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novel Schiff base metal complexes

Posted in Bacterial Resistance, Curation, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Infectious Disease & New Antibiotic Targets, Microbiology, tagged , , , , on November 28, 2015| Leave a Comment »

novel Schiff base metal complexes

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Synthesis and Characterisation of some novel Schiff base metal complexes: Spectral, XRD, Photoluminescence and Antimicrobial Studies
Rajendran Jayalakshmi and Rangappan Rajavel*  – Department of chemistry, Periyar University, Salem-636 011, Tamil Nadu, India

Chem Sci Rev Lett 2015; 4(15); 851-859        Article CS072046073        http://chesci.com/articles/csrl/v4i15/11_CS072046073.pdf

Schiff base ligands are potentially capable of forming stable complexes with most transition metal ions, which act as model compounds for biologically important species. Cu (II), Co (II), Ni (II) and Mn (II) Schiff base metal complexes was prepared by the condensation of benzil and 2,6-diamino pyridine in 1:1 molar ratio. The chemical structures of the Schiff base ligand and its metal complexes were confirmed by various spectroscopic studies like IR, UV-VIS, 1H NMR, TGA/DTA, Powder XRD, Molar conductance, and Photo luminescence. The free Schiff base ligand and its complexes have been tested for their antibacterial activity using disc diffusion method. From the biological studies, the complexes exhibit more activity than the ligand.

 

Metal-chelate Schiff base complexes have continued to play the role of one of the most important stereo chemical models in main group and transition metal coordination chemistry due to their preparative accessibility, diversity and structural variability(Garnovskii.,1993). Schiff bases have gained importance because of physiological and pharmacological activities associated with them. Schiff base metal complexes have ability to reversibly bind oxygen in epoxidation reactions [1], biological activity [2-4], catalytic activity in hydrogenation of olefins [5, 6] non-linear optical materials and [7] and photochromic properties [8]. The Schiff base complexes were also used as drugs and they possess a wide variety of antimicrobial activity against bacteria, fungi and it also inhibits the growth of certain type of tumours [9, 10]. The symmetric nature of a number of homo dinuclear transition metal derived metallobiosites and of the ability of the individual metal ions to have quite distinct roles in the functioning of the metalloenzyme concerned has led to a search for symmetrical dinucleating ligands which will give binuclear complexes capable of acting as models for the metallobiosites [11, 12]. 2, 6-Diamino-pyridine is a mediumproduction-volume chemical used as a pharmaceutical intermediate and a hair dye coupler in oxidation/permanent formulations. Although mutagenic activity has been reported, here in the present work we report the formation of Schiff base ligand from the condensation of 2, 6-diamino pyridine with benzil and the complexation with metal ions to form potentially active macrocyclic binuclear Schiff base metal complexes.

 

Synthesis of Ligand ((6E)-N2-((E)-2-(6-aminopyridin-2-ylimino)-1, 2-diphenylethyidine) pyridine-2, 6-diamine) The Schiff base ligand ((6E)-N2-((E)-2-(6-aminopyridin-2-ylimino)-1,2-diphenylethylidine)pyridine-2,6-diamine) were prepared by the drop wise addition of a solution of 2,6-diaminopyridine (0.22 g, 2 mmol) in ethanol (20 ml) to a stirred solution of benzil (0. 21 g, 1 mmol) in ethanol (20 ml). After the addition was completed, the mixture was condensed for 3 h at 900C. A brown precipitate solution was formed. The solution was kept for slow evaporation. The formed brown precipitate was filtered and washed with ethanol and then dried in air. Yield: 0.44 g (53%). Anal Calcd. For C24H20N6: C-73.45, H-5.14, and N-21.41. Found: C-73.38, H- 5.09, and N-21.40.

 

Synthesis of Schiff base metal complexes ([M2 (L) 2].4(OAc)) The macrocyclic binuclear Schiff base metal complexes (Cu(II), Ni(II), Co(II) and Mn(II)) were prepared by the condensation of 20 ml DMF solution of synthesized ligand (2mmol) adding to the constant stirring of 20 ml of ethanolic solution of metal salt (2 mmol M (where M = Cu2+, Ni2+, Co2+, Mn2+)) which was boiled for 3 hour under reflux. The coloured solution was formed. It was kept for slow evaporation and then collected the precipitate. It was filtered and washed with ethanol and then dried in vacuum.

 

The resultant macro cyclic Schiff metal complexes were colored powders, and stable for a long time in the open atmosphere. The analytical data and some of the physical properties of the Schiff base ligands and their binuclear metal complexes were summarized. All the metal complexes were sparingly soluble in general organic solvents, and soluble in DMF and DMSO, but insoluble in H2O, EtOH and MeOH. From the molar conductivity data, we clearly found the metal complexes were electrolytic in nature. The structural studies of the ligand and their complexes were done by spectroscopic methods.

Molar conductance The molar conductivity measurements commonly employed in the determination of the geometrical structure of inorganic compounds at infinite dilution. The molar conductance of binuclear Schiff base complexes was dissolved in DMSO and recorded (10-3M molar conductivity solution) at room temperature (Table 1). The complexes showed the range of molar conductance (127-134 ohm1 cm2mol1 ). From these values, we concluded that the complexes were electrolytic in nature. From the molar conductance, we concluded that the anions were outside the coordination sphere and not bonded to the metal ion therefore, these complexes may be formulated as [M2L2]4Z where, Z = acetate ion.

Table 1    Molar conductance and magnetic moment data of Schiff base binuclear metal complexes

S.No    Compounds                   Solvent      Molar conductance            Type of electrolyte        Magnetic moment            Geometry
Λm (ohm1 cm2 mol-1 )                                                          μ eff  B.M

1. [Cu2(L)2]4(OCOCH3)        DMSO                      132                                    1 :2  electrolyte                          1.74
2. [CO2(L)2]4(OCOCH3)      DMSO                      127                                     1 : 2 electrolyte                          4.83
3. [Ni2(L)2]4(OCOCH3)       DMSO                      134                                     1 : 2 electrolyte                          2.91
4. [Mn2(L)2]4(OCOCH3)     DMSO                     129                                      1 : 2 electrolyte                          5.82                          Octahedral 

 

IR Spectra of the free ligand and their binuclear metal complexes Vibrational spectra provide valuable information regarding the nature of functional group attached to the metal ion in the complexes. The IR spectra of the complexes show very similar spectra to one another. These spectra indicates the replacement of Ѵ(NH2) and Ѵ(C=O) of the starting materials with Ѵ(C=N) which suggest the occurs of the condensation reaction between amine and carbonyl groups [13]. Selected vibration bands of ligands and their metal complexes are given in Table 2. From the IR spectral analysis, the assignment of the important bands was made and recorded. In order to give a conclusive idea about the structure of the metal complexes, the IR bands of metal complexes were compared with free Schiff base ligand. The appearance of a strong, broad band at 3177 cm−1 in the spectra of the free ligands was assigned to ν (NH2). The IR band was shifted in the region (3063–3198 cm -1 ) shows the involvement of primary amine nitrogen atom coordinate to the metal ion for all the Schiff base metal complexes (Ray et al., 2009) after the complexation. The appearance of the band at 1629 cm -1 which may be assigned to the azomethine group Ѵ(C=N) vibration, indicate the condensation of the amino group of 2,6-diamino pyridine with the carbonyl group of benzil and formation of the proposed Schiff base. The IR spectra of all metal complexes show significant changes compared to free Schiff base ligand. After Complexation, the positions of the Ѵ(C=N) were shifted in the range (1660-1667cm1 ) indicates the participation of the azomethine group in complex formation (Singh et al., 2010). The position of an N – atom of the azomethine group and group of the pyridine ring in coordination is further supported by the presence of new bands in the range from 470–495cm-1which is assignable to (M-N) vibration. From the spectroscopic behaviour of metal complexes of pyridine, after the complexation the ring deformation found at 797 cm-1 and 711 cm−1. It was clearly indicate that the free pyridine is shifted to higher frequencies [14], and the coordination takes place via the pyridine nitrogen, as previously reported for pyridine complexes [15]. Therefore, this shift is clearly indicates the participation of pyridine in complex formation. The appearance of band range from 1660 cm−1 to 1438 cm−1 were due to symmetric stretching frequency and asymmetric stretching frequency of acetate ion. This clearly indicates that the acetate ions were coordinated outside of the coordination sphere.

Table 2 IR spectral data (cm-1 ) of the Schiff base (L) and their binuclear metal complexes

1H NMR spectrum of ligand and its macro cyclic binuclear metal complexes The 1H NMR data of the Schiff base (L) and the metal complexes were recorded in DMSO-d6 (Table 3). Assignment of 1H NMR signals were made according to their reported results for 2,6-diaminopyridine and its complexes [16-20]. The 1H-NMR spectra of ligand and its metal complexes show different peaks in the range 6.99-7.94 ppm corresponding to H3, H4, and H5 protons indicate unsymmetrical binding of the ligand to M (II) complexes. In the 1H NMR spectrum of M (II) complexes, singlet signal of the pyridine-NH2 (s, 3.1 to 3.7 ppm) and multiplet signals of aromatic protons (m, 6.72 to 7.94 ppm) of Schiff base (L) shifted compared to the starting material which suggests coordination through nitrogen atom of the azomethine group. For the metal complexes, a single sharp signal is appeared (region from 2.1 – 2.6 ppm) in the 1H NMR spectrum, suggest that the acetate ion is present in the outside coordination sphere of the metal complexes.

Table 3 1H NMR spectrum of ligand and its macro cyclic binuclear metal complexes

Electronic absorption spectra and magnetic moment measurements The electronic spectrum of the Schiff base ligand in DMSO (Table 4), the absorption band observed at 274 nm were assigned to π→π* transition and the band at 386 nm were assigned due to n→π* transition associated with the azomethine chromophore (-C=N).The absorption bands of the complexes are shift to longer wave numbers compared to that of the ligand [21]. For [M2 (L) 2]4(OCOCH3) complexes, the electronic absorption band occurs at 468-474 nm due to charge transfer from ligand to metal ion (LMCT). The obtained Cu (II) complexes exhibits a band at 652 nm assigned to 2Eg → 2T2g transition which is in conformity with octahedral geometry around the Cu (II) ion (Patil et al., 2010; Lever, 1968). The obtained magnetic moment value (µeff) for Cu(II)complex is 1.89 BM indicating that magnetic exchange occurs between the two copper sites and also supports octahedral geometry of Cu(II) complex [22]. The electronic absorption spectra of Co (II) complexes showed a band at 648 nm corresponding to 4T1g(F)→4A2g(F) transition and also the obtained magnetic moment value is 4.84 BM which confirm the octahedral geometry of the complex [23]. For the Ni (II) complex, it has the 3.06 BM magnetic moment value and the electronic spectrum showed a band at 645nm corresponding to 3A2g (F) →3T1g (F) transition which is consistent with the octahedral geometry of the complex. The Mn (II) binuclear complex shows bands at 633 nm corresponds to 6A1g→4T2g (4G) transitions and 5.82 BM magnetic value were compatible to an octahedral geometry of the ligand around manganese (II) ion [24].

Table 4 Electronic Spectral data of Schiff base ligand and their macro cyclic binuclear metal complexes

Compounds                    Electronic absorption spectra (nm)          Magnetic moment             Geometry of
π→π*   n→π*   L→M   d-d                          value(µeff)BM                  the complex
(nm)   (nm)      (nm)  (nm)
C12H12N6 (ligand)             274        342          –            –                                                                                       –
[Cu2(L)2]4(OCOCH3)      268       340        474     652                                1.89
[CO2(L)2]4(OCOCH3)     266        338        468    648                               4.84
[Ni2(L)2]4(OCOCH3)      256        339        471      645                               3.06                                        Octahedral
[Mn2(L)2]4(OCOCH3)   261         341         474     636                                5.82

 

TGA and DTA studies By using TGA and DTA analysis the thermal stability of the complexes were explained. The observation thermogram and curves (Table 5, Figure 2) were obtained at a heating rate of 100C/min over a temperature range of 40–7300C. The complex was stable up to 1600C and its decomposition started at this temperature. In the thermal decomposition process of the Cu (II) complex proceeds two steps of the mass losses corresponded to acetate, and NH2 leaving in the first, and second stages of the decomposition. The decomposition of the Cu (II) are irreversible. The Cobalt complexes were stable up to 2000C and its decomposition started at this temperature. The Cobalt (II) complex was decomposed in two steps with the temperature ranges from 200-470˚C corresponding to the loss of acetate and NH2 respectively. The Ni (II) complexes were stable up to 180oC and its decomposition started at this temperature. In the decomposition process of the Ni(II) complex, the estimated mass loss of the first step 6.85(6.91) corresponded to the loss of four acetate group and the second stage the liberation of four NH2 unit respectively, shown in table 6. The decomposition of the Nickel complex was irreversible. The thermal decomposition of the Manganese complex was stable up to 1700C and its decomposition started at this temperature. Thereafter, they start the decomposition process of the Mn (II) complex and weight loss observed in the temperature range 170-4600C, the mass loses corresponded to four acetate and four NH2 leaving in the first and second stages of the decomposition. The decomposition of the Mn (II) complexes are irreversible. The amount of acetate and NH2 groups stoichiometrically corresponding to the weight losses are given in the proposal chemical formulas of complexes.

Powder XRD Analysis Synthesized Schiff base metal (II) complexes were subjected to Powder X-ray diffractograms in the range (2ɵ = 10– 600 ) were shown in (Figure 3). Among the metal complexes Ni (II) complex shows well defined crystalline sharp peak which indicate the sample were crystalline nature. The appearance of crystallinity in the Schiff base metal complexes is due to the inherent crystalline nature of the metallic compounds. The average grain size (dXRD) of the Ni (II) complex is 32 nm which was calculated by using Scherer’s formula (Dhanaraj and Nair, 2009a,b) suggesting that the Ni(II) complex are nanocrystalline.

Table 5 Thermo gravimetric data of metal complexes

Figure 2 DTA/TGA Curve for metal complexes

Figure 3 Powder X-ray diffractogram for Ni complex

 

Fluorescence spectra The Schiff base and its binuclear metal complexes were analysed by the photoluminescence emission spectra (Figure 4) and recorded in DMSO at room temperature. Comparing with Schiff base ligand and its macro cyclic binuclear metal complexes, the metal complexes have strong fluorescence intensity than Schiff base. Among the metal complexes the Co (II) complex exhibited a strong fluorescence emission at 400 nm (Flourescence intensity 713) with excitation at 269 nm. The quenching of metal (II) complexes indicates that the ligand has a less potential photo active than metal (II) complexes.

Figure 4 Fluorescence spectra for all metal complexes

In vitro antimicrobial activity of Schiff base ligand and their metal complexes By using broth micro dilution procedures, the Schiff base ligand and their metal complexes were screened separately against for two Gram positive bacteria (Staphylococcus aureus and B. Subtilis), two Gram negative bacteria (E. Coli and S. typhi) and the fungi (A. fumigatus) for their antimicrobial activity. When the activity of Schiff base ligand and their metal complexes were increased by increasing the antimicrobial screening concentration (Table 6, Figure 5), because the concentration plays an important role in the zone of inhibition and the chelated metal complexes deactivate the various cellular enzyme [25]. Metal complexes show considerable antimicrobial activity even at low concentration and also more toxicity towards Gram-positive strains, Gram-negative strains and fungi compare with Schiff base ligand. The antimicrobial data shows that the copper complex noticed an excellent activity against bacteria and fungi than other metal complexes. The different antimicrobial activity of different metal complexes depends on the impermeability of the cell or the difference in ribosomes in microbial cell (Sengupta et al., 1998).

Table 6 Antimicrobial activity of Schiff base ligand and their metal complexes

Figure 5 Anti-Bacterial Activities of the Schiff Base and Its Binuclear Metal Complexes against Gram positive and negative Bacterias

Conclusion Macrocyclic binuclear metal (II) complexes was synthesized by using condensation method of a novel Schiff base ligand derived from 2, 6-diamino pyridine and benzil. The data which have been the physico chemical and spectral studies provides excellent structure and chemical composition of Schiff base and its metal complexes. The electronic absorption spectra, IR spectra and magnetic moment value reveals that the metal complexes were octahedral geometry and the Schiff base coordinated through six nitrogen atoms of azomethine group and pyridine ring. Powder XRD data reveals that the Ni(II) complex was nano crystalline structure. Based on the photo luminescence studies, we have confirmed the metal complexes were more potential photo active than Schiff base. The in vitro antimicrobial studies of metal (II) complexes showed better activity than Schiff base.

References

[1] Viswanathamurthi P, Natarajan K, Synth.React.Inorg.Met.-Org.Chem 2006; 36:415-418.

[2] Ren S, Wang R, Komastu K, Krause P.B, Zyrianov Y, Mckenna C. E, Csipke C, TokesZ. A, Lien E. J, J. Med. Chem 2002; 45: 410

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Hospital Acquired Infections

Posted in Curation, Microbiology, Pharmaceutical Analytics, Pharmaceutical Industry Competitive Intelligence, Population Health Management, tagged , on November 28, 2015| Leave a Comment »

Hospital Acquired Infections

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Hospital infection control in the era of superbug outbreaks
By Leslie Small

http://www.fiercehealthcare.com/special-reports/hospital-infection-control-era-superbug-outbreaks-special-report

 

Long before superbug outbreaks tied to a specialized medical scope sickened and killed patients across the country, infection control has been a major priority for hospitals.

But the need to curb infections has become even more pressing now that the shift from a fee-for-service model to value-based payments has led the federal government to increasingly tie reimbursements to patient outcomes. An industry trend toward transparency also has made it easier for the public to see the danger of a hospital stay.

One in 25 hospital patients acquires at least one healthcare-associated infection (HAI), according to data from the Centers for Disease Control and Prevention. There were an estimated 722,000 HAIs in U.S acute care hospitals in 2011, about 75,000 hospital patients with HAIs died during their hospitalizations, and more than half of all HAIs occurred outside of the intensive care unit.

The problem has gained more attention in recent months, when reports surfaced of patients contracting a particularly lethal antibiotic-resistant superbug, carbapenem-resistant Enterobacteriaceae (CRE), after undergoing procedures that involved a device known as a duodenoscope. A Food and Drug Administration advisory panel concluded this month what hospitals involved in the outbreak already knew–that the ability of CRE and other dangerous pathogens to stay on scopes after cleaning puts patients at a significant risk.

But while the problems posed by such outbreaks are clear, finding solutions to them–particularly in a seldom-static healthcare industry–is anything but. To help chart a way forward, this special report from FierceHealthcare examines advice from experts and hospital leaders who have learned valuable lessons from the front lines of hospital infection control.

 

Rise of a superbug jeopardizes patient safety

Hospital infection control in the era of superbug outbreaks
By Leslie Small
http://www.fiercehealthcare.com/special-reports/rise-superbug-jeopardizes-patient-safety

The recent carbapenem-resistant Enterobacteriaceae (CRE) outbreak burst onto the scene when reports surfaced in February that it caused two patient deaths at UCLA’s Ronald Reagan Medical Center. In addition to the California outbreak–which also sickened patients at Cedars-Sinai Medical Center in Los Angeles–cases of the superbug linked to duodenoscopes also cropped up at hospitals in North Carolina, Pittsburgh, Chicago and Seattle.

The Centers for Disease Control and Prevention (CDC) has cautioned hospitals that they must do more to mitigate the threat of CRE, which it dubbed “nightmare bacteria” due to their resistance to even last-resort antibiotics. When it reaches the bloodstream, CRE can kill up to half of all patients it infects.

The Food and Drug Administration (FDA) issued a warning in February that the complex design of duodenoscopes makes them difficult to sterilize even when hospitals follow the device manufacturers’ instructions. However, the FDA has refused to take the devices off the market because they are used for the potentially life-saving procedure known as endoscopic retrograde cholangiopancreatography (ERCP), a technique that diagnoses and treats cancers and other digestive diseases. The agency estimates that 500,000 ERCPs are performed each year. A special advisory panel recently endorsed this decision, though it urged the FDA to better protect patients from the infection risk posed by duodenoscopes,FierceHealthcare has reported.

The panel was also critical of major duodenoscope manufacturer Olympus, which declined to participate in the advisory panel’s forum but says it has supplied the FDA with data to prove that its updated cleaning instructions and new cleaning brush allow for safe reprocessing.

Indeed, news surfaced recently that the company was aware of the infection risk associated with the devices in 2013, which it communicated to European hospitals two years before the UCLA outbreak. The situation has led California lawmaker, Rep. Ted Lieu (D-Los Angeles) to call for congressional hearings into the matter. Meanwhile, Olympus faces two patient-driven lawsuits, and Virginia Mason Hospital in Seattle also has pursued legal action against the manufacturer.

The outbreaks have left many hospitals wondering what to do to make sure patients are safe and still have access to important medical devices. For its part, the FDA panel did not outright endorse any specific sterilization method.

Jackie Caynon, pictured right, a lawyer with more than 18 years of health law experience, and partner and co-chair of Mirick O’Connell’s Health Law Group, told FierceHealthcare in an exclusive interview that the answer has to come from each hospital’s unique risk management assessment.

“I’ve heard some hospitals say, you know these things are really life-saving, so if we get rid of the product we won’t be able to, obviously, save lives,” he said. But for others, he said, the risk may be too great.

“To me it just seems too risky to use it,” Caynon said. “If you’re going to do informed consent, I could see you saying to the patient ‘oh you know, this could save your life, but we won’t know until we actually go in there and look, but you run the risk of having a CRE infection because we cannot guarantee that we can properly clean this device.'”

And now that the infection risk surrounding the devices has been made public, “I think you’re going to have a lot of patients that are going to say ‘I don’t want you to use that device, period,'” he said.

Regardless of what each individual facility decides to do about the scopes, it would be a mistake to hold hospitals responsible for manufacturers’ mistakes or regulatory failures, according to Caynon.

“Holding hospitals and physicians liable here is kind of going after the wrong folks,” he said, because “the hospital is just as much of a customer as patients (are).”

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newly developed oxazolidinone antibiotics

Posted in Bacterial Resistance, Clinical & Translational, Commercialization, Curation, Disease Biology, Small Molecules in Development of Therapeutic Drugs, FDA Regulatory Affairs, Glycobiology: Biopharmaceutical Production, Infectious Disease & New Antibiotic Targets, Microbiology, Pharmaceutical Analytics, Pharmaceutical Industry Competitive Intelligence, tagged , , , on November 27, 2015| Leave a Comment »

newly developed oxazolidinone antibiotics

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

New Antibacterial oxazolidinones in pipeline by Wockhardt

by DR ANTHONY MELVIN CRASTO Ph.D

 

WCK ?

(5S)-N-{3-[3,5-difluoro-4-(4-hydroxy-4-methoxymethyl-piperidin-1-yl)-phenyl]-2-oxo-oxazolidin-5-ylmethyl}-acetamide

MF C19 H25 F2 N3 O5, MW 413.42

Acetamide, N-​[[(5S)​-​3-​[3,​5-​difluoro-​4-​[4-​hydroxy-​4-​(methoxymethyl)​-​1-​piperidinyl]​phenyl]​-​2-​oxo-​5-​oxazolidinyl]​methyl]​-

CAS 957796-51-9

Antibacterial oxazolidinones

THIS MAY BE WCK 4086?????

PATENT

WO 2015173664, US8217058, WO 2012059823, 

 

Oxazolidinone represent a novel chemical class of synthetic antimicrobial agents.Linezolid represents the first member of this class to be used clinically. Oxazolidinones display activity against important Gram-positive human and veterinary pathogens including Methicillin-Resistant Staphylococcus aureus (MRSA), Vancomycin Resistant Enterococci (VRE) and β-lactam Resistant Streptococcus pneumoniae (PRSP). The oxazolidinones also show activity against Gram-negative aerobic bacteria, Gram-positive and Gram-negative anaerobes. (Diekema D J et al., Lancet 2001 ; 358: 1975-82).

Various oxazolidinones and their methods of preparation are disclosed in the literature. International Publication No. WO 1995/25106 discloses substituted piperidino phenyloxazolidinones and International Publication No. WO 1996/13502 discloses phenyloxazolidinones having a multisubstituted azetidinyl or pyrrolidinyl moiety. US Patent Publication No. 2004/0063954, International Publication Nos. WO 2004/007489 and WO 2004/007488 disclose piperidinyl phenyl oxazolidinones for antimicrobial use.

Pyrrolidinyl/piperidinyl phenyl oxazohdinone antibacterial agents are also described in Kim H Y et al., Bioorg. & Med. Chem. Lett., (2003), 13:2227-2230. International Publication No. WO 1996/35691 discloses spirocyclic and bicyclic diazinyl and carbazinyl oxazolidinone derivatives. Diazepeno phenyloxazolidinone derivatives are disclosed in the International Publication No. WO 1999/24428. International Publication No. WO 2002/06278 discloses substituted aminopiperidino phenyloxazolidinone derivatives.

Various other methods of preparation of oxazolidinones are reported in US Patent No. 7087784, US Patent No. 6740754, US Patent No. 4948801 , US Patent No. 3654298, US Patent No. 5837870, Canadian Patent No. 681830, J. Med. Chem., 32, 1673 (1989), Tetrahedron, 45, 1323 (1989), J. Med. Chem., 33, 2569 (1990), Tetrahedron Letters, 37, 7937-40 (1996) and Organic Process Research and Development, 11 , 739-741(2007).

Indian Patent Application No. 2534/MUM/2007 discloses a process for the preparation of substituted piperidino phenyloxazolidinones. International Publication No. WO2012/059823 further discloses the process for the preparation of phosphoric acid mono-(L-{4-[(5)-5-(acetylaminomethyl)-2-oxo-oxazolidin-3-yl]-2,6-difluorophenyl}4-methoxymethyl piperidine-4-yl)ester.

US Patent No. 8217058 discloses (5S)-N-{3-[3,5-difluoro-4-(4-hydroxy-4-methoxymethyl-piperidin-l-yl)-phenyl]-2-oxo-oxazolidin-5-ylmethyl}-acetamide as an antibacterial agent and its process for preparation.

PATENT

WO2015173664

https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2015173664&recNum=1&maxRec=&office=&prevFilter=&sortOption=&queryString=&tab=PCTDescription

 

 

PATENT

http://www.google.st/patents/WO2007132314A2?cl=en

 

Figure imgf000004_0001

Wockhardt Ltd,

Figure imgf000006_0001
Figure imgf000006_0002

(3) (4)

 

PATENT

WO 2012059823

http://www.google.co.in/patents/WO2012059823A1?cl=en

Phosphoric acid mono-(l-{4-[(S)-5-(acetylamino- methyl)-2-oxo-oxazolidin-3-yl]-2,6-difluorophenyl}-4-methoxymethyl-piperidin-4-yl) ester of Formula (A),
Figure imgf000022_0001
the process comprising the steps of:
a) Converting intermediate of Formula (1) into intermediate of Formula (3)
Figure imgf000022_0002
b) Converting intermediate of Formula (3) into intermediate of Formula (5)
Figure imgf000022_0003

c) Converting intermediate of Formula (5) into intermediate of structure (6)

Figure imgf000022_0004
(5) <6> d) Converting intermediate of Formula (6) into intermediate of Formula (10)
Figure imgf000023_0001
e) Converting intermediate of Formula (10) into intermediate of Formula (11),
Figure imgf000023_0002

f) Converting intermediate of Formula (11) into compound of Formula (A) or Pharmaceutically acceptable salts thereof

Figure imgf000023_0003

 

 

Figure imgf000006_0001
Figure imgf000006_0002
Figure imgf000006_0003

 

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Protein regulator of HIV replication

Posted in Curation, Proteins, Viral diseases, Virology, tagged , , , , , , , , , , , , , , on November 25, 2015| Leave a Comment »

Protein regulator of HIV replication

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Updated 11/26/2015

 

Closing the loop on an HIV escape mechanism

University of Delaware

http://www.rdmag.com/news/2015/11/closing-loop-hiv-escape-mechanism

 

Tatyana Polenova, professor of chemistry and biochemistry at UD (background, left), with her UD research team involved in the HIV study. Next to her is Huilan Zhang. In the foreground, from left, are Guangjin Hou and Manman Lu.

http://www.rdmag.com/sites/rdmag.com/files/newsletter-ads/CHEM-Polenova_Research_Groups-111015-015.jpg

Tatyana Polenova, professor of chemistry and biochemistry at UD (background, left), with her UD research team involved in the HIV study. Next to her is Huilan Zhang. In the foreground, from left, are Guangjin Hou and Manman Lu.

 

Nearly 37 million people worldwide are living with HIV. When the virus destroys so many immune cells that the body can’t fight off infection, AIDS will develop. The disease took the lives of more than a million people last year.

For the past three and a half years, a team of researchers from six universities, led by the University of Delaware and funded by the National Institutes of Health and the National Science Foundation, has been working to uncover new information about a protein that regulates HIV’s capability to hijack a cell and start replicating. Their findings, reported recently in the Proceedings of the National Academy of Sciences, point to a new avenue for developing potential strategies to thwart the virus.

The team included scientists from UD, the University of Pittsburgh School of Medicine, University of Illinois at Urbana-Champaign, Carnegie Mellon University, the National High Magnetic Field Laboratory at Florida State University and Vanderbilt University School of Medicine. They used a combination of high-tech tools and techniques, including magic-angle-spinning nuclear magnetic resonance (NMR) spectroscopy and computer simulations of molecules, to examine the interactions between HIV and the host-cell protein cyclophilin A (CypA), right down to the movement of individual atoms.

“In a nutshell, we found that the infectivity of HIV is regulated by the motions of these proteins,” says Tatyana Polenova, professor of chemistry and biochemistry at the University of Delaware, who led the study. “It’s a subtle regulation strategy that does not involve major structural changes in the virus.”

Sixty times smaller than a red blood cell, HIV contains a cone-shaped shell, or capsid, made of protein, which surrounds two strands of RNA and the enzymes the virus needs for replication. Like any virus, HIV can only produce copies of itself once it has invaded a host organism. Then it will begin directing certain host cells to begin producing the virus.

But how does HIV invade a cell? In humans, the protein CypA can either promote or inhibit viral infection through interactions with the HIV capsid, although the exact mechanism is not yet known. A portion of the HIV capsid protein, called the CypA loop, is responsible for binding to the CypA in the human host cell. Once this occurs, the virus typically becomes infectious.

However, a change of just one amino acid in the CypA loop can cause the virus to operate opposite from how it does normally, allowing the virus to become non-infectious when CypA is present, and to become infectious when there is no CypA present. Such changes are called “escape mutations,” Polenova says, because they allow the virus to “escape” from its dependence on CypA.

To home in on this escape mechanism, the research team examined assemblies of different variants of HIV capsid protein complexed with CypA. Using magic-angle-spinning NMR, they recorded the motions in these assemblies, atom by atom, on time scales ranging from nanoseconds to milliseconds, from a billionth of a second to a thousandth of a second.

The team found that a reduction in the naturally occurring motions in the binding region due to the mutations allowed the virus to escape from CypA dependence. Magic-angle-spinning NMR experiments provided a direct probe of these motions, recording the changes in the magnetic interactions between nuclei. Computer simulations allowed the team to visualize the motions.

Some portions of the capsid protein do not move at all or move only a little while other portions undergo large-amplitude motions distributed over a wide range of time scales, with the most dynamic region being the CypA loop. Polenova says it is rather surprising that such extensive motions are present in the assembled capsid, and that these dynamics could be detected by both NMR and computer simulations.

“It is the first time that quantitative agreement between experiment and computation was achieved in a dynamics study, and it’s particularly exciting that this was attained for such a complex system,” Polenova says. “We hope this work may guide the development of new therapeutic interventions, such as small molecules that would serve as interactors with the HIV capsid and inhibit these dynamics.”

Polenova says the diverse team of researchers, with expertise in HIV virology, structural biology, biophysics and biochemistry, was critical to the study’s success, along with access to national high-field NMR facilities through the National High Magnetic Field Laboratory. The team was assembled through the NIH-funded Pittsburgh Center for HIV Protein Interactions. Led by Prof. Angela Gronenborn, the center brings together high-caliber scientists and facilities to elucidate the interactions of HIV proteins with host cell factors.

 

Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy

Si Yana,1, Changmiao Guoa,1, Guangjin Houa, Huilan Zhanga, Xingyu Lua, John Charles Williamsb, and Tatyana Polenovaa,2  Author Affiliations

PNAS Nov 24, 2015; 112(47): 14611–14616    http://dx.doi.org:/10.1073/pnas.1509852112

 

Significance

Microtubules and their associated proteins are central to most cellular functions. They have been extensively studied at multiple levels of resolution; however, significant knowledge gaps remain. Structures of microtubule-associated proteins bound to microtubules are not known at atomic resolution. We used magic angle spinning NMR to solve a structure of dynactin’s cytoskeleton-associated protein glycine-rich (CAP-Gly) domain bound to microtubules and to determine the intermolecular interface, the first example, to our knowledge, of the atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. The results reveal remarkable structural plasticity of CAP-Gly, which enables CAP-Gly’s binding to microtubules and other binding partners. This approach offers atomic-resolution information of microtubule-binding proteins on microtubules and opens up the possibility to study critical parameters such as protonation states, strain, and dynamics on multiple time scales.

 

Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

 

How Viruses Commandeer Human Proteins

http://www.technologynetworks.com/Proteomics/news.aspx?ID=185156

 

Researchers have produced the first image of an important human protein as it binds with ribonucleic acid (RNA), a discovery that could offer clues to how some viruses, including HIV, control expression of their genetic material.

 

RNA is one of three macromolecules — along with DNA and proteins — essential to all forms of life. By understanding how hnRNP A1 binds to RNA, the scientists may find ways to jam up components of the replication machinery when the protein is coopted by disease.

The team of scientists reveals the mechanism used by the protein, hnRNP A1 to link to the section of RNA, called the ‘hairpin loop.’

They found that hnRNP A1, a protein essential to cell function and virus replication, has a significantly different structure than its only previously known form: binding to DNA.

“We solved the three-dimensional structure of the protein bound to an RNA hairpin derived from the HIV virus,” said Blanton Tolbert, a chemistry professor at Case Western Reserve. “But because the hairpin loop is found in other viruses and throughout healthy cells, our findings may help explain how the protein connects to the other hairpin targets.”

Tolbert began this research six years ago, frustrated that the only information available was the structure of the protein bound to a synthetic DNA, which isn’t its natural target.

Proteins that bind hairpins sense both the structure and the sequence information presented in the loop. The structure of the DNA complex did not demonstrate the molecular recognition that must take place to bind RNA hairpins.

The process

To discover the structure bound to RNA, the researchers combined three techniques: X-ray crystallography, nuclear magnetic resonance spectroscopy and small angle x-ray scattering. Each technique yielded a piece of the puzzle.

To bind to RNA, hnRNP A1 has two domains, RRM1 and RRM2, which are akin to hands. Scientists already knew both hands are needed to connect to RNA.

But the researchers found that, instead of each domain grabbing a section of the loop, only RRM1 makes contact with the RNA. RRM2 acts as support, helping organize RRM1 into the structure needed to conform to a certain section of the loop.

To confirm that the structures are key to binding, the researchers inserted mutations by changing amino acids on the surface of the domains.

Surprisingly, mutations on the far side of RRM1 — the surface not in contact with the RNA but with the RRM2 — caused decoupling at that site and substantially weakened the affinity for RNA.

Without the normal connection between the two domains, RRM1 fails to adopt the geometric shape that conforms to the RNA hairpin loop.

The researchers are further investigating how the protein transmits the effects of RRM2 to RRM1 and bind. They are also exploring the development of antagonistic agents that would disrupt the interaction of the protein with viruses.

 

Natural defense protein against HIV discovered

HIV-1, ERManI, antiretroviral, defense protein

Earlier research had shown that it was possible to interfere with HIV spread but the exact molecular mechanisms had not been identified. For the first time, scientists have identified ERManI (Endoplasmic Reticulum Class I α-Mannosidase) as the essential host protein that slows the spread of HIV-1. Scientists investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the HIV-1 envelope (Env) degradation process. Ectopic expression of these four α-mannosidases uncovered that only ERManI inhibited HIV-1 Env expression in a dose-dependent manner. Basically, ERManI is a host enzyme that adds sugars to proteins. The Env glycoprotein is targeted to the endoplasmic reticulum-associated protein degradation pathway for degradation after infecting cells. And ERManI was found to interact with the Env and initiate this degradation pathway.

With this discovery, ERManI has the potential as a new antiretroviral treatment option. Currently there is no cure for HIV-1 and once patients are infected, they have it for life. Current antiretroviral therapies can prolong life but cannot fully cure a patient. ERManI is different from current treatments in the sense that it can help the body protect itself.

 

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway (Sep 2015)

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway.
Zhou T1, Frabutt DA2, Moremen KW3, Zheng YH4.  Author information
 J Biol Chem. 2015 Sep 4;290(36):22184-92.    http://dx.doi.org:/ 10.1074/jbc.M115.675207. Epub 2015 Jul 23

Previously, we reported that the mitochondrial translocator protein (TSPO) induces HIV-1 envelope (Env) degradation via the endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway, but the mechanism was not clear. Here we investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the Env degradation process. Ectopic expression of these four α-mannosidases uncovers that only ERManI inhibits HIV-1 Env expression in a dose-dependent manner. In addition, genetic knock-out of the ERManI gene MAN1B1 using CRISPR/Cas9 technology disrupts the TSPO-mediated Env degradation. Biochemical studies show that HIV-1 Env interacts with ERManI, and between the ERManI cytoplasmic, transmembrane, lumenal stem, and lumenal catalytic domains, the catalytic domain plays a critical role in the Env-ERManI interaction. In addition, functional studies show that inactivation of the catalytic sites by site-directed mutagenesis disrupts the ERManI activity. These studies identify ERManI as a critical GH47 α-mannosidase in the ER-associated protein degradation pathway that initiates the Env degradation and suggests that its catalytic domain and enzymatic activity play an important role in this process.

 

T cell editing using CRISPR/Cas9 could revolutionize HIV therapeutics
September 15, 2015   

T cell therapy, HIV

Reinforcing the immune system by engineering lymphocytes to target and destroy viruses has the potential to be an effective therapy for many diseases. One potential approach to this strategy is to alter the genome of lymphocytes so that proteins that are typically hijacked by viruses are no longer present. While conceptually feasible, editing T cells has been challenging in practice; however, with the advent of mammalian cell editing using CRISPR/Cas9, T-cell editing is closer to becoming a reality.

How can CRISPR/Cas9 bring us closer to finding a cure for HIV?

In a study recently published in PNAS, scientists have optimized a protocol to introduce nucleotide replacements that would inhibit CXCR4 expression. The authors streamlined the CRISPR/Cas9 editing process by electroporating Cas9 ribonucleoproteins (RNPs) into CD4+ T cells. The RNPs, consisting of both a recombinant Cas9 enzyme and guide RNA, vastly improved editing efficiency, ultimately promoting knock-out of the CXCR4 cell-surface receptor. Taken together, these result suggest the potential of a new cell therapy approach for the fight against HIV.

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins
Kathrin Schumann a , b , 1 , Steven Lin c , 1 , Eric Boyer a , b , Dimitre R. Simeonov a , b , d , Meena Subramaniam e , f , Rachel E. Gate e , f , et al.  PNAS. 2015; 112(33): 10437-10442. http://dx.doi.org:/10.1073/pnas.1512503112

Significance

T-cell genome engineering holds great promise for cancer immunotherapies and cell-based therapies for HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been inefficient. We achieved efficient genome editing by delivering Cas9 protein pre-assembled with guide RNAs. These active Cas9 ribonucleoproteins (RNPs) enabled successful Cas9-mediated homology-directed repair in primary human T cells. Cas9 RNPs provide a programmable tool to replace specific nucleotide sequences in the genome of mature immune cells—a longstanding goal in the field. These studies establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

 

T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently “knock out” genes and “knock in” targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4+ T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved in CXCR4 and PD-1 (PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

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Experience with Trauma Surgery

Posted in Curation, Diagnostics and Lab Tests, Infectious Disease & New Antibiotic Targets, Innovations, Microbiology, Patient Experience, Patient Experience: Personal Memories of Invasive Medical Intervantion, Patient’s Voice: Personal Experience with Invasive Medical Procedures, Pharmaceutical Analytics, tagged , , , , on November 23, 2015| 1 Comment »

Experience with Trauma Surgery

Author: Larry H. Bernstein, MD, FCAP

 

 

In 1987, I went on vacation to Bermuda with my wife and two children.  It was a beautiful place, and the weather and the ocean were wonderful to experience.  One could travel by bus, which was very safe, which I preferred. My older daughter wanted to use a moped, which we allowed on the condition that she first be trained.  On the last day, she went to return the moped, but the station was out for lunch.  I was a photograper and wanted to photograph the white bird of Burmuda. I put my camera in the rear, but as I left the station my moped was hit by an oncoming moped that I failed to see, unaccustomed to the British style driving.  An ambulance arrived within a few minutes as I lay on the ground. My wife sent the kids home and made arrangements for my secretary to look after them.  I was impressed with the surgeon when I arrived at the hospital. He wheeled me to the bed I was to stay in. I had two blood transfusions.  He took me to the operating room, but I don’t recall any details. He had a McGill University resident who later wrote a thesis about the experience.  I was pretty knocked out, but there was another patient in the room who had fallen down his steps. He was a WWII RAF veteran who had bombed the Germans. He told me the stories about his experience.  We contacted the burn surgeon, Walter Pleban, who arranged to have me flown to Bridgeport, CT, and he arranged for the best orthopedic surgeons to admit me on arrival.  In my flight there was another patient who was dying of endstage HIV AIDS.

Herbert Hermele observed how serious this was because there were three fractures of the right tibia. The good news was that there was no need to amputate because I had the nervous innervation, but I lost a popliteal artery.  I was admitted, and at first there was only a small room. The nurse was a very competent young woman of Portuguese descent. She was able to move me as needed. I was moved when a better room became available.  It was very good when the night shift nurse came in because I was able to talk to her with some attachment.  The Vice President had me provided with good meals, as I was the director of blood bank and chemistry.  I also had visits by my supervisors and other staff.

It was not an easy time, but I was privileged because of my standing with the medical and laboratory staff.  I had a longer stay than usual because I had an infection with two gram negative resistant strains of bacteria –serratia marcesans and Enterobacter. I was put on a gram negative penicillin and the next morning I felt dizzy. When Dr. Pleban came to see me I told him that I was having a penicillin reaction because I was aware that my twin sister was allergic to penicillin. As a result, the prescription was changed and it was an improved situation.  I underwent 10 operative procedures in some weeks. Dr. Hermeles partner put an antibiotic plug into the wound and it healed.  It was only after the infection cleared that a superb reconstructive surgeon was called in and he made skin grafts to close the wound after he disconnected a tendon and pulled muscle over the wound.  I also had a call from IJ Good, University Professor of Statistics at Virginia Polytech, who had completed writing a program to analyze data that I had provided him 2 years earlier – of MB isoenzyme CK at 6 hours and 12 hours later for diagnosis of heart attack.  We published the work in the prestigious journal, Clinical Chemistry and the President of the College of American Pathologists took note of the paper. I was finally sent home, without needing excess stay to the hospital environment.  I had physical therapy at home, and my bed was made on the first floor.  When I returned to work my infection site oozed, so I went to the Chief of Infectious Disease.  He prescribed a new quinolone antibiotic that could be taken orally. The infection subsided and it has never returned.

My sister came from San Diego, California and she brought me a recording she made for imaging to heal.  It went on that I was climbing a step to the heavens and getting better and better.  She also emphases laughing.

I can only look back and recall how fortunate I was to have the attention and kindness at that time. It was in excess of what many patients experience.  I do recall that the Hungarian-Cuban music teacher my daughter had had thousands of musical pieces and thousands of stories so that she was one of the most entertaining patients ever admitted to Bridgeport Hospital.

 

 

 

 

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Kurzweill Reports in Medical Science I

Posted in Alzheimer's Disease, Bacterial Resistance, Behavioral Genetics, Cardiac and Cardiovascular Surgical Procedures, Clinical & Translational, Clinical Genomics, Curation, Developmental biology, Embryology, Genetics & Pharmaceutical, Genome Biology, Human aging, Infectious Disease & New Antibiotic Targets, Innovations in Neurophysiology & Neuropsychology, Investment in Technological Breakthrough, Medical Imaging Technology, Microbiologial genetics, Microbiology, Molecular Genetics & Pharmaceutical, Myocardial Ischemia, Neurodegenerative Diseases, Neurological Diseases, Neuroscience, PCI, Pharmacotherapy and Cell Activity, tagged , , , , , , on November 21, 2015| Leave a Comment »

Kurzweill Reports in Medical Science I

Curator: Larry H. Bernstein, MD, FCAP

 

 

 

E-coli bacteria found in some China farms and patients cannot be killed with antiobiotic drug of last resort

“One of the most serious global threats to human health in the 21st century” — could spread around the world, requiring “urgent coordinated global action”
November 20, 2015

http://www.kurzweilai.net/e-coli-bacteria-found-in-some-china-farms-and-patients-cannot-be-killed-with-antiobiotic-drug-of-last-resort

Colistin antibiotic overused in farm animals in China apparently caused E-coli bacteria to become completely resistant to treatment; E-coli strain has already spread to Laos and Malaysia (credit: Yi-Yun Liu et al./Lancet Infect Dis)

Widespread E-coli bacteria that cannot be killed with the antiobiotic drug of last resort — colistin — have been found in samples taken from farm pigs, meat products, and a small number of patients in south China, including bacterial strains with epidemic potential, an international team of scientists revealed in a paper published Thursday Nov. 19 in the journal The Lancet Infectious Diseases.

The scientists in China, England, and the U.S. found a new gene, MCR-1, carried in E-coli bacteria strain SHP45. MCR-1 enables bacteria to be highly resistant to colistin and other polymyxins drugs.

“The emergence of the MCR-1 gene in China heralds a disturbing breach of the last group of antibiotics — polymixins — and an end to our last line of defense against infection,” said Professor Timothy Walsh, from the Cardiff University School of Medicine, who collaborated on this research with scientists from South China Agricultural University.

Walsh, an expert in antibiotic resistance, is best known for his discovery in 2011 of the NDM-1 disease-causing antibiotic-resistant superbug in New Delhi’s drinking water supply. “The rapid spread of similar antibiotic-resistant genes such as NDM-1 suggests that all antibiotics will soon be futile in the face of previously treatable gram-negative bacterial infections such as E.coli and salmonella,” he said.

Likely to spread worldwide; already found in Laos and Malaysia

The MCR-1 gene was found on plasmids — mobile DNA that can be easily copied and transferred between different bacteria, suggesting an alarming potential to spread and diversify between different bacterial populations.

Structure of plasmid pHNSHP45 carrying MCR-1 from Escherichia coli strain SHP45 (credit: Yi-Yun Liu et al./Lancet Infect Dis)

“We now have evidence to suggest that MCR-1-positive E.coli has spread beyond China, to Laos and Malaysia, which is deeply concerning,” said Walsh.  “The potential for MCR-1 to become a global issue will depend on the continued use of polymixin antibiotics, such as colistin, on animals, both in and outside China; the ability of MCR-1 to spread through human strains of E.coli; and the movement of people across China’s borders.”

“MCR-1 is likely to spread to the rest of the world at an alarming rate unless we take a globally coordinated approach to combat it. In the absence of new antibiotics against resistant gram-negative pathogens, the effect on human health posed by this new gene cannot be underestimated.”

“Of the top ten largest producers of colistin for veterinary use, one is Indian, one is Danish, and eight are Chinese,” The Lancet Infectious Diseases notes. “Asia (including China) makes up 73·1% of colistin production with 28·7% for export including to Europe.29 In 2015, the European Union and North America imported 480 tonnes and 700 tonnes, respectively, of colistin from China.”

Urgent need for coordinated global action

“Our findings highlight the urgent need for coordinated global action in the fight against extensively resistant and pan-resistant gram-negative bacteria,” the journal paper concludes.

“The implications of this finding are enormous,” an associated editorial comment to the The Lancet Infectious Diseases paper stated. “We must all reiterate these appeals and take them to the highest levels of government or face increasing numbers of patients for whom we will need to say, ‘Sorry, there is nothing I can do to cure your infection.’”

Margaret Chan, MD, Director-General of the World Health Organization, warned in 2011 that “the world is heading towards a post-antibiotic era, in which many common infections will no longer have a cure and, once again, kill unabated.”

“Although in its 2012 World Health Organization Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR) report the WHO concluded that colistin should be listed under those antibiotics of critical importance, it is regrettable that in the 2014 Global Report on Surveillance, the WHO did not to list any colistin-resistant bacteria as part of their ‘selected bacteria of international concern,’” The Lancet Infectious Diseases paper says, reflecting WHO’s inaction in Ebola-stricken African countries, as noted last September by the international medical humanitarian organization Médecins Sans Frontières.

Funding for the E-coli bacteria study was provided by the Ministry of Science and Technology of China and National Natural Science Foundation of China.

Abstract of Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

Until now, polymyxin resistance has involved chromosomal mutations but has never been reported via
horizontal gene transfer. During a routine surveillance project on antimicrobial resistance in commensal Escherichia coli from food animals in China, a major increase of colistin resistance was observed. When an E coli strain, SHP45, possessing colistin resistance that could be transferred to another strain, was isolated from a pig, we conducted further analysis of possible plasmid-mediated polymyxin resistance. Herein, we report the emergence of the first plasmid-mediated polymyxin resistance mechanism, MCR-1, in Enterobacteriaceae.

The mcr-1 gene in E coli strain SHP45 was identified by whole plasmid sequencing and subcloning. MCR-1 mechanistic studies were done with sequence comparisons, homology modelling, and electrospray ionisation mass spectrometry. The prevalence of mcr-1 was investigated in E coli and Klebsiella pneumoniae strains collected from five provinces between April, 2011, and November, 2014. The ability of MCR-1 to confer polymyxin resistance in vivo was examined in a murine thigh model.

Polymyxin resistance was shown to be singularly due to the plasmid-mediated mcr-1 gene. The plasmid carrying mcr-1 was mobilised to an E coli recipient at a frequency of 10−1 to 10−3 cells per recipient cell by conjugation, and maintained in K pneumoniae and Pseudomonas aeruginosa. In an in-vivo model, production of MCR-1 negated the efficacy of colistin. MCR-1 is a member of the phosphoethanolamine transferase enzyme family, with expression in E coli resulting in the addition of phosphoethanolamine to lipid A. We observed mcr-1 carriage in E coli isolates collected from 78 (15%) of 523 samples of raw meat and 166 (21%) of 804 animals during 2011–14, and 16 (1%) of 1322 samples from inpatients with infection.

The emergence of MCR-1 heralds the breach of the last group of antibiotics, polymyxins, by plasmid-mediated resistance. Although currently confined to China, MCR-1 is likely to emulate other global resistance mechanisms such as NDM-1. Our findings emphasise the urgent need for coordinated global action in the fight against pan-drug-resistant Gram-negative bacteria.

references:

 

Researchers discover signaling molecule that helps neurons find their way in the developing brain

November 20, 2015

http://www.kurzweilai.net/researchers-discover-signaling-molecule-that-helps-neurons-find-their-way-in-the-developing-brain

This image shows a section of the spinal cord of a mouse embryo. Neurons appear green. Commissural axons (which connect the two sides of the brain) appear as long, u-shaped threads, and the bottom, yellow segment of the structure represents the midline (between brain hemispheres). (credit: Laboratory of Brain Development and Repair/ The Rockefeller University)

Rockefeller University researchers have discovered a molecule secreted by cells in the spinal cord that helps guide axons (neuron extensions) during a critical stage of central nervous system development in the embryo. The finding helps solve the mystery: how do the billions of neurons in the embryo nimbly reposition themselves within the brain and spinal cord, and connect branches to form neural circuits?

Working in mice, the researchers identified an axon guidance factor, NELL2, and explained how it makes commissural axons (which connect the two sides of the brain).

The findings could help scientists understand what goes wrong in a rare disease called horizontal gaze palsy with progressive scoliosis. People affected by the condition often suffer from abnormal spine curvature, and are unable to move their eyes horizontally from side to side. The study was published Thursday Nov. 19 in the journal Science.

Abstract of Operational redundancy in axon guidance through the multifunctional receptor Robo3 and its ligand NELL2

Axon pathfinding is orchestrated by numerous guidance cues, including Slits and their Robo receptors, but it remains unclear how information from multiple cues is integrated or filtered. Robo3, a Robo family member, allows commissural axons to reach and cross the spinal cord midline by antagonizing Robo1/2–mediated repulsion from midline-expressed Slits and potentiating deleted in colorectal cancer (DCC)–mediated midline attraction to Netrin-1, but without binding either Slits or Netrins. We identified a secreted Robo3 ligand, neural epidermal growth factor-like-like 2 (NELL2), which repels mouse commissural axons through Robo3 and helps steer them to the midline. These findings identify NELL2 as an axon guidance cue and establish Robo3 as a multifunctional regulator of pathfinding that simultaneously mediates NELL2 repulsion, inhibits Slit repulsion, and facilitates Netrin attraction to achieve a common guidance purpose.

references:

Topics: Cognitive Science/Neuroscience

A sensory illusion that makes yeast cells self-destruct

A possible tactic for cancer therapeutics
November 20, 2015

http://www.kurzweilai.net/a-sensory-illusion-that-makes-yeast-cells-self-destruct

 

Effects of osmotic changes on yeast cell growth. (A) Schematic of the flow chamber used to create osmotic level oscillations for different periods of time. (B) Cell growth for these periods. The graphs show the average number of progeny cells (blue) before and after applying stress for different periods (gray shows orginal “no stress” line). The inset shows representative images of cells for two periods. (credit: Amir Mitchell et al./Science)

UC San Francisco researchers have discovered that even brainless single-celled yeast have “sensory biases” that can be hacked by a carefully engineered illusion — a finding that could be used to develop new approaches to fighting diseases such as cancer.

In the new study, published online Thursday November 19 in Science Express, Wendell Lim, PhD, the study’s senior author*, and his team discovered that yeast cells falsely perceive a pattern of osmotic levels (by applying potassium chloride) that alternate in eight minute intervals as massive, continuously increasing stress. In response, the microbes over-respond and kill themselves. (In their natural environment, salt stress normally gradually increases.)

The results, Lim says, suggest a whole new way of looking at the perceptual abilities of simple cells and this power of illusion could even be used to develop new approaches to fighting cancer and other diseases.

“Our results may also be relevant for cellular signaling in disease, as mutations affecting cellular signaling are common in cancer, autoimmune disease, and diabetes,” the researchers conclude in the paper. “These mutations may rewire the native network, and thus could modify its activation and adaptation dynamics. Such network rewiring in disease may lead to changes that can be most clearly revealed by simulation with oscillatory inputs or other ‘non-natural’ patterns.

“The changes in network response behaviors could be exploited for diagnosis and functional profiling of disease cells, or potentially taken advantage of as an Achilles’ heel to selectively target cells bearing the diseased network.”

https://youtu.be/CuDjZrM8xtA
UC San Francisco (UCSF) | Sensory Illusion Causes Cells to Self-Destruct

* Chair of the Department of Cellular and Molecular Pharmacology at UCSF, director of the UCSF Center for Systems and Synthetic Biology, and a Howard Hughes Medical Institute (HHMI) investigator.

** Normally, sensor molecules in a yeast cell detect changes in salt concentration and instruct the cell to respond by producing a protective chemical. The researchers found that the cells were perfectly capable of adapting when they flipped the salt stress on and off every minute or every 32 minutes. But to their surprise, when they tried an eight-minute oscillation of precisely the same salt level the cells quickly stopped growing and began to die off.

Abstract of Oscillatory stress stimulation uncovers an Achilles’ heel of the yeast MAPK signaling network

Cells must interpret environmental information that often changes over time. We systematically monitored growth of yeast cells under various frequencies of oscillating osmotic stress. Growth was severely inhibited at a particular resonance frequency, at which cells show hyperactivated transcriptional stress responses. This behavior represents a sensory misperception—the cells incorrectly interpret oscillations as a staircase of ever-increasing osmolarity. The misperception results from the capacity of the osmolarity-sensing kinase network to retrigger with sequential osmotic stresses. Although this feature is critical for coping with natural challenges—like continually increasing osmolarity—it results in a tradeoff of fragility to non-natural oscillatory inputs that match the retriggering time. These findings demonstrate the value of non-natural dynamic perturbations in exposing hidden sensitivities of cellular regulatory networks.

references:

Topics: Biotech

Google Glass helps cardiologists complete difficult coronary artery blockage surgery

November 20, 2015

http://www.kurzweilai.net/google-glass-helps-cardiologists-in-challenging-coronary-artery-blockage-surgery

 

Google Glass allowed the surgeons to clearly visualize the distal coronary vessel and verify the direction of the guide wire advancement relative to the course of the occluded vessel segment. (credit: Maksymilian P. Opolski et al./Canadian Journal of Cardiology

Cardiologists from the Institute of Cardiology, Warsaw, Poland have used Google Glass in a challenging surgical procedure, successfully clearing a blockage in the right coronary artery of a 49-year-old male patient and restoring blood flow, reports the Canadian Journal of Cardiology.

Chronic total occlusion, a complete blockage of the coronary artery, sometimes referred to as the “final frontier in interventional cardiology,” represents a major challenge for catheter-based percutaneous coronary intervention (PCI), according to the cardiologists.

That’s because of the difficulty of recanalizing (forming new blood vessels through an obstruction) combined with poor visualization of the occluded coronary arteries.

Coronary computed tomography angiography (CTA) is increasingly used to provide physicians with guidance when performing PCI for this procedure. The 3-D CTA data can be projected on monitors, but this technique is expensive and technically difficult, the cardiologists say.

So a team of physicists from the Interdisciplinary Centre for Mathematical and Computational Modelling of theUniversity of Warsaw developed a way to use Google Glass to clearly visualize the distal coronary vessel and verify the direction of the guide-wire advancement relative to the course of the blocked vessel segment.

Three-dimensional reconstructions displayed on Google Glass revealed the exact trajectory of the distal right coronary artery (credit: Maksymilian P. Opolski et al./Canadian Journal of Cardiology)

The procedure was completed successfully, including implantation of two drug-eluting stents.

“This case demonstrates the novel application of wearable devices for display of CTA data sets in the catheterization laboratory that can be used for better planning and guidance of interventional procedures, and provides proof of concept that wearable devices can improve operator comfort and procedure efficiency in interventional cardiology,” said lead investigatorMaksymilian P. Opolski, MD, PhD, of the Department of Interventional Cardiology and Angiology at the Institute of Cardiology, Warsaw, Poland.

“We believe wearable computers have a great potential to optimize percutaneous revascularization, and thus favorably affect interventional cardiologists in their daily clinical activities,” he said. He also advised that “wearable devices might be potentially equipped with filter lenses that provide protection against X-radiation.

Abstract of First-in-Man Computed Tomography-Guided Percutaneous Revascularization of Coronary Chronic Total Occlusion Using a Wearable Computer: Proof of Concept

We report a case of successful computed tomography-guided percutaneous revascularization of a chronically occluded right coronary artery using a wearable, hands-free computer with a head-mounted display worn by interventional cardiologists in the catheterization laboratory. The projection of 3-dimensional computed tomographic reconstructions onto the screen of virtual reality glass allowed the operators to clearly visualize the distal coronary vessel, and verify the direction of the guide wire advancement relative to the course of the occluded vessel segment. This case provides proof of concept that wearable computers can improve operator comfort and procedure efficiency in interventional cardiology.

references:

Topics: Biomed/Longevity | VR/Augmented Reality/Computer Graphics

Modulating brain’s stress circuity might prevent Alzheimer’s disease

Drug significantly prevented onset of cognitive and cellular effects in mice
November 17, 2015

http://www.kurzweilai.net/modulating-brains-stress-circuity-might-prevent-alzheimers-disease

 

Effect of drug treatment on AD mice in control group (left) or drug (right) on Ab plaque load. (credit: Cheng Zhang et al./Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association)

In a novel animal study design that mimicked human clinical trials, researchers at University of California, San Diego School of Medicine report that long-term treatment using a small-molecule drug that reduces activity of  the brain’s stress circuitry significantly reduces Alzheimer’s disease (AD) neuropathology and prevents onset of cognitive impairment in a mouse model of the neurodegenerative condition.

The findings are described in the current online issue of the journal Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association.

Previous research has shown a link between the brain’s stress signaling pathways and AD. Specifically, the release of a stress-coping hormone called corticotropin-releasing factor (CRF), which is widely found in the brain and acts as a neurotransmitter/neuromodulator, is dysregulated in AD and is associated with impaired cognition and with detrimental changes in tau protein and increased production of amyloid-beta protein fragments that clump together and trigger the neurodegeneration characteristic of AD.

“Our work and that of our colleagues on stress and CRF have been mechanistically implicated in Alzheimer’s disease, but agents that impact CRF signaling have not been carefully tested for therapeutic efficacy or long-term safety in animal models,” said the study’s principal investigator and corresponding author Robert Rissman, PhD, assistant professor in the Department of Neurosciences and Biomarker Core Director for the Alzheimer’s Disease Cooperative Study (ADCS).

The researchers determined that modulating the mouse brain’s stress circuitry mitigated generation and accumulation of amyloid plaques widely attributed with causing neuronal damage and death. As a consequence, behavioral indicators of AD were prevented and cellular damage was reduced.  The mice began treatment at 30-days-old — before any pathological or cognitive signs of AD were present — and continued until six months of age.

One particular challenge, Rissman noted, is limiting exposure of the drug to the brain so that it does not impact the body’s ability to respond to stress. “This can be accomplished because one advantage of these types of small molecule drugs is that they readily cross the blood-brain barrier and actually prefer to act in the brain,” Rissman said.

“Rissman’s prior work demonstrated that CRF and its receptors are integrally involved in changes in another AD hallmark, tau phosphorylation,” said William Mobley, MD, PhD, chair of the Department of Neurosciences and interim co-director of the Alzheimer’s Disease Cooperative Study at UC San Diego. “This new study extends those original mechanistic findings to the amyloid pathway and preservation of cellular and synaptic connections.  Work like this is an excellent example of UC San Diego’s bench-to-bedside legacy, whereby we can quickly move our basic science findings into the clinic for testing,” said Mobley.

Rissman said R121919 was well-tolerated by AD mice (no significant adverse effects) and deemed safe, suggesting CRF-antagonism is a viable, disease-modifying therapy for AD. Drugs like R121919 were originally designed to treat generalized anxiety disorder, irritable bowel syndrome and other diseases, but failed to be effective in treating those disorders.

Rissman noted that repurposing R121919 for human use was likely not possible at this point. He and colleagues are collaborating with the Sanford Burnham Prebys Medical Discovery Institute to design new assays to discover the next generation of CRF receptor-1 antagonists for testing in early phase human safety trials.

“More work remains to be done, but this is the kind of basic research that is fundamental to ultimately finding a way to cure — or even prevent —Alzheimer’s disease,” said David Brenner, MD, vice chancellor, UC San Diego Health Sciences and dean of UC San Diego School of Medicine. “These findings by Dr. Rissman and his colleagues at UC San Diego and at collaborating institutions on the Mesa suggest we are on the cusp of creating truly effective therapies.”

Abstract of Corticotropin-releasing factor receptor-1 antagonism mitigates beta amyloid pathology and cognitive and synaptic deficits in a mouse model of Alzheimer’s disease

Introduction: Stress and corticotropin-releasing factor (CRF) have been implicated as mechanistically involved in Alzheimer’s disease (AD), but agents that impact CRF signaling have not been carefully tested for therapeutic efficacy or long-term safety in animal models.

Methods: To test whether antagonism of the type-1 corticotropin-releasing factor receptor (CRFR1) could be used as a disease-modifying treatment for AD, we used a preclinical prevention paradigm and treated 30-day-old AD transgenic mice with the small-molecule, CRFR1-selective antagonist, R121919, for 5 months, and examined AD pathologic and behavioral end points.

Results: R121919 significantly prevented the onset of cognitive impairment in female mice and reduced cellular and synaptic deficits and beta amyloid and C-terminal fragment-β levels in both genders. We observed no tolerability or toxicity issues in mice treated with R121919.

Discussion: CRFR1 antagonism presents a viable disease-modifying therapy for AD, recommending its advancement to early-phase human safety trials.

references:

Topics: Cognitive Science/Neuroscience

Allen Institute researchers decode patterns that make our brains human
Conserved gene patterning across human brains provide insights into health and disease
November 17, 2015

http://www.kurzweilai.net/allen-institute-researchers-decode-patterns-that-make-our-brains-human

 

Percentage of known neuron-, astrocyte- and oligodendrocyte-enriched genes in 32 modules, ordered by proportion of neuron-enriched gene membership. (credit: Michael Hawrylycz et al./Nature Neuroscience)

Allen Institute researchers have identified a surprisingly small set of just 32 gene-expression patterns for all 20,000 genes across 132 functionally distinct human brain regions, and these patterns appear to be common to all individuals.

In research published this month in Nature Neuroscience, the researchers used data for six brains from the publicly available Allen Human Brain Atlas. They believe the study is important because it could provide a baseline from which deviations in individuals may be measured and associated with diseases, and could also provide key insights into the core of the genetic code that makes our brains distinctly human.

While many of these patterns were similar in human and mouse, many genes showed different patterns in human. Surprisingly, genes associated with neurons were most conserved (consistent) across species, while those for the supporting glial cells showed larger differences. The most highly stable genes (the genes that were most consistent across all brains) include those associated with diseases and disorders like autism and Alzheimer’s, and these genes include many existing drug targets.

These patterns provide insights into what makes the human brain distinct and raise new opportunities to target therapeutics for treating disease.

The researchers also found that the pattern of gene expression in cerebral cortex is correlated with “functional connectivity” as revealed by neuroimaging data from the Human Connectome Project.

“The human brain is phenomenally complex, so it is quite surprising that a small number of patterns can explain most of the gene variability across the brain,” says Christof Koch, Ph.D., President and Chief Scientific Officer at the Allen Institute for Brain Science. “There could easily have been thousands of patterns, or none at all. This gives us an exciting way to look further at the functional activity that underlies the uniquely human brain.”

Abstract of Canonical genetic signatures of the adult human brain

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry.

references:

Topics: Biotech

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Evolutionary Change

Posted in Curation, Gene Regulation and Evolution, Genome Biology, Metabolism, Microbiology, Parasitology, Pharmaceutical Analytics, Pharmacogenomics, tagged , , , on November 20, 2015| Leave a Comment »

Evolutionary Change

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

Change accelerates stalled evolution

biomolbioandco    https://biomolbioandco.wordpress.com/2015/11/17/change-accelerates-stalled-evolution/

Evolution can get stuck. When no mutations are available that can improve the fitness of an organism, evolution cannot proceed. However, using environmental fluctuations that are ubiquitous in nature, evolution can proceed. In the preprint that we posted earlier on the bioRxiv and which has recently been published in PNAS we describe how a transcription factor and its binding site, constraint in the different constant environments, can evolve in fluctuating environments.

Stalled evolution

Concept of fitness landscape. From de Visser & Krug,Nature Reviews Genetics 15, 480–490 (2014)

Concept of fitness landscape. From de Visser & Krug, Nature Reviews Genetics 15, 480–490 (2014)

 

 

The accessibility of phenotypes in different environments depends on the wiring of the genotype-phenotype map and the translation of this map into fitness. When sub-optimal genotypes are surrounded by valleys in the adaptive landscape, neighboring genotypes are inaccessible and evolution is unable to proceed by single mutational step-by-step positive Darwinian evolution (Figure 1).

To investigate the connectedness of the fitness increasing genotypes in sequence space we used the lac regulatory system in Escherichia coli. Decades of work have elucidated the physiology of the lac regulatory system. And it is known that a few base pairs in the operator DNA, and a few amino acid residues in the transcription factor are responsible for specificity of binding of these operator-repressor pairs. We here experimentally constructed mutants with mutations in these specific residues (6 residues, yielding 26=64 mutants in total) that together constitute 6!=720 direct trajectories.

Assessing the ability to repress the lac operon in one environment (without a lactose-sugar-derivative), and the ability to express the lac operon in the other environment (with a lactose-sugar-derivative), we find that none of the mutational trajectories allows continuous improvements along the mutational trajectories in one of the constant environments. Interestingly, we find that alternating between these environments doesallow for constant improvements along the mutational trajectories. We find that the shortest route towards the final genotype is of Hamming distance 6, there is thus a direct mutational trajectory from the starting sequence to the final combination of transcription-factor and binding site. With a computational method that describes the mutational and environmental transitions as a Markov process, we can further calculate the crossing rates from the initial to the final genotype for all trajectories in the landscape, allowing mutational detours. We find that the crossing rate is maximal when the environmental switches are on the order of the mutation rate (or the rate at which a sweep can be completed).

Tradeoffs are crucial for crossing the adaptive landscape in fluctuating environments

Cross-environmental tradeoffs are responsible for these continuous improvements. In the most extreme case, suboptimal peaks are translated into valleys, by which constraints are resolved. In the more subtle case, descending slopes are turned into ascending slopes upon environmental change, allowing adaptive trajectories to surf over the slopes with positive selective coefficients. Evolutionary constraints can thus be overcome by the environment-dependent ‘ratcheting’ that allows the crossing of otherwise inaccessible regions in sequence space (Figure 2).

 

multipeaked_trajectory_2env

 

We think that this research not only aids the fundamental understanding of ecological and evolutionary transitions in fluctuating environments, but that it can also help rethinking the evolutionary optimization of certain biotechnological processes (for instance the production of antibodies). And in addition, it cautions against the use of cyclic multi-drug protocols in clinical treatments, as these might potentially increase the speed of adaptation to the drugs, instead of halting it.

Breaking evolutionary constraint with a tradeoff ratchet
M.G.J. de Vos, A. Dawid, V. Sunderlikova, S.J. Tans
PNAS, (2015) | http://dx.doi.org/10.1073/pnas.1510282112

 

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Antibiotic Resistance

Posted in Bacterial Resistance, Biological Networks, Gene Regulation and Evolution, Cell Biology, Chemical Genetics, Clinical & Translational, Clinical Genomics, Curation, Disease Biology, Gene Regulation and Evolution, Genetics & Pharmaceutical, Microbiologial genetics, Microbiology, Molecular Genetics & Pharmaceutical, tagged on November 19, 2015| Leave a Comment »

Antibiotic Resistance

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Resistance Gene to Last Line of Antibiotic Defense Has Emerged

http://www.genengnews.com/gen-news-highlights/resistance-gene-to-last-line-of-antibiotic-defense-has-emerged/81252000/

Drug resistance can often emerge due to the selective pressure of antibiotic use on a microbial population. [NIAID]

 

Until recently, resistance to the polymyxin class of antibiotics—the last line of microbial defense—was thought to be highly improbable. However now, Chinese scientists have discovered a new gene, called mcr-1 that is widespread among Enterobacteriaceae, a large family of Gram-negative bacteria that include a variety of human pathogens, after taking samples from pigs and patients in South China.

“These are extremely worrying results. The polymyxins (colistin and polymyxin B) were the last class of antibiotics in which resistance was incapable of spreading from cell to cell. Until now, colistin resistance resulted from chromosomal mutations, making the resistance mechanism unstable and incapable of spreading to other bacteria,” explained co-author Jian-Hua Liu, Ph.D., a professor at the South China Agricultural University in Guangzhou, China. “Our results reveal the emergence of the first polymyxin resistance gene that is readily passed between common bacteria such as Escherichia coli and Klebsiella pneumoniae, suggesting that the progression from extensive drug resistance to pandrug resistance is inevitable.”

The investigators found the mcr-1 gene on plasmids within various bacterial strains, suggesting an alarming potential to spread and differentiate between diverse microbial populations.

The findings from this study were published recently in The Lancet Infectious Diseases through an article entitled “Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study.”

The researchers stumbled across the mcr-1 gene while performing routine testing of livestock for antimicrobial resistance on a pig farm in Shanghai. This prompted the researchers to collect bacteria samples from pigs at slaughter across four provinces, and from pork and chicken sold in 30 open markets and 27 supermarkets across Guangzhou between 2011 and 2014. Additionally, the scientists analyzed bacteria samples from patients presenting with infections at two hospitals in Guangdong and Zhejiang provinces.

What they found was troubling to say the least, as a high prevalence of the mcr-1 gene in E. coli was observed in isolates from animal (166 of 804) and raw meat samples (78 of 523). Moreover, the proportion of positive samples has been observed to be increasing from year to year.

The scientists also found that the transfer rate of the mcr-1 gene was very high between E. coli strains and that it has a strong potential to spread into other epidemic pathogenic bacterial species such asK. pneumoniae and Pseudomonas aeruginosa—making the rapid dissemination into humans very likely.

“Because of the relatively low proportion of positive samples taken from humans compared with animals, it is likely that mcr-1 mediated colistin resistance originated in animals and subsequently spread to humans,” noted senior author Jianzhong Shen, Ph.D., professor at the China Agricultural University in Beijing, China. “The selective pressure imposed by increasingly heavy use of colistin in agriculture in China could have led to the acquisition of mcr-1 by E. coli.”

The importance of selective pressure on this resistance gene becomes even more evident when considering the fact that China is one of the world’s largest users and producers of colistin for agriculture and veterinary use. Worldwide, the demand for colistin in agriculture is expected to reach almost 12,000 tons per year by the end of 2015, rising to 16,500 tons by 2021.

“The emergence of mcr-1 heralds the breach of the last group of antibiotics,” the authors stated. “Although currently confined to China, mcr-1 is likely to emulate other resistance genes such as blaNDM-1 and spread worldwide. There is a critical need to re-evaluate the use of polymyxins in animals and for very close international monitoring and surveillance of mcr-1 in human and veterinary medicine.”

 

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study  

Yi-Yun Liu, Yang Wang, Timothy R Walsh, Ling-Xian Yi, Rong Zhang, James Spencer, et al.

DOI: http://dx.doi.org/10.1016/S1473-3099(15)00424-7      http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(15)00424-7/abstract

Background

Until now, polymyxin resistance has involved chromosomal mutations but has never been reported via horizontal gene transfer. During a routine surveillance project on antimicrobial resistance in commensal Escherichia coli from food animals in China, a major increase of colistin resistance was observed. When an E coli strain, SHP45, possessing colistin resistance that could be transferred to another strain, was isolated from a pig, we conducted further analysis of possible plasmid-mediated polymyxin resistance. Herein, we report the emergence of the first plasmid-mediated polymyxin resistance mechanism, MCR-1, in Enterobacteriaceae.

Methods

The mcr-1 gene in E coli strain SHP45 was identified by whole plasmid sequencing and subcloning. MCR-1 mechanistic studies were done with sequence comparisons, homology modelling, and electrospray ionisation mass spectrometry. The prevalence of mcr-1 was investigated in E coli andKlebsiella pneumoniae strains collected from five provinces between April, 2011, and November, 2014. The ability of MCR-1 to confer polymyxin resistance in vivo was examined in a murine thigh model.

Findings

Polymyxin resistance was shown to be singularly due to the plasmid-mediated mcr-1 gene. The plasmid carrying mcr-1 was mobilised to an E coli recipient at a frequency of 10−1 to 10−3 cells per recipient cell by conjugation, and maintained in K pneumoniae and Pseudomonas aeruginosa. In an in-vivo model, production of MCR-1 negated the efficacy of colistin. MCR-1 is a member of the phosphoethanolamine transferase enzyme family, with expression in E coli resulting in the addition of phosphoethanolamine to lipid A. We observed mcr-1 carriage in E coli isolates collected from 78 (15%) of 523 samples of raw meat and 166 (21%) of 804 animals during 2011–14, and 16 (1%) of 1322 samples from inpatients with infection.

Interpretation

The emergence of MCR-1 heralds the breach of the last group of antibiotics, polymyxins, by plasmid-mediated resistance. Although currently confined to China, MCR-1 is likely to emulate other global resistance mechanisms such as
NDM-1. Our findings emphasise the urgent need for coordinated global action in the fight against pan-drug-resistant Gram-negative bacteria.

 

Colistin resistance: a major breach in our last line of defence

David L Paterson, Patrick N A Harris
DOI: http://dx.doi.org/10.1016/S1473-3099(15)00463-6http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(15)00463-6/abstract
In hospital practice, clinicians have been buoyed by the recent development of new antibiotics active against multidrug resistant Gram-negative bacilli. However, recently approved antibiotics like ceftazidime-avibactam or ceftolozane-tazobactam do not provide activity against all Gram-negative bacilli, with notable gaps in their coverage, including the notorious New Delhi metallo-β-lactamase 1-producing organisms and many strains of carbapenem resistant Acinetobacter baumannii. For this reason, the polymyxins (colistin and polymyxin B) remain the last line of defence against many Gram-negative bacilli.
References
  1. The White House Office of the Press Secretary. FACT SHEET: Obama Administration Releases National Action Plan to Combat Antibiotic-Resistant Bacteria. https://www.whitehouse.gov/the-press-office/2015/03/27/fact-sheet-obama-administration-releases-national-action-plan-combat-ant. ((accessed Oct 20, 2015).)
  2. Walsh, F. Antibiotic resistance: Cameron warns of medical ‘dark ages’.http://www.bbc.co.uk/news/health-28098838. ((accessed Oct 20, 2015).)
  3. WHO. Antimicrobial resistance: global report on surveillance 2014. Wolrd Health Organization,Geneva; 2014http://www.who.int/drugresistance/documents/surveillancereport/en/. ((accessed Oct 20, 2015).)
  4. McKenna, M. CDC Threat Report: We will soon be in a post-antibiotic era. Wired. Sept 16, 2013;http://www.wired.com/2013/09/cdc-amr-rpt1/. ((accessed Oct 20, 2015).)
  5. Kumarasamy, KK, Toleman, MA, Walsh, TR et al. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study.Lancet Infect Dis. 2010; 10: 597–602
  6. Munoz-Price, LS, Poirel, L, Bonomo, RA et al. Clinical epidemiology of the global expansion ofKlebsiella pneumoniae carbapenemases. Lancet Infect Dis. 2013; 13: 785–796
  7. Falagas, ME, Karageorgopoulos, DE, and Nordmann, P. Therapeutic options for infections with Enterobacteriaceae producing carbapenem-hydrolyzing enzymes. Future Microbiol. 2011; 6: 653–666
  8. Halaby, T, Al Naiemi, N, Kluytmans, J, van der Palen, J, and Vandenbroucke-Grauls, CM.Emergence of colistin resistance in Enterobacteriaceae after the introduction of selective digestive tract decontamination in an intensive care unit. Antimicrob Agents Chemother. 2013; 57: 3224–3229

 

https://www.reddit.com/r/science/comments/3tdyaz/emergence_of_plasmidmediated_colistin_resistance/

This is my second attempt at my first time contributing a link so hopefully this is the correct subreddit. This really highlights why research focused on discovery of novel antibiotics and resistance modifying agents is so important.  The article is summarized in the BBC: http://www.bbc.com/news/health-34857015

 

What a shame this isn’t getting any more attention in the news, antibiotic resistance is becoming more and more of a problem, and nobody is giving a fuck it seems. Colistin is used as a last defense against extensive resistant Gram-negative bacteria, and if resistance against it now also comes in a plasmid flavor, implications could be big.

 

Yes, the gene has been known for a fair amount of time but the fact it is now in plasmids that can easily transfect other bacteria is a bit disconcerting. Hopefully some of the new soil cultured classes of antibiotics make it into clinical settings soon.

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Genomic Pathogen Typing

Posted in Clinical & Translational, Clinical Diagnostics, Computational Biology/Systems and Bioinformatics, CRISPR/Cas9 & Gene Editing, Curation, Genetics & Pharmaceutical, Genome Biology, Infectious Disease & New Antibiotic Targets, Microbiologial genetics, Microbiology, tagged , , , , , , , on November 16, 2015| Leave a Comment »

Genomic Pathogen Typing, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

Genomic Pathogen Typing

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Genomic Pathogen Typing Using Solid-State Nanopores

Allison H. Squires, Evrim Atas, Amit Meller

PLOS  Nov 12, 2015   DOI: http://dx.doi.org:/1371/journal.pone.0142944

Citation: Squires AH, Atas E, Meller A (2015) Genomic Pathogen Typing Using Solid-State Nanopores. PLoS ONE 10(11): e0142944.   http://dx.doi.org:/10.1371/journal.pone.0142944

Editor: Niyaz Ahmed, University of Hyderabad, INDIA

In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based “fingerprints” of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.

 

Subtle genetic changes in bacteria can produce large variations in factors affecting pathogenicity, such as toxicity, antibiotic resistance, and virulence. These genetic variations are not only used to trace the epidemic and phylogenetic relationships among strains of bacteria, but are also critically important in clinical settings for proper patient diagnosis and treatment. Most existing approaches require sample incubation and growth over the course of multiple days prior to testing, and nearly all require expert handling of samples and interpretation of results. Traditional phenotypic typing techniques such as serotypes, biotypes, phage-types, and antibiograms lack the necessary sensitivity to distinguish between closely related pathogen strains, and therefore fail to adequately capture these critical variations for clinical applications. Gel-based techniques such as restriction fragment length polymorphism (RFLP) or cleaved amplified polymorphic sequences (CAPS) require a large amount of time and results are not easily compared or transferred among labs. Next-generation sequencing is an increasingly popular method of fully characterizing bacterial strains [1] and may be used for typing strains according to the sequences of a panel of housekeeping genes, as in multi-locus sequence typing (MLST) [2], but this approach is more commonly used to trace post hoc epidemic and phylogenetic relationships among clinical isolates. Furthermore, the complexity and quantity of sequencing data far exceeds the minimum information required to efficiently and accurately diagnose a patient. For example, bioinformatics studies suggest that a panel of just 30–50 single nucleotide variations (SNVs) could be used to uniquely identify thousands of strains of Mycobacterium tuberculosis [3, 4]. Yet SNVs are not the only source of variation among pathogens; polymorphisms from SNVs and short indels up to genetic changes as large as whole plasmids or sets of genes may be responsible for critical changes to pathogenicity. Thus there exists a clear clinical need for a novel approach to molecular typing that can quickly and simply screen patient samples for a panel of widely varying known genetic polymorphisms of dangerous pathogens.

Solid-state nanopores may be used to discriminate the lengths of unlabeled individual biopolymers such as DNA molecules across a wide range of lengths [5, 6]. Biopolymers are electrophoretically attracted and threaded through a voltage-biased nanoscale pore drilled in an ultrathin freestanding SiNx membrane [7, 8]. When a DNA molecule is threaded through a nanopore, it partially blocks the flow of ions moving through the pore, allowing real-time detection of the analyte by monitoring changes in the ion current. Nanopore sensing is biochemically simple, as it does not require labeling of the analyte with radioactive or fluorescent probes, yet it can be used to detect minute quantities of nucleic acid molecules, surpassing the sensitivity of bulk methods [8]. Moreover, nanopore sensing involves relatively simple instrumentation (primarily a current amplifier) and may be used to analyze thousands of molecules in just a few minutes, making this technique an ideal candidate for applications such as nucleic acid based diagnostics.

Here we describe and practice a novel detection scheme (Fig 1) for molecular typing of pathogens using solid-state nanopores, and demonstrate its ability to discriminate a wide range of critical genetic polymorphisms in closely related organisms with starkly different pathogenicities. In the first sensing mode of our approach (Mode I), large insertions or deletions are detected by directly classifying the length of DNA in the nanopore. In the second sensing mode (Mode II), small indels down to SNVs may be detected by sequence-specific digestion at the site of the polymorphism to produce either one or two DNA fragments, which are then detected in the nanopore. We first characterize the practical range of our nanopore system for detecting variation in DNA length, and show that fragment length differences are more readily apparent for shorter DNA lengths and for asymmetric cut sites. We then demonstrate that statistical analysis tools such as Bayesian classifiers, commonly used for automated classification, are highly effective for rapid and statistically robust discrimination among different lengths and combinations of DNA fragments translocating through a nanopore, even in cases where significant portions of these distributions overlap. We apply these techniques to demonstrate polymorphism discrimination down to the single nucleotide level in prototypical strains of Mycobacterium tuberculosis (virulent vs. avirulent) and Streptococcus aureus(methicillin-resistant vs. multi-drug resistant). This highly versatile combination of rapid length and digest discrimination, spanning several orders of magnitude of possible genomic variation size, in a single, parallelizable device, could be extended to probe a large panel of critical sites within a genome for point-of-care determination of critical pathogenic properties and sequence typing.

Fig 1. Two Principal Modes for Nanopore Discrimination of Pathogen Genomic Variation.

http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0142944.g001

Fig 1. Two Principal Modes for Nanopore Discrimination of Pathogen Genomic Variation.

Mode I: Direct length detection according to analyte translocation dwell time and depth enables discrimination of longer vs. shorter fragments; i.e: whether or not an insertion or deletion is present (left). Mode II: Prior to translocation, samples are exposed to a restriction enzyme that cuts at the site of a SNV or short indel or mutation. Detection of cleaved vs. uncleaved DNA fragments in the nanopore reveals whether or not the critical genomic variation is present.

http://dx.doi.org:/10.1371/journal.pone.0142944.g001

Detection of DNA Sequence Polymorphisms in Solid-State Nanopores  

The simplest form of nanopore translocation analysis involves the measurement of the depth of each current blockade (ΔIB) and the dwell time of each molecule within the pore (tD). Both parameters have been shown to grow nonlinearly with DNA length, forming the basis for fragment length separation in the nanopore system. The statistical distributions of these independently measured quantities may be used to distinguish between analytes of different lengths, such as DNAs [5, 6, 9], or proteins having identical molecular weight but slightly different charge or 3D structure [10–13]. Variation in the translocation dwell-time (tD) in solid-state nanopores measured for different DNA lengths (l), are empirically described by a power law: tD ∼ lα where α = 1.38±0.02, which has been reproduced by multiple experimental approaches [5, 9, 14]. Using a log-scale distribution of translocation times to estimate the distribution of tD, note that the difference in log(tD) for two sequences (lengths l0 and l0 + Δl) is more apparent for shorter length l0 as compared with the insertions and deletions Δl (i.e. when Δl/l0 ∼ 1) according to Eq 1:(1)

If the presence of two fragment lengths must be identified from within a single sample, it is desirable that their distributions of ΔIB or tD should be as well-separated as possible. Furthermore, if the presence of a cut sample must be distinguished from an uncut sample, then by Eq 1 the peak produced by the shorter part of a cut sample will appear farther away from the uncut peak than the longer part of a cut sample. To statistically distinguish the samples, it is desirable for the peak of the shorter part to be as dissimilar as possible from the uncut peak. Therefore, asymmetrically cut DNA pieces from a restriction digest are more readily distinguished from the original uncut length than those produced by symmetrically positioned restriction sites, provided that the shorter piece is of sufficient length to be detected by the nanopore. In cases where separation between two similar length biopolymers (Δl/l0 ∼ 1) is required, the measured histograms of either ΔIB or tD may overlap significantly, making discrimination between these molecules difficult. Combinations of multiple fragment lengths within a sample pose additional challenges, as their more complicated distributions may overlap or otherwise preclude simple contour cluster separation.

In the context of sequence typing, identification of fragments by sizing will indicate the presence of specific insertions and deletions that may enhance or reduce pathogenicity or otherwise uniquely identify a pathogenic strain. Upper bounds on Δl are set by: 1) sample preparation parameters and limitations; for example, robust and fast PCR amplification is most easily achieved for fragment lengths of ~102–103 bp [15] and 2) nanopore stability considerations; for example, nanopores are more frequently clogged by very long DNA (>20 kbp). Lower bounds on l0 are set by nanopore sensitivity; while several groups have demonstrated detection of small DNA fragments (<50 bp) [16] we find that a minimum l0 on the order of ~100 bp is more reliable since it is readily detectable in small nanopores with no additional modifications [5], producing an extremely small fraction of missed events due to the finite system bandwidth. Thus a reasonable design range for sequence typing fragments is ~100 bp minimum length forl0, ranging up to a few thousand base pairs maximum length for l0 + Δl. Many types of common genetic variations used for strain typing fall within this size range. For example, one complete IS6110 (insertion-like sequence element) insertion in M. tuberculosis is 1358 bp [17]. At the other end of this range, multi-drug resistant strains of methicillin-resistant S. aureus (MRSA) have many insertions and deletions in the range 47 bp—643 bp that affect their pathogenicity [18]. To detect the smallest indels, which fall below the minimum detectable Δl, we turn to the exquisite sequence specificity of digestion by restriction enzymes, which can identify sequence polymorphisms down to a single nucleotide variation.

Using these design principles, we present here two alternative modes of detection that illustrate the wide range of genomic variations that may be detected using a single sensor. For large insertions or deletions (Fig 1: Mode I, left panel), a nanopore may be used to discriminate the raw change in DNA length caused by the presence or absence of this sequence according to the duration of translocation events. For short indels, mutations, or single nucleotide variations (SNVs) (Fig 1: Mode II, right panel), which are more difficult to identify solely by length as discussed above, we utilize a restriction enzyme. The sample is only cut in the presence (or absence) of the critical sequence, and subsequent detection in a nanopore reveals either one or two fragments in the nanopore according to the observed durations and blockage levels of translocation events.

Event Diagram Discrimination of Sample Length and Composition

We first experimentally illustrate the practical length resolution of the nanopore platform for identifying sample length and composition. We analyzed samples containing mixtures of DNA fragments composed of one or two well-defined lengths. The resulting event diagrams create unique fingerprints that can be used to distinguish different lengths of DNA (Mode I) or whether or not a fragment of DNA has been cut (Mode II). Fig 2A–2E show event diagrams for 100 bp, 200 bp, 900 bp, 1000 bp, and 100+900 bp DNA in a single nanopore (diameter 4.8 nm, effective height 7 nm) at +300 mV bias (for additional examples, see Figs B-E in S1 File). Here, each translocation event is represented by its corresponding ion current event amplitude (ΔIB) and dwell time (tD). From comparison of Fig 2A and 2D, it is evident that insertions and deletions Δl several times larger than the base length (here: Δl:l0 = 9:1) are indeed easily distinguishable (Fig C in S1 File). Comparison of Fig 2A and 2B illustrates that Δl = 100 bp results in reasonably distinct event diagrams for l0 = 100 bp, which may be distinguished to >95% confidence with just a few events each, taking both dwell time and current amplitude into consideration (Fig D in S1 File). However, at l0 = 900 bp a minimum of several hundred events are required to confidently (>95%) differentiate l0 (Fig 2C) from l0 + Δl (1000 bp, Fig 2D), since their event diagrams overlap significantly (Fig E in S1 File). Returning to Eq 1, for Δl = 100 bp, we expect Δlog(tD) = 0.415 for l0 = 100 bp, and Δlog(tD) = 0.063 for l0 = 900 bp. For the data shown in Fig 2F, Δlog(tD) = 0.1 for l0 = 100 bp, and Δlog(tD) = 0.03 for l0 = 900 bp. The inability to easily and quickly discriminate the 900 bp DNA from the 1000 bp DNA demonstrates the practical limits set on Mode I sample identification according to the size of the insertion or deletion that must be detected.

Fig 2. Translocation Event Diagrams Uniquely Identify DNA Fragment Lengths in a Single Nanopore.

http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0142944.g002

Fig 2. Translocation Event Diagrams Uniquely Identify DNA Fragment Lengths in a Single Nanopore.

(a) 100 bp at 1 nM. (b) 200 bp at 1 nM. (c) 900 bp at 1 nM. (d) 1000 bp at 1 nM. (e) 1:1 combination of 100 bp and 900 bp, total concentration 2 nM. (f) Semilog(x) distributions of translocation dwell times for all samples (a)-(e). Translocations for all samples were collected in a single nanopore (4.8 nm diameter, effective thickness ~7 nm) with a +300 mV bias relative to trans (open pore current: 13 nA). To facilitate visualization of population density, a random white noise offset below the acquisition rate of this data (-2 μs < Δt < +2 μs, acquisition rate 250 kHz) has been added to each tD.    http://dx.doi.org:/10.1371/journal.pone.0142944.g002

Fig 2E illustrates how Mode II may overcome these limitations by digesting DNA into fragments: here, a highly asymmetric ratio of lengths in a mixed sample (100+900 bp) clearly facilitates sample identification as compared to the full length 1000 bp DNA (Fig 2D). However, Mode II also presents a more challenging case for quantitative discrimination between an uncut and a cut sample. Whereas single-length samples can be identified using either their tD or IB distribution (as shown in Fig 2F), the longer fragment in a cut sample may share significant overlap with the uncut sample. This is particularly true in the case of a highly asymmetric cut site.

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http://journals.plos.org/plosone/article/figure/image?size=inline&id=info:doi/10.1371/journal.pone.0142944.g003

Fig 3. Gaussian Mixture Models for Mode II Classification of 1000 bp vs. 900+100 bp DNA Fragments.

(a) 2-D GMM for 1000 bp DNA fragment translocations. (b) 2-D GMM for 900+100 bp DNA fragment translocations. (c) Bayesian posterior estimates p(A|Θ) of correctly identifying a data set Θ as Case A, calculated for each increment of N points in Θ, repeated 1000 times (first 50 shown in gray) and averaged (blue), each using M = 1500 points in the model data set. (d) Bayesian posterior estimates p(B|Θ) of correctly identifying a data set Θ as Case B, calculated for each increment of N points in Θ, repeated 1000 times (first 50 shown in gray) and averaged (red), all using M = 1500 points in the model data set. (e) Bayesian posterior estimates p(A|Θ) for test data sets ofN points given a model based on data set size M. Each point represents the average of 1000 separate bootstrap simulations. (f) Bayesian posterior estimates p(A|Θ) for test data sets of N points given a model based on data set size M. Each point represents the average of 1000 separate bootstrap simulations. Insets: range of N for which p(A|Θ) reaches 0.95. See Methods and S1 File for complete numerical simulation details.    http://dx.doi.org:/10.1371/journal.pone.0142944.g003

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http://journals.plos.org/plosone/article/figure/image?size=inline&id=info:doi/10.1371/journal.pone.0142944.g004

Fig 4. Gaussian Mixture Models of DNA Fragments for Actual Mode II Pathogen Typing at the SNV Level.

(a) Diagram of the main steps in sample preparation, detection, and classification: PCR fragments from isolated pathogens are subjected to a restriction digest, which recognizes and cuts only one genomic variant. Nanopore translocations are used to classify the pathogen according to the combination of fragment lengths detected. (b) ThemazG gene of the avirulent M. tuberculosis strain H37Ra is not cut by NaeI (942 bp), while the same gene in the closely related virulent strain H37Rv, which differs by only a single A-to-C mutation, is cut by NaeI (621bp + 321 bp). (c) Gaussian mixture model (one component) fit to translocations of mazG fragments from H37Ra. (d) Gaussian mixture model (two components) fit to translocations of mazG fragments from H37Rv. (e) Posterior probabilities for correctly identifying the H37Ra and H37Rv strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data. (f) The parC gene of the multi-drug-resistant MRSA strain FPR3757 is not cut by BseRI (886 bp) due to a single C-to-A mutation, while the closely related and less resistant strain HOU-MR is cut by BseRI (640bp + 245 bp). (g) Gaussian mixture model (one component) fit to translocations of parC fragments from FPR3757. (h) Gaussian mixture model (two components) fit to translocations of parC fragments from HOU-MR. (i) Posterior probabilities for correctly identifying the FPR3757 and HOU-MR strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data.    http://dx.doi.org:/10.1371/journal.pone.0142944.g004

Conclusion

Solid-state nanopore based biosensing is a rapidly growing field due to its practical and conceptual simplicity, portability and versatility. To date, few reports have demonstrated the utility of the method towards clinical diagnostic applications. Yet as we have shown here, nanopores are well-suited to make statistically robust diagnostic classifications among different DNA lengths with real single-molecule data, even in cases where the distributions significantly overlap. Utilizing a Bayesian statistical model, we have demonstrated that nanopore sensing can be used to discriminate among pathogens based on well-known genomic variations. Both large indels (Mode I) or short indels and single nucleotide variations (Mode II) can be targeted using proper sequence-specific digestion with off-the-shelf restriction enzymes. Furthermore, the Bayesian classifiers indicate the statistical confidence of each classification as a function of the number of nanopore events obtained in each measurement. Even at this preliminary stage of development we find that only a few tens of events (obtained in just a few minutes using a single pore) are sufficient to produce a statistically reliable result with well-defined and small error margins.

Our method is general and can be adapted to address many different “multiple-choice” clinical questions using a nanopore biosensor or other single molecule approaches. Future extensions of this work may seek to design and implement large panels of critical sites that represent the minimum sets necessary to characterize genomic variation for various applications in healthcare and research, and to develop additional sensing modalities. Although the primary design challenge currently remains linked to the location and availability of restriction digestion sites, we expect that the ongoing development of designer restriction enzymes, for example systems based on modular zinc fingers [27], TALENs [28], or CRISPR-like proteins will provide additional design flexibility for this technique.

The nanopore fingerprinting approach presented here addresses clear needs in clinical molecular diagnostics for a rapid and simple sensor that can identify a wide range of genomic variation in pathogens to inform treatment options. We have shown here discrimination of both large and small scale genomic variations between pathogen strains, down to single SNVs. The large, flexible sample design space for lengths, cut sites, and enzyme selection at each critical locus ensures that the technique is highly customizable for different genomic variation panels that could profile pathogenicity, antibiotic resistance, or even sequence type. The inherent scalability, minimal sample requirements, speed, and simple readout of the nanopore platform would all facilitate on-site and perhaps even automated use: As successive events are recorded, an increasingly clear fingerprint of translocation times and blockage levels will permit online software to “call” the sample as soon as enough events have been accumulated. Our technique is highly portable and customizable, and the binary data would be readily transferrable among different labs.

 

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Clinical Laboratory Challenges

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Clinical Laboratory Challenges

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

CLINICAL LABORATORY NEWS   

The Lab and CJD: Safe Handling of Infectious Prion Proteins

Author: Mari DeMarco, PhD  // Date: NOV.1.2015  // Source: Clinical Laboratory News

https://www.aacc.org/publications/cln/articles/2015/november/the-lab-and-cjd-safe-handling-of-infectious-prion-proteins

https://www.aacc.org/~/media/images/cln/articles/2015/november/prion-protiens.jpg

Body fluids from individuals with possible Creutzfeldt-Jakob disease (CJD) present distinctive safety challenges for clinical laboratories. Sporadic, iatrogenic, and familial CJD (known collectively as classic CJD), along with variant CJD, kuru, Gerstmann-Sträussler-Scheinker, and fatal familial insomnia, are prion diseases, also known as transmissible spongiform encephalopathies. Prion diseases affect the central nervous system, and from the onset of symptoms follow a typically rapid progressive neurological decline. While prion diseases are rare, it is not uncommon for the most prevalent form—sporadic CJD—to be included in the differential diagnosis of individuals presenting with rapid cognitive decline. Thus, laboratories may deal with a significant number of possible CJD cases, and should have protocols in place to process specimens, even if a confirmatory diagnosis of CJD is made in only a fraction of these cases.

The Lab’s Role in Diagnosis

Laboratory protocols for handling specimens from individuals with possible, probable, and definitive cases of CJD are important to ensure timely and appropriate patient management. When the differential includes CJD, an attempt should be made to rule-in or out other causes of rapid neurological decline. Laboratories should be prepared to process blood and cerebrospinal fluid (CSF) specimens in such cases for routine analyses.

Definitive diagnosis requires identification of prion aggregates in brain tissue, which can be achieved by immunohistochemistry, a Western blot for proteinase K-resistant prions, and/or by the presence of prion fibrils. Thus, confirmatory diagnosis is typically achieved at autopsy. A probable diagnosis of CJD is supported by elevated concentration of 14-3-3 protein in CSF (a non-specific marker of neurodegeneration), EEG, and MRI findings. Thus, the laboratory may be required to process and send CSF samples to a prion surveillance center for 14-3-3 testing, as well as blood samples for sequencing of the PRNP gene (in inherited cases).

Processing Biofluids

Laboratories should follow standard protective measures when working with biofluids potentially containing abnormally folded prions, such as donning standard personal protective equipment (PPE); avoiding or minimizing the use of sharps; using single-use disposable items; and processing specimens to minimize formation of aerosols and droplets. An additional safety consideration is the use of single-use disposal PPE; otherwise, re-usable items must be either cleaned using prion-specific decontamination methods, or destroyed.

Blood. In experimental models, infectivity has been detected in the blood; however, there have been no cases of secondary transmission of classical CJD via blood product transfusions in humans. As such, blood has been classified, on epidemiological evidence by the World Health Organization (WHO), as containing “no detectible infectivity,” which means it can be processed by routine methods. Similarly, except for CSF, all other body fluids contain no infectivity and can be processed following standard procedures.

In contrast to classic CJD, there have been four cases of suspected secondary transmission of variant CJD via transfused blood products in the United Kingdom. Variant CJD, the prion disease associated with mad cow disease, is unique in its distribution of prion aggregates outside of the central nervous system, including the lymph nodes, spleen, and tonsils. For regions where variant CJD is a concern, laboratories should consult their regulatory agencies for further guidance.

CSF. Relative to highly infectious tissues of the brain, spinal cord, and eye, infectivity has been identified less often in CSF and is considered to have “low infectivity,” along with kidney, liver, and lung tissue. Since CSF can contain infectious material, WHO has recommended that analyses not be performed on automated equipment due to challenges associated with decontamination. Laboratories should perform a risk assessment of their CSF processes, and, if deemed necessary, consider using manual methods as an alternative to automated systems.

Decontamination

The infectious agent in prion disease is unlike any other infectious pathogen encountered in the laboratory; it is formed of misfolded and aggregated prion proteins. This aggregated proteinacious material forms the infectious unit, which is incredibly resilient to degradation. Moreover, in vitro studies have demonstrated that disrupting large aggregates into smaller aggregates increases cytotoxicity. Thus, if the aim is to abolish infectivity, all aggregates must be destroyed. Disinfectant procedures used for viral, bacterial, and fungal pathogens such as alcohol, boiling, formalin, dry heat (<300°C), autoclaving at 121°C for 15 minutes, and ionizing, ultraviolet, or microwave radiation, are either ineffective or variably effective against aggregated prions.

The only means to ensure no risk of residual infectious prions is to use disposable materials. This is not always practical, as, for instance, a biosafety cabinet cannot be discarded if there is a CSF spill in the hood. Fortunately, there are several protocols considered sufficient for decontamination. For surfaces and heat-sensitive instruments, such as a biosafety cabinet, WHO recommends flooding the surface with 2N NaOH or undiluted NaClO, letting stand for 1 hour, mopping up, and rinsing with water. If the surface cannot tolerate NaOH or NaClO, thorough cleaning will remove most infectivity by dilution. Laboratories may derive some additional benefit by using one of the partially effective methods discussed previously. Non-disposable heat-resistant items preferably should be immersed in 1N NaOH, heated in a gravity displacement autoclave at 121°C for 30 min, cleaned and rinsed in water, then sterilized by routine methods. WHO has outlined several alternate decontamination methods. Using disposable cover sheets is one simple solution to avoid contaminating work surfaces and associated lengthy decontamination procedures.

With standard PPE—augmented by a few additional safety measures and prion-specific decontamination procedures—laboratories can safely manage biofluid testing in cases of prion disease.

 

The Microscopic World Inside Us  

Emerging Research Points to Microbiome’s Role in Health and Disease

Author: Deborah Levenson  // Date: NOV.1.2015  // Source: Clinical Laboratory News

https://www.aacc.org/publications/cln/articles/2015/november/the-microscopic-world-inside-us-emerging-research-points-to-microbiomes-role-in-health-and-disease

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Thousands of species of microbes—bacteria, viruses, fungi, and protozoa—inhabit every internal and external surface of the human body. Collectively, these microbes, known as the microbiome, outnumber the body’s human cells by about 10 to 1 and include more than 1,000 species of microorganisms and several million genes residing in the skin, respiratory system, urogenital, and gastrointestinal tracts. The microbiome’s complicated relationship with its human host is increasingly considered so crucial to health that researchers sometimes call it “the forgotten organ.”

Disturbances to the microbiome can arise from nutritional deficiencies, antibiotic use, and antiseptic modern life. Imbalances in the microbiome’s diverse microbial communities, which interact constantly with cells in the human body, may contribute to chronic health conditions, including diabetes, asthma and allergies, obesity and the metabolic syndrome, digestive disorders including irritable bowel syndrome (IBS), and autoimmune disorders like multiple sclerosis and rheumatoid arthritis, research shows.

While study of the microbiome is a growing research enterprise that has attracted enthusiastic media attention and venture capital, its findings are largely preliminary. But some laboratorians are already developing a greater appreciation for the microbiome’s contributions to human biochemistry and are considering a future in which they expect to measure changes in the microbiome to monitor disease and inform clinical practice.

Pivot Toward the Microbiome

Following the National Institutes of Health (NIH) Human Genome Project, many scientists noted the considerable genetic signal from microbes in the body and the existence of technology to analyze these microorganisms. That realization led NIH to establish the Human Microbiome Project in 2007, said Lita Proctor, PhD, its program director. In the project’s first phase, researchers studied healthy adults to produce a reference set of microbiomes and a resource of metagenomic sequences of bacteria in the airways, skin, oral cavities, and the gastrointestinal and vaginal tracts, plus a catalog of microbial genome sequences of reference strains. Researchers also evaluated specific diseases associated with disturbances in the microbiome, including gastrointestinal diseases such as Crohn’s disease, ulcerative colitis, IBS, and obesity, as well as urogenital conditions, those that involve the reproductive system, and skin diseases like eczema, psoriasis, and acne.

Phase 1 studies determined the composition of many parts of the microbiome, but did not define how that composition affects health or specific disease. The project’s second phase aims to “answer the question of what microbes actually do,” explained Proctor. Researchers are now examining properties of the microbiome including gene expression, protein, and human and microbial metabolite profiles in studies of pregnant women at risk for preterm birth, the gut hormones of patients at risk for IBS, and nasal microbiomes of patients at risk for type 2 diabetes.

Promising Lines of Research

Cystic fibrosis and microbiology investigator Michael Surette, PhD, sees promising microbiome research not just in terms of evidence of its effects on specific diseases, but also in what drives changes in the microbiome. Surette is Canada research chair in interdisciplinary microbiome research in the Farncombe Family Digestive Health Research Institute at McMaster University
in Hamilton, Ontario.

One type of study on factors driving microbiome change examines how alterations in composition and imbalances in individual patients relate to improving or worsening disease. “IBS, cystic fibrosis, and chronic obstructive pulmonary disease all have periods of instability or exacerbation,” he noted. Surette hopes that one day, tests will provide clinicians the ability to monitor changes in microbial composition over time and even predict when a patient’s condition is about to deteriorate. Monitoring perturbations to the gut microbiome might also help minimize collateral damage to the microbiome during aggressive antibiotic therapy for hospitalized patients, he added.

Monitoring changes to the microbiome also might be helpful for “culture negative” patients, who now may receive multiple, unsuccessful courses of different antibiotics that drive antibiotic resistance. Frustration with standard clinical biology diagnosis of lung infections in cystic fibrosis patients first sparked Surette’s investigations into the microbiome. He hopes that future tests involving the microbiome might also help asthma patients with neutrophilia, community-acquired pneumonia patients who harbor complex microbial lung communities lacking obvious pathogens, and hospitalized patients with pneumonia or sepsis. He envisions microbiome testing that would look for short-term changes indicating whether or not a drug is effective.

Companion Diagnostics

Daniel Peterson, MD, PhD, an assistant professor of pathology at Johns Hopkins University School of Medicine in Baltimore, believes the future of clinical testing involving the microbiome lies in companion diagnostics for novel treatments, and points to companies that are already developing and marketing tests that will require such assays.

Examples of microbiome-focused enterprises abound, including Genetic Analysis, based in Oslo, Norway, with its high-throughput test that uses 54 probes targeted to specific bacteria to measure intestinal gut flora imbalances in inflammatory bowel disease and irritable bowel syndrome patients. Paris, France-based Enterome is developing both novel drugs and companion diagnostics for microbiome-related diseases such as IBS and some metabolic diseases. Second Genome, based in South San Francisco, has developed an experimental drug, SGM-1019, that the company says blocks damaging activity of the microbiome in the intestine. Cambridge, Massachusetts-based Seres Therapeutics has received Food and Drug Administration orphan drug designation for SER-109, an oral therapeutic intended to correct microbial imbalances to prevent recurrent Clostridium difficile infection in adults.

One promising clinical use of the microbiome is fecal transplantation, which both prospective and retrospective studies have shown to be effective in patients with C. difficile infections who do not respond to front-line therapies, said James Versalovic, MD, PhD, director of Texas Children’s Hospital Microbiome Center and professor of pathology at Baylor College of Medicine in Houston. “Fecal transplants and other microbiome replacement strategies can radically change the composition of the microbiome in hours to days,” he explained.

But NIH’s Proctor discourages too much enthusiasm about fecal transplant. “Natural products like stool can have [side] effects,” she pointed out. “The [microbiome research] field needs to mature and we need to verify outcomes before anything becomes routine.”

Hurdles for Lab Testing

While he is hopeful that labs someday will use the microbiome to produce clinically useful information, Surette pointed to several problems that must be solved beforehand. First, molecular methods commonly used right now should be more quantitative and accurate. Additionally, research on the microbiome encompasses a wide variety of protocols, some of which are better at extracting particular types of bacteria and therefore can give biased views of communities living in the body. Also, tests may need to distinguish between dead and live microbes. Another hurdle is that labs using varied bioinfomatic methods may produce different results from the same sample, a problem that Surette sees as ripe for a solution from clinical laboratorians, who have expertise in standardizing robust protocols and in automating tests.

One way laboratorians can prepare for future, routine microbiome testing is to expand their notion of clinical chemistry to include both microbial and human biochemistry. “The line between microbiome science and clinical science is blurring,” said Versalovic. “When developing future assays to detect biochemical changes in disease states, we must consider the contributions of microbial metabolites and proteins and how to tailor tests to detect them.” In the future, clinical labs may test for uniquely microbial metabolites in various disease states, he predicted.

 

Automated Review of Mass Spectrometry Results  

Can We Achieve Autoverification?

Author: Katherine Alexander and Andrea R. Terrell, PhD  // Date: NOV.1.2015  // Source:Clinical Laboratory News

https://www.aacc.org/publications/cln/articles/2015/november/automated-review-of-mass-spectrometry-results-can-we-achieve-autoverification

 

Paralleling the upswing in prescription drug misuse, clinical laboratories are receiving more requests for mass spectrometry (MS) testing as physicians rely on its specificity to monitor patient compliance with prescription regimens. However, as volume has increased, reimbursement has declined, forcing toxicology laboratories both to increase capacity and lower their operational costs—without sacrificing quality or turnaround time. Now, new solutions are available enabling laboratories to bring automation to MS testing and helping them with the growing demand for toxicology and other testing.

What is the typical MS workflow?

A typical workflow includes a long list of manual steps. By the time a sample is loaded onto the mass spectrometer, it has been collected, logged into the lab information management system (LIMS), and prepared for analysis using a variety of wet chemistry techniques.

Most commercial clinical laboratories receive enough samples for MS analysis to batch analyze those samples. A batch consists of a calibrator(s), quality control (QC) samples, and patient/donor samples. Historically, the method would be selected (i.e. “analysis of opiates”), sample identification information would be entered manually into the MS software, and the instrument would begin analyzing each sample. Upon successful completion of the batch, the MS operator would view all of the analytical data, ensure the QC results were acceptable, and review each patient/donor specimen, looking at characteristics such as peak shape, ion ratios, retention time, and calculated concentration.

The operator would then post acceptable results into the LIMS manually or through an interface, and unacceptable results would be rescheduled or dealt with according to lab-specific protocols. In our laboratory we perform a final certification step for quality assurance by reviewing all information about the batch again, prior to releasing results for final reporting through the LIMS.

What problems are associated with this workflow?

The workflow described above results in too many highly trained chemists performing manual data entry and reviewing perfectly acceptable analytical results. Lab managers would prefer that MS operators and certifying scientists focus on troubleshooting problem samples rather than reviewing mounds of good data. Not only is the current process inefficient, it is mundane work prone to user errors. This risks fatigue, disengagement, and complacency by our highly skilled scientists.

Importantly, manual processes also take time. In most clinical lab environments, turnaround time is critical for patient care and industry competitiveness. Lab directors and managers are looking for solutions to automate mundane, error-prone tasks to save time and costs, reduce staff burnout, and maintain high levels of quality.

How can software automate data transfer from MS systems to LIMS?

Automation is not a new concept in the clinical lab. Labs have automated processes in shipping and receiving, sample preparation, liquid handling, and data delivery to the end user. As more labs implement MS, companies have begun to develop special software to automate data analysis and review workflows.

In July 2011, AIT Labs incorporated ASCENT into our workflow, eliminating the initial manual peak review step. ASCENT is an algorithm-based peak picking and data review system designed specifically for chromatographic data. The software employs robust statistical and modeling approaches to the raw instrument data to present the true signal, which often can be obscured by noise or matrix components.

The system also uses an exponentially modified Gaussian (EMG) equation to apply a best-fit model to integrated peaks through what is often a noisy signal. In our experience, applying the EMG results in cleaner data from what might appear to be poor chromatography ultimately allows us to reduce the number of samples we might otherwise rerun.

How do you validate the quality of results?

We’ve developed a robust validation protocol to ensure that results are, at minimum, equivalent to results from our manual review. We begin by building the assay in ASCENT, entering assay-specific information from our internal standard operating procedure (SOP). Once the assay is configured, validation proceeds with parallel batch processing to compare results between software-reviewed data and staff-reviewed data. For new implementations we run eight to nine batches of 30–40 samples each; when we are modifying or upgrading an existing implementation we run a smaller number of batches. The parallel batches should contain multiple positive and negative results for all analytes in the method, preferably spanning the analytical measurement range of the assay.

The next step is to compare the results and calculate the percent difference between the data review methods. We require that two-thirds of the automated results fall within 20% of the manually reviewed result. In addition to validating patient sample correlation, we also test numerous quality assurance rules that should initiate a flag for further review.

What are the biggest challenges during implementation and continual improvement initiatives?

On the technological side, our largest hurdle was loading the sequence files into ASCENT. We had created an in-house mechanism for our chemists to upload the 96-well plate map for their batch into the MS software. We had some difficulty transferring this information to ASCENT, but once we resolved this issue, the technical workflow proceeded fairly smoothly.

The greater challenge was changing our employees’ mindset from one of fear that automation would displace them, to a realization that learning this new technology would actually make them more valuable. Automating a non-mechanical process can be a difficult concept for hands-on scientists, so managers must be patient and help their employees understand that this kind of technology leverages the best attributes of software and people to create a powerful partnership.

We recommend that labs considering automated data analysis engage staff in the validation and implementation to spread the workload and the knowledge. As is true with most technology, it is best not to rely on just one or two super users. We also found it critical to add supervisor level controls on data file manipulation, such as removing a sample that wasn’t run from the sequence table. This can prevent inadvertent deletion of a file, requiring reinjection of the entire batch!

 

Understanding Fibroblast Growth Factor 23

Author: Damien Gruson, PhD  // Date: OCT.1.2015  // Source: Clinical Laboratory News

https://www.aacc.org/publications/cln/articles/2015/october/understanding-fibroblast-growth-factor-23

What is the relationship of FGF-23 to heart failure?

A Heart failure (HF) is an increasingly common syndrome associated with high morbidity, elevated hospital readmission rates, and high mortality. Improving diagnosis, prognosis, and treatment of HF requires a better understanding of its different sub-phenotypes. As researchers gained a comprehensive understanding of neurohormonal activation—one of the hallmarks of HF—they discovered several biomarkers, including natriuretic peptides, which now are playing an important role in sub-phenotyping HF and in driving more personalized management of this chronic condition.

Like the natriuretic peptides, fibroblast growth factor 23 (FGF-23) could become important in risk-stratifying and managing HF patients. Produced by osteocytes, FGF-23 is a key regulator of phosphorus homeostasis. It binds to renal and parathyroid FGF-Klotho receptor heterodimers, resulting in phosphate excretion, decreased 1-α-hydroxylation of 25-hydroxyvitamin D, and decreased parathyroid hormone (PTH) secretion. The relationship to PTH is important because impaired homeostasis of cations and decreased glomerular filtration rate might contribute to the rise of FGF-23. The amino-terminal portion of FGF-23 (amino acids 1-24) serves as a signal peptide allowing secretion into the blood, and the carboxyl-terminal portion (aa 180-251) participates in its biological action.

How might FGF-23 improve HF risk assessment?

Studies have shown that FGF-23 is related to the risk of cardiovascular diseases and mortality. It was first demonstrated that FGF-23 levels were independently associated with left ventricular mass index and hypertrophy as well as mortality in patients with chronic kidney disease (CKD). FGF-23 also has been associated with left ventricular dysfunction and atrial fibrillation in coronary artery disease subjects, even in the absence of impaired renal function.

FGF-23 and FGF receptors are both expressed in the myocardium. It is possible that FGF-23 has direct effects on the heart and participates in the physiopathology of cardiovascular diseases and HF. Experiments have shown that for in vitro cultured rat cardiomyocytes, FGF-23 stimulates pathological hypertrophy by activating the calcineurin-NFAT pathway—and in wild-type mice—the intra-myocardial or intravenous injection of FGF-23 resulted in left ventricular hypertrophy. As such, FGF-23 appears to be a potential stimulus of myocardial hypertrophy, and increased levels may contribute to the worsening of heart failure and long-term cardiovascular death.

Researchers have documented that HF patients have elevated FGF-23 circulating levels. They have also found a significant correlation between plasma levels of FGF-23 and B-type natriuretic peptide, a biomarker related to ventricular stretch and cardiac hypertrophy, in patients with left ventricular hypertrophy. As such, measuring FGF-23 levels might be a useful tool to predict long-term adverse cardiovascular events in HF patients.

Interestingly, researchers have documented a significant relationship between FGF-23 and PTH in both CKD and HF patients. As PTH stimulates FGF-23 expression, it could be that in HF patients, increased PTH levels increase the bone expression of FGF-23, which enhances its effects on the heart.

 

The Past, Present, and Future of Western Blotting in the Clinical Laboratory

Author: Curtis Balmer, PhD  // Date: OCT.1.2015  // Source: Clinical Laboratory News

https://www.aacc.org/publications/cln/articles/2015/october/the-past-present-and-future-of-western-blotting-in-the-clinical-laboratory

Much of the discussion about Western blotting centers around its performance as a biological research tool. This isn’t surprising. Since its introduction in the late 1970s, the Western blot has been adopted by biology labs of virtually every stripe, and become one of the most widely used techniques in the research armamentarium. However, Western blotting has also been employed in clinical laboratories to aid in the diagnosis of various diseases and disorders—an equally important and valuable application. Yet there has been relatively little discussion of its use in this context, or of how advances in Western blotting might affect its future clinical use.

Highlighting the clinical value of Western blotting, Stanley Naides, MD, medical director of Immunology at Quest Diagnostics observed that, “Western blotting has been a very powerful tool in the laboratory and for clinical diagnosis. It’s one of many various methods that the laboratorian brings to aid the clinician in the diagnosis of disease, and the selection and monitoring of therapy.” Indeed, Western blotting has been used at one time or the other to aid in the diagnosis of infectious diseases including hepatitis C (HCV), HIV, Lyme disease, and syphilis, as well as autoimmune disorders such as paraneoplastic disease and myositis conditions.

However, Naides was quick to point out that the choice of assays to use clinically is based on their demonstrated sensitivity and performance, and that the search for something better is never-ending. “We’re constantly looking for methods that improve detection of our target [protein],” Naides said. “There have been a number of instances where we’ve moved away from Western blotting because another method proves to be more sensitive.” But this search can also lead back to Western blotting. “We’ve gone away from other methods because there’s been a Western blot that’s been developed that’s more sensitive and specific. There’s that constant movement between methods as new tests are developed.”

In recent years, this quest has been leading clinical laboratories away from Western blotting toward more sensitive and specific diagnostic assays, at least for some diseases. Using confirmatory diagnosis of HCV infection as an example, Sai Patibandla, PhD, director of the immunoassay group at Siemens Healthcare Diagnostics, explained that movement away from Western blotting for confirmatory diagnosis of HCV infection began with a technical modification called Recombinant Immunoblotting Assay (RIBA). RIBA streamlines the conventional Western blot protocol by spotting recombinant antigen onto strips which are used to screen patient samples for antibodies against HCV. This approach eliminates the need to separate proteins and transfer them onto a membrane.

The RIBA HCV assay was initially manufactured by Chiron Corporation (acquired by Novartics Vaccines and Diagnostics in 2006). It received Food and Drug Administration (FDA) approval in 1999, and was marketed as Chiron RIBA HCV 3.0 Strip Immunoblot Assay. Patibandla explained that, at the time, the Chiron assay “…was the only FDA-approved confirmatory testing for HCV.” In 2013 the assay was discontinued and withdrawn from the market due to reports that it was producing false-positive results.

Since then, clinical laboratories have continued to move away from Western blot-based assays for confirmation of HCV in favor of the more sensitive technique of nucleic acid testing (NAT). “The migration is toward NAT for confirmation of HCV [diagnosis]. We don’t use immunoblots anymore. We don’t even have a blot now to confirm HCV,” Patibandla said.

Confirming HIV infection has followed a similar path. Indeed, in 2014 the Centers for Disease Control and Prevention issued updated recommendations for HIV testing that, in part, replaced Western blotting with NAT. This change was in response to the recognition that the HIV-1 Western blot assay was producing false-negative or indeterminable results early in the course of HIV infection.

At this juncture it is difficult to predict if this trend away from Western blotting in clinical laboratories will continue. One thing that is certain, however, is that clinicians and laboratorians are infinitely pragmatic, and will eagerly replace current techniques with ones shown to be more sensitive, specific, and effective. This raises the question of whether any of the many efforts currently underway to improve Western blotting will produce an assay that exceeds the sensitivity of currently employed techniques such as NAT.

Some of the most exciting and groundbreaking work in this area is being done by Amy Herr, PhD, a professor of bioengineering at University of California, Berkeley. Herr’s group has taken on some of the most challenging limitations of Western blotting, and is developing techniques that could revolutionize the assay. For example, the Western blot is semi-quantitative at best. This weakness dramatically limits the types of answers it can provide about changes in protein concentrations under various conditions.

To make Western blotting more quantitative, Herr’s group is, among other things, identifying losses of protein sample mass during the assay protocol. About this, Herr explains that the conventional Western blot is an “open system” that involves lots of handling of assay materials, buffers, and reagents that makes it difficult to account for protein losses. Or, as Kevin Lowitz, a senior product manager at Thermo Fisher Scientific, described it, “Western blot is a [simple] technique, but a really laborious one, and there are just so many steps and so many opportunities to mess it up.”

Herr’s approach is to reduce the open aspects of Western blot. “We’ve been developing these more closed systems that allow us at each stage of the assay to account for [protein mass] losses. We can’t do this exactly for every target of interest, but it gives us a really good handle [on protein mass losses],” she said. One of the major mechanisms Herr’s lab is using to accomplish this is to secure proteins to the blot matrix with covalent bonding rather than with the much weaker hydrophobic interactions that typically keep the proteins in place on the membrane.

Herr’s group also has been developing microfluidic platforms that allow Western blotting to be done on single cells, “In our system we’re doing thousands of independent Westerns on single cells in four hours. And, hopefully, we’ll cut that down to one hour over the next couple years.”

Other exciting modifications that stand to dramatically increase the sensitivity, quantitation, and through-put of Western blotting also are being developed and explored. For example, the use of capillary electrophoresis—in which proteins are conveyed through a small electrolyte-filled tube and separated according to size and charge before being dropped onto a blotting membrane—dramatically reduces the amount of protein required for Western blot analysis, and thereby allows Westerns to be run on proteins from rare cells or for which quantities of sample are extremely limited.

Jillian Silva, PhD, an associate specialist at the University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, explained that advances in detection are also extending the capabilities of Western blotting. “With the advent of fluorescence detection we have a way to quantitate Westerns, and it is now more quantitative than it’s ever been,” said Silva.

Whether or not these advances produce an assay that is adopted by clinical laboratories remains to be seen. The emphasis on Western blotting as a research rather than a clinical tool may bias advances in favor of the needs and priorities of researchers rather than clinicians, and as Patibandla pointed out, “In the research world Western blotting has a certain purpose. [Researchers] are always coming up with new things, and are trying to nail down new proteins, so you cannot take Western blotting away.” In contrast, she suggested that for now, clinical uses of Western blotting remain “limited.”

 

Adapting Next Generation Technologies to Clinical Molecular Oncology Service

Author: Ronald Carter, PhD, DVM  // Date: OCT.1.2015  // Source: Clinical Laboratory News

https://www.aacc.org/publications/cln/articles/2015/october/adapting-next-generation-technologies-to-clinical-molecular-oncology-service

Next generation technologies (NGT) deliver huge improvements in cost efficiency, accuracy, robustness, and in the amount of information they provide. Microarrays, high-throughput sequencing platforms, digital droplet PCR, and other technologies all offer unique combinations of desirable performance.

As stronger evidence of genetic testing’s clinical utility influences patterns of patient care, demand for NGT testing is increasing. This presents several challenges to clinical laboratories, including increased urgency, clinical importance, and breadth of application in molecular oncology, as well as more integration of genetic tests into synoptic reporting. Laboratories need to add NGT-based protocols while still providing old tests, and the pace of change is increasing.What follows is one viewpoint on the major challenges in adopting NGTs into diagnostic molecular oncology service.

Choosing a Platform

Instrument selection is a critical decision that has to align with intended test applications, sequencing chemistries, and analytical software. Although multiple platforms are available, a mainstream standard has not emerged. Depending on their goals, laboratories might set up NGTs for improved accuracy of mutation detection, massively higher sequencing capacity per test, massively more targets combined in one test (multiplexing), greater range in sequencing read length, much lower cost per base pair assessed, and economy of specimen volume.

When high-throughput instruments first made their appearance, laboratories paid more attention to the accuracy of base-reading: Less accurate sequencing meant more data cleaning and resequencing (1). Now, new instrument designs have narrowed the differences, and test chemistry can have a comparatively large impact on analytical accuracy (Figure 1). The robustness of technical performance can also vary significantly depending upon specimen type. For example, LifeTechnologies’ sequencing platforms appear to be comparatively more tolerant of low DNA quality and concentration, which is an important consideration for fixed and processed tissues.

https://www.aacc.org/~/media/images/cln/articles/2015/october/carter_fig1_cln_oct15_ed.jpg

Figure 1 Comparison of Sequencing Chemistries

Sequence pile-ups of the same target sequence (2 large genes), all performed on the same analytical instrument. Results from 4 different chemistries, as designed and supplied by reagent manufacturers prior to optimization in the laboratory. Red lines represent limits of exons. Height of blue columns proportional to depth of coverage. In this case, the intent of the test design was to provide high depth of coverage so that reflex Sanger sequencing would not be necessary. Courtesy B. Sadikovic, U. of Western Ontario.

 

In addition, batching, robotics, workload volume patterns, maintenance contracts, software licenses, and platform lifetime affect the cost per analyte and per specimen considerably. Royalties and reagent contracts also factor into the cost of operating NGT: In some applications, fees for intellectual property can represent more than 50% of the bench cost of performing a given test, and increase substantially without warning.

Laboratories must also deal with the problem of obsolescence. Investing in a new platform brings the angst of knowing that better machines and chemistries are just around the corner. Laboratories are buying bigger pieces of equipment with shorter service lives. Before NGTs, major instruments could confidently be expected to remain current for at least 6 to 8 years. Now, a major instrument is obsolete much sooner, often within 2 to 3 years. This means that keeping it in service might cost more than investing in a new platform. Lease-purchase arrangements help mitigate year-to-year fluctuations in capital equipment costs, and maximize the value of old equipment at resale.

One Size Still Does Not Fit All

Laboratories face numerous technical considerations to optimize sequencing protocols, but the test has to be matched to the performance criteria needed for the clinical indication (2). For example, measuring response to treatment depends first upon the diagnostic recognition of mutation(s) in the tumor clone; the marker(s) then have to be quantifiable and indicative of tumor volume throughout the course of disease (Table 1).

As a result, diagnostic tests need to cover many different potential mutations, yet accurately identify any clinically relevant mutations actually present. On the other hand, tests for residual disease need to provide standardized, sensitive, and accurate quantification of a selected marker mutation against the normal background. A diagnostic panel might need 1% to 3% sensitivity across many different mutations. But quantifying early response to induction—and later assessment of minimal residual disease—needs a test that is reliably accurate to the 10-4 or 10-5 range for a specific analyte.

Covering all types of mutations in one diagnostic test is not yet possible. For example, subtyping of acute myeloid leukemia is both old school (karyotype, fluorescent in situ hybridization, and/or PCR-based or array-based testing for fusion rearrangements, deletions, and segmental gains) and new school (NGT-based panel testing for molecular mutations).

Chemistries that cover both structural variants and copy number variants are not yet in general use, but the advantages of NGTs compared to traditional methods are becoming clearer, such as in colorectal cancer (3). Researchers are also using cell-free DNA (cfDNA) to quantify residual disease and detect resistance mutations (4). Once a clinically significant clone is identified, enrichment techniques help enable extremely sensitive quantification of residual disease (5).

Validation and Quality Assurance

Beyond choosing a platform, two distinct challenges arise in bringing NGTs into the lab. The first is assembling the resources for validation and quality assurance. The second is keeping tests up-to-date as new analytes are needed. Even if a given test chemistry has the flexibility to add analytes without revalidating the entire panel, keeping up with clinical advances is a constant priority.

Due to their throughput and multiplexing capacities, NGT platforms typically require considerable upfront investment to adopt, and training staff to perform testing takes even more time. Proper validation is harder to document: Assembling positive controls, documenting test performance criteria, developing quality assurance protocols, and conducting proficiency testing are all demanding. Labs meet these challenges in different ways. Laboratory-developed tests (LDTs) allow self-determined choice in design, innovation, and control of the test protocol, but can be very expensive to set up.

Food and Drug Administration (FDA)-approved methods are attractive but not always an option. More FDA-approved methods will be marketed, but FDA approval itself brings other trade-offs. There is a cost premium compared to LDTs, and the test methodologies are locked down and not modifiable. This is particularly frustrating for NGTs, which have the specific attraction of extensive multiplexing capacity and accommodating new analytes.

IT and the Evolution of Molecular Oncology Reporting Standards

The options for information technology (IT) pipelines for NGTs are improving rapidly. At the same time, recent studies still show significant inconsistencies and lack of reproducibility when it comes to interpreting variants in array comparative genomic hybridization, panel testing, tumor expression profiling, and tumor genome sequencing. It can be difficult to duplicate published performances in clinical studies because of a lack of sufficient information about the protocol (chemistry) and software. Building bioinformatics capacity is a key requirement, yet skilled people are in short supply and the qualifications needed to work as a bioinformatician in a clinical service are not yet clearly defined.

Tumor biology brings another level of complexity. Bioinformatic analysis must distinguish tumor-specific­ variants from genomic variants. Sequencing of paired normal tissue is often performed as a control, but virtual normal controls may have intriguing advantages (6). One of the biggest challenges is to reproducibly interpret the clinical significance of interactions between different mutations, even with commonly known, well-defined mutations (7). For multiple analyte panels, such as predictive testing for breast cancer, only the performance of the whole panel in a population of patients can be compared; individual patients may be scored into different risk categories by different tests, all for the same test indication.

In large scale sequencing of tumor genomes, which types of mutations are most informative in detecting, quantifying, and predicting the behavior of the tumor over time? The amount and complexity of mutation varies considerably across different tumor types, and while some mutations are more common, stable, and clinically informative than others, the utility of a given tumor marker varies in different clinical situations. And, for a given tumor, treatment effect and metastasis leads to retesting for changes in drug sensitivities.

These complexities mean that IT must be designed into the process from the beginning. Like robotics, IT represents a major ancillary decision. One approach many labs choose is licensed technologies with shared databases that are updated in real time. These are attractive, despite their cost and licensing fees. New tests that incorporate proprietary IT with NGT platforms link the genetic signatures of tumors to clinically significant considerations like tumor classification, recommended methodologies for monitoring response, predicted drug sensitivities, eligible clinical trials, and prognostic classifications. In-house development of such solutions will be difficult, so licensing platforms from commercial partners is more likely to be the norm.

The Commercial Value of Health Records and Test Data

The future of cancer management likely rests on large-scale databases that link hereditary and somatic tumor testing with clinical outcomes. Multiple centers have such large studies underway, and data extraction and analysis is providing increasingly refined interpretations of clinical significance.

Extracting health outcomes to correlate with molecular test results is commercially valuable, as the pharmaceutical, insurance, and healthcare sectors focus on companion diagnostics, precision medicine, and evidence-based health technology assessment. Laboratories that can develop tests based on large-scale integration of test results to clinical utility will have an advantage.

NGTs do offer opportunities for net reductions in the cost of healthcare. But the lag between availability of a test and peer-evaluated demon­stration of clinical utility can be considerable. Technical developments arise faster than evidence of clinical utility. For example, immuno­histochemistry, estrogen receptor/progesterone receptor status, HER2/neu, and histology are still the major pathological criteria for prognostic evaluation of breast cancer at diagnosis, even though multiple analyte tumor profiling has been described for more than 15 years. Healthcare systems need a more concerted assessment of clinical utility if they are to take advantage of the promises of NGTs in cancer care.

Disruptive Advances

Without a doubt, “disruptive” is an appropriate buzzword in molecular oncology, and new technical advances are about to change how, where, and for whom testing is performed.

• Predictive Testing

Besides cost per analyte, one of the drivers for taking up new technologies is that they enable multiplexing many more analytes with less biopsy material. Single-analyte sequential testing for epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase, and other targets on small biopsies is not sustainable when many more analytes are needed, and even now, a significant proportion of test requests cannot be completed due to lack of suitable biopsy material. Large panels incorporating all the mutations needed to cover multiple tumor types are replacing individual tests in companion diagnostics.

• Cell-Free Tumor DNA

Challenges of cfDNA include standardizing the collection and processing methodologies, timing sampling to minimize the effect of therapeutic toxicity on analytical accuracy, and identifying the most informative sample (DNA, RNA, or protein). But for more and more tumor types, it will be possible to differentiate benign versus malignant lesions, perform molecular subtyping, predict response, monitor treatment, or screen for early detection—all without a surgical biopsy.

cfDNA technologies can also be integrated into core laboratory instrumentation. For example, blood-based EGFR analysis for lung cancer is being developed on the Roche cobas 4800 platform, which will be a significant change from the current standard of testing based upon single tests of DNA extracted from formalin-fixed, paraffin-embedded sections selected by a pathologist (8).

• Whole Genome and Whole Exome Sequencing

Whole genome and whole exome tumor sequencing approaches provide a wealth of biologically important information, and will replace individual or multiple gene test panels as the technical cost of sequencing declines and interpretive accuracy improves (9). Laboratories can apply informatics selectively or broadly to extract much more information at relatively little increase in cost, and the interpretation of individual analytes will be improved by the context of the whole sequence.

• Minimal Residual Disease Testing

Massive resequencing and enrichment techniques can be used to detect minimal residual disease, and will provide an alternative to flow cytometry as costs decline. The challenge is to develop robust analytical platforms that can reliably produce results in a high proportion of patients with a given tumor type, despite using post-treatment specimens with therapy-induced degradation, and a very low proportion of target (tumor) sequence to benign background sequence.

The tumor markers should remain informative for the burden of disease despite clonal evolution over the course of multiple samples taken during progression of the clinical course and treatment. Quantification needs to be accurate and sensitive down to the 10-5 range, and cost competitive with flow cytometry.

• Point-of-Care Test Methodologies

Small, rapid, cheap, and single use point-of-care (POC) sequencing devices are coming. Some can multiplex with analytical times as short as 20 minutes. Accurate and timely testing will be possible in places like pharmacies, oncology clinics, patient service centers, and outreach programs. Whether physicians will trust and act on POC results alone, or will require confirmation by traditional laboratory-based testing, remains to be seen. However, in the simplest type of application, such as a patient known to have a particular mutation, the advantages of POC-based testing to quantify residual tumor burden are clear.

Conclusion

Molecular oncology is moving rapidly from an esoteric niche of diagnostics to a mainstream, required component of integrated clinical laboratory services. While NGTs are markedly reducing the cost per analyte and per specimen, and will certainly broaden the scope and volume of testing performed, the resources required to choose, install, and validate these new technologies are daunting for smaller labs. More rapid obsolescence and increased regulatory scrutiny for LDTs also present significant challenges. Aligning test capacity with approved clinical indications will require careful and constant attention to ensure competitiveness.

References

1. Liu L, Li Y, Li S, et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012; doi:10.1155/2012/251364.

2. Brownstein CA, Beggs AH, Homer N, et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014;15:R53.

3. Haley L, Tseng LH, Zheng G, et al. Performance characteristics of next-generation sequencing in clinical mutation detection of colorectal ­cancers. [Epub ahead of print] Modern Pathol July 31, 2015 as doi:10.1038/modpathol.2015.86.

4. Butler TM, Johnson-Camacho K, Peto M, et al. Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary ­disease. PLoS One 2015;10:e0136407.

5. Castellanos-Rizaldos E, Milbury CA, Guha M, et al. COLD-PCR enriches low-level variant DNA sequences and increases the sensitivity of genetic testing. Methods Mol Biol 2014;1102:623–39.

6. Hiltemann S, Jenster G, Trapman J, et al. Discriminating somatic and germline mutations in tumor DNA samples without matching normals. Genome Res 2015;25:1382–90.

7. Lammers PE, Lovly CM, Horn L. A patient with metastatic lung adenocarcinoma harboring concurrent EGFR L858R, EGFR germline T790M, and PIK3CA mutations: The challenge of interpreting results of comprehensive mutational testing in lung cancer. J Natl Compr Canc Netw 2015;12:6–11.

8. Weber B, Meldgaard P, Hager H, et al. Detection of EGFR mutations in plasma and biopsies from non-small cell lung cancer patients by allele-specific PCR assays. BMC Cancer 2014;14:294.

9. Vogelstein B, Papadopoulos N, Velculescu VE, et al. Cancer genome landscapes. Science 2013;339:1546–58.

10. Heitzer E, Auer M, Gasch C, et al. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res 2013;73:2965–75.

11. Healy B. BRCA genes — Bookmaking, fortunetelling, and medical care. N Engl J Med 1997;336:1448–9.

 

 

 

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