Intact proviral DNA assay analysis of large cohorts of people with HIV provides a benchmark for the frequency and composition of persistent proviral DNA.

A scalable approach for quantifying intact HIV-1 proviruses is critical for basic research and clinical trials directed at HIV-1 cure. The intact proviral DNA assay (IPDA) is a novel approach to characterizing the HIV-1 reservoir, focusing on the genetic integrity of individual proviruses independent of transcriptional status. It uses multiplex digital droplet PCR to distinguish and separately quantify intact proviruses, defined by a lack of overt fatal defects such as large deletions and APOBEC3G-mediated hypermutation, from the majority of proviruses that have such defects. This distinction is important because only intact proviruses cause viral rebound on ART interruption. To evaluate IPDA performance and provide benchmark data to support its implementation, we analyzed peripheral blood samples from 400 HIV-1+ adults on ART from several diverse cohorts, representing a robust sample of treated HIV-1 infection in the United States. We provide direct quantitative evidence that defective proviruses greatly outnumber intact proviruses (by >12.5 fold). However, intact proviruses are present at substantially higher frequencies (median, 54/106 CD4+ T cells) than proviruses detected by the quantitative viral outgrowth assay, which requires induction and in vitro growth (∼1/106 CD4+ T cells). IPDA amplicon signal issues resulting from sequence polymorphisms were observed in only 6.3% of individuals and were readily apparent and easily distinguished from low proviral frequency, an advantage of the IPDA over standard PCR assays which generate false-negative results in such situations. The large IPDA dataset provided here gives the clearest quantitative picture to date of HIV-1 proviral persistence on ART.

Impact of backbone linkage positions on the molecular aggregation behavior of polymer photovoltaic materials.

It is imperative to advance the structural design of conjugated materials to achieve a practical impact on the performance of photovoltaic devices. However, the effect of the linkage positions (meta-, para-) of the backbone on the molecular packing has been relatively little explored. In this study, we have synthesized two wide-bandgap polymer photovoltaic materials from identical monomers with different linkage positions, using dibenzo[c,h][2,6]-naphthyridine-5,11-(6H,12H)-dione (DBND) as the building block. This study shows that the para-connected polymer exhibits an unexpected 0.2 eV higher ionization potential and a resultant higher open-circuit voltage than the meta-connected counterpart. We found that different linkage positions result in different intermolecular binding energies and molecular aggregation conformations, leading to different HOMO energy levels and photovoltaic performances. Specifically, theoretical calculations and 2D-NMR indicate that P(p-DBND-f-2T) performs a segregated stacking of f-2T and DBND units, while P(m-DBND-f-2T) films form π-overlaps between f-2T and DBND. These results show that linkage position adjustment on the polymeric backbone exerts a profound influence on the molecular aggregation of the materials. Also, the effect of isomerism on the polymer backbone is crucial in designing polymer structures for photovoltaic applications.

Anemia and Low Albumin Levels Are Associated with Severe Community-Acquired Pneumonia in Pregnancy: A Case-Control Study.

Community-acquired pneumonia (CAP) is the most common form of pneumonia in pregnancy and may lead to severe adverse maternal and fetal outcomes. Severe CAP (SCAP) is defined as the need for invasive mechanical ventilation and with septic shock with the need for vasopressors. This study aimed to analyze the clinical characteristics and factors associated with SCAP in pregnancy. The present study was a case-control study of pregnant women hospitalized between September 2012 and September 2017 at nine tertiary hospitals in China. Among 358,424 pregnant women, we found 35 SCAP cases and 393 common CAP cases. The 35 SCAP cases were matched 1:4 with common CAP cases (n = 140), based on patient age and gestational weeks. Infection indicators, hemoglobin, platelets, coagulation function, liver, and kidney function markers, myocardial enzyme, arterial oxygen pressure/fraction inspired oxygen (PO2/FiO2), and partial echocardiographic results were different between the two groups at admission (all P < 0.05). The univariable analyses indicated significant differences for hemoglobin, BMI, irregular obstetric examination, albumin, and white blood cells (all P < 0.05) between the common CAP and SCAP groups. The multivariable logistic regression analysis showed that hemoglobin (OR = 0.87, 95% CI: 0.77-0.97, P = 0.01), BMI (OR = 0.42, 95% CI: 0.22-0.81, P = 0.01), and serum albumin (OR = 0.37, 95% CI: 0.19-0.69, P = 0.002) were independently associated with SCAP. Anemia and low serum albumin are possibly associated with SCAP in pregnancy. The results indicate that anemia and albumin levels should be examined and properly treated in pregnant women with CAP.

Thiazoloisoindigo: A Building Block that Merges the Merits of Thienoisoindigo and Diazaisoindigo for Conjugated Polymers.

Thiazoloisoindigo, a novel structural variation of isoindigo, is for the first time utilized to synthesize conjugated polymers. The polymer based on thiazoloisoindigo merges the advantages of the one based on thienoisoindigo and diazaisoindigo; it not only exhibits a greatly redshifted UV/Vis absorption to the near-infrared region owing to its strong tendency to form quinoidal structures, similar to that based on thienoisoindigo, but also shows excellent ambipolar mobility (hole: 3.93, electron: 1.07 cm2 V-1 s-1 ) in organic field-effect transistors (OFETs), superior to that based on diazaisoindigo, showing the strong electron-withdrawing capability of thiazoloisoindigo.

Aqueous extract from a Chaga medicinal mushroom, Inonotus obliquus (higher Basidiomycetes), prevents herpes simplex virus entry through inhibition of viral-induced membrane fusion.

Chaga medicinal mushroom, Inonotus obliquus, a popular prescription in traditional medicine in Europe and Asia, was used to reduce inflammation in the nasopharynx and to facilitate breathing. The aqueous extract from I. obliquus (AEIO) exhibited marked decrease in herpes simplex virus (HSV) infection (the 50% inhibitory concentration was 3.82 µg/mL in the plaque reduction assay and 12.29 µg/mL in the HSV-1/blue assay) as well as safety in Vero cells (the 50% cellular cytotoxicity was > 1 mg/mL, and selection index was > 80). Using a time course assay, effective stage analysis, and fusion inhibition assay, the mechanism of anti-HSV activity was found against the early stage of viral infection through inhibition of viral-induced membrane fusion. Therefore, AEIO could effectively prevent HSV-1 entry by acting on viral glycoproteins, leading to the prevention of membrane fusion, which is different from nucleoside analog antiherpetics.

Enhancing organic cathodes of aqueous zinc-ion batteries via utilizing steric hindrance and electron cloud equalization.

Polyaniline (PANI), with merits of high electronic conductivity and capacity, is a promising material for zinc (Zn)-ion batteries. However, its redox window in Zn batteries is often limited, mainly due to the oxidative degradation at high potentials-in which imine groups can be attacked by water molecules. Here, we introduce phytic acid, a kind of supermolecule acid radical ion, as a dopant and electrolyte additive. Various in/ex situ analyses and theoretical calculations prove that the steric hindrance effect can prevent electroactive sites from the attack by water molecules. Meanwhile, the redox reaction can be stabilized by an even distribution of electron cloud due to the conjugated structure of phenazine groups. Accordingly, the assembled Zn-PANI battery can allow stable and long-term charge-discharge reactions to occur at a potential as high as 2.0 V with a discharged plateau of 1.5 V, and it also shows high rate performance and stable long cycle life (75% capacity retention after 1000 cycles at 10 A g-1).

Electrochemical Performance of Graphitic Multi-walled Carbon Nanotubes with Different Aspect Ratios as Cathode Materials for Aluminum-ion Batteries.

Graphitic multi-walled carbon nanotubes (MWCNTs) can function as high-performance cathode materials for rechargeable Al-ion batteries with well-defined discharging plateaus and reasonable charge/discharge C-rates. However, the main intercalation/deintercalation or adsorption/desorption path of AlCl4- anions into or onto G-MWCNTs has not been elucidated. Herein, we used battery cells comprised of G-MWCNTs with different aspect ratios, Al metal, and AlCl3/1-ethyl-3-methylimidazolium chloride ionic liquid as the cathode, anode, and electrolyte, respectively. The electrochemical performance of the Al||G-MWCNT cell increased as the aspect ratio of the G-MWCNT cathode increased (i. e., longer and thinner). The degree of defects of the G-MWCNTs was similar (0.15-0.22); hence, the results confirm that the main and alternate paths for the AlCl4- intercalation/de-intercalation or adsorption/desorption into/from or onto/from the G-MWCNT are the basal and edge planes, respectively. The step-like structures of defects on the basal plane provide the main reaction site for AlCl4- anions.

Pathogen profiling: rapid molecular characterization of Staphylococcus aureus by PCR/electrospray ionization-mass spectrometry and correlation with phenotype.

There are few diagnostic methods that readily distinguish among community-acquired methicillin (meticillin)-resistant Staphylococcus aureus strains, now frequently transmitted within hospitals. We describe a rapid and high-throughput method for bacterial profiling of staphylococcal isolates. The method couples PCR to electrospray ionization-mass spectrometry (ESI-MS) and is performed on a platform suitable for use in a diagnostic laboratory. This profiling technology produces a high-resolution genetic signature indicative of the presence of specific genetic elements that represent distinctive phenotypic features. The PCR/ESI-MS signature accurately identified genotypic determinants consistent with phenotypic traits in well-characterized reference and clinical isolates of S. aureus. Molecular identification of the antibiotic resistance genes correlated strongly with phenotypic in vitro resistance. The identification of toxin genes correlated with independent PCR analyses for the toxin genes. Finally, isolates were correctly classified into genotypic groups that correlated with genetic clonal complexes, repetitive-element-based PCR patterns, or pulsed-field gel electrophoresis types. The high-throughput PCR/ESI-MS assay should improve clinical management of staphylococcal infections.

N-Alkylation vs. O-alkylation: influence on the performance of the photovoltaic cells based on a tetracyclic lactam polymer donor.

Lactam-containing acceptors, which could provide two potential alkylation positions (N-alkylation and O-alkylation), are important building blocks for polymeric donors in high performance polymer solar cells (PSCs). However, the influence of alkylation positions on the PSC performance has seldom been studied. Herein, we investigated the influence of O-alkylation and N-alkylation on a novel bislactam acceptor, namely dibenzonaphthyridinedione (DBND), on the physical properties of the corresponding polymers and hence their PSC performance. Besides O-alkylated and N-alkylated DBND, half-N-alkylated-half-O-alkylated DBND (N,O-DBND) was also prepared and copolymerized with stannyl bithiophene (2T). It was found that by varying the alkylation positions, the optical, crystalline and aggregation properties of the corresponding polymers were greatly altered. In comparison with P(N-DBND-2T) and P(O-DBND-2T), P(N,O-DBND-2T) shows both better solubility and shorter π-π stacking distance. By blending with PC71BM, P(N,O-DBND-2T) forms better nano-fibrillar phase separation so that less charge recombination is observed, thus leading to a much better power conversion efficiency (PCE) around 5%, which is the highest value of the conjugated system based on N,O-alkylated acceptors. The results show that the asymmetric N,O-alkylation protocol is a promising way to adjust the properties of the bislactam-containing conjugated polymers.

Protein folding intermediates of invasin protein IbeA from Escherichia coli.

IbeA of Escherichia coli K1 was cloned, expressed and purified as a His(6)-tag fusion protein. The purified fusion protein inhibited E. coli K1 invasion of human brain microvascular endothelial cells and was heat-modifiable. The structural and functional aspects, along with equilibrium unfolding of IbeA, were studied in solution. The far-UV CD spectrum of IbeA at pH 7.0 has a strong negative peak at 215 nm, indicating the existence of beta-sheet-like structure. The acidic unfolding curve of IbeA at pH 2.0 shows the existence of a partially unfolded molecule (molten globule-like structure) with beta-sheet-like structure and displays strong 8-anilino-2-naphthyl sulfonic acid (ANS) binding. The pH dependent intrinsic fluorescence of IbeA was biphasic. At pH 2.0, IbeA exists in a partially unfolded state with characteristics of a molten globule-like state, and the protein is in extended beta-sheet conformation and exhibits strong ANS binding. Guanidine hydrochloride denaturation of IbeA in the molten globule-like state is noncooperative, contrary to the cooperativity seen with the native protein, suggesting the presence of two domains (possibly) in the molecular structure of IbeA, with differential unfolding stabilities. Furthermore, tryptophan quenching studies suggested the exposure of aromatic residues to solvent in this state. Acid denatured unfolding of IbeA monitored by far-UV CD is non-cooperative with two transitions at pH 3.0-1.5 and 1.5-0.5. At lower pH, IbeA unfolds to the acid-unfolded state, and a further decrease in pH to 2.0 drives the protein to the A state. The presence of 0.5 m KCl in the solvent composition directs the transition to the A state by bypassing the acid-unfolded state. Additional guanidine hydrochloride induced conformational changes in IbeA from the native to the A-state, as monitored by near- and far-UV CD and ANS-fluorescence.

Comparison of the BD GeneOhm methicillin-resistant Staphylococcus aureus (MRSA) PCR assay to culture by use of BBL CHROMagar MRSA for detection of MRSA in nasal surveillance cultures from an at-risk community population.

We compared the BD GeneOhm methicillin-resistant Staphylococcus aureus (MRSA) PCR assay to culture with BBL CHROMagar MRSA for nasal surveillance among 602 arrestees from the Baltimore City Jail. The sensitivity and specificity were 88.5% and 91.0%, respectively, and after secondary analysis using enrichment broth, they were 89.0% and 91.7%, respectively. Twenty-three of 42 false-positive PCR lysates contained methicillin-susceptible S. aureus.

Staphylococcus aureus colonization among healthcare workers at a tertiary care hospital.

We describe the epidemiology of Staphylococcus aureus colonization among 200 healthcare workers. The prevalence of S. aureus was 28%, and the prevalence of methicillin-resistant S. aureus (MRSA) was 2%. The incidence of MRSA colonization was extremely low. This study suggests that the risk of MRSA transmission to healthcare workers is low in a hospital where MRSA is endemic.

Efficient Route toward N-Unsubstituted Thienoisoindigo Suitable for Side-Chain Engineering.

A highly efficient and easily scalable synthetic method toward N-unsubstituted thienoisoindigo (TII) is developed with more than 25% overall yield, which is higher than the reported cases, and allows facile side-chain manipulation of the thienoisoindigo core.

Severe community-onset pneumonia in healthy adults caused by methicillin-resistant Staphylococcus aureus carrying the Panton-Valentine leukocidin genes.

BACKGROUND: Recent worldwide reports of community-onset skin abscesses, outbreaks of furunculosis, and severe pneumonia associated with methicillin-resistant Staphylococcus aureus (MRSA) carrying Panton-Valentine leukocidin (PVL) genes and the staphylococcal cassette chromosome mec (SCCmec) type IV indicate that MRSA infections are evolving into a community-related problem. The majority of cases reported to date involve skin and soft-tissue infections, with severe pneumonia representing a relatively rare phenomenon. During a 2-month period in the winter of 2003-2004, four healthy adults presented to 1 of 2 Baltimore hospitals with severe necrotizing MRSA pneumonia in the absence of typical risk factors for MRSA infection. METHODS: Patients' MRSA isolates were characterized by strain typing with use of pulsed-field gel electrophoresis and SCCmec typing with use of a multiplex polymerase chain reaction (PCR) assay and detection of PVL genes by PCR. RESULTS: All 4 patients' MRSA isolates carried the PVL genes and the SCCmec type IV element and belonged to the USA300 pulsed-field type. These 3 findings are among the typical characteristics of community-onset MRSA strains. In addition, 2 of our patients had concomitant influenza A diagnosed, which likely contributed to the severity of their presentation. CONCLUSIONS: To our knowledge, these patients represent the first reported North American adults with severe community-onset MRSA pneumonia caused by strains carrying the PVL genes.

Anticancer activity of Amauroderma rude.

More and more medicinal mushrooms have been widely used as a miraculous herb for health promotion, especially by cancer patients. Here we report screening thirteen mushrooms for anti-cancer cell activities in eleven different cell lines. Of the herbal products tested, we found that the extract of Amauroderma rude exerted the highest activity in killing most of these cancer cell lines. Amauroderma rude is a fungus belonging to the Ganodermataceae family. The Amauroderma genus contains approximately 30 species widespread throughout the tropical areas. Since the biological function of Amauroderma rude is unknown, we examined its anti-cancer effect on breast carcinoma cell lines. We compared the anti-cancer activity of Amauroderma rude and Ganoderma lucidum, the most well-known medicinal mushrooms with anti-cancer activity and found that Amauroderma rude had significantly higher activity in killing cancer cells than Ganoderma lucidum. We then examined the effect of Amauroderma rude on breast cancer cells and found that at low concentrations, Amauroderma rude could inhibit cancer cell survival and induce apoptosis. Treated cancer cells also formed fewer and smaller colonies than the untreated cells. When nude mice bearing tumors were injected with Amauroderma rude extract, the tumors grew at a slower rate than the control. Examination of these tumors revealed extensive cell death, decreased proliferation rate as stained by Ki67, and increased apoptosis as stained by TUNEL. Suppression of c-myc expression appeared to be associated with these effects. Taken together, Amauroderma rude represented a powerful medicinal mushroom with anti-cancer activities.

Clinical validation of the molecular BD GeneOhm StaphSR assay for direct detection of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus in positive blood cultures.

The rapid detection of Staphylococcus aureus bacteremia and a swift determination of methicillin susceptibility has serious clinical implications affecting patient mortality. This study evaluated the StaphSR assay (BD GeneOhm, San Diego, CA), a real-time PCR assay, for the identification and differentiation of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) from 300 positive blood cultures. The BD GeneOhm StaphSR assay was performed and interpreted according to the manufacturer's recommendations. Positive blood cultures (containing predominantly gram-positive cocci in clusters) were subcultured on 5% sheep blood agar plates. After 18 to 24 h of incubation, isolates morphologically consistent with S. aureus were presumptively identified by latex agglutination (Staphaurex Plus; Remel, Lenexa, KS). Susceptibility testing was initially performed with the Phoenix automated microbiology system (BD Diagnostics, Sparks, MD). Additional susceptibility testing of samples with discrepant results was done using BBL oxacillin screen agar (BD Diagnostics, Sparks, MD), oxacillin and cefoxitin Etests (AB Biodisk, Solna, Sweden) on Mueller-Hinton agar, an immunoassay for penicillin binding protein 2' (Denka Seiken Co., Tokyo, Japan), and mecA PCR. The sensitivity, specificity, and positive and negative predictive values of the BD GeneOhm StaphSR assay for MSSA detection were 98.9, 96.7, 93.6, and 99.5%, respectively. For the detection of MRSA, the BD GeneOhm StaphSR assay was 100% sensitive and 98.4% specific; positive and negative predictive values for MRSA detection were 92.6 and 100%, respectively. Inhibition was seen with only one sample, and the issue was resolved upon retesting. The BD GeneOhm StaphSR assay appears to be a valuable diagnostic tool for quickly differentiating bacteremia caused by MSSA and MRSA from that caused by other gram-positive cocci.

Comparison of the BD GeneOhm VanR assay to culture for identification of vancomycin-resistant enterococci in rectal and stool specimens.

Active screening for vancomycin-resistant enterococci (VRE) in rectal and stool specimens has been recommended to limit the spread of antimicrobial resistance within certain high-risk populations. Directly from 502 rectal swabs and stool specimens, we evaluated the diagnostic performance of the BD GeneOhm VanR assay (BD GeneOhm, San Diego, CA), a rapid real-time PCR test that detects the presence of vanA and/or vanB genes. The VanR assay was compared to culture consisting of both bile-esculin-azide agar with 6 mug/ml vancomycin (BEAV agar) (BD Diagnostics, Sparks, MD) and BEAV broth with 8 mug/ml vancomycin (Hardy Diagnostics, Santa Maria, CA). Enterococci were identified to the species level using standard biochemical tests and a Phoenix automated microbiology system (BD Diagnostics, Sparks, MD). The susceptibility of the enterococci to vancomycin and teicoplanin was determined using an Etest (AB Biodisk, Solna, Sweden). VRE were initially isolated from 147 cultures, and the VanR assay detected 142 of the 147 positive cultures for a sensitivity of 96.6%. The specificity was 87.0% (309/355) largely due to false positives seen with the vanB portion of the assay. The sensitivity when testing rectal swabs was 98.3%, and the sensitivity for stool samples was 95.4% (P = 0.643). The specificity of rectal swabs was comparable to that of the stool specimens (87.5% and 86.5%, respectively). When used only to detect VanA resistance, the VanR assay was 94.4% (136/144) sensitive and 96.4% (345/358) specific, with positive and negative predictive values of 91.3% and 97.7%, respectively. In summary, the BD GeneOhm VanR assay is a good screening test for VRE in our population of predominantly vanA-colonized patients. However, patient samples testing only vanB positive should be confirmed by another method for the presence of VRE.

Yield of stool culture with isolate toxin testing versus a two-step algorithm including stool toxin testing for detection of toxigenic Clostridium difficile.

We examined the incremental yield of stool culture (with toxin testing on isolates) versus our two-step algorithm for optimal detection of toxigenic Clostridium difficile. Per the two-step algorithm, stools were screened for C. difficile-associated glutamate dehydrogenase (GDH) antigen and, if positive, tested for toxin by a direct (stool) cell culture cytotoxicity neutralization assay (CCNA). In parallel, stools were cultured for C. difficile and tested for toxin by both indirect (isolate) CCNA and conventional PCR if the direct CCNA was negative. The "gold standard" for toxigenic C. difficile was detection of C. difficile by the GDH screen or by culture and toxin production by direct or indirect CCNA. We tested 439 specimens from 439 patients. GDH screening detected all culture-positive specimens. The sensitivity of the two-step algorithm was 77% (95% confidence interval [CI], 70 to 84%), and that of culture was 87% (95% CI, 80 to 92%). PCR results correlated completely with those of CCNA testing on isolates (29/29 positive and 32/32 negative, respectively). We conclude that GDH is an excellent screening test and that culture with isolate CCNA testing detects an additional 23% of toxigenic C. difficile missed by direct CCNA. Since culture is tedious and also detects nontoxigenic C. difficile, we conclude that culture is most useful (i) when the direct CCNA is negative but a high clinical suspicion of toxigenic C. difficile remains, (ii) in the evaluation of new diagnostic tests for toxigenic C. difficile (where the best reference standard is essential), and (iii) in epidemiologic studies (where the availability of an isolate allows for strain typing and antimicrobial susceptibility testing).

Effects of ompA deletion on expression of type 1 fimbriae in Escherichia coli K1 strain RS218 and on the association of E. coli with human brain microvascular endothelial cells.

We have previously shown that outer membrane protein A (OmpA) and type 1 fimbriae are the bacterial determinants involved in Escherichia coli K1 binding to human brain microvascular endothelial cells (HBMEC), which constitute the blood-brain barrier. In investigating the role of OmpA in E. coli K1 binding to HBMEC, we showed for the first time that ompA deletion decreased the expression of type 1 fimbriae in E. coli K1. Decreased expression of type 1 fimbriae in the ompA deletion mutant was largely the result of driving the fim promoter toward the type 1 fimbrial phase-OFF orientation. mRNA levels of fimB and fimE were found to be decreased with the OmpA mutant compared to the parent strain. Of interest, the ompA deletion further decreased the abilities of E. coli K1 to bind to and invade HBMEC under the conditions of fixing type 1 fimbria expression in the phase-ON or phase-OFF status. These findings suggest that the decreased ability of the OmpA mutant to interact with HBMEC is not entirely due to its decreased type 1 fimbrial expression and that OmpA and type 1 fimbriae facilitate the interaction of E. coli K1 with HBMEC at least in an additive manner.

Escherichia coli outer membrane protein A adheres to human brain microvascular endothelial cells.

Escherichia coli K1 is the most common gram-negative bacterium causing neonatal meningitis. The outer membrane protein A (OmpA) assembles a beta-barrel structure having four surface-exposed loops in E. coli outer membrane. OmpA of meningitis-causing E. coli K1 is shown to contribute to invasion of the human brain microvascular endothelial cells (HBMEC), the main cellular component of the blood-brain barrier (BBB). However, the direct evidence of OmpA protein interacting with HBMEC is not clear. In this study, we showed that OmpA protein, solubilized from the outer membrane of E. coli, adhered to HBMEC surface. To verify OmpA interaction with the HBMEC, we purified N-terminal membrane-anchoring beta-barrel domain of OmpA and all surface-exposed loops deleted OmpA proteins, and showed that the surface-exposed loops of OmpA were responsible for adherence to HBMEC. These findings indicate that the OmpA is the adhesion molecule with HBMEC and the surface-exposed loops of OmpA are the determinant of this interaction.