Intra-genomic internal transcribed spacer region sequence heterogeneity and molecular diagnosis in clinical microbiology

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study.published_or_final_versio

Genotypic analysis of Klebsiella pneumoniae isolates in a Beijing hospital reveals high genetic diversity and clonal population structure of drug-resistant isolates.

Background The genetic diversity and the clinical relevance of the drug-resistant Klebsiella pneumoniae isolates from hospital settings are largely unknown. We thus conducted this prospective study to analyze the molecular epidemiology of K. pneumoniae isolates from patients being treated in the 306 Hospital in Beijing, China for the period of November 1, 2010–October 31, 2011. Methodology/Principal Findings Antibiotic susceptibility testing, PCR amplification and sequencing of the drug resistance-associated genes, and multilocus sequence typing (MLST) were conducted. A total of 163 isolates were analyzed. The percentage of MDR, XDR and PDR isolates were 63.8% (104), 20.9 (34), and 1.8% (3), respectively. MLST results showed that 60 sequence types (STs) were identified, which were further separated by eBURST into 13 clonal complexes and 18 singletons. The most dominant ST was ST15 (10.4%). Seven new alleles and 24 new STs were first identified in this study. Multiple logistic regression analysis revealed that certain clinical characteristics were associated with those prevalent STs such as: from ICU, from medical ward, from community acquired infection, from patients without heart disease, from patients with treatment success, susceptible to extended spectrum cephalosporin, susceptible to cephamycins, susceptible to fluoroquinolones, and with MDR. Conclusions/Significance Our data indicate that certain drug-resistant K. pneumoniae clones are highly prevalent and are associated with certain clinical characteristics in hospital settings. Our study provides evidence demonstrating that intensive nosocomial infection control measures are urgently needed.published_or_final_versio

First genome sequences of buffalo coronavirus from water buffaloes in Bangladesh

AbstractWe report the complete genome sequences of a buffalo coronavirus (BufCoV HKU26) detected from the faecal samples of two domestic water buffaloes (Bubalus bubalis) in Bangladesh. They possessed 98–99% nucleotide identities to bovine coronavirus (BCoV) genomes, supporting BufCoV HKU26 as a member of Betacoronavirus 1. Nevertheless, BufCoV HKU26 possessed distinct accessory proteins between spike and envelope compared to BCoV. Sugar-binding residues in the N-terminal domain of S protein in BCoV are conserved in BufCoV HKU26

Clinical characteristics, laboratory identification, and in vitro antifungal susceptibility of Yarrowia (Candida) lipolytica isolates causing fungemia: a multicenter, prospective surveillance study

Our case series showed that uncomplicated Yarrowia lipolytica fungemia might be treated with catheter removal alone. The Vitek 2 YST identification (ID) card system, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), and internal transcribed spacer and 25S nuclear ribosomal DNA (nrDNA) gene sequencing provided reliable identification. All isolates had low MICs to voriconazole, echinocandins, and amphotericin B

Monolithically Integratable Colliding Pulse Modelocked Laser Source for O-CDMA Photonic Chip Development

We demonstrate modelocking of a colliding-pulse mode-locked laser formed by 3-μm-deep etched-mirrors on an InP platform for integration with passive waveguide components. Timing jitter of 243 fs and pulse width of 10 ps were measured

Monolithically Integratable Colliding Pulse Modelocked Laser Source for O-CDMA Photonic Chip Development

We demonstrate modelocking of a colliding-pulse mode-locked laser formed by 3-μm-deep etched-mirrors on an InP platform for integration with passive waveguide components. Timing jitter of 243 fs and pulse width of 10 ps were measured

Addition of Amines to a Carbonyl Ligand: Syntheses, Characterization, and Reactivities of Iridium(III) Porphyrin Carbamoyl Complexes

Treatment of (carbonyl)chloro(meso-tetra-p-tolylporphyrinato)iridium(III), (TTP)Ir(CO)Cl (1), with excess primary amines at 23 °C in the presence of Na2CO3 produces the trans-amine-coordinated iridium carbamoyl complexes (TTP)Ir(NH2R)[C(O)NHR] (R = Bn (2a), n-Bu (2b), i-Pr (2c), t-Bu (2d)) with isolated yields up to 94%. The trans-amine ligand is labile and can be replaced with quinuclidine (1-azabicyclo[2.2.2]octane, ABCO), 1-methylimidazole (1-MeIm), triethyl phosphite (P(OEt)3), and dimethylphenylphosphine (PMe2Ph) at 23 °C to afford the hexacoordinated carbamoyl complexes (TTP)Ir(L)[C(O)NHR] (for R = Bn: L = ABCO (3a), 1-MeIm (4a), P(OEt)3 (5a), PMe2Ph (6a)). On the basis of ligand displacement reactions and equilibrium studies, ligand binding strengths to the iridium metal center were found to decrease in the order PMe2Ph \u3e P(OEt)3 \u3e 1-MeIm \u3e ABCO \u3e BnNH2 ≫ Et3N, PCy3. The carbamoyl complexes (TTP)Ir(L)[C(O)NHR] (L = RNH2 (2a,b), 1-MeIm (4a)) undergo protonolysis with HBF4 to give the cationic carbonyl complexes [(TTP)Ir(NH2R)(CO)]BF4 (7a,b) and [(TTP)Ir(1-MeIm)(CO)]BF4 (8), respectively. In contrast, the carbamoyl complexes (TTP)Ir(L)[C(O)NHR] (L = P(OEt)3 (5a), PMe2Ph (6a,c)) reacted with HBF4 to afford the complexes [(TTP)Ir(PMe2Ph)]BF4 (9) and [(TTP)IrP(OEt)3]BF4 (10), respectively. The carbamoyl complexes (TTP)Ir(L)[C(O)NHR] (L = RNH2 (2a–d), 1-MeIm (4a), P(OEt)3 (5b), PMe2Ph (6c)) reacted with methyl iodide to give the iodo complexes (TTP)Ir(L)I (L = RNH2 (11a–d), 1-MeIm (12), P(OEt)3(13), PMe2Ph (14)). Reactions of the complexes [(TTP)Ir(PMe2Ph)]BF4 (9) and [(TTP)IrP(OEt)3]BF4 (10) with [Bu4N]I, benzylamine (BnNH2), and PMe2Ph afforded (TTP)Ir(PMe2Ph)I (14), (TTP)Ir[P(OEt)3]I (13), [(TTP)Ir(PMe2Ph)(NH2Bn)]BF4 (16), and trans-[(TTP)Ir(PMe2Ph)2]BF4 (17), respectively. Metrical details for the molecular structures of 4a and17 are reported

The Homeobox Protein CEH-23 Mediates Prolonged Longevity in Response to Impaired Mitochondrial Electron Transport Chain in C. elegans

Recent findings indicate that perturbations of the mitochondrial electron transport chain (METC) can cause extended longevity in evolutionarily diverse organisms. To uncover the molecular basis of how altered METC increases lifespan in C. elegans, we performed an RNAi screen and revealed that three predicted transcription factors are specifically required for the extended longevity of mitochondrial mutants. In particular, we demonstrated that the nuclear homeobox protein CEH-23 uniquely mediates the longevity but not the slow development, reduced brood size, or resistance to oxidative stress associated with mitochondrial mutations. Furthermore, we showed that ceh-23 expression levels are responsive to altered METC, and enforced overexpression of ceh-23 is sufficient to extend lifespan in wild-type background. Our data point to mitochondria-to-nucleus communications to be key for longevity determination and highlight CEH-23 as a novel longevity factor capable of responding to mitochondrial perturbations. These findings provide a new paradigm for how mitochondria impact aging and age-dependent diseases

Osteoinduction of Human Mesenchymal Stem Cells by Bioactive Composite Scaffolds without Supplemental Osteogenic Growth Factors

The development of a new family of implantable bioinspired materials is a focal point of bone tissue engineering. Implant surfaces that better mimic the natural bone extracellular matrix, a naturally nano-composite tissue, can stimulate stem cell differentiation towards osteogenic lineages in the absence of specific chemical treatments. Herein we describe a bioactive composite nanofibrous scaffold, composed of poly-caprolactone (PCL) and nano-sized hydroxyapatite (HA) or beta-tricalcium phosphate (TCP), which was able to support the growth of human bone marrow mesenchymal stem cells (hMSCs) and guide their osteogenic differentiation at the same time. Morphological and physical/chemical investigations were carried out by scanning, transmission electron microscopy, Fourier-transform infrared (FTIR) spectroscopy, mechanical and wettability analysis. Upon culturing hMSCs on composite nanofibers, we found that the incorporation of either HA or TCP into the PCL nanofibers did not affect cell viability, meanwhile the presence of the mineral phase increases the activity of alkaline phosphatase (ALP), an early marker of bone formation, and mRNA expression levels of osteoblast-related genes, such as the Runt-related transcription factor 2 (Runx-2) and bone sialoprotein (BSP), in total absence of osteogenic supplements. These results suggest that both the nanofibrous structure and the chemical composition of the scaffolds play a role in regulating the osteogenic differentiation of hMSCs

Impact of Tai Chi exercise on multiple fracture-related risk factors in post-menopausal osteopenic women: a pilot pragmatic, randomized trial

Background: Tai Chi (TC) is a mind-body exercise that shows potential as an effective and safe intervention for preventing fall-related fractures in the elderly. Few randomized trials have simultaneously evaluated TC's potential to reduce bone loss and improve fall-predictive balance parameters in osteopenic women. Methods: In a pragmatic randomized trial, 86 post-menopausal osteopenic women, aged 45-70, were recruited from community clinics. Women were assigned to either nine months of TC training plus usual care (UC) vs. UC alone. Primary outcomes were changes between baseline and nine months of bone mineral density (BMD) of the proximal femur and lumbar spine (dual-energy X-ray absorptiometry) and serum markers of bone resorption and formation. Secondary outcomes included quality of life. In a subsample (n = 16), quiet standing fall-predictive sway parameters and clinical balance tests were also assessed. Both intent-to-treat and per-protocol analyses were employed. Results: For BMD, no intent-to-treat analyses were statistically significant; however, per protocol analyses (i.e., only including TC participants who completed $\geq$ 75% training requirements) of femoral neck BMD changes were significantly different between TC and UC (+0.04 vs. -0.98%; P = 0.05). Changes in bone formation markers and physical domains of quality of life were also more favorable in per protocol TC vs. UC (P = 0.05). Changes in sway parameters were significantly improved by TC vs. UC (average sway velocity, P = 0.027; anterior-posterior sway range, P = 0.014). Clinical measures of balance and function showed non-significant trends in favor of TC. Conclusions: TC training offered through existing community-based programs is a safe, feasible, and promising intervention for reducing multiple fracture risks. Our results affirm the value of a more definitive, longer-term trial of TC for osteopenic women, adequately powered to detect clinically relevant effects of TC on attenuation of BMD loss and reduction of fall risk in this population