Identification of Peptides from a Phage Display Library for Differentiating Newcastle Disease Virus Pathotypes

Newcastle disease virus (NDV) strains can be classified as virulent or avirulent based upon the severity of the disease.Biopanning experiments were performed using a disulfide constrained phage display heptapeptide library against three pathotypes of NDV strains: velogenic (highly virulent), mesogenic (moderately virulent) and lentogenic (avirulent).A phage clone bearing the peptide sequence SWGEYDM was isolated and shown to be able to differentiate virulent from avirulent NDV strains.This phage clone was employed as a capturing reagent in a dot-blot assay to detect virulent NDV strains in allantoic fluid of embryonated chicken eggs. The performance of the dot blot assay was compared with that of mean death time (MDT) in embryonated chicken eggs and the reverse transcription-polymerase chain reaction (RT-PCR) methods.The dot blot was shown to be specific for virulent NDV strains and able to differentiate between the virulent and avirulent NDV strain

spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity

R-loops affect transcription and genome stability. Dysregulation of R-loops is related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive ribonuclease H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq) to map R-loops by taking advantage of the presence of a ssDNA in the triplex structure. We show that spKAS-seq detects R-loops and their dynamics at coding sequences, enhancers, and other intergenic regions with as few as 50,000 cells. A joint analysis of R-loops and chromatin-bound RNA binding proteins (RBPs) suggested that R-loops can be RBP binding hotspots on the chromatin

Immunological hotspots analyzed by docking simulations: evidence for a general mechanism in pemphigus vulgaris pathology and transformation

<p>Abstract</p> <p>Background</p> <p>Pemphigus vulgaris (PV) is an acquired autoimmune blistering disorder in which greater than 80% of active patients produce autoantibodies to the desmosomal protein desmogelin 3 (Dsg3). As the disease progresses, 40–50% of patients may also develop reactivity to a second component of the desmosomal complex, desmogelin 1 (Dsg1). T cells are clearly required for the production of autoantibodies in PV. However, few T-cell specificities within Dsg3 or Dsg1 have been reported to date, and the precise role of T-cells in disease pathogenesis and evolution remains poorly understood. In particular, no studies have addressed the immunological mechanisms that underlie the observed clinical heterogeneity in pemphigus. We report here a structure-based technique for the screening of DRB1*0402-specific immunological (T-cell epitope) hotspots in both Dsg3 and Dsg1 glycoproteins.</p> <p>Results</p> <p>High predictivity was obtained for DRB1*0402 (<it>r</it>²= 0.90, <it>s </it>= 1.20 kJ/mol, <it>q</it>²= 0.82, <it>s</it>_{<it>press </it>}= 1.61 kJ/mol) predictive model, compared to experimental data. <it>In silico </it>mapping of the T-cell epitope repertoires in Dsg3 and Dsg1 glycoproteins revealed that the potential immunological hotspots of both target autoantigens are highly conserved, despite limited sequence identity (54% identical, 72% similar). A similar number of well-conserved (18%) high-affinity binders were predicted to exist within both Dsg3 and Dsg1, with analogous distribution of binding registers.</p> <p>Conclusion</p> <p>This study provides interesting new insights into the possible mechanism for PV disease progression. Our data suggests that the potential T-cell epitope repertoires encoded in Dsg1 and Dsg3 is substantially overlapping, and it may be possible to apply a common, antigen-specific therapeutic strategy with efficacy across distinct clinical phases of disease.</p

Teleconsultation by a Team of Physicians: The Intricacy of Hierarchy

Teleconsultations delivered by a team of physicians can yield various benefits over individual-based teleconsultations, such as rapid response, diverse expertise, workload distribution, and a learning environment for junior physicians. However, formal hierarchical barriers may inhibit junior physicians from actively participating in consultations in the presence of their senior counterparts. Drawing upon the lens of hierarchy, this study investigates strategies for mitigating formal hierarchical obstacles by examining the influence of medical rank-based formal hierarchy on physician participation and exploring the moderating effects of three informal hierarchical factors: gender stereotypes, platform-given informal hierarchy, and reputation-given informal hierarchy. We analyzed data from a prominent Chinese teleconsultation platform to derive our findings. This research aims to contribute to the literature on hierarchy, online health IT, and gender stereotypes while providing practical insights for effectively motivating and managing physicians in team-based teleconsultation services

Direct and Indirect Use of Information Systems in Organizations: An Empirical Investigation of System Usage in a Public Hospital

A user’s interaction with an Information System (IS) could transpire in two ways: direct and indirect. While most prior literature examines the direct interaction between a user and the system, few have examined and differentiated between direct and indirect use. In this study, we anchor on the theory of psychological attachment to study the effects of various external social factors on direct-usage and indirect-usage of an organizational IS. Survey results from 102 physicians in a public hospital reveal that punishment and informational influence are significantly related to direct-usage of the Electronic Medical Record System (EMRS) by physicians. Punishment and image are significantly associated with indirect-usage of EMRS

Understanding peptide specificity through structural immunoinformatics

Ph.DDOCTOR OF PHILOSOPH

Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage

Background: Type I signal peptidases (SPases) are essential membrane-bound serine proteases responsible for the cleavage of signal peptides from proteins that are translocated across biological membranes. The crystal structure of SPase in complex with signal peptide has not been solved and their substrate-binding site and binding specificities remain poorly understood. We report here a structure-based model for Escherichia coli DsbA 13–25 in complex with its endogenous type I SPase. Results: The bound structure of DsbA 13–25 in complex with its endogenous type I SPase reported here reveals the existence of an extended conformation of the precursor protein with a pronounced backbone twist between positions P3 and P1'. Residues 13–25 of DsbA occupy, and thereby define 13 subsites, S7 to S6', within the SPase substrate-binding site. The newly defined subsites, S1' to S6' play critical roles in the substrate specificities of E. coli SPase. Our results are in accord with available experimental data. Conclusion: Collectively, the results of this study provide interesting new insights into the binding conformation of signal peptides and the substrate-binding site of E. coli SPase. This is the first report on the modeling of a precursor protein into the entire SPase binding site. Together with the conserved precursor protein binding conformation, the existing and newly identified substrate binding sites readily explain SPase cleavage fidelity, consistent with existing biochemical results and solution structures of inhibitors in complex with E. coli SPase. Our data suggests that both signal and mature moiety sequences play important roles and should be considered in the development of predictive tools.7 page(s

Carbon dioxide dynamics from sediment, sediment-water interface and overlying water in the aquaculture shrimp ponds in subtropical estuaries, southeast China

Aquaculture ponds can emit a large amount carbon dioxide (CO2), with the consequence of exacerbating global climate change. Many studies about CO2 dynamics across the water-air interface, but CO2 in sediment and overlying water received relative less attention. In this study, CO2 concentration in sediment porewater, the diffusive CO2 fluxes across the sediment-water interface (SWI), and the CO2 production rates in the overlying water (CO2_WP) were determined in the shrimp ponds in the Min River Estuary (MRE) and Jiulong River Estuary (JRE), southeast China, to analyze the dynamics of CO2 among different growth stages of shrimps. Our results showed large variations in porewater CO2 concentrations, CO2 diffusive fluxes and CO2_WP rates among different growth stages, with markedly larger values in the middle stage of shrimp growth. The temporal variation of CO2 in both estuarine ponds followed closely the seasonal change of temperature. The internal CO2 production (CO2_IP) in these ponds was dominated by sediments. A significantly larger mean porewater CO2 concentrations, diffusive fluxes and production rate were observed in the MRE ponds than those in the JRE ponds, which could be attributed to the lower water salinity and a larger source of carbon substrates in the former estuary. Considering a total surface area of 6.63 × 103 km2 across the mariculture ponds in subtropical estuaries, it is estimated conservatively that approximately 100 Gigagram (Gg) of dissolved organic carbon and 190 Gg of dissolved inorganic carbon were transported annually from the mariculture ponds into China's coastal areas. Because of the substantial supply of dissolved carbon, the adjacent coastal waters receiving effluent discharge from the mariculture ponds could become “hotspots” of CO2 emissions. Our results highlight the role of aquaculture pond as a major CO2 source in China's coastal areas, and effective actions are needed to alleviate the greenhouse gas (GHG) emissions from these ponds