Mutagenesis of the fusion peptide-like domain of hepatitis C virus E1 glycoprotein: involvement in cell fusion and virus entry

<p>Abstract</p> <p>Background</p> <p>Envelope (E) glycoprotein E2 of the hepatitis C virus (HCV) mediates binding of the virus to target cell receptors. Nevertheless, the precise role of E1 in viral entry remains elusive.</p> <p>Methods</p> <p>To understand the involvement of the fusion peptide-like domain positioned at residues 264 to 290 within envelope glycoprotein E1 in HCV infection, mutants with Ala and Asn substitutions for residues conserved between HCV and E proteins of flaviviruses or the fusion proteins of paramyxoviruses were constructed by site-directed mutagenesis and their effects on membrane fusion and viral infectivity were examined.</p> <p>Results</p> <p>None of these mutations affected the synthesis or cell surface expression of envelope proteins, nor did they alter the formation of a non-covalent E1-E2 heterodimer or E2 binding to the large extracellular loop of CD81. The Cys residues located at positions 272 and 281 were unlikely involved in intra- or intermolecular disulfide bond formation. With the exception of the G267A mutant, which showed increased cell fusion, other mutants displayed reduced or marginally inhibited cell fusion capacities compared to the wild-type (WT) E1E2. The G267A mutant was also an exception in human immunodeficiency virus type 1 (HIV-1)/HCV E1E2 pseudotyping analyses, in that it showed higher one-cycle infectivity; all other mutants exhibited greatly or partially reduced viral entry versus the WT pseudotype. All but the G278A and D279N mutants showed a WT-like profile of E1E2 incorporation into HIV-1 particles. Since C272A, C281A, G282A, and G288A pseudotypes bound to Huh7 cells as effectively as did the WT pseudotype, the reduced infectivity of these pseudotypes was due to their ability to inhibit cell fusion.</p> <p>Conclusion</p> <p>Our results indicate that specific residues, but not the structure, of this fusion peptide-like domain are required for mediating cell fusion and viral entry.</p

Granger causal connectivity dissociates navigation networks that subserve allocentric and egocentric path integration

Studies on spatial navigation demonstrate a significant role of the retrosplenial complex (RSC) in the transformation of egocentric and allocentric information into complementary spatial reference frames (SRFs). The tight anatomical connections of the RSC with a wide range of other cortical regions processing spatial information support its vital role within the human navigation network. To better understand how different areas of the navigational network interact, we investigated the dynamic causal interactions of brain regions involved in solving a virtual navigation task. EEG signals were decomposed by independent component analysis (ICA) and subsequently examined for information flow between clusters of independent components (ICs) using direct short-time directed transfer function (sdDTF). The results revealed information flow between the anterior cingulate cortex and the left prefrontal cortex in the theta (4-7 Hz) frequency band and between the prefrontal, motor, parietal, and occipital cortices as well as the RSC in the alpha (8-13 Hz) frequency band. When participants prefered to use distinct reference frames (egocentric vs. allocentric) during navigation was considered, a dominant occipito-parieto-RSC network was identified in allocentric navigators. These results are in line with the assumption that the RSC, parietal, and occipital cortices are involved in transforming egocentric visual-spatial information into an allocentric reference frame. Moreover, the RSC demonstrated the strongest causal flow during changes in orientation, suggesting that this structure directly provides information on heading changes in humans

Cerebro-Cerebellar Pathways for Verbal Working Memory

The current study examined the structural and functional connectivity of the cerebro-cerebellar network of verbal working memory as proposed by Chen and Desmond (2005a). Diffusion spectrum imaging was employed to establish structural connectivity between cerebro-cerebellar regions co-activated during a verbal working memory task. The inferior frontal gyrus, inferior parietal lobule, pons, thalamus, superior cerebellum and inferior cerebellum were used as regions of interest to reconstruct and segment the contralateral white matter cerebro-cerebellar circuitry. The segmented pathways were examined further to establish the relationship between structural and effective connectivity as well as the relationship between structural connectivity and verbal working memory performance. No direct relationship between structural and effective connectivity was found but the results demonstrated that structural connectivity is indirectly related to effective connectivity as DCM models that resembled more closely with underlying white matter pathways had a higher degree of model inference confidence. Additionally, it was demonstrated that the structural connectivity of the ponto-cerebellar tract was associated with individual differences in response time for verbal working memory. The findings of the study contribute to further our understanding of the relationship between structural and functional connectivity and the impact of variability in verbal working memory performance

An Overview of Regional Experiments on Biomass Burning Aerosols and Related Pollutants in Southeast Asia: From BASE-ASIA and the Dongsha Experiment to 7-SEAS

By modulating the Earth-atmosphere energy, hydrological and biogeochemical cycles, and affecting regional-to-global weather and climate, biomass burning is recognized as one of the major factors affecting the global carbon cycle. However, few comprehensive and wide-ranging experiments have been conducted to characterize biomass-burning pollutants in Southeast Asia (SEA) or assess their regional impact on meteorology, the hydrological cycle, the radiative budget, or climate change. Recently, BASEASIA (Biomass-burning Aerosols in South-East Asia: Smoke Impact Assessment) and the 7-SEAS (7- South-East Asian Studies) Dongsha Experiment were conducted during the spring seasons of 2006 and 2010 in northern SEA, respectively, to characterize the chemical, physical, and radiative properties of biomass-burning emissions near the source regions, and assess their effects. This paper provides an overview of results from these two campaigns and related studies collected in this special issue, entitled Observation, modeling and impact studies of biomass burning and pollution in the SE Asian Environment. This volume includes 28 papers, which provide a synopsis of the experiments, regional weatherclimate, chemical characterization of biomass-burning aerosols and related pollutants in source and sink regions, the spatial distribution of air toxics (atmospheric mercury and dioxins) in source and remote areas, a characterization of aerosol physical, optical, and radiative properties, as well as modeling and impact studies. These studies, taken together, provide the first relatively complete dataset of aerosol chemistry and physical observations conducted in the sourcesink region in the northern SEA, with particular emphasis on the marine boundary layer and lower free troposphere (LFT). The data, analysis and modeling included in these papers advance our present knowledge of source characterization of biomass-burning pollutants near the source regions as well as the physical and chemical processes along transport pathways. In addition, we raise key questions to be addressed by a coming deployment during springtime 2013 in northern SEA, named 7-SEASBASELInE (Biomass-burning Aerosols Stratocumulus Environment: Lifecycles and Interactions Experiment). This campaign will include a synergistic approach for further exploring many key atmospheric processes (e.g., complex aerosol-cloud interactions) and impacts of biomass burning on the surface-atmosphere energy budgets during the lifecycles of biomass burning emissions

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The Effect of Haemodialysis Access Types on Cardiac Performance and Morbidities in Patients with Symptomatic Heart Disease.

Little is known about whether the arteriovenous type haemodialysis access affects cardiac function and whether it is still advantageous to the uremic patient with symptomatic heart disease.We conducted a retrospective comparative study. Patients with heart disease and end-stage renal disease that had a new chronic access created between January 2007 and December 2008 and met the inclusion criteria were assessed. The endpoint was major adverse event (MAE)-free survivals of arteriovenous access (AVA) and tunneled cuffed double-lumen central venous catheter (CVC) groups. Whether accesses worsened heart failure was also evaluated.There were 43 CVC patients and 60 AVA patients. The median follow-up time from access creation was 27.6 months (IQR 34.7, 10.9~45.6). Although CVC patients were older than AVA patients (median age 78.0, IQR 14.0 vs. 67.5, IQR 16.0, respectively, p = .009), they manifested non-inferior MAE-free survival (mean 17.1, 95% CI 10.3~24.0 vs. 12.9, 95% CI 8.5~17.4 months in CVC and AVA patients, respectively, p = .290). During follow-up, more patients in the AVA group than in the CVC group deteriorated in heart failure status (35 of 57 vs. 10 of 42, respectively, odds ratio 5.1, p < .001). Preoperative-postoperative pairwise comparison of echocardiographic scans revealed an increased number of abnormal findings in the AVA group (Z = 3.91, p < .001), but not in the CVC group.In patients with both symptomatic heart disease and end stage renal disease (ESRD), CVC patients showed non-inferior MAE-free survival in comparison to those in the AVA group. AV type access could deteriorate heart failure. Accordingly, uremic patients with symptomatic heart disease are not ideal candidates for AV type access creation

The J-Domain of Heat Shock Protein 40 Can Enhance the Transduction Efficiency of Arginine-Rich Cell-Penetrating Peptides

Sense and antisense oligonucleotide pairs encoding cell-penetrating peptides PTD (Tat47–57), DPV3A, E162, pVEC, R11, and TP13 were used to construct two sets of pET22b-CPP-DsRed and pET22b-CPP-J-DsRed vectors for CPP-DsRed and CPP-J-DsRed recombinant proteins expression. PTD-DsRed, DPV3A-DsRed, PTD-J-DsRed, and DPV3A-J-DsRed recombinant proteins were expressed in a soluble form. PTD-J-DsRed and DPV3A-J-DsRed recombinant proteins were able to escape from E. coli host cells into the culture medium. The membrane-penetrating activity of PTD-J-DsRed and DPV3A-J-DsRed recombinant proteins to mammalian cells was more effective than that of PTD-DsRed and DPV3A-DsRed. The route of the cellular membrane translocation of these recombinant proteins is suggested via macropinocytosis followed by an endosomal escape pathway