A standardised sampling protocol for robust assessment of reach-scale fish community diversity in wadeable New Zealand streams

The New Zealand fish fauna contains species that are affected not only by river system connectivity, but also by catchment and local-scale changes in landcover, water quality and habitat quality. Consequently, native fish have potential as multi-scale bioindicators of human pressure on stream ecosystems, yet no standardised, repeatable and scientifically defensible methods currently exist for effectively quantifying their abundance or diversity in New Zealand stream reaches. Here we report on the testing of a back-pack electrofishing method, modified from that used by the United States Environmental Protection Agency, on a wide variety of wadeable stream reaches throughout New Zealand. Seventy-three first- to third-order stream reaches were fished with a single pass over 150-345 m length. Time taken to sample a reach using single-pass electrofishing ranged from 1-8 h. Species accumulation curves indicated that, irrespective of location, continuous sampling of 150 stream metres is required to accurately describe reach-scale fish species richness using this approach. Additional species detection beyond 150 m was rare (<10%) with a single additional species detected at only two out of the 17 reaches sampled beyond this distance. A positive relationship was also evident between species detection and area fished, although stream length rather than area appeared to be the better predictor. The method tested provides a standardised and repeatable approach for regional and/or national reporting on the state of New Zealand's freshwater fish communities and trends in richness and abundance over time

Identification of Trypanosome Proteins in Plasma from African Sleeping Sickness Patients Infected with T. b. rhodesiense

Control of human African sleeping sickness, caused by subspecies of the protozoan parasite Trypanosoma brucei, is based on preventing transmission by elimination of the tsetse vector and by active diagnostic screening and treatment of infected patients. To identify trypanosome proteins that have potential as biomarkers for detection and monitoring of African sleeping sickness, we have used a ‘deep-mining” proteomics approach to identify trypanosome proteins in human plasma. Abundant human plasma proteins were removed by immunodepletion. Depleted plasma samples were then digested to peptides with trypsin, fractionated by basic reversed phase and each fraction analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). This sample processing and analysis method enabled identification of low levels of trypanosome proteins in pooled plasma from late stage sleeping sickness patients infected with Trypanosoma brucei rhodesiense. A total of 254 trypanosome proteins were confidently identified. Many of the parasite proteins identified were of unknown function, although metabolic enzymes, chaperones, proteases and ubiquitin-related/acting proteins were found. This approach to the identification of conserved, soluble trypanosome proteins in human plasma offers a possible route to improved disease diagnosis and monitoring, since these molecules are potential biomarkers for the development of a new generation of antigen-detection assays. The combined immuno-depletion/mass spectrometric approach can be applied to a variety of infectious diseases for unbiased biomarker identification

Plasma proteomic signature predicts who will get persistent symptoms following SARS-CoV-2 infection

BACKGROUND: The majority of those infected by ancestral Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) during the UK first wave (starting March 2020) did not require hospitalisation. Most had a short-lived mild or asymptomatic infection, while others had symptoms that persisted for weeks or months. We hypothesized that the plasma proteome at the time of first infection would reflect differences in the inflammatory response that linked to symptom severity and duration. METHODS: We performed a nested longitudinal case-control study and targeted analysis of the plasma proteome of 156 healthcare workers (HCW) with and without lab confirmed SARS-CoV-2 infection. Targeted proteomic multiple-reaction monitoring analysis of 91 pre-selected proteins was undertaken in uninfected healthcare workers at baseline, and in infected healthcare workers serially, from 1 week prior to 6 weeks after their first confirmed SARS-CoV-2 infection. Symptom severity and antibody responses were also tracked. Questionnaires at 6 and 12 months collected data on persistent symptoms. FINDINGS: Within this cohort (median age 39 years, interquartile range 30-47 years), 54 healthcare workers (44% male) had PCR or antibody confirmed infection, with the remaining 102 (38% male) serving as uninfected controls. Following the first confirmed SARS-CoV-2 infection, perturbation of the plasma proteome persisted for up to 6 weeks, tracking symptom severity and antibody responses. Differentially abundant proteins were mostly coordinated around lipid, atherosclerosis and cholesterol metabolism pathways, complement and coagulation cascades, autophagy, and lysosomal function. The proteomic profile at the time of seroconversion associated with persistent symptoms out to 12 months. Data are available via ProteomeXchange with identifier PXD036590. INTERPRETATION: Our findings show that non-severe SARS-CoV-2 infection perturbs the plasma proteome for at least 6 weeks. The plasma proteomic signature at the time of seroconversion has the potential to identify which individuals are more likely to suffer from persistent symptoms related to SARS-CoV-2 infection. FUNDING INFORMATION: The COVIDsortium is supported by funding donated by individuals, charitable Trusts, and corporations including Goldman Sachs, Citadel and Citadel Securities, The Guy Foundation, GW Pharmaceuticals, Kusuma Trust, and Jagclif Charitable Trust, and enabled by Barts Charity with support from University College London Hospitals (UCLH) Charity. This work was additionally supported by the Translational Mass Spectrometry Research Group and the Biomedical Research Center (BRC) at Great Ormond Street Hospital

Heterologous infection and vaccination shapes immunity against SARS-CoV-2 variants

[Figure: see text].The impact of initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infecting strain on downstream immunity to heterologous variants of concern (VOC) is unknown. Studying a longitudinal healthcare worker cohort, we found that after three antigen exposures (infection+two vaccine doses), S1 antibody, memory B cells and heterologous neutralization of B.1.351, P.1 and B.1.617.2 plateaued, while B.1.1.7 neutralization and spike T cell responses increased. Serology using Wuhan Hu-1 spike receptor binding domain poorly predicted neutralizing immunity against VOCs. Neutralization potency against VOCs changed with heterologous virus encounter and number of antigen exposures. Neutralization potency fell differentially depending on targeted VOCs over 5-months from the second vaccine dose. Heterologous combinations of spike encountered during infection and vaccination shape subsequent cross-protection against VOC, with implications for future-proof next-generation vaccines

Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Breusing, C., Mitchell, J., Delaney, J., Sylva, S. P., Seewald, J. S., Girguis, P. R., & Beinart, R. A. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. Isme Journal, (2020), doi:10.1038/s41396-020-0707-2.Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host–symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.We thank the Schmidt Ocean Institute, the crew of the R/V Falkor and the pilots of the ROV ROPOS for facilitating the sample collections and shipboard experiments, and the Broad Institute Microbial ‘Omics Core for preparing and sequencing the transcriptomic libraries. This material is based in part upon work supported by the National Science Foundation under Grant Numbers NSF OCE-1536653 (to PRG), OCE-1536331 (to RAB and JSS), OCE-1819530 and OCE-1736932 (to RAB)

Patient, informal caregiver and care provider acceptance of a hospital in the home program in Ontario, Canada

<p>Abstract</p> <p>Background</p> <p>Hospital in the home programs have been implemented in several countries and have been shown to be safe substitutions (alternatives) to in-patient hospitalization. These programs may offer a solution to the increasing demands made on tertiary care facilities and to surge capacity. We investigated the acceptance of this type of care provision with nurse practitioners as the designated principal home care providers in a family medicine program in a large Canadian urban setting.</p> <p>Methods</p> <p>Patients requiring hospitalization to the family medicine service ward, for any diagnosis, who met selection criteria, were invited to enter the hospital in the home program as an alternative to admission. Participants in the hospital in the home program, their caregivers, and the physicians responsible for their care were surveyed about their perceptions of the program. Nurse practitioners, who provided care, were surveyed and interviewed.</p> <p>Results</p> <p>Ten percent (104) of admissions to the ward were screened, and 37 patients participated in 44 home hospital admissions. Twenty nine patient, 17 caregiver and 38 provider surveys were completed. Most patients (88%–100%) and caregivers (92%–100%) reported high satisfaction levels with various aspects of health service delivery. However, a significant proportion in both groups stated that they would select to be treated in-hospital should the need arise again. This was usually due to fears about the safety of the program. Physicians (98%–100%) and nurse practitioners also rated the program highly. The program had virtually no negative impact on the physician workload. However nurse practitioners felt that the program did not utilize their full expertise.</p> <p>Conclusion</p> <p>Provision of hospital level care in the home is well received by patients, their caregivers and health care providers. As a new program, investment in patient education about program safety may be necessary to ensure its long term success. A small proportion of hospital admissions were screened for this program. Appropriate dissemination of program information to family physicians should help buy-in and participation. Nurse practitioners' skills may not be optimally utilized in this setting.</p

A System Dynamics Approach for Hospital Waste Management in a City in a Developing Country: The Case of Nablus, Palestine

Hospitals and health centers provide a variety of healthcare services and normally generate hazardous waste as well as general waste. General waste has a similar nature to that of municipal solid waste and therefore could be disposed of in municipal landfills. However, hazardous waste poses risks to public health, unless it is properly managed. The hospital waste management system encompasses many factors, i.e., number of beds, number of employees, level of service, population, birth rate, fertility rate, and not in my back yard (NIMBY) syndrome. Therefore, this management system requires a comprehensive analysis to determine the role of each factor and its influence on the whole system. In this research, a hospital waste management simulation model is presented based on the system dynamics technique to determine the interaction among these factors in the system using a software package, ithink. This model is used to estimate waste segregation as this is important in the hospital waste management system to minimize risk to public health. Real data has been obtained from a case study of the city of Nablus, Palestine to validate the model. The model exhibits wastes generated from three types of hospitals (private, charitable, and government) by considering the number of both inpatients and outpatients depending on the population of the city under study. The model also offers the facility to compare the total waste generated among these different types of hospitals and anticipate and predict the future generated waste both infectious and non-infectious and the treatment cost incurred

Bim Nuclear Translocation and Inactivation by Viral Interferon Regulatory Factor

Viral replication efficiency is in large part governed by the ability of viruses to counteract pro-apoptotic signals induced by infection of the host cell. Human herpesvirus 8 (HHV-8) uses several strategies to block the host's innate antiviral defenses via interference with interferon and apoptotic signaling. Contributors include the four viral interferon regulatory factors (vIRFs 1–4), which function in dominant negative fashion to block cellular IRF activities in addition to targeting IRF signaling-induced proteins such as p53 and inhibiting other inducers of apoptosis such as TGFβ receptor-activated Smad transcription factors. Here we identify direct targeting by vIRF-1 of BH3-only pro-apoptotic Bcl-2 family member Bim, a key negative regulator of HHV-8 replication, to effect its inactivation via nuclear translocation. vIRF-1-mediated relocalization of Bim was identified in transfected cells, by both immunofluorescence assay and western analysis of fractionated cell extracts. Also, co-localization of vIRF-1 and Bim was detected in nuclei of lytically infected endothelial cells. In vitro co-precipitation assays using purified vIRF-1 and Bim revealed direct interaction between the proteins, and Bim-binding residues of vIRF-1 were mapped by deletion and point mutagenesis. Generation and experimental utilization of Bim-refractory vIRF-1 variants revealed the importance of vIRF-1:Bim interaction, specifically, in pro-replication and anti-apoptotic activity of vIRF-1. Furthermore, blocking of the interaction with cell-permeable peptide corresponding to the Bim-binding region of vIRF-1 confirmed the relevance of vIRF-1:Bim association to vIRF-1 pro-replication activity. To our knowledge, this is the first report of an IRF protein that interacts with a Bcl-2 family member and of nuclear sequestration of Bim or any other member of the family as a means of inactivation. The data presented reveal a novel mechanism utilized by a virus to control replication-induced apoptosis and suggest that inhibitory targeting of vIRF-1:Bim interaction may provide an effective antiviral strategy

GPS-CCD: A Novel Computational Program for the Prediction of Calpain Cleavage Sites

As one of the most essential post-translational modifications (PTMs) of proteins, proteolysis, especially calpain-mediated cleavage, plays an important role in many biological processes, including cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. Experimental identification of calpain targets with bona fide cleavage sites is fundamental for dissecting the molecular mechanisms and biological roles of calpain cleavage. In contrast to time-consuming and labor-intensive experimental approaches, computational prediction of calpain cleavage sites might more cheaply and readily provide useful information for further experimental investigation. In this work, we constructed a novel software package of GPS-CCD (Calpain Cleavage Detector) for the prediction of calpain cleavage sites, with an accuracy of 89.98%, sensitivity of 60.87% and specificity of 90.07%. With this software, we annotated potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. In this regard, GPS-CCD 1.0 is considered to be a useful tool for experimentalists. The online service and local packages of GPS-CCD 1.0 were implemented in JAVA and are freely available at: http://ccd.biocuckoo.org/

Functional Neuromuscular Junctions Formed by Embryonic Stem Cell-Derived Motor Neurons

A key objective of stem cell biology is to create physiologically relevant cells suitable for modeling disease pathologies in vitro. Much progress towards this goal has been made in the area of motor neuron (MN) disease through the development of methods to direct spinal MN formation from both embryonic and induced pluripotent stem cells. Previous studies have characterized these neurons with respect to their molecular and intrinsic functional properties. However, the synaptic activity of stem cell-derived MNs remains less well defined. In this study, we report the development of low-density co-culture conditions that encourage the formation of active neuromuscular synapses between stem cell-derived MNs and muscle cells in vitro. Fluorescence microscopy reveals the expression of numerous synaptic proteins at these contacts, while dual patch clamp recording detects both spontaneous and multi-quantal evoked synaptic responses similar to those observed in vivo. Together, these findings demonstrate that stem cell-derived MNs innervate muscle cells in a functionally relevant manner. This dual recording approach further offers a sensitive and quantitative assay platform to probe disorders of synaptic dysfunction associated with MN disease