Biology subjects

Wiley, M.

Publications and source records attributed to Wiley, M..

6 recordsLinked to original sources

bioRxiv2022

Detection of Dugbe virus from ticks in Ghana

Vector-borne pathogens historically have impacted U.S. warfighters and active-duty personnel stationed both domestically and globally during deployments or forward operations. Tick-borne diseases continue to spread to new geographical regions affecting both animal and human health. In Ghana, there is limited information on the circulating tick-borne pathogens and their risk of infections. This military-to-military vector surveillance study focused on seven sites in Ghana: Navrongo, Airforce Base, 6th Battalion Infantry, Air Borne Force, Army Recruit Training School, 1st Battalion Infantry and 5th Battalion Infantry for detection of tick-borne pathogens. Ticks from these sites were collected by hand-picking with a pair of forceps from domesticated animals including cattle, sheep, goats and dogs. A total of 2,016 ticks were collected from two main ecological zones; the northern Sahel savannah and the coastal savannah. Amblyomma variegatum was the predominant species, accounting for 59.5% of the collected ticks. Next-generation sequencing allowed for Dugbe virus whole genome detection. This study reports the second detection of Dugbe virus in Ghana, which is closely related to Dugbe virus strains from Kenya and Nigeria. This study (sponsored by the Armed Forces Health Surveillance Branch-Global Emerg-ing Infections Surveillance Section) aimed to better inform Force Health Protection (FHP) decisions within the U.S. AFRICOM area of responsibility, the Ghana Armed Forces, and enhance global health security countermeasures. Further surveillance needs to be conducted within the country to determine the distribution of tick-borne pathogens to formulate effective control measures. Author summaryThe prevalence of Dugbe virus in tick species within Ghana was investigated. This study involved seven sampling sites that covered two ecological zones, the northern Sahel savannah and the coastal savannah. About 2,000 ticks were collected from cattle, sheep, goats and dogs and identified using a dissecting microscope. The most predominant tick species was Amblyomma variegatum (59.5%) also known as the tropical bont tick. Using Next-generation sequencing, the full genome of Dugbe virus was for the first time in Ghana identified in A. variegatum. This positive Amblyomma variegatum was collected from the Greater Accra region of Ghana within a military site. The virus was found to be related to Dugbe virus strains from Kenya and Nigeria. Findings from this study show that the trade of livestock across borders facilitates the spread of tick-borne pathogens hence there is a need to enforce measures that prevent the importation of potentially harmful ticks and tick-borne pathogens.

scientific communication and education↗

bioRxiv2019

Analysis of Practices to Promote Reproducibility and Transparency in Anaesthesiology Research: Are Important Aspects Hidden Behind the Drapes?

IntroductionReliable, high-quality research is essential to the field of anaesthesiology. Reproducibility and transparency has been investigated in the biomedical domain and in the social sciences, with both lacking to provide necessary information to reproduce the study findings. In this study, we investigated 14 indicators of reproducibility in anaesthesiology research.\n\nMethodsWe used the National Library of Medicine (NLM) catalogue to search for all anaesthesiology journals that are MEDLINE indexed and provided English texts. PubMed was searched with the list of journals to identify all publications from January 1, 2014 to December 31, 2018. We randomly sampled 300 publications that fit the inclusion criteria for our analysis. Data extraction was then conducted in a blinded, duplicate fashion using a pilot-tested Google form.\n\nResultsThe PubMed search of these journals identified 171,441 publications, with 28,310 being within the time frame. From the 300 publications sampled, 296 full-text publications were accessible. Most of the studies did not include materials or protocol availability statements. The majority of publications did not provide a data analysis script statement (121/122, 99% [98% to 100%]) or a preregistration statement (94/122, 77% [72% to 81%]).\n\nConclusionAnaesthesiology research needs to drastically improve indicators of reproducibility and transparency. By making research publically available and improving accessibility to detailed study components, primary research can be reproduced in subsequent studies and help contribute to the development of new practice guidelines.

scientific communication and education↗

bioRxiv2018

Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry

In 2012, the genome of a novel rhabdovirus, Bas-Congo virus, was discovered in the acute-phase serum of a Congolese patient with presumed viral hemorrhagic fever. In the absence of a replicating virus isolate, fulfilling Kochs postulates to determine whether Bas-Congo virus is indeed a human virus and/or pathogen has been impossible. However, experiments with vesiculoviral particles pseudotyped with Bas-Congo glycoprotein suggested that Bas-Congo virus particles can enter cells from multiple animals, including humans. In 2015, genomes of two related viruses, Ekpoma virus 1 and Ekpoma virus 2, were detected in human sera in Nigeria. Isolates could not be obtained. Phylogenetic analyses led to the classification of Bas-Congo virus, Ekpoma virus 1, and Ekpoma virus 2 in the same genus, Tibrovirus, together with five biting midge-borne rhabdoviruses (i.e., Beatrice Hill virus, Bivens Arm virus, Coastal Plains virus, Sweetwater Branch virus, and Tibrogargan virus) not known to infect humans. Using individual recombinant vesiculoviruses expressing the glycoproteins of all eight known tibroviruses and more than 75 cell lines representing different animal species, we demonstrate that the glycoproteins of all tibroviruses can mediate vesiculovirus particle entry into human, bat, nonhuman primate, cotton rat, boa constrictor, and Asian tiger mosquito cells. Using four of five isolated authentic tibroviruses (i.e., Bivens Arm virus, Coastal Plains virus, Sweetwater Branch virus, and Tibrogargan virus), our experiments indicate that many cell types may be partially resistant to tibrovirus replication after virion cell entry. Consequently, experimental data solely obtained from experiments using tibrovirus surrogate systems (e.g., vesiculoviral pseudotypes, recombinant vesiculoviruses) cannot be used to predict whether Bas-Congo virus, or any other tibrovirus, infects humans.

microbiology↗

bioRxiv2018

Evidence of an Unusual Poly(A) RNA Signature Detected by High-throughput Chemical Mapping

Homopolymeric adenosine RNA plays numerous roles in both cells and non-cellular genetic material, and for lack of evidence to the contrary, it is generally accepted to form a random coil under physiological conditions. However, chemical mapping data generated by the Eterna Massive Open Laboratory indicates that a poly (A) sequence of length seven or more, at pH 8.0 and MgCl concentrations of 10 mM, develops unexpected protection to selective 2-hydroxyl acylation read out by primer extension (SHAPE) and dimethyl sulfate (DMS) chemical probing. This protection first appears in poly(A) sequences of length 7 and grows to its maximum strength at length ~10. In a long poly(A) sequence, substitution of a single A by any other nucleotide disrupts the protection, but only for the 6 or so nucleotides on the 5 side of the substitution. The authors are grateful for pre-publication comments; please use https://docs.google.com/document/d/14972Q36IDTYMglwMXTOrqd4P9orQ6-P3bPbCuITdv6A.

biochemistry↗

bioRxiv2018

bpRNA: Large-scale Automated Annotation and Analysis of RNA Secondary Structure

While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, \"bpRNA-1m\", of over 100,000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar ([≥]90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

bioinformatics↗

bioRxiv2017

Interferon Regulatory Factor 5 (IRF5) Interacts with the Translation Initiation Complex and Promotes mRNA Translation During the Integrated Stress Response to Amino Acid Deprivation

Interferon Regulatory Factor 5 (IRF5) plays an important role in limiting pathogenic infection and tumor development. Host protection by IRF5 can occur through a variety of mechanisms including production of type I interferon and cytokines as well as the regulation of cell survival, growth, proliferation, and differentiation. While modulation of these cellular processes is attributed to IRF5 transcription factor function in the nucleus, emerging evidence suggests that IRF5 may also retain non-transcriptional regulatory properties within the cytoplasmic compartment. Consistent with this notion, we report the ability of IRF5 to control gene expression at the level of mRNA translation. Our findings demonstrate that IRF5 interacts with the translation initiation complex in the absence of the m7GTP cap-binding protein, eIF4E. We observed that under nutrient deprivation-induced cell stress, IRF5 promoted mRNA translation of the master integrated stress response (ISR) regulator, Activating Transcription Factor 4 (ATF4). Enhanced ATF4 protein expression correlated with increased levels of downstream target genes including CHOP and GADD34 and was associated with amplification of eIF2 de-phosphorylation and translational de-repression under stress. The novel mechanism we describe broadens our understanding of how IRF5 regulates gene expression and may govern diverse cellular processes in the absence of stimuli that trigger IRF5 nuclear translocation.

biochemistry↗