bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Hsp90 chaperone system from the African trypanosome,Trypanosoma brucei
Authors: Jamabo Miebaka , Bentley Stephen J. , Macucule-Tinga Paula , Edkins Adrienne L. , Boshoff Aileen 
Published: March 2021

AbstractAfrican Trypanosomiasis is a neglected tropical disease caused byTrypanosoma brucei(T. brucei) and is spread by the tsetse fly in sub-Saharan Africa. The disease is fatal if left untreated and the currently approved drugs for treatment are toxic and difficult to administer. The trypanosome must survive in the insect vector and its mammalian host, and to adapt to these different conditions, the parasite relies on molecular chaperones called heat shock proteins. Heat shock proteins mediate the folding of newly synthesized proteins as well as prevent misfolding of proteins under normal conditions and during stressful conditions. Heat shock protein 90 (Hsp90) is one of the major molecular chaperones of the stress response at the cellular level. It functions with other chaperones and co-chaperones and inhibition of its interactions is being explored as a potential therapeutic target for numerous diseases. This study provides an in-silico overview of Hsp90 and its co-chaperones in bothT. brucei brucei and T. brucei gambiensein relation to human and other kinetoplastid parasites. The evolutionary, functional, and structural analyses of Hsp90 were also shown. The updated information on Hsp90 and its co-chaperones from recently published proteomics onT. bruceiwas examined for the different life cycle stages and subcellular localisations. The results show a difference betweenT. b. brucei and T. b. gambiensewithT. b. bruceiencoding 12 putativeHsp90genes, 10 of which are cytosolic and located on a single chromosome whileT. gambienseencodes 5Hsp90genes, 3 of which are located in the cytosol. Eight putative co-chaperones were identified in this study, 6 TPR-containing and 2 non-TPR-containing co-chaperones. This study provides an updated context for studying the biology of the African trypanosome and evaluating Hsp90 and its interactions as potential drug targets.
Functionally distinct T-helper cell phenotypes predict resistance to different types of parasites in a wild mammal
Authors: Corripio-Miyar Yolanda , Hayward Adam , Lemon Hannah , Sweeny Amy R. , Bal Xavier , Kenyon Fiona , Pilkington Jill G , Pemberton Josephine M. , Nussey Daniel H , McNeilly Tom N 
Published: March 2021

ABSTRACTThe adaptive immune system is critical to an effective, long-lasting ability to respond to infection in vertebrates and T-helper (Th) cells play a key role in orchestrating the adaptive immune response. Laboratory studies show that functionally distinct Th responses provide protection against different kinds of parasites (i.e., Th1 responses against microparasites and Th2 against macroparasites).Natural populations must deal with challenges from a wide range of infectious agents and co-infection with different types of parasite is the norm, so different Th responses are likely to play an important and dynamic role in maintaining host health and fitness. However, the relationship between T helper immune phenotypes and infection with different types of parasites remains poorly understood in wild animals.In this study, we characterised variation in functionally distinct Th responses (Th1, Th2, Th17 and regulatory responses) in a wild population of Soay sheep using flow cytometry to detect Th-subset specific transcription factors, andex vivolymphocyte stimulation to quantify release of Th-associated cytokines. We specifically tested the prediction that raised Th1 and Th2 responses should predict reduced apicomplexan (coccidian) and helminth (nematode) parasite burdens, respectively.Cell counts of different Th subsets measured by flow cytometry did not vary with age or sex. However, all measures of Th-associatedex vivocytokine production increased with age, and Th17- and regulatory Th-associated cytokine production increased more rapidly with age in males than females.Independent of age and sex, Th2-associated immune measures negatively predicted gastro-intestinal strongyle nematode faecal egg count, while production of the Th1-associated cytokine IFN-γ negatively predicted coccidian faecal oocyst count.Our results provide important support from outside the laboratory that Th1 and Th2 responses confer resistance to different kinds of parasites (micro- and macro-parasites, respectively). They also add to mounting evidence from wild populations that Th1/Th2 trade-offs often observed in controlled laboratory experiments may not readily translate to more complex natural systems.Our study illustrates that harnessing more specific reagents and tools from laboratory immunology has the potential to illuminate our understanding of epidemiology and host-parasite co-evolution in the wild.
Open source timed pressure control hardware and software for delivery of air mediated distensions in animal models
Authors: Patel Trishna , Hendren Jamie , Lee Nathan , Mickle Aaron D 
Published: March 2021

AbstractStudying the visceral sensory component of peripheral nervous systems can be challenging due to limited options for consistent and controlled stimulation. One method for mechanical stimulation of hollow organs, including colon and bladder, are controlled distensions mediated by compressed air. For example, distension of the bladder can be used as an assay for bladder nociception. Bladder distension causes a corresponding increase in abdominal electromyography, which increases with distension pressure and is attenuated with analgesics. However, the hardware used to control these distensions are primarily all one-off custom builds, without clear directions how to build your own. This has made it difficult for these methods to be fully utilized and replicated as not everyone has access, knowledge and resources required to build this controller. Here we show an open-source Arduino based system for controlling a solenoid valve to deliver timed pressure distensions in the experimental model. This device can be controlled by one of two methods through direct TTL pulses from the experimenters data acquisition software (ex. CED Spike2) or by a graphical user interface, where the user can set the time before, during, and after distension as well as the number of cycles. This systems low cost and relative ease to build will allow more groups to utilize timed pressure distensions in their experiments.Specifications table
Late Anisian microbe-metazoan build-ups (“stromatolites”) in the Germanic Basin – aftermath of the Permian – Triassic Crisis
Authors: Pei Yu , Duda Jan-Peter , Schönig Jan , Luo Cui , Reitner Joachim 
Published: March 2021

AbstractThe so-called Permian – Triassic mass extinction was followed by a prolonged period of ecological recovery that lasted until the Middle Triassic. Triassic stromatolites from the Germanic Basin seem to be an important part of the puzzle, but have barely been investigated so far. Here we analyzed late Anisian (upper Middle Muschelkalk) stromatolites from across the Germanic Basin by combining petrographic approaches (optical microscopy, micro X-ray fluorescence, Raman imaging) and geochemical analyses (sedimentary hydrocarbons, stable carbon and oxygen isotopes). Paleontological and sedimentological evidence, such asPlacunopsisbivalves, intraclasts and disrupted laminated fabrics, indicate that the stromatolites formed in subtidal, shallow marine settings. This interpretation is consistent with δ13Ccarbof about −2.1‰ to −0.4‰. Occurrences of calcite pseudomorphs after gypsum suggest slightly evaporitic environments, which is well in line with the relative rarity of fossils in the host strata. Remarkably, the stromatolites are composed of microbes (perhaps cyanobacteria and sulfate reducing bacteria) and metazoans such as non-spicular demosponges,Placunopsisbivalves, and/orSpirobis-likeworm tubes. Therefore, these “stromatolites” should more correctly be referred to as microbe-metazoan build-ups. They are characterized by diverse lamination types, including planar, wavy, domal and conical ones. Microbial mats likely played an important role in forming the planar and wavy laminations. Domal and conical laminations commonly show clotted to peloidal features and mesh-like fabrics, attributed to fossilized non-spicular demosponges. Our observations not only point up that non-spicular demosponges are easily overlooked and might be mistakenly interpreted as stromatolites, but also demonstrate that microbe-metazoan build-ups were widespread in the Germanic Basin during Early to Middle Triassic times. In the light of our findings, it appears plausible that the involved organisms benefited from elevated salinities. Another (not necessarily contradictory) possibility is that the mutualistic relationship between microbes and non-spicular demosponges enabled these organisms to fill ecological niches cleared by the Permian – Triassic Crisis. If that is to be the case, it means that such microbe-metazoan associations maintained their advantage until the Middle Triassic.
Allele frequency divergence reveals ubiquitous influence of positive selection inDrosophila
Authors: Bertram Jason 
Published: March 2021

AbstractResolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally resolved allele frequency measurements from laboratory and wildDrosophilapopulations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantial at intermediate allele frequencies, which we argue is most parsimoniously explained by positive — not purifying — selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as a purging of deleterious mutations.Author summaryNatural selection is the process fundamentally driving evolutionary adaptation; yet the specifics of how natural selection molds the genome are contentious. A prevailing neutralist view holds that the evolution of most mutations is essentially random. Here, we develop new theory that looks past the stochasticity of individual mutations and instead analyzes the behavior of mutations across the genome as a collective. We find that selection has a strong non-random influence on most of theDrosophilagenome over short timescales (tens of generations), including the bulk of mutations that are not themselves directly targeted by selection. We show that this likely involves ongoing positive selection.
Genomic Surveillance ofAcinetobacter baumanniiin the Philippines, 2013-2014
Authors: Chilam Jeremiah , Argimón Silvia , Limas Marilyn T. , Masim Melissa L. , Gayeta June M. , Lagrada Marietta L. , Olorosa Agnettah M. , Cohen Victoria , Hernandez Lara T. , Jeffrey Benjamin , Abudahab Khalil , Hufano Charmian M. , Sia Sonia B. , Holden Matthew T.G. , Stelling John , Aanensen David M. , Carlos Celia C. 
Published: March 2021

AbstractAcinetobacter baumanniiis an opportunistic nosocomial pathogen that has increasingly become resistant to carbapenems worldwide. In the Philippines, carbapenem resistance and multi-drug resistance (MDR) rates are above 50%. We undertook a genomic study of carbapenem resistantA. baumanniiin the Philippines to characterize the population diversity and antimicrobial resistance (AMR) mechanisms.We sequenced the whole genomes of 117A. baumanniiisolates recovered by 16 hospitals in the Philippines between 2013 and 2014. We determined the multi-locus sequence type (MLST), presence of acquired AMR determinants and relatedness between isolates from the genome sequences. We also compared the phenotypic and genotypic resistance results.Carbapenem resistance was mainly explained by the acquisition of class-D beta-lactamase geneblaOXA-23. The concordance between phenotypic and genotypic resistance to imipenem was 98.15% and 94.97% overall for the seven antibiotics analysed. Twenty-two different sequence types (ST) were identified, including 7 novel STs. The population was dominated by high-risk international clone 2 (i.e., clonal complex 92), in particular by ST195 and ST208 and their single locus variants. With WGS we identified local clusters representing potential undetected nosocomial outbreaks, as well as multi-hospital clusters indicating inter-hospital transmission. Comparison with global genomes suggested that the establishment of carbapenem-resistant IC2 clones in the Philippines is likely the result of clonal expansion and geographical dissemination and at least partly explained by inadequate hospital infection control and prevention.This study is the first extensive genomic study of carbapenem-resistantA. baumanniiin the Philippines and underscores the importance of hospital infection control and prevention to contain high-risk clones.
Genetically Encoded CRISPR components Yield Efficient Gene Editing in the Invasive Pest,Drosophila suzukii
Authors: Kandul Nikolay P. , Belikoff Esther J. , Liu Junru , Buchman Anna , Li Fang , Yamamoto Akihiko , Yang Ting , Shriner Isaiah , Scott Maxwell J. , Akbari Omar S. 
Published: March 2021

AbstractOriginally from Asia,Drosophila suzukii(Matsumura, 1931, Diptera:Drosophilidae) is presently a global pest of economically important soft-skinned fruits. Also commonly known as spotted wingDrosophila(SWD), it is largely controlled through repeated applications of broad-spectrum insecticides. There is a pressing need for a better understanding of SWD biology and for developing alternative environmentally-friendly methods of control. The RNA-guided Cas9 nuclease has revolutionized functional genomics and is an integral component of several recently developed genetic strategies for population control of insects. Here we have developed transgenic strains that encode three different terminators and four different promoters to express Cas9 in both the soma and/or germline of SWD. The Cas9 lines were evaluated through genetic crossing to transgenic lines that encode single guide RNAs targeting the conserved X-linkedyellowbody andwhiteeye genes. We find that several Cas9/gRNA lines display very high editing capacity. Going forward, these tools will be instrumental for evaluating gene function in SWD and may provide tools useful for the development of new genetic strategies for control of this invasive species.
Identification of Japanese Encephalitis Virus Genotype V and Other Mosquito-borne Viruses in Camp Humphreys, Republic of Korea, using Metagenomic Analysis
Authors: Sanborn Mark A. , Wuertz Kathryn McGuckin , Kim Heung-Chul , Yang Yu , Li Tao , Pollett Simon D. , Jarman Richard G. , Berry Irina Maljkovic , Klein Terry A. , Hang Jun 
Published: March 2021

ABSTRACTRecent outbreaks of emerging and re-emerging viruses such as Zika, West Nile and Japanese encephalitis (JEV) viruses have shown that timely detection of novel arboviruses with epidemic potential is essential to mitigate human health risks. There have been rising concerns that an emergent JEV genotype (genotype V, GV) is circulating in Asia, against which the current US-FDA-approved JEV vaccine may not be efficacious. To ascertain if JEV GV and other arboviruses are circulating in East Asia, we conducted next-generation sequencing on 260 pools ofCulex tritaeniorhynchusandCulex bitaeniorhynchusmosquitoes (6,540 specimens) collected at Camp Humphreys, Republic of Korea (ROK), from mid-May - October 2018. Metagenomic analysis demonstrated a highly abundant and diverse virome with correlates of health and ecological relevance. Additionally, two complete JEV GV genome sequences were obtained from separate mosquito pools, indicating that JEV GV is circulating in the Pyeongtaek area near Seoul, ROK. Retrospective sample and sequence analyses showed that JEV GV was also present in 2016 mosquito pools collected in Seoul, ROK. Sequence-based analysis of JEV GV indicates a divergent genotype that is the most distant from the GIII derived live attenuated SA14-14-2 vaccine strain. A GV E protein investigation and 3D modeling in context to SA14-14-2 indicated likely regions responsible for reduced antibody affinity, including clusters of significant amino acid changes at externally exposed domains. These data highlight the critical need for continued mosquito surveillance as a means of detecting and identifying emerging and re-emerging arboviruses of public health relevance. Importantly, our results emphasize recent concerns that there may be a possible shift in the circulating JEV genotype in East Asia and highlights the critical need for a vaccine proven to be efficacious against this re-emergent virus.
CNPY4 inhibits the Hedgehog pathway by modulating membrane sterol lipids
Authors: Lo Megan , Sharir Amnon , Paul Michael D. , Torosyan Hayarpi , Agnew Christopher , Raleigh David R. , Jura Natalia , Klein Ophir D. 
Published: March 2021

Introductory paragraphThe Hedgehog (HH) pathway is critical for development and adult tissue homeostasis1. Aberrant HH signaling can cause congenital malformations, such as digit anomalies and holoprosencephaly2, and other diseases, including cancer3. Signal transduction is initiated by HH ligand binding to the Patched 1 (PTCH1) receptor on primary cilia, thereby releasing inhibition of Smoothened (SMO), a HH pathway activator4. Although cholesterol and several oxysterol lipids, which are enriched in the ciliary membrane, play a crucial role in HH activation4,5, the molecular mechanisms governing the regulation of these lipid molecules remain unresolved. Here, we identify Canopy 4 (CNPY4), a Saposin-like protein, as a regulator of the HH pathway that controls membrane sterol lipid levels.Cnpy4−/−embryos exhibit multiple defects consistent with HH signaling perturbations, most notably changes in digit number. Knockdown ofCnpy4hyperactivates the HH pathway at the level of SMOin vitro, and elevates membrane levels of accessible sterol lipids such as cholesterol, an endogenous ligand involved in SMO activation6. Thus, our data demonstrate that CNPY4 is a negative regulator that fine-tunes the initial steps of HH signal transduction, revealing a previously undescribed facet of HH pathway regulation that operates through control of membrane composition.
Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity
Authors: Blazie Stephen M , Takayanagi-Kiya Seika , McCulloch Katherine A , Jin Yishi 
Published: March 2021

AbstractThe translation initiation complex eIF3 imparts specialized functions to regulate protein expression. However, understanding of eIF3 activities in neurons remains limited despite widespread dysregulation of eIF3 subunits in neurological disorders. Here, we report a selective role of theC. elegansRNA-binding subunit EIF-3.G in shaping the neuronal protein landscape. We identify a missense mutation in the conserved Zinc-Finger (ZF) of EIF-3.G that acts in a gain-of-function manner to dampen neuronal hyperexcitation. Using neuron type-specific seCLIP, we systematically mapped EIF-3.G-mRNA interactions and identified EIF-3.G occupancy on GC-rich 5′UTRs of a select set of mRNAs enriched in activity-dependent functions. We demonstrate that the ZF mutation in EIF-3.G alters translation in a 5′UTR dependent manner. Our study reveals anin vivomechanism for eIF3 in governing neuronal protein levels to control activity states and offers insights into how eIF3 dysregulation contributes to neuronal disorders.
Automated Modeling of Protein Accumulation at DNA Damage Sites using qFADD.py
Authors: Bowerman Samuel , Mahadevan Jyothi , Benson Philip , Rudolph Johannes , Luger Karolin 
Published: March 2021

AbstractCells are exposed to a plethora of influences that can cause damage to DNA and alter the genome, often with detrimental consequences for health. Cells mitigate this damage through a variety of repair protein pathways, and accurate measurement of the accumulation, action, and dissipation timescales of these repair proteins is required to fully understand the DNA damage response. Recently, we described the Q-FADD (Quantitation ofFluorescenceAccumulation afterDNADamage) method, which enhances the analytical power of the widely used laser microirradiation technique. In that study, Q-FADD and its preprocessing operations required licensed software and a significant amount of user overhead to find the model of best fit. Here, we present “qFADD.py”, an open-source implementation of the Q-FADD algorithm that is available as both a stand-alone software package and on a publicly accessible webserver (https://qfadd.colorado.edu/). Furthermore, we describe significant improvements to the fitting and preprocessing methods that include corrections for nuclear drift and an automated grid-search for the model of best fit. To improve statistical rigor, the grid-search algorithm also includes automated simulation of replicates. As an example, we discuss the recruitment dynamics of the signaling protein PARP1 to DNA damage sites, and we show how to compare different populations of qFADD.py models.Statement of SignificanceCells are constantly bombarded by factors that can alter or damage their genome, and they have evolved a variety of proteins that can identify and fix this damage. To fully understand how these proteins interact in repair pathways, we need robust methods to quantify the timescales between the initial identification of the DNA damage event and the subsequent protein-protein interactions that lead to repair. Laser microirradiation is a popular method for studying these repair protein cascades in vivo, and methods for quantifying the timescales of recruitment in these experiments have historically been simple to implement but lacking in physical interpretation. Here, we present qFADD.py, the next iteration of the Q-FADD method, which uses Monte Carlo diffusion models to interpret repair protein recruitment timescales to sites of DNA damage. By moving towards automated fitting procedures with minimal bias from the user, qFADD.py provides a statistically robust but low-effort means to analyze laser microirradiation experiments through a biophysical framework.