bluuebunny/crossref_metadata_2025_split huggingface dataset:
Editing of the TRIM5 gene decreases the permissiveness of human T lymphocytic cells to HIV-1
Authors: Désaulniers Kevin , Ortiz Levine , Dufour Caroline , Claudel Alix , Plourde Mélodie B. , Merindol Natacha , Berthoux Lionel 
Published: December 2020

AbstractTRIM5α is a cytoplasmic antiretroviral effector upregulated by type I interferons (IFN-I). We previously showed that two points mutations, R332G/R335G, in the retroviral capsid-binding region confer human TRIM5α the capacity to target and strongly restrict HIV-1 upon over-expression of the mutated protein. Here, we used CRISPR-Cas9-mediated homology-directed repair (HDR) to introduce these two mutations in the endogenous human TRIM5 gene. We found 6 out of 47 isolated cell clones containing at least one HDR-edited allele. One clone (Clone 6) had both alleles containing R332G but only one of the two alleles containing R335G. Upon challenge with an HIV-1 vector, clone 6 was significantly less permissive compared to unmodified cells, whereas the cell clones with monoallelic modifications were only slightly less permissive. Following IFN-β treatment, inhibition of HIV-1 infection in clone 6 was significantly enhanced (~40-fold inhibition). TRIM5α knockdown confirmed that HIV-1 was inhibited by the edited TRIM5 gene products. Quantification of HIV-1 reverse transcription products showed that inhibition occurred through the expected mechanism. In conclusion, we demonstrate the feasibility of potently inhibiting a viral infection through editing of innate effector genes. Our results also emphasize the importance of biallelic modification in order to reach significant levels of inhibition by TRIM5α.
On a wing and a prayer: limitations and gaps in global bat wing morphology trait data
Authors: Crane Matt , Silva Inês , Grainger Matthew J. , Gale George A. 
Published: December 2020

AbstractSpecies’ life history traits have a wide variety of applications in ecological and conservation research, particularly when assessing threats. The development and growth of global species trait databases are critical for improving trait-based analyses; however, it is vital to understand the gaps and biases of available data. Bats are an extremely diverse and widely distributed mammalian order, with many species facing local declines and extinction. We conducted a literature review for bat wing morphology, specifically wing loading and aspect ratio, to identify issues with data reporting and ambiguity. We collected data on field methodology, trait terminology, and data reporting and quality. We found several issues regarding semantic ambiguity in trait definitions and data reporting. Globally we found that bat wing morphology trait coverage was low. Only six bat families had over 40% trait coverage, and of those none consisted of more than 11 total species. We found similar biases in trait coverage across IUCN Redlist categories with threatened species having lower coverage. Geographically, North America, Europe, and the Indomalayan regions showed higher overall trait coverage, while both the Afrotropical and Neotropical ecoregions showed poor trait coverage. The underlying biases and gaps with bat wing morphology data have implications for researchers conducting global trait-based assessments. Implementing imputation techniques may address missing data, but only for smaller regional subsets with substantial trait coverage. However, due to the low overall trait coverage, increasing species representation in the database should be prioritized. We suggest adopting an Ecological Trait Standard vocabulary to reduce semantic ambiguity in bat wing morphology traits to improve data compilation and clarity. Additionally, we advocate that researchers adopt an Open Science approach to facilitate the growth of a bat wing morphology trait database.
Molecular and physiological responses predict acclimation limits in juvenile brook trout (Salvelinus fontinalis)
Authors: Mackey Theresa E. , Hasler Caleb T. , Durhack Travis , Jeffrey Jennifer D. , Macnaughton Camille J. , Ta Kimberly , Enders Eva C. , Jeffries Ken M. 
Published: December 2020

AbstractBrook trout (Salvelinus fontinalis) populations are at risk of exposure to high water temperatures in the species’ native range in eastern North America. We quantified the physiological and molecular responses of juvenile brook trout to six acclimation temperatures that span the thermal distribution of the species (5, 10, 15, 20, 23, and 25°C). Using quantitative PCR (qPCR), we measured the mRNA transcript abundance of temperature-induced cellular stress genes to identify a potential sub-lethal temperature threshold for brook trout between 20–23°C. Brook trout exhibited an upregulation of stress-related genes (heat shock protein 90-beta;heat shock cognate 71 kDa protein;glutathione peroxidase 1) and a downregulation of transcription factors and osmoregulation-related genes (Na+/K+/2Cl−co-transporter-1-a;nuclear protein 1) at temperatures ≥20°C. We also used respirometry to assess the effects of the acclimation temperatures on oxygen consumption. Standard metabolic rate results indicated that energy expenditure was higher at temperatures ≥20°C. We then examined the effects of acclimation temperature on metabolic rate and blood plasma parameters in fish exposed to an acute exhaustive exercise and air exposure stress. Fish acclimated to temperatures ≥20°C exhibited elevated levels of plasma cortisol, muscle lactate, and plasma glucose after exposure to the acute stressors. After 24 h of recovery, fish showed longer metabolic recovery times at 15 and 20°C and cortisol levels remaining elevated at temperatures ≥20°C. Our findings suggest that brook trout may have a limited ability to acclimate to temperatures >20°C and increases in temperatures beyond 20°C may impact brook trout populations.
Neuropredictome: a data-driven predictome for cognitive, psychiatric, medical, and lifestyle factors on the brain
Authors: Sultan Syed Fahad , Parodi Lilianne R. Mujica , Skiena Steven 
Published: December 2020

ABSTRACTMost neuroimaging studies individually provide evidence on a narrow aspect of the human brain function, on distinct data sets that often suffer from small sample sizes. More generally, the high technical and cost demands of neuroimaging studies (combined with the statistical unreliability of neuroimaging pilot studies) may lead to observational bias, discouraging discovery of less obvious associations that nonetheless have important neurological implications. To address these problems, we built a machine-learning based classification framework,NeuroPredictome, optimized for the reliability and robustness of its associations. NeuroPredictome is grounded in a large-scale dataset, UK-Biobank (N=19,831), which includes resting and task functional MRI as well as structural T1-weighted and diffusion tensor imaging. Participants were assessed with respect to a comprehensive set of 5,034 phenotypes, including the physical and lifestyle factors most relevant to general medicine. Results generated by data-driven classifiers were then cross-validated, using deep-learning textual analyses, against 14,371 peer-reviewed research articles, providing an unbiased hypothesis-generator of linkages between diverse phenotypes and the brain. Our results show that neuroimaging reveals as many neurological links to physical and lifestyle factors as to cognitive factors, supporting a more integrative approach to medicine that considers disease interactions between multiple organs and systems.
Distant Residues Modulate Conformational Opening in SARS-CoV-2 Spike Protein
Authors: Ray Dhiman , Le Ly , Andricioaei Ioan 
Published: December 2020

Infection by SARS-CoV-2 involves the attachment of the receptor binding domain (RBD) of its spike proteins to the ACE2 receptors on the peripheral membrane of host cells. Binding is initiated by a down-to-up conformational change in the spike protein, the change that presents the RBD to the receptor. To date, computational and experimental studies that search for therapeutics have concentrated, for good reason, on the RBD. However, the RBD region is highly prone to mutations, and is therefore a hotspot for drug resistance. In contrast, we here focus on the correlations between the RBD and residues distant to it in the spike protein. This allows for a deeper understanding of the underlying molecular recognition events and prediction of the highest-effect key mutations in distant, allosteric sites, with implications for therapeutics. Also, these sites can appear in emerging mutants with possibly higher transmissibility and virulence, and pre-identifying them can give clues for designing pancoronavirus vaccines against future outbreaks. Our model, based on time-lagged independent component analysis (tICA) and protein graph connectivity network, is able to identify multiple residues that exhibit long-distance coupling with the RBD opening. Residues involved in the most ubiquitous D614G mutation and the A570D mutation of the highly contagious UK SARS-CoV-2 variant are predictedab-initiofrom our model. Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can target these key distant-but-conserved regions of the spike protein.Significance StatementThe novel coronavirus (SARS-CoV-2) pandemic resulted in the largest public health crisis in recent times. Significant drug design effort against SARS-CoV-2 is focused on the receptor binding domain (RBD) of the spike protein, although this region is highly prone to mutations causing therapeutic resistance. We applied deep data analysis methods on all-atom molecular dynamics simulations to identify key non-RBD residues that play a crucial role in spike-receptor binding and infection. textcol-orredBecause the non-RBD residues are typically conserved across multiple coronaviruses, they can be targeted by broad spectrum antibodies and drugs to treat infections from new strains that might appear during future epidemics.
Conserved tandem arginines for PbgA/YejM allowSalmonellato regulate LpxC and control lipopolysaccharide biogenesis during infection
Authors: Giordano Nicole P. , Mettlach Joshua A. , Dalebroux Zachary D. 
Published: December 2020

ABSTRACTSalmonella entericaserovar Typhimurium uses PbgA/YejM, a conserved multi-pass transmembrane protein with a soluble periplasmic domain (PD), to balance the glycerophospholipid (GPL) and lipopolysaccharide (LPS) concentrations within the outer membrane (OM). The lipid homeostasis and virulence defects ofpbgAΔ191-586mutants, which are deleted for the PD, can be suppressed by substitutions in three LPS regulators, LapB/YciM, FtsH, and LpxC. We reasoned thatS. Typhimurium uses the PbgA PD to regulate LpxC through functional interactions with LapB and FtsH. In the stationary phase of growth,pbgAΔ191-586mutants accumulated LpxC and overproduced LPS precursors, known as lipid A-core molecules. Trans-complementation fully decreased the LpxC and lipid A-core levels for the mutants, while substitutions in LapB, FtsH, and LpxC variably reduced the concentrations. PbgA binds lipid A-core, in part, using dual arginines, R215 and R216, which are located near the plasma membrane. Neutral, conservative, and non-conservative substitutions were engineered at these positions to test whether the side-chain charges for residues 215 and 216 influenced LpxC regulation. Salmonellae that expressed PbgA with dual alanines or aspartic acids overproduced LpxC, accumulated lipid A-core and short-LPS molecules, and were severely attenuated in mice. Bacteria that expressed PbgA with tandem lysines were fully virulent in mice and yielded LpxC and lipid A-core levels that were similar to the wild type. Thus,S.Typhimurium uses the cationic charge of PbgA R215 and R216 to down-regulate LpxC and decrease lipid A-core biosynthesis in response to host stress and this regulatory mechanism enhances their virulence during bacteremia.IMPORTANCESalmonella entericaserovar Typhimurium causes self-limiting gastroenteritis in healthy individuals and severe systemic disease in immunocompromised humans. The pathogen manipulates the immune system of its host by regulating the lipid, protein, and polysaccharide content of the outer membrane (OM) bilayer. Lipopolysaccharides (LPS) comprise the external leaflet of the OM, and are essential for establishing the OM barrier and providing gram-negative microbes with intrinsic antimicrobial resistance. LPS molecules are potent endotoxins and immunomodulatory ligands that bind host-pattern receptors, which control host resistance and adaptation during infection. Salmonellae use the cationic charge of dual arginines for PbgA/YejM to negatively regulate LPS biosynthesis. The mechanism involves PbgA binding to an LPS precursor and activating a conserved multi-protein signal transduction network that cues LpxC proteolysis, the rate-limiting enzyme. The cationic charge of the tandem arginines is critical for the ability of salmonellae to survive intracellularly and to cause systemic disease in mice.
The prevalence and distribution in genomes of low-complexity, amyloid-like, reversible, kinked segment (LARKS), a common structural motif in amyloid-like fibrils
Authors: Hughes Michael P. , Goldschmidt Luki , Eisenberg David S. 
Published: December 2020

AbstractMembraneless Organelles (MLOs) are vital and dynamic reaction centers in cells that organize metabolism in the absence of a membrane. Multivalent interactions between protein Low-Complexity Domains (LCDs) contribute to MLO organization. Our previous work used computational methods to identify structural motifs termed Low-complexity Amyloid-like Reversible Kinked Segments (LARKS) that can phase-transition to form hydrogels and are common in human proteins that participate in MLOs. Here we searched for LARKS in proteomes of six model organisms:Homo sapiens, Drosophila melanogaster, Plasmodium falciparum, Saccharomyces cerevisiae, Mycobacterium tuberculosis, andEscherichia coli. We find LARKS are abundant inM. tuberculosis, D. melanogaster, andH. sapiens, but not inS. cerevisiaeorP. falciparum. Abundant LARKS require high glycine content, which enables kinks to form in LARKS as is illustrated in the known LARKS-rich amyloid structures of TDP43, FUS, and hnRNPA2, three proteins that participate in MLOs. These results support the idea of LARKS as an evolved structural motif and we offer the LARKSdb webserver which permits users to search for LARKS in their protein sequences of interest.
Anti-SARS-CoV-2 activity ofAndrographis paniculataextract and its major component Andrographolide in human lung epithelial cells and cytotoxicity evaluation in major organ cell representatives
Authors: Sa-ngiamsuntorn Khanit , Suksatu Ampa , Pewkliang Yongyut , Thongsri Piyanoot , Kanjanasirirat Phongthon , Manopwisedjaroen Suwimon , Charoensutthivarakul Sitthivut , Wongtrakoongate Patompon , Pitiporn Supaporn , Khemawoot Phisit , Chutipongtanate Somchai , Borwornpinyo Suparerk , Thitithanyanont Arunee , Hongeng Suradej 
Published: December 2020

ABSTRACTThe coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2) has become a major health problem affecting more than fifty million cases with over one million deaths globally. The effective antivirals are still lacking. Here, we optimized a high-content imaging platform and the plaque assay for viral output study using the legitimate model of human lung epithelial cells, Calu-3, to determine anti-SARS-CoV–2 activity ofAndrographis paniculataextract and its major component andrographolide. SARS-CoV-2 at 25TCID50was able to reach the maximal infectivity of 95% in Calu-3 cells. Post-infection treatment ofA. paniculataand andrographolide in SARS-CoV–2 infected Calu-3 cells significantly inhibited the production of infectious virions with the IC50of 0.036 μg/mL and 0.034 μM, respectively, as determined by plaque assay. The cytotoxicity profile developed over the cell line representatives of major organs, including liver (HepG2 and imHC), kidney (HK-2), intestine (Caco-2), lung (Calu-3) and brain (SH-SY5Y), showed the CC50of >100 μg/mL forA. paniculataextract and 13.2-81.5 μM for andrographolide, respectively, corresponding to the selectivity index over 380. In conclusion, this study provided experimental evidence in favor ofA. paniculataand andrographolide for further development as a monotherapy or in combination with other effective drugs against SARS-CoV–2 infection.
A Draft Genome forHirudo verbana, the Medicinal Leech
Authors: Paulsen Riley T. , Agany Diing D.M. , Petersen Jason , Davis Christel M. , Ehli Erik A. , Gnimpieba Etienne , Burrell Brian D. 
Published: December 2020

AbstractThe medicinal leech,Hirudo verbana, is a powerful model organism for investigating fundamental neurobehavioral processes. The well-documented arrangement and properties ofH. verbana’s nervous system allows changes at the level of specific neurons or synapses to be linked to physiological and behavioral phenomena. Juxtaposed to the extensive knowledge ofH. verbana’snervous system is a limited, but recently expanding, portfolio of molecular and multi-omics tools. Together, the advancement of genetic databases forH. verbanawill complement existing pharmacological and electrophysiological data by affording targeted manipulation and analysis of gene expression in neural pathways of interest. Here, we present the first draft genome assembly forH. verbana, which is approximately 250 Mbp in size and consists of 61,282 contigs. Whole genome sequencing was conducted using an Illumina sequencing platform followed by genome assembly with CLC-Bio Genomics Workbench and subsequent functional annotation. Ultimately, the diversity of organisms for which we have genomic information should parallel the availability of next generation sequencing technologies to widen the comparative approach to understand the involvement and discovery of genes in evolutionarily conserved processes. Results of this work hope to facilitate comparative studies withH.verbanaand provide the foundation for future, more complete, genome assemblies of the leech.
The spatio-temporal axis for phenotypic change: a comparison of source and translocated Arctic charr populations after 25 generations
Authors: Hassve Marius H. , Hagenlund Mari , Østbye Kjartan , Häkli Katja , Vogler Thomas , Gregersen Finn , Andersen Gørli B. , Stegarud Svein O. , Langdal Kjell , Waalberg Max E. , Langevoll Karl C. , Præbel Kim 
Published: December 2020

AbstractEvolution of morphological traits is hypothesized to act on an extended time scale, yet studies have suggested that these changes are possible within a few generations. Trophic polymorphism enabled through niche adaptations and ecological opportunity is one phenomenon that facilitate occurrence of rapid adaptive variation, common in many northern freshwater fish species. One such species is Arctic charr, which is known for its extensive variation in morphology and the occurrence of morphs. However, the speed at which such morphological variation arises is poorly studied despite the importance for understanding the onset of evolution. The aim of this study was to elucidate this process in a gradient of eight lakes that was stocked with Arctic charr in the period from 1910 to 1917 from Lake Tinnsjøen, Norway. We used morphological measurements to test for differences in traits between populations and Haldane and Darwin’s evolutionary rates to estimate divergence rates in traits. We also tested for correlation between putative genetic and morphological divergence. In addition, we contrasted the morphological divergence with that expected under neutral genetic expectations, using 12 microsatellite markers, to analyze whether and which morphological differences that is following early genetic divergence. A significant genetic differentiation was found between the source population and five of the translocated populations with corresponding differences in morphological traits for four of the populations. Population genetic structuring indicated six different genetic clusters. The translocated populations also exhibited trait divergence estimated with both Haldane and Darwin’s rates. Differences in morphological traits showed a significant correlation with genetic divergence, and the morphological differences were most likely affected by differences in lake parameters such as maximum depth, lake size and fish community. We conclude that intraspecific morphological and genetic divergence can form on short evolutionary time scales with important implications for conservation and management practices.
Srsf3 mediates alternative RNA splicing downstream of PDGFRα signaling
Authors: Dennison Brenna J.C. , Larson Eric D. , Fu Rui , Mo Julia , Fantauzzo Katherine A. 
Published: December 2020

SummarySignaling through the platelet-derived growth factor receptor alpha (PDGFRα) is critical for mammalian craniofacial development, though the mechanisms by which the activity of downstream intracellular effectors is regulated to mediate gene expression changes have not been defined. We find that the RNA-binding protein Srsf3 is phosphorylated at Akt consensus sites downstream of PI3K-mediated PDGFRα signaling in palatal mesenchyme cells, leading to its nuclear translocation. We further demonstrate that ablation ofSrsf3in the neural crest lineage leads to facial clefting due to defective cranial neural crest cell specification and survival. Finally, we show that Srsf3 regulates the alternative RNA splicing of transcripts encoding protein kinases in the facial process mesenchyme to negatively regulate PDGFRα signaling. Collectively, our findings reveal that PI3K/Akt-mediated PDGFRα signaling primarily modulates gene expression through alternative RNA splicing in the facial mesenchyme and identify Srsf3 as a critical regulator of craniofacial development.
Extracellular spreading of Wingless is required forDrosophilaoogenesis
Authors: Wang Xiaoxi , LaFever Kimberly S. , Waghmare Indrayani , Page-McCaw Andrea 
Published: December 2020

AbstractRecent studies have investigated whether the Wnt family of extracellular ligands can signal at long range, spreading from their source and acting as morphogens, or whether they signal only in a juxtacrine manner to neighboring cells. The original evidence for long-range Wnt signaling arose from studies of Wg, aDrosophilaWnt protein, which patterns the wing disc over several cell diameters from a central source of Wg ligand. However, the requirement of long-range Wg for patterning was called into question when it was reported that replacing the secreted protein Wg with a membrane-tethered version, NRT-Wg, results in flies with normally patterned wings. We and others previously reported that Wg spreads in the ovary about 50 μm or 5 cell diameters, from the cap cells to the follicle stem cells (FSCs) and that Wg stimulates FSC proliferation. We used theNRT-wgflies to analyze the consequence of tethering Wg to the cap cells.NRT-wghomozygous flies are sickly, but we found that hemizygousNRT-wg/nullflies, carrying only one copy of tethered Wingless, were significantly healthier. Despite their overall improved health, these hemizygous flies displayed dramatic reductions in fertility and in FSC proliferation. Further, FSC proliferation was nearly undetectable when thewglocus was converted toNRT-wgonly in adults, and the resulting germarium phenotype was consistent with a previously reportedwgloss-of-function phenotype. We conclude that Wg protein spreads from its source cells in the germarium to promote FSC proliferation.