bluuebunny/crossref_metadata_2025_split huggingface dataset:
TnCentral: A Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis
Authors: Ross Karen , Varani Alessandro M. , Snesrud Erik , Huang Hongzhan , Alvarenga Danillo Oliveira , Zhang Jian , Wu Cathy , McGann Patrick , Chandler Mick 
Published: May 2021

AbstractWe describe here the structure and organization of TnCentral (https://tncentral.proteininformationresource.org/). a web resource for prokaryotic transposable elements (TE). TnCentral currently contains ~400 carefully annotated TE, including transposons from the Tn3, Tn7, Tn402 and Tn554 families, compound transposons, integrons and associated insertion sequences (IS). These TE carry passenger genes, including genes conferring resistance to over 25 classes of antibiotics and nine types of heavy metal as well as genes responsible for pathogenesis in plants, toxin/antitoxin gene pairs, transcription factors and genes involved in metabolism. Each TE has its own entry page providing details about its transposition genes, passenger genes, and other sequence features required for transposition as well as a graphical map of all features. TnCentral content can be browsed and queried through text and sequence-based searches with a graphic output. We describe three use cases, which illustrate how the search interface, results tables, and entry pages can be used to explore and compare TEs.TnCentral also includes downloadable software to facilitate user-driven identification, with manual annotation, of certain types of TE in genomic sequences. Through the TnCentral homepage, users can also access TnPedia which provides comprehensive reviews of the major TE families including an extensive general section, and specialised sections with descriptions of insertion sequence and transposon families. TnCentral and TnPedia are intuitive resources that can be used by clinicians and scientists to assess TE diversity in clinical, veterinary and environmental samples.ImportanceThe ability of bacteria to undergo rapid evolution and adapt to changing environmental circumstances drives the public health crisis of multiple antibiotic resistance as well as outbreaks of disease in economically important agricultural crops and animal husbandry. Prokaryotic transposable elements (TE) play a critical role in this. Many carry “passenger genes” (not required for the transposition process) conferring resistance to antibiotics or heavy metals or causing disease in plants and animals. Passenger genes are spread by the normal TE transposition activities, by insertion into plasmids which then spread via conjugation within and across bacterial populations. Thus, an understanding of TE composition and transposition mechanisms is key to developing strategies to combat bacterial pathogenesis. Toward this end, we have developed TnCentral, a bioinformatics resource dedicated to describing and exploring the structural and functional features of prokaryotic TE and whose use is intuitive and accessible to users with or without bioinformatics expertise.
Neuron-radial glial cell communication via BMP/Id1 signaling maintains the regenerative capacity of the adult zebrafish telencephalon
Authors: Zhang Gaoqun , Lübke Luisa , Chen Fushun , Beil Tanja , Takamiya Masanari , Diotel Nicolas , Strähle Uwe , Rastegar Sepand 
Published: May 2021

AbstractThe mechanisms of the management of the neural stem cell (NSC) pool underlying the regenerative capacity of the adult zebrafish brain are not understood. We show that Bone Morphogenetic Proteins (BMPs) which are exclusively expressed by neurons in the adult telencephalon and the helix-loop-helix (HLH) transcription co-regulator, Inhibitor of differentiation 1 (Id1), control quiescence of NSCs. Upon injury, lack ofid1function leads to an initial over-proliferation and subsequent loss of NSCs and the regenerative capacity. BMP/Id1 signaling up-regulates the transcription factorher4.1which is also a target of Notch signaling mediating short-range control of NSC quiescence. Hence, the two signaling systems converge onto Her4.1. Our data show that neurons feedback on NSC proliferation. BMP1/Id1 signaling appears as the predominant safeguard of the NSC pool under regenerative conditions while Notch signaling is sufficient to maintain NSCs under homeostatic baseline neurogenesis in the uninjured animal.
Genome-wide functional analysis reveals key roles for kinesins in the mammalian and mosquito stages of the malaria parasite life cycle
Authors: Zeeshan Mohammad , Rashpa Ravish , Ferguson David J , Abel Steven , Chahine Zeinab , Brady Declan , Vaughan Sue , Moores Carolyn A. , Le Roch Karine G. , Brochet Mathieu , Holder Anthony A. , Tewari Rita 
Published: May 2021

AbstractKinesins are microtubule-based motors important in cell division, motility, polarity, and intracellular transport in many eukaryotes. However, they are poorly studied in the divergent eukaryotic pathogens-Plasmodium spp.,the causative agents of malaria, which manifest atypical aspects of cell division and plasticity of morphology throughout the lifecycle in both mammalian and mosquito hosts. Here we describe a genome-wide screen ofPlasmodiumkinesins, revealing diverse subcellular locations and functions in spindle assembly, axoneme formation and cell morphology. Surprisingly, only kinesin-13 is essential for growth in the mammalian host while the other eight kinesins are required during the proliferative and invasive stages of parasite transmission through the mosquito vector. In-depth analyses of kinesin-13 and kinesin-20 revealed functions in microtubule dynamics during apical cell polarity formation, spindle assembly, and axoneme biogenesis. These findings help us to understand the importance of microtubule motors and may be exploited to discover new therapeutic interventions against malaria.
Plasmodium falciparumand helminth coinfections increase IgE and parasite-specific IgG responses
Authors: Santano Rebeca , Rubio Rocío , Grau-Pujol Berta , Escola Valdemiro , Muchisse Osvaldo , Cuamba Inocência , Vidal Marta , Cisteró Pau , Ruiz-Olalla Gemma , Aguilar Ruth , Demontis Maria , Jamine Jose Carlos , Cossa Anélsio , Sacoor Charfudin , Cano Jorge , Izquierdo Luis , Chitnis Chetan E , Coppel Ross L , Chauhan Virander , Cavanagh David , Dutta Sheetij , Angov Evelina , Gaur Deepak , van Lieshout Lisette , Zhan Bin , Muñoz José , Moncunill Gemma , Dobaño Carlota 
Published: May 2021

ABSTRACTCoinfection withPlasmodium falciparumand helminths may impact the immune response to these parasites since they induce different immune profiles. We studied the effects of coinfections on the antibody profile in a cohort of 715 Mozambican children and adults using the Luminex technology with a panel of 16 antigens fromP. falciparumand 11 antigens from helminths (Ascaris lumbricoides, hookworm,Trichuris trichiura,Strongyloides stercoralisandSchistosomaspp.) and measured antigen-specific IgG and total IgE responses. We compared the antibody profile between groups defined byP. falciparumand helminth previous exposure (based on serology) and/or current infection (determined by microscopy and/or qPCR). In multivariable regression models adjusted by demographic, socioeconomic, water and sanitation variables, individuals exposed/infected withP. falciparumand helminths had significantly higher total IgE and antigen-specific IgG levels, magnitude (sum of all levels) and breadth of response to both types of parasites compared to individuals exposed/infected with only one type of parasite (p≤ 0.05). There was a positive association between exposure/infection toP. falciparumand exposure/infection to helminths or the number of helminth species, andvice versa(p≤ 0.001). In addition, children coexposed/coinfected tended (p= 0.062) to have higherP. falciparumparasitemia than those single exposed/infected. Our results suggest that an increase in the antibody responses in coexposed/coinfected individuals may reflect higher exposure and be due to a more permissive immune environment to infection in the host.GRAPHICAL ABSTRACT
Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin
Authors: Yang Weizhao , Feiner Nathalie , Salvi Daniele , Laakkonen Hanna , Jablonski Daniel , Pinho Catarina , Carretero Miguel A. , Sacchi Roberto , Zuffi Marco A. L. , Scali Stefano , Plavos Konstantinos , Pafilis Panayiotis , Poulakakis Nikos , Lymberakis Petros , Jandzik David , Schulte Ulrich , Aubret Fabien , Badiane Arnaud , i de Lanuza Guillem Perez , Abalos Javier , While Geoffrey M. , Uller Tobias 
Published: May 2021

AbstractThe Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (~5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flow have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.
Dissociating the impact of movement time and energy costs on decision-making and action initiation in humans
Authors: Lunazzi Clara Saleri , Reynaud Amélie J. , Thura David 
Published: May 2021

ABSTRACTRecent theories and data suggest that adapted behavior involves economic computations during which multiple trade-offs between reward value, accuracy requirement, energy expenditure and elapsing time are solved so as to obtain rewards as soon as possible while spending the least possible amount of energy. However, the relative impact of movement energy and duration costs on perceptual decision-making and movement initiation is poorly understood. Here, we tested 31 healthy subjects on a perceptual decision-making task in which they executed reaching movements to report probabilistic choices. In three distinct blocks of trials, the reaching time and energy costs were independently varied while decision difficulty was maintained similar at the block level. Participants also performed a fully instructed delayed-reaching (DR) task in each motor condition. Results in that DR task show that time-consuming movements extended reaction times (RTs) in most subjects, whereas energy-consuming movements led to mixed effects on RTs. In the choice task, about half of the subjects decreased their decision durations (DDs) in the time consuming condition, while the impact of energy costs on DDs were again mixed across subjects. Decision accuracy was overall similar across motor conditions. These results indicate that movement duration and, to a lesser extent, energy expenditure, idiosyncratically affect perceptual decision-making and action initiation. We propose that subjects who shortened their decisions in the time consuming condition of the choice task did so to limit a drop of their rate of reward.
Purification of immunostimulatory glucose homopolymer from broccoli (Brassica oleracea var. italica)
Authors: Miyashita Atsushi , Kataoka Keiko , Tsuchida Toshio , Ogasawara Akihiko Ano , Hamamoto Hiroshi , Takahashi Megumu , Sekimizu Kazuhisa 
Published: May 2021

AbstractWe prepared broccoli (Brassica oleracea var. italica) neutral polysaccharides (flow-through fractions of anion exchange column chromatography from hot water extracts) from different broccoli cultivars and compared their immunostimulatory effects in the silkworm muscle contraction assay. The cultivars showed a wide range of activity, with the cultivar ‘Winter dome’ showing the highest specific activity (more than 100 times higher than curdlan). Furthermore, the active substance was purified by gel filtration column chromatography. The active substance showed heterogeneous molecular weights of more than 270 kDa. Sugar composition analysis of the purified fraction revealed that more than 95% of its sugar component was glucose, suggesting that the immunostimulatory neutral polysaccharide from broccoli cultivar ‘Winter dome’ was a homopolymer of glucose. The purified fraction also induced TNFα production in cultured mouse macrophage cells. These results suggest that the glucose homopolymer in broccoli has an immunostimulatory effect on both arthropod and mammalian immune system.
Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity
Authors: Catela Catarina , Weng Yifei , Wen Kailong , Feng Weidong , Kratsios Paschalis 
Published: May 2021

ABSTRACTSpinal motor neurons (MNs) constitute cellular substrates for several movement disorders. Although their early development has received much attention, how spinal MNs become and remain terminally differentiated is poorly understood. Here, we determined the transcriptome of mouse brachial MNs at embryonic and postnatal stages. We found that genes encoding homeodomain (HOX, LIM) transcription factors (TFs), previously implicated in early MN development, continue to be expressed postnatally, suggesting later functions. To test this, we inactivated Hoxc8 at successive stages of MN development. We found that Hoxc8 is not only required to establish but also maintain expression of several MN terminal differentiation markers. Furthermore, we uncovered novel TFs with continuous MN expression, a Hoxc8 dependency for maintained expression of Iroquois (Irx) homeodomain TFs, and a new role for Irx2 in MN development. Our findings dovetail recent observations in C. elegans MNs, pointing toward an evolutionarily conserved role for Hox in neuronal terminal differentiation.
Variable Induction of Pro-inflammatory Cytokines by Commercial SARS CoV-2 Spike Protein Reagents: Potential Impacts of LPS on In Vitro Modeling and Pathogenic Mechanisms In Vivo
Authors: Ouyang Weiming , Xie Tao , Fang Hui , Gao Chunling , Stantchev Tzanko , Clouse Kathleen A. , Yuan Kun , Ju Tongzhong , Frucht David M. 
Published: May 2021

AbstractProinflammatory cytokine production following infection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is associated with poor clinical outcomes. Like SARS CoV-1, SARS CoV-2 enters host cells via its spike protein, which attaches to angiotensin-converting enzyme 2 (ACE2). As SARS CoV-1 spike protein is reported to induce cytokine production, we hypothesized that this pathway could be a shared mechanism underlying pathogenic immune responses. We herein compared the capabilities of Middle East Respiratory Syndrome (MERS), SARS CoV-1 and SARS CoV-2 spike proteins to induce cytokine expression in human peripheral blood mononuclear cells (PBMC). We observed that only specific commercial lots of SARS CoV-2 induce cytokine production. Surprisingly, recombinant SARS CoV-2 spike proteins from different vendors and batches exhibited different patterns of cytokine induction, and these activities were not inhibited by blockade of spike protein-ACE2 binding using either soluble ACE2 or neutralizing anti-S1 antibody. Moreover, commercial spike protein reagents contained varying levels of endotoxin, which correlated directly with their abilities to induce cytokine production. The lipopolysaccharide (LPS) inhibitor, polymyxin B, blocked this cytokine induction activity. In addition, SARS CoV-2 spike protein avidly bound soluble LPS in vitro, rendering it a cytokine inducer. These results not only suggest caution in monitoring the purity of SARS CoV-2 spike protein reagents, but they indicate the possibility that interactions of SARS CoV-2 spike protein with LPS from commensal bacteria in virally infected mucosal tissues could promote pathogenic inflammatory cytokine production.
Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism
Authors: Tejedor-Sanz Sara , Stevens Eric T. , Finnegan Peter , Nelson James , Knoessen Andre , Light Samuel H. , Ajo-Franklin Caroline M. , Marco Maria L. 
Published: May 2021

ABSTRACTEnergy conservation in microorganisms is classically categorized into respiration and fermentation, however recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the utility of a flavin-based extracellular electron transport (FLEET) system for energy conservation within diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD+/NADH ratio, generate more ATP through substrate-level phosphorylation and accumulate biomass more rapidly. This novel, hybrid metabolism was dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally required a flavin-binding extracellular lipoprotein (PplA) in the FLEET system to confer increased fermentation yield, metabolic flux, and environmental acidification in both laboratory media and food fermentation. The discovery of a single pathway that blends features of fermentation and respiration expands our knowledge of energy conservation metabolism and provides immediate biotechnology applications.
Evidence of neutralizing antibodies against SARS-CoV-2 in domestic cats living with owners with a history of COVID-19 in Lima – Peru
Authors: Jara Luis M. , Ferradas Cusi , Schiaffino Francesca , Sánchez-Carrión Camila , Martinez Ana , Ulloa Alexandra , Isasi-Rivas Gisela , Montalván Angela , Sarmiento Luis Guevara , Fernández Manolo , Zimic Mirko 
Published: May 2021

AbstractSARS-CoV-2 can infect a variety of wild and domestic animals worldwide. Of these, domestic cats are highly susceptible species and potential viral reservoirs. As such, it is important to investigate disease exposure in areas with active community transmission and high disease prevalence. In this report we demonstrate the presence of serum neutralizing antibodies against the receptor binding-domain (RBD) of the SARS-CoV-2 in cats whose owners had been infected with SARS-CoV-2 in Lima, Peru, using a commercial competitive ELISA SARS-CoV-2 Surrogate Virus Neutralization Test. Out of 41 samples, 17.1% (7/41) and 31.7% (13/41) were positive, using the cut-off inhibition value of 30% and 20%, respectively. Not all cats living in a single house had detectable neutralizing antibodies showing that heterogenous exposure and immune among cohabiting animals. This is the first report of SARS-COV-2 exposure of domestic cats in Lima, Peru. Further studies are required to ascertain the prevalence of SARS-COV-2 exposure among domestic cats of Lima, Peru.
Phage-Derived Depolymerase as an Antibiotic Adjuvant Against Multidrug-Resistant Acinetobacter Baumannii
Authors: Chen Xi , Liu Miao , Zhang Pengfei , Xu Miao , Yuan Weihao , Bian Liming , Liu Yannan , Xia Jiang , Leung Sharon S.Y. 
Published: May 2021

ABSTRACTBacteriophage-encoded depolymerases are responsible for degrading capsular polysaccharides (CPS), lipopolysaccharides (LPS) and exopolysachcharides (EPS) of the host bacteria during phage invasion. They have been considered as promising antivirulence agents in controlling bacterial infections, including those caused by drug-resistant bacteria. This feature inspires a hope of utilizing these enzymes to disarm the polysaccharide capsid of the bacterial cells, which then strengthens the action of antibiotics. Here we have identified, cloned, and expressed a depolymerase Dpo71 from a bacteriophage specific for the gram-negative (G-ve) bacterium Acinetobacter baumannii in the heterologous host E. coli. Dpo71 sensitizes the multidrug-resistant (MDR) A. baumannii to the host immune attack, and also acts as an adjuvant to assist or boost the action of antibiotics, for example colistin. Specifically, Dpo71 at 10 µg/ml enables a complete bacterial eradication by human serum at 50% volume ratio. Dpo71 inhibits biofilm formation and disrupts the pre-formed biofilm. Combination of Dpo71 could significantly enhance the antibiofilm activity of colistin, and improve the survival rate of A. baumannii infected Galleria mellonella. Dpo71 retains the strain-specificity of the parent phage from which Dpo71 is derived: the phage-sensitive A. baumannii strains respond to Dpo71 treatment, whereas the phage-insensitive strains do not. This indicates that Dpo71 indeed is responsible for the host specificity of bacteriophages. In summary, our work demonstrates the feasibility of using recombinant depolymerases as an antibiotic adjuvants to supplement the development of new antibacterials and to battle against MDR pathogens.
Genomic signatures of recent adaptation in a wild bumblebee
Authors: Colgan Thomas J. , Arce Andres N. , Gill Richard J. , Rodrigues Ana Ramos , Kanteh Abdoulie , Duncan Elizabeth J. , Li Li , Chittka Lars , Wurm Yannick 
Published: May 2021

AbstractBehavioral experiments and analyses of observation records have shown that environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects or other animals can adapt in response to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes ofBombus terrestrisbumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome. More specifically, we find that selection recently affected key processes underpinning environmental interactions, including neurobiology, wing development, and response to xenobiotics. We also discover unusual features of the genome, including a 53-gene region that lacks genetic diversity in many bee species, and a horizontal gene transfer from aWolbachiabacteria. The genetic diversity and gene flow we observe for this species could support its resilience to ongoing and future challenges. Overall, we provide important insight on the genetic health of an ecologically and economically important pollinator and reveal mechanisms by which it has recently adapted. The approach we used could help to understand how species differ in their adaptive potential, and to develop conservation strategies for those most at risk.