bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protistan plankton communities in the Galápagos Archipelago respond to changes in deep water masses resulting from the 2015/16 El Niño
Authors: Neave Erika F. , Seim Harvey , Gifford Scott , Torano Olivia , Johnson Zackary I. , Páez-Rosas Diego , Marchetti Adrian 
Published: May 2021

AbstractThe Galápagos Archipelago lies within the eastern equatorial Pacific Ocean at the convergence of major ocean currents that are subject to changes in circulation. The nutrient-rich Equatorial Undercurrent upwells from the west onto the Galápagos platform, stimulating primary production, but this source of deep water weakens during El Niño events. From measurements collected on repeat cruises, the 2015/16 El Niño was associated with declines in phytoplankton biomass at most sites throughout the archipelago and reduced utilization of nitrate, particularly in large-sized phytoplankton in the western region. Protistan assemblages were identified by sequencing the V4 region of the 18S rRNA gene. Dinoflagellates, chlorophytes, and diatoms dominated most sites. Shifts in dinoflagellate communities were most apparent between the years; parasitic dinoflagellates,Syndiniales, were highly detected during the El Niño (2015) while the dinoflagellate genus,Gyrodiniumdominated many sites during the neutral period (2016). Variations in protistan communities were most strongly correlated with changes in subthermocline water density. These findings indicate that marine protistan communities in this region are regimented by deep water mass sources and thus could be profoundly affected by altered ocean circulation.
CommensalStreptococcus mitisproduces two different lipoteichoic acids of type I and type IV
Authors: Gisch Nicolas , Peters Katharina , Thomsen Simone , Vollmer Waldemar , Schwudke Dominik , Denapaite Dalia 
Published: May 2021

ABSTRACTThe opportunistic pathogenStreptococcus mitispossesses, like other members of the Mitis group of viridans streptococci, phosphorylcholine (P-Cho)-containing teichoic acids (TAs) in its cell wall. Bioinformatic analyses predicted the presence of TAs that are almost identical with those identified in the pathogenS. pneumoniae, but a detailed analysis ofS. mitislipoteichoic acid (LTA) was not performed to date. Here we determined the structures of LTA from twoS. mitisstrains, the high-level beta-lactam and multiple antibiotic resistant strain B6 and the penicillin-sensitive strain NCTC10712. In agreement with bioinformatic predictions we found that the structure of one LTA (type IV) was like pneumococcal LTA, except the exchange of a glucose moiety with a galactose within the repeating units. Further genome comparisons suggested that the majority ofS. mitisstrains should contain the same type IV LTA asS. pneumoniae, providing a more complete understanding of the biosynthesis of theseP-Cho-containing TAs in members of the Mitis group of streptococci. Remarkably, we observed besides type IV LTA an additional polymer belonging to LTA type I in both investigatedS. mitisstrains. This LTA consists of β-galactofuranosyl-(1,3)-diacylglycerol as glycolipid anchor and a poly-glycerol-phosphate chain at theO-6 position of the furanosidic galactose. Hence, these bacteria are capable of synthesizing two different LTA polymers, most likely produced by distinct biosynthesis pathways. Our bioinformatics analysis revealed the prevalence of the LTA synthase LtaS, most probably responsible for the second LTA version (type I), amongstS. mitisandS. pseudopneumoniaestrains.
Direct comparison of contralateral bias and face/scene selectivity in human occipitotemporal cortex
Authors: Silson Edward H , Groen Iris I A , Baker Chris I 
Published: May 2021

AbstractHuman visual cortex is organised broadly according to two major principles: retinotopy (the spatial mapping of the retina in cortex) and category-selectivity (preferential responses to specific categories of stimuli). Historically, these principles were considered anatomically separate, with retinotopy restricted to the occipital cortex and category-selectivity emerging in the lateral-occipital and ventral-temporal cortex. However, recent studies show that category-selective regions exhibit systematic retinotopic biases, for example exhibiting stronger activation for stimuli presented in the contra- compared to the ipsilateral visual field. It is unclear, however, whether responseswithincategory-selective regions are more strongly driven by retinotopic location or by category preference, and if there are systematic differencesbetweencategory-selective regions in the relative strengths of these preferences. Here, we directly compare contralateral and category preferences by measuring fMRI responses to scene and face stimuli presented in the left or right visual field and computing two bias indices: a contralateral bias (response to the contralateral minus ipsilateral visual field) and a face/scene bias (preferred response to scenes compared to faces, or vice versa). We compare these biases within and between scene- and face-selective regions and across the lateral and ventral surfaces of visual cortex more broadly. We find an interaction between surface and bias: lateral surface regions show a stronger contralateral than face/scene bias, whilst ventral surface regions show the opposite. These effects are robust across and within subjects, and appear to reflect large-scale, smoothly varying gradients. Together, these findings support distinct functional roles for lateral and ventral visual cortex in terms of the relative importance of the spatial location of stimuli during visual information processing.
Host adaptation through hybridization: Genome analysis of triticale powdery mildew reveals unique combination of lineage-specific effectors
Authors: Müller Marion C. , Kunz Lukas , Graf Johannes , Schudel Seraina , Keller Beat 
Published: May 2021

AbstractThe emergence of new fungal pathogens through hybridization represents a serious challenge for agriculture. Hybridization between the wheat mildew (Blumeria graminis f.sp. tritici) and rye mildew (B.g. f.sp. secalis) pathogens have led to the emergence of a new mildew form (B.g. f.sp. triticale) growing on triticale, a man-made amphiploid crop derived from crossing rye and wheat which was originally resistant to the powdery mildew disease. The identification of the genetic basis of host-adaptation in triticale mildew has been hampered by the lack of a reference genome. Here we report the 141.4 Mb reference assembly ofB.g. triticaleisolate THUN-12 derived from long-read sequencing and genetic map-based scaffolding. All elevenB.g. triticalechromosomes were assembled from telomere-to-telomere and revealed that 19.7% of the hybrid genome was inherited from the rye mildew parental lineage. We identified lineage-specific regions in the hybrid, inherited from the rye or wheat mildew parental lineages, that harbour numerous bona fide candidate effectors. We propose that the combination of lineage-specific effectors in the hybrid genome is crucial for host-adaptation, allowing the fungus to simultaneously circumvent the immune systems contributed by wheat and rye in the triticale crop. In line with this we demonstrate the functional transfer of theSvrPm3effector from wheat to triticale mildew, a virulence effector that specifically suppresses resistance of the wheatPm3allelic series. This transfer is the likely underlying cause for the observed poor effectiveness of severalPm3alleles against triticale mildew and exemplifies the negative implications of pathogen hybridizations on resistance breeding.
The influence of the respiratory cycle on reaction times in sensory-cognitive paradigms
Authors: Johannknecht Michelle , Kayser Christoph 
Published: May 2021

AbstractBehavioural and electrophysiological studies point to widespread influence of the state of respiration on brain activity and cognitive performance. Still, the prevalence and relevance of such respiratory-behavioural relations in typical sensory-cognitive tasks remain unclear. We here used a battery of six tasks probing sensory detection, discrimination and short-term memory to address the questions of whether and by how much behaviour covaries with the respiratory cycle. Our results show that participants tended to align their respiratory cycle to the experimental paradigm. Furthermore, their reaction times, but not so much their response accuracy, consistently and significantly covaried with the respiratory cycle, and this effect was strongest when analyzed contingent on the respiratory state at participants’ responses. The respective effect sizes where comparable to those seen in many typical neurocognitive experimental manipulations. These results support a prominent relation between respiration and sensory-cognitive function and suggest that sensation is intricately linked to rhythmic bodily or interoceptive functions.
Squeegee: de-novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes
Authors: Liu Yunxi , Elworth R. A. Leo , Jochum Michael D. , Aagaard Kjersti M. , Treangen Todd J. 
Published: May 2021

ABSTRACTComputational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Our hypothesis is that contamination from DNA extraction kits or sampling lab environments will leave taxonomic “bread crumbs” across multiple distinct sample types, allowing for the detection of microbial contaminants when negative controls are unavailable. To test this hypothesis we implemented Squeegee, ade novocontamination detection tool. We tested Squeegee on simulated and real low biomass metagenomic datasets. On the low biomass samples, we compared Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers known contaminants. We also analyzed 749 metagenomic datasets from the Human Microbiome Project and identified likely previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision. Squeegee is open-source and available at:https://gitlab.com/treangenlab/squeegee
Limacus flavusyellow slug: bioactive molecules in the mucus
Authors: Hayashida Patricia Yumi , da Silva Júnior Pedro Ismael 
Published: May 2021

ABSTRACTBackgroundSnails and slugs were used as a treatment for many health problems therefore ancient times. Since the antimicrobial resistance became a major global thread, antimicrobial peptides have been considered as a potential source for development of new drugs, especially for drug-resistant bacteria. Nowadays reports confirm that the mucous secretions have antimicrobial, antiviral and antifungal properties.MethodsThe present study has the objective to characterize and evaluate antimicrobial peptides ofLimacus flavusmucus. The mucus was obtained by thermal shock and submitted to RP-HPLC. Fractions were used to perform the antimicrobial activity and hemolytic assays, electrophoresis (SDS-Page Gel) and submitted to mass spectrometry (LC-MS / MS). Identification and characterization was performed by PeaksX+ software. The physicochemical parameters were evaluated with bioinformatics tools, which predicted water solubility, iso-electric point, charge net and its primary structure.ResultsThree fractions were isolated from the mucus ofL. flavusand presented antifungal and antibacterial activity. The mucus showed greater inhibition for filamentous fungi (Aspergillus niger), yeast (Cryptococcus neoformans), Gram positive bacteria (Bacillus subtilis, Micrococcus luteus) and Gram negative bacteria (Enterobacter cloacae). These fractions also did not show hemolytic activity for human blood cells (erythrocytes). Fraction’s sequences were identified and presents Mw <3kDa, WLGH, DLQW, YLRW, respectively.ConclusionThis study revealed three antimicrobial peptides ofL. flavusmucus with a wide range of antimicrobial activity and its physic-chemical characterization.
From theory to experiment and back again — Challenges in quantifying a trait-based theory of predator-prey dynamics
Authors: Wootton K. L. , Curtsdotter Alva , Jonsson Tomas , Banks H.T. , Bommarco Riccardo , Roslin Tomas , Laubmeier A. N. 
Published: May 2021

AbstractFood webs map feeding interactions among species, providing a valuable tool for understanding and predicting community dynamics. Trait-based approaches to food webs are increasingly popular, using e.g. species’ body sizes to parameterize dynamic models. Although partly successful, models based on body size often cannot fully recover observed dynamics, suggesting that size alone is not enough. For example, differences in species’ use of microhabitat or non-consumptive effects of other predators may affect dynamics in ways not captured by body size.Here, we report on the results of a pre-registered study (Laubmeier et al., 2018) where we developed a dynamic food-web model incorporating body size, microhabitat use, and non-consumptive predator effects and used simulations to optimize the experimental design. Now, after performing the mesocosm experiment to generate empirical time-series of insect herbivore and predator abundance dynamics, we use the inverse method to determine parameter values of the dynamic model. We compare four alternative models with and without microhabitat use and non-consumptive predator effects. The four models achieve similar fits to observed data on herbivore population dynamics, but build on different estimates for the same parameters. Thus, each model predicts substantially different effects of each predator on hypothetical new prey species. These findings highlight the imperative of understanding the mechanisms behind species interactions, and the relationships mediating the effects of traits on trophic interactions. In particular, we believe that increased understanding of the estimates of optimal predator-prey body-size ratios and maximum feeding rates will improve future predictions. In conclusion, our study demonstrates how iterative cycling between theory, data and experiment may be needed to hone current insights into how traits affect food-web dynamics.
Integration of chemosensing and carbon catabolite repression impacts fungal enzyme regulation and plant associations
Authors: Hinterdobler Wolfgang , Li Guofen , Turrà David , Schalamun Miriam , Kindel Stefanie , Sauer Ursula , Beier Sabrina , Iglesias Aroa Rodriguez , Compant Stéphane , Vitale Stefania , Pietro Antonio Di , Schmoll Monika 
Published: May 2021

AbstractFungal metabolism and enzyme production are regulated by nutrient availability and by interactions with the living environment. We investigated the mechanisms underpinning adaptation of the biotechnological fungusTrichoderma reeseito decaying plant biomass versus living plants. We found that concentration-gated response to glucose, the main molecule sensed from dead plant biomass, is mediated by a conserved signaling pathway downstream of G protein-coupled receptors (GPCRs), while the carbon catabolite repressor CRE1 is critical for glucose concentration gating. The GPCRs CSG1 and CSG2 are further required for root colonization and formation of appressorium like structures on plant surfaces. Acceleration of sexual development in the presence of plant roots and their interactions with fruiting bodies indicates preferential association with plants. Our results reveal a complex sensing network governing resource distribution, enzyme production and fungal development that explains previously observed phenomena in fermentations and opens new perspectives for industrial strain improvement and agriculture.
GIV/Girdin, a Non-receptor Modulator for Gαi/s, Regulates Spatiotemporal Signaling during Sperm Capacitation and is Required for Male Fertility
Authors: Reynoso Sequoyah , Castillo Vanessa , Katkar Gajanan D. , Lopez-Sanchez Inmaculada , Taheri Sahar , Espinoza Celia R. , Rohena Christina , Sahoo Debashis , Gagneux Pascal , Ghosh Pradipta 
Published: May 2021

SUMMARYFor a sperm to successfully fertilize an egg, it must first undergo capacitation in the female reproductive tract, and later undergo acrosomal reaction (AR) upon encountering an egg surrounded by its vestment. How premature AR is avoided despite rapid surges in signaling cascades during capacitation remains unknown. Using a combination of KO mice and cell-penetrating peptides, we show that GIV (CCDC88A), a guanine nucleotide-exchange modulator (GEM) for trimeric GTPases, is highly expressed in spermatocytes and is required for male fertility. GIV is rapidly phosphoregulated on key tyrosine and serine residues in human and murine spermatozoa. These phosphomodifications enable GIV-GEM to orchestrate two distinct compartmentalized signaling programs in the sperm tail and head; in the tail, GIV enhances PI3K→ Akt signals, sperm motility and survival, whereas in the head it inhibits cAMP surge and premature AR. Furthermore, GIV transcripts are downregulated in the testis and semen of infertile men. These findings exemplify the spatiotemporally segregated signaling programs that support sperm capacitation and shed light on a hitherto unforeseen cause of infertility in men.GRAPHIC ABSTRACTHIGHLIGHTSGIV is highly expressed in spermatozoa, and is required for male fertilityGIV is rapidly phosphoregulated during sperm capacitationIt enhances tyrosine-based signals in sperm tail, enhances motilityIt suppresses cAMP in the sperm head, inhibits premature acrosome exocytosis
An Analysis of gRNA Sequence Dependent Cleavage Highlights the Importance of Genomic Context on CRISPR-Cas Activity
Authors: Moreb E.A , Lynch M.D. 
Published: May 2021

AbstractCRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. To better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 39 published data sets. We find strong evidence that the genomic context, which can be defined as the DNA content outside of the gRNA/target sequence itself, greatly contributes to differences in gRNA dependent activity. Context underlies variation in activity often attributed to differences in gRNA sequence. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.HighlightsSpecies-specific genomic context drives variability in gRNA activity in a PAM proximal sequence-dependent mannerIncreased PAM specificity of Cas9 and/or increased Cas9/gRNA expression reduces the impact of species-specific contextCurrent gRNA prediction algorithms trained on species are not expected to predict activity in another species
Physiological and genetic analysis of tomato from two cultivars differing in potassium deficiency resistance
Authors: Wang Xi , Zhang Honghui , Li Tianlai , Liu Xin , Jiang Jing 
Published: May 2021

AbstractPotassium (K) is one of the essential nutrients for tomato. Potassium deficiency will limit tomato growth and yield. So improving the low-K+(LK) resistance of tomato seems important. Two tomato cultivars (JZ18 and JZ34) differing in LK resistance were obtained to analyze the plant demonstration difference under LK treatment. According to the results, JZ34 showed lower accumulation of ROS, less membrane damage and higher antioxidant enzyme activity after LK treatment. Besides, JZ34 also keeps higher K+/Na+content, higher Ca2+and Mg2+content than JZ18 in both shoots and roots. Our genetic analysis revealed that the two additive-dominance-epistasis major genes plus additive-dominance polygene genetic model (E-1) was the optimum model associated with LK resistance based on root trait. The major QTL intervals were finally obtained by the bulked segregant sequencing (BSA-seq) analysis, which were 2.38 Mb at the end of chromosome 4 and 1.38 Mb at the chromosome 6. This is consistent with the analysis of the genetic model. A total of 8 genes were selected in the two candidate regions, which exhibited close related to ion and antioxidant signaling. These findings provided the inheritance pattern and foundation for further molecular mechanisms study of tomato LK resistance.
Single Cell Atlas of Human Putamen Reveals Disease Specific Changes in Synucleinopathies: Parkinson’s Disease and Multiple System Atrophy
Authors: Pande Rahul , Huang Yinyin , Teeple Erin , Joshi Pooja , Flores-Morales Amilcar , Latta-Mahieu Martine , Sardi S. Pablo , Cedazo-Minguez Angel , Klinger Katherine W. , Madden Stephen L. , Rajpal Deepak , Kumar Dinesh 
Published: May 2021

AbstractUnderstanding disease biology at a cellular level from disease specific tissues is imperative for effective drug development for complex neurodegenerative diseases. We profiled 87,086 nuclei from putamen tissue of healthy controls, Parkinson’s Disease (PD), and Multiple System Atrophy (MSA) subjects to construct a comprehensive single cell atlas. Although both PD and MSA are manifestations of α-synuclein protein aggregation, we observed that both the diseases have distinct cell-type specific changes. We see a possible expansion and activation of microglia and astrocytes in PD compared to MSA and controls. Contrary to PD microglia, we found absence of upregulated unfolded protein response in MSA microglia compared to controls. Differentially expressed genes in major cell types are enriched for genes associated with PD-GWAS loci. We found altered expression of major neurodegeneration associated genes — SNCA, MAPT, LRRK2, and APP — at cell-type resolution. We also identified disease associated gene modules using a network biology approach. Overall, this study creates an interactive atlas from synucleinopathies and provides major cell-type specific disease insights.Link to interactive atlas will be made available at the time of publication.
A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree
Authors: Revell Liam J. , Toyama Ken S. , Mahler D. Luke 
Published: May 2021

ABSTRACTNumerous questions in phylogenetic comparative biology revolve around the correlated evolution of two or more phenotypic traits on a phylogeny. In many cases, it may be sufficient to assume a constant value for the evolutionary correlation between characters across all the clades and branches of the tree. Under other circumstances, however, it is desirable or necessary to account for the possibility that the evolutionary correlation differs through time or in different sections of the phylogeny. Here, we present a method designed to fit a hierarchical series of models for heterogeneity in the evolutionary rates and correlation of two quantitative traits on a phylogenetic tree. We apply the method to two datasets: one for different attributes of the buccal morphology in sunfishes (Centrarchidae); and a second for overall body length and relative body depth in rock- and non-rock-dwelling South American iguanian lizards. We also examine the performance of the method for parameter estimation and model selection using a small set of numerical simulations.