bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implication of synaptotagmins 4 and 7 in activity-dependent somatodendritic dopamine release
Authors: Delignat-Lavaud Benoît , Ducrot Charles , Kouwenhoven Willemieke , Feller Nina , Trudeau Louis-Éric 
Published: January 2021

ABSTRACTDopamine (DA) neurons can release DA not just from axon terminals, but also from their somatodendritic (STD) compartment thought a mechanism that is still incompletely understood. Using voltammetry in mouse mesencephalic brain slices, we find that STD DA release has low capacity, is stable in response to electrical but not optogenetic train pulses and shows a calcium sensitivity that is comparable to that of axonal release. It is also strikingly more resilient compared to axonal release in a 6‐ hydroxydopamine model of Parkinson’s disease plasticity. We find that the molecular mechanism of STD DA release differs from axonal release with regards to the implication of synaptotagmin (Syt) calcium sensors. While individual constitutive knock-out Syt4 and Syt7 is not sufficient to reduce STD DA release, removal of both isoforms reduces this release by ~50%, leaving axonal release unimpaired. Our works unveils clear differences in the mechanisms of STD and axonal DA release.
Integrating Sample Similarities into Latent Class Analysis: A Tree-Structured Shrinkage Approach
Authors: Li Mengbing , Park Daniel E. , Aziz Maliha , Liu Cindy M. , Price Lance B. , Wu Zhenke 
Published: January 2021

SummaryThis paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter distances over the tree between the leaves indicatea priorihigher similarity in class probability vectors. We propose a novel data integrative extension to classical latent class models (LCMs) with tree-structured shrinkage. The proposed approach enables 1) borrowing of information across leaves, 2) estimating data-driven leaf groups with distinct vectors of class probabilities, and 3) individual-level probabilistic class assignment given the observed multivariate binary measurements. We derive and implement a scalable posterior inference algorithm in a variational Bayes framework. Extensive simulations show more accurate estimation of class probabilities than alternatives that suboptimally use the additional sample similarity information. A zoonotic infectious disease application is used to illustrate the proposed approach. The paper concludes by a brief discussion on model limitations and extensions.
LeafGo: Leaf to Genome, a quick workflow to produce high-qualityDe novogenomes with Third Generation Sequencing technology
Authors: Driguez Patrick , Bougouffa Salim , Carty Karen , Putra Alexander , Jabbari Kamel , Reddy Muppala , Soppe Richard , Cheung Nicole , Fukasawa Yoshinori , Ermini Luca 
Published: January 2021

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a completede novoplant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two differentEucalyptusspeciesE. rudis, andE. camaldulensisto chromosome level without using additional scaffolding technologies. For the rapid production ofde novogenome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.
TRPM7 is critical for short-term synaptic depression by regulating synaptic vesicle endocytosis
Authors: Jiang Zhong-Jiao , Li Wenping , Yao Li-Hua , Grewe Brian S. , McGinley Andrea , Varga Kelly , Alford Simon , Gong Liang-Wei 
Published: January 2021

AbstractTRPM7 contributes to a variety of physiological and pathological processes in many tissues and cells. With a widespread distribution in the nervous system, TRPM7 is involved in animal behaviors and neuronal death induced by ischemia. However, the physiological role of TRPM7 in CNS neuron remains unclear. Here, we identify endocytic defects in neuroendocrine cells and neurons from TRPM7 knockout (KO) mice, indicating a role of TRPM7 in synaptic vesicle endocytosis. Our experiments further pinpoint the importance of TRPM7 as an ion channel in synaptic vesicle endocytosis. Ca2+imaging detects a defect in presynaptic Ca2+dynamics in TRPM7 KO neuron, suggesting an importance of Ca2+influx via TRPM7 in synaptic vesicle endocytosis. Moreover, the short-term depression is enhanced in both excitatory and inhibitory synaptic transmission from TRPM7 KO mice. Taking together, our data suggests that Ca2+influx via TRPM7 may be critical for short-term plasticity of synaptic strength by regulating synaptic vesicle endocytosis in neurons.
Diet composition, body condition and sexual size dimorphism of the common African toad(Amietophrynus regularis)in urban and agricultural landscape
Authors: Ofori Benjamin Yeboah , Mensah John Bosu , Anderson Roger Sigismund , Attuquayefio Daniel Korley 
Published: January 2021

AbstractLand use and land cover change (LULCC) are major drivers of global biodiversity loss. The conversion of natural habitats into human-modified landscapes poses novel and multifaceted environmental stressors to organisms, influencing their ecology, physiology, life history and fitness. Although the effects of LULCC have been studied extensively at the community level, there is scant information about its effect on population and individual characteristics. We assessed the diet composition, body condition, and sexual size dimorphism of the common African toad(Amietophrynus regularis)in urban and agricultural landscape. Diet composition was evaluated using gut content analysis, while body condition was measured using residual mass index. Overall, 935 prey items comprising six classes, at least 18 orders and 31 families were obtained from toads. This broad dietary niche suggested thatAmietophrynus regularisis a generalist predator. The family Formicidae was the most consumed prey item, with a frequency of occurrence above 80% at both sites. We found no sex- or habitat-biased dietary partitioning in the toads. A statistically significant positive correlation existed between snout-vent-length (SVL) and diversity of prey items (Pearson’s correlation r = 0.999, p ≤ 0.0001) for toads from farmland, which also had better body conditions. The toads showed female-biased sexual size dimorphism, but males had longer tibio-fibula, radio-ulna, foot, and distal fore limbs. This study is probably the first to assess the diet composition, body condition and sexual size dimorphism ofAmietophrynus regularissimultaneously. The ecological, evolutionary and conservation implications of our findings are discussed.
Identification of developmentally important genes inSilene latifoliathrough chemical genetics and transcriptome profiling
Authors: Bačovský Václav , Čegan Radim , Tihlaříková Eva , Neděla Vilém , Hudzieczek Vojtěch , Smrža Lubomír , Beneš Vladimír , Hobza Roman 
Published: January 2021

AbstractDioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. InSilene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia induced by rapid demethylation in the parental generation. As the hermaphrodite flower trait is holandric (transmitted only from male to male, inherited on the Y chromosome), we screened for genes that are differentially expressed between male, female, and hermaphrodite flowers. Dozens of candidate genes that are upregulated in hermaphrodite flowers compared to male and female flowers were detected and found to have putative roles in floral organization, affecting the expression of floral MADS-box and other genes. Amongst these genes, eight candidates were found to promote gynoecium formation in female and hermaphrodite flowers, affecting organ size, whorl boundary, and the expression of mainly B class flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using a field emission environmental scanning electron microscope. Our results reveal the principal regulatory pathways involved in sex-specific flower development in the classical model of dioecy,S. latifolia.
Elucidation of an anaerobic pathway for metabolism of L-carnitine-derived γ-butyrobetaine to trimethylamine in human gut bacteria
Authors: Rajakovich Lauren J. , Fu Beverly , Bollenbach Maud , Balskus Emily P. 
Published: January 2021

ABSTRACTTrimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient L-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent L-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the L-carnitine-derived metabolite γ-butyrobetaine (γbb) by the human gut bacteriumEmergencia timonensis. We identify a set of genes upregulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a flavin cofactor to catalyze a redox neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess thebbugene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from L-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of thebbupathway provides the critical missing link in anaerobic metabolism of L-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.SIGNIFICANCETrimethylamine (TMA) is a disease-associated metabolite produced in the human body exclusively by microbes. Gut microbes generate TMA from essential nutrients consumed in the human diet, including L-carnitine. However, our understanding of the biochemical mechanisms involved in these transformations is incomplete. In this work, we define the biochemical pathway and genetic components in gut bacteria required for anaerobic production of TMA from γ-butyrobetaine, a metabolite derived from L-carnitine. This discovery identifies a new type of TMA-producing enzyme and fills a critical gap in our knowledge of L-carnitine metabolism to TMA in the anaerobic environment of the human gut. This knowledge will enable evaluation of the link between L-carnitine metabolism and human disease, and the design of potential therapeutics.
mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge
Authors: Meyer Michelle , Wang Yuan , Edwards Darin , Smith Gregory R. , Rubenstein Aliza B. , Ramanathan Palaniappan , Mire Chad E. , Pietzsch Colette , Chen Xi , Ge Yongchao , Cheng Wan Sze , Henry Carole , Woods Angela , Ma LingZhi , Stewart-Jones Guillaume B. E. , Bock Kevin W. , Minai Mahnaz , Nagata Bianca M. , Periasamy Sivakumar , Shi Pei-Yong , Graham Barney S. , Moore Ian N. , Ramos Irene , Troyanskaya Olga G. , Zaslavsky Elena , Carfi Andrea , Sealfon Stuart C. , Bukreyev Alexander 
Published: January 2021

ABSTRACTThe mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.
Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat
Authors: Saif Rashid , Henkel Jan , Mahmood Tania , Ejaz Aniqa , Zia Saeeda 
Published: January 2021

AbstractNatural and artificial selection fix certain genomic regions of reduce heterozygosity which is an initial process in breed development. Primary goal of the current study is to identify these genomic selection signatures under positive selection and harbor genes in Pakistani Kamori goat breed. High throughput whole genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files were undergone quality checks, trimming and mapping process against ARS1 reference followed by calling variant allele frequencies. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajima’s D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. Total 98,574 autosomal selection signals were detected; 32,838 fromHpand 32,868 from each FST& TD statistics. Annotation of the regions with threshold (−ZHp≥ 5, TD ≤ −2.72 & FST≤ 0.09) detected 60 candidate genes. The top hits harbor Chr.1, 6, 8 & 21 having genes associated with body weight (GLIS3, ASTE1), coat color (DOCK8,MIPOL1) & body height (SLC25A21). Other significant windows harbor milk production, wool production, immunity, adaptation and reproduction trait related genes. Current finding highlighted the under-selection genomic regions of Kamori breed and likely to be associated with its vested traits and further useful in breed improvement, and may be also propagated to other undefined goat breeds by adopting targeted breeding policies to improve the genetic potential of this valued species.
Redefining the roles of UDP-glycosyltransferases in auxin metabolism and homeostasis during plant development
Authors: Mateo-Bonmatí Eduardo , Casanova-Sáez Rubén , Šimura Jan , Ljung Karin 
Published: January 2021

ABSTRACTThe levels of the important plant growth regulator indole-3-acetic acid (IAA) are tightly controlled within plant tissues to spatiotemporally orchestrate concentration gradients that drive plant growth and development. Metabolic inactivation of bioactive IAA is known to participate in the modulation of IAA maxima and minima. IAA can be irreversibly inactivated by oxidation and conjugation to Aspartate and Glutamate. Usually overlooked because its reversible nature, the most abundant inactive IAA form is the IAA-glucose (IAA-glc) conjugate. Glycosylation of IAA is reported to be carried out by the UDP-glycosyltransferase 84B1 (UGT84B1), while UGT74D1 has been implicated in the glycosylation of the irreversibly formed IAA catabolite oxIAA. Here we demonstrate that both UGT84B1 and UGT74D1 modulate IAA levels throughout plant development by dual IAA and oxIAA glycosylation. Moreover, we identify a novel UGT subfamily whose members modulate IAA homeostasis during skotomorphogenesis by redundantly mediating the glycosylation of oxIAA.
A novel SARS-CoV-2 related coronavirus in bats from Cambodia
Authors: Hul Vibol , Delaune Deborah , Karlsson Erik A , Hassanin Alexandre , Tey Putita Ou , Baidaliuk Artem , Gámbaro Fabiana , Tu Vuong Tan , Keatts Lucy , Mazet Jonna , Johnson Christine , Buchy Philippe , Dussart Philippe , Goldstein Tracey , Simon-Lorière Etienne , Duong Veasna 
Published: January 2021

AbstractKnowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected inRhinolophusbats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in twoRhinolophus shamelibats sampled in Cambodia in 2010. Metagenomic sequencing identified nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a small region corresponding to the spike N terminal domain. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously understood, and suggests that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses.
The experimental manipulation of atmospheric drought: Teasing out the role of microclimate in biodiversity experiments
Authors: Aguirre Beatriz A. , Hsieh Brian , Watson Samantha J. , Wright Alexandra J. 
Published: January 2021

Abstract

Drought occurrence is increasing due to anthropogenic climate change. Drought can negatively affect plants via reduced water below‐ground and increased evaporative demand or vapour pressure deficit (VPD) above‐ground. Past work has shown that plant diversity can ameliorate the negative effects of drought in plant communities, but these results are inconsistent between experimental and natural drought studies. Furthermore, while studies on the negative effects of reduced soil moisture on plant growth in drought experiments are abundant, the effects of predicted increases in atmospheric VPD have been neglected.

We directly manipulated atmospheric relative humidity in a biodiversity and drought experiment at the California State University, Los Angeles (CA, USA) under three atmospheric conditions (ambient, dehumidified and humidified), two treatments of native perennial grass diversity (monoculture and eight species polyculture) and two soil drought treatments (control and drought). We assessed both polyculture plant community and individual species (Poa secunda) responses to atmospheric drought and soil drought.

We found that soil drought only limits above‐ground biomass production when atmospheric conditions are also dry. We also found that P. secunda was limited by increased competition in polyculture when ambient atmospheric conditions were humid but was facilitated by diversity when atmospheric conditions were dry.

Synthesis. Higher diversity ecosystems may be capable of protecting individual species from the negative effects of drought (facilitation). Without careful experimental manipulation of atmospheric drought, this important mechanism will be missed.
Quantifying nectar production by flowering plants in urban and rural landscapes
Authors: Tew Nicholas E. , Memmott Jane , Vaughan Ian P. , Bird Stephanie , Stone Graham N. , Potts Simon G. , Baldock Katherine C. R. 
Published: January 2021

Abstract

Floral resources (nectar and pollen) provide food for insect pollinators but have declined in the countryside due to land use change. Given widespread pollinator loss, it is important that we quantify their food supply to help develop conservation actions. While nectar resources have been measured in rural landscapes, equivalent data are lacking for urban areas, an important knowledge gap as towns and cities often host diverse pollinator populations.

We quantified the nectar supply of urban areas, farmland and nature reserves in the UK by combining floral abundance and nectar sugar production data for 536 flowering plant taxa, allowing us to compare landscape types and assess the spatial distribution of nectar sugar among land uses within cities.

The magnitude of nectar sugar production did not differ significantly among the three landscapes. In urban areas the nectar supply was more diverse in origin and predominantly delivered by non‐native flowering plants. Within cities, urban land uses varied greatly in nectar sugar production. Gardens provided the most nectar sugar per unit area and 85% of all nectar at a city scale, while gardens and allotments produced the most diverse supplies of nectar sugar. Floral abundance, commonly used as a proxy for pollinators’ food supply, correlated strongly with nectar resources, but left a substantial proportion of the variation in nectar supply unexplained.

Synthesis. We show that urban areas are hotspots of floral resource diversity rather than quantity and their nectar supply is underpinned by the contribution of residential gardens. Individual gardeners have an important role to play in pollinator conservation as ornamental plants, usually non‐native in origin, are a key source of nectar in towns and cities.
The potential value of dequalinium chloride in the treatment of cancer: Focus on malignant glioma
Authors: Pan Yuehai , Zhao Shuai , Chen Fan 
Published: January 2021

AbstractDequalinium chloride has been known as one kind of antibiotic that displays a broad antimicrobial spectrum and has been clinically proven to be very safe. In recent years, studies have shown that dequalinium chloride can inhibit the growth of malignant tumours, and reports were mainly used for solid tumours. Glioblastoma is the most common malignant neuroepithelial tumour of the central nervous system in adults, and the prognosis of glioblastoma is poor as it has a high resistance to apoptosis. This review summarizes the current understanding of dequalinium chloride‐induced cancer cell apoptosis and its potential role in glioblastoma resistance and progression. Particularly, we focus on dequalinium chloride as it exerts a wide range of anti‐cancer activity through its ability to target and accumulate in the mitochondria, and it effectively inhibits the growth of glioblastoma cells in vitro and vivo. Dequalinium chloride is an inhibitor of XIAP and can also act as a mitochondrial targeting agent, which gives it an interesting perspective regarding recent advances in the treatment of malignant glioma.