bluuebunny/crossref_metadata_2025_split huggingface dataset:
Horizontal transfer of a conservednpc-2like effector gene in rust fungi that suppresses cell death in plants
Authors: Jaswal Rajdeep , Dubey Himanshu , Kiran Kanti , Rawal Hukam , Kumar Gulshan , Rajarammohan Sivasubramanian , Deshmukh Rupesh , Sonah Humira , Prasad Pramod , Bhardwaj Subhash C , Gupta Naveen , Sharma Tilak Raj 
Published: August 2021

AbstractML/MD-2 is a conserved lipid/sterol-binding protein family having a role in sterol transfer and innate immunity in lower and higher eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 25 fungal and five oomycetes plant pathogen, having a different nutrition mode. All the fungal species were found to have varied numbers of family members, a distinctively substantial expansion of the ML gene family was observed inRhizophagus irregularis(RI) with 33 genes. Our analysis also showed that NPC2 like proteins, a subfamily of ML domain superfamily, were not only restricted to animals and insect species but also present in plant fungal pathogens, including members ofClavicipitaceae,Pucciniacease,andTremellaceaefamily. The phylogenetic analysis showed that these NPC2 like fungal proteins are more closely related to animals/insects than other fungal species. The molecular docking studies of these proteins with cholesterol and other derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. Further, the full length CDS of one of thenpc2like genes fromPuccinia triticina(Pt5643) was PCR amplified and further characterized using various studies such as qRT-PCR, expression in onion epidermal cells,Nicotiana benthamianafor subcellular localization studies, yeast functional complementation, and expression studies. The mRNA abundance ofPt5643was observed to be increased along with the infection progression and exhibits the highest expression at 5thday post-infection (dpi), suggesting its important role in theP. triticinainfection cycle in wheat. The fluorescent confocal microscopy of transiently expressed YFP taggedPt5643in onion epidermal cells andN. benthamianashows its location in cytoplasm and nucleus, indicating its involvement in the manipulation of host genes. The functional complementation ofPt5643innpc2mutant yeast showed its functional similarity to the eukaryotic npc2 gene. Further, the overexpression ofPt5643also suppressed the BAX and H2O2 induced program cell death inN. benthamianaand yeast, respectively thus proving to be a novel horizontally transferred effector in rust fungal pathogens. Altogether the present study reports the novel function of fungal NPC2 like proteins playing a crucial role in host defense manipulation possibly through lipid binding/transport similar to animals.
The genome of stress tolerant crop wild relativePaspalum vaginatumleads to increased biomass productivity in the cropZea mays
Authors: Sun Guangchao , Wase Nishikant , Shu Shengqiang , Jenkins Jerry , Zhou Bangjun , Chen Cindy , Sandor Laura , Plott Chris , Yoshinga Yuko , Daum Christopher , Qi Peng , Barry Kerrie , Lipzen Anna , Berry Luke , Gottilla Thomas , Foltz Ashley , Yu Huihui , O’Malley Ronan , Zhang Chi , Devos Katrien M. , Sigmon Brandi , Yu Bin , Obata Toshihiro , Schmutz Jeremy , Schnable James C. 
Published: August 2021

ABSTRACTA number of crop wild relatives can tolerate extreme stressed to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. PaspalumPaspalum vaginatumis a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession ofP. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologous conserved in 6 related grass species placed paspalum as an outgroup of the maize-sorghum clade demonstrating paspalum as their closest sequenced wild relative. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibited significant increases in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, resulting in autophagy dependent increases in biomass accumulation.
Distinct fastigial output channels and their impact on temporal lobe seizures
Authors: Streng Martha L. , Tetzlaff Madison , Krook-Magnuson Esther 
Published: August 2021

AbstractDespite being canonically considered a motor control structure, the cerebellum is increasingly recognized for important roles in processes beyond this traditional framework, including seizure suppression. Excitatory fastigial neurons project to a large number of downstream targets, and it is unclear if this broad targeting underlies seizure suppression, or if a specific output may be sufficient. To address this question, we used the intrahippocampal kainic acid mouse model of temporal lobe epilepsy, male and female animals, and a dual-virus approach to selectively label and manipulate fastigial outputs. We examined fastigial neurons projecting to the superior colliculus, medullary reticular formation, and central lateral nucleus of the thalamus, and found that these comprise largely non-overlapping populations of neurons which send collaterals to unique sets of additional thalamic and brainstem regions, creating distinct, somewhat overlapping, “output channels”. We found that neither optogenetic stimulation of superior colliculus nor reticular formation output channels attenuated hippocampal seizures. In contrast, on-demand stimulation of fastigial neurons targeting the central lateral nucleus robustly inhibited seizures. Our results indicate that fastigial control of hippocampal seizures does not require simultaneous modulation of many fastigial output channels. Rather, selective modulation of the fastigial output channel to the central lateral thalamus, specifically, is sufficient for seizure control. This may provide a means for more selective therapeutic interventions, which provide seizure control while minimizing unwanted side effects. More broadly, our data highlight the concept of specific cerebellar output channels, whereby discrete cerebellar nucleus neurons project to specific aggregates of downstream targets, with distinct functional outcomes.Significance statementThe cerebellum has an emerging relationship with non-motor systems and may represent a powerful target for therapeutic intervention in temporal lobe epilepsy. We find that fastigial neurons project to numerous brain regions via largely segregated output channels, and that excitation of fastigial neurons projecting to the central lateral nucleus of the thalamus, but not the superior colliculus or reticular formation, is sufficient to attenuate hippocampal seizures. These findings illustrate an important conceptual framework: fastigial neurons project to aggregates of downstream targets via distinct output channels, which cannot be predicted simply by somatic location within the nucleus, and these channels have distinct functional outcomes. This nuanced appreciation of fastigial outputs may provide a path for therapeutic interventions with minimized side effects.
Structure-Function in Helical Cardiac Musculature Using Additive Textile Manufacturing
Authors: Chang Huibin , Liu Qihan , Zimmerman John F. , Lee Keel Yong , Jin Qianru , Peters Michael M. , Rosnach Michael , Choi Suji , Kim Sean L. , Ardoña Herdeline Ann M. , MacQueen Luke A. , Chantre Christophe O. , Motta Sarah E. , Cordoves Elizabeth M. , Parker Kevin Kit 
Published: August 2021

AbstractFor more than fifty years, it has been hypothesized that the helical alignment of the heart gives rise to its mechanical function. Testing this hypothesis in an engineered environment is difficult, as the fine spatial features and complex three-dimensional (3D) structures of the cardiac musculature are challenging to reproduce using current biofabrication techniques. Addressing this, here we report a new form of additive textile manufacturing, Focused Rotary Jet Spinning (FRJS). FRJS allows for the rapid manufacturing of micro/nanofibers with controlled alignments. Using this method, we manufacture 3D models of the left ventricle, showing that helically aligned scaffolds display increased strain uniformity, axial shortening, cardiac output, and ejection fractions as compared to circumferential models. We then demonstrate how FRJS can enable the assembly of a full-sized model of the human heart’s musculature. This work experimentally confirms that ventricular alignment plays a critical role in ensuring healthy cardiac performance.
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments
Authors: Nishimura Yosuke , Yoshizawa Susumu 
Published: August 2021

AbstractMarine microorganisms are immensely diverse and play fundamental roles in global geochemical cycling. Recent metagenome-assembled genome studies, with special attention to large-scale projects such as Tara Oceans, have expanded the genomic repertoire of marine microorganisms. However, published marine metagenome data has not been fully explored yet. Here, we collected 2,057 marine metagenomes (>29 Tera bps of sequences) covering various marine environments and developed a new genome reconstruction pipeline. We reconstructed 52,325 qualified genomes composed of 8,466 prokaryotic species-level clusters spanning 59 phyla, including genomes from deep-sea deeper than 1,000 m (n=3,337), low-oxygen zones of <90 μmol O2 per kg water (n=7,884), and polar regions (n=7,752). Novelty evaluation using a genome taxonomy database shows that 6,256 species (73.9%) are novel and include genomes of high taxonomic novelty such as new class candidates. These genomes collectively expanded the known phylogenetic diversity of marine prokaryotes by 34.2% and the species representatives cover 26.5 - 42.0% of prokaryote-enriched metagenomes. This genome resource, thoroughly leveraging accumulated metagenomic data, illuminates uncharacterized marine microbial ‘dark matter’ lineages.
Does pollen limitation limit plant ranges? Evidence and implications
Authors: Dawson-Glass Emma , Hargreaves Anna L. 
Published: August 2021

AbstractRange limits often involve declines in sexual reproduction, reducing fitness, dispersal, and adaptive potential at range edges. For plants, sexual reproduction is frequently limited by inadequate pollination. While case studies show that pollen limitation can limit plant distributions, the extent to which pollination commonly declines toward plant range edges is unknown. Here, we leverage global databases of pollen-supplementation experiments and plant occurrence data to test whether pollen limitation increases toward plant range edges, using a phylogenetically controlled meta-analysis. While there was significant pollen limitation across studies, we found little evidence that pollen limitation increases toward plant range edges. Pollen limitation was not stronger toward the tropics, nor at species’ equatorward vs poleward range limits. Meta-analysis results are consistent with results from targeted experiments, in which pollen limitation increased significantly toward only 14% of 14 plant range edges, suggesting that pollination contributes to range limits less often than do other interactions. Together, these results suggest pollination is one of the rich variety of potential ecological factors that can contribute to range limits, rather than a generally important constraint on plant distributions.
Antarctic biodiversity predictions through substrate qualities and environmental DNA
Authors: Czechowski Paul , de Lange Michel , Knapp Micheal , Terauds Aleks , Stevens Mark I. 
Published: August 2021

AbstractAntarctic conservation science is important to enhance Antarctic policy and to understand alterations of terrestrial Antarctic biodiversity. Antarctic conservation will have limited long term effect in the absence of large-scale biodiversity data, but if such data were available, it is likely to improve environmental protection regimes. To enable Antarctic biodiversity prediction across continental spatial scales through proxy variables, in the absence of baseline surveys, we link Antarctic substrate-derived environmental DNA (eDNA) sequence data from the remote Antarctic Prince Charles Mountains to a selected range of concomitantly collected measurements of substrate properties. We achieve this using a statistical method commonly used in machine learning. We find neutral substrate pH, low conductivity, and some substrate minerals to be important predictors of presence for basidiomycetes, chlorophytes, ciliophorans, nematodes, or tardigrades. Our bootstrapped regression reveals how variations of the identified substrate parameters influence probabilities of detecting eukaryote phyla across vast and remote areas of Antarctica. We believe that our work may improve future taxon distribution modelling and aid targeting logistically challenging biodiversity surveys.
A comparison of the IgM and IgT repertoires reveals the structure of B cell communities in rainbow trout is a consequence of mechanistic and evolutionary forces
Authors: Costa Gregory R. , Poirier Annie , Bromage Erin S. 
Published: August 2021

AbstractIn rainbow trout (Oncorhynchus mykiss), three classes of antibodies have been identified: IgM, IgD, and IgT, which differ in their abundance and effector functions. Though the process of VDJ recombination that creates these antibodies is often described as a stochastic process, recent findings in mammals suggest that there are biases in antibody construction. Because class switching is absent in teleosts, studying the IgM and IgT communities of rainbow trout provides the opportunity to see how evolution has differentially shaped the IgM and IgT repertoires. Even though it has not yet been demonstrated that biases exist in variable region construction for trout immunoglobulins, it seems reasonable that both natural and artificial selection have driven preferential gene-segment usage and pairing biases in rainbow trout. In this study, we sequenced the heavy chain variable regions of membrane IgM and IgT from multiple fish and predicted that given the more generalist role of the abundant IgM there would be less pressure to bias V gene segment usage and DJ pairings; rather, natural selection would have favored diversity and the ability to respond to a plethora of pathogens. Conversely, as IgT is substantially less abundant in the serum than IgM and specialized in its function, there would be selective pressure to make the most out of a little, thus favoring biased V segment usage and preferential DJ pairings. In support of our hypotheses, for IgT, over 70% of DJ pairs were biased and over 60% of antibodies were constructed with just two V gene segments. These biases were not prevalent in the IgM repertoire, where only 4% of DJ pairs were biased and no single V gene segment was utilized in more than 10% of antibodies. We found that these biases have profound influences in the richness and evenness of the repertoires, with the IgM repertoire investing more equitably in nearly double the number of VDJ combinations compared with IgT.
Does plant diversity determine the diversity of the rhizosphere microbial community?
Authors: Zverev Aleksei , Kichko Arina , Shapkin Vasiliy , Pinaev Aleksandr , Provorov Nikolay , Andronov Evgeny 
Published: August 2021

AbstractThe rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Close connection and mutual influence in this communication allow to talk about the self-adjusting “plant-rhizosphere community” system, which should be be studied in connection. Diversity estimation is one of the ways of describing both bacterial and plant communities. Based on the literature, there are two assumptions of how the diversity of plant communities related to the diversity of bacterial communities: 1) an increase in the species richness of plants leads to an increase in the number of available micro-niches, and increasing of microbial diversity, 2) an increase in the species richness of plants is accompanied by the predominant development of bacteria from highly productive specific taxa and decreasing in the diversity of microorganisms. Experimental studies show controversial results.We analyzed field sites (rye crop field and two fallow sites), using DNA isolation of both the plant root mass (followed by sequencing of the ITS1 region) and rhizosphere microorganisms (followed by sequencing of the 16s rDNA V4 region). This allowed us to 1) accurately determine the abundance and taxonomic position of plant communities; 2) extract information about both plant and microbial communities from the same sample.There was no correlation between alpha-diversity indices of plants and rhizosphere communities. Alpha-diversity connection should be explored in similar plant communities, such as synusia. We hypothesize, that the significant differences in plant abundances lead to significant changes in exudation profiles, and the loss of diversity connection. The beta-diversity between rhizosphere communities and plant communities is highly correlated, in particular in terms of the abundance of taxa. This can be explained by a potential correlation (as reported in the literature) or by the presence of statistical artifacts.
The Troyer syndrome protein spartin mediates selective autophagy of lipid droplets
Authors: Chung Jeeyun , Park Joongkyu , Lai Zon Weng , Lambert Talley J. , Richards Ruth C. , Farese Robert V. , Walther Tobias C. 
Published: August 2021

AbstractLipid droplets (LDs) are crucial organelles for energy storage and lipid homeostasis. Autophagy of LDs is an important pathway for their catabolism, but the molecular mechanisms mediating targeting of LDs for degradation by selective autophagy (lipophagy) are unknown. Here we identify spartin as a receptor localizing to LDs and interacting with core autophagy machinery, and we show that spartin is required to deliver LDs to lysosomes for triglyceride (TG) mobilization. Mutations in SPART (encoding spartin) lead to Troyer syndrome, a form of hereditary spastic paraplegia. We find that interfering with spartin function leads to LD and TG accumulation in motor cortex neurons of mice. Our findings thus identify spartin as a lipophagy receptor and suggest that impaired LD turnover may contribute to Troyer syndrome development.
A bacterial genome and culture collection of gut microbial in weanling piglet
Authors: Dong Bo , Lin Xiaoqian , Jing Xiaohuan , Hu Tuanyuan , Zhou Jianwei , Chen Jianwei , Xiao Liang , Wang Bo , Chen Zhuang , Liu Jing , Hu Yiyin , Liu Guilin , Liu Shanshan , Liu Junnian , Wei Wenkang , Zou Yuanqiang 
Published: August 2021

ABSTRACTThe microbiota hosted in the pig gastrointestinal tract are important for productivity of livestock. However, the individual species and functional repertoires that make up the pig gut microbiome remain largely undefined. Here we comprehensively investigated the genomes and functions of the piglet gut microbiome using culture-based and metagenomics approaches. A collection included 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) that were clustered to 428 species across 10 phyla was established. Among these clustered species, 333 genomes represent potential new species. Less matches between cultured genomes and MAGs revealed a substantial bias for the acquisition of reference genomes by the two strategies. Glycoside hydrolases was the dominant category of carbohydrate-active enzymes. 445 secondary metabolite biosynthetic genes were predicted from 292 genomes with bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri uncover the biosynthesis of reuterin was strain-specific and the production was experimentally determined. These genomic resources will enable a comprehensive characterization of the microbiome composition and function of pig gut.
Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD
Authors: Larsen Joachim S. , Miller Michael , Oakley Aaron J. , Dixon Nicholas E. , Lewis Peter J. 
Published: August 2021

SUMMARYEfficient control of transcription is essential in all organisms. In bacteria, where DNA replication and transcription occur simultaneously, the replication machinery is at risk of colliding with highly abundant transcription complexes. This can be exacerbated by the fact that transcription complexes pause frequently. When pauses are long-lasting, the stalled complexes must be removed to prevent collisions with either another transcription complex or the replication machinery. HelD is a protein that represents a new class of ATP-dependent motor protein distantly related to helicases. It was first identified in the model Gram-positive bacterium Bacillus subtilis and is involved in removing and recycling stalled transcription complexes. To date, two classes of HelD have been identified: one in the low G+C and the other in the high G+C Gram-positive bacteria. In this work we have undertaken the first comprehensive investigation of the phylogenetic diversity of HelD proteins. We show that genes in certain bacterial classes have been inherited by horizontal gene transfer, many organisms contain multiple expressed isoforms of HelD, some of which are associated with antibiotic resistance, and that there is a third class of HelD protein found in Gram-negative bacteria. Therefore, HelD proteins represent an important new class of transcription factor associated with genome maintenance and antibiotic resistance that are conserved across the Eubacterial kingdom.
Estimating genetic correlation jointly using individual-level and summary-level GWAS data
Authors: Zhang Yiliang , Cheng Youshu , Ye Yixuan , Jiang Wei , Lu Qiongshi , Zhao Hongyu 
Published: August 2021

AbstractWith the increasing accessibility of individual-level data from genome wide association studies, it is now common for researchers to have individual-level data of some traits in one specific population. For some traits, we can only access public released summary-level data due to privacy and safety concerns. The current methods to estimate genetic correlation can only be applied when the input data type of the two traits of interest is either both individual-level or both summary-level. When researchers have access to individual-level data for one trait and summary-level data for the other, they have to transform the individual-level data to summary-level data first and then apply summary data-based methods to estimate the genetic correlation. This procedure is computationally and statistically inefficient and introduces information loss. We introduce GENJI (Genetic correlation EstimatioN Jointly using Individual-level and summary data), a method that can estimate within-population or transethnic genetic correlation based on individual-level data for one trait and summary-level data for another trait. Through extensive simulations and analyses of real data on within-population and transethnic genetic correlation estimation, we show that GENJI produces more reliable and efficient estimation than summary data-based methods. Besides, when individual-level data are available for both traits, GENJI can achieve comparable performance than individual-level data-based methods. Downstream applications of genetic correlation can benefit from more accurate estimates. In particular, we show that more accurate genetic correlation estimation facilitates the predictability of cross-population polygenic risk scores.