bluuebunny/crossref_metadata_2025_split huggingface dataset:
HSC-independent definitive hematopoietic cells persist into adult life
Authors: Kobayashi Michihiro , Wei Haichao , Yamanashi Takashi , Shih David J , Portilho Nathalia Azevedo , Cornelius Samuel , Valiente Noemi , Nishida Chika , Zheng Wenjin J , Kang Joonsoo , Seita Jun , Wu Jia Qian , Yoshimoto Momoko 
Published: December 2021

SummaryThe stem cell theory that all blood cells are derived from hematopoietic stem cell (HSC) is a central dogma in hematology. However, various types of blood cells are already produced from hemogenic endothelial cells (HECs) before the first HSCs appear at embryonic day (E)11 in the mouse embryo. This early blood cell production from HECs, called HSC-independent hematopoiesis, includes primitive and definitive erythromyeloid progenitors that transiently support fetal blood homeostasis until HSC-derived hematopoiesis is established. Lymphoid potential has traditionally been detected in the extra-embryonic yolk sac (YS) and/or embryos before HSC emergence, but the actual presence of lymphoid progenitors at this stage remains unknown. In addition, whether HSCs in the fetal liver are the main source of innate-like B-1a cells has been controversial. Here, using complementary lineage tracing mouse models, we show that HSC-independent multipotent progenitors (MPPs) and HSC-independent adoptive B-lymphoid progenitors persist into adult life. Furthermore, HSCs minimally contribute to the peritoneal B-1a cell pool; most B-1a cells are originated directly from ECs in the YS and embryo and HSC-independent for life. Our discovery of extensive HSC-independent MPP and B-lymphoid progenitors in adults attests to the complex blood developmental dynamics through embryo to adult that underpin the immune system and challenges the paradigm of HSC theory in hematology.
Self-confined expression in theArabidopsisroot stem cell niche
Authors: Mercadal Josep , Betegón-Putze Isabel , Bosch Nadja , Caño-Delgado Ana I. , Ibañes Marta 
Published: December 2021

AbstractStem cell niches are local microenvironments that preserve their unique identity while communicating with adjacent tissues. In the primary root ofArabidopsis thaliana, the stem cell niche comprises the expression of two transcription factors, BRAVO and WOX5, among others. Intriguingly, these proteins confine their own gene expression to the niche, as evidenced in each mutant background. Here we propose through mathematical modeling that BRAVO confines its own expression domain to the stem cell niche by attenuating its WOX5-dependent diffusible activator. This negative feedback drives WOX5 action to be spatially restricted as well. The results show that WOX5 diffusion and sequestration by binding to BRAVO is sufficient to drive realistic confinedBRAVOexpression at the stem cell niche. We propose that attenuation of a diffusible activator can be a general mechanism to confine genetic activity to a small region while at the same time maintain signaling within it and with the surrounding cells.
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Authors: Yang Rui , Das Arnav , Gao Vianne R. , Karbalayghareh Alireza , Noble William S. , Bilmes Jeffrey A. , Leslie Christina S. 
Published: December 2021

AbstractRecent deep learning models that predict the Hi-C contact map from DNA sequence achieve promising accuracy but cannot generalize to new cell types and indeed do not capture cell-type-specific differences among training cell types. We propose Epiphany, a neural network to predict cell-type-specific Hi-C contact maps from five epigenomic tracks that are already available in hundreds of cell types and tissues: DNase I hypersensitive sites and ChIP-seq for CTCF, H3K27ac, H3K27me3, and H3K4me3. Epiphany uses 1D convolutional layers to learn local representations from the input tracks, a bidirectional long short-term memory (Bi-LSTM) layers to capture long term dependencies along the epigenome, as well as a generative adversarial network (GAN) architecture to encourage contact map realism. To improve the usability of predicted contact matrices, we trained and evaluated models using multiple normalization and matrix balancing techniques including KR, ICE, and HiC-DC+ Z-score and observed-over-expected count ratio. Epiphany is trained with a combination of MSE and adversarial (i.a., a GAN) loss to enhance its ability to produce realistic Hi-C contact maps for downstream analysis. Epiphany shows robust performance and generalization to held-out chromosomes within and across cell types and species, and its predicted contact matrices yield accurate TAD and significant interaction calls. At inference time, Epiphany can be used to study the contribution of specific epigenomic peaks to 3D architecture and to predict the structural changes caused by perturbations of epigenomic signals.
A stepwise route to domesticate rice by controlling seed shattering and panicle shape
Authors: Ishikawa Ryo , Castillo Cristina Cobo , Htun Than Myint , Numaguchi Koji , Inoue Kazuya , Oka Yumi , Ogasawara Miki , Sugiyama Shohei , Takama Natsumi , Orn Chhourn , Inoue Chizuru , Nonomura Ken-ichi , Allaby Robin , Fuller Dorian Q , Ishii Takashige 
Published: December 2021

AbstractAsian rice (Oryza sativa L.) is consumed by more than half of the world’s population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (O. rufipogon Griff.) acquired non-seed-shattering behaviour, allowing humans to increase grain yield. Previous studies argued that the sh4 mutation triggered a reduction in seed shattering during rice domestication; but our experiments using wild introgression lines of O. rufipogon show that the domesticated sh4 allele alone is insufficient for shattering loss. Here, we identified the interaction between three key mutations associated with the interruption of abscission layer formation and panicle architecture that were causal in early rice domestication. An interruption of abscission layer formation requires both sh4 and qSH3 mutations, presenting an apparent barrier to the selection of shattering loss. We identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we demonstrated that seed shattering alone did not significantly impact yield; rather yield increases were observed with closed panicle formation controlled by SPR3, which is further augmented by the integration of sh4 and qSH3 alleles. Complementary manipulation of seed shattering and panicle shape result in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which led to the loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as those in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 alone is insufficient and other genes, such as qSH3, are required to cause abscission layer disruption. The evolution of non-seed-shattering therefore required multiple mutations. Furthermore, shattering loss in genetic backgrounds of wild rice does not correspondingly increase yields. We have identified an interaction in which a second trait, closed panicle formation controlled by SPR3, that both increases the yield and facilitates recruitment of sh4 and qSH3, which synergistically augment yield, leading to a stepwise model for rice domestication.
An ecological perspective on microbial genes of unknown function in soil
Authors: Holland-Moritz Hannah , Vanni Chiara , Fernandez-Guerra Antonio , Bissett Andrew , Fierer Noah 
Published: December 2021

AbstractGenes that remain hypothetical, uncharacterized, and unannotated comprise a substantial portion of metagenomic datasets and are likely to be particularly prevalent in soils where poorly characterized taxa predominate. Documenting the prevalence, distribution, and potential roles of these genes of unknown function is an important first step to understanding their functional contributions in soil communities. We identified genes of unknown function from 50 soil metagenomes and analyzed their environmental distributions and ecological associations. We found that genes of unknown function are prevalent in soils, particularly fine-textured, higher pH soils that harbor greater abundances of Crenarchaeota, Gemmatimonadota, Nitrospirota, and Methylomirabilota. We identified 43 dominant (abundant and ubiquitous) gene clusters of unknown function and determined their associations with soil microbial phyla and other “known” genes. We found that these dominant unknown genes were commonly associated with microbial phyla that are relatively uncharacterized, with the majority of these dominant unknown genes associated with mobile genetic elements. This work demonstrates a strategy for investigating genes of unknown function in soils, emphasizes the biological insights that can be learned by adopting this strategy, and highlights specific hypotheses that warrant further investigation regarding the functional roles of abundant and ubiquitous genes of unknown function in soil metagenomes.
Mitochondrial antiviral-signalling protein is a client of the BAG6 protein quality control complex
Authors: Roboti Peristera , Lawless Craig , High Stephen 
Published: December 2021

ABSTRACTThe heterotrimeric BAG6 complex coordinates the direct handover of newly synthesised tail-anchored (TA) membrane proteins from an SGTA-bound preloading complex to the endoplasmic reticulum (ER) delivery component TRC40. In contrast, defective precursors, including aberrant TA proteins, form a stable complex with this cytosolic protein quality control factor, enabling such clients to be either productively re-routed or selectively degraded. We identify the mitochondrial TA protein MAVS (mitochondrial antiviral-signalling protein) as an endogenous client of both SGTA and the BAG6 complex. Our data suggest that the BAG6 complex binds to a cytosolic pool of MAVS before its misinsertion into the ER membrane, from where it can subsequently be removed via ATP13A1-mediated dislocation. This BAG6- associated fraction of MAVS is dynamic and responds to the activation of an innate immune response, suggesting that BAG6 may modulate the pool of MAVS that is available for coordinating the cellular response to viral infection.SUMMARY STATEMENTMitochondrial antiviral-signalling (MAVS) protein is a favoured client of the cytosolic BAG6 complex. We discuss how this dynamic interaction may modulate MAVS biogenesis at signalling membranes.
Specific plasticity loci and their synergism mediate operant conditioning
Authors: Momohara Yuto , Neveu Curtis L. , Chen Hsin-Mei , Baxter Douglas A. , Byrne John H. 
Published: December 2021

AbstractDespite numerous studies examining the mechanisms of operant conditioning (OC), the diversity of plasticity loci and their synergism have not been examined sufficiently. In the well-characterized feeding neural circuit of Aplysia, appetitive OC increases neuronal excitability and electrical coupling among several neurons. Here we found OC decreased the intrinsic excitability of B4 and the strength of its inhibitory connection to a key decision-making neuron, B51. The OC-induced changes were specific without affecting the B4-to-B8 inhibitory connection or excitability of another neuron critical for feeding behavior, B8. A conductance-based circuit model indicated certain sites of plasticity mediated the OC phenotype more effectively and that plasticity loci acted synergistically. This synergy was specific in that only certain combinations of loci synergistically enhanced feeding. Taken together, these results suggest modifications of diverse loci work synergistically to mediate OC.Significance StatementThe diversity and synergism of plasticity loci mediating operant conditioning (OC) is poorly understood. Here we found that OC decreased the intrinsic excitability of a critical neuron mediating Aplysia feeding behavior and specifically reduced the strength of one of its inhibitory connections to a key decision-making neuron. A conductance-based computational model indicated that the known plasticity loci showed a surprising level of synergism to mediate the behavioral changes associated with OC. These results highlight the importance of understanding the diversity, specificity and synergy among different types of plasticity that encode memory. Also, because OC in Aplysia is mediated by dopamine (DA), the present study provides insights into specific and synergistic mechanisms of DA-mediated reinforcement of behaviors.
Microbial ecology of sulfur biogeochemical cycling at a mesothermic hot spring atop Northern Himalayas, India
Authors: Nagar Shekhar , Talwar Chandni , Motelica-Heino Mikael , Richnow Hans-Hermann , Shakarad Mallikarjun , Lal Rup , Negi Ram Krishan 
Published: December 2021

AbstractGraphical AbstractSulfur Related Prokaryotes (SRP) residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expand the phylogenetic breadth of these extraordinary sulfur metabolizing microorganisms, as well a their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on sulfur cycling genes through metagenomic analysis of sulfur (S) contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such asPseudomonas,Thioalkalivibrio,DesulfovibrioandDesulfobulbaceae(Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment and water were assigned toProteobacteriaas reflected from the RPKs (reads per kilobase) categorized into translation and ribosomal structure and biogenesis. Analysis of sequence similarity showed conserved pattern of bothdsrABgenes (n=178) retrieved from all metagenomes while other sulfur disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of sulfur oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrABsuggests for it to be an important adaptation for microbial fitness at this site. Here, we confirm that (i) SRBs belongs toδ-Proteobacteriaoccurring independent LGT ofdsrgenes to different and few novel lineages (ii) also, the oxidative and reductivedsrevolutionary time scale phylogeny, proved that the earliest (not first)dsrABproteins belong to anaerobicThiobacilluswith other (rdsr) oxidizers. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species ofDesulfovibrio(TM score= 0.86; 0.98; 0.96) andArchaeoglobus fulgidus(TM score= 0.97; 0.98). We proposed that the genetic repertoire might provide the basis of studying time scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling and the complementary genes could be implemented in biotechnology and bioremediation applications.
Aboveground impacts of a belowground invader: how invasive earthworms alter aboveground arthropod communities in a northern North American forest
Authors: Jochum Malte , Thouvenot Lise , Ferlian Olga , Zeiss Romy , Klarner Bernhard , Pruschitzki Ulrich , Johnson Edward A. , Eisenhauer Nico 
Published: December 2021

AbstractDeclining arthropod communities have recently gained a lot of attention with climate and land-use change among the most-frequently discussed drivers. Here, we focus on a seemingly underrepresented driver of arthropod-community decline: biological invasions. For ∼12,000 years, earthworms have been absent from wide parts of northern North America, but they have been re-introduced with dramatic consequences. Most studies investigating earthworm-invasion impacts focus on the belowground world, resulting in limited knowledge on aboveground-community changes. We present observational data on earthworm, plant, and aboveground-arthropod communities in 60 plots, distributed across areas with increasing invasion status (low, medium, high) in a Canadian forest. We analyzed how earthworm-invasion status and biomass impact aboveground arthropod community abundance, biomass, and species richness, and how earthworm impacts cascade across trophic levels. We sampled ∼13,000 arthropods, dominated by Hemiptera, Diptera, Araneae, Thysanoptera, and Hymenoptera. Total arthropod abundance, biomass, and species richness declined significantly from areas of low to those with high invasion status with reductions of 61, 27, and 18%, respectively. Structural Equation Models unraveled that earthworms directly and indirectly impact arthropods across trophic levels. We show that earthworm invasion can alter aboveground multitrophic arthropod communities and suggest that belowground invasions can be important drivers of aboveground-arthropod decline.
CV-containing vesicle budding from chloroplast inner envelope membrane is mediated by clathrin but inhibited by GAPC
Authors: Pan Ting , Liu Yangxuan , Ling Chengcheng , Tang Yuying , Tang Wei , Liu Yongsheng , Guo Liang , Kim Chanhong , Fang Jun , Lin Honghui , Blumwald Eduardo , Wang Songhu 
Published: December 2021

AbstractClathrin-mediated vesicular formation and trafficking are highly conserved in eukaryotic cells and are responsible for molecular cargo transport and signal transduction among organelles. It remains largely unknown whether clathrin-coated vesicles can be generated from chloroplasts. CHLOROPLAST VESICULATION (CV)-containing vesicles (CVVs) generate from chloroplasts and mediate chloroplast degradation under abiotic stress. In this study, we showed that CV interacted with the clathrin heavy chain (CHC) and induced vesicle budding from the chloroplast inner envelope membrane. Defects on CHC2 and the dynamin-encoding DRP1A gene affected CVV budding and releasing from chloroplast. CHC2 is also required for CV-induced chloroplast degradation and hypersensitivity to water stress. Moreover, GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPC) interacts with CV and impairs the CV-CHC2 interaction. GAPC1 overexpression inhibited CV-mediated chloroplast degradation and hypersensitivity to water stress. CV silencing alleviated the hypersensitivity of gapc1gapc2 plant to water stress. Together, our work revealed a pathway of clathrin-assisted CVV budding from the chloroplast inner envelope membrane, which mediated the stress-induced chloroplast degradation and stress response.
NamZ1 and NamZ2 from the oral pathogen Tannerella forsythia are peptidoglycan processing exo-β-N-acetylmuramidases with distinct substrate specificity
Authors: Borisova Marina , Balbuchta Katja , Lovering Andrew , Titz Alexander , Mayer Christoph 
Published: December 2021

ABSTRACTThe Gram-negative periodontal pathogen Tannerella forsythia is inherently auxotrophic for N-acetylmuramic acid (MurNAc), which is an essential carbohydrate constituent of the peptidoglycan (PGN) of the bacterial cell wall. Thus, to build up its cell wall, T. forsythia strictly depends on the salvage of exogenous MurNAc or sources of MurNAc, such as polymeric or fragmentary PGN, derived from cohabiting bacteria within the oral microbiome. In our effort to elucidate how T. forsythia satisfies its demand for MurNAc, we recognized that the organism possesses three putative orthologs of the exo-β-N-acetylmuramidase BsNamZ from Bacillus subtilis, which cleaves non-reducing end, terminal MurNAc entities from the artificial substrate pNP-MurNAc and the naturally-occurring disaccharide substrate MurNAc-β-1,4-N-acetylglucosamine (GlcNAc). TfNamZ1 and TfNamZ2 were successfully purified as soluble, pure recombinant His6-fusions and characterized as exo-lytic β-N-acetylmuramidases with distinct substrate specificities. The activity of TfNamZ1 was considerably lower compared to TfNamZ2 and BsNamZ, in the cleavage of pNP-MurNAc and MurNAc-GlcNAc. When peptide-free PGN glycans were used as substrates, we revealed striking differences in the specificity and mode of action of these enzymes, as analyzed by mass spectrometry. TfNamZ1, but not TfNamZ2 or BsNamZ, released GlcNAc-MurNAc disaccharides from these glycans. In addition, glucosamine (GlcN)-MurNAc disaccharides were generated when partially N-deacetylated PGN glycans from B. subtilis 168 were applied. This characterizes TfNamZ1 as a unique disaccharide-forming exo-lytic β-N-acetylmuramidase (exo-disaccharidase), and, TfNamZ2 and BsNamZ as sole MurNAc monosaccharide-lytic exo-β-N-acetylmuramidases.IMPORTANCETwo exo-β-N-acetylmuramidases from T. forsythia belonging to glycosidase family GH171 (www.cazy.org) were shown to differ in their activities, thus revealing a functional diversity within this family: NamZ1 releases disaccharides (GlcNAc-MurNAc/GlcN-MurNAc) from the non-reducing ends of PGN glycans, whereas NamZ2 releases terminal MurNAc monosaccharides. This work provides a better understanding of how T. forsythia may acquire the essential growth factor MurNAc by the salvage of PGN from cohabiting bacteria in the oral microbiome, which may pave avenues for the development of anti-periodontal drugs. On a broad scale, our study indicates that the utilization of PGN as a nutrient source, involving exo-lytic N-acetylmuramidases with different modes of action, appears to be a general feature of bacteria, particularly among the phylum Bacteroidetes.
Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cells
Authors: Cheng Huaitao , Pui Han-pin , Lentini Antonio , Kolbeinsdóttir Solrún , Andrews Nathanael , Pei Yu , Reinius Björn , Deng Qiaolin , Enge Martin 
Published: December 2021

AbstractJoint single-cell measurements of gene expression and DNA regulatory element activity holds great promise as a tool to understand transcriptional regulation. Towards this goal we have developed Smart3-ATAC, a highly sensitive method which allows joint mRNA and chromatin accessibility analysis genome wide in single cells. With Smart3-ATAC, we are able to obtain the highest possible quality measurements per cell. The method combines transcriptomic profiling based on the highly sensitive Smart-seq3 protocol on cytosolic mRNA, with a novel low-loss single-cell ATAC (scATAC) protocol to measure chromatin accessibility. Compared to current droplet multiome methods, the yield of both the scATAC protocol and mRNA-seq protocol is markedly higher.