bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic analysis betweenLeonurus japonicusandLeonurus sibiricus
Authors: Yang Dan-Jie , Yan Meng-Xiao , Li Peng , Liu Pan , Gao Yun , Jiang Yan , He Ze-Kun , Kong Yu , Zhong Xin , Wu Sheng , Yang Jun , Wang Hong-Xia , Huang Yan-Bo , Wang Le , Chen Xiao-Ya , Hu Yong-Hong , Zhao Qing , Xu Ping 
Published: November 2022

AbstractLeonurus japonicusHoutt. is an important medicinal plant in East Asia and is now widely recognized for its role in treating cerebral apoplexy and lowering blood lipids. Here, we report two sets of chromosome-level genome sequences for leonurine-producingLeonurus japonicusand for its closely related species leonurine-freeLeonurus sibiricus, where 99.78% of 518.19 Mb ofL. japonicuswas assembled into ten pseudochromosomes with a contig N50 of 17.62 Mb and 99.33% of 472.29 Mb ofL. sibiricuswas assembled into nine pseudochromosomes with a contig N50 of 13.29 MB. The reference genomes ofLeonuruswill accelerate the decoding of novel bioactive molecules in medicinal plants, especially in the Lamiaceae family.
Retention of visuo-proprioceptive recalibration in estimating hand position
Authors: Wali Manasi , Lee-Miller Trevor , Babu Reshma , Block Hannah J. 
Published: November 2022

AbstractThe brain estimates hand position using visual and proprioceptive cues, which are combined to give an integrated multisensory estimate. Spatial mismatches between cues elicit recalibration, a compensatory process where each unimodal estimate is shifted closer to the other. It is unclear how well visuo-proprioceptive recalibration is retained after mismatch exposure. Here we asked whether direct vision and/or active movement of the hand can undo visuo-proprioceptive recalibration, and whether recalibration is still evident 24 hours later. 75 participants performed two blocks of visual, proprioceptive, and combination trials, with no feedback or direct vision of the hand. In Block 1, a 70 mm visuo-proprioceptive mismatch was gradually imposed, and recalibration assessed. Block 2 tested retention. Between blocks, Groups 1-4 rested or made active movements with their directly visible or unseen hand for several minutes. Group 5 had a 24-hour gap between blocks. All five groups recalibrated both vision and proprioception in Block 1, and Groups 1-4 retained most of this recalibration in Block 2. Interestingly, Group 5 showed an offline increase in proprioceptive recalibration, but retained little visual recalibration. Our results suggested that visuo-proprioceptive recalibration is robustly retained in the short-term. In the longer term, contextual factors may affect retention.
Whole genome sequencing reveals fine-scale climate associated adaptive divergence near the range limits of a temperate reef fish
Authors: Nugent Cameron M. , Kess Tony , Brachmann Matthew K. , Langille Barbara L. , Duffy Steven J. , Lehnert Sarah J. , Wringe Brendan F. , Bentzen Paul , Bradbury Ian R. 
Published: November 2022

ABSTRACTAdaptation to ocean climate is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hindering management and conservation action. Cunner (Tautogolabrus adspersus), is a temperate reef fish that displays both pelagic early life history stages and strong site-associated homing as adults; the species is also presently of interest for use as a cleaner fish in salmonid aquaculture in Atlantic Canada. Here we produce a chromosome-level genome assembly for cunner and characterize spatial population structure throughout Atlantic Canada using whole genome resequencing. The genome assembly spanned 0.72 Gbp and resolved 24 chromosomes; whole genome resequencing of 803 individuals from 20 locations spanning from Newfoundland to New Jersey identified approximately 11 million genetic variants. Principal component analysis revealed four distinct regional groups in Atlantic Canada, including three near the range edge in Newfoundland. PairwiseFSTand selection scans revealed consistent signals of differentiation and selection at discrete genomic regions including adjacent peaks on chromosome 10 recurring across multiple pairwise comparisons (i.e.,FST0.5-0.75). Redundancy analysis suggested significant association of environmental variables related to benthic temperature and oxygen range with genomic structure, again highlighting the previously identified region on chromosome 10. Our results suggest that climate associated adaptation in this temperate reef fish drives regional diversity despite high early life history dispersal potential.
Population-level integration of single-cell datasets enables multi-scale analysis across samples
Authors: De Donno Carlo , Hediyeh-Zadeh Soroor , Wagenstetter Marco , Moinfar Amir Ali , Zappia Luke , Lotfollahi Mohammad , Theis Fabian J. 
Published: November 2022

AbstractThe increasing generation of population-level single-cell atlases with hundreds or thousands of samples has the potential to link demographic and technical metadata with high-resolution cellular and tissue data in homeostasis and disease. Constructing such comprehensive references requires large-scale integration of heterogeneous cohorts with varying metadata capturing demographic and technical information. Here, we presentsingle-cell population level integration (scPoli), a semi-supervised conditional deep generative model for data integration, label transfer and query-to-reference mapping. Unlike other models, scPoli learns both sample and cell representations, is aware of cell-type annotations and can integrate and annotate newly generated query datasets while providing an uncertainty mechanism to identify unknown populations. We extensively evaluated the method and showed its advantages over existing approaches. We applied scPoli to two population-level atlases of lung and peripheral blood mononuclear cells (PBMCs), the latter consisting of roughly 8 million cells across 2,375 samples. We demonstrate that scPoli allows atlas-level integration and automatic reference mapping with label transfer. It can explain sample-level biological and technical variations such as disease, anatomical location and assay by means of its novel sample embeddings. We use these embeddings to explore sample-level metadata, enable automatic sample classification and guide a data integration workflow. scPoli also enables simultaneous sample-level and cell-level analysis of gene expression patterns, revealing genes associated with batch effects and the main axes of between-sample variation. We envision scPoli becoming an important tool for population-level single-cell data integration facilitating atlas use but also interpretation by means of multi-scale analyses.
The human sperm head spins with a conserved direction during swimming in 3D
Authors: Corkidi G. , Montoya F. , González-Cota A.L. , Hernández-Herrera P. , Bruce N.C. , Bloomfield-Gadêlha H. , Darszon A. 
Published: November 2022

AbstractIn human sperm, head spinning is essential for sperm swimming and critical for fertilization. Measurement of head spinning has not been straightforward due to its symmetric head morphology, its translucent nature and fast 3D motion driven by its helical flagellum movement. Microscope image acquisition has been mostly restricted to 2D single focal plane images limited to head position tracing, in absence of head orientation and rotation in 3D. To date, human sperm spinning has been reported to be mono or bidirectional, and even intermittently changing direction. This variety in head spinning direction, however, appears to contradict observations of conserved helical beating of the human sperm flagellum. Here, we reconcile these observations by directly measuring the head spinning movement of freely swimming human sperm with multi-plane 4D microscopy. We show that 2D microscopy is unable to distinguish the spinning direction in human sperm. We evaluated the head spinning of 409 spermatozoa in four different conditions: in non-capacitating and capacitating solutions, for both aqueous and viscous media. All spinning spermatozoa, regardless of the experimental conditions spun counterclockwise (CCW) as seen from head-to-tail. Head spinning was suppressed in 57% of spermatozoa swimming in non-capacitating viscous media, though, interestingly, they recovered the CCW spinning after incubation in capacitating conditions within the same viscous medium. Our observations show that the spinning direction in human sperm is conserved, even when recovered from non-spin, indicating the presence of a robust and persistent helical driving mechanism powering the human sperm flagellum, thus of critical importance in future sperm motility assessments, human reproduction research and microorganism self-organised swimming.
A macrophage subpopulation promotes airineme-mediated intercellular communication in a Matrix Metalloproteinase-9 dependent manner
Authors: Bowman Raquel Lynn , Wang Daoqin , Eom Dae Seok 
Published: November 2022

AbstractTissue-resident macrophages are highly heterogenous and perform various dedicated functions depending on their locations. In particular, skin resident macrophages have intriguing roles in long-distance intercellular signaling by mediating cellular protrusions called ‘airinemes’ in zebrafish. During pigment pattern formation, macrophages relay signaling molecules containing ‘airineme vesicles’ from one pigment cell to another. Without macrophages, airineme-mediated signaling is abolished, disrupting pigment pattern formation. It remains unknown, however, if the same macrophage population controls both these signaling roles and typical immune functions or if a separate macrophage subpopulation functions in intercellular communication. In this study, with high-resolution confocal live-imaging and cell type-specific genetic ablation approachesin vivo, we have identified a macrophage subpopulation responsible for airineme-mediated signaling. These cells appear distinct from conventional skin resident macrophages by their amoeboid morphology and faster/expansive migratory behaviors. Instead, we show that they resemble ectoderm-derived macrophages termed metaphocytes. Metaphocyte ablation dramatically reduces airineme extension and signaling. In addition, these amoeboid/metaphocytes require high levels of MMP9 expression for their migration and airineme-mediated signaling. These results reveal a novel macrophage subpopulation with specialized functions in airineme-mediated signaling, which may play roles in many other aspects of intercellular communication.
Development and Evolution of Drosophila Chromatin Landscape in a 3D genome context
Authors: Ali Mujahid , Younas Lubna , Liu Jing , Zhou Qi 
Published: November 2022

AbstractChromatin states of genes and transposable elements (TEs) dictated by combinations of various histone modifications comprise key information for understanding the mechanisms of genome organization and regulation. However, little is known about the principles of their dynamic changes during development and evolution in a three-dimensional genome context. To address this, we studyDrosophila pseudoobscura, a Drosophila model species that diverged fromD. melanogasterabout 25 million years ago. We collected 71 epigenomic datasets targeting 11 histone modification marks and 4 Hi-C datasets, and projected 15 chromatin states across four different developmental stages and two adult tissues. We estimate that before zygotic genome activation, 41% of the genome has already been deposited with histone modifications, while 20% of the rest genome switches from a ‘null’ state to an active/inactive chromatin state after the zygotic genome activation. Over two thirds of the genomic region exhibit at least one transition between different chromatin states during development. And such transitions oncis-regulatory regions are associated with tissue- or stage-specific formation of chromatin loops or topologically associated domain borders (TABs), as well as specific activation of gene expression. We further demonstrate that while evolutionarily young TEs are preferentially targeted by silencing histone modifications, old TEs are more frequently domesticated as TABs or specific enhancers that further contribute to the genome organization or local gene regulation. Interestingly, this trend is reversed on the newly evolved X chromosome inD. pseudoobscura, due to the acquisition of dosage compensation mechanism. Overall we characterize the developmental and evolutionary dynamics of Drosophila epigenomic states, and highlight the roles of certain TEs of different evolutionary ages in genome organization and regulation.
Soft and stretchable organic bioelectronics for continuous intra-operative neurophysiological monitoring during microsurgery
Authors: Zhou Wenjianlong , Jiang Yuanwen , Xu Qin , Chen Liangpeng , Qiao Hui , Wang Yixuan , Lai Jiancheng , Zhong Donglai , Zhang Yuan , Li Weining , Du Yanru , Wang Xuecheng , Lei Jiaxin , Dong Gehong , Guan Xiudong , Ma Shunchang , Kang Peng , Yuan Linhao , Zhang Milin , Tok Jeffrey B.-H. , Li Deling , Bao Zhenan , Jia Wang 
Published: November 2022

AbstractContinuous intra-operative neurophysiological monitoring (CINM) that provides precise mapping of neural anatomy through the entire microsurgery process is essential to preserve the structural and functional integrity of the nerve. However, bulky and rigid electrodes used currently in clinics are usually unable to reliably maintain continuous and stable contacts with the vulnerable and complex nerve networks, thus often resulting in detrimental post-operative complications, such as hemiplegia and sensory disturbances. Here, we describe a biomechanically compatible, suture-free, and individually reconfigurable CINM based on soft and stretchable organic electronic materials. Due to both low impedance and modulus of our conducting polymer electrodes, we achievedfor the first timecontinuous recording of near-field action potential with high signal-to-noise ratio and minimal invasiveness during microsurgeries. Utilizing this unprecedented CINM modality, in conjunction with localized neurostimulation, we further demonstrated our approach in enabling optimal post-operative prognosis in preclinical animal models by preserving normal neural functions after a variety of tumor resection surgeries.
Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads
Authors: Homberger Christina , Hayward Regan J , Barquist Lars , Vogel Jörg 
Published: November 2022

ABSTRACTBulk RNA-sequencing technologies have provided invaluable insights into host and bacterial gene expression and associated regulatory networks. Nevertheless, the majority of these approaches report average expression across cell populations, hiding the true underlying expression patterns that are often heterogeneous in nature. Due to technical advances, single-cell transcriptomics in bacteria has recently become reality, allowing exploration of these heterogeneous populations, which are often the result of environmental changes and stressors. In this work, we have improved our previously published bacterial single-cell RNA-sequencing protocol that is based on MATQ-seq, achieving a higher throughput through the integration of automation. We also selected a more efficient reverse transcriptase, which led to reduced cell loss and higher workflow robustness. Moreover, we successfully implemented a Cas9-based ribosomal RNA depletion protocol into the MATQ-seq workflow. Applying our improved protocol on a large set of singleSalmonellacells sampled over growth revealed improved gene coverage and a higher gene detection limit compared to our original protocol and allowed us to detect the expression of small regulatory RNAs, such as GcvB or CsrB at a single-cell level. In addition, we confirmed previously described phenotypic heterogeneity inSalmonellain regards to expression of pathogenicity-associated genes. Overall, the low percentage of cell loss and high gene detection limit makes the improved MATQ-seq protocol particularly well suited for studies with limited input material, such as analysis of small bacterial populations in host niches or intracellular bacteria.IMPORTANCEGene expression heterogeneity among isogenic bacteria is linked to clinically-relevant scenarios, like biofilm formation and antibiotic tolerance. The recent development of bacterial single-cell RNA-sequencing (scRNA-seq) enables the study of cell-to-cell variability in bacterial populations and the mechanisms underlying these phenomena. Here, we report a scRNA-seq workflow based on MATQ-seq with increased robustness, reduced cell loss, improved transcript capture rate, and gene coverage. Use of a more efficient reverse transcriptase and the integration of a ribosomal RNA depletion step, which can be adapted to other bacterial single-cell workflows, was instrumental for these improvements. Applying the protocol to the foodborne-pathogenSalmonella, we confirmed transcriptional heterogeneity across and within different growth phases and demonstrated that our workflow captures small regulatory RNAs on the single-cell level. Due to low cell loss and high transcript capture rates, this protocol is uniquely suited for experimental settings in which the starting material is limited, such as infected tissues.
A conserved complex of microneme proteins mediates rhoptry discharge inToxoplasma
Authors: Sidik Saima M. , Valleau Dylan , Acevedo-Sánchez Yamilex , Godoy Luiz C. , Pasaje Charisse Flerida A. , Huynh My-Hang , Carruthers Vern B. , Niles Jacquin C. , Lourido Sebastian 
Published: November 2022

ABSTRACTApicomplexan parasites discharge specialized organelles called rhoptries upon host cell contact to mediate invasion. The events that drive rhoptry discharge are poorly understood, yet essential to sustain the apicomplexan parasitic life cycle. Rhoptry discharge appears to depend on proteins secreted from another set of organelles called micronemes, which inToxoplasma gondiiincludes MIC8 and the microneme-associated CRMP complex. Here, we examine the function of the microneme protein CLAMP, uncovering its essential role in rhoptry discharge. CLAMP forms a distinct complex with two other microneme proteins, the invasion-associated SPATR, and a previously uncharacterized protein we name CLAMP-linked invasion protein (CLIP). CLAMP-deficiency does not impact parasite adhesion or microneme protein secretion; however, knockdown of any member of the CLAMP complex affects rhoptry discharge. Phylogenetic analysis suggests orthologs of the essential complex components, CLAMP and CLIP, are ubiquitous across apicomplexans. Nevertheless, SPATR, which appears to act as an accessory factor inToxoplasma, is essential duringPlasmodium falciparumblood stages. Our results reveal a new protein complex that mediates rhoptry discharge following host-cell contact.
Theory on the rate equations of Michaelis-Menten type enzyme kinetics with competitive inhibition
Authors: Murugan R. 
Published: November 2022

AbstractWe derive approximate expressions under various conditions of validity over both pre- and post-steady state regimes of the velocity-substrate-inhibitor spaces of the Michaelis-Menten enzyme kinetic schemes with fully and partial competitive inhibition. Our refinement over the currently available standard quasi steady state approximations (sQSSA) seems to be valid over wide range of enzyme to substrate and enzyme to inhibitor ratios. Further, we show that under certain conditions the enzyme-inhibitor-substrate system can exhibit temporally well-separated two different steady states with respect to both enzyme-substrate and enzyme-inhibitor complexes. We define the ratiosfS=vmax⁄(KMS+e0) andfI=umax⁄(KMI+e0) as the acceleration factors with respect to the catalytic conversion of substrate and inhibitor into their respective products. HereKMSandKMIare the Michaelis-Menten parameters associated with the binding of substrate and inhibitor with the enzyme,vmaxandumaxare the respective maximum reaction velocities and e0, s0, and i0are total enzyme, substrate and inhibitor levels. When (fS⁄fI) < 1, then enzyme-substrate complex will show multiple steady states subsequently reaches the full-fledged steady state only after the depletion of enzyme-inhibitor complex. When (fS⁄fI) > 1, then the enzyme-inhibitor complex will show multiple steady states and subsequently reaches the full-fledged steady state only after the depletion of enzyme-substrate complex. This complex behavior exclusively when (fS⁄fI) ≠ 1 is the root cause of large amount of error in the estimation of various kinetic parameters both in the cases of fully and partial competitive inhibition schemes using the sQSSA methods. Remarkably, we show that our refined expressions for the reaction velocities over enzyme-substrate-inhibitor space can control this error more significantly than the currently available sQSSA velocity expressions.
An updated genome-scale model forXylella fastidiosasubsp.paucaDe Donno
Authors: Oliveira Alexandre , Cunha Emanuel , Silva Miguel , Faria Cristiana , Dias Oscar 
Published: November 2022

AbstractXylella fastidiosais a gram-negative phytopathogenic bacterium that caused a significant economic impact around the world. In the last decade, genome-scale metabolic models have become important systems biology tools for studying the metabolic behaviour of different pathogens and driving the discovery of novel drug targets. This work is a second iteration of the iMS508 model forX. fastidiosasubsp.paucaDe Donno. The model comprises 1138 reactions, 1234 metabolites, and 509 genes.in silicovalidation of the metabolic model was achieved through the comparison of simulations with available experimental data. Aerobic metabolism was simulated properly and fastidian gum production rates predicted accurately.
A dark matter insakebrewing: Origin of microbes producing aKimoto-style fermentation starter
Authors: Ito Kohei , Niwa Ryo , Kobayashi Ken , Nakagawa Tomoyuki , Hoshino Genki , Tsuchida Yuji 
Published: November 2022

AbstractInKimoto-style fermentation, a fermentation starter is produced before the primary brewing process to stabilize fermentation. Nitrate-reducing bacteria, mainly derived from brewing water, produce nitrite, and lactic acid bacteria such asLeuconostoccan proliferate because of their tolerance towards low temperature and their low nutritional requirements. Later,Lactobacillusbecomes the dominant genus, leading to weakly acidic conditions that contribute to control yeasts and undesired bacterial contaminants. However, the sources of these microorganisms that play a pivotal role inSakebrewing have not yet been revealed. Thus, comprehensive elucidation of the microbiome is necessary. In this study, we performed 16S rRNA amplicon sequencing analysis after sampling from floor, equipment surfaces, and raw materials for making fermentation starters, includingkoji, and water inTsuchida Sakebrewery, Gunma, Japan. Amplicon sequence variants (ASVs) between the external environments and the fermentation starter were compared, and it was verified that the microorganisms in the external environments, such as built environments, equipment surfaces, and raw materials in the sake brewery, were introduced into the fermentation starter. Furthermore, various adventitious microbes present in the fermentation starter of early days and from the external environments were detected in a nonnegligible proportion in the starter, which may impact the taste and flavor. These findings illuminate the uncharacterized microbial dark matter of sake brewing, the sources of microbes inKimoto-style fermentation.