bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field
Authors: Han Xu , Li Yingbin , Li Yuhui , Du Xiaofang , Li Bing , Li Qi , Bezemer T. Martijn 
Published: August 2021

AbstractThe importance of soil inoculation to engineer soil microbiomes and ultimately entire ecosystems is becoming widely acknowledged. Inoculation with soil from different ecosystems can induce directional changes in soil and plant communities and promote the restoration of degraded ecosystems. However, it is unknown how such inoculations influence the soil microbiome, how much inoculum is needed, and whether inocula collected from similar ecosystems will steer the microbiome in different directions. We conducted a three-year soil inoculation field experiment at a degraded grassland and used two different soil inocula both from grasslands with three inoculation rates. Our results show that inoculation with soil that originates from different donor grasslands steers the soil microbiome as well as the plant communities at the inoculated site which was a degraded grassland into different directions and that these effects were stronger with increasing amount of soil used to inoculate. Inoculation with upland meadow soil introduced more keystone genera and resulted in more complex biotic networks in the soil than inoculation with meadow steppe soil. Our experiment highlights that soil inoculation can steer soil microbiomes in the field and that the direction and speed of development depend on the origin and the amount of soil inoculum used.
A multiscale spatiotemporal model including a switch from aerobic to anaerobic metabolism reproduces succession in the early infant gut microbiota
Authors: Versluis David M. , Schoemaker Ruud , Looijesteijn Ellen , Muysken Daniël , Jeurink Prescilla V. , Paques Marcel , Geurts Jan M. W. , Merks Roeland M. H. 
Published: August 2021

ABSTRACTThe human intestinal microbiota starts to form immediately after birth, and is important for the health of the host. During the first days facultatively anaerobic bacterial species generally dominate, such as Enterobacteriaceae. These are succeeded by strictly anaerobic species, particularly Bifidobacterium species. An early transition to Bifidobacterium species is associated with health benefits: for example, Bifidobacterium species repress growth of pathogenic competitors and modulate the immune response. Succession to Bifidobacterium is thought to be due to consumption of intracolonic oxygen present in newborns by facultative anaerobes, including Enterobacteriaceae. To study if oxygen depletion suffices for the transition to Bifidobacterium species, here we introduce a multiscale mathematical model that considers metabolism, spatial bacterial population dynamics and cross-feeding. Using publicly available metabolic network data from the AGORA collection, the model simulates ab initio the competition of strictly and facultatively anaerobic species in a gut-like environment under the influence of lactose and oxygen. The model predicts that individual differences in intracolonic oxygen in newborn infants can explain the observed individual variation in succession to anaerobic species, in particular Bifidobacterium species. Bifidobacterium species become dominant in the model by using the bifid shunt, which allows Bifidobacterium to switch to sub-optimal yield metabolism with fast growth at high lactose concentrations as predicted here using flux-balance analysis. The computational model thus allows us to test the internal plausibility of hypotheses for bacterial colonization and succession in the infant colon.IMPORTANCEThe composition of the infant microbiota has a great impact on infant health, but its controlling factors are still incompletely understood. The frequently dominant anaerobic Bifidobacterium species benefit health, e.g., because they can keep harmful competitors under control and modulate the intestinal immune response. Controlling factors could include nutritional composition and intestinal mucus composition, as well as environmental factors, such as antibiotics. We introduce a modeling framework of a metabolically realistic intestinal microbial ecology in which hypothetical scenarios can be tested and compared. We present simulations that suggest that greater levels of intra-intestinal oxygenation more strongly delay the dominance of Bifidobacterium species, explaining the observed variety of microbial composition and demonstrating the use of the model for hypothesis generation. The framework allows us to test a variety of controlling factors, including intestinal mixing and transit time. Future versions will also include detailed modeling of oligosaccharide and mucin metabolism.
Defining the components of the miRNA156-SPL-miR172 aging pathway in pea and their expression relative to changes in leaf morphology
Authors: Vander Schoor J.K. , Hecht V. , Aubert G. , Burstin J. , Weller J.L. 
Published: August 2021

AbstractThe timing of developmental phase transitions is crucial for plant reproductive success, and two microRNAs (miRNA),miR156andmiR172, are implicated in the control of these changes, together with their respectiveSQUAMOSA promoter binding-like(SPL) andAPETALA2(AP2)-like targets. While their patterns of regulation have been studied in a growing range of species, to date they have not been examined in pea (Pisum sativum), an important legume crop and model species. We analysed the recently-released pea genome and defined ninemiR156, 21SPL, fourmiR172, and fiveAP2-likegenes. Phylogenetic analysis of theSPLgenes in pea,MedicagoandArabidopsisconfirmed the eight previously defined clades, and identified a ninth potentially legume-specificSPLclade in pea andMedicago. Among thePsSPL, 14 contain amiR156binding site and all fiveAP2-liketranscription factors in pea include amiR172binding site. Phylogenetic relationships, expression levels and temporal expression changes identifiedPsSPL2a/3a/3c/6b/9a/9b/13b/21, PsmiR156d/jandPsmiR172a/das the most likely of these genes to participate in phase change in pea. Comparisons with leaf morphology suggests that vegetative phase change is unlikely to be definitively marked by a change in leaflet number. In addition, the timing ofFTgene induction suggests that the shift from the juvenile to the adult vegetative phase may occur within fourteen days in plants grown under inductive conditions, and calls into question the contribution ofmiR172/AP2to the floral transition. This work provides the first insight into the nature of vegetative phase change in pea, and an important foundation for future functional studies.
Tracheal tube fusion inDrosophilainvolves release of extracellular vesicles from multivesicular bodies
Authors: Camelo Carolina , Körte Anna , Jacobs Thea , Luschnig Stefan 
Published: August 2021

SummaryExtracellular vesicles (EVs) comprise diverse types of cell-released membranous structures that are thought to play important roles in intercellular communication. Despite extensive work on the formation and functions of EVs in cultured cells, studies of EVsin vivohave remained scarce. We report here that EVs are present in the developing lumen of tracheal tubes inDrosophilaembryos. We defined two distinct EV subpopulations, one of which contains the Munc13-4 homologue Staccato (Stac) and is spatially and temporally associated with tracheal tube fusion events. The formation of Stac-positive luminal EVs depends on the tip-cell-specific GTPase Arl3, which is also required for the formation of Stac-positive multivesicular bodies, suggesting that Stac-EVs derive from fusion of Stac-MVBs with the luminal membrane in tip cells during anastomosis formation. The GTPases Rab27 and Rab35 cooperate downstream of Arl3 to promote Stac-MVB formation and tube fusion. We propose that Stac-MVBs act as membrane reservoirs that facilitate tracheal lumen fusion in a process regulated by Arl3, Rab27, Rab35, and Stac/Munc13-4.
The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines
Authors: Liu Yafei , Arase Noriko , Kishikawa Jun-ichi , Hirose Mika , Li Songling , Tada Asa , Matsuoka Sumiko , Arakawa Akemi , Akamatsu Kanako , Ono Chikako , Jin Hui , Kishida Kazuki , Nakai Wataru , Kohyama Masako , Nakagawa Atsushi , Yamagishi Yoshiaki , Nakagami Hironori , Kumanogoh Atsushi , Matsuura Yoshiharu , Standley Daron M. , Kato Takayuki , Okada Masato , Fujimoto Manabu , Arase Hisashi 
Published: August 2021

AbstractmRNA-based vaccines provide effective protection against most common SARS-CoV-2 variants. However, identifying likely breakthrough variants is critical for future vaccine development. Here, we found that the Delta variant completely escaped from anti-N-terminal domain (NTD) neutralizing antibodies, while increasing responsiveness to anti-NTD infectivity-enhancing antibodies. Although Pfizer-BioNTech BNT162b2-immune sera neutralized the Delta variant, when four common mutations were introduced into the receptor binding domain (RBD) of the Delta variant (Delta 4+), some BNT162b2-immune sera lost neutralizing activity and enhanced the infectivity. Unique mutations in the Delta NTD were involved in the enhanced infectivity by the BNT162b2-immune sera. Sera of mice immunized by Delta spike, but not wild-type spike, consistently neutralized the Delta 4+ variant without enhancing infectivity. Given the fact that a Delta variant with three similar RBD mutations has already emerged according to the GISAID database, it is necessary to develop vaccines that protect against such complete breakthrough variants.
Stretching and squeezing of neuronal log firing rate distribution by psychedelic and intrinsic brain state transitions
Authors: Dearnley Bradley , Dervinis Martynas , Shaw Melissa , Okun Michael 
Published: August 2021

AbstractHow psychedelic drugs change the activity of cortical neuronal populations and whether such changes are specific to transition into the psychedelic brain state or shared with other brain state transitions is not well understood. Here, we used Neuropixels probes to record from large populations of neurons in prefrontal cortex of mice given the psychedelic drug TCB-2. Drug ingestion significantly stretched the distribution of log firing rates of the population of recorded neurons. This phenomenon was previously observed across transitions between sleep and wakefulness, which suggested that stretching of the log-rate distribution can be triggered by different kinds of brain state transitions and prompted us to examine it in more detail. We found that modulation of the width of the log-rate distribution of a neuronal population occurred in multiple areas of the cortex and in the hippocampus even in awake drug-free mice, driven by intrinsic fluctuations in their arousal level. Arousal, however, did not explain the stretching of the log-rate distribution by TCB-2. In both psychedelic and naturally occurring brain state transitions, the stretching or squeezing of the log-rate distribution of an entire neuronal population reflected concomitant changes in two subpopulations, with one subpopulation undergoing a downregulation and often also stretching of its neurons’ log-rate distribution, while the other subpopulation undergoes upregulation and often also a squeeze of its log-rate distribution. In both subpopulations, the stretching and squeezing were a signature of a greater relative impact of the brain state transition on the rates of the slow-firing neurons. These findings reveal a generic pattern of reorganisation of neuronal firing rates by different kinds of brain state transitions.
Plasma Contains Ultra-short Single-stranded DNA in Addition to Nucleosomal cfDNA
Authors: Cheng Jordan , Morselli Marco , Huang Wei-Lun , Heo You Jeong , Pinheiro-Ferreira Thalyta , Li Feng , Wei Fang , Chia David , Jun Hua , Cole Kenneth , Su Wu-Chou , Pellegrini Matteo , Wong David TW 
Published: August 2021

ABSTRACTPlasma cell-free DNA is a widely used biomarker for diagnostic screening. We introduce uscfDNA-seq, a single-stranded cell-free DNA NGS pipeline, which bypasses previous limitations to reveal a novel population of ultrashort single-stranded cell-free DNA in plasma with a modal size of 50nt. This species of cfDNA aligns predominantly to the nuclear genome and could potentially be used for novel biomarker discovery.
Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas with Stenotrophomonas and Pseudoxanthomonas as misclassified relatives
Authors: Bansal Kanika , Kumar Sanjeet , Kaur Amandeep , Singh Anu , Patil Prabhu B. 
Published: August 2021

AbstractGenus Xanthomonas is a group of phytopathogens which is phylogenetically related to Xylella, Stenotrophomonas and Pseudoxanthomonas following diverse lifestyles. Xylella is a lethal plant pathogen with highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono-genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas species. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan genome analysis identified set of unique genes associated with sub-lineages representing plant associated Xanthomonas clade and nosocomial origin Stenotrophomonas. Overall, our study reveals importance to reconcile classical phenotypic data and genomic findings in reconstituting taxonomic status of these four genera.Significance StatementXylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. The pathogen is transmitted by an insect vector to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is extremely reduced both in terms of size (2Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria along with comparative studies, we assert the need of unification of Xanthomonas with its misclassified relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.
Modeling movie-evoked human brain activity using motion-energy and space-time vision transformer features
Authors: Nishimoto Shinji 
Published: August 2021

SummaryIn this paper, the process of building a model for predicting human brain activity under video viewing conditions was described as a part of an entry into the Algonauts Project 2021 Challenge. The model was designed to predict brain activity measured using functional MRI (fMRI) by weighted linear summations of the spatiotemporal visual features that appear in the video stimuli (video features). Two types of video features were used: (1) motion-energy features designed based on neurophysiological findings, and (2) features derived from a space-time vision transformer (TimeSformer). To utilize the features of various video domains, the features of the TimeSformer models pre-trained using several different movie sets were combined. Through these model building and validation processes, results showed that there is a certain correspondence between the hierarchical representation of the TimeSformer model and the hierarchical representation of the visual system in the brain. The motion-energy features are effective in predicting brain activity in the early visual areas, while TimeSformer-derived features are effective in higher-order visual areas, and a hybrid model that uses motion energy and TimeSformer features is effective for predicting whole brain activity.
Vegetation memory effects and their association with vegetation resilience in global drylands
Authors: Kusch Erik , Davy Richard , Seddon Alistair W. R. 
Published: August 2021

AbstractVegetation memory describes the effect of antecedent environmental and ecological conditions on the present ecosystem state and has been proposed as an important proxy for vegetation resilience. In particular, strong vegetation-memory effects have been identified in dryland regions, but the factors underlying the spatial patterns of vegetation memory remain unknown.We aim to map the components and drivers of vegetation memory in dryland regions using state-of-the-art climate reanalysis data and refined approaches to identify vegetation-memory characteristics across dryland regions worldwide.Using a framework which distinguishes between intrinsic and extrinsic ecological memory, we show that: (i) intrinsic memory is a much stronger component than extrinsic memory in the majority of dryland regions; and (ii) climate reanalysis data sets change the detection of extrinsic vegetation memory effects in some global dryland regions.Synthesis. Our study offers a global picture of the vegetation response to two climate forcing variables using satellite data, information which is potentially relevant for mapping components and properties of vegetation responses worldwide. However, the large differences in the spatial patterns in intrinsic vegetation memory in our study compared to previous analyses show the overall sensitivity of this component in particular to the initial choice of extrinsic forcing variables. As a result, we caution against using the oversimplified link between intrinsic vegetation-memory and vegetation recovery rates at large spatial scales.
Machine learning prediction of antiviral-HPV protein interactions for anti-HPV pharmacotherapy
Authors: Lin Hui-Heng , Zhang Qian-Ru , Kong Xiangjun , Zhang Liuping , Zhang Yong , Tang Yanyan , Xu Hongyan 
Published: August 2021

AbstractPersistent infection with high-risk types Human Papillomavirus could cause diseases including cervical cancers and oropharyngeal cancers. Nonetheless, so far there is no effective pharmacotherapy for treating the infection from high-risk HPV types, and hence it remains to be a severe threat to the health of female. Based on drug repositioning strategy, we trained and benchmarked multiple machine learning models so as to predict potential effective antiviral drugs for HPV infection in this work. Through optimizing models, measuring models’ predictive performance using 182 pairs of antiviral-target interaction dataset which were all approved by the United States Food and Drug Administration, and benchmarking different models’ predictive performance, we identified the optimized Support Vector Machine and K-Nearest Neighbor classifier with high precision score were the best two predictors (0.80 and 0.85 respectively) amongst classifiers of Support Vector Machine, Random forest, Adaboost, Naïve Bayes, K-Nearest Neighbors, and Logistic regression classifier. We applied these two predictors together and successfully predicted 57 pairs of antiviral-HPV protein interactions from 864 pairs of antiviral-HPV protein associations. Our work provided good drug candidates for anti-HPV drug discovery. So far as we know, we are the first one to conduct such HPV-oriented computational drug repositioning study.
Reconstitution of surface lipoprotein translocation reveals Slam as an outer membrane translocon in Gram-negative bacteria
Authors: Huynh Minh Sang , Hooda Yogesh , Li Raina , Jagielnicki Maciej , Lai Christine Chieh-Lin , Moraes Trevor F 
Published: August 2021

AbstractSurface lipoproteins (SLPs) are peripherally attached to the outer leaflet of the outer membrane in many Gram-negative bacteria, playing significant roles in nutrient acquisition and immune evasion in the host. While the factors that are involved in the synthesis and delivery of SLPs in the inner membrane are well characterized, the molecular machineries required for the movement of SLPs to the surface are still not fully elucidated. In this study, we investigated the translocation of a surface lipoprotein TbpB through a Slam1-dependent pathway. Using purified components, we developed an in vitro translocation assay where unfolded TbpB is transported through Slam1 containing proteoliposomes, confirming Slam1 as an outer membrane translocon. While looking to identify factors to increase translocation efficiency, we discovered the periplasmic chaperone Skp interacted with TbpB in the periplasm of Escherichia coli. The presence of Skp was found to increase the translocation efficiency of TbpB in the reconstituted translocation assays. A knockout of Skp in Neisseria meningitidis revealed that Skp is essential for functional translocation of TbpB to the bacterial surface. Taken together, we propose a pathway for surface destined lipoproteins, where Skp acts as a holdase for Slam-mediated TbpB translocation across the outer membrane.
Vapor cannabis exposure generationally affects male reproductive functions in mice
Authors: Shi Mingxin , Langholt Esther M. , Butler Logan C. , Harvey Madeleine E. , Wheeler Emma C. , Zhao Liang , MacLean James A. , Oh Yeongseok , Sabrowsky Emily , Yu Sue , Watson Shane , Davis Jon F. , Hayashi Kanako 
Published: August 2021

ABSTRACTThis study was performed to examine whether vapor exposure to cannabis plant matter negatively impacts male reproductive functions and testis development in mice. Adult CD-1 male mice (F0) were exposed to air (control) or 200 mg of vaporized cannabis plant matter 3x/day over a 10 day period. Subsequently, F0 males were bred with drug naïve CD-1 females to generate F1 males, and F1 offspring were used to generate F2 males. Cannabis vapor exposure decreased sperm count and/or motility in F0 and F1 males and disrupted the progression of germ cell development, as morphometric analyses exhibited an abnormal distribution of the stages of spermatogenesis in F0 males. Although plasma levels of testosterone were not affected by cannabis exposure in any ages or generations of males, dysregulated steroidogenic enzymes, Cyp11a1 and Cyp19a1, were observed in F0 testis. In the neonatal testis from F1 males, while apoptosis was not altered, DNA damage and DNMT1, but not DNMT3A and DNMT3B, were increased in germ cells following cannabis exposure. In contrast, the alterations of DNA damage and DNMT1 expression were not observed in F2 neonatal males. These results suggest that cannabis vapor exposure generationally affects male reproductive functions, probably due to disruption of spermatogenesis in the developing testis.GRAPHICAL ABSTRACTHIGHLIGHTSCannabis vapor exposure to adult males impairs sperm counts, motility and spermatogenesis.Cannabis vapor exposure to F0 males causes reduced sperm counts in F1, but not in F2 males.Plasma testosterone levels are not affected in F0, F1 and F2 males by cannabis exposure.Cannabis increases DNA damage and the expression of DNA methyltransferase (DNMT) 1 in the F1 neonatal testis.