bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-drug resistantE. colidisplace commensalE. colifrom the intestinal tract, a trait associated with elevated levels of genetic diversity in carbohydrate metabolism genes
Authors: Connor Christopher H. , Zucoloto Amanda Z. , Yu Ian-Ling , Corander Jukka , McDonald Braedon , McNally Alan 
Published: November 2022

AbstractExtra-intestinal pathogenicE. coli(ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multi-drug resistance (MDR) is not uniform across the phylogenetic spectrum ofE. coli. Instead AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model we demonstrate that an MDRE. coliST131 is capable out-competing and displacing non-MDRE. colifrom the gutin vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDRE. colistrains, challenge with MDRE. colieither by oral gavage or co-housing with MDRE. colicolonized mice results in displacement and dominant intestinal colonization by MDRE. coliST131. To investigate the genetic basis of this superior gut colonization ability by MDRE. coli, we used a functional pangenomic analysis of 19,571E. coligenomes revealing that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDRE. colidisplay a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages ofE. colivia carriage and spread.
Neural alpha oscillations and pupil size differentially index cognitive demand under competing audio-visual task conditions
Authors: Kraus Frauke , Tune Sarah , Obleser Jonas , Herrmann Björn 
Published: November 2022

AbstractCognitive demand is thought to modulate two often used, but rarely combined, measures: pupil size and neural alpha (8–12 Hz) oscillatory power. However, it is unclear whether these two measures capture cognitive demand in a similar way under complex audio-visual task conditions. Here we recorded pupil size and neural alpha power (using electroencephalography), while human participants of both sexes concurrently performed a visual multiple object-tracking task and an auditory gap-detection task. Difficulties of the two tasks were manipulated independent of each other. Participants’ performance decreased in accuracy and speed with increasing cognitive demand. Pupil size increased with increasing difficulty for both the auditory and the visual task. In contrast, alpha power showed diverging neural dynamics: Parietal alpha power decreased with increasing difficulty in the visual task, but not with increasing difficulty in the auditory task. Furthermore, independent of task difficulty, within-participant trial-by-trial fluctuations in pupil size were negatively correlated with alpha power. Difficulty-induced changes in pupil size and alpha power, however, did not correlate, which is consistent with their different cognitive-demand sensitivities. Overall, the current study demonstrates that the dynamics of the neurophysiological indices of cognitive demand and associated effort are multi-faceted and potentially modality-dependent under complex audio-visual task conditions.Significance StatementPupil size and oscillatory alpha power are associated with cognitive demand and effort, but their relative sensitivity under complex audio-visual task conditions is unclear as is the extent to which they share underlying mechanisms. Using an audio-visual dual-task paradigm, we show that pupil size increases with increasing cognitive demands for both audition and vision. In contrast, changes in oscillatory alpha power depend on the respective task demands: Parietal alpha power decreases with visual demand but not with auditory task demand. Hence, pupil size and alpha power show different sensitivity to cognitive demands, perhaps suggesting partly different underlying neural mechanisms.
All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity
Authors: Papon Nathan , Lasserre-Zuber Pauline , Rimbert Hélène , De Oliveira Romain , Paux Etienne , Choulet Frédéric 
Published: November 2022

AbstractBread wheat (Triticum aestivumL.) is a major crop and its genome is one of the largest ever assembled at reference-quality level. It is 15 Gb, hexaploid, with 85% of transposable elements (TEs). Wheat genetic diversity was mainly focused on genes and little is known about the extent of genomic variability affecting TEs, transposition rate, and the impact of polyploidy. Multiple chromosome-scale assemblies are now available for bread wheat and for its tetraploid and diploid wild relatives. In this study, we computed base pair-resolved, gene-anchored, whole genome alignments of A, B, and D lineages at different ploidy levels in order to estimate the variability that affects the TE space. We used assembled genomes of 13T. aestivumcultivars (6x=AABBDD),T. durum(4x=AABB),T. dicoccoides(4x=AABB),T. urartu(2x=AA), andAegilops tauschii(2x=DD). We show that 5 to 34% of the TE fraction is variable, depending on the species divergence. Between 400 and 13,000 novel TE insertions per subgenome were detected. We found lineage-specific insertions for nearly all TE families in di- tetra- and hexaploids. No burst of transposition was observed and polyploidization did not trigger any boost of transposition. This study challenges the prevailing idea of wheat TE dynamics and is more in agreement with an equilibrium model of evolution.
A RAF-like kinase mediates a deeply conserved, ultra-rapid auxin response
Authors: Kuhn Andre , Roosjen Mark , Mutte Sumanth , Dubey Shiv Mani , Carrasco Polet Carrillo , Monzer Aline , Kohchi Takayuki , Nishihama Ryuichi , Fendrych Matyáš , Friml Jiří , Sprakel Joris , Weijers Dolf 
Published: November 2022

SUMMARYThe plant signaling molecule auxin triggers both fast and slow cellular responses across the plant kingdom, including both land plants and algae. A nuclear response pathway mediates auxin-dependent gene expression, and controls a range of growth and developmental processes in land plants. It is unknown what mechanisms underlie both the physiological responses occurring within seconds, and the responses in algae, that lack the nuclear auxin response pathway. We discovered an ultra-fast proteome-wide phosphorylation response to auxin across 5 land plant and algal species, converging on a core group of shared target proteins. We find conserved rapid physiological responses to auxin in the same species and identified a RAF-like protein kinase as a central mediator of auxin-triggered phosphorylation across species. Genetic analysis allowed to connect this kinase to both auxin-triggered protein phosphorylation and a rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.
Public goods exploitation is reduced in species-rich microbial communities
Authors: O’Brien Siobhán , Culbert Chris , Barraclough Timothy G. 
Published: November 2022

AbstractIntraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e. interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence select for increased intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacteriumPseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2-15 species. We find, contrary to our prediction, that siderophore exploitation is reduced in high diversity communities, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains ofP. fluorescens. Our results suggest that maintaining a healthy soil microbiota could contribute to the maintenance of siderophore production in natural communities.
Chromatin activity identifies differential gene regulation across human ancestries
Authors: Pettie Kade P. , Mumbach Maxwell , Lea Amanda J. , Ayroles Julien , Chang Howard Y. , Kasowski Maya , Fraser Hunter B. 
Published: November 2022

AbstractCurrent evidence suggests thatcis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. To address this, we devised an approach to search for lineage-specific selection on chromatin activity, transcription factor binding, and chromosomal looping—critical steps in transcriptional regulation. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, we find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, we show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. Overall, our study indicates that somecis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This work provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species.
Screening of naturalWolbachiainfection in mosquitoes (Diptera: Culicidae) from Cape Verde Islands
Authors: Fernandes da Moura Aires Januário , Valadas Vera , Veiga Leal Silvania Da , Sousa Carla A. , Pinto João 
Published: November 2022

AbstractBackgroundWolbachia pipientisis an endosymbiont bacteria that induce cytoplasmic incompatibility and inhibit arboviral replication in mosquitoes. This study aimed at estimating the prevalence and genetic diversity ofWolbachiain different mosquito (Diptera: Culicidae) species from Cape Verde.MethodsMosquitoes were collected in six islands of Cape Verde using dippers/pipettes, BG-sentinel® traps, CDC light traps, and dorsal aspirators. Samples were identified to species using morphological keys and PCR-based molecular assays.Wolbachiawas detected by amplifying a fragment of the surface protein gene (wsp). Multilocus sequence typing (MLST) was performed with five housekeeping genes (coxA, gatB, ftsZ, hcpA and fbpA) and thewsphypervariable region (HVR) for strain identification. Identification ofwPip groups (wPip-I towPip-V) was performed using PCR-RFLP assay on the ankyrin-domain genepk1.ResultsNine mosquito species were collected, including the major vectorsAedes aegypti, Anopheles arabiensis, Culex pipiens s.s. andCulex quinquefasciatus. Wolbachiawas detected inCx. pipiens s.s. (100% prevalence),Cx. quinquefasciatus (98.3%), Cx. pipiens/quinquefasciatushybrids (100%) andCulex tigripes (100%). Results from MLST andwsphypervariable region typing showed thatWolbachiafromCx. pipiens s.l. belong to Sequence Type 9,wPip clade and supergroup BWolbachia. Phylogenetic analyses indicate thatWolbachiaisolated fromCx. tigripesbelongs to Supergroup B but integrates a distinct clade fromwPip with no attributed MLST profile. PCR-RFLP revealedwPip-II,wPip-III andwPip-IV groups inCulex pipiens s.l. wPip-IV was the dominant group, whilewPip-II andwPip-III were restricted to Maio and Fogo islands, respectively.ConclusionOur study showed a high prevalence and diversity ofWolbachiainCx pipiens s.l. from Cape Verde islands and, to the best of our knowledge, is the first to detectWolbachiainCx. tigripes, being represented in this species by a previously undescribed MLST Sequence Type.
Processing of the Same Narrative Stimuli Elicits Common Functional Connectivity Dynamics Between Individuals
Authors: Türker Başak , Belloli Laouen , Owen Adrian M. , Naci Lorina , Sitt Jacobo D. 
Published: November 2022

ABSTRACTIt has been suggested that the richness of conscious experience can be directly linked to the richness of brain state repertories. Brain states change depending on our environment and activities we engage in by taking both external and internally derived information into account. It has been shown that high-level sensory stimulation changes local brain activity and induces neural synchrony across participants. However, the dynamic interplay of cognitive processes that underlie moment-to-moment information processing remains poorly understood. Using naturalistic movies as an ecological laboratory model of the real world, here we assess how the processing of complex naturalistic stimuli alters the dynamics of brain networks’ interactions, and how these in turn support information processing. Participants underwent fMRI recordings during movie watching, scrambled movie watching, and rest. Measuring phase-synchrony between different brain networks, we computed whole-brain connectivity patterns. We showed that specific connectivity patterns were associated with each experimental condition. We found a higher synchronization of brain patterns across participants during movie watching compared to resting state and scrambled movie conditions. Moreover, synchronization increased during the most engaging parts of the movie. The synchronization dynamics across participants were associated with suspense; more suspenseful scenes induced higher synchronization. These results suggest that processing of the same high-level information elicits common neural dynamics among individuals and that whole-brain functional connectivity tracks variations in the processed information and the subjective experience.
Uncovering 2-D toroidal representations in grid cell ensemble activity during 1-D behavior
Authors: Hermansen Erik , Klindt David A. , Dunn Benjamin A. 
Published: November 2022

AbstractNeuroscience is pushing toward studying the brain during naturalistic behaviors with open-ended tasks. Grid cells are a classic example, where free behavior was key to observing their characteristic spatial representations in two-dimensional environments [1]. In contrast, it has been difficult to identify grid cells and study their computations in more restrictive experiments, such as head-fixed wheel running [2–6]. Here, we challenge this view by showing that shifting the focus from single neurons to the population level changes the minimal experimental complexity required to study grid cell representations. Specifically, we combine the manifold approximation in UMAP [7] with persistent homology [8] to study the topology of the population activity. With these methods, we show that the population activity of grid cells covers a similar two-dimensional toroidal state space during wheel running as in open field foraging [9, 10], with and without a virtual reality setup. Trajectories on the torus correspond to single trial runs in virtual reality and changes in experimental conditions are reflected in the internal representation, while the toroidal representation undergoes occasional shifts in its alignment to the environment. These findings show that our method can uncover latent topologies that go beyond the complexity of the task, allowing us to investigate internal dynamics in simple experimental settings in which the analysis of grid cells has so far remained elusive.
High pathogenicity island,aerandsitoperons: a “ménage à trois” inEscherichia coliextra-intestinal virulence
Authors: Royer Guilhem , Clermont Olivier , Condamine Bénédicte , Dion Sara , Galardini Marco , Denamur Erick 
Published: November 2022

AbstractThe intrinsic virulence of extra-intestinal pathogenicEscherichia coliis attributed to numerous chromosome and/or plasmid-borne virulence associated genes (VAGs), encoding diverse functions as adhesins, toxins, protectins and iron capture systems, which occur in specific genetic backgrounds. Little is however known on their respective contribution to virulence. Here, by analyzing genomes of 232 sequence type complex (STc) 58 strains, we show that virulence quantified in a mouse model of sepsis emerged in a sub-group of STc58 due to the presence of the siderophore encoding high-pathogenicity island (HPI). When extending our analysis to 370Escherichiastrains we show that full virulence is associated with the presence of theaerorsitoperons, in addition to the HPI. The prevalence of these operons, their co-occurrence and genomic location depend on the strain phylogeny. Selection of lineage-dependent specific associations of VAGs argues for strong epistatic interactions shaping the emergence of virulence inE. coli.
Uterine NK cells underexpress receptors recognizing HLA-C2 and HLA-G in reproductive failure
Authors: Woon Ee Von , Nikolaou Dimitrios , MacLaran Kate , Norman-Taylor Julian , Bhagwat Priya , Cuff Antonia O. , Johnson Mark R. , Male Victoria 
Published: November 2022

AbstractA significant proportion of recurrent miscarriage, recurrent implantation failure and infertility are unexplained, and these conditions have been proposed to have an etiology of immunological dysfunction at the maternal-fetal interface. Uterine Natural Killer cells (uNK) comprise three subsets and are the most numerous immune cells found in the uterine mucosa at the time of implantation. They are thought to play an important role in successful pregnancy by regulation of extravillous trophoblast (EVT) invasion and spiral artery remodelling. Here, we examine the frequency, phenotype and function of uNK1-3 from the uterine mucosa of 16 women with unexplained reproductive failure compared to 11 controls with no reproductive problems, during the window of implantation. We report that KIR2DL1/S1 and LILRB1 expression is lower in the reproductive failure group for both uNK (total uNK, uNK 2 and 3) and pNK. We also show that degranulation activity is significantly reduced in total uNK, and that TNF-α production is lower in all uNK subsets in the reproductive failure group. Taken together, our findings suggest that reproductive failure may be caused by global reduction in expression of uNK receptors important for interaction with HLA-C and HLA-G on EVT during early pregnancy, leading to reduced uNK activation. This is the first study to examine uNK subsets during the window of implantation in women with reproductive failure and will serve as a platform to focus on particular aspects of phenotype and function of uNK subsets in future studies. Further understanding of uNK dysregulation is important to establish potential diagnostic and therapeutic targets in the population of women with unexplained reproductive failure.
Self-Supervised Maize Kernel Classification and Segmentation for Embryo Identification
Authors: Dong David , Nagasubramanian Koushik , Wang Ruidong , Frei Ursula K , Jubery Talukder Z , Lübberstedt Thomas , Ganapathysubramanian Baskar 
Published: November 2022

ABSTRACTComputer vision and deep learning (DL) techniques have succeeded in a wide range of diverse fields. Recently, these techniques have been successfully deployed in plant science applications to address food security, productivity, and environmental sustainability problems for a growing global population. However, training these DL models often necessitates the large-scale manual annotation of data which frequently becomes a tedious and time-and-resource-intensive process. Recent advances in self-supervised learning (SSL) methods have proven instrumental in overcoming these obstacles, using purely unlabeled datasets to pre-train DL models. Here, we implement the popular self-supervised contrastive learning methods of NNCLR (Nearest neighbor Contrastive Learning of visual Representations) and SimCLR (Simple framework for Contrastive Learning of visual Representations) for the classification of spatial orientation and segmentation of embryos of maize kernels. Maize kernels are imaged using a commercial high-throughput imaging system. This image data is often used in multiple downstream applications across both production and breeding applications, for instance, sorting for oil content based on segmenting and quantifying the scutellum’s size and for classifying haploid and diploid kernels. We show that in both classification and segmentation problems, SSL techniques outperform their purely supervised transfer learning-based counterparts and are significantly more annotation efficient. Additionally, we show that a single SSL pre-trained model can be efficiently finetuned for both classification and segmentation, indicating good transferability across multiple downstream applications. Segmentation models with SSL-pretrained backbones produce DICE similarity coefficients of 0.81, higher than the 0.78 and 0.73 of those with ImageNet-pretrained and randomly initialized backbones, respectively. We observe that finetuning classification and segmentation models on as little as 1% annotation produces competitive results. These results show SSL provides a meaningful step forward in data efficiency with agricultural deep learning and computer vision.
NR5A2 connects genome activation to the first lineage segregation in early mouse development
Authors: Lai Fangnong , Li Lijia , Hu Xiaoyu , Liu Bofeng , Zhu Ziqi , Liu Ling , Fan Qiang , Tian Huabin , Xu Kai , Lu Xukun , Li Qing , Kong Feng , Wang Lijuan , Lin Zili , Deng Hongyu , Li Jinsong , Xie Wei 
Published: November 2022

AbstractAfter fertilization, zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which further gives rise to the pluripotent embryonic lineages and extraembryonic trophectoderm after the first lineage commitment. While much has been learned about pluripotency regulation, how ZGA is connected to the pluripotency commitment in early embryos remains elusive. Here, we investigated the role of nuclear receptor1family transcription factors (TFs) in mouse pre-implantation embryos, whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. We found NR5A2, an NR TF highly induced upon ZGA, is required for early development, as both the knockdown and knockout ofNr5a2from 1C embryos led to morula arrest. While the zygotic genome was largely activated at the 2C stage, 4-8C-specific gene activation (mid-preimplantation activation) was substantially impaired. Genome-wide chromatin binding and RNA-seq analyses showed NR5A2 preferentially regulates its binding targets including a subset of key pluripotency genes (i.e.,Nanog, Pou5f1, andTdgf1). Finally, NR5A2-occupied sites at the 2C and 8C stages predominantly reside in accessible B1 elements where its motif is embedded. Taken together, these data identify NR5A2 as a key regulator that connects ZGA to the first lineage segregation in early mouse development.