bluuebunny/crossref_metadata_2025 huggingface dataset:
Area per player in small-sided games to replicate the external load and estimated physiological match demands in elite soccer players
Authors: Riboli Andrea , Coratella Giuseppe , Rampichini Susanna , Cé Emiliano , Esposito Fabio
Published: February 2020

The current study determined the area-per-player during small- or large-sided games with or without goalkeeper that replicates the relative (m·min−1) total distance, high-intensity running distance, sprint distance and metabolic power covered during official matches. Time-motion analysis was performed on twenty-five élite soccer-players during 26 home-matches. A total of 2565 individual samples for SSGs using different pitch sizes and different number of players were collected and classified as SSGs with (SSG-G) or without goalkeeper (SSG-P). A between-position comparison was also performed. The area-per-player needed to replicate the official match demands waslargelygreater in SSG-GvsSSG-P for total distance [187±53 vs 115±35 m2, effect size (ES): 1.60 95%CI 0.94/2.21], high-intensity running distance [262±72 vs 166±39 m2, ES: 1.66(0.99/2.27)] and metabolic power [177±42 vs 94±40, ES: 1.99(1.31/2.67)], but similar for sprint distance [(316±75 vs 295±99 m2, ES: 0.24(−0.32/0.79)] with direction of larger area-per-player for sprint distance > high-intensity running > total distance ≅ metabolic power for both SSG-G and SSG-P. In SSG-G, forwards required greater area-per-player than central-defenders [ES: 2.96(1.07/4.35)], wide-midfielders [ES: 2.45(0.64/3.78)] and wide-defenders [ES: 3.45(1.13/4.99)]. Central-midfielders required greater area-per-player than central-defenders [ES: 1.69(0.20/2.90)] and wide-midfielders [ES: 1.35(−0.13/2.57)]. In SSG-P, central defenders need smaller area-per-player (ES: −6.01/−0.92) to overall replicate the match demands compared to all other positions. The current results highlight that soccer players need a specific area-per-player during the small-side games with or without goalkeeper to replicate the overall match demands, especially to perform high-intensity running or sprint distance. Additionally, central defenders, central midfielders and forwards need to be trained with tailored area-per-player or specific rules/additional exercises.
Polar opposites; bacterioplankton susceptibility and mycoplankton resistance to ocean acidification
Authors: de Scally Storme Zaviar , Chaffron Samuel , Makhalanyane Thulani Peter
Published: February 2020

Microorganisms form the basis of ocean ecosystems yet the effects of perturbations such as decreasing pH on microbial community structure, interactions and functionality remain compared to multicellular organisms. Using an experimental manipulation of Southern Ocean seawater, we subjected bacterioplankton and mycoplankton to artificial pH decreases, which are predicted to occur in the future. We show that acidification led to substantial increases of bacterioplankton diversity, while in contrast it had no effect on mycoplankton diversity. Our analyses revealed a loss of putative keystone taxa and a decrease in predicted community interactions as a response to lower pH levels. Bacterioplankton shifted from generalist to specialist community members, suggesting a specific stress response to unfavourable conditions. In addition, enzyme activities involved in nitrogen acquisition were lower at reduced pH levels, suggesting altered organic matter cycling in a more acidic ocean. Our findings suggest that bacterioplankton and mycoplankton may respond differentially to future ocean acidification, with potentially negative impacts on community structure and biogeochemical cycling in the Southern Ocean.

IMPORTANCE

Oceans absorb the majority of anthropogenically produced CO2, the consequence of which is ocean acidification, a phenomenon already negatively impacting key marine organisms. Marine microbial communities form the basis of ocean food webs by generating nutrients for higher trophic levels, yet the response of these key microbial drivers to acidification remains unclear. This knowledge deficit is particularly true for understudied marine ecosystems such as the Southern Ocean. Using a mesocosm approach, we found that acidification severely impacts microbial community stability, by altering bacterioplankton community structure, reducing network complexity, and augmenting enzyme activities associated with nitrogen acquisition. This study adds to our understanding of the effects of ocean acidification on microbial communities, particularly within an environment expected to be largely effected by future anthropogenically driven climate change.
Distinguishing Viruses Responsible for Influenza-Like Illness
Authors: Spencer Julie A. , Shutt Deborah P. , Moser Sarah K. , Clegg Hannah , Wearing Helen J. , Mukundan Harshini , Manore Carrie A.
Published: February 2020

The many respiratory viruses that cause influenza-like illness (ILI) are reported and tracked as one entity, defined by the CDC as a group of symptoms that include a fever of 100 degrees Fahrenheit and a cough and/or a sore throat. In the United States alone, ILI impacts 9-49 million people every year. While tracking ILI as a single clinical syndrome is informative in many respects, the underlying viruses differ in their parameters and outbreak properties. Most existing models treat either a single respiratory virus or ILI as a whole. However, there is a need for models capable of comparing several individual ILI viruses. To address this need, here we present a flexible model and simulations of epidemics for influenza, RSV, rhinovirus, seasonal coronavirus, adenovirus, and SARS/MERS, parameterized by a systematic literature review and accompanied by a global sensitivity analysis. We find that for these biological causes of ILI, their parameter values, timing, prevalence, and proportional contributions differ substantially. These results demonstrate that distinguishing the viruses that cause influenza-like illness will be an important aspect of future work on ILI diagnostics, mitigation, modeling, and preparation for future unknown pandemics.
Using predicted imports of 2019-nCoV cases to determine locations that may not be identifying all imported cases
Authors: De Salazar PM , Niehus R , Taylor A , Buckee C , Lipsitch M
Published: February 2020

Cases from the ongoing outbreak of atypical pneumonia caused by the 2019 novel coronavirus (2019-nCoV) exported from mainland China can lead to self-sustained outbreaks in other populations. Internationally imported cases are currently being reported in several different locations. Early detection of imported cases is critical for containment of the virus. Based on air travel volume estimates from Wuhan to international destinations and using a generalized linear regression model we identify locations which may potentially have undetected internationally imported cases.
Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding
Authors: Sales Naiara Guimarães , Wangensteen Owen Simon , Carvalho Daniel Cardoso , Deiner Kristy , Præbel Kim , Coscia Ilaria , McDevitt Allan D. , Mariani Stefano
Published: February 2020

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative “eDNA reservoirs” for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.
The Human LL-37(17-29) Antimicrobial Peptide Reveals a Functional Supramolecular Nanostructure
Authors: Engelberg Yizhaq , Landau Meytal
Published: February 2020

Protein fibrils that perform biological activities present attractive biomaterials. Here we demonstrate, by crystal structures, the self-assembly of the antibacterial human LL-37 active core (residues 17-29) into a stable structure of densely packed helices. The surface of the fibril encompasses alternating hydrophobic and positively charged zigzagged belts, which likely underlie interactions with and subsequent disruption of negatively charged lipid bilayers, such as bacterial membranes. LL-3717-29correspondingly formed wide, ribbon-like, thermostable fibrils in solution, which co-localized with bacterial cells, and structure-guided mutagenesis analyses supported the role of self-assembly in antibacterial activity. LL-3717-29resembled, in sequence and in the ability to form amphipathic helical fibrils, the bacterial cytotoxic PSMα3 peptide that assembles into cross-α amyloid fibrils. This suggests helical, self-assembling, basic building blocks across kingdoms of life and point to potential structural mimicry mechanisms. The findings offer a scaffold for functional and durable nanostructures for a wide range of medical and technological applications.
MiRNAs profiling and degradome sequencing between the CMS-line N816S and its maintainer line Ning5m during anther development in pepper (Capsicum annuumL.)
Authors: Zhang Hongyuan , Huang Shuping , Tan Jie , Chen Xia , Zhang Min
Published: February 2020

Utilization of cytoplasmic male sterility (CMS) is significant for agriculture. MiRNAs are a class of endogenously non-coding small RNAs (21-24 nt) that play key roles in the regulation of various growth and developmental processes in plants. The knowledge miRNA-guided CMS regulation is rather limited in pepper. To better understand the miRNAs involvement and regulatory mechanism of CMS, miRNA libraries from anther of CMS-line N816S and its maintainer line Ning5m were generated by miRNAome sequencing in pepper. A total of 76 differentially expressed miRNAs were detected, of which 18 miRNAs were further confirmed by quantitative real-time PCR (qRT-PCR). In addition, miRNA targets were identified by degradome sequencing. The result showed that 1292 targets that were potentially cleaved by 321 miRNAs (250 conserved miRNAs and 71 novel miRNAs). Gene Ontology (GO) and KEGG pathway analysis indicated that 35 differentially expressed miRNAs might play roles in the regulation of CMS sterility, by cleaving 77 target transcripts, such asMYBs, SPLs, andAFRs, of which targeted by miR156, miR167, miRNA858 family. Nineteen miRNA-cleaved targets were selectively examined by qRT-PCR, and the results showed that there were mostly negative correlations between miRNAs and their targets on the expression level. These findings provide a valuable information to understand miRNAs mechanism during anther development and CMS occurrence in pepper.
Haplotype Threading: Accurate Polyploid Phasing from Long Reads
Authors: Schrinner Sven D. , Mari Rebecca Serra , Ebler Jana , Rautiainen Mikko , Seillier Lancelot , Reimer Julia J. , Usadel Björn , Marschall Tobias , Klau Gunnar W.
Published: February 2020

Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. As a highly complex computational problem, polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.

We present WhatsHap polyphase, a novel two-stage approach that addresses these challenges by (i) clustering reads using a position-dependent scoring function and (ii) threading the haplotypes through the clusters by dynamic programming. We demonstrate on a simulated data set that this results in accurate haplotypes with switch error rates that are around three times lower than those obtainable by the current state-of-the-art and even around seven times lower in regions of collapsing haplotypes. Using a real data set comprising long and short read tetraploid potato sequencing data we show that WhatsHap polyphaseis able to phase the majority of the potato genes after error correction, which enables the assembly of local genomic regions of interest at haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap and ready to be included in production settings.
Mindfulness meditation experience is associated with increased ability to monitor covert somatosensory attention
Authors: Whitmarsh Stephen , Jensen Ole , Barendregt Henk
Published: February 2020

The distinguishing practice of mindfulness meditation is the intentional regulation of attention towards the present moment. Mindfulness meditation therefore emphasizes metacognitive functions, in particular the ability to monitor the attentional focus on a moment-by-moment basis. In this study we set out to test whether mindfulness meditation experience is associated with an increased ability to monitor moment-by-moment fluctuation in the attentional state. In response to auditory cues, participants maintained somatosensory attention to either their left or right hand. At random moments, trials were terminated by a probe sound to which participants reported their level of attention at that moment. MEG was recorded during the attention interval preceding probe onset. Using a beamformer approach, alpha activity in contralateral primary somatosensory regions was quantified. Alpha activity for self-reported high versus low attention trials was compared both within and between groups of either highly experienced experienced mindfulness meditators, novice meditators or meditation-naive participants (controls). As predicted, generally contralateral alpha power was associated with self-reported attention. Novice meditators (< 1000 h of meditation) showed temporal profiles similar to controls, displaying a correspondence between self-report and alpha power preceding probe onset. Expert meditators (≫ 1000 h) showed a strikingly different pattern, however. Their self-reported attentional state corresponded with alpha power during a more extended time interval preceding those of controls and novice meditators. In addition, self-reported low attention trials showed a distinctive alpha suppression preceding probe onset, suggesting that the ability for moment-by-moment monitoring of the attentional state permitted greater attentional control.
In cell architecture of the nuclear pore complex and snapshots of its turnover
Authors: Allegretti Matteo , Zimmerli Christian E. , Rantos Vasileios , Wilfling Florian , Ronchi Paolo , Fung Herman K.H. , Lee Chia-Wei , Hagen Wim , Turonova Beata , Karius Kai , Zhang Xiaojie , Müller Christoph , Schwab Yannick , Mahamid Julia , Pfander Boris , Kosinski Jan , Beck Martin
Published: February 2020

Nuclear pore complexes (NPCs) mediate exchange across the nuclear envelope. They consist of hundreds of proteins called nucleoporins (Nups) that assemble in multiple copies to fuse the inner and outer nuclear membranes. Elucidating the molecular function and architecture of NPCs imposes a formidable challenge and requires the convergence ofin vitroandin situapproaches. How exactly NPC architecture accommodates processes such as mRNA export or NPC assembly and turnover inside of cells remains poorly understood. Here we combine integratedin situstructural biology, correlative light and electron microscopy with yeast genetics to structurally analyze NPCs within the native context ofSaccharomyces cerevisiaecells under conditions of starvation and exponential growth. We find an unanticipatedin situlayout of nucleoporins with respect to overall dimensions and conformation of the NPC scaffold that could not have been predicted from previousin vitroanalysis. Particularly striking is the configuration of the Nup159 complex, which appears critical to spatially accommodate not only mRNA export but also NPC turnover by selective autophagy. We capture structural snapshots of NPC turnover, revealing that it occurs through nuclear envelope herniae and NPC-containing nuclear vesicles. Our study provides the basis for understanding the various membrane remodeling events that happen at the interface of the nuclear envelope with the autophagy apparatus and emphasizes the need of investigating macromolecular complexes in their cellular context.
Unravelling the developmental and functional significance of an ancient Argonaute duplication
Authors: Fridrich Arie , Modepalli Vengamanaidu , Lewandowska Magda , Aharoni Reuven , Moran Yehu
Published: February 2020

microRNAs (miRNAs), base-pair to messenger RNA targets and guide Argonaute proteins to mediate their silencing. This target regulation is considered crucial for animal physiology and development. However, this notion is based exclusively on studies in bilaterians, which comprise almost all lab model animals. To fill this glaring phylogenetic gap, we characterized the functions of two Argonaute paralogs in the sea anemoneNematostella vectensisof the phylum Cnidaria, which is separated from bilaterians by ∼600 million years. Using genetic manipulation, Argonaute-immunoprecipitations and high-throughput sequencing we provide experimental evidence for the developmental importance of miRNAs in a non-bilaterian animal. Additionally, we uncover unexpected differential distribution of distinct miRNAs between the two Argonautes and the ability of one of them to load additional types of small RNAs. This enables us to postulate a novel model for evolution of miRNA precursors in sea anemones and their relatives, revealing alternative trajectories for metazoan miRNA evolution.
RNA structure prediction using positive and negative evolutionary information
Authors: Rivas Elena
Published: February 2020

Knowing the structure of conserved structural RNAs is important to elucidate their function and mechanism of action. However, predicting a conserved RNA structure remains unreliable, even when using a combination of thermodynamic stability and evolutionary covariation information. Here we present a method to predict a conserved RNA structure that combines the following three features. First, it uses significant covariation due to RNA structure and removes spurious covariation due to phylogeny. Second, it uses negative evolutionary information: basepairs that have variation but no significant covariation are prevented from occurring. Lastly, it uses a battery of probabilistic folding algorithms that incorporate all positive covariation into one structure. The method, named CaCoFold (Cascade variation/covariation Constrained Folding algorithm), predicts a nested structure guided by a maximal subset of positive basepairs, and recursively incorporates all remaining positive basepairs into alternative helices. The alternative helices can be compatible with the nested structure such as pseudoknots, or overlapping such as competing structures, base triplets, or other 3D non-antiparallel interactions. We present evidence that CaCoFold predictions are consistent with structures modeled from crystallography.

Author Summary

The availability of deeper comparative sequence alignments and recent advances in statistical analysis of RNA sequence covariation have made it possible to identify a reliable set of conserved base pairs, as well as a reliable set of non-basepairs (positions that vary without covarying). Predicting an overall consensus secondary structure consistent with a set of individual inferred pairs and non-pairs remains a problem. Current RNA structure prediction algorithms that predict nested secondary structures cannot use the full set of inferred covarying pairs, because covariation analysis also identifies important non-nested pairing interactions such as pseudoknots, base triples, and alternative structures. Moreover, although algorithms for incorporating negative constraints exist, negative information from covariation analysis (inferred non-pairs) has not been systematically exploited.

Here I introduce an efficient approximate RNA structure prediction algorithm that incorporates all inferred pairs and excludes all non-pairs. Using this, and an improved visualization tool, I show that the method correctly identifies many non-nested structures in agreement with known crystal structures, and improves many curated consensus secondary structure annotations in RNA sequence alignment databases.
TRPV1 expressed throughout the arterial circulation enables inflammatory vasoconstriction
Authors: Phan Thieu X. , Ton Hoai T. , Gulyás Hajnalka , Pórszász Róbert , Tóth Attila , Russo Rebekah , Kay Matthew W. , Sahibzada Niaz , Ahern Gerard P.
Published: February 2020

The capsaicin receptor, TRPV1, is a key ion channel involved in inflammatory pain signaling. Although mainly studied in sensory nerves, there are reports of TRPV1 expression in isolated segments of the vasculature, but whether the channel localizes to vascular endothelium or smooth muscle is controversial and the distribution and functional roles of TRPV1 in arteries remain unknown. We mapped functional TRPV1 expression throughout the mouse arterial circulation. Analysis of reporter mouse lines TRPV1PLAP-nlacZand TRPV1-Cre:tdTomato combined with Ca2+imaging revealed specific localization of TRPV1 to smooth muscle of terminal arterioles in the heart, fat and skeletal muscle. Capsaicin evoked inward currents and raised intracellular Ca2+levels in arterial smooth muscle cells, constricted arteriolesex vivoandin vivoand increased systemic blood pressure in mice and rats. Further, capsaicin markedly and dose-dependently reduced coronary flow. Pharmacologic and/or genetic disruption of TRPV1 abolished all these effects of capsaicin as well as vasoconstriction triggered by lysophosphatidic acid, a bioactive lipid generated by platelets and atherogenic plaques. Notably, ablation of sensory nerves did not affect the responses to capsaicin revealing a vascular smooth muscle-restricted signaling mechanism. Moreover, unlike in sensory nerves, TRPV1 function in arteries was resistant to activity-induced desensitization. Thus, TRPV1 activation in vascular myocytes of resistance arterioles enables a persistent depolarizing current, leading to constriction of coronary, skeletal muscle, and adipose arterioles and a sustained increase in systemic blood pressure.
Bidirectional synaptic plasticity rapidly modifies hippocampal representations
Authors: Milstein Aaron D. , Li Yiding , Bittner Katie C. , Grienberger Christine , Soltesz Ivan , Magee Jeffrey C. , Romani Sandro
Published: February 2020

Learning requires neural adaptations thought to be mediated by activity-dependent synaptic plasticity. A relatively non-standard form of synaptic plasticity driven by dendritic plateau potentials has been reported to underlie place field formation in hippocampal CA1 neurons. Here we found that this behavioral timescale synaptic plasticity (BTSP) can also reshape existing place fields via bidirectional synaptic weight changes that depend on the temporal proximity of plateau potentials to pre-existing place fields. When evoked near an existing place field, plateau potentials induced less synaptic potentiation and more depression, suggesting BTSP might depend inversely on postsynaptic activation. However, manipulations of place cell membrane potential and computational modeling indicated that this anti-correlation actually results from a dependence on current synaptic weight such that weak inputs potentiate and strong inputs depress. A network model implementing this bidirectional synaptic learning rule suggested that BTSP enables population activity, rather than pairwise neuronal correlations, to drive neural adaptations to experience.
Cooperative policing behavior regulates reproductive division of labor in a termite
Authors: Sun Qian , Hampton Jordan D. , Haynes Kenneth F. , Merchant Austin , Zhou Xuguo
Published: February 2020

Reproductive conflicts are common in insect societies where helping castes retain reproductive potential. One of the mechanisms regulating the conflicts is policing, a coercive behavior that reduces direct reproduction by other individuals. In eusocial Hymenoptera (ants, bees, and wasps), workers or the queen act aggressively toward fertile workers, or destroy their eggs. In many termite species (order Blattodea), upon the death of primary queen and king, workers or nymphs can differentiate into neotenic reproductives and inherit the breeding position. During this process, competition among neotenics is inevitable, but how this conflict is resolved remains unclear. Here, we report a policing behavior that regulates reproductive division of labor in the eastern subterranean termite,Reticulitermes flavipes. Our results demonstrate that the policing behavior is a cooperative effort performed sequentially by successful neotenics and workers. A neotenic reproductive initiates the attack of the fellow neotenic by biting and displays alarm behavior. Workers are then recruited to cannibalize the injured neotenic. Furthermore, the initiation of policing is age-dependent, with older reproductives attacking younger ones, thereby inheriting the reproductive position. This study provides empirical evidence of policing behavior in termites, which represents a convergent trait shared between eusocial Hymenoptera and Blattodea.
Ribosome Profiling in Archaea Reveals Leaderless Translation, Novel Translational Initiation Sites, and Ribosome Pausing at Single Codon Resolution
Authors: Gelsinger Diego Rivera , Dallon Emma , Reddy Rahul , Mohammad Fuad , Buskirk Allen R. , DiRuggiero Jocelyne
Published: February 2020

High-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon,Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint ofH. volcaniito be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% ofH. volcaniitranscriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.
Joint Inference of Clonal Structure using Single-cell Genome and Transcriptome Sequencing Data
Authors: Bai Xiangqi , Duren Zhana , Wan Lin , Xia Li C.
Published: February 2020

Latest advancements in high-throughput single-cell genome (scDNA) and transcriptome (scRNA) sequencing technologies enabled cell-resolved investigation of tissue clones. However, it remains challenging to cluster and couple single cells for heterogeneous scRNA and scDNA data generated from the same specimen. In this study, we present a computational framework called CC-NMF, which employs a novel Coupled-Clone Non-negative Matrix Factorization technique to jointly infer clonal structure for matched scDNA and scRNA data. CCNMF couples multi-omics single cells by linking copy number and gene expression profiles through their general concordance. We validated CC-NMF using both simulated benchmarks and real-world applications, demon-strating its robustness and accuracy. We analyzed scRNA and scDNA data from an ovarian cancer cell lines mixture, a gastric cancer cell line, as well as a primary gastric cancer, successfully resolving underlying clonal structures and identifying high correlations of coexisting clones between genome and transcriptome. Overall, CCNMF is a coherent computational framework that simultaneously resolves genomic and transcriptomic clonal architecture, facilitating understanding of how cellular gene expression changes along with clonal genome alternations.
A neural circuit for flexible control of persistent behavioral states
Authors: Ji Ni , Madan Gurrein K. , Fabre Guadalupe I. , Dayan Alyssa , Baker Casey M. , Nwabudike Ijeoma , Flavell Steven W.
Published: February 2020

To adapt to their environments, animals must generate behaviors that are closely aligned to a rapidly changing sensory world. However, behavioral states such as foraging or courtship typically persist over long time scales to ensure proper execution. It remains unclear how neural circuits generate persistent behavioral states while maintaining the flexibility to select among alternative states when the sensory context changes. Here, we elucidate the functional architecture of a neural circuit controlling the choice between roaming and dwelling states, which underlie exploration and exploitation during foraging inC. elegans. By imaging ensemble-level neural activity in freely-moving animals, we identify stable, circuit-wide activity patterns corresponding to each behavioral state. Combining circuit-wide imaging with genetic analysis, we find that mutual inhibition between two antagonistic neuromodulatory systems underlies the persistence and mutual exclusivity of the opposing network states. Through machine learning analysis and circuit perturbations, we identify a sensory processing neuron that can transmit information about food odors to both the roaming and dwelling circuits and bias the animal towards different states in different sensory contexts, giving rise to context-appropriate state transitions. Our findings reveal a potentially general circuit architecture that enables flexible, sensory-driven control of persistent behavioral states.
Physiological and head motion signatures in static and time-varying functional connectivity and their subject discriminability
Authors: Xifra-Porxas Alba , Kassinopoulos Michalis , Mitsis Georgios D.
Published: February 2020

Human brain connectivity yields significant potential as a noninvasive biomarker. Several studies have used fMRI-based connectivity fingerprinting to characterize individual patterns of brain activity. However, it is not clear whether these patterns mainly reflect neural activity or the effect of physiological and motion processes. To answer this question, we capitalize on a large data sample from the Human Connectome Project and rigorously investigate the contribution of the aforementioned processes on functional connectivity (FC) and time-varying FC, as well as their contribution to subject identifiability. We find that head motion, as well as heart rate and breathing fluctuations, induce artifactual connectivity within distinct resting-state networks and that they correlate with recurrent patterns in time-varying FC. Even though the spatiotemporal signatures of these processes yield above-chance levels in subject identifiability, removing their effects at the preprocessing stage improves identifiability, suggesting a neural component underpinning the inter-individual differences in connectivity.
Altered Temporal Variability of Local and Large-scale Resting-state Brain Functional Connectivity Patterns in Schizophrenia and Bipolar Disorder
Authors: Long Yicheng , Liu Zhening , Chan Calais Kin-yuen , Wu Guowei , Xue Zhimin , Pan Yunzhi , Chen Xudong , Huang Xiaojun , Pu Weidan
Published: February 2020

Schizophrenia and bipolar disorder share some common clinical features and are both characterized by aberrant resting-state functional connectivity (FC). However, little is known about the common and specific aberrant features of the dynamic FC patterns in these two disorders. In this study, we explored the differences in dynamic FC among schizophrenia patients (n= 66), type I bipolar disorder patients (n= 53) and healthy controls (n= 66), by comparing temporal variabilities of FC patterns involved in specific brain regions and large-scale brain networks. Compared with healthy controls, both patient groups showed significantly increased regional FC variabilities in subcortical areas including the thalamus and basal ganglia, as well as increased inter-network FC variability between the thalamus and sensorimotor areas. Specifically, more widespread changes were found in the schizophrenia group, involving increased FC variabilities in sensorimotor, visual, attention, limbic and subcortical areas at both regional and network levels, as well as decreased regional FC variabilities in the default-mode areas. The observed alterations shared by schizophrenia and bipolar disorder may help to explain their overlapped clinical features; meanwhile, the schizophrenia-specific abnormalities in a wider range may support that schizophrenia is associated with more severe functional brain deficits than bipolar disorder.
Increased variation in sex organ positions can increase reciprocity and pollination success in heterostylous plant populations
Authors: Ganguly Shatarupa , Shreenidhi P.M. , Barua Deepak
Published: February 2020

Aims

The reciprocal position of sexual organs in complementary floral morphs is central to our understanding of heterostyly. Reciprocity indices are used to quantify the spatial match between complementary sex organs, but previous indices fail to appropriately account for variation in sex organ positions among individuals in a population. The objective of this study was to examine how reciprocity and consequently reproductive success change with an increase in intra-population variation in sex organ heights. To this end, we formulated a reciprocity index that incorporates variation in sex organ positions among individuals in a population and asked if estimates of reciprocity can predict reproductive success in naturally occurring heterostylous populations.

Methods

We developed a reciprocity index that assumed pollen transfer success equalled one for a perfectly matched stigma-anther pair, and decreased to zero with increasing mismatch. Reciprocity was quantified as the average pollen transfer success for all pair-wise combinations of complementary sex organs in the population. We examined the relationship between intra-population variation and reciprocity using simulated populations that varied in the distribution of sex organ positions, and with empirical data from natural populations. We compared previously proposed indices using the simulated and natural populations, and for a subset of natural populations we tested the ability of the indices to predict reproductive success.

Important Findings

In both simulated and natural populations we observed that when differences between mean anther and stigma heights of complementary morphs are small, increasing intra-population variation in heights resulted in a monotonous decrease in reciprocity. However, when differences between mean complementary anther and stigma heights are larger, reciprocity increased, reached a peak, and then decreased with increasing variation. Previous indices failed to capture this behaviour and were largely insensitive to variation or differences in mean complementary sex organ heights. Seed set was consistently positively related to reciprocity for our index, and for two of the four previous indices. These results highlight the importance of incorporating intra-population variation in sex organ dimensions in quantifying reciprocity, and challenge the current understanding that increasing variation will always decrease reciprocity in heterostylous populations. These results may help explain why heterostylous systems exhibit, and tolerate high amounts of intra-population variation in sex organ heights.
Segregation, connectivity, and gradients of deactivation in neural correlates of evidence in social decision making
Authors: Viviani Roberto , Dommes Lisa , Bosch Julia E. , Labek Karin
Published: February 2020

Functional imaging studies of sensory decision making have detected a signal associated with evidence for decisions that is consistent with data from single-cell recordings in laboratory animals. However, the generality of this finding and its implications on our understanding of the organization of the fMRI signal are not clear. In the present functional imaging study, we investigated decisions in an elementary social cognition domain to identify the neural correlates of evidence, their segregation, connectivity, and their relationship to task deactivations. Besides providing data in support of an evidence-related signal in a social cognition task, we were interested in embedding these neural correlates in models of supramodal associative cortex placed at the top of a hierarchy of processing areas. Participants were asked to decide which of two depicted individuals was saddest based on information rich in sensory features (facial expressions) or through contextual cues suggesting the mental state of others (stylized drawings of mourning individuals). The signal associated with evidence for the decision was located in two distinct networks differentially recruited depending on the information type. Using the largest peaks of the signal associated with evidence as seeds in a database of connectivity data, these two networks were retrieved. Furthermore, the hubs of these networks were located near or along a ribbon of cortex located between task activations and deactivations between areas affected by perceptual priming and the deactivated areas of the default network system. In associative cortex, these findings suggest gradients of progressive relative deactivation as a possible neural correlate of the cortical organization envisaged by structural models of cortical organization and by predictive coding theories of cortical function.
Species level enrichment of AnAOB and associated growth morphology under the effect of key metabolites
Authors: Lu Yang , Natarajan Gayathri , Nguyen Thi Quynh Ngoc , Thi Sara Swa , Arumugam Krithika , Seviour Thomas William , Williams Rohan B.H. , Wuertz Stefan , Law Yingyu
Published: February 2020

Nineteen anaerobic ammonium oxidizing bacteria (AnAOB) species have been identified, yet the environmental factors that select for each species within a specialized ecological niche have not been described. We enriched AnAOB from a single inoculum under standard enrichment conditions (reactor R1) with stepwise increase in nitrite and ammonia concentration, nitric oxide (NO) supplementation (reactor R2), or with complex organic carbon using wastewater collected from mainstream wastewater treatment facility (reactor R3). AnAOB were enriched up to 80%, 90% and 50% relative abundance in R1, R2 and R3 respectively.CandidatusBrocadia caroliniensis predominated in all reactors, but a shift towardsCa. Brocadia sinica was consistently observed with increasing ammonium and nitrite concentrations beyond 270 mg NH4-N L−1and 340 mg NO2-N L−1, respectively. In the presence of NO, growth of heterotrophs were inhibited, andCa. Jettenia could coexist withCa. B. caroliniensis before diminishing when nitrite increased to 160 mg NO2-N L−1. In contrast, supplementation of organic carbon led to the emergence of heterotrophic communities that coevolved withCa. B. caroliniensis.Ca. B. caroliniensis andCa. Jettenia preferentially form biofilms on reactor surfaces, whereasCa. Brocadia sinica forms granules in suspension. Our results thus indicate that multiple AnAOB species co-exist and occupy sub-niches in anaerobic ammonium oxidation reactors, that the dominant population can be reversibly shifted by, for example, changing the nitrogen load (i.e. high nitrite concentration favorsCa. Brocadia caroliniensis), and that speciation has implications for wastewater process design, with the optimum cell immobilization strategy (i.e. carriers vs granules) dependent on which species dominates.

IMPORTANCE

This study demonstrates how to reversibly and predictably shift dominant anammox population using operating parameters (e.g. high nitrite concentration favoursCa. Brocadia sinica), and that species selection has implications for wastewater process design, illustrated here in terms of dependence of optimum cell immobilization strategy (i.e. carriers vs granules) on which species dominates. The research informs the characterization of AnAOBs at species level as well process design and control strategies targeting Anammox species population dynamics in full scale waste water treatment systems.
Aggregation and Disaggregation Features of the Human Proteome
Authors: Määttä Tomi A , Rettel Mandy , Helm Dominic , Stein Frank , Savitski Mikhail M
Published: February 2020

Protein aggregates have negative implications in disease. While reductionist experiments have increased our understanding of aggregation processes, the systemic view in biological context is still limited. To extend this understanding, we used mass spectrometry-based proteomics to characterize aggregation and disaggregation in human cells after non-lethal heat shock. Aggregation-prone proteins were enriched in nuclear proteins, high proportion of intrinsically disordered regions, high molecular mass, high isoelectric point and hydrophilic amino acids. During recovery, most aggregating proteins disaggregated with a rate proportional to the aggregation propensity: larger loss in solubility was counteracted by faster disaggregation. High amount of intrinsically disordered regions also resulted in faster disaggregation. However, other characteristics enriched in aggregating proteins did not correlate with the disaggregation rates. In addition, we analyzed changes in protein thermal stability after heat shock. Soluble remnants of aggregated proteins were more thermally stable compared to control condition. Our results provide a rich resource of heat stress-related protein solubility data, propose novel roles for intrinsically disordered regions in protein quality control and reveal a protection mechanism to repress protein aggregation in heat stress.
The Wsp intermembrane complex mediates metabolic control of the swim-attach decision ofPseudomonas putida
Authors: Hueso-Gil Ángeles , Calles Belén , de Lorenzo Víctor
Published: February 2020

Pseudomonas putidaKT2440, a microorganism of interest for biotechnological purposes, is one amongst the many bacteria that attach to surfaces and produce biofilm. Although other mechanisms that contribute to this decision have been studied until now, a 7-genes-operon with a disposition and homology shared with thewspoperon inPseudomonas aeruginosaremained to be investigated. In this work, we characterized the function ofP. putida wspoperon by the combination of deletion mutants with complementations withP. aeruginosa’s genes and with deletions of 3 other genes: the genes that code for the transcription factorsfleQandfleNand the flagellar movement regulator,fglZ. Examining mutant behaviour at 6 and 24 hours under three different carbon regimes (citrate, glucose and fructose) we saw that this complex carries out a similar function in bothPseudomonas. InP. putida, the key components are WspR, a protein that harbours the domain for producing c-di-GMP, and WspF, which controls its activity. Transformation with the equivalent proteins ofP. aeruginosahad a significant impact on ofP. putidamutant phenotypes and could complement their functions under some conditions. These results contribute to the deeper understanding of the complex element network that regulate lifestyle decision inP. putida
Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
Authors: Li Runsheng , Ren Xiaoliang , Ding Qiutao , Bi Yu , Xie Dongying , Zhao Zhongying
Published: February 2020

Massively parallel sequencing of the polyadenylated RNAs has played a key role in delineating transcriptome complexity, including alternative use of an exon, promoter, 5′ or 3′ splice site or polyadenylation site, and RNA modification. However, reads derived from the current RNA-seq technologies are usually short and deprived of information on modification, compromising their potential in defining transcriptome complexity. Here, we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts. To utilize the full-length transcripts in defining transcriptome complexity, we devised a method to classify the long reads as the same as existing transcripts or as a novel transcript using sequence mapping tracks rather than existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. The sets of genes with differential expression versus differential isoform usage over development are largely different, implying a fine-tuned regulation at isoform level. We also observed an unexpected increase in putative RNA modification in all bases in the coding region relative to the UTR, suggesting their possible roles in translation. The RNA reads and the method for read classification are expected to deliver new insights into RNA processing and modification and their underlying biology in the future.
Crystal structures of the cell-division protein FtsZ from Klebsiella pneumoniae and Escherichia coli
Authors: Yoshizawa Takuya , Fujita Junso , Terakado Haruna , Ozawa Mayuki , Kuroda Natsuko , Tanaka Shun-ichi , Uehara Ryo , Matsumura Hiroyoshi
Published: February 2020

FtsZ, a tubulin-like GTPase, is essential for bacterial cell division. In the presence of GTP, FtsZ polymerizes into filamentous structures, which are key to generating force in cell division. However, the structural basis for the molecular mechanism underlying FtsZ function remains to be elucidated. In this study, crystal structures of the enzymatic domains of FtsZ from Klebsiella pneumoniae (KpFtsZ) and Escherichia coli (EcFtsZ) were determined at 1.75 and 2.50 Å resolution, respectively. Both FtsZs form straight protofilaments in the crystals, and the two structures adopted relaxed (R) conformations. The T3 loop, which is involved in GTP/GDP binding and FtsZ assembly/disassembly, adopted a unique open conformation in KpFtsZ, while the T3 loop of EcFtsZ was partially disordered. The crystal structure of EcFtsZ can explain the results from previous functional analyses using EcFtsZ mutants.