bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genome sequence of the octocoral Paramuricea clavata – a key resource to study the impact of climate change in the Mediterranean
Authors: Ledoux Jean-Baptiste , Cruz Fernando , Gomez-Garrido Jèssica , Antoni Regina , Blanc Julie , Gómez-Gras Daniel , López-Sendino Paula , Antunes Agostinho , Linares Cristina , Gut Marta , Alioto Tyler , Garrabou Joaquim 
Published: November 2019

AbstractThe octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e. varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes and genetic factors contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo hybrid assembly accounting for 712.4 Mb and 107,682 scaffolds. The contig and scaffold N50 are 15.85 Kb and 17.01 Kb, respectively. Despite of the low contiguity of the assembly, the gene completeness was relatively high, including 86% of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 76,508 protein-coding genes and 85,763 transcripts have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, the genome of P. clavata will help to understand various aspects of its evolutionary ecology and to elaborate effective conservation plans such as active restoration actions to overcome the threats of global change.
SVJedi: Genotyping structural variations with long reads
Authors: Lecompte Lolita , Peterlongo Pierre , Lavenier Dominique , Lemaitre Claire 
Published: November 2019

AbstractMotivationStudies on structural variants (SV) are expanding rapidly. As a result, and thanks to third generation sequencing technologies, the number of discovered SVs is increasing, especially in the human genome. At the same time, for several applications such as clinical diagnoses, it is important to genotype newly sequenced individuals on well defined and characterized SVs. Whereas several SV genotypers have been developed for short read data, there is a lack of such dedicated tool to assess whether known SVs are present or not in a new long read sequenced sample, such as the one produced by Pacific Biosciences or Oxford Nanopore Technologies.ResultsWe present a novel method to genotype known SVs from long read sequencing data. The method is based on the generation of a set of reference sequences that represent the two alleles of each structural variant. Long reads are aligned to these reference sequences. Alignments are then analyzed and filtered out to keep only informative ones, to quantify and estimate the presence of each SV allele and the allele frequencies. We provide an implementation of the method, SVJedi, to genotype insertions and deletions with long reads. The tool has been applied to both simulated and real human datasets and achieves high genotyping accuracy. We also demonstrate that SV genotyping is considerably improved with SVJedi compared to other approaches, namely SV discovery and short read SV genotyping approaches.Availabilityhttps://github.com/llecompte/SVJedi.gitContactlolita.lecompte@inria.fr
Mental travel in the social domain
Authors: Hayman Mordechai , Arzy Shahar 
Published: November 2019

“Mental travel” is the ability to imagine oneself in different places and times and to adopt other people’s point of view (POV), also termed “Theory of Mind (ToM)”. While ToM has been extensively investigated, self-projection with respect to ones’ own and others’ social networks has yet to be systematically studied.Here we asked participants to “project” themselves to four different POVs: a significant other, a non-significant other, a famous-person, and their own-self. From each POV they were asked to rate the level of affiliation (closeness) to different individuals in the respective social network while undergoing functional MRI.Participants were always faster making judgments from their own POV compared to other POVs (self-projection effect) and for people who were personally closer to their adopted POV (self-reference effect). Brain activity at the medial prefrontal and anterior cingulate cortex in the self POV condition was found to be higher compared to all other conditions. Activity at the right temporoparietal junction and medial parietal cortex was found to distinguish between the personally related (self, significant- and non-significant others) and unrelated (famous-person) individuals within the social network. Regardless of the POV, the precuneus, anterior cingulate cortex, prefrontal cortex, and temporoparietal junction distinguished between relatively closer and distant people. Representational similarity analysis (RSA) implicated the left retrosplenial cortex as crucial for social distance processing across all POVs.
Stimulus contrast information modulates sensorimotor decision making in goldfish
Authors: Coronel Santiago Otero , Martorell Nicolás , de Astrada Martín Berón , Medan Violeta 
Published: November 2019

AbstractAnimal survival relays on environmental information gathered by their sensory systems. We found that contrast information of a looming stimulus biases the type of defensive behavior goldfish (Carassius auratus) perform. Low contrast looms only evoke subtle alarm reactions whose probability is independent of contrast. As looming contrast increases, the probability of eliciting a fast escape maneuver, the C-start response, increases dramatically. Contrast information also modulates the decision of when to escape. Although looming retinal size is determinant of response latency, we found that contrast acts as an additional parameter influencing this decision. When presented progressively higher contrast stimuli, animals need shorter periods of stimulus integration to initiate the response. Our results comply the notion that the decision to escape is a flexible process initiated with stimulus detection and followed by assessment of the perceived risk posed by the stimulus. Highly disruptive behaviors as the C-start are only observed when a multifactorial threshold that includes stimulus contrast is surpassed.Summary statementThis study highlights that in fish, the decision of what to do after threat detection is a multifactorial non-binary process that includes assessing the relative contrast of the potential threat. Increasingly higher contrast stimuli produce a progressive increase in C-start escape probability and a decrease in response latency. More subtle alarm reactions are, on the contrary, mostly insensitive to changes in contrast. This might reflect that while subtle reactions have lower thresholds to be executed, disruptive behaviors as the C-start must surpass higher saliency thresholds that integrate multiple aspects including contrast.
Electron beam lithography fabrication of SU-8 polymer structures for cell studies
Authors: Vinje Jakob , Beckwith Kai S. , Sikorski Pawel 
Published: November 2019

AbstractFlat surfaces decorated with micro- and nanostructures are important tools in biomedical research used to control cellular shape, in studies of mechanotransduction, membrane mechanics, cell migration and cellular interactions with nanostructured surfaces. Existing methods to fabricate surface-bound nanostructures are typically limited either by resolution, aspect ratio or throughput. In this work, we explore electron beam lithography based structuring of the epoxy resist SU-8 on glass substrate. We focus on a systematic investigation of the process parameters and determine limits of the fabrication process, both in terms of spatial resolution, structure aspect ration and fabrication throughput. The described approach is capable of producing high-aspect ratio, surface bound nanostructures with height ranging from 100 nm to 4000 nm and with in-plane resolution below 100 nm directly on a transparent substrate. Fabricated nanostructured surfaces can be integrated with common techniques for biomedical research, such as high numerical aperture optical microscopy. Further more, we show how the described approach can be used to make nanostructures with multiple heights on the same surface, something which is not readily achievable using alternative fabrication approaches. Our research paves an alternative way of manufacturing nanostructured surfaces with applications in life science research.
Enhancing Gesture Decoding Performance Using Signals from Posterior Parietal Cortex: A Stereo-Electroencephalograhy (SEEG) Study
Authors: Wang Meng , Li Guangye , Jiang Shize , Wei Zixuan , Hu Jie , Chen Liang , Zhang Dingguo 
Published: November 2019

AbstractObjectiveHand movement is a crucial function for humans’ daily life. Developing brain-machine interface (BMI) to control a robotic hand by brain signals would help the severely paralyzed people partially regain the functional independence. Previous intracranial electroencephalography (iEEG)-based BMIs towards gesture decoding mostly used neural signals from the primary sensorimotor cortex while ignoring the hand movement related signals from posterior parietal cortex (PPC). Here, we propose combining iEEG recordings from PPC with that from primary sensorimotor cortex to enhance the gesture decoding performance of iEEG-based BMI.ApproachStereoelectroencephalography (SEEG) signals from 25 epilepsy subjects were recorded when they performed a three-class hand gesture task. Across all 25 subjects, we identified 524, 114 and 221 electrodes from three regions of interest (ROIs), including PPC, postcentral cortex (POC) and precentral cortex (PRC), respectively. Based on the time-varying high gamma power (55-150 Hz) of SEEG signal, both the general activation in the task and the fine selectivity to gestures of each electrode in these ROIs along time was evaluated by the coefficient of determinationr2. According to the activation along time, we further assessed the first activation time of each ROI. Finally, the decoding accuracy for gestures was obtained by linear support vector machine classifier to comparatively explore if the PPC will assist PRC and POC for gesture decoding.Main ResultsWe find that a majority(L: >60%,R: >40%) of electrodes in all the three ROIs present significant activation during the task. A large scale temporal activation sequence exists among the ROIs, where PPC activates first, PRC second and POC last. Among the activated electrodes, 15% (PRC), 26% (POC) and 4% (left PPC) of electrodes are significantly selective to gestures. Moreover, decoding accuracy obtained by combining the selective electrodes from three ROIs together is 5%, 3.6%, and 8% higher than that from only PRC and POC when decoding features across, before, and after the movement onset, were used.SignificanceThis is the first human iEEG study demonstrating that PPC contains neural information about fine hand movement, supporting the role of PPC in hand shape encoding. Combining PPC with primary sensorimotor cortex can provide more information to improve the gesture decoding performance. Our results suggest that PPC could be a rich neural source for iEEG-based BMI. Our findings also demonstrate the early involvement of human PPC in visuomotor task and thus may provide additional implications for further scientific research and BMI applications.
Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)
Authors: Moharana Kanhu C. , Venancio Thiago M. 
Published: November 2019

AbstractTranscription factors (TF) are essential for proper plant growth and development. Several legumes, particularly soybean, are rich sources of protein and oil, with great impact in the economy of several countries. Here we report a phylogenomic analysis of major TF families in legumes and their potential association with important traits such as nitrogen fixation and seed development. We used TF DNA-binding domains to systematically screen the genomes of 15 legume and 5 non-legume species. The percentage of TFs ranged from 3-8% of the gene complements. TF orthologous groups (OG) in extant species were used to estimate OG sizes in ancestor nodes using a gene birth-death model, which allowed us to identify lineage-specific expansions. Together, OG analysis and rate of synonymous substitutions (Ks) between gene pairs show that major TF expansions are strongly associated with known whole-genome duplication (WGD) events in the legume (∼58 mya) and Glycine (∼13 mya) lineages, which account for a large fraction of the Ph. vulgaris and Gl. max TF repertoires. Out of the 3407 Gl. max TFs, 1808 and 676 can be traced back to a single homeolog in Ph. vulgaris and Vi vinifera, respectively. We found a trend for TFs expanded in legumes to be preferentially transcribed in roots and nodules, suggesting their recruitment early in the evolution of nodulation in the legume clade. We also found TF expansions in the Glycine WGD that were followed by gene loss in the wild soybean Gl. soja, including genes located within important quantitative trait loci. Together, our findings strongly support the roles of two WGDs in shaping the TF repertoires in the legume and Glycine lineages, which are likely related to important aspects of legume and soybean biology.
The C-terminal RRM/ACT domain is crucial for fine-tuning the activation of ‘long’ RelA-SpoT Homolog enzymes by ribosomal complexes
Authors: Takada Hiraku , Roghanian Mohammad , Murina Victoriia , Dzhygyr Ievgen , Murayama Rikinori , Akanuma Genki , Atkinson Gemma C. , Garcia-Pino Abel , Hauryliuk Vasili 
Published: November 2019

AbstractThe (p)ppGpp-mediated stringent response is a bacterial stress response implicated in virulence and antibiotic tolerance. Both synthesis and degradation of the (p)ppGpp alarmone nucleotide are mediated by RelA-SpoT Homolog (RSH) enzymes which can be broadly divided in two classes: single-domain ‘short’ and multi-domain ‘long’ RSH. The regulatory ACT (Aspartokinase, Chorismate mutase and TyrA) / RRM (RNA Recognition Motif) domain is a near-universal C-terminal domain of long RSHs. Deletion of RRM in both monofunctional (synthesis-only) RelA as well as bifunctional (i.e. capable of both degrading and synthesising the alarmone) Rel renders the long RSH cytotoxic due to overproduction of (p)ppGpp. To probe the molecular mechanism underlying this effect we characterisedEscherichia coliRelA andBacillus subtilisRel RSHs lacking RRM. We demonstrate that, first, the cytotoxicity caused by the removal of RRM is counteracted by secondary mutations that disrupt the interaction of the RSH with the starved ribosomal complex – the ultimate inducer of (p)ppGpp production by RelA and Rel – and, second, that the hydrolytic activity of Rel is not abrogated in the truncated mutant. Therefore, we conclude that the overproduction of (p)ppGpp by RSHs lacking the RRM domain is not explained by a lack of auto-inhibition in the absence of RRM or/and a defect in (p)ppGpp hydrolysis. Instead, we argue that it is driven by misregulation of the RSH activation by the ribosome.
How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridis
Authors: Foucaud Julien , Hufbauer Ruth A. , Ravigné Virginie , Olazcuaga Laure , Loiseau Anne , Ausset Aurélien , Wang Su , Zang Lian-Sheng , Leménager Nicolas , Tayeh Ashraf , Weyna Arthur , Gneux Pauline , Bonnet Elise , Dreuilhe Vincent , Poutout Bastien , Estoup Arnaud , Facon Benoît 
Published: November 2019

ABSTRACTExperiments comparing native to introduced populations or distinct introduced populations to each other show that phenotypic evolution is common and often involves a suit of interacting phenotypic traits. We define such sets of traits that evolve in concert and contribute to the success of invasive populations as an ‘invasion syndrome’. The invasive Harlequin ladybirdHarmonia axyridisdisplays such an invasion syndrome with, for instance, females from invasive populations being larger and heavier than individuals from native populations, allocating more resources to reproduction, and spreading reproduction over a longer lifespan. Invasion syndromes could emerge due to selection acting jointly and directly on a multitude of traits, or due to selection on one or a few key traits that drive correlated indirect responses in other traits. Here, we investigated the degree to which theH. axyridisinvasion syndrome would emerge in response to artificial selection on either female body mass or on age at first reproduction, two traits involved in their invasion syndrome. To further explore the interaction between environmental context and evolutionary change in molding the phenotypic response, we phenotyped the individuals from the selection experiments in two environments, one with abundant food resources and one with limited resources. The two artificial selection experiments show that the number of traits showing a correlated response depends upon the trait undergoing direct selection. Artificial selection on female body mass resulted in few correlated responses and hence poorly reproduced the invasion syndrome. In contrast, artificial selection on age at first reproduction resulted in more widespread phenotypic changes, which nevertheless corresponded only partly to the invasion syndrome. The artificial selection experiments also revealed a large impact of diet on the traits, with effects dependent on the trait considered and the selection regime. Overall, our results indicate that direct selection on multiple traits was likely necessary in the evolution of theH. axyridisinvasion syndrome. Furthermore, they show the strength of using artificial selection to identify the traits that are correlated in different selective contexts, which represents a crucial first step in understanding the evolution of complex phenotypic patterns, including invasion syndromes.
“mir152hypomethylation, potentially triggered by embryonic hypoxia, as a common mechanism for non-syndromic cleft lip/palate”
Authors: Alvizi Lucas , Brito Luciano Abreu , Bischain Bárbara , da Silva Camila Bassi Fernandes , Ramos Sofia Ligia Guimaraes , Kobayashi Gerson Shigeru , Wang Jaqueline , Passos-Bueno Maria Rita 
Published: November 2019

AbstractNon-syndromic cleft lip/palate (NSCLP), the most common human craniofacial malformations, is a complex disorder given its genetic heterogeneity and multifactorial component revealed by genetic, epidemiological and epigenetic findings. Association of epigenetic variations with NSCLP has been made, however still of little functional investigation. Here we combined a reanalysis of NSCLP methylome data with genetic analysis and used bothin vitroandin vivoapproaches to dissect the functional effects of epigenetic changes. We found a frequent differentially methylated region inmir152, hypomethylated in NSCLP cohorts (21-26%), leading tomir152overexpression.In vivoanalysis using zebrafish embryos revealed thatmir152upregulation leads to craniofacial impairment analogue to palatal defects. Also, we demonstrated that zebrafish embryonic hypoxia leads tomir152upregulation combined withmir152hypomethylation and also analogue palatal alterations. We therefore suggestmir152hypomethylation, potentially induced by hypoxia in early development, as a novel and frequent predisposing factor to NSCLP.
Dorsal raphe oxytocin receptors regulate the neurobehavioral consequences of social touch
Authors: Grieb Z.A. , Ford E.G. , Manfredsson F.P. , Lonstein J.S. 
Published: November 2019

SummaryProsocial interactions are essential for group-living animals and are regulated by tactile cues shared among the group members. Neurobiological mechanisms through which social touch influences prosociality and related affective behaviors are relatively unknown. Using the evolutionarily ancient mother-young dyad as a model, we hypothesized that neurobehavioral consequences of social touch involves an interaction between central oxytocin (released during social touch) and serotonin (regulating affect and neuroplasticity). New mother rats showed upregulation of numerous aspects of the oxytocin system in the midbrain dorsal raphe (DR; source of forebrain serotonin) compared to non-maternal females. Preventing this upregulation by OTR knockdown in the maternal DR elicited infanticide, reduced nursing, increased aggression, and decreased active coping behavior. OTR knockdown also decreased serotonin-immunoreactive fibers, and increased neuroplasticity-restricting perineuronal nets, in the primary somatosensory cortex. Thus, oxytocin signaling in the DR regulates mechanisms involved in serotonin-induced cortical plasticity, which refines the tactile processing underlying prosocial behaviors.
Facile Accelerated Specific Therapeutic (FAST) Platform to Counter Multidrug-Resistant Bacteria
Authors: Eller Kristen A. , Aunins Thomas R. , Courtney Colleen M. , Campos Jocelyn K. , Otoupal Peter B. , Erickson Keesha E. , Madinger Nancy E. , Chatterjee Anushree 
Published: November 2019

ABSTRACTMultidrug-resistant (MDR) bacteria pose a grave concern to global health. This problem is further aggravated by a lack of new and effective antibiotics and countermeasure platforms that can sustain the creation of novel antimicrobials in the wake of new outbreaks or evolution of resistance to antibiotics. To address this, we have developed a Facile Accelerated Specific Therapeutic (FAST) platform that can develop effective therapies against MDR bacteria within a week. Our FAST platform combines four essential modules- design, build, test, and delivery-of drug development cycle. The design module comprises a bioinformatics toolbox that predicts sequence-specific peptide nucleic acids (PNAs) that target non-traditional pathways and genes of bacteria in minutes. The build module constitutes in-situ synthesis and validation of selected PNAs in less than four days and efficacy testing within a day. As a proof of concept, these PNAs were tested against MDR clinical isolates. Here we tested Enterobacteriaceae including carbapenem-resistant Escherichia coli, extended-spectrum beta-lactamase (ESBL) Klebsiella pneumoniae, New Delhi Metallo-beta-lactamase-1 carrying Klebsiella pneumoniae and MDR Salmonella enterica. PNAs showed significant growth inhibition for 82% of treatments, with nearly 18% of the treatments leading to more than 97% decrease. Further, these PNAs are capable of potentiating antibiotic activity in the clinical isolates despite presence of cognate resistance genes. Finally, FAST offers a novel delivery approach to overcome limited transport of PNAs into mammalian cells to clear intracellular infections. This method relies on repurposing the bacterial Type III secretion system in conjunction with a kill switch that is effective at eliminating 99.6% of an intracellular Salmonella infection in human epithelial cells. Our findings demonstrate the potential of the FAST platform in treating MDR bacteria in a rapid and effective manner.