bluuebunny/crossref_metadata_2025_split huggingface dataset:
ArabidopsisTopless-related 1 mitigates physiological damage and growth penalties of induced immunity
Authors: Griebel Thomas , Lapin Dmitry , Locci Federica , Kracher Barbara , Bautor Jaqueline , Qiu Jingde , Concia Lorenzo , Benhamed Moussa , Parker Jane E. 
Published: July 2021

SummaryTranscriptional corepressors of the Topless family are important regulators of plant hormone and immunity signaling. The lack of a genome-wide profile of their chromatin associations limits understanding of transcriptional regulation in plant immune responses. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed on GFP-tagged Topless-related 1 (TPR1) expressed inArabidopsis thalianalines with and without constitutive immunity dependent onEnhanced Disease Susceptibility 1(EDS1). RNA-seq profiling of pathogen-infectedtpl/tprmutants and assessments of growth and physiological parameters were employed to determine TPL/TPR roles in transcriptional immunity and defense homeostasis. TPR1 bound to promoter regions of ~1,400 genes and ~10% of the detected binding requiredEDS1immunity signaling. Atpr1 tpl tpr4(t3) mutant displayed mildly enhanced defense-related transcriptional reprogramming upon bacterial infection but not increased bacterial resistance. Bacteria or pep1 phytocytokine-challengedt3plants exhibited, respectively, photosystem II dysfunction and exacerbated root growth inhibition. Transgenic expression ofTPR1restored thet3physiological defects. We propose that TPR1 and TPL-family proteins function inArabidopsisto reduce detrimental effects associated with activated transcriptional immunity.
Structural-functional connectivity mapping of the insular cortex: A combined data-driven and meta-analytic topic mapping
Authors: Klugah-Brown Benjamin , Wang Pan , Jiang Yuan , Becker Benjamin , Hu Peng , Uddin Lucina Q. , Biswal Bharat 
Published: July 2021

AbstractIn this study, we examined structural and functional profiles of the insular cortex and mapped associations with well-described functional networks (FNs) throughout the brain using diffusion tensor imaging (DTI) and resting-state functional connectivity (RSFC) data. We used a data-driven method to independently estimate the structural-functional connectivity of the insular cortex. Data were obtained from the Human Connectome Project comprising 108 adult participants. Overall, we observed moderate to high associations between the structural and functional mapping scores of three different insular subregions: the posterior insula (associated with the sensorimotor network: RSFC, DTI = 50% and 72%, respectively), dorsal anterior insula (associated with ventral attention: RSFC, DTI = 83% and 83%, respectively), and ventral anterior insula (associated with the frontoparietal: RSFC, DTI = 42% and 89%, respectively). Further analyses utilized meta-analytic decoding maps to demonstrate specific cognitive and affective as well as gene expression profiles of the three subregions reflecting the core properties of the insular cortex. In summary, given the central role of the insular in the human brain, our results revealing correspondence between DTI and RSFC mappings provide a complementary approach and insight for clinical researchers to identify dysfunctional brain organization in various neurological disorders associated with insular pathology.
Feeding habits and the influence of pellet diameter on the feeding responses of the flathead grey mullet (Mugil cephalus) in captivity
Authors: Ramos-Júdez Sandra , Duncan Neil 
Published: July 2021

AbstractThe feeding habits and effect of the diameter of pelleted feeds on the feeding responses of wild juvenile and adult flathead grey mullet (Mugil cephalus) in captivity were examined. Optimal pellet size for feeding was defined according to the behavioural responses and ingestion of pellets with different diameters (2, 4, 6, 8 mm) that were dropped into the tank in a random sequence. Larger pellets (6 and 8 mm) were more attractive (lower reaction time, high percentage of capture), but the small to medium-sized pellets (2 and 4 mm) were consumed the most. The optimal size was the 2- and 4- mm pellet diameter for juvenile individuals (365.50 ± 36.90 g; 28.8 ± 0.84 cm) and the 4-mm diameter pellet for adults (937.49 ± 146.54 g; 40 ± 1.12 cm). The preferred feeding area of adult mullet was also studied to estimate preference in relation to pellet characteristics such as floating or sink. Two pellet types, floating or sinking, were offered simultaneously in the water column: at the surface, mid-water column and bottom of the tank. The flathead grey mullet had a preference to feed in the mid-water column and the bottom of the tanks indicating that sinking or slow-sinking pellets would be the optimal feed type in relation to mullet feeding behaviour.
Virtual meetings promise to eliminate the geographical and administrative barriers and increase accessibility, diversity, and inclusivity
Authors: Wu Juncheng , Rajesh Anushka , Huang Yu-Ning , Chhugani Karishma , Acharya Rajesh , Peng Kerui , Johnson Ruth D. , Fiscutean Andrada , Robles-Espinoza Carla Daniela , De La Vega Francisco M. , Bao Riyue , Mangul Serghei 
Published: July 2021

AbstractThe COVID-19 pandemic brought a new set of unprecedented challenges not only for healthcare, education, and everyday jobs but also in terms of academic conferences. In this study, we investigate the effect of the broad adoption of virtual platforms for academic conferences as a response to COVID-19 restrictions. We show that virtual platforms enable higher participation from underrepresented minority groups, increased inclusion, and broader geographic distribution. We also discuss emerging challenges associated with the virtual conference format resulting in a decreased engagement of social activities, limited possibilities of cross-fertilization between participants, and reduced peer-to-peer interactions. Lastly, we conclude that a novel comprehensive approach needs to be adopted by the conference organizers to ensure increased accessibility, diversity, and inclusivity of post-pandemic conferences. Our findings provide evidence favoring a hybrid format for future conferences, marrying the strength of both in-person and virtual platforms.
Genome binning of viral entities from bulk metagenomics data
Authors: Johansen Joachim , Plichta Damian , Nissen Jakob Nybo , Jespersen Marie Louise , Shah Shiraz A. , Deng Ling , Stokholm Jakob , Bisgaard Hans , Nielsen Dennis Sandris , Sørensen Søren , Rasmussen Simon 
Published: July 2021

AbstractDespite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal are not well understood. In addition, a paucity of whole-virome datasets from subjects with gastrointestinal diseases is preventing a deeper understanding of the virome’s role in disease and in gastrointestinal ecology as a whole. By combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets we developed the Phages from Metagenomics Binning (PHAMB) approach for binning thousands of viral genomes directly from bulk metagenomics data. Simultaneously our methodology enables clustering of viral genomes into accurate taxonomic viral populations. We applied this methodology on the Human Microbiome Project 2 (HMP2) cohort and recovered 6,077 HQ genomes from 1,024 viral populations and explored viral-host interactions. We show that binning can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.
The smooth transition from many-legged to bipedal locomotion - Gradual ground force reduction and its impact on total ground reaction forces, body dynamics and gait transitions
Authors: Weihmann Tom 
Published: July 2021

AbstractMost terrestrial animals move with a specific number of propulsive legs, which differs between clades. The reasons for these differences are often unknown and rarely queried, despite the underlying mechanisms being indispensable for understanding the evolution of multilegged locomotor systems in the animal kingdom and the development of swiftly moving robots. Moreover, when speeding up, a range of species change their number of propulsive legs. The reasons for this behaviour have proven equally elusive. In animals and robots, the number of propulsive legs also has a decisive impact on the movement dynamics of the centre of mass. Here, I use the leg force interference model to elucidate these issues by introducing gradually declining ground reaction forces in locomotor apparatuses with varying numbers of leg pairs in a first numeric approach dealing with these measures’ impact on locomotion dynamics. The effects caused by the examined changes in ground reaction forces and timing thereof follow a continuum. However, the transition from quadrupedal to a bipedal locomotor system deviates from those between multilegged systems with different numbers of leg pairs. Only in quadrupeds do reduced ground reaction forces beneath one leg pair result in increased reliability of vertical body oscillations and therefore increased energy efficiency and dynamic stability of locomotion.Significance statementThe model grants access to the effects of gradual ground force reduction on total ground reaction forces, body dynamics and gait transitions.
Adult medial habenula neurons require GDNF receptor GFRα1 for synaptic stability and function
Authors: Fernández-Suárez Diana , Krapacher Favio A. , Pietrajtis Katarzyna , Andersson Annika , Kisiswa Lilian , Diana Marco A. , Ibáñez Carlos F. 
Published: July 2021

AbstractThe medial habenula (mHb) is an understudied small brain nucleus linking forebrain and midbrain structures controlling anxiety and fear behaviors. The mechanisms that maintain the structural and functional integrity of mHb neurons and their synapses remain unknown. Using spatio-temporally controlled Cre-mediated recombination in adult mice, we found that the GDNF receptor alpha 1 (GFRα1) is required in adult mHb neurons for synaptic stability and function. mHb neurons express some of the highest levels of GFRα1 in the mouse brain, and acute ablation of GFRα1 results in loss of septo-habenular and habenulo-interpeduncular glutamatergic synapses, with the remaining synapses displaying reduced numbers of presynaptic vesicles. Chemo- and opto-genetic studies in mice lacking GFRα1 revealed impaired circuit connectivity, reduced AMPA receptor postsynaptic currents, and abnormally low rectification index of AMPARs, suggesting reduced Ca2+-permeability. Further biochemical and proximity ligation assay studies defined the presence of GluA1/GluA2 (Ca2+-impermeable) as well as GluA1/GluA4 (Ca2+-permeable) AMPAR complexes in mHb neurons, as well as clear differences in the levels and association of AMPAR subunits in mHb neurons lacking GFRα1. Finally, acute loss of GFRα1 in adult mHb neurons reduced anxiety-like behavior and potentiated context-based fear responses, phenocopying the effects of lesions to septal projections to the mHb. These results uncover an unexpected function for GFRα1 in the maintenance and function of adult glutamatergic synapses, and reveal a potential new mechanism for regulating synaptic plasticity in the septo-habenulo-interpeduncular pathway and attuning of anxiety and fear behaviors.
Characterization of the radiation desiccation response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses
Authors: Eugénie Nicolas , Zivanovic Yvan , Lelandais Gaelle , Coste Geneviève , de la Tour Claire Bouthier , Bentchikou Esma , Servant Pascale , Confalonieri Fabrice 
Published: July 2021

AbstractNumerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. The DdrO and IrrE proteins play a major role in regulating the expression of approximately predicted twenty of these genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. Bioinformatic analyzes showed that this mechanism seems to be conserved in several species of Deinococcus, but many questions remain as such the number of genes regulated by DdrO. Here, by RNA-seq and CHiP-seq assays performed at a genome-wide scale coupled with bioinformatic analyses, we show that, the DdrO regulon in D. radiodurans includes many other genes than those previously described. These results thus pave the way to better understand the radioresistance mechanisms encoded by this bacterium.Author SummaryThe main response pathway to genotoxic conditions in the radioresistant bacterium Deinococcus radiodurans is regulated by the constitutively expressed metalloprotease IrrE that cleaves the transcriptional repressor DdrO, leading to the expression of the genes repressed by DdrO. One of the major goals to better understand how pathways involved in radioresistance are coordinated into this fascinating bacterium is to highlight genes regulated by DdrO. In this study, we mapped in vivo the DdrO regulon in D. radiodurans by using two genome-scale approaches, ChIP-seq and RNA-seq analyses, coupled with bioinformatic analyses. As homologs of these two proteins are also found in many other bacteria, these results also pave the way to compare the stress-induced responses mediated by this couple of proteins in diverse bacteria.
All driven by energy demand? Integrative comparison of metabolism ofEnterococcus faecaliswildtype and a glutamine synthase mutant
Authors: Loghmani Seyed Babak , Zitzow Eric , Koh Gene Ching-Chiek , Ulmer Andreas , Veith Nadine , Großeholz Ruth , Rossnagel Madlen , Loesch Maren , Aebersold Ruedi , Kreikemeyer Bernd , Fiedler Tomas , Kummer Ursula 
Published: July 2021

AbstractLactic acid bacteria (LAB) play a significant role in biotechnology, e.g. food industry, but also in human health. Many LAB genera have developed a multidrug resistance in the past few years, becoming a serious problem in controlling hospital germs all around the world.Enterococcus faecalisaccounts for a large part of the human infections caused by LABs. Therefore, studying its adaptive metabolism under various environmental conditions is particularly important. In this study, we investigated the effect of glutamine auxotrophy (ΔglnAmutant) on metabolic and proteomic adaptations ofE. faecalisin response to a changing pH in its environment. Changing pH values are part of its natural environment in the human body, but also play a role in food industry. We compared the results to those of the wildtype. Our integrative method, using a genome-scale metabolic model, constrained by metabolic and proteomic data allows us to understand the bigger picture of adaptation strategies in this bacterium. The study showed that energy demand is the decisive factor in adapting to a new environmental pH. The energy demand of the mutant was higher at all conditions. It has been reported that ΔglnAmutants of bacteria are energetically less effective. With the aid of our data and model we are able to explain this phenomenon as a consequence of a failure to regulate glutamine uptake and the costs for the import of glutamine and the export of ammonium. Methodologically, it became apparent that taking into account the non-specificity of amino acid transporters is important for reproducing metabolic changes with genome-scale models since it affects energy balance.
A DEEP LEARNING APPROACH TO ESTIMATING INITIAL CONDITIONS OF BRAIN NETWORK MODELS IN REFERENCE TO MEASURED FMRI DATA
Authors: Kashyap Amrit , Plis Sergey , Schirner Michael , Ritter Petra , Keilholz Shella 
Published: July 2021

1.AbstractBrain Network Models (BNMs) are a family of dynamical systems that simulate whole brain activity using neural mass models to represent local activity in different brain regions that influence each other via a global structural network. Research has been interested in using these network models to explain measured whole brain activity measured via resting state functional magnetic resonance imaging (rs-fMRI). Properties computed over longer periods of simulated and measured data such as average functional connectivity (FC), have shown to be comparable with similar properties estimated from measured rs-fMRI data. While this shows that these network models have similar properties over the dynamical landscape, it is unclear how well simulated trajectories compare with empirical trajectories on a timepoint-by-timepoint basis. Previous studies have shown that BNMs are able to produce relevant features at shorter timescales, but analysis of short-term trajectories or transient dynamics as defined by synchronized predictions from BNM made at the same timescale as the collected data has not yet been conducted. Relevant neural processes exist in the time frame of measurements and are often used in task fMRI studies to understand neural responses to behavioral cues. Therefore, it is important to investigate how much of these dynamics are captured by our current brain simulations. To test the nature of BNMs short term trajectories against observed data, we utilize a deep learning technique known as Neural ODE that based on an observed sequence of fMRI measurements, estimates the initial conditions such that the BNM’s simulation is synchronized to produce the closest trajectory relative to the observed data. We test to see if the parameterization of a specific well studied BNM, the Firing Rate Model, calculated by maximizing its accuracy in reproducing observed short term trajectories matches with the parameterized model that produces the best average long-term metrics. Our results show that such an agreement between parameterization using long and short simulation analysis exists if also considering other factors such as the sensitivity in accuracy with relative to changes in structural connectivity. Therefore, we conclude that there is evidence that by solving for initial conditions, BNMs can be simulated in a meaningful way when comparing against measured data trajectories, although future studies are necessary to establish how BNM activity relate to behavioral variables or to faster neural processes during this time period.
H3K9me2 genome-wide distribution in the holocentric insect Spodoptera frugiperda (Lepidoptera: Noctuidae)
Authors: Nhim Sandra , Gimenez Sylvie , Nait-Saidi Rima , Severac Dany , Nam Kiwoong , d’Alençon Emmanuelle , Nègre Nicolas 
Published: July 2021

AbstractBackgroundEukaryotic genomes are packaged by Histone proteins in a structure called chromatin. There are different chromatin types. Euchromatin is typically associated with decondensed, transcriptionally active regions and heterochromatin to more condensed regions of the chromosomes. Methylation of Lysine 9 of Histone H3 (H3K9me) is a conserved biochemical marker of heterochromatin. In many organisms, heterochromatin is usually localized at telomeric as well as pericentromeric regions but can also be found at interstitial chromosomal loci. This distribution may vary in different species depending on their general chromosomal organization. Holocentric species such as Spodoptera frugiperda (Lepidoptera: Noctuidae) possess dispersed centromeres instead of a monocentric one and thus no observable pericentromeric compartment. To identify the localization of heterochromatin in such species we performed ChIP-Seq experiments and analyzed the distribution of the heterochromatin marker H3K9me2 in the Sf9 cell line and whole 4th instar larvae (L4) in relation to RNA-Seq data.ResultsIn both samples we measured an enrichment of H3K9me2 at the (sub) telomeres, rDNA loci, and satellite DNA sequences, which could represent dispersed centromeric regions. We also observed that density of H3K9me2 is positively correlated with transposable elements and protein-coding genes. But contrary to most model organisms, H3K9me2 density is not correlated with transcriptional repression.ConclusionThis is the first genome-wide ChIP-Seq analysis conducted in S. frugiperda for H3K9me2. Compared to model organisms, this mark is found in expected chromosomal compartments such as rDNA and telomeres. However, it is also localized at numerous dispersed regions, instead of the well described large pericentromeric domains, indicating that H3K9me2 might not represent a classical heterochromatin marker in Lepidoptera.
SufB intein splicing inMycobacterium tuberculosisis influenced by two remote conserved N-extein Histidines
Authors: Panda Sunita , Nanda Ananya , Sahu Nilanjan , Ojha Deepak , Pradhan Biswaranjan , Rai Anjali , Suryawanshi Amol R. , Banavali Nilesh , Nayak Sasmita 
Published: July 2021

AbstractInteins are auto-processing domains that implement a multi-step biochemical reaction termed protein splicing, marked by cleavage and formation of peptide bonds. They excise from a precursor protein, generating a functional protein via covalent bonding of flanking exteins. We report the kinetic study of splicing and cleavage reaction in [Fe-S] cluster assembly protein SufB fromMycobacterium tuberculosis. Although it follows a canonical intein splicing pathway, distinct features are added by extein residues present in the active site. Sequence analysis identified two conserved histidines in the N-extein region; His-5 and His-38. Kinetic analyses of His-5Ala and His-38Ala SufB mutants exhibited significant reductions in splicing and cleavage rates relative to the SufB wild-type precursor protein. Structural analysis and molecular dynamics simulations suggested thatMtuSufB displays a unique mechanism where two remote histidines work concurrently to facilitate N-terminal cleavage reaction. His-38 is stabilized by the solvent-exposed His-5, and can impact N-S acyl shift by direct interaction with the catalytic Cys1. Development of inteins as biotechnological tools or as pathogen specific novel antimicrobial targets requires a more complete understanding of such unexpected roles of conserved extein residues in protein splicing.
Spatially resolved transcriptomics reveals unique gene signatures associated with human temporal cortical architecture and Alzheimer’s pathology
Authors: Chen Shuo , Chang Yuzhou , Li Liangping , Acosta Diana , Morrison Cody , Wang Cankun , Julian Dominic , Hester Mark E. , Serrano Geidy E. , Beach Thomas G. , Ma Qin , Fu Hongjun 
Published: July 2021

AbstractAlzheimer’s disease (AD) is pathologically characterized by amyloid beta (Aβ) plaques, neurofibrillary tangles (tau aggregates), and alterations in microglia, astrocytes and oligodendrocytes. The mesial temporal lobe is a vulnerable brain region in early AD; however, little is known about the transcriptome-scale gene expression in this region and its relation to AD pathology. Here we use the 10x Genomics Visium platform in combination with co-immunofluorescence staining of AD-associated pathological markers to define the spatial topography of gene expression in the middle temporal gyrus (MTG) from both early AD and age- and gender-matched control cases. We identify unique marker genes for six cortical layers and the adjacent white matter as well as gene expression patterns and alterations that showcase unique gene signatures and pathways associated with a range of AD pathology. Also, gene co-expression analyses of differentially expressed genes (DEGs) between AD and controls reveal four unique gene modules, which significantly change their co-expression patterns in the presence of variations of AD pathology. Furthermore, we validate the changes of key representative DEGs that are associated with AD pathology in neurons, microglia, astrocytes and oligodendrocytes using single-molecule fluorescent in situ hybridization. In summary, we provide a rich resource for the spatial transcriptomic profile of the human MTG, which will contribute to our understanding of the complex architecture and AD pathology of this vulnerable brain region.