bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prolactin and DNA damage trigger an anti-breast cancer cell immune response
Authors: Atici Ödül Karayazi , Govindrajan Nayantara , Gonzalez Isbel Lopetegui , Finney Constance A. M. , Shemanko Carrie S. 
Published: September 2020

AbstractThere are conflicting reports on the role of prolactin (PRL) in breast cancer, and its role within the context of the tumour microenvironment is not well understood. In our previous study, we demonstrated a cross-talk between the ataxia telangiectasia-mutated (ATM) DNA damage response pathway and the PRL-Janus-kinase-2 (JAK2)-signal transducer and activator of transcription-5 (STAT5)-heat shock protein-90 (HSP90) pathway. To investigate the role of PRL in tumour initiation and the effect of DNA damage in vivo, we used a model of breast cancer initiation that assesses the ability of breast cancer cells to initiate orthotopic xenograft tumour formation after DNA damage. Breast cancer cells engineered to secrete human PRL or the control cells, were treated with the DNA damaging agent doxorubicin or vehicle and injected into the mammary fat pad of immune-deficient SCID mice. PRL secretion from human breast cancer cells did not change the tumour latency compared to controls, although combined doxorubicin and PRL treatment increased tumour latency. Depletion of glycolipid asialo ganglioside-GM1 positive immune cells using anti-asialo GM1 antibody resulted in faster tumour formation only in the PRL-secreting breast cancer cells that were pre-treated with doxorubicin, and not in the PRL-only or empty vector controls. Additionally, doxorubicin plus PRL treatment of breast cancer cells were shownin vitroto attract cytotoxic NK cells compared to controls, and that this was dependent on the PRLR. These results may shed light on the conflicting reports of PRL in breast cancer and demonstrate that combined breast cancer cell DNA damage and PRL exposure results in anti-tumour activity of asialo-GM1-positive immune cells.
Deficient spermiogenesis in mice lackingRlim
Authors: Wang Feng , Gervasi Maria G. , Bošković Ana , Sun Fengyun , Rinaldi Vera D. , Yu Jun , Wallingford Mary C. , Tourzani Darya A. , Mager Jesse , Zhu Lihua J. , Rando Oliver J. , Visconti Pablo E. , Strittmatter Lara , Bach Ingolf 
Published: September 2020

SummaryThe X-linked geneRlimplays major roles in female mouse development and reproduction, where it is crucial for the maintenance of imprinted X chromosome inactivation in extraembryonic tissues of embryos. However, while females carrying a systemicRlimknockout (KO) die around implantation, maleRlimKO mice appear healthy and are fertile, raising questions as to the pressures drivingRlimgene selection during evolution. Here we report an important role forRlimin testis where it is highly expressed in post-meiotic round spermatids as well as in Sertoli cells. Systemic deletion of theRlimgene leads to lower numbers of mature sperm that contains excess cytoplasm, leading to decreased sperm motility andin vitrofertilization rates. Targeting the conditionalRlimcKO specifically to the spermatogenic cell lineage largely recapitulates this phenotype. These results reveal functions ofRlimin male reproduction specifically in round spermatids during spermiogenesis with likely evolutionary implications.
F-box protein At1g08710 negatively regulates root length and imparts drought stress tolerance inArabidopsis thaliana
Authors: Rao Venkateswara , Vijaybhaskar Virupapuram 
Published: September 2020

AbstractPlants experience abiotic stresses throughout their life cycle and accordingly respond to tide over the unfavorable conditions. Drought or water deficit is one such condition to which plants respond in various ways including the ubiquitin proteasome system (UPS). Ubiquitin E3 ligases are a diverse family of protein complexes of which Skp1□Cullin□F□box (SCF) class mediate the ubiquitination and subsequent proteolytic turnover of proteins. F□box protein subunit plays crucial role in imparting specificity for selective degradation of target proteins. Here we report the function ofArabidopsisF-box proteinAt1g08710in drought stress adaptation. As F-box protein is a constituent of SCF complex, here it is shown interacting with ASK1 and Cullin1. F-box protein localizes to both nucleus and membrane. F-box gene transcript accumulates highly in root and is altered in response to drought stress conditions. F-box protein interacts with a transcriptional co-activator protein ADA2b. F-box mutant plants displayed better growth under drought stress conditions compared to the wild type with a reduced accumulation of H2O2and malondialdehyde (MDA). Drought responsive genesRD29A, RD22, ABI3expression is also induced in F-box mutant plants. These results indicate F-box protein At1g08710 plays a role in drought stress adaptation inArabidopsis thaliana.HighlightsF-box geneAt1g08710encodes a nuclear, membrane localized protein.F-box protein At1g08710 interacts with transcriptional co-activator protein ADA2b.F-box protein imparts drought stress tolerance by modulating H2O2and MDA content.Drought response genesRD29A, RD22, ABI3expression is induced in F-box mutant plants.
The relationship between microbiomes and selective regimes in the sponge genusIrcinia
Authors: Kelly Joseph B. , Carlson David , Low Jun Siong , Rice Tyler , Thacker Robert W. 
Published: September 2020

AbstractSponges are often densely populated by microbes that benefit their hosts through nutrition and bioactive secondary metabolites; however, sponges must simultaneously contend with the toxicity of microbes and thwart microbial overgrowth. Despite these fundamental tenets of sponge biology, the patterns of selection in the host sponges’ genomes that underlie tolerance and control of their microbiomes are still poorly understood. To elucidate these patterns of selection, we performed a population genetic analysis on multiple species ofIrciniafrom Belize, Florida, and Panama using anFST-outlier approach on transcriptome-annotated RADseq loci. As part of the analysis, we delimited species boundaries among seven growth forms ofIrcinia. Our analyses identified balancing selection in immunity genes that have implications for the hosts’ tolerance of high densities of microbes. Additionally, our results support the hypothesis that each of the seven growth forms constitutes a distinctIrciniaspecies that is characterized by a unique microbiome. These results illuminate the evolutionary pathways that promote stable associations between host sponges and their microbiomes, and that potentially facilitate ecological divergence amongIrciniaspecies.
Strategies of grain number determination differentiate barley row-types
Authors: Thirulogachandar Venkatasubbu , Koppolu Ravi , Schnurbusch Thorsten 
Published: September 2020

AbstractGaining knowledge on intrinsic interactions of various yield components is crucial to improve the yield potential in small grain cereals. It is well known in barley that increasing the grain number (GN) preponderantly improves their yield potential; however, the yield components determining GN and their association in barley row-types are less explored. In this study, we assessed different yield components like potential spikelet number (PSN), spikelet survival (SSL), spikelet number (SN), grain set (GS), and grain survival (GSL), as well as their interactions with GN by using a selected panel of two- and six-rowed barley types. Also, to analyze the stability of these interactions, we performed the study in two growth conditions, greenhouse and field. From this study, we found that in two-rowed, GN determination is strongly influenced by PSN rather than SSL and/or GS in both growth conditions. Conversely, in six-rowed, GN is associated with SSL instead of PSN and/or GS. Thus, our study exemplified that increasing GN might be possible by augmenting PSN in two-rowed genotypes, while for six-rowed genotypes, the ability of SSL needs to be improved. We speculate that this disparity of GN determination in barley row-types might be due to the fertility of lateral spikelets. Collectively, this study revealed that the GN of two-rowed largely depends on the developmental trait, PSN, while in six-rowed, it mainly follows the ability of SSL.HighlightIn cereals, understanding the interactions of different yield components that influence the grain number is essential to increase their yield by modulating the components. We show in this study that the grain number of two-rowed barley is predominantly determined by the potential spikelet number while in six-rowed by spikelet survival.
Spontaneous rate of clonal mutations inDaphnia galeata
Authors: Pfenninger Markus , Doria Halina Binde , Nickel Jana , Thielsch Anne , Schwenk Klaus , Cordellier Mathilde 
Published: September 2020

AbstractMutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct estimates exist only for few species. We estimated the spontaneous nucleotide mutation rate among clonal generations in the waterfleaDaphnia galeatawith a short term mutation accumulation approach. Individuals from eighteen mutation accumulation lines over five generations were deep genome sequenced to count de novo mutations that were not present in a pool of F1 individuals, representing the parental genotype. We identified 12 new nucleotide mutations in 90 clonal generational passages. This resulted in an estimated haploid mutation rate of 0.745 x 10-9(95% c.f. 0.39 x 10-9− 1.26 x 10-9), which is slightly lower than recent estimates for otherDaphniaspecies. We discuss the implications for the population genetics of Cladocerans.
An Approach to Automatically Label & Order Brain Activity/Component Maps
Authors: Salman Mustafa S. , Wager Tor D. , Damaraju Eswar , Calhoun Vince D. 
Published: September 2020

AbstractFunctional magnetic resonance imaging (fMRI) is a brain imaging technique which provides detailed in-sights into brain function and its disruption in various brain disorders. fMRI data can be analyzed using data-driven or region-of-interest based methods. The data-driven analysis of brain activity maps involves several steps, the first of which is identifying whether the maps capture what might be interpreted as intrinsic connectivity networks (ICNs) or artifacts. This is followed by linking the ICNs to known anatomical and/or functional parcellations. Optionally, as in the study of functional network connectivity (FNC), rearranging the connectivity graph is also necessary for systematic interpretation. Here we present a toolbox that automates all these processes under minimal or no supervision with high accuracy. We provide a pretrained cross-validated elastic-net regularized general linear model for the noisecloud toolbox to separate the ICNs from artifacts. We include several well-known anatomical and functional parcellations from which researchers can choose to label the activity maps. Finally, we integrate a method for maximizing the within-domain modularity to generate a more systematically structured FNC matrix. We improve upon and integrate existing techniques and new methods to design this toolbox which can take care of all the above needs. Specifically, we show that our pretrained model achieves 89% accuracy and 100% precision at classifying ICNs from artifacts in a validation dataset. Researchers are generating brain imaging data and analyzing brain activity at an ever-increasing rate. The Autolabeller toolbox can help automate such analyses for faster and reproducible research.
Steady-state visually evoked potentials and feature-based attention: Pre-registered null results and a focused review of methodological considerations
Authors: Adam Kirsten C.S. , Chang Lillian , Rangan Nicole , Serences John T. 
Published: September 2020

AbstractFeature-based attention is the ability to selectively attend to a particular feature (e.g., attend to red but not green items while looking for the ketchup bottle in your refrigerator), and steady-state visually evoked potentials (SSVEPs) measured from the human electroencephalogram (EEG) signal have been used to track the neural deployment of feature-based attention. Although many published studies suggest that we can use trial-by-trial cues to enhance relevant feature information (i.e., greater SSVEP response to the cued color), there is ongoing debate about whether participants may likewise use trial-by-trial cues to voluntarily ignore a particular feature. Here, we report the results of a pre-registered study in which participants either were cued to attend or to ignore a color. Counter to prior work, we found no attention-related modulation of the SSVEP response in either cue condition. However, positive control analyses revealed that participants paid some degree of attention to the cued color (i.e., we observed a greater P300 component to targets in the attended versus the unattended color). In light of these unexpected null results, we conducted a focused review of methodological considerations for studies of feature-based attention using SSVEPs. In the review, we quantify potentially important stimulus parameters that have been used in the past (e.g., stimulation frequency; trial counts) and we discuss the potential importance of these and other task factors (e.g., feature-based priming) for SSVEP studies.
Reduced anterior cingulate cortex volume induced by chronic stress correlates with increased behavioral emotionality and decreased synaptic puncta density
Authors: Misquitta Keith A. , Miles Amy , Prevot Thomas D. , Knoch Jaime K. , Fee Corey , Newton Dwight F. , Ellegood Jacob , Lerch Jason P. , Sibille Etienne , Nikolova Yuliya S. , Banasr Mounira 
Published: September 2020

AbstractClinical and preclinical studies report that chronic stress induces behavioral deficits as well as volumetric and synaptic alterations in corticolimbic brain regions including the anterior cingulate cortex (ACC), amygdala (AMY), nucleus accumbens (NAc) and hippocampus (HPC). Here, we aimed to investigate the volumetric changes associated with chronic restraint stress (CRS) and link these changes to the CRS-induced behavioral and synaptic deficits. We first confirmed that CRS increases behavioral emotionality, defined as collective scoring of anxiety- and anhedonia-like behaviors. We then demonstrated that CRS induced a reduction of total brain volume which negatively correlated with behavioral emotionality. Region-specific analysis identified that only the ACC showed significant decrease in volume following CRS (p<0.05). Reduced ACC correlated with increased behavioral emotionality (r=-0.56; p=0.0003). Although not significantly altered by CRS, AMY and NAc (but not the HPC) volumes were negatively correlated with behavioral emotionality. Finally, using structural covariance network analysis to assess shared volumetric variances between the corticolimbic brain regions and associated structures, we found a progressive decreased ACC degree and increased AMY degree following CRS. At the cellular level, reduced ACC volume correlated with decreased PSD95 (but not VGLUT1) puncta density (r=0.35, p<0.05), which also correlated with increased behavioral emotionality (r=-0.44, p<0.01), suggesting that altered synaptic strength is an underlying substrate of CRS volumetric and behavioral effects. Our results demonstrate that CRS effects on ACC volume and synaptic density are linked to behavioral emotionality and highlight key ACC structural and morphological alterations relevant to stress-related illnesses including mood and anxiety disorders.HighlightsChronic restraint stress (CRS) decreases anterior cingulate cortex (ACC) volumeACC and amygdala (AMY) volumes negatively correlate with behavioral emotionalityCRS decreased the strength and degree of the ACC structural covariance networkCRS increased the strength and degree of the AMY structural covariance networkPSD95 puncta density correlates with behavioral emotionality and ACC volume.
Evaluation of the effect of SiO2 and Fe3O4 nanoparticles onPisum sativumseeds in laboratory and field experiments
Authors: Galaktionova L.V. , Korotkova A.M. , Voskobulova N.I. , Lebedev S.V. , Terehova N.A. , Vershinina I.A. 
Published: September 2020

ABSTRACTThe present study assessed the toxic effects and prospects of using nanoparticles of SiO2 and Fe3O4 by studying the influence of pre-sowing priming ofPisum sativum L. seeds with a suspension of nanoparticles of SiO2and Fe3O4in a concentration range of 10−2to 10−5mg/l. The results demonstrated the stimulating effect of the SiO2suspension (10−3mg/l and 10−4mg/l) and the mix of Fe3O4+SiO2at the corresponding concentrations of 10−3mg/l and 10−4mg/l on the length of roots and seedlings, and the increase in the viability of plant cells under the influence of a stress factor (based on Evans blue staining). Field experience has shown the ambiguous effect of nano-printing of seeds on plant productivity.
A genome-wide CRISPR-Cas9 screen identifies CENPJ as a host regulator of altered microtubule organization duringPlasmodiumliver infection
Authors: Vijayan Kamalakannan , Arang Nadia , Wei Ling , Morrison Robert , Geiger Rechel , Parks K. Rachael , Lewis Adam J , Mast Fred D , Douglass Alyse N , Kain Heather S , Aitchison John D , Johnson Jarrod S , Aderem Alan , Kaushansky Alexis 
Published: September 2020

SummaryPrior to initiating symptomatic malaria, a singlePlasmodiumsporozoite infects a hepatocyte and develops into thousands of merozoites, in part by scavenging host resources. We show that host microtubules dynamically reorganize around the developing liver stage (LS) parasite. Using a genome-wide CRISPR-Cas9 screen, we identified host regulators of cytoskeleton organization, vesicle trafficking, ER/Golgi stress and lipid biogenesis that regulatePlasmodiumLS development. These novel regulators of infection, including Centromere Protein J (CENPJ), led us to interrogate how microtubule organizing centers (MTOCs) are regulated during infection. Foci of γ-tubulin localized to the parasite periphery; depletion of CENPJ exacerbated this re-localization and increased infection. Further, we show that the Golgi acts as a non-centrosomal MTOC by organizing γ-tubulin and stimulating microtubule nucleation at the parasite periphery. Collectively, we show that thePlasmodiumLS recruits the host Golgi to form MT mediated conduits along which host organelles are recruited to the PVM, to support liver stage development. Our findings suggest many host-targeted pharmacological inhibitors may inhibit LS infection.
Structural and functional insights into nitrosoglutathione reductase fromChlamydomonas reinhardtii
Authors: Tagliani Andrea , Rossi Jacopo , Marchand Christophe H. , De Mia Marcello , Tedesco Daniele , Libero Gurrieri , Meloni Maria , Falini Giuseppe , Trost Paolo , Lemaire Stéphane D. , Fermani Simona , Zaffagnini Mirko 
Published: September 2020

ABSTRACTProtein S-nitrosylation plays a fundamental role in cell signaling and nitrosoglutathione (GSNO) is considered as the main nitrosylating signaling molecule. Enzymatic systems controlling GSNO homeostasis are thus crucial to indirectly control the formation of protein S-nitrosothiols. GSNO reductase (GSNOR) is the key enzyme controlling GSNO levels by catalyzing its degradation in the presence of NADH. Here, we found that protein extracts from the microalgaChlamydomonas reinhardtiicatabolize GSNOviatwo enzymatic systems having specific reliance on NADPH or NADH and different biochemical features. Scoring the Chlamydomonas genome for orthologs of known plant GSNORs, we found two genes encoding for putative and almost identical GSNOR isoenzymes. One of the two, here named CrGSNOR1, was heterologously expressed and purified. The kinetic properties of CrGSNOR1 were determined and the high-resolution three-dimensional structures of the apo and NAD+-bound forms of the enzyme were solved. These analyses revealed that CrGSNOR1 has a strict specificity towards GSNO and NADH, and a conserved 3D-folding with respect to other plant GSNORs. The catalytic zinc ion, however, showed an unexpected variability of the coordination environment. Furthermore, we evaluated the catalytic response of CrGSNOR1 to thermal denaturation, thiol-modifying agents and oxidative modifications as well as the reactivity and position of accessible cysteines. Despite being a cysteine-rich protein, CrGSNOR1 contains only two solvent-exposed/reactive cysteines. Oxidizing and nitrosylating treatments have null or limited effects on CrGSNOR1 activity, highlighting a certain resistance of the algal enzyme to redox modifications. The molecular mechanisms and structural features underlying the response to thiol-based modifications are discussed.One-sentence summaryGSNOR1 fromChlamydomonas reinhardtiidisplays an unusual variability of the catalytic zinc coordination environment and an unexpected resistance to thiol-based redox modifications
Resetting of the 24-nt siRNA landscape in rice zygotes
Authors: Li Chenxin , Gent Jonathan I. , Xu Hengping , Fu Hong , Russell Scott D. , Sundaresan Venkatesan 
Published: September 2020

ABSTRACTBackgroundThe zygote, a totipotent stem cell, constitutes a critical stage of the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells — the egg and sperm, which in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Due to technical challenges, the epigenetic changes that accompany the zygotic transition are poorly understood.ResultsHere, we characterized the small RNA transcriptome of rice zygotes. We found widespread redistribution of 24-nt siRNAs relative to gametes, including absence of sperm signature siRNAs, reduction at egg signature siRNA loci, and upregulation at seedling signature siRNA loci. Loci with reduced siRNAs in zygote relative to egg were gene-distal and heterochromatic, while loci with increased siRNAs relative to egg had a similar genomic distribution to canonical siRNA loci. Although both egg and zygote siRNA loci had higher mCHH level in wildtype than indrm2embryo, zygote but not egg siRNA loci were associated with hypermethylation in mature embryo. A small fraction of siRNA loci (~1%) called siren loci accounted for 60% of all siRNAs within zygote siRNA loci, that likely arose from maternal carryover as they had similarly abundant siRNAs in egg; these siren loci were not associated with embryo hypermethylation.ConclusionsTaken together, our results indicate re-distribution of siRNAs in rice zygotes towards the canonical vegetative profile, that are consistent with the initiation of resetting of the gametic epigenome before the first embryonic division.