bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mother Brain is Wired for Social Moments
Authors: Shimon-Raz Ortal , Salomon Roy , Bloch Miki , Romano Gabi Aisenberg , Hendler Talma , Yeshurun Yaara , Ulmer-Yaniv Adi , Zagoory-Sharon Orna , Feldman Ruth 
Published: June 2020

AbstractReorganization of the maternal brain, primed by oxytocin surge during childbirth, triggers the species-typical maternal social behavior. These brief social moments carry profound effects on the infant’s social brain and likely have a distinct signature in the maternal brain. Utilizing a double-blind, oxytocin/placebo administration crossover design, we imaged mothers twice while observing three naturalistic maternal-infant contexts in the home ecology; “unavailable”, “unresponsive”, and “social”, when mothers engaged in synchronous pick-a-boo play. We found four processes by which mother’s brain registers social moments.Salience- social moments increased activations throughout the maternal brain network;Brain-behavior coupling- caregiving behavior linked with socially-driven neural response;Oxytocin sensitivity– administration impacted neural response mainly to the social context; andTemporal engrams–consistent temporal patterns in insula and TP characterized response to social play. Findings describe how mother’s brain compiles and amplifies these precious social moments to generate dyad-specific brain-behavior patterns that initiate the cross-generational transmission of human sociality.
Functional characterization of a “plant-like” HYL1 homolog in the cnidarianNematostella vectensisindicates a conserved involvement in microRNA biogenesis
Authors: Tripathi Abhinandan Mani , Admoni Yael , Fridrich Arie , Lewandowska Magda , Surm Joachim M. , Aharoni Reuven , Moran Yehu 
Published: June 2020

AbstractWhile the biogenesis of microRNAs (miRNAs) in both animals and plants depends on the RNase III Dicer, its partner proteins are considered distinct for each kingdom. Nevertheless, recent discovery of homologs of Hyponastic Leaves1 (HYL1), a “plant-specific” Dicer partner, in the metazoan phylum Cnidaria, challenges the view that miRNAs evolved convergently in animals and plants. Here we show that the HYL1 homolog Hyl1-like a (Hyl1La) is crucial for development and miRNA biogenesis in the cnidarian modelNematostella vectensis. Inhibition of Hyl1La by morpholinos resulted in metamorphosis arrest inNematostellaembryos and a significant reduction in levels of most miRNAs. Further, meta-analysis of morphants of miRNA biogenesis components, like Dicer1, shows clustering of their miRNA profiles with Hyl1La morphants. Strikingly, immunoprecipitation of Hyl1La followed by quantitative PCR revealed that in contrast to the plant HYL1, Hyl1La interacts only with precursor miRNAs and not with primary miRNAs. This was complemented by an in vitro binding assay of Hyl1La to synthetic precursor miRNA. Altogether, these results suggest that the last common ancestor of animals and plants carried a HYL1 homolog that took essential part in miRNA biogenesis and indicate early emergence of the miRNA system before plants and animals separated.Impact statementPresence of a functional homolog of HYL1 inNematostellavectensis, a basal animal model, indicates divergent evolution of miRNA biogenesis pathway in plants and animals from an ancestral miRNA system
The Amphibian Antimicrobial Peptide Uperin 3.5 is a Cross-α/Cross-β Chameleon Functional Amyloid
Authors: Salinas Nir , Tayeb-Fligelman Einav , Sammito Massimo , Bloch Daniel , Jelinek Raz , Noy Dror , Uson Isabel , Landau Meytal 
Published: June 2020

AbstractAntimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic-resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 were comprised of parallel and anti-parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. Uperin 3.5 demonstrated chameleon properties, with a secondary structure switch to cross-β fibrils with reduced antibacterial activity in the absence of lipids or after heat shock. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.
Impacts of host phylogeny, feeding styles, and parasite attachment site on isotopic discrimination in helminths infecting coral reef fish hosts
Authors: Riekenberg Philip M. , Briand Marine J. , Moléana Thibaud , Sasal Pierre , van der Meer Marcel , Thieltges David W. , Letourneur Yves 
Published: June 2020

AbstractStable isotopes of carbon and nitrogen characterize trophic relationships in predator-prey relationships, with clear differences between consumer and diet (discrimination factor, Δ13C, Δ15N). However, parasite-host isotopic relationships remain unclear, with Δ13C and Δ15N remaining incompletely characterized, especially for helminths. In this study, we used stable isotopes to determine discrimination factors for 13 parasite-host pairings of helminths in coral reef fish. Δ15N differences grouped according to phylogeny and attachment site on the hosts: Δ15N was positive for trematodes and nematodes from the digestive tract and varied for cestodes and nematodes from the general cavity. Δ13C showed more complex patterns with no effect of phylogeny or attachment site. A negative relationship was observed between Δ15N and host δ15N value among different host-parasite pairings as well as within 7 out of the 13 parings, indicating that host metabolic processing affects host-parasite discrimination values. In contrast, no relationships were observed for Δ13C. Our results indicate that host phylogeny, attachment site and host stable isotope value drive Δ15N of helminths in coral reef fish while Δ13C is more idiosyncratic. These results call for use of taxon- or species-specific and scaled framework for bulk stable isotopes in the trophic ecology of parasites.
A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates
Authors: Banu Sofia , Jolly Bani , Mukherjee Payel , Singh Priya , Khan Shagufta , Zaveri Lamuk , Shambhavi Sakshi , Gaur Namami , Mishra Rakesh K , Scaria Vinod , Sowpati Divya Tej 
Published: June 2020

AbstractFrom an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. The availability of whole genomes from multiple states in India prompted us to analyse the phylogenetic clusters of genomes in India. We performed whole-genome sequencing for 64 genomes making a total of 361 genomes from India, followed by phylogenetic clustering, substitution analysis, and dating of the different phylogenetic clusters of viral genomes. We describe a distinct phylogenetic cluster (Clade I / A3i) of SARS-CoV-2 genomes from India, which encompasses 41% of all genomes sequenced and deposited in the public domain from multiple states in India. Globally 3.5% of genomes, which till date could not be mapped to any distinct known cluster fall in this newly defined clade. The cluster is characterized by a core set of shared genetic variants – C6312A (T2016K), C13730T (A88V/A97V), C23929T, and C28311T (P13L). Further, the cluster is also characterized by a nucleotide substitution rate of 1.4 × 10−3variants per site per year, lower than the prevalent A2a cluster, and predominantly driven by variants in the E and N genes and relative sparing of the S gene. Epidemiological assessments suggest that the common ancestor emerged in the month of February 2020 and possibly resulted in an outbreak followed by countrywide spread, as evidenced by the low divergence of the genomes from across the country. To the best of our knowledge, this is the first comprehensive study characterizing the distinct and predominant cluster of SARS-CoV-2 in India.
LINE elements are a reservoir of regulatory potential in mammalian genomes
Authors: Roller Maša , Stamper Ericca , Villar Diego , Izuogu Osagie , Martin Fergal , Redmond Aisling , Ramachanderan Raghavendra , Harewood Louise , Odom Duncan T. , Flicek Paul 
Published: June 2020

SUMMARYTo investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in liver, brain, muscle, and testis from ten diverse mammals. The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species. Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.HIGHLIGHTSTissue-specific regulatory regions evolve faster than tissue-sharedSwitching promoter and enhancer regulatory roles is frequent in evolutionLINE L1s contribute to the evolution of tissue-specific regulatory regionsLINE L2s are associated with broad tissue activity and dynamic regulatory signatures
LIN28B controls the regenerative capacity of neonatal murine auditory supporting cells through activation of mTOR signaling
Authors: Li Xiaojun , Doetzlhofer Angelika 
Published: June 2020

ABSTRACTMechano-sensory hair cells within the inner ear cochlea are essential for the detection of sound. In mammals, cochlear hair cells are only produced during development and their loss, due to disease or trauma, is a leading cause of deafness. In the immature cochlea, prior to the onset of hearing, hair cell loss stimulates neighboring supporting cells to act as hair cell progenitors and produce new hair cells. However, for reasons unknown, such regenerative capacity (plasticity) is lost once supporting cells undergo maturation. Here, we demonstrate that the RNA binding protein LIN28B plays an important role in the production of hair cells by supporting cells and provide evidence that the developmental drop in supporting cell plasticity in the mammalian cochlea is, at least in part, a product of declining LIN28B-mTOR activity. Employing murine cochlear organoid and explant cultures to model mitotic and non-mitotic mechanisms of hair cell generation, we show that loss ofLin28bfunction, due to its conditional deletion, or due to overexpression of the antagonistic miRNAlet-7g, suppressed Akt-mTORC1 activity and renders young, immature supporting cells incapable of generating hair cells. Conversely, we found that LIN28B overexpression increased Akt-mTORC1 activity and allowed supporting cells that were undergoing maturation to de-differentiate into progenitor-like cells and to produce hair cells via mitotic and non-mitotic mechanisms. Finally, using the mTORC1 inhibitor rapamycin, we demonstrate that LIN28B promotes supporting cell plasticity in an mTORC1-dependent manner.SIGNIFICANCE STATEMENTCochlear hair cell loss is a leading cause of deafness in humans and other mammals. In the immature cochlea lost hair cells are regenerated by neighboring glia-like supporting cells. However, for reasons unknown, such regenerative capacity is rapidly lost as supporting cells undergo maturation. Here we identify a direct link between LIN28B-mTOR activity and supporting cell plasticity. Mimicking later developmental stages, we found that loss of the RNA binding protein LIN28B attenuated mTOR signaling and rendered young, immature supporting cells incapable of producing hair cells. Conversely, we found that re-expression of LIN28B reinstated the ability of maturing supporting cells to revert to a progenitor-like state and generate hair cells via activation of mTOR signaling.
Population structure of eulachonThaleichthys pacificusfrom Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing
Authors: Sutherland Ben J. G. , Candy John , Mohns Kayla , Cornies Olivia , Jonsen Kim , Le Khai , Gustafson Richard G. , Nichols Krista M. , Beacham Terry D. 
Published: June 2020

ABSTRACTEulachonThaleichthys pacificus, a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published RADseq-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1,989 individuals from 14 populations ranging from Northern California through Central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations, and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel, and thus will be used in future mixed-stock analyses of eulachon in order to provide new insights for management and conservation of eulachon.
Molecular Dynamics Study of Dehydrated Lipopolysaccharide Membrane
Authors: Liu Changjiang , Elvati Paolo , Violi Angela 
Published: June 2020

AbstractThe outer membrane of bacteria is known to play an important role in the rapid response to desiccation, although the causes and the extent of these effects are still mostly unclear. For this reason, in this work we study the desiccation response of the Gram-negative lipopolysaccha-ride (LPS) bacterial outer membranes. By analyzing molecular dynamics simulations of LPS membranes of different composition during desiccation, we identified the formation of a rigid protective layer of polysaccharides that not only reduces the water evaporation but is also able to indirectly preserve several structural features and as such membrane functionality. Overall, we found that the presence of polysaccharide layer is critical in the conservation of a layer of water in proximity of the hydrophobic region as well as the structure of the lipids acyl chain structure.
Physiological responses of two accessions of tomato to three distance regimes in juvenile oil palm-tomato intercrop in rainforest zone of nigeria
Authors: Oluwatobi Ayodele Samuel 
Published: June 2020

ABSTRACTThis study was conducted during the rainy season of 2017 within the alleys of juvenile oil palms that were 2-year-old at the oil palm plantation located in Ala, Akure-North Local Government, Ondo State. Tomato accessions (NGB 01665 and NG/AA/SEP/09/053) were intercropped at 1, 2 and 3 m from the juvenile oil palm within the alley in a randomized complete block design. The results showed that tomato (NGB 01665 and NG/AA/SEP/09/053) planted at 3 m from the juvenile oil palm performed better than those at other planting distances in terms of growth and yield attributes with number of fruit; fruit weight and yield per hectare of 39.50, 2265.8 g and 3.74 ton/ha respectively. However, the control (sole) recorded the best yield but was not significantly different from those planted at 3 m from the juvenile oil palm. Varietal advantage was recorded by tomato (NGB 01665) with higher number of fruits, fruit weight and yield per hectare (26.94, 1834 g and 3.158 ton/ha) respectively. Intercropping advantage was not recorded for any of the intercropping distance regimes during the trial (when the juvenile oil palms were 2-year-old), with LER values less than unity.
Cyclin-dependent kinase 2 (Cdk2) controls phosphatase-regulated signaling and function in platelets
Authors: Woods Paul R. , Hood Brian L. , Shiva Sruti , Conrads Thomas P. , Suchko Sarah , Steinman Richard 
Published: June 2020

AbstractCell cycle regulatory molecules including cyclin-dependent kinases can be recruited into non-nuclear pathways to coordinate cell cycling with the energetic state of the cell or with functions such as motility. Little is known about the role of cell cycle regulators in anucleate cells such as platelets. We report that cyclin-dependent kinase (cdk2) is robustly expressed in human platelets, is activated by thrombin and is required for platelet activation. Cdk2 activation required Src signaling downstream of the platelet thrombin receptor PAR1. Kinase-active cdk2 promoted the activation of downstream platelet kinases by phosphorylating and inactivating the catalytic subunit of protein phosphatase 1 (PP1). Erk was bound to PP1 in a complex with the PP1 regulator PPP1R12a (MYPT1) in platelets, and cdk2 inhibited the phosphatase activity of PP1 and PPP1R12a bound complexes. The requirement for cdk2 in Erk activation could be replaced by the phosphatase inhibitor calyculin if cdk2 was inhibited. Blockade of cdk2 kinase with chemical and peptide cdk2 inhibitors resulted in suppression of thrombin-induced platelet aggregation, and partially inhibited GPIIb/IIIa integrin activation as well as platelet secretion of P-Selectin and ATP. Together, these data indicate a requirement for cdk2 in platelet activation.
Depression polygenic scores are associated with major depressive disorder diagnosis and depressive episode in Mexican adolescents
Authors: Rabinowitz Jill A. , Campos Adrian I. , Benjet Corina , Su Jinni , Macias-Kauffer Luis , Méndez Enrique , Martinez-Levy Gabriela A. , Cruz-Fuentes Carlos S. , Rentería Miguel E. 
Published: June 2020

AbstractObjectiveLarge-scale genome-wide association studies have uncovered genetic variants associated with depression; however, most of this work has been limited to adults of European ancestry. We investigate the ability of depression polygenic risk scores (PRS) to predict both lifetime and past year major depressive disorder (MDD) diagnosis and the experience of a major depressive episode (MDE) in a sample of adolescents with admixed ancestry from Mexico City, and explore whether adverse life events moderate these relations.MethodsThe study sample consisted of adolescents (N = 1,152) aged 12–17 from Mexico City who were interviewed and genotyped as part of a general population survey on adolescent mental health. PRS for depression were derived using summary statistics from a large-scale discovery genome-wide association study (GWAS) conducted on depressive symptoms that included over 800,000 individuals of European ancestry (Howard et al., 2019).ResultsHigher depression PRS were associated with a higher likelihood of both past year MDD and MDE and lifetime MDE, accounting for 1.5%-2.5% of the variance in these outcomes. Adversity did not moderate the relationship between depression PRS and lifetime or past year MDD or MDE.LimitationsThis study is cross-sectional. As such, a few participants might have experience MDD/MDE after the interview. In addition, our sample comprised only Mexican youth and thus it may not generalize to other populations.ConclusionOur results indicate that depression PRS derived from a European ancestry GWAS are associated with MDD and MDE risk among Mexican adolescents and have the potential to aid in the identification of youth who may be genetically prone to developing depressive symptoms.
Characterisation of the Renal Cortical Transcriptome Following Roux-en-Y Gastric Bypass Surgery in Experimental Diabetic Kidney Disease
Authors: Nair Meera , Martin William P. , Zhernovkov Vadim , Elliott Jessie A. , Fearon Naomi , Eckhardt Hans , McCormack Janet , Godson Catherine , Brennan Eoin Patrick. , Fändriks Lars , Docherty Neil G. , le Roux Carel W. 
Published: June 2020

ABSTRACTIntroductionRoux-en-Y Gastric Bypass Surgery (RYGB) reduces albuminuria and the long-term incidence of end-stage renal disease in patients with obesity and diabetes. Preclinical modelling in experimental diabetic kidney disease (DKD) demonstrates that improvements in glomerular structure likely underpin these findings.Research Design & MethodsIn adult male Zucker Diabetic Fatty (ZDF) rats, we profiled the effect of RYGB on weight and metabolic control as well biochemical, structural and ultrastructural indices of diabetic renal injury. Furthermore, we sequenced the renal cortical transcriptome in these rats and used bioinformatic pathway analyses to characterise the transcriptional alterations governing the renal reparative response to RYGBResultsIn parallel with improvements in weight and metabolic control, RYGB reduced albuminuria, glomerulomegaly, podocyte stress, and podocyte foot process effacement. Pathway analysis of RYGB-induced transcriptomic changes in the renal cortex highlighted correction of disease-associated alterations in fibrosis, inflammation and biological oxidation pathways. RYGB reversed disease-associated changes in the expression of TGF-β superfamily genes that strongly correlated with improvements in structural measures of glomerulopathy.ConclusionsImproved glomerular structure in ZDF rats following RYGB is underpinned by pathway level changes, including interruption of the TGF-β driven pro-fibrotic programme. Our data provide an important layer of experimental support for clinical evidence demonstrating that RYGB arrests renal damage in patients with obesity and Type 2 Diabetes.KEY MESSAGESWhat is already known about this subject?RYGB is an effective treatment for obesity and type 2 diabetes and longitudinal cohort studies have demonstrated it’s albuminuria lowering effect and evidence of longer term reno-protection.Studies in pre-clinical models of diabetic kidney disease have described favourable changes in measures of renal structure and ultrastructure following RYGB.What are the new findings?The present study directly correlates structural and ultrastructural improvements in the ZDF rat kidney following RYGB with corrective shifts in the global renal transcriptome.Chronic renal remodelling responses in experimental DKD that are governed by TGF-β signalling are interrupted and reversed by RYGB.How might these results change the focus of research or clinical practice?These data will support further interrogation of RYGB specific shifts in the renal transcriptome with a view to identifying tractable targets for treatment response biomarkers and bariatric mimetic based diet and pharmacotherapy based interventions.