bluuebunny/crossref_metadata_2025_split huggingface dataset:
Piezo1 activation attenuates thrombin-induced blebbing in breast cancer cells
Authors: O’Callaghan Paul , Engberg Adam , Fatsis-Kavalopoulos Nikos , Sanchez Gonzalo , Idevall-Hagren Olof , Kreuger Johan 
Published: May 2020

AbstractCancer cells exploit a variety of migration modes to leave primary tumors and establish metastases, including amoeboid cell migration facilitated by bleb formation. Here we demonstrate that thrombin induces dynamic blebbing in the MDA-MB-231 breast cancer cell line, and confirm that PAR2 activation is sufficient to induce this effect. Cell confinement has been implicated as a driving force in bleb-based migration. Unexpectedly, we find that gentle contact compression, exerted using a “Cell Press” to mechanically stimulate cells, attenuated thrombin-induced blebbing with an associated increase in cytosolic calcium. Thrombin-induced blebbing was similarly attenuated using Yoda1, an agonist of the mechanosensitive calcium channel Piezo1, and its capacity to attenuate blebbing was impaired in Piezo1 depleted cells. Additionally, Piezo1 activation suppressed and reversed the thrombin-induced phosphorylation of ERM proteins, which are implicated in the blebbing process, and this activity was in part mediated through activation of the PP1A/PP2A family of serine/threonine phosphatases. Our results provide mechanistic insights into Piezo1 activation as a suppressor of dynamic blebbing, specifically that which is induced by thrombin.
Structural basis of Rgg protein binding to their regulatory pheromones and target DNA promoters
Authors: Capodagli Glenn C. , Tylor Kaitlyn M. , Kaelber Jason T. , Petrou Vasileios I. , Federle Michael J. , Neiditch Matthew B. 
Published: May 2020

AbstractRgg family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors inStreptococcusspecies, controlling virulence, antimicrobial resistance, and biofilm formation. Rgg2 and Rgg3 function is regulated by their interaction with oligopeptide quorum-sensing signals called short hydrophobic peptides (SHPs). The molecular basis of Rgg-SHP and Rgg-target DNA promoter specificity was unknown. To close this gap, we determined the cryo-EM structure ofStreptococcus thermophilusRgg3 bound to its quorum-sensing signal, SHP3, and the X-ray crystal structure of Rgg3 alone. Comparison of these structures to that of an Rgg in complex with cyclosporin A (CsA), an inhibitor of SHP-induced Rgg activity, reveals the molecular basis of CsA function. Furthermore, to determine how Rgg proteins recognize DNA promoters, we determined X-ray crystal structures of bothS. dysgalactiaeRgg2 andS. thermophilusRgg3 in complex with their target DNA promoters. The physiological importance of the observed Rgg-DNA interactions was dissected usingin vivogenetic experiments andin vitrobiochemical assays. Based on these structure-function studies, we present a revised unifying model of Rgg regulatory interplay. In contrast to existing models, where Rgg2 proteins are transcriptional activators and Rgg3 proteins are transcriptional repressors, we propose that both are capable of transcriptional activation. However, when Rgg proteins with different activation requirements compete for the same DNA promoters, those with more stringent activation requirements function as repressors by blocking promoter access of the SHP-bound conformationally active Rgg proteins. While a similar gene expression regulatory scenario has not been previously described, in all likelihood it is not unique to streptococci.Significance StatementSecreted peptide pheromones regulate critical biological processes in Gram-positive bacteria. In streptococci such as the human pathogenS. pyogenes, oligopeptide pheromones, like the short hydrophobic peptides (SHPs), regulate virulence, antimicrobial resistance, and biofilm formation. SHPs directly regulate the activity of transcription factors called Rgg2 and Rgg3. We present the cryo-EM structure of Rgg3 in complex with SHP3, as well as X-ray crystal structures of Rgg2 bound to target promoter DNA, Rgg3 bound to target promoter DNA, and Rgg3 alone. Based on the cryo-EM, X-ray crystallographic, biochemical, and genetic studies presented here, we provide not only detailed mechanistic insight into the molecular basis of Rgg3-SHP3, Rgg2-DNA, and Rgg3-DNA binding specificity, but also a new model of transcription factor regulatory interplay.
DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution
Authors: Liu Hanqing , Zhou Jingtian , Tian Wei , Luo Chongyuan , Bartlett Anna , Aldridge Andrew , Lucero Jacinta , Osteen Julia K. , Nery Joseph R. , Chen Huaming , Rivkin Angeline , Castanon Rosa G , Clock Ben , Li Yang Eric , Hou Xiaomeng , Poirion Olivier B. , Preissl Sebastian , O’Connor Carolyn , Boggeman Lara , Fitzpatrick Conor , Nunn Michael , Mukamel Eran A. , Zhang Zhuzhu , Callaway Edward M. , Ren Bing , Dixon Jesse R. , Behrens M. Margarita , Ecker Joseph R. 
Published: May 2020

SummaryMammalian brain cells are remarkably diverse in gene expression, anatomy, and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. We carried out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single nucleus DNA methylation sequencing to profile 110,294 nuclei from 45 regions of the mouse cortex, hippocampus, striatum, pallidum, and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements, and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types, and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, an artificial neural network model was constructed that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data allowed prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse brain.
Excitatory GABAergic modulation of calyx terminals in the vestibular sensory end organ
Authors: Ramakrishna Yugandhar , Sadeghi Soroush G. 
Published: May 2020

ABSTRACTGABAergic sources have been identified in the vestibular sensory neuroepithelium, mainly in the supporting cells. However, existence of GABA receptors or any possible GABAergic effects on vestibular nerve afferents has not been investigated. The current study was conducted to determine whether activation of GABA-B receptors affects calyx afferent terminals in the central region of the cristae of the semicircular canals in rats. We used patch clamp recording in P13 – P18 Sprague-Dawley rats of either sex. Application of GABA-B receptor agonist baclofen inhibited voltage activated outward potassium currents. This effect was blocked by selective GABA-B receptor antagonist CGP 35348. Antagonists of small (SK) and large (BK) current potassium channels resulted in an almost complete block of baclofen effect. The remaining baclofen effect was due to inhibition of voltage gated calcium channels and was blocked by cadmium chloride. Furthermore, baclofen had no effect in the absence of calcium in the extracellular fluid. Inhibition of potassium currents by GABA-B activation resulted in an excitatory effect on calyx terminal action potential firing. While in the control condition calyces could only fire a single action potential during step depolarizations, in the presence of baclofen they fired continuously during steps and a few even showed spontaneous discharge. We also found a decrease in threshold for action potential generation and a decrease in first spike latency during step depolarization. These results provide the first evidence for the presence of GABA-B receptors on calyx terminals, show that their activation results in an unusual excitatory effect and that GABA inputs could be used to modulate calyx response properties.
The heart microbiome of insectivorous bats from Central and South Eastern Europe
Authors: Corduneanu Alexandra , Mihalca Andrei Daniel , Sándor Attila D. , Hornok Sándor , Malmberg Maja , Viso Natalia Pin , Bongcam-Rudloff Erik 
Published: May 2020

AbstractHost associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic reservoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reservoirs of multiple pathogens such as viruses, bacteria and parasites, showing in the same time robust immunity against many of them. The microbiota plays a fundamental role on the induction, training and function of the host immune system and the immune system has largely evolved in order to maintain the symbiotic relationship of the host with these diverse microbes. Thus, expanding our knowledge on bat-associated microbiome it can be usefully in understanding bats’ outstanding immune capacities. The aim of this study was to investigate the presence of different bacterial communities in heart tissue of insectivorous bats,Nyctalus noctula, Pipistrellus pipistrellusandRhinoplophus hipposideros, from Central and Eastern Europe using high-throughput sequencing of variable regions of the 16S rRNA. In addition, species-specific PCRs were used to validate the presence of the vector-borne pathogensBartonellaspp. andRickettsiaspp. In this study we identified a wide variety of bacterial groups, with the most abundant phyla being Proteobacteria and Firmicutes. The results showed that at individual level, the year or location had no effect on the diversity and composition of the microbiome, however host species determined both structure and abundance of the bacterial community. We report the presence of vector-borne bacteriaBartonellaspp. in samples ofN. noctulaand indications ofRickettsiaspp. inR. hipposideros. Our results provide a first insight into the bacterial community found in heart tissue of bats from Central and South Eastern Europe.
Grain Fe and Zn Contents Linked SSR Markers Based Genetic Diversity Reveal Perspective for Marker Assisted Biofortification Breeding in Rice
Authors: Raza Qasim , Riaz Awais , Saher Hira , Bibi Ayesha , Ali Syed Sultan , Sabar Muhammad 
Published: May 2020

AbstractRice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. Here, we assessed genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in 56 fine and coarse grain rice accessions of different geographical origin. Aromatic fine gain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions. Genotyping with 24 SSR markers identified 21 polymorphic markers, among which seventeen demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulations. Single marker analysis recognized four ZnBR and single FeBR significant marker-trait associations (MTAs), contributing 15.41–39.72% in total observed phenotypic variance. Furthermore, high grain Fe and Zn contents linked marker alleles from significant MTAs were also identified. Collectively, these results indicate availability of wide genetic diversity in rice germplasm and perspective for marker-assisted biofortification breeding.
Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita
Authors: Kozlowski Djampa KL , Hassanaly-Goulamhoussen Rahim , Rocha Martine Da , Koutsovoulos Georgios D , Bailly-Bechet Marc , Danchin Etienne GJ 
Published: May 2020

AbstractDespite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability without sex remain poorly known and only low variation at the single nucleotide polymorphism level have been observed so far across different geographical isolates with distinct ranges of compatible hosts. Hence, other mechanisms than the accumulation of point mutations are probably involved in the genomic dynamics and plasticity necessary for adaptability. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE content, and used population genomics approach to estimate the mobility of these TEs across 12 geographical isolates, presenting phenotypic variations. The TE content is more abundant in DNA transposons and the distribution of TE copies identity to their consensuses sequence suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed variations across the different isolates. Compared to the M. incognita reference genome, we detected the insertion of some TEs either within genic regions or in the upstream regulatory regions. These predicted TEs insertions might thus have a functional impact. We validated by PCR the insertion of some of these TEs, confirming TE movements probably play a role in the genome plasticity with possible functional impacts.
Intact nucleosomal context enables chromodomain reader MRG15 to distinguish H3K36me3 from -me2
Authors: Faulkner Sarah , Couturier Antony M. , Josephson Brian , Watts Tom , Davis Benjamin G. , Esashi Fumiko 
Published: May 2020

AbstractA wealth ofin vivoevidence demonstrates the physiological importance of histone H3 trimethylation at lysine 36 (H3K36me3), to which chromodomain-containing proteins, such as MRG15, bind preferentially compared to their dimethyl (H3K36me2) counterparts. However,in vitrostudies using isolated H3 peptides have failed to recapitulate a causal interaction. Here, we show that MRG15 can clearly discriminate between synthetic, fully intact model nucleosomes containing H3K36me2 and H3K36me3. MRG15 docking studies, along with experimental observations and nucleosome structure analysis suggest a model where the H3K36 side chain is sequestered in intact nucleosomes via a hydrogen bonding interaction with the DNA backbone, which is abrogated when the third methyl group is added to form H3K36me3. Hence, this mechanism provides a ‘methyl-switch’ for contextdependent reader selectivity. These results highlight the importance of such intra-chromatin interactions in understanding epigenetic regulation, a feature which is absent in commonly-used peptide or histone-only models.
YTHDF2 is essential for spermatogenesis and fertility through mediating a wave of transcript transition during spermatogonial differentiation
Authors: Zhao Xin-Xi , Lin Zhen , Fan Yong , Zhang Yu-Jie , Li Fei , Hong Tong , Feng Hua , Tong Ming-Han , Wang Ning-Ling , Kuang Yan-Ping , Lyu Qi-Feng 
Published: May 2020

AbstractThe dynamic and reversible regulation roles of m6A modification, and the characterization of m6A readers have provided new insights into spermatogenesis at post-transcriptional level. YTHDF2 has been reported to recognize and mediate the m6A-containing transcripts decay during the mouse oocyte mature, embryonic stem cell differentiation, neural development, and zebrafish maternal-to-zygotic transition. However, the roles of YTHDF2 in mammalian spermatogenesis are uncertain. Here, we generated germ cell-specificYthdf2mutants (Ythdf2-vKO) at a C57BL/6J background, and demonstrated that YTHDF2 was essential for mouse spermatogenesis and fertility.Ythdf2-vKOprovided oligoasthenoteratozoospermia (OAT) phenotype with increased apoptosis in germ cells. High-throughput RNA-seq of the testis tissue showed the failure of the degradation of a wave of YTHDF2 target mRNA. Interestingly, RNA-seq analysis combined with our previous single-cell transcriptomics data of mouse spermatogenesis pointed out the failure of a wave of transcript transition during the spermatogenesis ofYthdf2-vKO, which was confirmed by gene expression analysis of diplotene spermatocytes and round spermatids obtained through fluorescence-activated cell sorting using qPCR. Our study demonstrates the fundamental role of YTHDF2 during mouse spermatogenesis and provides a potential candidate for the diagnosis of male infertility with OAT syndrome.Author summaryMale infertility is becoming a worldwide health problem. Male gamete is generated through spermatogenesis, which is a complicated developmental process with dynamic transcriptome changes. RNA m6A modification has been reported as the most prominently internal mRNA modification, which control the tune of gene expression through mRNA splicing, export, translation and decay. RNA m6A modification is catalyzed by “writers”, and could be removed by “erasers”. The m6A modification enzymes are reported to play important roles during spermatogenesis. Given that the biological function of m6A modification are mediated through its “readers”, its readers might be proposed to be involved in the regulation of spermatogenesis. YTHDF2, as a reader of m6A modification, has been reported to mediate the m6A-containing transcripts decay. To explore the roles of YTHDF2 in spermatogenesis, we used germ cell-specific mutation strategy to knock out the mouseYthdf2. The mutants provided oligoasthenoteratozoospermia phenotype. Our study demonstrate that YTHDF2 is essential for mouse spermatogenesis. YTHDF2 could be a potential candidate for the diagnosis of oligoasthenoteratozoospermia syndrome.
Optimization of human papillomavirus-based pseudovirus techniques for efficient gene transfer
Authors: Gilson Timra D. , Gibson Ryan T. , Androphy Elliot J. 
Published: May 2020

AbstractHuman papillomavirus (HPV) L1 and L2 capsid proteins self-assemble into virions capable of efficiently packaging either its 8 kilobase genome or non-viral DNA. The ability of HPV capsids to package non-viral DNA makes these a useful tool for delivering plasmids to study proteins of interest in a variety of cell types. We describe optimization of current methods and present new protocols for using HPV capsids to deliver non-viral DNA thereby providing an alternative to DNA transfection. Using keratinocyte generated extracellular matrices can enhance infection efficiency in keratinocytes, hepatocytes and neuronal cells. Furthermore, we describe a suspension-based efficient technique for infecting different cell types.
The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold
Authors: Steckelberg Anna-Lena , Vicens Quentin , Costantino David A. , Nix Jay C. , Kieft Jeffrey S. 
Published: May 2020

ABSTRACTExonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5’ to 3’ exonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
Complementary and divergent roles for Ctage5 and Tango1 in zebrafish
Authors: Clark Eric M. , Link Brian A. 
Published: May 2020

AbstractCoat protein complex II (COPII) factors mediate cargo export from the endoplasmic reticulum (ER), but bulky collagens and lipoproteins are too large for traditional COPII vesicles. Mammalian CTAGE5 and TANGO1 have been well characterized individually as specialized cargo receptors at the ER that function with COPII coats to facilitate trafficking of bulky cargoes. Here, we present a genetic interaction study in zebrafish of deletions inctage5,tango1, or both to investigate their potential distinct and complimentary functions. We found that Ctage5 and Tango1 have different roles related to organogenesis, collagen versus lipoprotein trafficking, stress-pathway activation, and survival. While deletion of bothctage5andtango1compounded phenotype severity, deletion of either factor alone revealed novel tissue specific defects in the building of heart, muscle, lens, and intestine, in addition to the previously described roles in the development of neural and cartilage tissues. Together, our results suggest that Ctage5 and Tango1 have overlapping, but also divergent roles in tissue development and homeostasis.SummaryIn this genetic study Ctage5 and Tango1 endoplasmic reticulum cargo receptors were investigated togetherin vivofor the first time. Cell differentiation, survival, trafficking, and stress pathway activation were investigated.
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions
Authors: Metzig Marie Oliver , Tang Ying , Mitchell Simon , Taylor Brooks , Foreman Robert , Wollman Roy , Hoffmann Alexander 
Published: May 2020

ABSTRACTBalancing cell death is essential to maintain healthy tissue homeostasis and prevent disease. Tumor necrosis factor (TNF) not only activates nuclear factor κB (NFκB), which coordinates the cellular response to inflammation, but may also trigger necroptosis, a pro-inflammatory form of cell death. Whether TNF-induced NFκB cross-regulates TNF-induced necroptosis fate decisions is unclear. Live-cell microscopy and model-aided analysis of death kinetics identified a molecular circuit that interprets TNF-induced NFκB/RelA dynamics to control necroptosis decisions. Inducible expression of TNFAIP3/A20 forms an incoherent feedforward loop to interfere with the RIPK3-containing necrosome complex and protect a fraction of cells from transient, but not long-term TNF exposure. Furthermore, dysregulated NFκB dynamics often associated with disease diminish TNF-induced necroptosis. Our results suggest that TNF’s dual roles in either coordinating cellular responses to inflammation, or further amplifying inflammation are determined by a dynamic NFκB-A20-RIPK3 circuit, that could be targeted to treat inflammation and cancer.