bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does methylation of NFATC1 and C-FOS genes are associated with post-menopausal osteoporosis?
Authors: Kalkan Rasime , Tosun Özgür 
Published: February 2020

ABSTRACTGenetic and epigenetic factors have an important role during the development of osteoporosis. RANK/RANKL pathway is important for the bone remodeling and NFATC1 and c-FOS are the downtargets of this pathway. Here, we report methylation status ofNFATC1andC-FOSgenes in post and premenopausal cases. In this study 30 pre-menopausal and 35 post-menopausal cases were included. MS-HRM was used for identification ofNFATC1andC-FOSmetyhylation.NFATC1 were methylated in 11 of the 35 post-menopausal women and C-FOS were methylated in 6 of the postmenopausal women (p >0.005). Here, we found statistically significant association between unmethylation of NFATC1 and post-menopausal status. This result explains the epigenetic regulation of osteoclasts during the menopausal transition and our results can be used for epigenetic explanation of post-menopausal osteoporosis for the first time in the literature. Although the limited number of studies in this field makes our results crucial. Therefore, our results showed great value of epigenetic profile of post-menopausal women.
Bidirectional control of fear memories by the cerebellum through the ventrolateral periaqueductal grey
Authors: Frontera Jimena L. , Aissa Hind Baba , Sala Romain William , Mailhes-Hamon Caroline , Georgescu Ioana Antoaneta , Léna Clément , Popa Daniela 
Published: February 2020

AbstractFear conditioning is a form of associative learning that is known to involve brain areas, notably the amygdala, the prefrontal cortex and the periaqueductal grey (PAG). Here, we describe the functional role of pathways that link the cerebellum with the fear network. We found that the cerebellar fastigial nucleus (FN) sends glutamatergic projections to vlPAG that synapse onto glutamatergic and GABAergic vlPAG neurons. Chemogenetic and optogenetic manipulations revealed that the FN-vlPAG pathway controls bi-directionally the strength of the fear memory, indicating a role in the association of the conditioned and unconditioned stimuli, a function consistent with vlPAG encoding of fear prediction error. In addition, we found that a FN - thalamic parafascicular nucleus pathway, which may relay cerebellar influence to the amygdala, is involved in anxiety and fear expression but not in fear memory. Our results reveal the contributions to the emotional system of the cerebellum, which exerts a potent control on the strength of the fear memory through excitatory FN-vlPAG projections.
New pathogenic variants and insights into pathogenic mechanisms in GRK1-related Oguchi disease
Authors: Poulter James A. , Gravett Molly S. C. , Taylor Rachel L. , Fujinami Kaoru , De Zaeytijd Julie , Bellingham James , Rehman Atta Ur , Hayashi Takaaki , Kondo Mineo , Rehman Abdur , Ansar Muhammad , Donnelly Dan , Toomes Carmel , Ali Manir ,   UK Inherited Retinal Disease Consortium,   Genomics England Research Consortium, De Baere Elfride , Leroy Bart P. , Davies Nigel P. , Henderson Robert H. , Webster Andrew R. , Rivolta Carlo , Mahroo Omar A. , Arno Gavin , Black Graeme C. , McKibbin Martin , Harris Sarah A. , Khan Kamron N. , Inglehearn Chris F. 
Published: February 2020

AbstractPurposeBiallelic mutations in G-Protein coupled receptor kinase 1 (GRK1) cause Oguchi disease, a rare subtype of congenital stationary night blindness (CSNB). The purpose of this study was to identify pathogenic GRK1 variants and use in-depth bioinformatic analyses to evaluate how their impact on protein structure could lead to pathogenicity.MethodsPatients’ genomic DNA was sequenced by whole genome, whole exome or focused exome sequencing. Pathogenic variants, published and novel, were compared to nondisease associated missense variants. The impact ofGRK1missense variants at the protein level were then predicted using a series of computational tools.ResultsWe identified eleven previously unpublished cases with biallelic pathogenic GRK1 variants, including seven novel variants, and reviewed allGRK1pathogenic variants. Further structure-based scoring revealed a hotspot for missense variants in the kinase domain. Additionally, to aid future clinical interpretation, we identified the bioinformatics tools best able to differentiate pathogenic from non-pathogenic variants.ConclusionWe identified newGRK1pathogenic variants in Oguchi disease patients and investigated how disease-causing variants may impede protein function, giving new insights into the mechanisms of pathogenicity. All pathogenic GRK1 variants described to date have been collated into a Leiden Open Variation Database (http://dna2.leeds.ac.uk/GRK1_LOVD/genes/GRK1).
The helix bundle domain of primase RepB’ is required for dinucleotide formation and extension
Authors: Banchenko Sofia , Weise Chris , Lanka Erich , Saenger Wolfram , Geibel Sebastian 
Published: February 2020

ABSTRACTDuring DNA replication, primases synthesize oligonucleotide primers on single-stranded template DNA, which are then extended by DNA polymerases to synthesize a complementary DNA strand. Primase RepB’ of plasmid RSF1010 initiates DNA replication on two 40 nucleotide long inverted repeats, termed ssiA and ssiB, within the oriV of RSF1010. RepB’ consists of a catalytic domain and a helix bundle domain which are connected by long α-helix 6 and an unstructured linker. Previous work has demonstrated that RepB’ requires both domains for initiation of dsDNA synthesis in DNA replication assays. However, the precise functions of these two domains in primer synthesis have been unknown. Here we report that both domains of RepB’ are required to synthesizes a 10–12 nucleotide long DNA primer whereas the isolated domains are inactive. Mutational analysis of the catalytic domain indicates that the solvent-exposed W50 plays a critical role in resolving a hairpin structures formed by ssiA and ssiB. Three structurally conserved aspartates (D77, D78 and D134) of RepB’ catalyse the nucleotidyl transfer reaction. Mutations on the helix bundle domain are identified that either reduce the primer length to a dinucleotide (R285A) or abolish primer synthesis (D238A) indicating that the helix bundle domain is required to form and extend the initial dinucleotide synthesized by the catalytic domain.
Tudor staphylococcal nuclease acts as a docking platform for stress granule components inArabidopsis thaliana
Authors: Gutierrez-Beltran Emilio , Elander Pernilla H. , Dalman Kerstin , Crespo Jose Luis , Moschou Panagiotis N. , Uversky Vladimir N. , Bozhkov Peter V. 
Published: February 2020

SUMMARYAdaptation to stress depends on the modulation of gene expression. Regulation of mRNA stability and degradation in stress granules (SGs), - cytoplasmic membraneless organelles composed of messenger ribonucleoprotein (mRNP) complexes, - plays an important role in fine-tuning of gene expression. In addition, SG formation can modulate stress signaling pathways by protein sequestration. Molecular composition, structure, and function of SGs in plants remain obscure. Recently, we established Tudor Staphylococcal Nuclease (TSN or Tudor-SN; also known as SND1) as integral component of SGs inArabidopsis thaliana. Here, we combined purification of TSN interactome with cell biology, reverse genetics and bioinformatics to study composition and function of SGs in plants. We found that under both normal (in the absence of stress) and stress conditions TSN interactome is enriched in the homologues of known mammalian and yeast SG proteins, in addition to novel or plant-specific SG components. We estimate that upon stress perception, approximately half of TSN interactors are recruited to SGsde novo, in a stress-dependent manner, while another half represent a dense protein-protein interaction network pre-formed before onset of stress. Almost all TSN-interacting proteins are moderately or highly disordered and approximately 20% of them are predisposed for liquid-liquid phase separation (LLPS). This suggests that plant SGs, similarly to mammalian and yeast counterparts, are multicomponent viscous liquid droplets. Finally, we have discovered that evolutionary conserved SNF1-related protein kinase 1 (SnRK1) interacts with TSN in heat-induced SGs and that SnRK1 activation critically depends on the presence of TSN and formation of SGs. Altogether, our results establish TSN as a docking platform for SG-associated proteins and important stress signal mediator in plants.
Commensal oralRothia mucilaginosaproduces enterobactin – a metal chelating siderophore
Authors: Uranga Carla , Arroyo Pablo , Duggan Brendan M. , Gerwick William H. , Edlund Anna 
Published: February 2020

AbstractNext-generation sequencing studies of saliva and dental plaque from subjects in both healthy and diseased states have identified bacteria belonging to theRothiagenus as ubiquitous members of the oral microbiota. To gain a deeper understanding of molecular mechanisms underlying the chemical ecology of this unexplored group, we applied a genome mining approach that targets functionally important biosynthetic gene clusters (BGCs). All 45 genomes that were mined, representingRothia mucilaginosa, R. dentocariosaandR. aeria, harbored a catechol-siderophore-like BGC. To explore siderophore production further we grew the previously characterizedR. mucilaginosaATCC 25296 in liquid cultures, amended with glycerol, which led to the identification of the archetype siderophore enterobactin by using tandem Liquid Chromatography Mass Spectrometry (LC/MS/MS), High Performance Liquid Chromatography (HPLC), and Nuclear Magnetic Resonance (NMR) spectroscopy. Normally attributed to pathogenic gut bacteria,R. mucilaginosais the first commensal oral bacterium found to produce enterobactin. Co-cultivation studies includingR. mucilaginosaor purified enterobactin revealed that enterobactin reduced growth of certain strains of cariogenicStreptococcus mutansand pathogenic strains ofStaphylococcus aureus. Commensal oral bacteria were either unaffected by, reduced in growth, or induced to grow adjacent to enterobactin producingR. mucilaginosaor the pure compound. Taken together withRothia’s known capacity to ferment a variety of carbohydrates and amino acids, our findings of enterobactin production adds an additional level of explanation toR. mucilaginosa’s colonization success of the oral cavity. Enterobactin is the strongest Fe(III)-binding siderophore known, and its role in oral health requires further investigation.ImportanceThe communication language of the human oral microbiota is vastly underexplored. However, a few studies have shown that specialized small molecules encoded by BGCs have critical roles such as in colonization resistance against pathogens and quorum sensing. Here, by using a genome mining approach in combination with compound screening of growth cultures, we identified that the commensal oral community membermucilaginosaharbors a catecholate-siderophore BGC, which is responsible for the biosynthesis of enterobactin. The iron-scavenging role of enterobactin is known to have positive effects on the host’s iron pool and negative effects on host immune function, however its role in oral health remains unexplored.R. mucilaginosawas previously identified as an abundant community member in cystic fibrosis, where bacterial iron cycling plays a major role in virulence development. With respect to iron’s broad biological importance, iron-chelating enterobactin may explainR. mucilaginosa’s colonization success in both health and disease.
Automated identification of multinucleated germ cells with U-Net
Authors: Bell Samuel , Zsom Andras , Conley Justin , Spade Daniel 
Published: February 2020

AbstractPhthalic acid esters (phthalates) are male reproductive toxicants, which exert their most potent toxicity during a critical window of sensitivity in fetal development. In the fetal rat, exposure to phthalates reduces testosterone biosynthesis, alters the development of seminiferous cords and other male reproductive tissues, and induces the formation of abnormal multinucleated germ cells (MNGs). Identification of MNGs is a time-intensive process, and it requires specialized training to identify MNGs in histological sections. As a result, MNGs are not routinely quantified in phthalate toxicity experiments. In order to speed up and standardize this process, we have developed an improved method for automated detection of MNGs. Using hand-labeled histological section images with human-identified MNGs, we trained a convolutional neural network with a U-Net architecture to identify MNGs on unlabeled images. With unseen hand-labeled images not used in model training, we assessed the performance of the model, using five different configurations of the data. On average, the model reached near human accuracy, and in the best model, it exceeded it. The use of automated image analysis will allow data on this histopathological endpoint to be more readily collected for analysis of phthalate toxicity. Our trained model application code is available for download at github.com/brown-ccv/mngcount.
Tree bark scrape fungus: A potential source of laccase for application in bioremediation of non-textile dyes
Authors: Bhamare H.M. , Sayyed R. Z. , Marraiki Najat , Elgorban Abdallah M. , Syed Asad , El-Enshasy Hesham Ali 
Published: February 2020

AbstractAlthough laccase has been recognized as a wonder molecule, and green enzyme, the use of low yielding fungal strains, poor production, purification, and low enzyme kinetics have hampered its larger-scale applications. Hence the present research was aimed to select high yielding fungal strains and to optimize the production, purification, and kinetics of laccase ofAspergillussp. HB_RZ4.Aspergillussp. HB_RZ4 produced a copious amount of laccase on under meso-acidophillic shaking conditions in a medium containing glucose and yeast extract. A 25 µM of CuSO4enhanced the enzyme yield. The enzyme was best purified on Sephadex G-100 column. Purified enzyme resembled with the laccase ofA. flavus. Kinetics of purified enzyme revealed the high substrate specificity and good velocity of reaction with ABTS as substrate. The enzyme was stable over a wide range of pH and temperature. The peptide structure of the purified enzyme resembled with the laccase ofA. kawachiiIFO 4308. The fungus decolorized various dyes independent of the requirement of a laccase mediator system (LMS).Aspergillussp. HB_RZ4 came out as a potent natural producer of laccase, it decolorized the dyes even in absence of LMS and thus can be used for bioremediation.
Allergen Extraction: Factors Influencing the Yield, Allergenicity and Sensitivity of Immunoassays
Authors: Soares João Ricardo Almeida , Guimarães Isabelle Mazza , de Souza Oliveira Ana Luísa , das Neves Faccini Claudia Regina Josetti , de Aquino Mattos Erika Bertozzi , Rodrigues Sónia Kristy Pinto Melo , e Silva Airton Pereira , Marmello Bárbara Oliveira , Teixeira Gerlinde Agate Platais Brasil 
Published: February 2020

AbstractFood allergy is an IgE and or IgG immune-mediated reaction to food antigens. Knowledge of the allergenicity properties of proteins, how they react in the body and in diagnostic tests is necessary to adequately assess the allergenic potential of both natural foods and those produced through biotechnological processes. Thus, our aim was analyze the factors those influence the protein extraction of foods in terms of yield, allergenicity and sensitivity in immunoassays. Peanut proteins were extracted using 4 distinct extraction buffers (physiological saline, tris buffer, borate buffer with and without β-mercaptoethanol). The protein concentration of the obtained extracts was determined by the Lowry method. Polyacrylamide electrophoresis (SDS-PAGE) was used to compare the protein profile of each extract. Immunogenicity of each extract was verified by sensitizing two mouse strains (Balb/c and C57/BL6) with 100μg of the proteins, and the immunoreactivity was determined by ELISA. Our results show that extraction with the distinct buffers resulted in protein solutions with different yields and profiles. The antigenicity of the different extracts in a murine model of systemic immunization also demonstrated distinct patterns that varied depending on the extraction methods and mouse strain. The immunoreactivity varied in accordance to the protein extract used to coat the microtitration plates. In conclusion,the protein yield and profile in the extracts is critically influenced by the salt composition and pH of the extraction buffers. This in turn influences both in vivo immunogenicity and in vitro immunoreactivity.
Cooperation between CRISPR-Cas types enables adaptation in an RNA-targeting system
Authors: Hoikkala Ville , Ravantti Janne , Díez-Villaseñor César , Tiirola Marja , Conrad Rachel A. , McBride Mark J. , Sundberg Lotta-Riina 
Published: February 2020

AbstractCRISPR-Cas immune systems adapt to new threats by acquiring spacers from invading nucleic acids such as phage genomes. However, some CRISPR-Cas loci lack genes necessary for spacer acquisition, despite apparent variation in spacer content between strains. It has been suggested that such loci may use acquisition machinery from co-occurring CRISPR-Cas systems. Here, using a lytic dsDNA phage, we observe spacer acquisition in the native host Flavobacterium columnare that carries an acquisition-deficient subtype VI-B locus and a complete subtype II-C locus. We characterize acquisition events in both loci and show that the RNA-targeting VI-B locus acquires spacers in trans using acquisition machinery from the DNA-targeting II-C locus. Our observations reinforce the concept of modularity in CRISPR-Cas systems and raise further questions regarding plasticity of adaptation modules.
Modulation of bacterial multicellularity via spatiotemporal polysaccharide secretion
Authors: Islam Salim T. , Alvarez Israel Vergara , Saïdi Fares , Giuseppi Annick , Vinogradov Evgeny , Morrone Castrese , Brasseur Gael , Sharma Gaurav , Benarouche Anaïs , Bridot Jean-Luc , Ravicoularamin Gokulakrishnan , Cagna Alain , Gauthier Charles , Singer Mitchell , Fierobe Henri-Pierre , Mignot Tâm , Mauriello Emilia M. F. 
Published: February 2020

AbstractThe development of multicellularity is a key evolutionary transition allowing for differentiation of physiological functions across a cell population that confers survival benefits; among unicellular bacteria, this can lead to complex developmental behaviours and the formation of higher-order community structures. Herein, we demonstrate that in the social δ-proteobacteriumMyxococcus xanthus, the secretion of a novel secreted biosurfactant polysaccharide (BPS) is temporally and spatially modulated within communities, mediating swarm migration as well as the formation of multicellular swarm biofilms and fruiting bodies. BPS is a type IV pilus-inhibited acidic polymer built of randomly-acetylated β-linked tetrasaccharide repeats. Both BPS and the “shared good” EPS are produced by dedicated Wzx/Wzy-dependent polysaccharide assembly pathways distinct from that responsible for spore coat assembly. To our knowledge, such pathways have never-before been explicitly shown to synthesize a biosurfactant. Together, these data reveal the central role of secreted polysaccharides in the intricate behaviours coordinating bacterial multicellularity.
Proteome overabundance enables respiration but limitation onsets carbon overflow
Authors: Kumar Rahul , Lahtvee Petri-Jaan 
Published: February 2020

AbstractCentral carbon metabolism produces energy and precursor metabolites for biomass in heterotrophs. Carbon overflow yields metabolic byproducts and, here, we examined its dependency on nutrient and growth using the unicellular eukaryotic model organismSaccharomyces cerevisiae. We performed quantitative proteomics analysis together with metabolic modeling and found that proteome overabundance enabled respiration, and variation in energy efficiency caused distinct composition of biomass at different carbon to nitrogen ratio and growth rate. Our results showed that ceullar resource allocation for ribosomes was determinative of growth rate, but energy constrains on protein synthesis incepted carbon overflow by prioritizing abundance of ribosomes and glycolysis over mitochondria. We proved that glycolytic efficiency affected energy metabolism by making a trade-off between low and high energy production pathways. Finally, we summarized cellular energy budget underlying nutrient-responsive and growth rate-dependent carbon overflow, and suggested implications of results for bioprocesses and pathways relevant in cancer metabolism in humans.
Kinfitr – an open source tool for reproducible PET modelling: validation and evaluation of test-retest reliability
Authors: Tjerkaski Jonathan , Cervenka Simon , Farde Lars , Matheson Granville James 
Published: February 2020

AbstractIn positron emission tomography (PET) imaging, binding is typically estimated by fitting pharmacokinetic models to the series of measurements of radioactivity in the target tissue following intravenous injection of a radioligand. However, there are multiple different models to choose from and numerous analytical decisions which must be made when modelling PET data. Therefore, full communication of all the steps involved is often not feasible within the confines of a scientific publication. As such, there is a need to improve analytical transparency.Kinfitr, written in the open-source programming language R, is a tool developed for flexible and reproducible kinetic modelling of PET data, i.e. performing all steps using code which can be publicly shared in analysis notebooks. In this study, we compared outcomes obtained usingkinfitrwith those obtained using PMOD: a widely-used commercial tool.Using previously-collected test-retest data obtained with four different radioligands, a total of six different kinetic models were fitted to time-activity curves derived from different brain regions. We observed high agreement between the two kinetic modelling tools both for binding estimates and for microparameters. Likewise, no substantial differences were observed in the test-retest reliability estimates between the two tools.In summary, we showed excellent agreement between the open source R packagekinfitr, and the widely-used commercial application PMOD. We therefore conclude thatkinfitris a valid and reliable tool for kinetic modelling of PET data.
High-throughput behavioral screen inC. elegansreveals novel Parkinson’s disease drug candidates
Authors: Sohrabi Salman , Mor Danielle E. , Kaletsky Rachel , Keyes William , Murphy Coleen T. 
Published: February 2020

AbstractWe recently linked branched-chain amino acid transferase 1 (BCAT1) with the movement disorder Parkinson’s disease (PD), and found that reduction ofC. elegans bcat-1causes abnormal spasm-like ‘curling’ behavior with age. Here, we report the development of a high-throughput automated curling assay and its application to the discovery of new potential PD therapeutics. Four FDA-approved drugs were identified as candidates for late-in-life intervention, with metformin showing the greatest promise for repurposing to PD.