bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793)
Authors: de-Dios Toni , van Dorp Lucy , Charlier Philippe , Morfopoulou Sofia , Lizano Esther , Bon Celine , Le Bitouzé Corinne , Alvarez-Estape Marina , Marquès-Bonet Tomas , Balloux François , Lalueza-Fox Carles 
Published: October 2019

AbstractThe French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens.
The short-term high fat diet-induced increase in %5-methylcytosine expression in peripheral blood T lymphocytes, is attenuated by low-dose aspirin
Authors: Mutize Tinashe , Dludla Phiwayinkosi V. , Mkandla Zibusiso , Nkambule Bongani B. 
Published: October 2019

AbstractObjectiveTo assess peripheral lymphocyte DNA methylation profiles in prediabetes using a high fat-diet-fed C57BL/6 animal model. We further evaluated whether low dose-aspirin, or low-dose aspirin in combination with metformin, could modulate global DNA methylation levels in peripheral blood lymphocytes.MethodsTwenty-eight (28) male C57BL/6 mice were used in two experimental phases. The first experiment involved animals (n=16) which were randomised to receive a low-fat diet (LFD) or high-fat diet (HFD) (n = 8/group) for 10 weeks. Whereas in the second experiment, HFD-fed mice (n=15) were randomised into 3 treatment groups, a low-dose aspirin (LDA), LDA and metformin group, and a clopidogrel group. DNA methylation profiles of were determined using flow cytometry.ResultsThe HFD group showed moderate weight gain and elevated postprandial blood glucose levels when compared to the LFD group after 2 weeks of HFD-feeding (p < 0.05). Interestingly, the HFD group had elevated levels of T cells expressing high levels %5-methylcytosine (p<0, 05). Notably, these elevated levels were lowered by short-term low-dose aspirin treatment.DiscussionT cells are involved in the propagation of the inflammatory response. Persistent T cell activation promotes chronic inflammation and insulin resistance. Low-dose aspirin may be effective in modulating T cell-specific global methylation.
CRISPR/Cas9 mediated intersectional knockout of GSK3β in D2 receptor expressing mPFC neurons reveals contributions to emotional regulation
Authors: Khlghatyan Jivan , Beaulieu Jean-Martin 
Published: October 2019

AbstractBackgroundGlycogen synthase kinase 3β (GSK3β) regulates neurodevelopment, synaptic plasticity as well as mood, cognition, social interaction, and depressive-like behaviors. Inhibition of GSK3β is a shared consequence of treatment by lithium, SSRIs, ketamine and antipsychotics. GSK3β activity is regulated by dopamine D2 receptor signaling and can be inhibited by psychoactive drugs in a D2 receptor dependent manner. Functions of GSK3β in striatal D2 neurons has been studied extensively. However, GSK3β is ubiquitously expressed in the brain and D2 receptor expressing cells are distributed as a mosaic in multiple cortical regions. This complicates the interrogation of GSK3β functions in cortical D2 cells in a circuit defined manner using conventional animal models.MethodsWe have used a CRISPR/Cas9 mediated intersectional approach to achieve targeted deletion of GSK3β in D2 expressing neurons of the adult medial prefrontal cortex (mPFC).ResultsIsolation and analysis of ribosome associated RNA specifically from mPFC D2 neurons lacking GSK3β demonstrated large scale translatome alterations. Deletion of GSK3β in mPFC D2 neurons revealed its contribution to anxiety-related, cognitive, and social behaviors.ConclusionsOur results underscore the viability of intersectional knockout approach to study functions of a ubiquitous gene in a network defined fashion while uncovering a contribution of GSK3β expressed in mPFC D2 neurons in the regulation of behavioral dimensions related to mood and emotions. This advances our understanding of GSK3β action at a brain circuit level and can potentially lead to the development of circuit selective therapeutics.
Ubiquitin and SUMO conjugation as biomarkers of Acute Myeloid Leukemias response to chemotherapies
Authors: Gâtel Pierre , Brockly Frédérique , Reynes Christelle , Pastore Manuela , Hicheri Yosr , Cartron Guillaume , Piechaczyk Marc , Bossis Guillaume 
Published: October 2019

AbstractUbiquitin and the ubiquitin-like SUMO are covalently conjugated to thousands of proteins to modulate their function and fate. Many of the enzymes involved in their conjugation are dysregulated in cancers and involved in cancer cells response to therapies. We describe here the identification of biomarkers of the activity of these enzymes and their use to predict Acute Myeloid Leukemias (AML) response to standard chemotherapy (daunorubicine-DNR and cytarabine-Ara-C). We compared the ability of extracts from chemosensitive and chemoresistant AML cells to conjugate ubiquitin or SUMO-1 on 9000 proteins spotted on protein-arrays. We identified 122 proteins whose conjugation by these post-translational modifiers marks AML resistance to DNR and/or Ara-C. Based on this modifomic signature, we defined a statistical score able to predict AML patient response to standard chemotherapy. We finally developed a miniaturized assay to easily assess the modification level of the selected biomarkers and validated it in patient cell extracts. Thus, our work identifies a new type of ubiquitin-based biomarkers that could be used to predict cancer patients response to treatments.Summary blurbThis study describes the identification of a new class of biomarkers of cancer response to therapies based on protein modification by Ubiquitin and SUMO and provides the tools to analyze them in Acute Myeloid Leukemia patient samples.
Short-wavelength violet light (420nm) stimulates melanopsin-dependent acute alertness responses in zebrafish
Authors: Contreras Jorge E. , Lisse Thomas S. , Bouzidi Chifaa , Cavanaugh Ann M. , Matynia Anna , Rieger Sandra 
Published: October 2019

AbstractSunlight throughout the day and seasons strongly influences our biological rhythms and activity. In recent years, it has become evident that night-time overexposure to bright light in urban environments can profoundly affect physiology and behaviour in humans and animals. In particular, the artificial emission of short-wavelength light has been shown to stimulate alertness in humans, but the mechanisms remain largely unknown. Utilising a diurnal larval zebrafish model, we identified instant, non-image-forming (NIF) responses to short-wavelength violet light (~420nm), which are activated only during light exposure, and are reminiscent of alertness, including increased heart rate, enhanced locomotor activity, and pectoral fin beating (for increased oxygen supply). We further determined that these responses are driven by sympathetic neuronal circuits and depend on the zebrafish melanopsin homologue Opn4a. We also found that these responses can be modulated by the sleep-regulatory hormone melatonin, but that melatonin is not essential. Our findings reveal a previously unknown mechanism for violet light-dependent acute alertness.
Cockroaches show individuality in learning and memory during classical and operant conditioning
Authors: Arican Cansu , Bulk Janice , Deisig Nina , Nawrot Martin Paul 
Published: October 2019

AbstractAnimal personality and individuality are intensively researched in vertebrates and both concepts are increasingly applied to behavioral science in insects. However, only few studies have looked into individuality with respect to performance in learning and memory tasks. In vertebrates individual learning capabilities vary considerably with respect to learning speed and learning rate. Likewise, honeybees express individual learning abilities in a wide range of classical conditioning protocols. Here, we study individuality in the learning and memory performance of cockroaches, both in classical and operant conditioning tasks. We implemented a novel classical (olfactory) conditioning paradigm where the conditioned response is established in the maxilla-labia response (MLR). Operant spatial learning was investigated in a forced two-choice task using a T-maze. Our results confirm individual learning abilities in classical conditioning of cockroaches that was reported for honeybees and vertebrates but contrast long-standing reports on stochastic learning behavior in fruit flies. In our experiments, most learners expressed a correct behavior after only a single learning trial showing a consistent high performance during training and test. We can further show that individual learning differences in insects are not limited to classical conditioning but equally appear in operant conditioning of the cockroach.
RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting
Authors: Quintero-Cadena Porfirio , Lenstra Tineke L. , Sternberg Paul W. 
Published: October 2019

AbstractRNA Polymerase II contains a disordered C-terminal domain (CTD) whose length enigmatically correlates with genome size. The CTD is crucial to eukaryotic transcription, yet the functional and evolutionary relevance of this variation remains unclear. Here, we use smFISH, live imaging, and RNA-seq to investigate how CTD length and disorder influence transcription. We find that length modulates the size and frequency of transcriptional bursting. Disorder is highly conserved and mediates CTD-CTD interactions, an ability we show is separable from protein sequence and necessary for efficient transcription. We build a data-driven quantitative model, simulations of which recapitulate experiments and support CTD length promotes initial polymerase recruitment to the promoter but slows down its release from it, and that CTD-CTD interactions enable promoter recruitment of multiple polymerases. Our results reveal how these tunable parameters provide access to a range of transcriptional activity, offering a new perspective for the mechanistic significance of CTD length and disorder in transcription across eukaryotes.
Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons
Authors: Fischer Sylvia E. J. , Ruvkun Gary 
Published: October 2019

ABSTRACTEndogenous retroviruses and LTR retrotransposons are mobile genetic elements that are closely related to retroviruses. Desilenced endogenous retroviruses are associated with human autoimmune disorders and neurodegenerative diseases. C. elegans and related Caenorhabdites contain LTR retrotransposons and, as described here, numerous integrated viral genes including viral envelope genes that are part of LTR retrotransposons. We found that both LTR retrotransposons and endogenous viral elements are silenced by ADARs (adenosine deaminases acting on double-stranded RNA (dsRNA)) together with the endogenous RNAi factor ERI-6/7, a homolog of Mov10 helicase, a retrotransposon and retrovirus restriction factor in human. siRNAs corresponding to integrated viral genes and LTR retrotransposons, but not to DNA transposons, are dependent on the ADARs and ERI-6/7; on the contrary, siRNAs corresponding to palindromic repeats are increased in adar-eri mutants because of an antiviral RNAi response to dsRNA. Silencing of LTR retrotransposons is dependent on downstream RNAi factors and P granule components but is independent of the viral sensor DRH-1/RIG-I and the nuclear Argonaute NRDE-3. The activation of retrotransposons in the ADAR- and ERI-6/7/MOV10-defective mutant is associated with the induction of the Unfolded Protein Response (UPR), a common response to viral infection. The overlap between genes induced upon viral infection and infection with intracellular pathogens, and genes co-expressed with retrotransposons, suggests that there is a common response to different types of foreign elements that includes a response to proteotoxicity presumably caused by the burden of replicating pathogens and expressed retrotransposons.SIGNIFICANCESilencing of transposable elements and viruses is critical for the maintenance of genome integrity, cellular homeostasis and organismal health. Here we describe multiple factors that control different types of transposable elements, providing insight into how they are regulated. We also identify stress response pathways that are triggered upon mis-regulation of these transposable elements. The conservation of these factors and pathways in human suggests that our studies in C. elegans can provide general insight into the regulation of and response to transposable elements and viruses.
Genome-wide diversity of coconut from northern South America uncovers genotypes present in Colombia and strong population structure
Authors: Muñoz-Pérez Jorge Mario , Cañas Gloria Patricia , López Lorena , Arias Tatiana 
Published: October 2019

SummaryCoconut palms (Cocos nucifera) are a combination of wild admixed populations and perennial crops with a worldwide distribution. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) for at least four different commercially important and widely cultivated coconut varieties and hybrids growing in northern South America. We present a comprehensive catalog of approximately 27K SNPs to conduct genetic diversity, population structure and linkage disequilibrium analysis. A relatively fast LD decay for the Atlantic accessions within ~250Kb was observed in comparison to the Pacific accessions ~ 1500 Kb.The complete SNPs sampling showed a strong population structure at K = 2, separating accessions from the Pacific and Atlantic coasts as it has been found in previous studies. At higher K values, one non-admixed group was observed for the Atlantic while further substructures emerged for the Pacific accessions, where three non-admixed groups were found. Population structure analysis also showed a great degree of admixture between the Atlantic and Pacific populations, and SNPs of the Pacific non-admixed genetic groups were mostly introgressed into the Atlantic individuals but the contrary was rarely observed. The results of principal component analysis and Neighbor-Joining Hierarchical Clustering were consistent with the results from Structure and provided a measure of genetic relationships among individual genotypes. The Pacific group has a lower genetic diversity and a higher rate of inbreeding than the Atlantic group. These results suggest that the Pacific coconuts of Colombia belong to the pre-Columbian population found on the Pacific coast of Panama and Peru. If it had been introduced after Columbus (as in Mexico), genetic diversity would have been higher than on the Atlantic coast.
Prediction of druggable proteins using machine learning and functional enrichment analysis: a focus on cancer-related proteins and RNA-binding proteins
Authors: López-Cortés Andrés , Cabrera-Andrade Alejandro , Cruz-Segundo Carlos M. , Dorado Julian , Pazos Alejandro , Gonzáles-Díaz Humberto , Paz-y-Miño César , Pérez-Castillo Yunierkis , Tejera Eduardo , Munteanu Cristian R. 
Published: October 2019

ABSTRACTBackgroundDruggable proteins are a trending topic in drug design. The druggable proteome can be defined as the percentage of proteins that have the capacity to bind an antibody or small molecule with adequate chemical properties and affinity. The screening and in silico modeling are critical activities for the reduction of experimental costs.MethodsThe current work proposes a unique prediction model for druggable proteins using amino acid composition descriptors of protein sequences and 13 machine learning linear and non-linear classifiers. After feature selection, the best classifier was obtained using the support vector machine method and 200 tri-amino acid composition descriptors.ResultsThe high performance of the model is determined by an area under the receiver operating characteristics (AUROC) of 0.975 ± 0.003 and accuracy of 0.929 ± 0.006 (3-fold cross-validation). Regarding the prediction of cancer-associated proteins using this model, the best ranked druggable predicted proteins in the breast cancer protein set were CDK4, AP1S1, POLE, HMMR, RPL5, PALB2, TIMP1, RPL22, NFKB1 and TOP2A; in the cancer-driving protein set were TLL2, FAM47C, SAGE1, HTR1E, MACC1, ZFR2, VMA21, DUSP9, CTNNA3 and GABRG1; and in the RNA-binding protein set were PLA2G1B, CPEB2, NOL6, LRRC47, CTTN, CORO1A, SCAF11, KCTD12, DDX43 and TMPO.ConclusionsThis powerful model predicts several druggable proteins which should be deeply studied to find better therapeutic targets and thus improve clinical trials. The scripts are freely available at https://github.com/muntisa/machine-learning-for-druggable-proteins.
Inline Liquid Chromatography-Fast Photochemical Oxidation of Proteins Allows for Targeted Structural Analysis of Conformationally Heterogeneous Mixtures
Authors: Tadi Surendar , Misra Sandeep K. , Sharp Joshua S. 
Published: October 2019

AbstractStructural analysis of proteins in a conformationally heterogeneous mixture has long been a difficult problem in structural biology. In structural analysis by covalent labeling mass spectrometry, conformational heterogeneity results in data reflecting a weighted average of all conformers, complicating data analysis and potentially causing misinterpretation of results. Here, we describe a method coupling size exclusion chromatography (SEC) with hydroxyl radical protein footprinting using inline fast photochemical oxidation of proteins (FPOP). Using a controlled synthetic mixture of holomyoglobin and apomyoglobin, we demonstrate that we can achieve accurate footprints of each conformer using LC-FPOP when compared to off-line FPOP of each pure conformer. We then applied LC-FPOP to analyze the adalimumab heat-shock aggregation process. We found that the LC-FPOP footprint of unaggregated adalimumab was consistent with a previously published footprint of the native IgG. The LC-FPOP footprint of the aggregation product indicated that heat shock aggregation primarily protected the hinge region, suggesting this region is involved with the heat shock aggregation process of this molecule. LC-FPOP offers a new method to probe dynamic conformationally heterogeneous mixtures such as biopharmaceutical aggregates, and obtain accurate information on the topography of each conformer.
Phosphorylation on PstP regulates cell wall metabolism and antibiotic tolerance in Mycobacterium smegmatis
Authors: Shamma Farah , Papavinasasundaram Kadamba , Quintanilla Samantha Y. , Bandekar Aditya , Sassetti Christopher , Boutte Cara C. 
Published: October 2019

AbstractMycobacterium tuberculosis and its relatives, like many bacteria, have dynamic cell walls that respond to environmental stresses. Modulation of cell wall metabolism in stress is thought to be responsible for decreased permeability and increased tolerance to antibiotics. The signaling systems that control cell wall metabolism under stress, however, are poorly understood. Here, we examine the cell wall regulatory function of a key cell wall regulator, the Serine Threonine Phosphatase PstP, in the model organism Mycobacterium smegmatis. We show that the peptidoglycan regulator CwlM is a substrate of PstP. We find that a phospho-mimetic mutation, pstP T171E, slows growth, mis-regulates both mycolic acid and peptidoglycan metabolism in different conditions, and interferes with antibiotic tolerance. These data suggest that phosphorylation on PstP affects its activity against various substrates and is important in the transition between growth and stasis.ImportanceRegulation of cell wall assembly is essential for bacterial survival and contributes to pathogenesis and antibiotic tolerance in mycobacteria, including pathogens such as Mycobacterium tuberculosis. However, little is known about how the cell wall is regulated in stress. We describe a pathway of cell wall modulation in Mycobacterium smegmatis through the only essential Ser/Thr phosphatase, PstP. We showed that phosphorylation on PstP is important in regulating peptidoglycan metabolism in the transition to stasis and mycolic acid metabolism in growth. This regulation also affects antibiotic tolerance in growth and stasis. This work helps us to better understand the phosphorylation-mediated cell wall regulation circuitry in Mycobacteria.
Cortical morphology predicts placebo response in multiple sclerosis
Authors: Cherkasova Mariya V. , Fu Jessie F. , Jarrett Michael , Johnson Poljanka , Abel Shawna , Tam Roger , Rauscher Alexander , Sossi Vesna , Kolind Shannon , Li David , Sadovnick A. Dessa , Machan Lindsay , Girard J. Marc , Emond Francois , Vosoughi Reza , Traboulsee Anthony , Stoessl A. Jon 
Published: October 2019

ABSTRACTAlthough significant insights have been gained into the neural mechanisms of acute placebo responses, less is known about the mechanisms of longer-term placebo responses, such as those seen in clinical trials, or the interactions between these mechanisms and brain disease. We examined neuropathological and morphological brain correlates of placebo responses in a randomized clinical trial of a controversial endovascular treatment (“liberation therapy”) for multiple sclerosis. Patients were randomized to receive either balloon or sham extracranial venoplasty and followed for 48 weeks. The trial did not support therapeutic efficacy of venoplasty, but a subset of both venoplasty- and sham-treated patients reported an improvement in health-related quality of life that peaked at 12 weeks following treatment, suggesting a placebo response. Placebo responders had higher lesion activity than placebo non-responders. Although placebo responders did not differ from non-responders in terms of total normalized brain volume, regional grey or white matter volume or cortical thickness, graph theoretical analysis of cortical thickness covariance showed that placebo non-responders had a more homogenous cortical thickness topology with a more small-world-like architecture. In placebo non-responders, lesion load inversely predicted cortical thickness in primary somatosensory and motor areas, association areas, precuneus and insula, primarily in the right hemisphere. In placebo responders, lesion load was unrelated to cortical thickness. The neuropathological process in MS may result in a cortical configuration that is less suited to functional integration and less capable of generating a sustained placebo response.