bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq
Authors: Schwarzl Thomas , Sahadevan Sudeep , Lang Benjamin , Miladi Milad , Backofen Rolf , Huber Wolfgang , Hentze Matthias W , Tartaglia Gian G 
Published: November 2022

AbstractEnhanced crosslinking and immunoprecipitation (eCLIP) sequencing is a powerful method for transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). However, identified crosslink sites can profoundly deviate from experimentally established functional elements of even well-studied RBPs. Current peak-calling strategies result in low replication and high false-positive rates. Here, we present the R/Bioconductor packageDEWSeqthat makes full use of replicate information and size-matched input controls. We benchmarkedDEWSeqon 107 RBPs for which both eCLIP data and RNA sequence motifs are available and were able to more than double the number of motif-containing binding regions relative to standard eCLIP processing (2.3-fold median). The improvement not only relates to the number of binding sites (e.g., 3.1-fold of known motifs for RBFOX2), but also their subcellular localisation (e.g., 1.9-fold of mitochondrial genes for FASTKD2) and structural targets (e.g., 2.2-fold increase of stem-loop regions for SLBP). DEWSeq therefore shows promise as an improved processing method for eCLIP protein–RNA interaction data.
Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning
Authors: Maasch Jacqueline R. M. A. , Torres Marcelo D. T. , Melo Marcelo C. R. , de la Fuente-Nunez Cesar 
Published: November 2022

SummaryMolecular de-extinction could offer new avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted as subsequences of extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observedin vitrofor modern and archaic protein fragments identified with panCleave. Lead peptides were tested for mechanism of action, resistance to proteolysis, and anti-infective efficacy in two pre-clinical mouse models. These results suggest that machine learning-based encrypted peptide prospection can identify stable, nontoxic antimicrobial peptides. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.HighlightsMachine learning guides bioinspired prospection for encrypted antimicrobial peptides.Modern and extinct human proteins harbor antimicrobial subsequences.Ancient encrypted peptides displayin vitroandin vivoactivity with low host toxicity.Paleoproteome mining offers a new framework for antibiotic discovery.
Genome-wide single-molecule analysis of long-read DNA methylation reveals heterogeneous patterns at heterochromatin
Authors: Kerr Lyndsay , Kafetzopoulos Ioannis , Grima Ramon , Sproul Duncan 
Published: November 2022

AbstractHigh-throughput sequencing technology is central to our current understanding of the human methylome. The vast majority of studies use chemical conversion to analyse bulk-level patterns of DNA methylation across the genome from a population of cells. While this technology has been used to probe single-molecule methylation patterns, such analyses are limited to short reads of a few hundred basepairs. DNA methylation can also be directly detected using Nanopore sequencing which can generate reads measuring megabases in length. However, thus far these analyses have largely focused on bulk-level assessment of DNA methylation. Here, we analyse DNA methylation in single Nanopore reads with a mean length of 24.6kb, to show that bulk-level metrics underestimate large-scale heterogeneity in the methylome. We use the correlation in methylation state between neighbouring sites to quantify single-molecule heterogeneity and find that heterogeneity varies significantly across the human genome, with some regions having heterogeneous methylation patterns at the single-molecule level and others possessing more homogeneous methylation patterns. By comparing the genomic distribution of the correlation to epigenomic annotations, we find that the greatest heterogeneity in single-molecule patterns is observed within heterochromatic partially methylated domains (PMDs). In contrast, reads originating from euchromatic regions and gene bodies have more ordered DNA methylation patterns. By analysing the patterns of single molecules in more detail, we show the existence of a 185bp periodicity in DNA methylation that accounts for some of the heterogeneity we uncover in long single-molecule DNA methylation patterns. We find that this periodic structure is partially masked in bulk data in a manner that is consistent with imperfect phasing of nucleosomes between molecules. Our findings demonstrate the power of single-molecule analysis of long-read data to understand the structure of the human methylome.
Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing inSaccharomyces cerevisisae
Authors: Sapède Elena , Sugawara Neal , Tyers Randall G. , Nakajima Yuko , Afreen Mosammat Faria , Escobar Jesselin Romero , Haber James E. 
Published: November 2022

ABSTRACTSingle-strand annealing (SSA) is initiated when a double strand break (DSB) occurs between two flanking repeated sequences, resulting in a deletion that leaves a single copy of the repeat. We studied budding yeast strains carrying two 200-bpURA3sequences separated by 2.3-kb of phage lambda DNA in which a site-specific DSB can be created by HO or Cas9 endonucleases. Repeat-mediated deletion requires removal of long 3’-ended single-stranded tails (flaps) by Rad1-Rad10 with the assistance of Msh2-Msh3 and Slx4. A natural 3% divergence between repeats (designated F and A) causes a significant reduction in the frequency of SSA repair. This decrease is caused by heteroduplex rejection in which mismatches (MMs) in the annealed intermediate are recognized by the MutSα (Msh2 and Msh6) components of the MM repair (MMR) pathway coupled to unwinding of the duplex by the Sgs1-Rmi1-Top3 helicase. MutL homologs, Mlh1-Pms1 (MutLα) are not required for rejection but play their expected role in mismatch correction. Remarkably, heteroduplex rejection is very low in strains where the identical repeats were immediately adjacent (Tailless strains) and the DSB was induced by Cas9. These results suggest that the presence of nonhomologous tails strongly stimulates heteroduplex rejection in SSA. DNA sequencing analysis of SSA products from the FA Tailed strain, where the F variant carries six single-base mutations and one +1(T) insertion within a run of 10 Ts showed a gradient of correction favoring the sequence opposite each 3’ end of the annealed strand. Mismatches (MMs) located in the center of the repair intermediate were corrected by Msh2-Msh6 mediated mismatch correction, while correction of MMs at the extremity of the SSA intermediate often appears to use a different mechanism, using either 3’ nonhomologous tail removal or 3’ to 5’ “proofreading” resection by DNA polymerase δ followed by synthesis to fill in the gap. In contrast, in FA Tailless strains there was a uniform repair of the MMs across the repeat, with a bias in favor of the “left” copy. A distinctive pattern of correction was found in the absence ofMSH2, in both Tailed and Tailless strains, while the deletion ofMSH6resulted in unrepaired MMs.
The UBP5 histone H2A deubiquitinase counteracts PRC2-mediated repression to regulate Arabidopsis development and stress responses
Authors: Godwin James , March Eduardo , Govindasamy Mohan , Bourbousse Clara , Wolff Léa , Fort Antoine , Krzyszton Michal , López Jesús , Swiezewski Szymon , Barneche Fredy , Schubert Daniel , Farrona Sara 
Published: November 2022

AbstractPolycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. However, there is limited knowledge about PRCs’ interacting proteins and their interplay with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a novel interactor of the PRC2 subunit SWINGER and its associated factor PWO1 inArabidopsis thaliana. As inferred from the functional analyses ofubp5CRISPR-Cas9 mutant plants, UBP5 regulates plant development and stress responses, notably by promoting H2A monoubiquitination erasure, leading to transcriptional de-repression. Preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining inubp5mutant plants further suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, UBP5 provides novel insights to disentangle the complex PRC2 interaction network and is a crucial regulator of the pivotal epigenetic repressive marks H2Aub and H3K27me3.
Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia
Authors: Vuillemin Aurèle 
Published: November 2022

AbstractProductive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases.Here, geochemical data are combined with metagenomes, metatranscriptomes and stable-isotope probing incubations from the water column and subseafloor of the Benguela Upwelling System. Taxonomic assemblages and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated withCandidatusNitrosopumilus andCandidatusNitrosopelagicus among Archaea, andNitrospina, Nitrosomonas, Nitrosococcus, andNitrospiraamong Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity towards mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification prevails over canonical denitrification when Namibian coastal waters are ventilated during austral winter.
Food recognition in a blood-feeding insect: characterization of the pharyngeal taste organ
Authors: Ortega-Insaurralde Isabel , Latorre-Estivalis José Manuel , Costa-da-Silva Andre Luis , Cano Agustina , Insausti Teresita C. , Morales Hector Salas , Pontes Gina , de Astrada Martín Berón , Ons Sheila , DeGennaro Matthew , Barrozo Romina B. 
Published: November 2022

AbstractBackgroundObligate blood-feeding insects obtain the nutrients and water necessary to ensure survival from the vertebrate blood. The internal taste sensilla, situated in the pharynx, evaluate the suitability of the ingested food. Here, through multiple approaches, we characterized the pharyngeal organ (PO) of the hematophagous kissing bugRhodnius prolixusto determine its role in food assessment. The PO, located antero-dorsally in the pharynx, comprises 8 taste sensilla that become bathed with the incoming blood.ResultsWe showed that these taste sensilla house gustatory receptor neurons projecting their axons through the labral nerves to reach the subesophageal zone in the brain. We found that these neurons are electrically activated by relevant appetitive and aversive gustatory stimuli such as NaCl, ATP and caffeine. Using RNA-Seq, we examined the expression of sensory-related gene families in the PO. We identified gustatory receptors, ionotropic receptors, transient receptor potential channels, pickpocket channels, opsins, takeouts, neuropeptide precursors, neuropeptide receptors and biogenic amine receptors. RNA interference assays demonstrated that the pickpocket channelRproppk014276is necessary for salt detection during feeding.ConclusionWe provide evidence of the role of the pharyngeal organ in food evaluation. This work shows the first comprehensive characterization of a pharyngeal taste organ in a hematophagous insect.
Single-cell RNA-sequencing implicates venous endothelial cells as a source of VEGF-A-mediated neo-angiogenesis in neuroinflammation
Authors: Shahriar S. , Biswas S. , Zhao K. , Akcan U. , Tuohy M. C. , Glendinning M. D. , Kurt A. , Wayne C. R. , Prochilo G. , Price M. Z. , Brekken R. A. , Menon V. , Agalliu D. 
Published: November 2022

ABSTRACTHistopathological studies of multiple sclerosis (MS), a demyelinating disease of the central nervous system (CNS), and its animal model, experimental autoimmune encephalomyelitis (EAE), have found newly formed leaky vessels in demyelinated acute and chronic plaques, in addition to blood-brain barrier (BBB) damage in existing vessels, that exacerbate disease pathology by increasing infiltration of immune cells. Which vessel subtypes and signaling pathways generate these aberrant vessels is poorly understood. Using single-cell RNA-sequencing andin vivovalidation, we find that transcriptome signatures of neo-angiogenesis arise in venous endothelial cells in both acute and chronic EAE, and correlate with upregulation in VEGF-A signaling. These neo-angiogenic markers are also increased in acute and chronic MS lesions. Treatment with a VEGF-A blocking antibody diminishes neo-angiogenic transcriptomic signatures and vascular proliferationin vivo, but does not restore BBB function or ameliorate significantly EAE pathology. Therefore, anti-angiogenic therapies in combination with immunomodulatory therapies may benefit MS progression.
Cell-type specific developmental defects inPTEN-mutant cortical organoids converge on abnormal circuit activity
Authors: Pigoni Martina , Uzquiano Ana , Paulsen Bruna , Kedaigle Amanda , Yang Sung Min , Symvoulidis Panagiotis , Adiconis Xian , Velasco Silvia , Sartore Rafaela , Kim Kwanho , Tucewicz Ashley , Tsafou Kalliopi , Jin Xin , Barrett Lindy , Chen Fei , Boyden Ed , Regev Aviv , Levin Joshua Z. , Arlotta Paola 
Published: November 2022

AbstractDe novoheterozygous loss-of-function mutations inPTENare strongly associated with Autism spectrum disorders (ASD); however, it is unclear how heterozygous mutations in this gene affects different cell types during human brain development, and how these effects vary across individuals. Here, we used human cortical organoids from different donors to identify cell-type-specific developmental events that are affected by heterozygous mutations inPTEN. We profiled individual organoids by single-cell RNA-seq, proteomics and spatial transcriptomics, and revealed abnormalities in developmental timing in human outer radial glia progenitors and deep layer cortical projection neurons, which varied with the donor genetic background. Calcium imaging in intact organoids showed that both accelerated and delayed neuronal development phenotypes resulted in similar abnormal activity of local circuits, irrespective of genetic background. The work reveals donor-dependent, cell-type specific developmental phenotypes ofPTENheterozygosity that later converge on disrupted neuronal activity.
Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling inGrin2amutant mice
Authors: Farsi Zohreh , Nicolella Ally , Simmons Sean K , Aryal Sameer , Shepard Nate , Brenner Kira , Lin Sherry , Herzog Linnea , Shin Wangyong , Gazestani Vahid , Song Bryan , Bonanno Kevin , Keshishian Hasmik , Carr Steven A , Macosko Evan , Datta Sandeep Robert , Dejanovic Borislav , Kim Eunjoon , Levin Joshua Z , Sheng Morgan 
Published: November 2022

SUMMARYSchizophrenia disease mechanisms remain poorly understood, in large part due to a lack of valid animal models. Rare heterozygous loss-of-function mutations inGRIN2A, encoding a subunit of the NMDA (N-methyl-d-aspartate) receptor, greatly increase the risk of schizophrenia. By transcriptomic, proteomic, electroencephalogram (EEG) recording and behavioral analysis, we report that heterozygousGrin2amutant mice show: (i) large-scale gene expression changes across multiple brain regions and in neuronal (excitatory and inhibitory) and non-neuronal cells (astrocytes, oligodendrocytes); (ii) evidence of reduced activity in prefrontal cortex and increased activity in hippocampus and striatum; (iii) elevated dopamine signaling in striatum; (iv) altered cholesterol biosynthesis in astrocytes; (v) reduction of glutamatergic receptor signalin g proteins in the synapse; (iv) heightened gamma oscillation power in EEG; (vi) aberrant locomotor behavioral pattern opposite of that induced by antipsychotic drugs. These findings reveal potential pathophysiologic mechanisms, provide support for both the “hypo-glutamate” and “hyper-dopamine” hypotheses of schizophrenia, and underscore the utility ofGrin2a-deficient mice as a new genetic model of schizophrenia.
A review of reviews exploring patient and public involvement in population health research
Authors: Vinnicombe Soo , Noyes Jane 
Published: November 2022

AbstractIntroductionPatient and public involvement (PPI) is increasingly seen as something that is integral to research and of importance to research funders. There is general recognition that PPI is the right thing to do for both moral and practical reasons. The aim of this review of reviews is to examine how PPI can be done ‘properly’ by looking at the evidence that exists from published reviews and assessing it against the UK Standards for Public Involvement in Research, as well as examining the specific features of population health research that can make PPI more challenging.MethodsA review of reviews was carried out following the 5-stage Framework Synthesis method.ResultsIn total 31 reviews were included. There is a lack of current research or clarity around Governance and Impact when findings are mapped against UK Standards for Public Involvement in Research. It was also clear that there is little knowledge around PPI with under-represented groups. There are gaps in knowledge about how to ensure key specific attributes of population health research are addressed for PPI team members – particularly around how to deal with complexity and the data-driven nature of the research. Two tools were produced for researchers and PPI members to further improve their PPI activity within population health research and health research more generally: A framework of recommended actions to address PPI in population health research, and guidance on integrating PPI based on the UK Standards for Public Involvement in Research.ConclusionsFacilitating PPI in population health research is challenging due to the nature of this type of research and there is far less evidence on how to do PPI well in this context. The tools can help researchers identify key aspects of PPI that can be integrated when designing PPI within projects. Findings also highlight specific areas where more research or discussion is needed.
iSupport-J, the Japanese version of an internet-based self-learning and psychological assessment program for dementia caregivers: study protocol for a randomized, waiting-list controlled study
Authors: Yamashita Shingo , Yokoi Yuma , Matsui Makoto , Nozaki Kazumi , Fujimaki Chinatsu , Wada Ayumu , Iwata Naoya , Sugawara Norio , Omachi Yoshie 
Published: November 2022

AbstractBackgroundThe number of people with dementia in Japan will estimate to increase to roughly 20% of those aged 65 and over (approximately 7 million people) by 2025. Around the world, the number of people with dementia is increasing by 7.7 million per year, and caregivers’ depression, stress, social isolation, and sleep disorders due to the burden of caregiving are also increasing. Economic losses worldwide due to physical and mental health problems of dementia caregivers, reduced work hours due to caregiving, and job loss are estimated to be $252 billion in 2010. In addition, the risk of abuse against the caregiver increases as the caregiver is affected by physical and mental illness. Psychosocial interventions such as cognitive behavioral therapy have reportedly reduced caregivers’ mental distress and improved their health. Since caregivers have significant time and physical limitations due to caregiving, it is promising that interventions using the internet, which have few limitations in terms of location and time, will be helpful, along with its low cost.MethodsThis is a two-arm, randomized, waitlist-controlled trial. Participants will be randomized with a 1:1 ratio to either the immediate or late access group. The early intervention group will be able to use iSupport for three months, followed by allocation and follow-ups until six months. In the waitlist group, iSupport can be available for three months from the end of the Month 3 evaluation. Scheduled evaluation periods are Months 1, 3, and 6.DiscussionWe plan to begin recruiting for the trial in January 2021. We plan to finish the inclusion by June 2021 and complete all data collection by December 2021. Once all data collection is complete, we plan to analyze the data by April 2022; we aim to publish the results in a manuscript by the end of 2022.Trial RegistrationUMIN-CTR, UMIN000042957, registered on January 9, 2021.
β-Cyclodextrins as affordable antivirals to treat coronavirus infection
Authors: Raïch-Regué Dalia , Tenorio Raquel , Fernández de Castro Isabel , Perez -Zsolt Daniel , Muñoz-Basagoiti Jordana , Sachse Martin , Fernández-Sánchez Sara Y. , Gallemí Marçal , Ortega-González Paula , Fernández-Oliva Alberto , Gabaldón José A. , Nuñez-Delicado Estrella , Casas Josefina , Tarrés Ferran , Alert Júlia-Vergara , Segalés Joaquim , Carillo Jorge , Blanco Julià , Sala Bonaventura Clotet , Cerón-Carrasco José P. , Izquierdo-Useros Nuria , Risco Cristina 
Published: November 2022

AbstractThe SARS-CoV-2 pandemic made evident that we count with few coronavirus-fighting drugs. Here we aimed to identify a cost-effective antiviral with broad spectrum activity and high safety and tolerability profiles. We began elaborating a list of 116 drugs previously used to treat other pathologies or characterized in pre-clinical studies with potential to treat coronavirus infections. We next employed molecular modelling tools to rank the 44 most promising inhibitors and tested their efficacy as antivirals against a panel of α and β coronavirus, e.g., the HCoV-229E and SARS-CoV-2 viruses. Four drugs, OSW-1, U18666A, hydroxypropyl-β-cyclodextrin (HβCD) and phytol, showed antiviral activity against both HCoV-229E (in MRC5 cells) and SARS-CoV-2 (in Vero E6 cells). The mechanism of action of these compounds was studied by transmission electron microscopy (TEM) and by testing their capacity to inhibit the entry of SARS-CoV-2 pseudoviruses in ACE2-expressing HEK-293T cells. The entry was inhibited by HβCD and U18666A, yet only HβCD could inhibit SARS-CoV-2 replication in the pulmonary cells Calu-3. With these results and given that cyclodextrins are widely used for drug encapsulation and can be safely administered to humans, we further tested 6 native and modified cyclodextrins, which confirmed β-cyclodextrins as the most potent inhibitors of SARS-CoV-2 replication in Calu-3 cells. All accumulated data points to β-cyclodextrins as promising candidates to be used in the therapeutic treatments for SARS-CoV-2 and possibly other respiratory viruses.