bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cockayne syndrome group B deficiency reduces H3K9me3 chromatin remodeler SETDB1 and exacerbates cellular aging
Authors: Lee Jong-Hyuk , Demarest Tyler G , Babbar Mansi , Kim Edward W , Okur Mustafa N , De Supriyo , Croteau Deborah L , Bohr Vilhelm A 
Published: June 2019

Abstract
Cockayne syndrome is an accelerated aging disorder, caused by mutations in the CSA or CSB genes. In CSB-deficient cells, poly (ADP ribose) polymerase (PARP) is persistently activated by unrepaired DNA damage and consumes and depletes cellular nicotinamide adenine dinucleotide, which leads to mitochondrial dysfunction. Here, the distribution of poly (ADP ribose) (PAR) was determined in CSB-deficient cells using ADPr-ChAP (ADP ribose-chromatin affinity purification), and the results show striking enrichment of PAR at transcription start sites, depletion of heterochromatin and downregulation of H3K9me3-specific methyltransferases SUV39H1 and SETDB1. Induced-expression of SETDB1 in CSB-deficient cells downregulated PAR and normalized mitochondrial function. The results suggest that defects in CSB are strongly associated with loss of heterochromatin, downregulation of SETDB1, increased PAR in highly-transcribed regions, and mitochondrial dysfunction.
RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit
Authors: Allepuz-Fuster Paula , O’Brien Michael J , González-Polo Noelia , Pereira Bianca , Dhoondia Zuzer , Ansari Athar , Calvo Olga 
Published: June 2019

AbstractGene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in the rpb4Δ mutant. In contrast to the other looping-defective mutants, rpb4Δ cells do not exhibit a transcription termination defect. RPB4 overexpression, however, rescued the transcription termination and gene looping defect of sua7-1, a mutant of TFIIB. Furthermore, RPB4 overexpression rescued the ssu72-2 gene looping defect, while SSU72 overexpression restored the formation of gene loops in rpb4Δ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised in rpb4Δ cells. These results suggest that the TFIIB–Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB–Ssu72 mediated gene looping.
Using Transcriptome to Discover a Novel Melatonin-Induced Sodic Alkaline Stress Resistant Pathway in Solanum lycopersicum L.
Authors: Yan Yanyan , Jing Xin , Tang Huimeng , Li Xiaotong , Gong Biao , Shi Qinghua 
Published: June 2019

AbstractMelatonin plays important roles in multiple stress responses. However, the downstream signaling pathway and molecular mechanism are unclear until now. Here, we not only revealed the transcriptional control of melatonin-induced sodic alkaline stress tolerance, but also described a screen for key downstream transcriptional factors of melatonin through transcriptome analysis. The melatonin-induced transcriptional network of hormone, transcriptional factors and functional genes has been established under both control and stress conditions. Among these, six candidates of transcriptional factors have been identified via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Using the virus-induced gene silencing approach, we confirmed that DREB1α and IAA3 were key downstream transcriptional factors of melatonin-induced sodic alkaline stress tolerance at the genetic level. The transcriptions of DREB1α and IAA3 could be activated by melatonin or sodic alkaline treatment. Interestingly, we found that DREB1α could directly upregulate the expression of IAA3 by binding to its promoters. Moreover, several physiological processes of Na+ detoxification, dehydration resistance, high pH buffering and reactive oxygen species scavenging were confirmed to depend or partly depend on DREB1α and IAA3 pathway in melatonin-induced stress tolerance. Taken together, this study suggested that DREB1α and IAA3 are positive resistant modulators, and provided a direct link among melatonin, DREB1α and IAA3 in the sodic alkaline stress tolerance activating in tomato plants.
Source Strength Modulates Fruit Set by Starch Turnover and Export of Both Sucrose and Amino Acids in Pepper
Authors: de ï¿½vila Silva Lucas , Condori-Apfata Jorge A , Costa Paulo Mafra de Almeida , Martino Pedro Brandï¿½o , Tavares Ana C Azevedo , Marcelino Mariana Marques , Raimundi Sï¿½bata C Januï¿½rio , Picoli Edgard A de Toledo , Araï¿½jo Wagner L , Zsï¿½gï¿½n Agustin , Sulpice Ronan , Nunes-Nesi Adriano 
Published: June 2019

AbstractFruit set is an important yield-related parameter, which varies drastically due to genetic and environmental factors. Here, two commercial cultivars of Capsicum chinense (Biquinho and Habanero) were evaluated in response to light intensity (unshaded and shaded) and N supply (deficiency and sufficiency) to understand the role of source strength on fruit set at the metabolic level. We assessed the metabolic balance of primary metabolites in source leaves during the flowering period. Furthermore, we investigated the metabolic balance of the same metabolites in flowers to gain more insights into their influence on fruit set. Genotype and N supply had a strong effect on fruit set and the levels of primary metabolites, whereas light intensity had a moderate effect. Higher fruit set was mainly related to the export of both sucrose and amino acids from source leaves to flowers. Additionally, starch turnover in source leaves, but not in flowers, had a central role on the sucrose supply to sink organs at night. In flowers, our results not only confirmed the role of the daily supply of carbohydrates on fruit set but also indicated a potential role of the balance of amino acids and malate.
Nanobody stability engineering by employing the ΔTm shift; a comparison with apparent rate constants of heat-induced aggregation
Authors: Kunz Patrick , Ortale Aurelio , Mücke Norbert , Zinner Katinka , Hoheisel Jörg D 
Published: June 2019

Abstract
The antigen-binding domains of camelid heavy-chain antibodies, also called nanobodies, gained strong attention because of their unique functional and biophysical properties. They gave rise to an entire spectrum of applications in biotechnology, research and medicine. Despite several reports about reversibly refolding nanobodies, protein aggregation plays a major role in nanobody thermoresistance, asking for strategies to engineer their refolding behavior. Here, we use measurements of nanobody aggregation kinetics to validate structural features in the nanobody fold that are suppressing heat-induced nanobody aggregation. Furthermore, the kinetic measurements yielded a detailed insight into the concept of the ΔTm shift, a metric for protein aggregation propensities obtained from differential scanning fluorimetry measurements. By relating the equilibrium measurements of the ΔTm shift to the kinetic measurements of heat-induced nanobody aggregation, a distinct relationship could be identified that allows a prediction of nanobody aggregation rates from a simple equilibrium measurement of ΔTm.
QuantTB – A method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data
Authors: Anyansi Christine , Keo Arlin , Walker Bruce , Straub Timothy J. , Manson Abigail L. , Earl Ashlee M. , Abeel Thomas 
Published: June 2019

AbstractBackgroundMixed infections of Mycobacterium tuberculosis, and antibiotic heteroresistance, continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains of M. tuberculosis within a sample. Although metagenomic tools exist to classify strains in a metagenomic sample, most tools have been developed for more divergent species, and therefore cannot provide the sensitivity required to disentangle strains within closely related bacterial species such as M. tuberculosis.Here we present QuantTB, a method to identify and quantify individual M. tuberculosis strains in whole genome sequencing data. QuantTB uses SNP markers to determine the combination of strains that best explain the allelic variation observed in a sample. QuantTB outputs a list of identified strains, their corresponding relative abundances, as well as a list of drugs for which resistance-conferring mutations (or heteroresistance) has been predicted within the sample.ResultsWe show that QuantTB has a high degree of resolution, and is capable of differentiating communities differing by less than 25 SNPs and identifying strains down to 1× coverage. Using simulated data, we found QuantTB outperformed other metagenomic strain identification tools at detecting strains and quantifying strain multiplicity. In a real-world scenario, using a dataset of paired clinical isolates from a study of patients with either reinfections or relapses, we found that QuantTB could detect mixed infections and reinfections at rates concordant with a manually curated approach.ConclusionQuantTB can determine infection multiplicity, identify hetero-resistance patterns, enable differentiation between relapse and re-infection, and clarify transmission events across seemingly unrelated patients – even in low-coverage (1x) samples. QuantTB outperforms existing tools and promises to serve as a valuable resource for both clinicians and researchers working with clinical TB samples.
Identifying epigenetic biomarkers of established prognostic factors and survival in a clinical cohort of individuals with oropharyngeal cancer
Authors: Langdon Ryan , Richmond Rebecca , Elliott Hannah R. , Dudding Tom , Kazmi Nabila , Penfold Chris , Ingarfield Kate , Ho Karen , Bretherick Andrew , Haley Chris , Zeng Yanni , Walker Rosie M , Pawlita Michael , Waterboer Tim , Ring Sue , Gaunt Tom , Smith George Davey , Suderman Matthew , Thomas Steve , Ness Andy , Relton Caroline 
Published: June 2019

AbstractSmoking status, alcohol consumption and HPV infection (acquired through sexual activity) are the predominant risk factors for oropharyngeal cancer and are thought to alter the prognosis of the disease. Here, we conduct epigenome-wide association studies (EWAS) of these factors and ∼3-year survival using Illumina Methylation EPIC blood DNA methylation profiles from 409 individuals in the Head and Neck 5000 (HN5000) study. CpG site associations below our multiple-testing threshold (PBonferroni< 0.05) with both a prognostic factor and with survival were observed in four gene regions:SPEG(smoking),GFI1(smoking),PPT2(smoking), andKHD3CL(alcohol consumption). These were further analysed using 2-step Mendelian randomization to assess whether methylation may be a causal mediator of cancer survival. Evidence for mediation was observed only in theSPEGgene region, showing an association with decreased survival (mortality HR: 1.28, 95% CI: 1.14 to 1.43,P:2.12×10−05). Replication in data from independent datasets, and from HN5000 participants with longer follow-up times is needed to confirm these findings.
Proteomic studies of the Arabidopsis TRAPP complexes reveal conserved organization and a novel plant-specific component with a role in plant development
Authors: Garcia Veder J. , Xu Shou-Ling , Ravikumar Raksha , Wang Wenfei , Elliott Liam , Fesenko Mary , Altmann Melina , Falter-Braun Pascal , Moore Ian , Assaad Farhah F. , Wang Zhi-Yong 
Published: June 2019

AbstractHow the membrane trafficking system spatially organizes intracellular activities and intercellular signaling networks is not well understood in plants. The Transport Protein Particle (TRAPP) complexes are known to play key roles in selective delivery of membrane vesicles to various subcellular compartments in yeast and animals, but remain to be fully characterized in plants. Here we interrogate the TRAPP complexes in Arabidopsis using quantitative proteomic approaches. TRS33 is a component shared by all TRAPP complexes in yeast and animals, and the Arabidopsis AtTRS33 is essential for the subcellular dynamics of other TRAPP components. Affinity purification of AtTRS33 followed by quantitative mass spectrometry identified fourteen interacting proteins; these include not only thirteen homologs of all known TRAPP components in yeast and mammals but also a novel protein we named TRAPP-interacting plant protein (TRIPP), which is conserved in multi-cellular photosynthetic organisms. Proteomic and molecular analyses showed that TRIPP specifically associates with the TRAPPII complexin vivoand directly interacts with the TRAPPII-specific subunits but not the subunits shared with TRAPPIII. TRIPP co-localizes with a subset of TRS33 compartments, and its localization is disrupted in thetrs33mutant. Loss-of-functiontrippmutation caused growth and reproductive development defects, including partial photomorphogenesis in the dark. Our study demonstrates that plants possess at least two distinct TRAPP complexes similar to metazoan, and identifies TRIPP as a novel plant-specific component of the TRAPPII complex with important functions in plant growth and development.
H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
Authors: Cai Yichao , Zhang Ying , Loh Yan Ping , Tng Jia Qi , Lim Mei Chee , Cao Zhendong , Raju Anandhkumar , Lieberman-Aiden Erez , Li Shang , Manikandan Lakshmanan , Tergaonkar Vinay , Tucker-Kellogg Greg , Fullwood Melissa Jane 
Published: June 2019

AbstractGene repression and silencers are poorly understood. We reasoned that H3K27me3-rich regions (MRRs) of the genome defined from clusters of H3K27me3 peaks may be used to identify silencers that can regulate gene expression via proximity or looping. MRRs were associated with chromatin interactions and interact preferentially with each other. MRR component removal at interaction anchors by CRISPR led to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. The MRR knockout cells also showed changes in phenotype associated with cell identity, and altered xenograft tumor growth. MRR-associated genes and long-range chromatin interactions were susceptible to H3K27me3 depletion. Our results characterized H3K27me3-rich regions and their mechanisms of functioning via looping.
Hotspot prioritizations show sensitivity to data type
Authors: Norman Kari EA , White Ethan P 
Published: June 2019

ABSTRACTPrioritizing regions for conservation is essential for effectively allocating limited conservation resources. One of the most common approaches to prioritization is identifying regions with the highest biodiversity, or hotspots, typically using global range map data. Range maps are readily available at large scales for an array of taxa, but are also known to differ from local-scale survey data in the same regions. We examined how prioritizations may differ between range map and survey data using the North American Breeding Bird survey (BBS) and BirdLife International range maps as a case study. Hotspot prioritizations were generated for species richness and the richness of rare species at two scales.Total species richness patterns differed substantially between data types with at most a 41% overlap in identified hotspots. Some regions had few or no hotspots for one data type and a significant number for the other. Hotspots for rare species were more similar across the data types with 44% overlap at the larger scale. Future efforts to prioritize areas for conservation should consider differences between local-scale survey data and range maps, match data to the scale of interest, and develop methods to better downscale range map-based prioritizations to the scale of conservation decisions.
The whale shark genome reveals patterns of vertebrate gene family evolution
Authors: Tan Milton , Redmond Anthony K. , Dooley Helen , Nozu Ryo , Sato Keiichi , Kuraku Shigehiro , Koren Sergey , Phillippy Adam M. , Dove Alistair D.M. , Read Timothy D. 
Published: June 2019

AbstractChondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new Toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.
Diagnostic optical sequencing
Authors: Korshoj Lee E. , Nagpal Prashant 
Published: June 2019

AbstractAdvances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multi-omics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances towards such diagnostics. However, the inability to squeeze light with several hundred-nanometer wavelengths into angstrom-scale volume for single nucleotide measurements has hindered further progress. Recently, a block optical sequencing (BOS) method has been shown for determining relative nucleobase content in DNA k-mer blocks with Raman spectroscopy, and a block optical content scoring (BOCS) algorithm was developed for robust content-based genetic biomarker database searching. Here, we performed BOS measurements on positively-charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in DNA k-mer blocks (where k=10), as well as measurements on RNA and chemically-modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy BOS measurements were then used with BOCS to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 content measurements (<15% coverage) of the gene. These results prove the integration of BOS/BOCS as a diagnostic optical sequencing platform. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.
α2δ-2 protein controls structure and function at the cerebellar climbing fiber synapse
Authors: Beeson Kathleen A. , Beeson Ryne , Westbrook Gary L. , Schnell Eric 
Published: June 2019

Abstractα2δ proteins (Cacna2d1-4) are auxiliary subunits of voltage-dependent calcium channels that also drive synapse formation and maturation. Because cerebellar Purkinje cells (PCs) only express one isoform of this family, α2δ-2 (Cacna2d2), we used PCs as a model system to examine roles of α2δ in excitatory synaptic function in a Cacna2d2 knockout mouse. Whole-cell recordings of PCs from acute cerebellar slices revealed altered climbing fiber (CF)-evoked complex spike generation, as well as increased amplitude and faster decay of CF-evoked excitatory postsynaptic currents (EPSCs). CF terminals in the KO were localized more proximally on PC dendrites, as indicated by VGLUT2+ immunoreactive puncta, and computational modeling demonstrated that the increased EPSC amplitude can be partly attributed to the more proximal location of CF terminals. In addition, CFs in KO mice exhibited increased multivesicular transmission, corresponding to greater sustained responses during repetitive stimulation, despite a reduction in the measured probability of release. Electron microscopy demonstrated that mutant CF terminals had twice as many vesicle release sites, providing a morphologic explanation for the enhanced glutamate release. Though KO CFs evoked larger amplitude EPSCs, the charge transfer was the same as wildtype as a result of increased glutamate re-uptake, producing faster decay kinetics. Together, the larger, faster EPSCs in the KO explain the altered complex spike responses, which degrade information transfer from PCs and likely contribute to ataxia in Cacna2d2 KO mice. Our results also illustrate the multidimensional synaptic roles of α2δ proteins.Significance Statementα2δ proteins (Cacna2d1-4) regulate synaptic transmission and synaptogenesis, but co-expression of multiple α2δ isoforms has obscured a clear understanding of how various α2δ proteins control synaptic function. We focused on roles of the α2δ-2 protein (Cacna2d2), whose deletion causes cerebellar ataxia and epilepsy in mice and humans. Because cerebellar Purkinje cells only expresses this single isoform, we studied excitatory climbing fiber synaptic function onto Purkinje cells in Cacna2d2 knockout mice. Using optical and electrophysiological analysis, we provide a detailed description of the changes in Purkinje cells lacking α2δ-2, and provide a comprehensive mechanistic explanation for how functional synaptic phenotypes contribute to the altered cerebellar output.