bluuebunny/crossref_metadata_2025_split huggingface dataset:
Splatter: simulation of single-cell RNA sequencing data
Authors: Zappia Luke , Phipson Belinda , Oshlack Alicia 
Published: May 2017

AbstractAs single-cell RNA sequencing technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, their similarity to real data is not demonstrated, or reproducible code is not available.Here we present the Splatter Bioconductor package for simple, reproducible and well-documented simulation of single-cell RNA-seq data. Splatter provides an interface to multiple simulation methods including Splat, our own simulation, based on a gamma-Poisson distribution. Splat can simulate single populations of cells, populations with multiple cell types or differentiation paths.
Redox-Dependent Condensation Of the Mycobacterial Nucleoid By WhiB4
Authors: Chawla Manbeena , Mishra Saurabh , Parikh Pankti , Mehta Mansi , Shukla Prashant , Vij Manika , Singh Parul , Jakkala Kishore , Verma H N , AjitKumar Parthasarathi , Ganguli Munia , Seshasayee Aswin Sai Narain , Singh Amit 
Published: May 2017

AbstractOxidative stress response in bacteria is generally mediated through coordination between the regulators of oxidant-remediation systems (e.g.OxyR, SoxR) and nucleoid condensation (e.g.Dps, Fis). However, these genetic factors are either absent or rendered nonfunctional in the human pathogenMycobacterium tuberculosis(Mtb). Therefore, howMtborganizes genome architecture and regulates gene expression to counterbalance oxidative imbalance during infection is not known. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response inMtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central carbon metabolism (CCM), respiration, cell wall biogenesis, DNA repair and protein quality control under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNAin vitroandin vivo. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findingsin vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of theMtbgenome. Lastly, data indicate that WhiB4 deletion affected the expression of only a fraction of genes preferentially bound by the protein, suggesting its indirect effect on gene expression. We propose that WhiB4 is a novel redox-dependent nucleoid condensing protein that structurally couplesMtb’sresponse to oxidative stress with genome organization and transcription.Significance StatementMycobacterium tuberculosis (Mtb)needs to adapt in response to oxidative stress encountered inside human phagocytes. In other bacteria, condensation state of nucleoids modulates gene expression to coordinate oxidative stress response. However, this relation remains elusive inMtb. We performed molecular dissection of a mechanism controlled by an intracellular redox sensor, WhiB4, in organizing both chromosomal structure and selective expression of adaptive traits to counter oxidative stress inMtb. Using high-resolution sequencing, transcriptomics, imaging, and redox biosensor, we describe how WhiB4 modulates nucleoid condensation, global gene expression, and redox-homeostasis. WhiB4 over-expression hypercondensed nucleoids and perturbed redox homeostasis whereas WhiB4 disruption had an opposite effect. Our study discovered an empirical role for WhiB4 in integrating redox signals with nucleoid condensation inMtb.
Mitochondria are physiologically maintained at close to 50 °C
Authors: Chrétien Dominique , Bénit Paule , Ha Hyung-Ho , Keipert Susanne , El-Khoury Riyad , Chang Young-Tae , Jastroch Martin , Jacobs Howard T , Rustin Pierre , Rak Malgorzata 
Published: May 2017

AbstractIn endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, while a noticeable proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperaturein situunder different physiological conditions. At a constant external temperature of 38 °C, mitochondria were more than 10 °C warmer when the respiratory chain was fully functional, both in HEK293cells and primary skin fibroblasts. This differential was abolished in cells lacking mitochondrial DNA or by respiratory inhibitors, but preserved or enhanced by expressing thermogenic enzymes such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at, or slightly above, 50 °C. Our study prompts a re-examination of the literature on mitochondria, taking account of the inferred high temperature.
Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient
Authors: Hannon Colleen E. , Blythe Shelby A. , Wieschaus Eric F. 
Published: May 2017

ABSTRACTInDrosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classesin vitroand genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations.
Deconvolution of Transcriptional Networks Identifies TCF4 as a Master Regulator in Schizophrenia
Authors: Torshizi Abolfazl Doostparast , Armoskus Chris , Zhang Hanwen , Forrest Marc P. , Zhang Siwei , Souaiaia Tade , Evgrafov Oleg V. , Knowles James A. , Duan Jubao , Wang Kai 
Published: May 2017

AbstractTissue-specific reverse engineering of transcriptional networks has uncovered master regulators (MRs) of cellular networks in various cancers, yet the application of this method to neuropsychiatric disorders is largely unexplored. Here, using RNA-Seq data on postmortem dorsolateral prefrontal cortex (DLPFC) from schizophrenia (SCZ) patients and control subjects, we deconvolved the transcriptional network to identify MRs that mediate expression of a large body of target genes. Together with an independent RNA-Seq data on cultured cells derived from olfactory neuroepithelium, we identifiedTCF4, a leading SCZ risk locus implicated by genome-wide association studies, as one of the top candidate MRs that may be potentially dysregulated in SCZ. We validated the dysregulated TCF4-related transcriptional network through examining the transcription factor binding footprints inferred from human induced pluripotent stem cell (hiPSC)-derived neuronal ATAC-Seq data, as well as direct binding sites obtained from ChIP-seq data in SH-SY5Y cells. The predictedTCF4transcriptional targets were enriched for genes showing transcriptomic changes upon knockdown ofTCF4in hiPSC-derived neural progenitor cells (NPC) and glutamatergic neurons (Glut_N), based on observations from three separate cell lines. The alteredTCF4gene network perturbations in NPC, as compared to that in Glut_N, was more similar to the expression differences in theTCF4gene network observed in the DLPFC of individuals with SCZ. Moreover,TCF4-associated gene expression changes in NPC were more enriched than Glut_N for pathways involved in neuronal activity, genome-wide significant SCZ risk genes, and SCZ-associatedde novomutations. Our results suggest thatTCF4may potentially serve as a MR of a gene network that confers susceptibility to SCZ at early stage of neurodevelopment, highlighting the importance of network dysregulation involving core genes and many hundreds of peripheral genes in conferring susceptibility to neuropsychiatric diseases.
Large-Scale Concatenation cDNA Sequencing
Authors: Yu Wei , Andersson Björn , Worley Kim C. , Muzny Donna M. , Ding Yan , Liu Wen , Ricafrente Jennifer Y. , Wentland Meredith A. , Lennon Greg , Gibbs Richard A. 
Published: May 2017

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching.[All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.]
A Differential Hybridization Scheme to Identify Photoreceptor-Specific Genes
Authors: Swanson Deborah A. , Freund Carol L. , Steel Jason M. , Xu Shunbin , Ploder Lynda , McInnes Roderick R. , Valle David 
Published: May 2017

Identification of genes expressed preferentially or exclusively in photoreceptors will facilitate the understanding of photoreceptor biology as well as provide candidate genes for inherited retinal degenerations. To achieve this goal we performed a differential hybridization screen of 3717 well-isolated phage clones from a human retinal cDNA library. Clones were selected for further study if they hybridized exclusively or strongly preferentially to a probe derived from RNA isolated from the cone-predominant retina of 13-line ground squirrels as compared to a probe derived from human fibroblast RNA. Twenty percent of clones (9/45) identified by this screen were derived from photoreceptor-specific genes and an additional 24.4% (11/45) were from neural-specific genes, demonstrating the utility of this strategy in identifying genes important for retinal biology.[The sequence tags of cDNAs identified in this screen have been deposited in GenBank under accession nos. U89715, U89878–U89888, andU89951–U89955.]
Identification and Chromosomal Localization of Human Genes Containing CAG/CTG Repeats Expressed in Testis and Brain
Authors: Bulle Frédérique , Chiannilkulchai Nuchanard , Pawlak André , Weissenbach Jean , Gyapay Gabor , Guellaën Georges 
Published: May 2017

Human genes containing triplet repeats have been demonstrated to be involved in several neurodegenerative diseases by expansion of the repeat in succeeding generations. To identify novel genes involved in such pathologies, we have isolated transcripts containing (CAG/CTG)n repeats using two approaches. First, we screened 4 × 106 clones representing 10 copies of a human testis cDNA library using a (CAG)14 oligonucleotide probe. Among the 910 clones identified, the 243 clones with the strongest hybridization signal were sequenced partially from 3′ or 5′ ends. This provided us with 251 partial sequences that grouped into clusters corresponding to 39 genes, of which 19 represent unknown species. Second, we selected 203 additional ESTs containing (CAG/CTG)n repeats representing 121 clusters from the IMAGE consortium infant brain cDNA library. From these two series of sequences, we have localized 95 genes on human chromosomes using a panel of whole genome radiation hybrid (Genebridge 4). These genes are located on all of the chromosomes except for chromosome X, the highest density being observed on chromosome 19.[The sequence data described in this paper have been submitted to GenBank under accession nos. AA065241–AA065346.]
A Transcript Map for the 2.8-Mb Region Containing the Multiple Endocrine Neoplasia Type 1 Locus
Authors: Guru Siradanahalli C. , Agarwal Sunita K. , Manickam Pachiappan , Olufemi Shodimu-Emmanuel , Crabtree Judy S. , Weisemann Jane M. , Kester Mary Beth , Kim Young S. , Wang Yingping , Emmert-Buck Michael R. , Liotta Lance A. , Spiegel Allen M. , Boguski Mark S. , Roe Bruce A. , Collins Francis S. , Marx Stephen J. , Burns Lee , Chandrasekharappa Settara C. 
Published: May 2017

Multiple endocrine neoplasia type 1 (MEN 1) is an inherited cancer syndrome in which affected individuals develop multiple parathyroid, enteropancreatic, and pituitary tumors. The locus for MEN1 is tightly linked to the marker PYGM on chromosome 11q13, and linkage analysis places the MEN1 gene within a 2-Mb interval flanked by the markers D11S1883 and D11S449. Loss of heterozygosity studies in MEN 1 and sporadic tumors suggest that theMEN1 gene encodes a tumor suppressor and have helped to narrow the location of the gene to a 600-kb interval between PYGM andD11S449. Focusing on this smaller MEN1 interval, we have identified and mapped 12 transcripts to this 600-kb region. A precise ordered map of 33 transcripts, including 12 genes known to map to this region, was generated for the 2.8-Mb D11S480–D11S913interval. Fifteen candidate genes (of which 10 were examined exhaustively) were evaluated by Southern blot and/or dideoxy fingerprinting analysis to identify the gene harboring disease-causing mutations.[The sequence data described in this paper have been submitted to GenBank under accession nos. EST06996, U93236,AF001540–AF001547, AF001433–AF001436, AF001891–AF001893,N55476, R19205, and W37647 (see Table 1 for listing of transcripts). The BAC clone sequences have been submitted to GenBank under accession nos. AC000134, AC000159, and AC000353.]
Detection of RAPD Markers Correlated with Chloroquine Resistance in Plasmodium falciparum
Authors: Lescuyer Pierre , Picot Stéphane , Bracchi Valérie , Burnod Josette , Austin Juliet , Pérard Alain , Ambroise-Thomas Pierre 
Published: May 2017

We described the use of the random amplified polymorphic DNA (RAPD) technique on Plasmodium falciparum DNA to detect genetic markers for chloroquine-resistant strains. Fourteen RAPD primers were tested, three of which generated banding patterns correlated with chloroquine resistance. To measure this correlation, the RAPD profiles were analyzed using the Nei and Li similarity coefficient. Detection of distinctive RAPD bands allowed us to synthesize specific PCR primers to be used on whole-blood samples. Two primer sets were synthesized and tested on sensitive and resistant strains for their ability to amplify the DNA fragment corresponding to the RAPD marker. These results suggest that RAPD and PCR techniques can be used as powerful tools for the detection of genetic markers associated with drug resistance.[The nucleotide sequence data described in this paper have been submitted to the EMBL, GenBank, and DDBJ Nucleotide Sequence databases under accession nos. A863W25C and U854T571.]
Genotator: A Workbench for Sequence Annotation
Authors: Harris Nomi L. 
Published: May 2017

Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signals such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching.[Further details for obtaining Genotator are available at http://www.cshl.org/gr.]
A 3-Mb Contig from D11S987 to MLK3, a Gene-Rich Region in 11q13: Figure 1.
Authors: Smith Carissa M. , Ma Nancy S. , Nowak Norma J. , Shows Thomas B. , Gerhard Daniela S. 
Published: May 2017

We have combined genetic, radiation-reduced somatic cell hybrid (RRH), fluorescent in situ hybridization (FISH), and physical mapping methods to generate a contig of overlapping YAC, PAC, and cosmid clones corresponding to >3 continuous Mb in 11q13. A total of 15 STSs [7 genes (GSTP1, ACTN, PC, MLK3, FRA1, SEA, HNP36), 4 polymorphic loci (D11S807, D11S987, GSTP1, D11S913), 3 ESTs (D11S1956E, D11S951E, and WI-12191), and 1 anonymous STS (D11S703)], mapping to three independent RRH segregation groups, identified 26 YAC, 7 PAC, and 16 cosmid clones from the CGM, Roswell Park, CEPH Mark I, and CEPH MegaYAC YAC libraries, a 5 genome equivalent PAC library, and a chromosome 11-specific cosmid library. Thirty-six Alu–PCR products derived from 10 anonymous bacteriophage λ clones, a cosmid containing the polymorphic markerD11S460, or STS-positive YAC or cosmid clones were identified and used to screen selected libraries by hybridization, resulting in the identification of 19 additional clones. The integrity and relative position of a subset of clones was confirmed by FISH and were found to be consistent with the physical and RRH mapping results. The combination of STS and Alu–PCR-based approaches has proven to be successful in attaining contiguous cloned coverage in this very GC-rich region, thereby establishing for the first time the absolute order and distance between the markers: CEN–MLK3–(D11S1956E/D11S951E/WI-12191)–FRA1–D11S460–SEA–HNP36/D11S913–ACTN–PCD11S703–GSTP1–D11S987–TEL.[On-line supplementary material concerning screening materials and clones referred to in the text as Table 1 is available athttp://genome.wustl.edu/gerhard/gerhard.html or http://www.cshl.org/gr. The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF009361.]
Mutations in myostatin (GDF8) in Double-Muscled Belgian Blue and Piedmontese Cattle
Authors: Kambadur Ravi , Sharma Mridula , Smith Timothy P.L. , Bass John J. 
Published: May 2017

A visibly distinct muscular hypertrophy (mh), commonly known as double muscling, occurs with high frequency in the Belgian Blue and Piedmontese cattle breeds. The autosomal recessive mh locus causing double-muscling condition in these cattle maps to bovine chromosome 2 within the same interval as myostatin, a member of the TGF-β superfamily of genes. Because targeted disruption ofmyostatin in mice results in a muscular phenotype very similar to that seen in double-muscled cattle, we have evaluated this gene as a candidate gene for double-muscling condition by cloning the bovine myostatin cDNA and examining the expression pattern and sequence of the gene in normal and double-muscled cattle. The analysis demonstrates that the levels and timing of expression do not appear to differ between Belgian Blue and normal animals, as both classes show expression initiating during fetal development and being maintained in adult muscle. Moreover, sequence analysis reveals mutations in heavy-muscled cattle of both breeds. Belgian Blue cattle are homozygous for an 11-bp deletion in the coding region that is not detected in cDNA of any normal animals examined. This deletion results in a frame-shift mutation that removes the portion of the Myostatin protein that is most highly conserved among TGF-β family members and that is the portion targeted for disruption in the mouse study. Piedmontese animals tested have a G–A transition in the same region that changes a cysteine residue to a tyrosine. This mutation alters one of the residues that are hallmarks of the TGF-β family and are highly conserved during evolution and among members of the gene family. It therefore appears likely that the mh allele in these breeds involves mutation within the myostatin gene and that myostatin is a negative regulator of muscle growth in cattle as well as mice.[The sequence data for bovine myostatin has been submitted to GenBank under accession no. AF019761.]
Characterization of Short Tandem Repeats from Thirty-One Human Telomeres
Authors: Rosenberg Marjorie , Hui Lester , Ma Junli , Nusbaum Harris C. , Clark Kevin , Robinson Louise , Dziadzio Laura , Swain Pamela M. , Keith Tim , Hudson Thomas J. , Biesecker Leslie G. , Flint Jonathan 
Published: May 2017

Completion of genetic and physical maps requires markers from the ends (telomeres) of every human chromosome. We have searched for short tandem repeats (microsatellites) in cosmid and P1 clones and generated 661 sequence-tagged sites (STS) from the terminal 300 kb of 31 human chromosome ends. PCR assays were successfully designed for 58 microsatellites and mapped both genetically and on radiation hybrids (RHs) to confirm their telomeric location. Sequence analysis revealed marked variation in sequence composition, consistent with the hypothesis that even very highly GC-rich chromosome bands (the T bands) are not homogenous. The STSs that we have generated will be a necessary resource for the construction of physical maps of these complex regions of the genome.[Information about the microsatellites is available electronically athttp://www.cshl.org/grand sequence has been deposited in the Genome Database (GDB).]