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https://www.readbyqxmd.com/read/29048483/draft-genome-of-the-gayal-bos-frontalis
#1
Ming-Shan Wang, Yan Zeng, Xiao Wang, Wen-Hui Nie, Jin-Huan Wang, Wei-Ting Su, Newton O Otecko, Zi-Jun Xiong, Sheng Wang, Kai-Xing Qu, Shou-Qing Yan, Min-Min Yang, Wen Wang, Yang Dong, Dong-Dong Wu, Ya-Ping Zhang
Background: Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history as well as genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. Findings: We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29047802/intermode-beating-mode-locking-technique-for-a-rare-earth-doped-fiber-pulsed-laser
#2
Zhengqian Luo, Runhua Yang, Tuanjie Du, Qiujun Ruan, Weiwei Li, Nan Chen
In this paper, we report the intermode beating mode-locking of a 2  μm Tm(3+)-doped fiber laser (TDFL) pumped by a 1565 nm continuous-wave multi-longitudinal-mode laser. Because strong intermode beating of the 1565 nm pump source induces the periodic modulation of 2 μm intracavity power, stable mode-locking of the TDFL is successfully established by precisely matching the 2 μm cavity frequency with the intermode-beating frequency of the 1565 nm pump source. The mode-locked laser, without requiring any specific mode-locking element, can stably emit the rectangular nanosecond pulses...
August 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/29046683/the-diversity-of-sequence-and-chromosomal-distribution-of-new-transposable-element-related-segments-in-the-rye-genome-revealed-by-fish-and-lineage-annotation
#3
Yingxin Zhang, Chengming Fan, Shuangshuang Li, Yuhong Chen, Richard R-C Wang, Xiangqi Zhang, Fangpu Han, Zanmin Hu
Transposable elements (TEs) in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29046624/designing-thin-ultrastretchable-electronics-with-stacked-circuits-and-elastomeric-encapsulation-materials
#4
Renxiao Xu, Jung Woo Lee, Taisong Pan, Siyi Ma, Jiayi Wang, June Hyun Han, Yinji Ma, John A Rogers, Yonggang Huang
Many recently developed soft, skin-like electronics with high performance circuits and low modulus encapsulation materials can accommodate large bending, stretching, and twisting deformations. Their compliant mechanics also allows for intimate, nonintrusive integration to the curvilinear surfaces of soft biological tissues. By introducing a stacked circuit construct, the functional density of these systems can be greatly improved, yet their desirable mechanics may be compromised due to the increased overall thickness...
January 26, 2017: Advanced Functional Materials
https://www.readbyqxmd.com/read/29046454/mechanisms-of-herv-k-hml-2-transcription-during-human-mammary-epithelial-cell-transformation
#5
Meagan Montesion, Neeru Bhardwaj, Zachary H Williams, Charlotte Kuperwasser, John M Coffin
Increasing evidence suggests that repetitive elements may play a role in host gene regulation, particularly through the donation of alternative promoters, enhancers, splice sites, and termination signals. Elevated transcript expression of the endogenous retrovirus group HERV-K (HML-2) is seen in many human cancers, although the identity of the individual proviral loci contributing to this expression as well as their mechanism of activation has been unclear. Using high-throughput next-generation sequencing techniques optimized for the capture of HML-2 expression, we characterized the HML-2 transcriptome and means of activation in an in vitro model of human mammary epithelial cell transformation...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29042551/integrating-evolutionary-and-regulatory-information-with-a-multispecies-approach-implicates-genes-and-pathways-in-obsessive-compulsive-disorder
#6
Hyun Ji Noh, Ruqi Tang, Jason Flannick, Colm O'Dushlaine, Ross Swofford, Daniel Howrigan, Diane P Genereux, Jeremy Johnson, Gerard van Grootheest, Edna Grünblatt, Erik Andersson, Diana R Djurfeldt, Paresh D Patel, Michele Koltookian, Christina M Hultman, Michele T Pato, Carlos N Pato, Steven A Rasmussen, Michael A Jenike, Gregory L Hanna, S Evelyn Stewart, James A Knowles, Stephan Ruhrmann, Hans-Jörgen Grabe, Michael Wagner, Christian Rück, Carol A Mathews, Susanne Walitza, Daniëlle C Cath, Guoping Feng, Elinor K Karlsson, Kerstin Lindblad-Toh
Obsessive-compulsive disorder is a severe psychiatric disorder linked to abnormalities in glutamate signaling and the cortico-striatal circuit. We sequenced coding and regulatory elements for 608 genes potentially involved in obsessive-compulsive disorder in human, dog, and mouse. Using a new method that prioritizes likely functional variants, we compared 592 cases to 560 controls and found four strongly associated genes, validated in a larger cohort. NRXN1 and HTR2A are enriched for coding variants altering postsynaptic protein-binding domains...
October 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29041293/improved-self-referenced-biosensing-with-emphasis-on-multiple-resonance-nanorod-sensors
#7
Ahmed Abumazwed, Wakana Kubo, Takuo Tanaka, Andrew G Kirk
We present a novel approach to improve self-referenced sensing based on multiple-resonance nanorod structures. The method employs the maximum likelihood estimation (MLE) alongside a linear response model (LM), relating the sensor response (shifts in resonance wavelengths) to the changes due to surface binding and bulk refractive index. We also provide a solution to avoid repetitive simulations, that have been previously needed to determine the adlayer thickness sensitivity when measuring biological samples of different refractive indices...
October 2, 2017: Optics Express
https://www.readbyqxmd.com/read/29037846/altered-bone-density-and-stress-distribution-patterns-in-long-standing-cubitus-varus-deformity-and-their-effect-during-early-osteoarthritis-of-the-elbow
#8
Satoshi Miyamura, Kunihiro Oka, Shingo Abe, Atsuo Shigi, Hiroyuki Tanaka, Kazuomi Sugamoto, Hideki Yoshikawa, Tsuyoshi Murase
OBJECTIVE: To quantify the bone density and stress distribution patterns in long-standing cubitus varus and clarify the effects of the deformity on bone density. DESIGN: We created three-dimensional computed tomography elbow models from 21 patients with long-standing cubitus varus deformities without advanced osteoarthritis (OA) and assessed the deformity by superimposing the affected humerus onto a mirror-image of the contralateral normal. Elbows were divided into 13 regions before measuring the bone density of each region and comparing the percentage of high-density volume (%HDV) between affected and normal sides...
October 13, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/29037165/sequencing-flow-sorted-short-arm-of-haynaldia-villosa-chromosome-4v-provides-insights-into-its-molecular-structure-and-virtual-gene-order
#9
Jin Xiao, Keli Dai, Lian Fu, Jan Vrána, Marie Kubaláková, Wentao Wan, Haojie Sun, Jing Zhao, Chunyan Yu, Yufeng Wu, Michael Abrouk, Haiyan Wang, Jaroslav Doležel, Xiue Wang
BACKGROUND: Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. RESULTS: In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29036468/exponential-propagation-of-large-circular-dna-by-reconstitution-of-a-chromosome-replication-cycle
#10
Masayuki Su'etsugu, Hiraku Takada, Tsutomu Katayama, Hiroko Tsujimoto
Propagation of genetic information is a fundamental property of living organisms. Escherichia coli has a 4.6 Mb circular chromosome with a replication origin, oriC. While the oriC replication has been reconstituted in vitro more than 30 years ago, continuous repetition of the replication cycle has not yet been achieved. Here, we reconstituted the entire replication cycle with 14 purified enzymes (25 polypeptides) that catalyze initiation at oriC, bidirectional fork progression, Okazaki-fragment maturation and decatenation of the replicated circular products...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29034434/genomic-analyses-reveal-low-mitochondrial-and-high-nuclear-diversity-in-the-cyclosporin-producing-fungus-tolypocladium-inflatum
#11
Yong-Jie Zhang, Xiao-Qing Yang, Shu Zhang, Richard A Humber, Jianping Xu
Mitochondrial DNA is generally regarded to evolve faster than nuclear DNA in animals, whereas if this is also true in fungi remains unclear. Herein, we annotate the first complete mitochondrial genome (mitogenome) of the cyclosporin-producing fungus Tolypocladium inflatum and report the genome-wide sequence variations among five isolates originating from distantly separated localities. We found that T. inflatum has among the most compact of fungal mitogenomes; its 25 kb DNA molecule encodes all standard fungal mitochondrial genes and harbors only one intron...
October 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29030623/monitoring-cerebral-hemodynamic-change-during-transcranial-ultrasound-stimulation-using-optical-intrinsic-signal-imaging
#12
Evgenii Kim, Eloise Anguluan, Jae Gwan Kim
Transcranial ultrasound stimulation (tUS) is a promising non-invasive approach to modulate brain circuits. The application is gaining popularity, however the full effect of ultrasound stimulation is still unclear and further investigation is needed. This study aims to apply optical intrinsic signal imaging (OISI) for the first time, to simultaneously monitor the wide-field cerebral hemodynamic change during tUS on awake animal with high spatial and temporal resolution. Three stimulation paradigms were delivered using a single-element focused transducer operating at 425 kHz in pulsed mode having the same intensity (ISPPA = 1...
October 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29023226/contrasting-evolutionary-paths-among-indo-pacific-pomacentrus-species-promoted-by-extensive-pericentric-inversions-and-genome-organization-of-repetitive-sequences
#13
Nuntaporn Getlekha, Marcelo de Bello Cioffi, Nuntiya Maneechot, Luiz Antônio Carlos Bertollo, Weerayuth Supiwong, Alongklod Tanomtong, Wagner Franco Molina
Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends...
October 12, 2017: Zebrafish
https://www.readbyqxmd.com/read/29021958/complete-mitochondrial-genome-sequence-of-fruit-piercing-moth-eudocima-phalonia-linnaeus-1763-lepidoptera-noctuoidea
#14
Kuppusamy Sivasankaran, Pratheesh Mathew, Sekar Anand, Stanislaus Antony Ceasar, Soosaimanikam Mariapackiam, Savarimuthu Ignacimuthu
The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575 bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), 22 transfer RNA (tRNA) genes and an A + T-rich region (D-loop). The nucleotide composition of the genome is highly A + T biased, accounting for 80.67% of nucleotides...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/29021213/whats-hows-and-whys-of-programmed-dna-elimination-in-tetrahymena
#15
REVIEW
Tomoko Noto, Kazufumi Mochizuki
Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in Tetrahymena thermophila removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in cis by the small RNA-mediated genome comparison of the MIC to the MAC...
October 2017: Open Biology
https://www.readbyqxmd.com/read/29017452/whole-genome-sequencing-for-the-molecular-characterization-of-carbapenem-resistant-klebsiella-pneumoniae-strains-isolated-at-the-italian-asst-fatebenefratelli-sacco-hospital-2012-2014
#16
Sara Giordana Rimoldi, Bernardina Gentile, Cristina Pagani, Annamaria Di Gregorio, Anna Anselmo, Anna Maria Palozzi, Antonella Fortunato, Valentina Pittiglio, Anna Lisa Ridolfo, Maria Rita Gismondo, Giuliano Rizzardini, Florigio Lista
BACKGROUND: The emergence of carbapenem-resistant Klebsiella pneumoniae strains is threatening antimicrobial treatment. METHODS: Sixty-eight carbapenemase-producing K. pneumoniae strains isolated at Luigi Sacco University Hospital-ASST Fatebenefratelli Sacco (Milan, Italy) between 2012 and 2014 were characterised microbiologically and molecularly. They were tested for drug susceptibility and carbapenemase phenotypes, investigated by means of repetitive extra-genic palindromic polymerase chain reaction (REP-PCR), and fully sequenced by means of next-generation sequencing for the in silico analysis of multi-locus sequence typing (MLST), their resistome, virulome and plasmid content, and their core single nucleotide polymorphism (SNP) genotypes...
October 10, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29017438/hsd11b2-runx3-and-line-1-methylation-in-placental-dna-of-hypertensive-disorders-of-pregnancy-patients
#17
Aleksandra Majchrzak-Celińska, Katarzyna Kosicka, Julia Paczkowska, Franciszek K Główka, Grzegorz H Bręborowicz, Mariola Krzyścin, Anna Siemiątkowska, Marcin Szaumkessel, Wanda Baer-Dubowska
Hypertensive Disorders of Pregnancy (HDsP) remain leading causes of maternal and perinatal morbidity and mortality. Growing evidence suggests the involvement of epigenetic factors, such as gene-specific and global DNA methylation changes, both in the etiology and as an effect of HDsP. In this study, we investigated the potential association between placental DNA methylation status in selected CpGs of HSD11B2 cortisol level controlling gene, RUNX3 tumor suppressor gene, and long interspersed nucleotide element-1 (LINE-1) repetitive elements and HDsP-preeclampsia (PE), gestational hypertension (GH), and chronic hypertension (CH)...
November 2017: Reproductive Sciences
https://www.readbyqxmd.com/read/28992625/b-chromosome-variants-of-the-grasshopper-xyleus-discoideus-angulatus-are-potentially-derived-from-pericentromeric-dna
#18
Andrezza C S Bernardino, Diogo C Cabral-de-Mello, Carolina B Machado, Octavio M Palacios-Gimenez, Neide Santos, Vilma Loreto
B chromosomes, extra elements present in the karyotypes of some eukaryote species, have been described in the grasshopper Xyleus discoideus angulatus. Although some studies have proposed an autosomal origin of the B chromosome in X. d. angulatus, little is known about its repetitive DNA composition and evolutionary dynamics. The aim of the present work was to shed light on the B chromosome evolution in X. d. angulatus by cytogenetic analysis of 27 populations from Pernambuco and Ceará states (Brazil). The frequency of B chromosomes in the different populations was determined, and chromosome measurements and fluorescence in situ hybridization (FISH) with C0t-DNA and telomeric and B chromosome sequences were performed in cells from B-carrying individuals...
October 10, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28984711/genomic-organization-of-tbk1-copy-number-variations-in-glaucoma-patients
#19
Adam P DeLuca, L M Alward Wallace, Jeffrey Liebmann, Robert Ritch, Kazuhide Kawase, Young H Kwon, Alan L Robin, Edwin M Stone, Todd E Scheetz, John H Fingert
BACKGROUND: Approximately 1% of normal tension glaucoma cases are caused by TANK binding kinase 1 (TBK1) gene duplications and triplications. However, the precise borders and orientation of these TBK1 gene copy number variations (CNVs) on chromosome 12 are unknown. METHODS: We determined the exact borders of TBK1 CNVs and the orientation of duplicated or triplicated DNA segments in five NTG patients with different TBK1 mutations using whole genome sequencing. RESULTS: Tandemly duplicated chromosome segments spanning the TBK1 gene were detected in four NTG patients, each with unique borders...
September 3, 2017: Journal of Glaucoma
https://www.readbyqxmd.com/read/28980937/correction-a-team-of-heterochromatin-factors-collaborates-with-small-rna-pathways-to-combat-repetitive-elements-and-germline-stress
#20
Alicia N McMurchy, Przemyslaw Stempor, Tessa Gaarenstroom, Brian Wysolmerski, Yan Dong, Darya Aussianikava, Alex Appert, Ni Huang, Paulina Kolasinska-Zwierz, Alexandra Sapetschnig, Eric A Miska, Julie Ahringer
No abstract text is available yet for this article.
October 5, 2017: ELife
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