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Weicheng Li, Qiangchuan Hou, Yanjie Wang, Huimin Ma, Yahua Liu, Feiyan Zhao, Jing Li, Lai-Yu Kwok, Jie Yu, Zhihong Sun, Tiansong Sun
BACKGROUND: The gut microbes of dairy cows are strongly associated with their health, but the relationship between milk production and the intestinal microbiota has seldom been studied. Thus, we explored the diversity of the intestinal microbiota during peak lactation of dairy cows. METHODS: The intestinal microbiota of nine dairy cows at peak lactation was evaluated using the Pacific Biosciences single-molecule real-time (PacBio SMRT) sequencing approach. RESULTS: A total of 32,670 high-quality 16S rRNA gene sequences were obtained, belonging to 12 phyla, 59 families, 107 genera, and 162 species...
June 15, 2018: Current Microbiology
Qiang Zhuang, Wenjuan Li, Christina Benda, Zhijian Huang, Tanveer Ahmed, Ping Liu, Xiangpeng Guo, David P Ibañez, Zhiwei Luo, Meng Zhang, Mazid Md Abdul, Zhongzhou Yang, Jiayin Yang, Yinghua Huang, Hui Zhang, Dehao Huang, Jianguo Zhou, Xiaofen Zhong, Xihua Zhu, Xiuling Fu, Wenxia Fan, Yulin Liu, Yan Xu, Carl Ward, Muhammad Jadoon Khan, Shahzina Kanwal, Bushra Mirza, Micky D Tortorella, Hung-Fat Tse, Jiayu Chen, Baoming Qin, Xichen Bao, Shaorong Gao, Andrew P Hutchins, Miguel A Esteban
In the version of this Article originally published, in Fig. 2c, the '+' sign and 'OSKM' were superimposed in the label '+OSKM'. In Fig. 4e, in the labels, all instances of 'Ant' should have been 'Anti-'. And, in Fig. 7a, the label '0.0' was misplaced; it should have been on the colour scale bar. These figures have now been corrected in the online versions.
June 15, 2018: Nature Cell Biology
Mian Xia, Xue Han, Hang He, Renbo Yu, Gang Zhen, Xiping Jia, Beijiu Cheng, Xing Wang Deng
Background: Luo-han-guo (Siraitia grosvenorii), also called monk fruit, is a member of the Cucurbitaceae family. Monk fruit has become an important area for research because of the pharmacological and economic potential of its non-caloric, extremely sweet components (mogrosides). It is also commonly used in traditional Chinese medicine for the treatment of lung congestion, sore throat and constipation. Recently, a single reference genome became available for monk fruit, assembled from 36...
June 8, 2018: GigaScience
Faten A Al-Aqil, Maria J Monte, Ana Peleteiro-Vigil, Oscar Briz, Ruben Rosales, Raquel Gonzalez, Carlos J Aranda, Borja Ocon, Iker Uriarte, Fermin Sanchez de Medina, Olga Martinez-Augustin, Matias A Avila, Jose J G Marin, Marta R Romero
At high doses, glucocorticoids (GC) have been associated with enhanced serum bile acids and liver injury. We have evaluated the effect of GC, in the absence of hepatotoxicity, on FXR/Fgf15/Fgf21-mediated ileum-liver crosstalk. Rats and mice (wild type and Fxr-/- , Fgf15-/- and int-Gr-/- strains; the latter with GC receptor (Gr) knockout selective for intestinal epithelial cells), were treated (i.p.) with dexamethasone, prednisolone or budesonide. In both species, high doses of GC caused hepatotoxicity. At a non-hepatotoxic dose, GC induced ileal Fgf15 down-regulation and liver Fgf21 up-regulation, without affecting Fxr expression...
June 5, 2018: Biochimica et Biophysica Acta
Tianyi Xin, Zhichao Xu, Jing Jia, Christine Leon, Songnian Hu, Yulin Lin, Subramanyam Ragupathy, Jingyuan Song, Steven G Newmaster
Global concerns have been paid to the potential hazard of traditional herbal medicinal products (THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed...
May 2018: Acta Pharmaceutica Sinica. B
Liqiong Liu, Yizhou Zhang, Dongxu Jiang, Shiming Du, Zixin Deng, Lianrong Wang, Shi Chen
Bacterial epigenetic modifications play key roles in cellular processes such as stress responses, DNA replication, segregation, antimicrobial resistance, etc. In recent years, emerging new sequencing technologies, including single-molecule real-time (SMRT) sequencing and nanopore sequencing, have enabled the directed reading of epigenetic modifications without pre-treatment of DNA or DNA amplification. The applications of SMRT and nanopore sequencing open the door for the identification of more diverse epigenetic modifications of DNA bases and backbones and potentially facilitate the understanding of the novel functions of these epigenetic markers in cell physiology...
June 7, 2018: Biotechnology Journal
Yuko Yoshinaga, Christopher Daum, Guifen He, Ronan O'Malley
Strategies for sequencing fungal genomes on next-generation sequencing (NGS) platforms depend on the characteristics of the genome of the targeted species, quantity and quality of the genomic DNA, and cost considerations. Massively parallel sequencing with sequencing by synthesis (SBS) approach by Illumina produces terabases of short read sequences (i.e., ~300 bp) in a time and cost-effective manner, though the read length can limit the assembly particularly in repetitive regions. The single molecule, real-time (SMRT) sequencing approach by Pacific Biosciences (PacBio) produces longer reads (i...
2018: Methods in Molecular Biology
Thomas D Otto, Ulrike Böhme, Mandy Sanders, Adam Reid, Ellen I Bruske, Craig W Duffy, Pete C Bull, Richard D Pearson, Abdirahman Abdi, Sandra Dimonte, Lindsay B Stewart, Susana Campino, Mihir Kekre, William L Hamilton, Antoine Claessens, Sarah K Volkman, Daouda Ndiaye, Alfred Amambua-Ngwa, Mahamadou Diakite, Rick M Fairhurst, David J Conway, Matthias Franck, Chris I Newbold, Matt Berriman
Background : Although thousands of clinical isolates of Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. Methods : Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15 P...
2018: Wellcome Open Research
Sheetal Ambardar, Malali Gowda
The human HLA genes are among the most polymorphic genes in the human genome. Therefore, it is very difficult to find two unrelated individuals with identical HLA molecules. As a result, HLA Class I and Class II genes are routinely sequenced or serotyped for organ transplantation, autoimmune disease-association studies, drug hypersensitivity research, and other applications. However, these methods were able to give two or four digit data, which was not sufficient enough to understand the completeness of haplotypes of HLA genes...
2018: Methods in Molecular Biology
Kemal Eren, Ben Murrell
Motivation: Protein coding genes can be studied using long-read next generation sequencing. However, high rates of indel sequencing errors are problematic, corrupting the reading frame. Even the consensus of multiple independent sequence reads retains indel errors. To solve this problem, we introduce RIFRAF, a sequence consensus algorithm that takes a set of error-prone reads and a reference sequence and infers an accurate in-frame consensus. RIFRAF uses a novel structure, analogous to a two-layer hidden Markov model: the consensus is optimized to maximize alignment scores with both the set of noisy reads and with a reference...
May 29, 2018: Bioinformatics
Sin-Gi Park, Seung Il Yoo, Dong Sung Ryu, Hyunsung Lee, Yong Ju Ahn, Hojin Ryu, Junsu Ko, Chang Pyo Hong
Lentinula edodes is one of the most popular edible mushrooms in the world and contains useful medicinal components such as lentinan. The whole-genome sequence of L. edodes has been determined with the objective of discovering candidate genes associated with agronomic traits, but experimental verification of gene models with correction of gene prediction errors is lacking. To improve the accuracy of gene prediction, we produced 12.6 Gb of long-read transcriptome data of variable lengths using PacBio single-molecule real-time (SMRT) sequencing and generated 36,946 transcript clusters with an average length of 2...
December 2017: Data in Brief
M J A Weerts, E C Timmermans, A van de Stolpe, R H A M Vossen, S Y Anvar, J A Foekens, S Sleijfer, J W M Martens
The use of blood-circulating cell-free DNA (cfDNA) as a "liquid biopsy" in oncology is being explored for its potential as a cancer biomarker. Mitochondria contain their own circular genomic entity (mitochondrial DNA, mtDNA), up to even thousands of copies per cell. The mutation rate of mtDNA is several orders of magnitude higher than that of the nuclear DNA. Tumor-specific variants have been identified in tumors along the entire mtDNA, and their number varies among and within tumors. The high mtDNA copy number per cell and the high mtDNA mutation rate make it worthwhile to explore the potential of tumor-specific cf-mtDNA variants as cancer marker in the blood of cancer patients...
May 26, 2018: Neoplasia: An International Journal for Oncology Research
Gabriel Dario Damilano, Omar Sued, Maria Julia Ruiz, Yanina Ghiglione, Flavia Canitano, Maria Pando, Gabriela Turk, Pedro Cahn, Horacio Salomón, Dario Dilernia
BACKGROUND: Recent studies indicate that there is selection bias for transmission of viral polymorphisms associated with higher viral fitness. Furthermore, after transmission and before a specific immune response is mounted in the recipient, the virus undergoes a number of reversions which allow an increase in their replicative capacity. These aspects, and others, affect the viral population characteristic of early acute infection. METHODS: 160 singlegag-gene amplifications were obtained by limiting-dilution RT-PCR from plasma samples of 8 ARV-naïve patients with early acute infection (<30 days, 22 days average) and 8 ARV-naive patients with approximately a year of infection (10 amplicons per patient)...
May 22, 2018: Vaccine
Ze-Gang Wei, Shao-Wu Zhang
BACKGROUND: PacBio sequencing platform offers longer read lengths than the second-generation sequencing technologies. It has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. Due to its extremely wide range of application areas, fast sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of subsequent analysis tools. Although there are several available simulators (e...
May 22, 2018: BMC Bioinformatics
Tslil Gabrieli, Hila Sharim, Dena Fridman, Nissim Arbib, Yael Michaeli, Yuval Ebenstein
Next generation sequencing (NGS) is challenged by structural and copy number variations larger than the typical read length of several hundred bases. Third-generation sequencing platforms such as single-molecule real-time (SMRT) and nanopore sequencing provide longer reads and are able to characterize variations that are undetected in NGS data. Nevertheless, these technologies suffer from inherent low throughput which prohibits deep sequencing at reasonable cost without target enrichment. Here, we optimized Cas9-Assisted Targeting of CHromosome segments (CATCH) for nanopore sequencing of the breast cancer gene BRCA1...
May 18, 2018: Nucleic Acids Research
Liang Zhao, Yulong Song, Lin Li, Nanqin Gan, Jerry J Brand, Lirong Song
The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98...
May 2018: Harmful Algae
Gengmi Li, Li Yang, Tao Zhang, Xiaojiao Guo, Jian Qin, Yingjiang Cao, Qianhua Yang, Shumei You, Guoliang Yuan, Xianqi Wan, Jing Luo, Zhaoxiang Li, Lei Gao, Ying Liu, Kaifeng Jiang, Jiakui Zheng
OBJECTIVES: Achromobacter spanius is a new described, non-fermenting Gram-negative and coccoid pathogen that isolated from patient blood. In order to investigate the pathogenesis of this strain in genomic level, whole genome sequencing was carried out on this strain. METHODS: In this study, complete genome of the type strain of this species DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. RESULTS: Complete genome of DSM 23806T consists of one circular DNA chromosome of 6,425,783bp with a GC content of 64...
May 15, 2018: Journal of Global Antimicrobial Resistance
Marina Suzuki, Nanae Shinozuka, Tomohiro Hirakata, Miyuki T Nakata, Taku Demura, Hirokazu Tsukaya, Gorou Horiguchi
Organ size regulation is dependent on the precise spatial and temporal regulation of cell proliferation and cell expansion. A number of transcription factors have been identified that play a key role in the determination of aerial lateral organ size, but their functional relationship to various chromatin modifiers has not been well understood. To understand how leaf size is regulated, we previously isolated the oligocellula1 ( oli1 ) mutant of Arabidopsis thaliana that develops smaller first leaves than the wild type (WT) mainly due to a reduction in the cell number...
2018: Frontiers in Plant Science
Alexander Q Wixom, N Carol Casavant, Joseph C Kuhl, Fangming Xiao, Louise-Marie Dandurand, Allan B Caplan
Solanum sisymbriifolium , also known as "Litchi Tomato" or "Sticky Nightshade," is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, S. sisymbriifolium induces eggs of the cyst nematode, Globodera pallida , to hatch and migrate into its roots, but then arrests further nematode maturation. In order to provide researchers with a partial blueprint of its genetic make-up so that the mechanism of this response might be identified, we used single molecule real time (SMRT) sequencing to compile a high quality de novo transcriptome of 41,189 unigenes drawn from individually sequenced bud, root, stem, and leaf RNA populations...
May 16, 2018: G3: Genes—Genomes—Genetics
Phillip W L Tai, Jun Xie, Kaiyuen Fong, Matthew Seetin, Cheryl Heiner, Qin Su, Michael Weiand, Daniella Wilmot, Maria L Zapp, Guangping Gao
Recombinant adeno-associated virus (rAAV)-based gene therapy has entered a phase of clinical translation and commercialization. Despite this progress, vector integrity following production is often overlooked. Compromised vectors may negatively impact therapeutic efficacy and safety. Using single molecule, real-time (SMRT) sequencing, we can comprehensively profile packaged genomes as a single intact molecule and directly assess vector integrity without extensive preparation. We have exploited this methodology to profile all heterogeneic populations of self-complementary AAV genomes via bioinformatics pipelines and have coined this approach AAV-genome population sequencing (AAV-GPseq)...
June 15, 2018: Molecular Therapy. Methods & Clinical Development
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