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https://www.readbyqxmd.com/read/29151258/clinical-significance-of-disease-specific-myd88-mutations-in-circulating-dna-in-primary-central-nervous-system-lymphoma
#1
Keiichiro Hattori, Mamiko Sakata-Yanagimoto, Yasuhito Suehara, Yasuhisa Yokoyama, Takayasu Kato, Naoki Kurita, Hidekazu Nishikii, Naoshi Obara, Shingo Takano, Eiichi Ishikawa, Akira Matsumura, Yuichi Hasegawa, Shigeru Chiba
Recent sequencing studies demonstrated the MYD88 L265P mutation in more than 70% of primary central nervous system lymphomas (PCNSL), and the clinical significance of this mutation has been proposed as diagnostic and prognostic markers in PCNSL. On the other hand, mutational analyses using cell-free DNAs have been reported in a variety of systemic lymphomas. To investigate how sensitively the MYD88 L265P mutation can be identified in cell-free DNA from PCNSL patients, we performed droplet digital PCR (ddPCR) and targeted deep sequencing (TDS) in consecutive 14 PCNSL patients from whom paired tumor-derived DNA and cell-free DNA was available at diagnosis...
November 19, 2017: Cancer Science
https://www.readbyqxmd.com/read/29151156/deep-rnaseq-indicates-protective-mechanisms-of-cold-tolerant-indica-rice-plants-during-early-vegetative-stage
#2
Raul Antonio Sperotto, Artur Teixeira de Araújo Junior, Janete Mariza Adamski, Denise Cargnelutti, Felipe Klein Ricachenevsky, Ben-Hur Neves de Oliveira, Renata Pereira da Cruz, Rinaldo Pires Dos Santos, Leila Picolli da Silva, Janette Palma Fett
Cold-tolerance in rice may be related to increased cellulose deposition in the cell wall, membrane fatty acids unsaturation and differential expression of several newly identified genes. Low temperature exposure during early vegetative stages limits rice plant's growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated (10 °C) leaves from two genotypes, cold-tolerant (CT) and cold-sensitive (CS), was performed...
November 18, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29151135/classification-of-g-protein-coupled-receptors-based-on-a-rich-generation-of-convolutional-neural-network-n-gram-transformation-and-multiple-sequence-alignments
#3
Man Li, Cheng Ling, Qi Xu, Jingyang Gao
Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithms. To improve prediction accuracy, these algorithms must confront the key challenge of extracting valuable features. In this work, we propose a feature-enhanced protein classification approach, considering the rich generation of multiple sequence alignment algorithms, N-gram probabilistic language model and the deep learning technique...
November 18, 2017: Amino Acids
https://www.readbyqxmd.com/read/29150892/expanding-the-neurodevelopmental-phenotype-of-pura-syndrome
#4
Bo Hoon Lee, Margot R F Reijnders, Oluwatobi Abubakare, Emily Tuttle, Brynn Lape, Kelly Q Minks, Christopher Stodgell, Loisa Bennetto, Jennifer Kwon, Chin-To Fong, Karen W Gripp, Eric D Marsh, Wendy E Smith, Ahm M Huq, Stephanie A Coury, Wen-Hann Tan, Orestes Solis, Rupal I Mehta, Richard J Leventer, Diana Baralle, David Hunt, Alex R Paciorkowski
PURA syndrome is a recently described developmental encephalopathy presenting with neonatal hypotonia, feeding difficulties, global developmental delay, severe intellectual disability, and frequent apnea and epilepsy. We describe 18 new individuals with heterozygous sequence variations in PURA. A neuromotor disorder starting with neonatal hyptonia, but ultimately allowing delayed progression to walking, was present in nearly all individuals. Congenital apnea was present in 56% during infancy, but all cases in this cohort resolved during the first year of life...
November 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29149252/shared-genomic-variants-identification-of-transmission-routes-using-pathogen-deep-sequence-data
#5
Colin J Worby, Marc Lipsitch, William P Hanage
Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiologic investigations. Identifying who infected whom sheds considerable light on transmission patterns, high-risk settings and subpopulations, and the effectiveness of infection control. Genomic data shed new light on transmission dynamics and can be used to identify clusters of individuals likely to be linked by direct transmission. However, identification of individual routes of infection via single genome samples typically remains uncertain...
November 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29147808/maribacter-marinus-sp-nov-isolated-from-a-deep-sea-seamount
#6
Dan-Yang Wang, Ya-Wen Sun, Jie Liu, De-Chao Zhang
A Gram-stain negative, rod-shaped, aerobic strain, designated YC973(T), was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain YC973(T) is related to the genus Maribacter and has high 16S rRNA gene sequence similarity to Maribacter orientalis KMM 3947(T) (97.6%). The predominant cellular fatty acids were iso-C15:0, iso-C15:1 G and an unidentified fatty acid of equivalent chain-length 13.565. The polar lipid profile contained phosphatidylethanolamine and five unidentified lipids...
November 17, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29147655/magnetic-resonance-colonography-may-predict-the-need-for-bowel-resection-in-colorectal-endometriosis
#7
Arnaldo Scardapane, Filomenamila Lorusso, Mariantonietta Francavilla, Stefano Bettocchi, Fabiana Divina Fascilla, Giuseppe Angelelli, Marco Scioscia
Purpose: To define if MRI findings in patients with deep pelvic endometriosis (DPE) may be predictive for the need of bowel resection. Material and Methods: A retrospective survey of 196 pelvic MRIs of women who received laparoscopic procedures for DPE was carried out. A pelvic MRI was performed in all patients: it consisted in T2w-TSE sequences in axial, sagittal, and coronal planes and T1w and THRIVE sequences in the axial plane; the exam was completed by MR-Colonography...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29145794/analysis-of-bacterial-and-fungal-nucleic-acid-in-canine-sterile-granulomatous-and-pyogranulomatous-dermatitis-and-panniculitis
#8
Fabio B Rosa, Caitlin E Older, Courtney Meason-Smith, Jan S Suchodolski, Sonia Lingsweiler, Joanne E Mansell, Aline Rodrigues Hoffmann
Next generation sequencing (NGS) studies are revealing a diverse microbiota on the skin of dogs. The skin microbiota of canine sterile granulomatous and pyogranulomatous dermatitis (SGPD) has yet to be investigated using NGS techniques. NGS targeting the 16S rRNA and ITS-1 region of bacterial and fungal DNA, respectively, were used to investigate if bacterial and fungal DNA were associated with skin lesions in cases of canine SGPD. The study included 20 formalin-fixed paraffin-embedded (FFPE) skin samples and 12 fresh samples from SGPD-affected dogs, and 10 FFPE and 10 fresh samples from healthy dogs...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/29145046/genetic-and-clinical-characteristics-of-phyllodes-tumors-of-the-breast
#9
Ji-Yeon Kim, Jong Han Yu, Seok Jin Nam, Seok Won Kim, Se Kyung Lee, Woong-Yang Park, Dong-Young Noh, Do-Hyun Nam, Yeon Hee Park, Wonshik Han, Jeong Eon Lee
PURPOSE: Phyllodes tumors (PTs) of the breast are rare, accounting for less than 1% of all breast tumors. Among PTs, malignant PTs (MPTs) have malignant characteristics and distant metastases occur in about 20% to 30% of MPTs. However, there is no effective treatment for MPTs with distant metastasis, resulting in an abject prognosis. We performed targeted deep sequencing on PTs to identify the associations between genetic alterations and clinical prognosis. METHODS: We performed targeted deep sequencing to evaluate the genetic characteristics of PTs and analyzed the relationships between clinical and genetic characteristics...
November 12, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29145028/the-complete-mitochondrial-genome-of-the-alvinocaridid-shrimp-shinkaicaris-leurokolos-decapoda-caridea-insight-into-the-mitochondrial-genetic-basis-of-deep-sea-hydrothermal-vent-adaptation-in-the-shrimp
#10
Shao'e Sun, Ming Hui, Minxiao Wang, Zhongli Sha
Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi & Hashimoto, 2000) was determined through Illumina sequencing...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29144541/genetic-landscape-of-papillary-thyroid-carcinoma-in-the-chinese-population
#11
Jialong Liang, Wanshi Cai, Dongdong Feng, Huajing Teng, Fengbiao Mao, Yi Jiang, Shanshan Hu, Xianfeng Li, Yujie Zhang, Baoguo Liu, Zhong Sheng Sun
Improvement in the clinical outcome of human cancers requires characterization of genetic alterations underlying their pathogenesis. Large-scale genomic and transcriptomic characterization of papillary thyroid carcinomas (PTCs) in Western populations has revealed multiple oncogenic drivers which are essential for understanding pathogenic mechanisms of this disease; while so far, the genetic landscape in Chinese patients with PTC remains uncharacterized. Here, we conducted a largescale genetic analysis of PTCs from patients in China to determine the mutational landscape of this cancer...
November 16, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29144536/isolation-and-whole-genome-sequencing-of-fetal-cells-from-maternal-blood-towards-the-ultimate-non-invasive-prenatal-testing
#12
Fang Chen, Ping Liu, Ying Gu, Zhu Zhu, Amulya Nanisetti, Zhangzhang Lan, Zhiwei Huang, Sophie Jia Liu, Xiongbin Kang, Yuqing Deng, Liqiong Luo, Dan Jiang, Yong Qiu, Jianchang Pan, Jun Xia, Ken Xiong, Chao Liu, Lin Xie, Qianyu Shi, Jing Li, Xiuqing Zhang, Wei Wang, Snezana Drmanac, Hui Jiang, Radoje Drmanac, Xun Xu
OBJECTIVE: To develop a methodology of isolating fetal cells from maternal blood and use deep sequencing demonstrating the promise for more complete and accurate genetic screening compared to other non-invasive prenatal testing (NIPT). METHODS: Here in this study, we developed a double negative selection (DNS) procedure to unbiasedly enrich fetal cells. After validated by short tandem repeat (STR), the isolated CFCs were subjected to deep whole genome sequencing analysis (WGS)...
November 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29142136/size-composition-and-evolution-of-hiv-dna-populations-during-early-antiretroviral-therapy-and-intensification-with-maraviroc
#13
Antoine Chaillon, Sara Gianella, Steven M Lada, Josué Perez-Santiago, Parris Jordan, Caroline Ignacio, Maile Karris, Douglas Richman, Sanjay R Mehta, Susan J Little, Joel O Wertheim, Davey M Smith
Residual viremia is common during antiretroviral therapy (ART), and could be caused by ongoing low-level virus replication or by release of viral particles from infected cells. ART Intensification should impact ongoing viral propagation but not virion release. Eighteen acutely infected men were enrolled in a randomized controlled trial, and followed for a median of 107 weeks. Participants started ART with (n=9) or without (n=9) intensification with maraviroc (MVC) within 90 days of infection. Levels of HIV DNA and cell-free RNA were quantified by droplet digital PCR...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29141996/the-distinct-transcriptomes-of-slow-and-fast-adult-muscles-are-delineated-by-noncoding-rnas
#14
Vered Raz, Muhammad Riaz, Zuotian Tatum, Szymon M Kielbasa, Peter A C 't Hoen
Adult muscles have a vast adaptation capacity, enabling function switches in response to altered conditions. During intensive physical activity, disease, or aging, adult skeletal muscles change and adjust their functions. The competence to adjust varies among muscles. Muscle-specific molecular mechanisms in healthy and normal conditions could designate changes in physiologic and pathologic conditions. We generated deep mRNA-sequencing data in adult fast and slow mouse muscles, and applying paired analysis, we identified that the muscle-specific signatures are composed of half of the muscle transcriptome...
November 15, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29141909/local-fitness-landscapes-predict-yeast-evolutionary-dynamics-in-directionally-changing-environments
#15
Florien A Gorter, Mark G M Aarts, Bas J Zwaan, J Arjan G M de Visser
The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analysed their phenotypic and genomic changes...
November 15, 2017: Genetics
https://www.readbyqxmd.com/read/29141638/diffusion-weighted-imaging-of-the-brains-of-dogs-with-idiopathic-epilepsy
#16
Antje Hartmann, Steffen Sager, Klaus Failing, Marion Sparenberg, Martin J Schmidt
BACKGROUND: Idiopathic epilepsy is one of the most common neurological disorders in dogs. Unfortunately, up to 30% of dogs with idiopathic epilepsy show no improvement under antiepileptic drug treatment. Diffusion-weighted imaging is used in human medicine to identify epileptogenic foci in the brain to allow for more invasive treatments such as deep brain stimulation or surgical removal. The aim of this study was to ass the feasibility of interictal diffusion-weighted MRI in dogs and to evaluate the distribution of diffusion in the brains of dogs with idiopathic epilepsy (IE) and to compare these values to previously published values from healthy beagle dogs...
November 15, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29141589/reconstructing-cancer-karyotypes-from-short-read-data-the-half-empty-and-half-full-glass
#17
Rami Eitan, Ron Shamir
BACKGROUND: During cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions.The result is a highly complex, patient-specific cancer karyotype. Using high-throughput technologies of deep sequencing and microarrays it is possible to interrogate a cancer genome and produce chromosomal copy number profiles and a list of breakpoints ("jumps") relative to the normal genome...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29138302/disruption-of-the-opal-stop-codon-attenuates-chikungunya-virus-induced-arthritis-and-pathology
#18
Jennifer E Jones, Kristin M Long, Alan C Whitmore, Wes Sanders, Lance R Thurlow, Julia A Brown, Clayton R Morrison, Heather Vincent, Kayla M Peck, Christian Browning, Nathaniel Moorman, Jean K Lim, Mark T Heise
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus responsible for several significant outbreaks of debilitating acute and chronic arthritis and arthralgia over the past decade. These include a recent outbreak in the Caribbean islands and the Americas that caused more than 1 million cases of viral arthralgia. Despite the major impact of CHIKV on global health, viral determinants that promote CHIKV-induced disease are incompletely understood. Most CHIKV strains contain a conserved opal stop codon at the end of the viral nsP3 gene...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29136015/the-influences-of-walking-running-and-stair-activity-on-knee-articular-cartilage-quantitative-mri-using-t1-rho-and-t2-mapping
#19
Meng Chen, Lin Qiu, Si Shen, Fei Wang, Jing Zhang, Cici Zhang, Sirun Liu
OBJECTIVE: To explore the different influences of walking, running and stair activity on knee articular cartilage with T1 rho and T2 mapping sequences. MATERIALS AND METHODS: MRI (3.0-T) scans of the right knee were performed in twenty-three young healthy adults immediately after 30 minutes of rest, walking, running and stair activity respectively. Articular cartilage was quantitatively assessed based on T1 rho and T2 relaxation times. Analysis of variance for random block design data, bonferroni test and paired samples t tests were performed to estimate the different influences of physiological activities on articular cartilage...
2017: PloS One
https://www.readbyqxmd.com/read/29134273/o-cdc7-kinase-where-art-thou
#20
Robert A Sclafani, Jay R Hesselberth
Although Cdc7 protein kinase is important for regulating DNA replication in all eukaryotes and is a target for cancer therapy, it has never been localized in cells. Recently, a novel molecular genomic method used by our laboratory to localize Cdc7 to regions of chromosomes. Originally, mutations in the CDC7 gene were found in the classic cdc mutant collection of Hartwell et al. (Genetics 74:267-286, 1973). The CDC7 gene was found to encode a protein kinase called DDK that has been studied for many years, establishing its precise role in the initiation of DNA replication at origins...
November 13, 2017: Current Genetics
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