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https://www.readbyqxmd.com/read/29044880/targeted-deep-sequencing-of-effusion-cytology-samples-is-feasible-informs-spatiotemporal-tumor-evolution-and-has-clinical-and-diagnostic-utility
#1
Jonas Leichsenring, Anna-Lena Volckmar, Martina Kirchner, Daniel Kazdal, Mark Kriegsmann, Fabian Stögbauer, Teresa Bockmayr, Frederick Klauschen, Felix J F Herth, Roland Penzel, Arne Warth, Peter Schirmacher, Volker Endris, Albrecht Stenzinger
During the course of disease, many cancer patients eventually present with metastatic disease including peritoneal or pleural spread. In this context, cytology specimens derived from ascites or pleural effusion may help to differentiate malignant from benign conditions and sometimes yield diagnosis of a malignancy. However, even when supported by immunohistochemistry, cytological interpretation can be challenging, especially if tumor cellularity is low. Here, we investigated whether targeted deep sequencing of formalin-fixed and paraffin embedded (FFPE) cytology specimens of cancer patients is feasible, and has diagnostic and clinical impact...
October 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29044127/engineered-in-vitro-cell-line-mixtures-and-robust-evaluation-of-computational-methods-for-clonal-decomposition-and-longitudinal-dynamics-in-cancer
#2
Hossein Farahani, Camila P E de Souza, Raewyn Billings, Damian Yap, Karey Shumansky, Adrian Wan, Daniel Lai, Anne-Marie Mes-Masson, Samuel Aparicio, Sohrab P Shah
Characterization and quantification of tumour clonal populations over time via longitudinal sampling are essential components in understanding and predicting the response to therapeutic interventions. Computational methods for inferring tumour clonal composition from deep-targeted sequencing data are ubiquitous, however due to the lack of a ground truth biological data, evaluating their performance is difficult. In this work, we generate a benchmark data set that simulates tumour longitudinal growth and heterogeneity by in vitro mixing of cancer cell lines with known proportions...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043626/dna-replication-profiling-using-deep-sequencing
#3
Xanita Saayman, Cristina Ramos-Pérez, Grant W Brown
Profiling of DNA replication during progression through S phase allows a quantitative snap-shot of replication origin usage and DNA replication fork progression. We present a method for using deep sequencing data to profile DNA replication in S. cerevisiae.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043025/diversity-and-distribution-of-genetic-variation-in-gammarids-comparing-patterns-between-invasive-and-non-invasive-species
#4
Miguel Baltazar-Soares, Filipa Paiva, Yiyong Chen, Aibin Zhan, Elizabeta Briski
Biological invasions are worldwide phenomena that have reached alarming levels among aquatic species. There are key challenges to understand the factors behind invasion propensity of non-native populations in invasion biology. Interestingly, interpretations cannot be expanded to higher taxonomic levels due to the fact that in the same genus, there are species that are notorious invaders and those that never spread outside their native range. Such variation in invasion propensity offers the possibility to explore, at fine-scale taxonomic level, the existence of specific characteristics that might predict the variability in invasion success...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29040274/a-quadratically-regularized-functional-canonical-correlation-analysis-for-identifying-the-global-structure-of-pleiotropy-with-ngs-data
#5
Nan Lin, Yun Zhu, Ruzong Fan, Momiao Xiong
Investigating the pleiotropic effects of genetic variants can increase statistical power, provide important information to achieve deep understanding of the complex genetic structures of disease, and offer powerful tools for designing effective treatments with fewer side effects. However, the current multiple phenotype association analysis paradigm lacks breadth (number of phenotypes and genetic variants jointly analyzed at the same time) and depth (hierarchical structure of phenotype and genotypes). A key issue for high dimensional pleiotropic analysis is to effectively extract informative internal representation and features from high dimensional genotype and phenotype data...
October 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29039843/acetoclastic-methanosaeta-are-dominant-methanogens-in-organic-rich-antarctic-marine-sediments
#6
Stephanie A Carr, Florence Schubotz, Robert B Dunbar, Christopher T Mills, Robert Dias, Roger E Summons, Kevin W Mandernack
Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment...
October 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/29038972/interactions-of-plant-growth-promoting-rhizobacteria-and-soil-factors-in-two-leguminous-plants
#7
Xiao Xiao, Miaochun Fan, Entao Wang, Weimin Chen, Gehong Wei
Although the rhizomicrobiome has been extensively studied, little is known about the interactions between soil properties and the assemblage of plant growth-promoting microbes in the rhizosphere. Herein, we analysed the composition and structure of rhizomicrobiomes associated with soybean and alfalfa plants growing in different soil types using deep Illumina 16S rRNA sequencing. Soil pH, P and K significantly affected the composition of the soybean rhizomicrobiome, whereas soil pH and N had a significant effect on the alfalfa rhizomicrobiome...
October 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29038627/characterization-and-antibiotic-sensitivity-profile-of-bacteria-in-orofacial-abscesses-of-odontogenic-origin
#8
H Jagadish Chandra, B H Sripathi Rao, A P Muhammed Manzoor, A B Arun
BACKGROUND: Odontogenic infections range from peripheral abscess to superficial and deep infections leading to severe infections in head and neck region. This study was aimed to assess bacterial isolates responsible for orofacial infection of odontogenic origin and their drug susceptibility patterns so as to provide better perceptive for the management of odontogenic infections. METHODS: The study was made in a selected cohort of patients, irrespective of age and gender having moderate and severe orofacial infections of odontogenic origin admitted to Yenepoya University Hospital...
December 2017: Journal of Maxillofacial and Oral Surgery
https://www.readbyqxmd.com/read/29037144/trypanosoma-cruzi-specific-mrna-amplification-by-in-vitro-transcription-improves-parasite-transcriptomics-in-host-parasite-rna-mixtures
#9
Rafael Luis Kessler, Daniela Parada Pavoni, Marco Aurelio Krieger, Christian Macagnan Probst
BACKGROUND: Trypanosomatids are a group of protozoan parasites that includes the etiologic agents of important human illnesses as Chagas disease, sleeping sickness and leishmaniasis. These parasites have a significant distinction from other eukaryotes concerning mRNA structure, since all mature mRNAs have an identical species-specific sequence of 39 nucleotides at the 5' extremity, named spliced leader (SL). Considering this peculiar aspect of trypanosomatid mRNA, the aim of the present work was to develop a Trypanosoma cruzi specific in vitro transcription (IVT) linear mRNA amplification method in order to improve parasite transcriptomics analyses...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29036709/deep-learning-of-the-splicing-epi-genetic-code-reveals-a-novel-candidate-mechanism-linking-histone-modifications-to-esc-fate-decision
#10
Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036617/arrayed-mutant-haploid-embryonic-stem-cell-libraries-facilitate-phenotype-driven-genetic-screens
#11
Guang Liu, Xue Wang, Yufang Liu, Meili Zhang, Tao Cai, Zhirong Shen, Yuyan Jia, Yue Huang
Forward genetic screens using mammalian embryonic stem (ES) cells have identified genes required for numerous cellular processes. However, loss-of-function screens are more difficult to conduct in diploid cells because, in most cases, both alleles of a gene must be mutated to exhibit a phenotype. Recently, mammalian haploid ES cell lines were successfully established and applied to several recessive genetic screens. However, all these screens were performed in mixed pools of mutant cells and were mainly based on positive selection...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036616/deeploc-prediction-of-protein-subcellular-localization-using-deep-learning
#12
José Juan Almagro Armenteros, Casper Kaae Sønderby, Søren Kaae Sønderby, Henrik Nielsen, Ole Winther
Motivation: The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036529/itsonedb-a-comprehensive-collection-of-eukaryotic-ribosomal-rna-internal-transcribed-spacer-1-its1-sequences
#13
Monica Santamaria, Bruno Fosso, Flavio Licciulli, Bachir Balech, Ilaria Larini, Giorgio Grillo, Giorgio De Caro, Sabino Liuni, Graziano Pesole
A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036382/musitedeep-a-deep-learning-framework-for-general-and-kinase-specific-phosphorylation-site-prediction
#14
Duolin Wang, Shuai Zeng, Chunhui Xu, Wangren Qiu, Yanchun Liang, Trupti Joshi, Dong Xu
Motivation: Computational methods for phosphorylation site prediction play important roles in protein function studies and experimental design. Most existing methods are based on feature extraction, which may result in incomplete or biased features. Deep learning as the cutting-edge machine learning method has the ability to automatically discover complex representations of phosphorylation patterns from the raw sequences, and hence it provides a powerful tool for improvement of phosphorylation site prediction...
August 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036205/characterization-of-micrornas-of-beta-macrocarpa-and-their-responses-to-beet-necrotic-yellow-vein-virus-infection
#15
Jun-Ying Liu, Hui-Yan Fan, Ying Wang, Yong-Liang Zhang, Da-Wei Li, Jia-Lin Yu, Cheng-Gui Han
Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development, defense, and symptom development. Here, 547 known miRNAs representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. A phylogenetic analysis was performed, and 8 Beta lineage-specific miRNAs were identified. Through a differential expression analysis, miRNAs associated with Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis and stem-loop RT-qPCR...
2017: PloS One
https://www.readbyqxmd.com/read/29035212/a-deep-cascade-of-convolutional-neural-networks-for-dynamic-mr-image-reconstruction
#16
Jo Schlemper, Jose Caballero, Joseph V Hajnal, Anthony Price, Daniel Rueckert
Inspired by recent advances in deep learning, we propose a framework for reconstructing dynamic sequences of 2D cardiac magnetic resonance (MR) images from undersampled data using a deep cascade of convolutional neural networks (CNNs) to accelerate the data acquisition process. In particular, we address the case where data is acquired using aggressive Cartesian undersampling. Firstly, we show that when each 2D image frame is reconstructed independently, the proposed method outperforms state-of-the-art 2D compressed sensing approaches such as dictionary learning-based MR image reconstruction, in terms of reconstruction error and reconstruction speed...
October 13, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/29034851/nitrosopumilus-maritimus-gen-nov-sp-nov-nitrosopumilus-cobalaminigenes-sp-nov-nitrosopumilus-oxyclinae-sp-nov-and-nitrosopumilus-ureiphilus-sp-nov-four-marine-ammonia-oxidizing-archaea-of-the-phylum-thaumarchaeota
#17
Wei Qin, Katherine R Heal, Rasika Ramdasi, Julia N Kobelt, Willm Martens-Habbena, Anthony D Bertagnolli, Shady A Amin, Christopher B Walker, Hidetoshi Urakawa, Martin Könneke, Allan H Devol, James W Moffett, E Virginia Armbrust, Grant J Jensen, Anitra E Ingalls, David A Stahl
Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1(T), HCA1(T), HCE1(T) and PS0(T), were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0(T) possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions...
October 16, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29034847/aurantimonas-aggregata-sp-nov-isolated-from-deep-sea-sediment
#18
An-Zhang Li, Long-Zhen Lin, Ming-Xia Zhang, Hong-Hui Zhu
A novel bacterium, designated R14M6(T), was isolated from deep-sea sediment collected from the Ross Sea, Antarctica. Cells are Gram-stain-negative, aerobic, pale yellow, short-rod-shaped, polar-flagellated and aggregate-forming. Growth occurs at 4-36 °C, pH 6.0-8.3, and in 1-15 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain R14M6(T) clustered together with Aurantimonas endophytica EGI6500337(T) and fell within the genus Aurantimonas. The 16S rRNA gene sequence of strain R14M6(T) shared similarity with A...
October 16, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29032347/vocalic-transitions-as-markers-of-speech-acoustic-changes-with-stn-dbs-in-parkinson-s-disease
#19
Vincent Martel-Sauvageau, Kris Tjaden
PURPOSE: Deep Brain Stimulation of the subthalamic nucleus (STN-DBS) effectively treats cardinal symptoms of idiopathic Parkinson's disease (PD) that cannot be satisfactorily managed with medication. Research is equivocal regarding speech changes associated with STN-DBS. This study investigated the impact of STN-DBS on vocalic transitions and the relationship to intelligibility. METHODS: Eight Quebec-French speakers with PD and eight healthy controls participated...
October 7, 2017: Journal of Communication Disorders
https://www.readbyqxmd.com/read/29032046/past-present-and-future-of-genetic-research-in-borderline-personality-disorder
#20
REVIEW
Anahita Bassir Nia, Matthew C Eveleth, Jonathan M Gabbay, Yonis J Hassan, Bosi Zhang, M Mercedes Perez-Rodriguez
Borderline Personality Disorder (BPD) is a major mental illness with a lifetime prevalence of approximately 1-3%, characterized by a persistent pattern of instability in relationships, mood, impulse regulation, and sense of self. This results in impulsive self-damaging behavior, high suicide rates, and severe functional impairment. BPD has a complex, multifactorial etiology, resulting from an interaction among genetic and environmental substrates, and has moderate to high heritability based on twin and family studies...
September 12, 2017: Current Opinion in Psychology
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