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https://www.readbyqxmd.com/read/27923066/somatic-genomics-and-clinical-features-of-lung-adenocarcinoma-a-retrospective-study
#1
Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J Bouk, Joseph Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal Marconett, Ite Laird-Offringa, Ian Mills, Neil E Caporaso, Mitchell H Gail, Angela C Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J Chanock, Maria Teresa Landi
BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27918537/the-genome-and-transcriptome-of-japanese-flounder-provide-insights-into-flatfish-asymmetry
#2
Changwei Shao, Baolong Bao, Zhiyuan Xie, Xinye Chen, Bo Li, Xiaodong Jia, Qiulin Yao, Guillermo Ortí, Wenhui Li, Xihong Li, Kristin Hamre, Juan Xu, Lei Wang, Fangyuan Chen, Yongsheng Tian, Alex M Schreiber, Na Wang, Fen Wei, Jilin Zhang, Zhongdian Dong, Lei Gao, Junwei Gai, Takashi Sakamoto, Sudong Mo, Wenjun Chen, Qiong Shi, Hui Li, Yunji Xiu, Yangzhen Li, Wenteng Xu, Zhiyi Shi, Guojie Zhang, Deborah M Power, Qingyin Wang, Manfred Schartl, Songlin Chen
Flatfish have the most extreme asymmetric body morphology of vertebrates. During metamorphosis, one eye migrates to the contralateral side of the skull, and this migration is accompanied by extensive craniofacial transformations and simultaneous development of lopsided body pigmentation. The evolution of this developmental and physiological innovation remains enigmatic. Comparative genomics of two flatfish and transcriptomic analyses during metamorphosis point to a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways...
December 5, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27911943/enhanced-in-planta-fitness-through-adaptive-mutations-in-efpr-a-dual-regulator-of-virulence-and-metabolic-functions-in-the-plant-pathogen-ralstonia-solanacearum
#3
Anthony Perrier, Rémi Peyraud, David Rengel, Xavier Barlet, Emmanuel Lucasson, Jérôme Gouzy, Nemo Peeters, Stéphane Genin, Alice Guidot
Experimental evolution of the plant pathogen Ralstonia solanacearum, where bacteria were maintained on plant lineages for more than 300 generations, revealed that several independent single mutations in the efpR gene from populations propagated on beans were associated with fitness gain on bean. In the present work, novel allelic efpR variants were isolated from populations propagated on other plant species, thus suggesting that mutations in efpR were not solely associated to a fitness gain on bean, but also on additional hosts...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27911816/rapid-emergence-and-mechanisms-of-resistance-by-u87-glioblastoma-cells-to-doxorubicin-in-an-in-vitro-tumor-microfluidic-ecology
#4
Jeonghun Han, Yukyung Jun, So Hyun Kim, Hong-Hoa Hoang, Yeonjoo Jung, Suyeon Kim, Jaesang Kim, Robert H Austin, Sanghyuk Lee, Sungsu Park
In vitro prediction of the probable rapid emergence of resistance to a drug in tumors could act to winnow out potential candidates for further costly development. We have developed a microfluidic device consisting of ∼500 hexagonal microcompartments that provides a complex ecology with wide ranges of drug and nutrient gradients and local populations. This ecology of a fragmented metapopulation induced the drug resistance in stage IV U87 glioblastoma cells to doxorubicin in 7 d. Exome and transcriptome sequencing of the resistant cells identified mutations and differentially expressed genes...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911792/transcriptomics-and-neuroanatomy-of-the-clonal-raider-ant-implicate-an-expanded-clade-of-odorant-receptors-in-chemical-communication
#5
Sean K McKenzie, Ingrid Fetter-Pruneda, Vanessa Ruta, Daniel J C Kronauer
A major aim of sociogenomic research is to uncover common principles in the molecular evolution of sociality. This endeavor has been hampered by the small number of specific genes currently known to function in social behavior. Here we provide several lines of evidence suggesting that ants have evolved a large and novel clade of odorant receptor (OR) genes to perceive hydrocarbon-based pheromones, arguably the most important signals in ant communication. This genomic expansion is also mirrored in the ant brain via a corresponding expansion of a specific cluster of glomeruli in the antennal lobe...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27905446/genomic-evolution-and-chemoresistance-in-germ-cell-tumours
#6
Amaro Taylor-Weiner, Travis Zack, Elizabeth O'Donnell, Jennifer L Guerriero, Brandon Bernard, Anita Reddy, G Celine Han, Saud AlDubayan, Ali Amin-Mansour, Steven E Schumacher, Kevin Litchfield, Clare Turnbull, Stacey Gabriel, Rameen Beroukhim, Gad Getz, Scott L Carter, Michelle S Hirsch, Anthony Letai, Christopher Sweeney, Eliezer M Van Allen
Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27903126/potential-evolution-of-neurosurgical-treatment-paradigms-for-craniopharyngioma-based-on-genomic-and-transcriptomic-characteristics
#7
Leslie C Robinson, Sandro Santagata, Todd C Hankinson
The recent genomic and transcriptomic characterization of human craniopharyngiomas has provided important insights into the pathogenesis of these tumors and supports that these tumor types are distinct entities. Critically, the insights provided by these data offer the potential for the introduction of novel therapies and surgical treatment paradigms for these tumors, which are associated with high morbidity rates and morbid conditions. Mutations in the CTNNB1 gene are primary drivers of adamantinomatous craniopharyngioma (ACP) and lead to the accumulation of β-catenin protein in a subset of the nuclei within the neoplastic epithelium of these tumors...
December 2016: Neurosurgical Focus
https://www.readbyqxmd.com/read/27886141/comprehensive-transcriptome-analysis-provides-evidence-of-local-thermal-adaptation-in-three-loaches-genus-misgurnus
#8
Shaokui Yi, Sai Wang, Jia Zhong, Weimin Wang
The geographic distribution of three Misgurnus species, M. anguillicaudatus, M. bipartitus, and M. mohoity, displays a specific pattern in China, coincident with temperature zones. In this study, we sequenced the transcriptomes of these three species and used the sequences to investigate the lineage-specific adaptations within the genus Misgurnus. In total, 51 orphan genes (19 in M. anguillicaudatus, 18 in M. bipartitus, and 14 in M. mohoity) that may contribute to the species-specific adaptations were identified...
November 24, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27883053/measuring-intratumor-heterogeneity-by-network-entropy-using-rna-seq-data
#9
Youngjune Park, Sangsoo Lim, Jin-Wu Nam, Sun Kim
Intratumor heterogeneity (ITH) is observed at different stages of tumor progression, metastasis and reouccurence, which can be important for clinical applications. We used RNA-sequencing data from tumor samples, and measured the level of ITH in terms of biological network states. To model complex relationships among genes, we used a protein interaction network to consider gene-gene dependency. ITH was measured by using an entropy-based distance metric between two networks, nJSD, with Jensen-Shannon Divergence (JSD)...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27880757/redefining-the-invertebrate-rna-virosphere
#10
Mang Shi, Xian-Dan Lin, Jun-Hua Tian, Liang-Jun Chen, Xiao Chen, Ci-Xiu Li, Xin-Cheng Qin, Jun Li, Jian-Ping Cao, John-Sebastian Eden, Jan Buchmann, Wen Wang, Jianguo Xu, Edward C Holmes, Yong-Zhen Zhang
Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence...
November 23, 2016: Nature
https://www.readbyqxmd.com/read/27876851/the-genome-transcriptome-and-proteome-of-the-nematode-steinernema-carpocapsae-evolutionary-signatures-of-a-pathogenic-lifestyle
#11
Alejandra Rougon-Cardoso, Mitzi Flores-Ponce, Hilda Eréndira Ramos-Aboites, Christian Eduardo Martínez-Guerrero, You-Jin Hao, Luis Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu-Goodger, Norberto Chavarría-Hernández, Nelson Simões, Rafael Montiel
The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode's genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27875998/transcriptome-profiling-and-comparison-of-maize-ear-heterosis-during-the-spikelet-and-floret-differentiation-stages
#12
Xiaojiao Hu, Hongwu Wang, Xizhou Diao, Zhifang Liu, Kun Li, Yujin Wu, Qianjin Liang, Hui Wang, Changling Huang
BACKGROUND: Hybridization is a prominent process in the evolution of crop plants that can give rise to gene expression variation, phenotypic novelty and heterosis. Maize is the most successful crop in utilizing heterosis. The development of hybrid maize ears exhibits strong heterotic vigor and greatly affects maize yield. However, a comprehensive perspective on transcriptional variation and its correlation with heterosis during maize ear development is not available. RESULTS: Using RNA sequencing technology, we investigated the transcriptome profiles of maize ears in the spikelet and floret differentiation stages of hybrid ZD808 and its parents CL11 and NG5...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27871139/glycerol-stress-in-saccharomyces-cerevisiae-cellular-responses-and-evolved-adaptations
#13
Florian Mattenberger, Beatriz Sabater-Muñoz, John E Hallsworth, Mario A Fares
Glycerol synthesis is key to central metabolism and stress biology in Saccharomyces cerevisiae, yet the cellular adjustments needed to respond and adapt to glycerol stress are little understood. Here, we determined impacts of acute and chronic exposures to glycerol stress in S. cerevisiae. Glycerol stress can result from an increase of glycerol concentration in the medium due to the S. cerevisiae fermenting activity or other yeast metabolic activities. Acute glycerol-stress led to a 50% decline in growth rate and altered transcription of more than 40% of genes...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27867198/probing-the-evolution-ecology-and-physiology-of-marine-protists-using-transcriptomics
#14
David A Caron, Harriet Alexander, Andrew E Allen, John M Archibald, E Virginia Armbrust, Charles Bachy, Callum J Bell, Arvind Bharti, Sonya T Dyhrman, Stephanie M Guida, Karla B Heidelberg, Jonathan Z Kaye, Julia Metzner, Sarah R Smith, Alexandra Z Worden
Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of cultured species, complemented by meta-omics analyses of natural communities, have increased the amount of genetic information available for poorly represented branches on the tree of eukaryotic life. This information is providing insights into the adaptations and interactions between protists and other microorganisms and macroorganisms, but many of the genes sequenced show no similarity to sequences currently available in public databases...
November 21, 2016: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/27866097/current-therapy-and-the-evolving-molecular-landscape-of-paediatric-ependymoma
#15
REVIEW
Soumen Khatua, Vijay Ramaswamy, Eric Bouffet
Ependymomas are the third commonest paediatric central nervous system (CNS) tumour, accounting for 6-12% of brain tumours in children. The management of these tumours has seen considerable changes over the last two decades, leading to a significant improvement in outcomes. However, despite advances in neurosurgical, neuroimaging and postoperative adjuvant therapy, management of these tumours remain challenging, and recurrence occurs in over 50% of cases, particularly when complete resection is not achieved prior to conformal radiotherapy...
November 17, 2016: European Journal of Cancer
https://www.readbyqxmd.com/read/27865053/neural-progenitor-cells-and-their-role-in-the-development-and-evolutionary-expansion-of-the-neocortex
#16
REVIEW
Takashi Namba, Wieland B Huttner
The evolutionary expansion of the mammalian brain, notably the neocortex, provides a platform for the higher cognitive abilities that characterize humans. Cortical expansion is accompanied by increased folding of the pial surface, which gives rise to a gyrencephalic (folded) rather than lissencephalic (unfolded) neocortex. This expansion reflects the prolonged and increased proliferation of neural stem and progenitor cells (NPCs). Distinct classes of NPCs can be distinguished based on either cell biological criteria (apical progenitors [APs], basal progenitors [BPs]) or lineage (primary progenitors and secondary progenitors)...
November 16, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27862511/sperm-competition-shapes-gene-expression-and-sequence-evolution-in-the-ocellated-wrasse
#17
Rebecca Dean, Alison E Wright, Susan E Marsh-Rollo, Bridget M Nugent, Suzanne H Alonzo, Judith E Mank
Gene expression differences between males and females often underlie sexually dimorphic phenotypes and the expression levels of genes that are differentially expressed between the sexes is thought to respond to sexual selection. Most studies on the transcriptomic response to sexual selection treat sexual selection as a single force, but post-mating sexual selection in particular is expected to specifically target gonadal tissue. The three male morphs of the ocellated wrasse (Symphodus ocellatus) make it possible to test the role of post-mating sexual selection in shaping the gonadal transcriptome...
November 14, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27859288/exploring-key-cellular-processes-and-candidate-genes-regulating-the-primary-thickening-growth-of-moso-underground-shoots
#18
Qiang Wei, Chen Jiao, Lin Guo, Yulong Ding, Junjie Cao, Jianyuan Feng, Xiaobo Dong, Linyong Mao, Honghe Sun, Fen Yu, Guangyao Yang, Peijian Shi, Guodong Ren, Zhangjun Fei
The primary thickening growth of Moso (Phyllostachys edulis) underground shoots largely determines the culm circumference. However, its developmental mechanisms remain largely unknown. Using an integrated anatomy, mathematics and genomics approach, we systematically studied cellular and molecular mechanisms underlying the growth of Moso underground shoots. We discovered that the growth displayed a spiral pattern and pith played an important role in promoting the primary thickening process of Moso underground shoots and driving the evolution of culms with different sizes among different bamboo species...
November 12, 2016: New Phytologist
https://www.readbyqxmd.com/read/27856652/evolution-of-rosaceae-fruit-types-based-on-nuclear-phylogeny-in-the-context-of-geological-times-and-genome-duplication
#19
Yezi Xiang, Chien-Hsun Huang, Yi Hu, Jun Wen, Shisheng Li, Tingshuang Yi, Hongyi Chen, Jun Xiang, Hong Ma
Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ~3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution...
November 17, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27855630/structural-differences-and-differential-expression-among-rhabdomeric-opsins-reveal-functional-change-after-gene-duplication-in-the-bay-scallop-argopecten-irradians-pectinidae
#20
Anita J Porath-Krause, Autum N Pairett, Davide Faggionato, Bhagyashree S Birla, Kannan Sankar, Jeanne M Serb
BACKGROUND: Opsins are the only class of proteins used for light perception in image-forming eyes. Gene duplication and subsequent functional divergence of opsins have played an important role in expanding photoreceptive capabilities of organisms by altering what wavelengths of light are absorbed by photoreceptors (spectral tuning). However, new opsin copies may also acquire novel function or subdivide ancestral functions through changes to temporal, spatial or the level of gene expression...
November 17, 2016: BMC Evolutionary Biology
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