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https://www.readbyqxmd.com/read/28548128/genomic-profiling-of-breast-secretory-carcinomas-reveals-distinct-genetics-from-other-breast-cancers-and-similarity-to-mammary-analog-secretory-carcinomas
#1
Gregor Krings, Nancy M Joseph, Gregory R Bean, David Solomon, Courtney Onodera, Eric Talevich, Iwei Yeh, James P Grenert, Elizabeth Hosfield, Emily D Crawford, Richard C Jordan, Annemieke van Zante, Charles Zaloudek, Sandra J Shin, Yunn-Yi Chen
Secretory carcinomas of the breast are rare tumors with distinct histologic features, recurrent t(12;15)(p13;q25) translocation resulting in ETV6-NTRK3 gene fusion and indolent clinical behavior. Mammary analog secretory carcinomas arising in other sites are histopathologically similar to the breast tumors and also harbor ETV6-NTRK3 fusions. Breast secretory carcinomas are often triple (estrogen and progesterone receptor, HER2) negative with a basal-like immunophenotype. However, genomic studies are lacking, and whether these tumors share genetic features with other basal and/or triple negative breast cancers is unknown...
May 26, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28547909/identification-and-expression-of-conserved-and-novel-rna-variants-of-medaka-pax6b-gene
#2
Tiansheng Chen, Benzion Cavari, Manfred Schartl, Yunhan Hong
Gene duplication is a major driving force of evolution. How gene duplicates have evolved remains a mystery. A highly conserved gene such as Pax6 is an ideal model to study functional conservation and divergence via comparisons among diverse organisms. One pax6 gene has been characterized in the Japanese medaka (Oryzias latipes), which is annotated as pax6b on chromosome 3. Here, we report that Medaka pax6b is homolog to Pax6 of mammals in sequence, chromosomal synteny, and genomic organization. Cloning and sequencing led to the identification of up to 43 pax6b RNA variants predicting six protein isoforms, 22 of which are similar to those reported in other organisms and 21 represent novel RNA variants...
May 26, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28547583/genome-wide-identification-and-characterization-of-phospholipase-c-gene-family-in-cotton-gossypium-spp
#3
Bing Zhang, Yanmei Wang, Jin-Yuan Liu
Phospholipase C (PLC) are important regulatory enzymes involved in several lipid and Ca(2+)-dependent signaling pathways. Previous studies have elucidated the versatile roles of PLC genes in growth, development and stress responses of many plants, however, the systematic analyses of PLC genes in the important fiber-producing plant, cotton, are still deficient. In this study, through genome-wide survey, we identified twelve phosphatidylinositol-specific PLC (PI-PLC) and nine non-specific PLC (NPC) genes in the allotetraploid upland cotton Gossypium hirsutum and nine PI-PLC and six NPC genes in two diploid cotton G...
May 19, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28546386/assessment-of-gene-flow-between-gossypium-hirsutum-and-gossypium-herbaceum-evidence-of-unreduced-gametes-in-the-diploid-progenitor
#4
E Montes, O Coriton, F Eber, V Huteau, J M Lacape, C Reinhardt, D Marais, J L Hofs, A M Chèvre, C Pannetier
In the framework of a gene flow assessment, we investigated the natural hybridization rate between Gossypium hirsutum (AADD genome) and G. herbaceum (AA genome). The latter species, a diploid progenitor of G. hirsutum, is spontaneously present in South Africa. Reciprocal crosses were performed without emasculation between G. herbaceum and G. hirsutum Neither examination of the morphological characteristics nor flow cytometry analysis of the 335 plants resulting from the G. hirsutum x G. herbaceum cross showed any hybrid features...
May 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28546004/a-transfer-rna-gene-rearrangement-in-the-lepidopteran-mitochondrial-genome
#5
Qiu-Ning Liu, Zhao-Zhe Xin, Xiao-Yu Zhu, Xin-Yue Chai, Xiao-Ming Zhao, Chun-Lin Zhou, Bo-Ping Tang
Gene arrangements in the mitochondrial genomes (mitogenomes) of insects are conserved across the major lineages, but can be rearranged within derived groups and may provide valuable phylogenetic characters. In this study, we sequenced the entire mitogenome of Parasa consocia, a moth of the family Limacodidae (Lepidoptera: Zygaenoidea). Compared with other lepidopterans and ancestral insects, the P. consocia mitogenome features a transfer RNA gene arrangement novel among lepidopterans between the ND3 and ND5 genes: RANSEF (the underline signifies an inverted gene), which differs from the ARNSEF arrangement of ancestral insects...
May 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28544882/inference-and-evolutionary-analysis-of-genome-scale-regulatory-networks-in-large-phylogenies
#6
Christopher Koch, Jay Konieczka, Toni Delorey, Ana Lyons, Amanda Socha, Kathleen Davis, Sara A Knaack, Dawn Thompson, Erin K O'Shea, Aviv Regev, Sushmita Roy
Changes in transcriptional regulatory networks can significantly contribute to species evolution and adaptation. However, identification of genome-scale regulatory networks is an open challenge, especially in non-model organisms. Here, we introduce multi-species regulatory network learning (MRTLE), a computational approach that uses phylogenetic structure, sequence-specific motifs, and transcriptomic data, to infer the regulatory networks in different species. Using simulated data from known networks and transcriptomic data from six divergent yeasts, we demonstrate that MRTLE predicts networks with greater accuracy than existing methods because it incorporates phylogenetic information...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544683/comprehensive-genetic-study-of-cystic-fibrosis-in-slovak-patients-in-25-years-of-genetic-diagnostics
#7
Andrea Soltysova, Eva Tothova Tarova, Andrej Ficek, Marian Baldovic, Helena Polakova, Hana Kayserova, Ludevit Kadasi
INTRODUCTION: Cystic fibrosis (CF) has one of the longest histories in hereditary disease molecular diagnostics. However, identification of causative mutations in the CFTR gene is complicated by over two thousand currently identified mutations; with more still being discovered. Knowledge of mutation spectrum may improve effective routine diagnostics and is obligatory in mutation-specific treatment. OBJECTIVES: This study presents comprehensive mutation screening of the CFTR gene; with 275 unrelated, clinically confirmed and treated cystic fibrosis (CF) patients diagnosed in 25 years genetic testing in Slovakia...
May 20, 2017: Clinical Respiratory Journal
https://www.readbyqxmd.com/read/28544607/spotted-gar-and-the-evolution-of-innate-immune-receptors
#8
Dustin J Wcisel, Tatsuya Ota, Gary W Litman, Jeffrey A Yoder
The resolution of the gar genome affords an opportunity to examine the diversification and functional specialization of immune effector molecules at a distant and potentially informative point in phylogenetic development. Although innate immunity is effected by a particularly large number of different families of molecules, the focus here is to provide detailed characterization of several families of innate receptors that are encoded in large multigene families, for which orthologous forms can be identified in other species of bony fish but not in other vertebrate groups as well as those for which orthologs are present in other vertebrate species...
May 24, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28544363/expression-patterns-of-sterol-transporters-npc1-and-npc2-in-the-cnidarian-dinoflagellate-symbiosis
#9
Vincent Dani, Fabrice Priouzeau, Marjolijn Mertz, Magali Mondin, Sophie Pagnotta, Sandra Lacas-Gervais, Simon K Davy, Cécile Sabourault
The symbiotic interaction between cnidarians (e.g. corals and sea anemones) and photosynthetic dinoflagellates of the genus Symbiodinium is triggered by both host-symbiont recognition processes and metabolic exchange between the two partners. The molecular communication is crucial for homeostatic regulation of the symbiosis, both under normal conditions and during stresses that further lead to symbiosis collapse. It is therefore important to identify and fully characterize the key players of this intimate interaction at the symbiotic interface...
May 22, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28542515/a-novel-frameshift-mutation-of-smpx-causes-a-rare-form-of-x-linked-nonsyndromic-hearing-loss-in-a-chinese-family
#10
Zhijie Niu, Yong Feng, Lingyun Mei, Jie Sun, Xueping Wang, Juncheng Wang, Zhengmao Hu, Yunpeng Dong, Hongsheng Chen, Chufeng He, Yalan Liu, Xinzhang Cai, Xuezhong Liu, Lu Jiang
X-linked hearing impairment is the rarest form of genetic hearing loss (HL) and represents only a minor fraction of all cases. The aim of this study was to investigate the cause of X-linked inherited sensorineural HL in a four-generation Chinese family. A novel duplication variant (c.217dupA, p.Ile73Asnfs*5) in SMPX was identified by whole-exome sequencing. The frameshift mutation predicted to result in the premature truncation of the SMPX protein was co-segregated with the HL phenotype and was absent in 295 normal controls...
2017: PloS One
https://www.readbyqxmd.com/read/28542513/structural-features-of-phox-one-of-the-phosphate-binding-proteins-from-pho-regulon-of-xanthomonas-citri
#11
Vanessa R Pegos, Rodrigo M L Santos, Francisco J Medrano, Andrea Balan
In Escherichia coli, the ATP-Binding Cassette transporter for phosphate is encoded by the pstSCAB operon. PstS is the periplasmic component responsible for affinity and specificity of the system and has also been related to a regulatory role and chemotaxis during depletion of phosphate. Xanthomonas citri has two phosphate-binding proteins: PstS and PhoX, which are differentially expressed under phosphate limitation. In this work, we focused on PhoX characterization and comparison with PstS. The PhoX three-dimensional structure was solved in a closed conformation with a phosphate engulfed in the binding site pocket between two domains...
2017: PloS One
https://www.readbyqxmd.com/read/28542282/expression-patterns-of-members-of-the-ethylene-signaling-related-gene-families-in-response-to-dehydration-stresses-in-cassava
#12
Meng Yun Ren, Ren Jun Feng, Hou Rui Shi, Li Fang Lu, Tian Yan Yun, Ming Peng, Xiao Guan, Heng Zhang, Jing Yi Wang, Xi Yan Zhang, Cheng Liang Li, Yan Jun Chen, Peng He, Yin Dong Zhang, Jiang Hui Xie
Drought is the one of the most important environment stresses that restricts crop yield worldwide. Cassava (Manihot esculenta Crantz) is an important food and energy crop that has many desirable traits such as drought, heat and low nutrients tolerance. However, the mechanisms underlying drought tolerance in cassava are unclear. Ethylene signaling pathway, from the upstream receptors to the downstream transcription factors, plays important roles in environmental stress responses during plant growth and development...
2017: PloS One
https://www.readbyqxmd.com/read/28541905/inferring-gene-species-assignments-in-the-presence-of-horizontal-gene-transfer
#13
Agnieszka Mykowiecka, Pawel Szczesny, Pawel Gorecki
BACKGROUND: Microbial communities from environmental samples show great diversity as bacteria quickly response to changes in their ecosystems. To assess the scenario of the actual changes, metagenomics experiments aimed at sequencing genomic DNA from such samples are performed. These new obtained sequences together with already known are used to infer phylogenetic trees assessing the taxonomic groups the species with these genes belong to. Here we propose the first approach to the gene-species assignment problem by using reconciliation with horizontal gene transfer...
May 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28541576/rapidly-evolving-toll-3-4-genes-encode-male-specific-toll-like-receptors-in-drosophila
#14
Tera C Levin, Harmit S Malik
Animal Toll-like receptors (TLRs) have evolved through a pattern of duplication and divergence. Whereas mammalian TLRs directly recognize microbial ligands, Drosophila Tolls bind endogenous ligands downstream of both developmental and immune signaling cascades. Here, we find that most Toll genes in Drosophila evolve slowly with little gene turnover (gains/losses), consistent with their important roles in development and indirect roles in microbial recognition. In contrast, we find that the Toll-3/4 genes have experienced an unusually rapid rate of gene gains and losses, resulting in lineage-specific Toll-3/4s and vastly different gene repertoires among Drosophila species, from zero copies (e...
May 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28541223/efficient-algorithms-for-genomic-duplication-models
#15
Jaroslaw Paszek, Pawel Gorecki
An important issue in evolutionary molecular biology is to discover genomic duplication episodes and their correspondence to the species tree. Existing approaches vary in the two fundamental aspects: the choice of evolutionary scenarios that model allowed locations of duplications in the species tree, and the rules of clustering gene duplications from gene trees into a single multiple duplication event. Here we study the method of clustering called minimum episodes for several models of allowed evolutionary scenarios with a focus on interval models in which every gene duplication has an interval consisting of allowed locations in the species tree...
May 23, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28540588/proteomic-analysis-of-the-phycobiliprotein-antenna-of-the-cryptophyte-alga-guillardia-theta-cultured-under-different-light-intensities
#16
Thomas Kieselbach, Otilia Cheregi, Beverley R Green, Christiane Funk
Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active α1β·α2β-tetramer...
May 24, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28539927/a-comprehensive-analysis-of-alternative-splicing-in-paleopolyploid-maize
#17
Wenbin Mei, Sanzhen Liu, James C Schnable, Cheng-Ting Yeh, Nathan M Springer, Patrick S Schnable, William B Barbazuk
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28539513/evidence-for-parallel-evolution-of-a-gene-involved-in-the-regulation-of-spermatogenesis
#18
Xin Rui Wang, Li Bin Ling, Hsiao Han Huang, Jau Jyun Lin, Sebastian D Fugmann, Shu Yuan Yang
PHD finger protein 7 (Phf7) is a male germline specific gene in Drosophila melanogaster that can trigger the male germline sexual fate and regulate spermatogenesis, and its human homologue can rescue fecundity defects in male flies lacking this gene. These findings prompted us to investigate conservation of reproductive strategies through studying the evolutionary origin of this gene. We find that Phf7 is present only in select species including mammals and some insects, whereas the closely related G2/M-phase specific E3 ubiquitin protein ligase (G2e3) is in the genome of most metazoans...
May 31, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28538869/potential-mechanisms-linking-probiotics-to-diabetes-a-narrative-review-of-the-literature
#19
Maryam Miraghajani, Somayeh Shahraki Dehsoukhteh, Nahid Rafie, Sahar Golpour Hamedani, Sima Sabihi, Reza Ghiasvand
CONTEXT AND OBJECTIVE: Some studies have suggested a wide range of possible mechanisms through which probiotics may play a role in diabetes prevention and treatment. However, the underlying mechanisms are not fully understood. We conducted this study to review the potential mechanisms suggested for the effect of probiotics in diabetes. DESIGN AND SETTING: Narrative review conducted at the Food Security Research Center of Isfahan. METHODS: A search in the electronic databases MEDLINE (PubMed), Cochrane Library, Web of Science and Google scholar was performed up to October 2016...
March 2017: São Paulo Medical Journal, Revista Paulista de Medicina
https://www.readbyqxmd.com/read/28538728/the-sunflower-genome-provides-insights-into-oil-metabolism-flowering-and-asterid-evolution
#20
Hélène Badouin, Jérôme Gouzy, Christopher J Grassa, Florent Murat, S Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory L Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill, Nolan C Kane, John E Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile Donnadieu, Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven J Knapp, Zhao Lai, Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer R Mandel, Gwenola Marage, Gwenaëlle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savithri Nambeesan, Thuy Nguyen, Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas, Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John M Burke, Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren H Rieseberg, Nicolas B Langlade
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs...
May 22, 2017: Nature
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