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Chromosome homology search

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https://www.readbyqxmd.com/read/27902773/genomic-landscape-of-experimental-bladder-cancer-in-rodents-and-its-application-to-human-bladder-cancer-gene-amplification-and-potential-overexpression-of-cyp2a5-cyp2a6-are-associated-with-the-invasive-phenotype
#1
Kazuhiro Kanemoto, Katsuhiro Fukuta, Noriyasu Kawai, Keiichi Tozawa, Masako Ochiai, Koji Okamoto, Sumiko Ohnami, Hiromi Sakamoto, Teruhiko Yoshida, Yae Kanai, Masaru Katoh, Takahiro Yasui, Kenjiro Kohri, Tadao Kakizoe, Hitoshi Nakagama
Non-muscle invasive (superficial) bladder cancer is a low-grade malignancy with good prognosis, while muscle invasive (invasive) bladder cancer is a high-grade malignancy with poor prognosis. N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) induces superficial bladder cancers with papillary morphology in rats and invasive bladder cancers with infiltrating phenotype in mice. In this study, we analyzed genomic landscapes of rodent BBN-induced bladder cancers using array-based comparative genomic hybridization (array CGH)...
2016: PloS One
https://www.readbyqxmd.com/read/27900493/mining-the-cicer-arietinum-genome-for-the-mildew-locus-o-mlo-gene-family-and-comparative-evolutionary-analysis-of-the-mlo-genes-from-medicago-truncatula-and-some-other-plant-species
#2
Reena Deshmukh, V K Singh, Brahma Deo Singh
The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn...
November 30, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27892792/e2fl1-is-a-meiosis-specific-transcription-factor-in-the-protist-tetrahymena-thermophila
#3
Jing Zhang, Miao Tian, Guan-Xiong Yan, Anura Shodhan, Wei Miao
Members of the E2F family of transcription factors have been reported to regulate the expression of genes involved in cell cycle control, DNA replication, and DNA repair in multicellular eukaryotes. Here, E2FL1, a meiosis-specific E2F transcription factor gene, was identified in the model ciliate Tetrahymena thermophila. Loss of this gene resulted in meiotic arrest prior to anaphase I. The cytological experiments revealed that the meiotic homologous pairing was not affected in the absence of E2FL1, but the paired homologous chromosomes did not separate and assumed a peculiar tandem arrangement...
November 28, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27833625/dart-markers-effectively-target-gene-space-in-the-rye-genome
#4
Piotr Gawroński, Magdalena Pawełkowicz, Katarzyna Tofil, Grzegorz Uszyński, Saida Sharifova, Shivaksh Ahluwalia, Mirosław Tyrka, Maria Wędzony, Andrzej Kilian, Hanna Bolibok-Brągoszewska
Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27831816/genome-wide-analysis-of-the-dna-binding-with-one-zinc-finger-dof-transcription-factor-family-in-bananas
#5
Chen Dong, Huigang Hu, Jianghui Xie
DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. In this study, we report a genome-wide search for Musa acuminata Dof (MaDof) genes and their expression profiles at different developmental stages and in response to various abiotic stresses. In addition, a complete overview of the Dof gene family in bananas is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences...
September 14, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27818673/identification-of-nitrogen-use-efficiency-genes-in-barley-searching-for-qtls-controlling-complex-physiological-traits
#6
Mei Han, Julia Wong, Tao Su, Perrin H Beatty, Allen G Good
Over the past half century, the use of nitrogen (N) fertilizers has markedly increased crop yields, but with considerable negative effects on the environment and human health. Consequently, there has been a strong push to reduce the amount of N fertilizer used by maximizing the nitrogen use efficiency (NUE) of crops. One approach would be to use classical genetics to improve the NUE of a crop plant. This involves both conventional breeding and quantitative trait loci (QTL) mapping in combination with marker-assisted selection (MAS) to track key regions of the chromosome that segregate for NUE...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27811955/cytological-basis-of-sterility-in-male-and-female-hybrids-between-sibling-species-of-grey-voles-microtus-arvalis-and-m-levis
#7
Anna A Torgasheva, Pavel M Borodin
To make insight into the cytological basis of reproductive isolation, we examined chromosome synapsis and recombination in sterile male and female hybrids between Microtus arvalis and M. levis. These sibling species differ by a series of chromosomal rearrangements (fusions, inversions, centromere shifts and heterochromatin insertions). We found that meiosis in male hybrids was arrested at leptotene with complete failure of chromosome pairing and DNA double-strand breaks repair. In the female hybrids meiosis proceeded to pachytene; however, the oocytes varied in the degree of pairing errors...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27791086/chromosome-refolding-model-of-mating-type-switching-in-yeast
#8
Barış Avşaroğlu, Gabriel Bronk, Kevin Li, James E Haber, Jane Kondev
Chromosomes are folded into cells in a nonrandom fashion, with particular genetic loci occupying distinct spatial regions. This observation raises the question of whether the spatial organization of a chromosome governs its functions, such as recombination or transcription. We consider this general question in the specific context of mating-type switching in budding yeast, which is a model system for homologous recombination. Mating-type switching is induced by a DNA double-strand break (DSB) at the MAT locus on chromosome III, followed by homologous recombination between the cut MAT locus and one of two donor loci (HMLα and HMRa), located on the same chromosome...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27790846/identifying-homomorphic-sex-chromosomes-from-wild-caught-adults-with-limited-genomic-resources
#9
Alan Brelsford, Guillaume Lavanchy, Roberto Sermier, Anna Rausch, Nicolas Perrin
We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on non-invasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered dataset (411,446 RADtags) was more successful than searches from a filtered dataset (33,073 RADtags) for markers showing sex differences in heterozygosity or in allele frequencies...
October 28, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27788356/hypothesis-homologous-recombination-depends-on-parallel-search
#10
Johan Elf
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose a solution based on freely diffusing molecules that are programmed with sequences corresponding to those flanking the break site. In such a process, the target search would be parallelized.
October 26, 2016: Cell Systems
https://www.readbyqxmd.com/read/27768699/multiple-pairwise-analysis-of-non-homologous-centromere-coupling-reveals-preferential-chromosome-size-dependent-interactions-and-a-role-for-bouquet-formation-in-establishing-the-interaction-pattern
#11
Philippe Lefrançois, Beth Rockmill, Pingxing Xie, G Shirleen Roeder, Michael Snyder
During meiosis, chromosomes undergo a homology search in order to locate their homolog to form stable pairs and exchange genetic material. Early in prophase, chromosomes associate in mostly non-homologous pairs, tethered only at their centromeres. This phenomenon, conserved through higher eukaryotes, is termed centromere coupling in budding yeast. Both initiation of recombination and the presence of homologs are dispensable for centromere coupling (occurring in spo11 mutants and haploids induced to undergo meiosis) but the presence of the synaptonemal complex (SC) protein Zip1 is required...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27733861/genome-wide-analysis-and-expression-profiling-of-the-suc-and-sweet-gene-families-of-sucrose-transporters-in-oilseed-rape-brassica-napus-l
#12
Hongju Jian, Kun Lu, Bo Yang, Tengyue Wang, Li Zhang, Aoxiang Zhang, Jia Wang, Liezhao Liu, Cunmin Qu, Jiana Li
Sucrose is the principal transported product of photosynthesis from source leaves to sink organs. SUTs/SUCs (sucrose transporters or sucrose carriers) and SWEETs (Sugars Will Eventually be Exported Transporters) play significant central roles in phloem loading and unloading. SUTs/SUCs and SWEETs are key players in sucrose translocation and are associated with crop yields. The SUT/SUC and SWEET genes have been characterized in several plant species, but a comprehensive analysis of these two gene families in oilseed rape has not yet been reported...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27672335/the-association-of-pten-hypermethylation-and-breast-cancer-a-meta-analysis
#13
Shanshan Luo, Jiansi Chen, Xianwei Mo
OBJECTIVE: Phosphatase and tensin homolog (PTEN) deleted on chromosome 10, as a tumor suppressor gene, is crucial for the development of both familial and sporadic breast cancer (BC). The aim of this study was to perform a meta-analysis to evaluate the clinicopathological significance of PTEN promoter hypermethylation in BC. METHODS: A comprehensive literature search was made in PubMed, Embase, Google Scholar, Chinese database (China National Knowledge Infrastructure [CNKI]), and Web of Science...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27667292/runx1-truncation-resulting-from-a-cryptic-and-novel-t-6-21-q25-q22-chromosome-translocation-in-acute-myeloid-leukemia-a-case-report
#14
Ioannis Panagopoulos, Synne Torkildsen, Ludmila Gorunova, Aina Ulvmoen, Anne Tierens, Bernward Zeller, Sverre Heim
Fluorescence in situ hybridization examination of a pediatric AML patient whose bone marrow cells carried trisomy 4 and FLT3-ITD mutation, demonstrated that part of the RUNX1 probe had unexpectedly moved to chromosome band 6q25 indicating a cryptic t(6;21)(q25;q22) translocation. RNA sequencing showed fusion of exon 7 of RUNX1 with an intergenic sequence of 6q25 close to the MIR1202 locus, something that was verified by RT-PCR together with Sanger sequencing. The RUNX1 fusion transcript encodes a truncated protein containing the Runt homology domain responsible for both heterodimerization with CBFB and DNA binding, but lacking the proline-, serine-, and threonine-rich (PST) region which is the transcription activation domain at the C terminal end...
September 22, 2016: Oncology Reports
https://www.readbyqxmd.com/read/27549916/genome-wide-identification-phylogeny-and-expressional-profiles-of-mitogen-activated-protein-kinase-kinase-kinase-mapkkk-gene-family-in-bread-wheat-triticum-aestivum-l
#15
Meng Wang, Hong Yue, Kewei Feng, Pingchuan Deng, Weining Song, Xiaojun Nie
BACKGROUND: Mitogen-activated protein kinase kinase kinases (MAPKKKs) are the important components of MAPK cascades, which play the crucial role in plant growth and development as well as in response to diverse stresses. Although this family has been systematically studied in many plant species, little is known about MAPKKK genes in wheat (Triticum aestivum L.), especially those involved in the regulatory network of stress processes. RESULTS: In this study, we identified 155 wheat MAPKKK genes through a genome-wide search method based on the latest available wheat genome information, of which 29 belonged to MEKK, 11 to ZIK and 115 to Raf subfamily, respectively...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27519956/unique-clustering-genes-in-the-bacterial-chromosome-affecting-the-type-iii-secretion-of-enterohaemorrhagic-escherichia-coli
#16
I-Ting Lin, Yi-Ming Chiou, Yen-Chia Liang, Ching-Nan Lin, Wei-Sheng W Sun, Shiaowen Li, Chuan-Hsiung Chang, Wan-Jr Syu, Jenn-Wei Chen
Bioinformatics analysis was used to search for unknown genes that might influence the phenotypic presentations of enterohaemorrhagic Escherichia coli (EHEC). By so doing and using the known genomic data from EHEC O157  : H7 and K-12, it has been deduced that genes Z4863 to Z4866 of EHEC do not exist in K-12 strains. These four gene sequences have low degrees of homology (18-40 % amino acid identities) to a set of genes in K-12, which have been known to encode fatty acid biosynthesis enzymes. We referred these four consecutive genes as a fasyn cluster and found that deletion of fasyn from EHEC resulted in a defective type-III secretion (T3S)...
October 2016: Microbiology
https://www.readbyqxmd.com/read/27506936/pten-expression-is-a-prognostic-marker-for-patients-with-non-small-cell-lung-cancer-a-systematic-review-and-meta-analysis-of-the-literature
#17
Jian Xiao, Cheng-Ping Hu, Bi-Xiu He, Xi Chen, Xiao-Xiao Lu, Ming-Xuan Xie, Wei Li, Shu-Ya He, Shao-Jin You, Qiong Chen
Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a known tumor suppressor in non-small cell lung cancer (NSCLC). By performing a systematic review and meta-analysis of the literature, we determined the prognostic value of decreased PTEN expression in patients with NSCLC. We comprehensively and systematically searched through multiple online databases up to May 22, 2016 for NSCLC studies reporting on PTEN expression and patient survival outcome. Several criteria, including the Newcastle-Ottawa Quality Assessment Scale (NOS), were used to discriminate between studies...
August 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27491801/in-vivo-imaging-of-dna-double-strand-break-induced-telomere-mobility-during-alternative-lengthening-of-telomeres
#18
Nam Woo Cho, Michael A Lampson, Roger A Greenberg
Repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) requires mobilization of chromatin for homology searches that allow interaction of the sequence to be repaired and its template DNA. Here we describe a system to rapidly induce DSBs at telomeres and track their movement, as well as a semi-automated workflow for quantitative analysis. We have successfully used this approach to show that DSBs targeted to telomeres in cells utilizing the alternative lengthening of telomeres (ALT) mechanism increase their diffusion and subsequent long-range directional movement to merge with telomeres on other chromosomes...
August 1, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27488242/first-genetic-linkage-map-of-taraxacum-koksaghyz-rodin-based-on-aflp-ssr-cos-and-est-ssr-markers
#19
Marina Arias, Monica Hernandez, Naroa Remondegui, Koen Huvenaars, Peter van Dijk, Enrique Ritter
Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27473680/genome-wide-identification-and-expression-analysis-of-sulfate-transporter-sultr-genes-in-potato-solanum-tuberosum-l
#20
Recep Vatansever, Ibrahim Koc, Ibrahim Ilker Ozyigit, Ugur Sen, Mehmet Emin Uras, Naser A Anjum, Eduarda Pereira, Ertugrul Filiz
Solanum tuberosum genome analysis revealed 12 StSULTR genes encoding 18 transcripts. Among genes annotated at group level ( StSULTR I-IV), group III members formed the largest SULTRs-cluster and were potentially involved in biotic/abiotic stress responses via various regulatory factors, and stress and signaling proteins. Employing bioinformatics tools, this study performed genome-wide identification and expression analysis of SULTR (StSULTR) genes in potato (Solanum tuberosum L.). Very strict homology search and subsequent domain verification with Hidden Markov Model revealed 12 StSULTR genes encoding 18 transcripts...
December 2016: Planta
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