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Chromosome pairing

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https://www.readbyqxmd.com/read/29470932/precise-identification-of-wheat-i-thinopyrum-intermedium-i-translocation-chromosomes-carrying-resistance-to-wheat-stripe-rust-in-line-z4-and-its-derived-progenies
#1
Tao Lang, Shixiao La, Bin Li, Zhihui Yu, Qiheng Chen, Jianbo Li, Ennian Yang, Guangrong Li, Zujun Yang
2 The wheat- Thinopyrum intermedium derived line Z4 has displayed novel and effective stripe rust resistance for over 40 years. This study aimed to precisely identify the chromosome constitution of Z4 and determine the stripe rust resistance contribution using multicolor fluorescent in situ hybridization (FISH) and molecular marker analysis. The results indicated that the Z4 line (2n=44) contained two pairs of non-Robertsonian translocations without the 3A chromosomes of wheat. FISH karyotypes of F3 progenies derived from crosses between Z4 and MY11 indicated that the transmission of the translocated chromosomes appeared normal and the number of wheat chromosomes 3A and 3D frequently varied...
February 22, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29466359/cdk-activity-provides-temporal-and-quantitative-cues-for-organizing-genome-duplication
#2
Anthony Perrot, Christopher Lee Millington, Blanca Gómez-Escoda, Diane Schausi-Tiffoche, Pei-Yun Jenny Wu
In eukaryotes, the spatial and temporal organization of genome duplication gives rise to distinctive profiles of replication origin usage along the chromosomes. While it has become increasingly clear that these programs are important for cellular physiology, the mechanisms by which they are determined and modulated remain elusive. Replication initiation requires the function of cyclin-dependent kinases (CDKs), which associate with various cyclin partners to drive cell proliferation. Surprisingly, although we possess detailed knowledge of the CDK regulators and targets that are crucial for origin activation, little is known about whether CDKs play a critical role in establishing the genome-wide pattern of origin selection...
February 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29464982/rcc1-regulates-inner-centromeric-composition-in-a-ran-independent-fashion
#3
Michael Shaofei Zhang, Maiko Furuta, Alexei Arnaoutov, Mary Dasso
RCC1 associates to chromatin dynamically within mitosis and catalyzes Ran-GTP production. Exogenous RCC1 disrupts kinetochore structure in Xenopus egg extracts (XEEs), but the molecular basis of this disruption remains unknown. We have investigated this question, utilizing replicated chromosomes that possess paired sister kinetochores. We find that exogenous RCC1 evicts a specific subset of inner KT proteins including Shugoshin-1 (Sgo1) and the chromosome passenger complex (CPC). We generated RCC1 mutants that separate its enzymatic activity and chromatin binding...
February 21, 2018: Cell Cycle
https://www.readbyqxmd.com/read/29464042/yap-associated-chromosomal-instability-and-cholangiocarcinoma-in-mice
#4
Sumera Rizvi, Samantha R Fischbach, Steven F Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B Smadbeck, Rory L Smoot, George Vasmatzis, Gregory J Gores
Deregulated Hippo pathway signaling is associated with aberrant activation of the downstream effector yes-associated protein (YAP), an emerging key oncogenic mediator in cholangiocarcinoma (CCA). In our prior work, we have demonstrated that biliary transduction of YAP along with Akt as a permissive factor induces CCA in mice. To further delineate the mechanisms associated with YAP-associated biliary oncogenesis, we have established seven malignant murine cell lines from our YAP-driven murine CCA model. These cells express the CCA markers SRY (Sex Determining Region Y)-Box 9 (SOX9), cytokeratin (CK)-7 and 19 but lack hepatocyte nuclear factor 4 alpha and alpha-smooth muscle actin, markers of hepatocellular carcinoma and cancer-associated fibroblasts, respectively...
January 19, 2018: Oncotarget
https://www.readbyqxmd.com/read/29462803/chromosome-painting-in-tyrant-flycatchers-confirms-a-set-of-inversions-shared-by-oscines-and-suboscines-aves-passeriformes
#5
Benilson S Rodrigues, Rafael Kretschmer, Ricardo J Gunski, Analia D V Garnero, Patricia C M O'Brien, Malcolm Ferguson-Smith, Edivaldo H C de Oliveira
Tyrannidae is the largest family of Passeriformes in the Neotropical region. However, despite an interesting chromosomal diversity, there are only few cytogenetic studies of this family, and most of these are based on conventional cytogenetics. Hence, we analyzed here the chromosomal diversity and karyotypical evolution of this group by chromosome painting in 3 different species - Pitangus sulphuratus, Serpophaga subcristata, and Satrapa icterophrys - and make comparisons with previous data. In addition to chromosome painting with Gallus gallus (GGA) and Leucopternis albicollis (LAL) probes, karyotypes were analyzed by conventional staining, C-banding, and FISH with 18S rDNA and telomeric probes...
February 21, 2018: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/29460287/chromosomal-aberrations-and-cnvs-in-twin-fetuses-with-cardiovascular-anomalies-comparison-between-monochorionic-diamniotic-and-dichorionic-diamniotic-twins
#6
Yi Zhang, Linhuan Huang, Xuan Huang, Zhiming He, Shaobin Lin, Ye Wang, Lin Li, Yanmin Luo, Qun Fang
OBJECTIVE: To investigate the types of cardiovascular anomalies and the results of invasive prenatal diagnosis in twin fetuses. METHODS: A total of 298 fetuses in 149 twin pairs were enrolled, in which 1 or 2 fetuses of a twin pair had cardiovascular anomalies. Prenatal diagnosis was performed on 290 fetuses of 149 twin pairs, including 150 monochorionic diamniotic (MCDA) fetuses (79 pairs) and 140 dichorionic diamniotic (DCDA) fetuses (70 pairs). G-banding karyotyping and/or chromosomal microarray analysis (CMA) were performed...
February 19, 2018: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29458871/dna-sequence-specific-dimeric-bisbenzimidazoles-dbp-n-and-dbpa-n-as-inhibitors-of-h-ns-silencing-in-bacterial-cells
#7
Olga E Melkina, Vasilii S Koval, Alexander A Ivanov, Alexei L Zhuze, Gennadii B Zavilgelsky
DNA sequence-specific fluorescent dimeric bisbenzimidazoles DBP(n) and DBPA(n), noncovalently interacting with A-T pairs in the minor groove of double-stranded DNA were used for studying and monitoring the expression of histone-like H-NS-dependent promoters. Histone-like H-NS selectively binds to AT-rich segments of DNA and silences a large number of genes in bacterial chromosomes. The H-NS-dependent promoters of Quorum Sensing (QS)-regulated lux operons of the marine bacteria mesophilic Aliivibrio fischeri, psychrophilic Aliivibrio logei were used...
March 2018: Microbiological Research
https://www.readbyqxmd.com/read/29455040/a-simple-method-for-calculating-the-likelihood-ratio-in-a-kinship-test-using-x-chromosomal-markers-incorporating-linkage-linkage-disequilibrium-and-mutation
#8
Mamiko Fukuta, Mohammed Hassan Gaballah, Hideaki Kato, Yasuhiro Aoki
X-chromosomal short tandem repeats (X-STRs) are useful for personal identification and kinship tests. However, it has not yet been fully established how to incorporate linkage and linkage disequilibrium (LD) into the calculation of the likelihood ratio (LR). In this paper, we describe a simple calculation method of LR for X-STRs that incorporated linkage, LD, and mutations. Initially, Japanese population data of 27 X-STRs (DXS6807, DXS9902, DXS6795, DXS6810, DXS10076, DXS10077, DXS10078, DXS10162, DXS10163, DXS10164, DXS7132, DXS981, DXS6800, DXS6803, DXS6809, DXS6789, DXS6799, DXS7424, DXS101, DXS7133, GATA172D05, DXS10103, HPRTB, GATA31E08, DXS8377, DXS10147, and DXS7423) were collected from 748 unrelated individuals to estimate the influence of LD...
February 12, 2018: Legal Medicine
https://www.readbyqxmd.com/read/29449410/conserved-microrna-targeting-reveals-preexisting-gene-dosage-sensitivities-that-shaped-amniote-sex-chromosome-evolution
#9
Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29447163/paternal-lineage-early-onset-hereditary-ovarian-cancers-a-familial-ovarian-cancer-registry-study
#10
Kevin H Eng, J Brian Szender, John Lewis Etter, Jasmine Kaur, Samantha Poblete, Ruea-Yea Huang, Qianqian Zhu, Katherine A Grzesik, Sebastiano Battaglia, Rikki Cannioto, John J Krolewski, Emese Zsiros, Peter J Frederick, Shashikant B Lele, Kirsten B Moysich, Kunle O Odunsi
Given prior evidence that an affected woman conveys a higher risk of ovarian cancer to her sister than to her mother, we hypothesized that there exists an X-linked variant evidenced by transmission to a woman from her paternal grandmother via her father. We ascertained 3,499 grandmother/granddaughter pairs from the Familial Ovarian Cancer Registry at the Roswell Park Cancer Institute observing 892 informative pairs with 157 affected granddaughters. We performed germline X-chromosome exome sequencing on 186 women with ovarian cancer from the registry...
February 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29444174/chromosome-evolution-in-cophomantini-amphibia-anura-hylinae
#11
Juan M Ferro, Dario E Cardozo, Pablo Suárez, Juan M Boeris, Ailin Blasco-Zúñiga, Gastón Barbero, Anderson Gomes, Thiago Gazoni, William Costa, Cleusa Y Nagamachi, Miryan Rivera, Patricia P Parise-Maltempi, John E Wiley, Julio C Pieczarka, Celio F B Haddad, Julián Faivovich, Diego Baldo
The hylid tribe Cophomantini is a diverse clade of Neotropical treefrogs composed of the genera Aplastodiscus, Boana, Bokermannohyla, Hyloscirtus, and Myersiohyla. The phylogenetic relationships of Cophomantini have been comprehensively reviewed in the literature, providing a suitable framework for the study of chromosome evolution. Employing different banding techniques, we studied the chromosomes of 25 species of Boana and 3 of Hyloscirtus; thus providing, for the first time, data for Hyloscirtus and for 15 species of Boana...
2018: PloS One
https://www.readbyqxmd.com/read/29444111/genome-wide-identification-and-role-of-mkk-and-mpk-gene-families-in-clubroot-resistance-of-brassica-rapa
#12
Yinglan Piao, Kaining Jin, Ying He, Jiaxiu Liu, Shuang Liu, Xiaonan Li, Zhongyun Piao
Mitogen-activated protein kinase (MAPK or MPK) cascades play key roles in responses to various biotic stresses, as well as in plant growth and development. However, the responses of MPK and MPK kinase (MKK) in Chinese cabbage (Brassica rapa ssp. pekinensis) to Plasmodiophora brassicae, a causal agent of clubroot disease in Brassica crops, are still not clear. In the present study, a total of 11 B. rapa MKK (BraMKK) and 30 BraMPK genes were identified and unevenly distributed in 6 and 10 chromosomes, respectively...
2018: PloS One
https://www.readbyqxmd.com/read/29434621/extensive-karyotype-reorganization-in-the-fish-gymnotus-arapaima-gymnotiformes-gymnotidae-highlighted-by-zoo-fish-analysis
#13
Milla de Andrade Machado, Julio C Pieczarka, Fernando H R Silva, Patricia C M O'Brien, Malcolm A Ferguson-Smith, Cleusa Y Nagamachi
The genus Gymnotus (Gymnotiformes) contains over 40 species of freshwater electric fishes exhibiting a wide distribution throughout Central and South America, and being particularly prevalent in the Amazon basin. Cytogenetics has been an important tool in the cytotaxonomy and elucidation of evolutionary processes in this genus, including the unraveling the variety of diploid chromosome number (2n = from 34 to 54), the high karyotype diversity among species with a shared diploid number, different sex chromosome systems, and variation in the distribution of several Repetitive DNAs and colocation and association between those sequences...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29428890/construction-and-forensic-genetic-characterization-of-11-autosomal-haplotypes-consisting-of-22-tri-allelic-indels
#14
Xiaohong Zhao, Xiaogang Chen, Yuancun Zhao, Shu Zhang, Zehua Gao, Yiwen Yang, Yufang Wang, Ji Zhang
Insertion/deletion polymorphisms (indels), which combine the advantages of both short tandem repeats and single-nucleotide polymorphisms, are suitable for parentage testing. To overcome the limitations of the low polymorphism of di-allelic indels, we constructed a set of haplotypes with physically linked, multi-allelic indels. Candidate haplotypes were selected from the 1000 Genomes Project database, and were subject to the following criteria for inclusion: (i) each marker must have a minimum allele frequency (MAF) of ≥0...
February 6, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29427756/crispr-cas9-ablation-of-individual-mirnas-from-a-mirna-family-reveals-their-individual-efficacies-for-regulating-cardiac-differentiation
#15
Ziyao Zhang, Rebecca Ursin, Samiksha Mahapatra, G Ian Gallicano
Although it is well understood that genetic mutations, chromosomal abnormalities, and epigenetic miscues can cause congenital birth defects, many defects are still labeled idiopathic, meaning their origin is not yet understood. microRNAs are quickly entering the causal fray of developmental defects. miRNAs use a 7-8 base-pair seed sequence to target a corresponding sequence on one or multiple mRNAs resulting in rapid down-regulation of translation. miRNAs can also control protein 'amounts' in cells. As a result if miRNAs are over or under expressed during development protein homeostasis can be compromised resulting in defects in the development of organ systems...
February 7, 2018: Mechanisms of Development
https://www.readbyqxmd.com/read/29425824/salt-and-drought-stress-and-aba-responses-related-to-bzip-genes-from-v-radiata-and-v-angularis
#16
Lanfen Wang, Jifeng Zhu, Xiaoming Li, Shumin Wang, Jing Wu
Mung bean and adzuki bean are warm-season legumes widely cultivated in China. However, bean production in major producing regions is limited by biotic and abiotic stress, such as drought and salt stress. Basic leucine zipper (bZIP) genes play key roles in responses to various biotic and abiotic stresses. However, only several bZIP genes involved in drought and salt stress in legumes, especially Vigna radiata and Vigna angularis, have been identified. In this study, we identified 54 and 50 bZIP proteins from whole-genome sequences of V...
February 6, 2018: Gene
https://www.readbyqxmd.com/read/29423657/qtl-delineation-for-five-fiber-quality-traits-based-on-an-intra-specific-gossypium-hirsutum-l-recombinant-inbred-line-population
#17
Xiaoyun Jia, Hantao Wang, Chaoyou Pang, Qifeng Ma, Junji Su, Hengling Wei, Meizhen Song, Shuli Fan, Shuxun Yu
Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Marker-assisted selection (MAS) is an effective approach for improving fiber quality, and quantitative trait loci (QTL) mapping of fiber quality traits is important for cotton breeding. In this study, a permanent intra-specific recombinant inbred line (RIL) population containing 137 families was used for fiber quality testing. Based on a previously reported high-density genetic map with an average marker distance of 0...
February 8, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29423054/copy-number-profiles-of-paired-primary-and-metastatic-colorectal-cancers
#18
Futoshi Kawamata, Ann-Marie Patch, Katia Nones, Catherine Bond, Diane McKeone, Sally-Ann Pearson, Shigenori Homma, Cheng Liu, Lochlan Fennell, Troy Dumenil, Gunter Hartel, Nozomi Kobayasi, Hideki Yokoo, Moto Fukai, Hiroshi Nishihara, Toshiya Kamiyama, Matthew E Burge, Christos S Karapetis, Akinobu Taketomi, Barbara Leggett, Nicola Waddell, Vicki Whitehall
Liver metastasis is the major cause of death following a diagnosis of colorectal cancer (CRC). In this study, we compared the copy number profiles of paired primary and liver metastatic CRC to better understand how the genomic structure of primary CRC differs from the metastasis. Paired primary and metastatic tumors from 16 patients and their adjacent normal tissue samples were analyzed using single nucleotide polymorphism arrays. Genome-wide chromosomal copy number alterations were assessed, with particular attention to 188 genes known to be somatically altered in CRC and 24 genes that are clinically actionable in CRC...
January 9, 2018: Oncotarget
https://www.readbyqxmd.com/read/29421795/production-and-molecular-cytogenetic-characterization-of-a-durum-wheat-thinopyrum-elongatum-7e-disomic-addition-line-with-resistance-to-fusarium-head-blight
#19
Huiping Liu, Yi Dai, Dawn Chi, Shuai Huang, Haifeng Li, Yamei Duan, Wenguang Cao, Yong Gao, George Fedak, Jianmin Chen
Wheatgrass, Thinopyrum elongatum (2n = 2x = 14, EE), is an important wild relative of wheat with many excellent traits, including resistance to Fusarium head blight (FHB), that can be used for durum wheat improvement. Through hybridization of the durum cultivar "Langdon" with the amphiploid 8801 (AABBEE), a disomic alien addition line (2n = 30) with a pair of Th. elongatum 7E chromosomes was obtained and confirmed using chromosome-specific molecular markers of Th. elongatum and genomic in situ hybridization (GISH)...
February 9, 2018: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/29419817/investigation-of-the-spatial-structure-and-interactions-of-the-genome-at-sub-kilobase-pair-resolution-using-t2c
#20
Petros Kolovos, Rutger W W Brouwer, Christel E M Kockx, Michael Lesnussa, Nick Kepper, Jessica Zuin, A M Ali Imam, Harmen J G van de Werken, Kerstin S Wendt, Tobias A Knoch, Wilfred F J van IJcken, Frank Grosveld
Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio...
March 2018: Nature Protocols
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