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https://www.readbyqxmd.com/read/28812561/widespread-maintenance-of-genome-heterozygosity-in-schmidtea%C3%A2-mediterranea
#1
Longhua Guo, Shasha Zhang, Boris Rubinstein, Eric Ross, Alejandro Sánchez Alvarado
Loss of heterozygosity through inbreeding or mitotic errors leads to reductions in progeny survival and fertility. Loss of heterozygosity is particularly exacerbated in geographically isolated populations, which are prone to inbreeding depression and faster rates of extinction. The regenerative capacities of the hermaphroditic biotype of the planarian Schmidtea mediterranea allowed us to perform a systematic genetic test of Mendelian segregation and study the loss of heterozygosity in the Spiralian superclade in general and planarians in particular...
December 5, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812536/edgar-a-database-of-disease-gene-associations-with-annotated-relationships-among-genes
#2
Giulia Babbi, Pier Luigi Martelli, Giuseppe Profiti, Samuele Bovo, Castrense Savojardo, Rita Casadio
BACKGROUND: Genetic investigations, boosted by modern sequencing techniques, allow dissecting the genetic component of different phenotypic traits. These efforts result in the compilation of lists of genes related to diseases and show that an increasing number of diseases is associated with multiple genes. Investigating functional relations among genes associated with the same disease contributes to highlighting molecular mechanisms of the pathogenesis. RESULTS: We present eDGAR, a database collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28811599/histone-deacetylase-6-hdac6-is-an-essential-factor-for-oocyte-maturation-and-asymmetric-division-in-mice
#3
Dongjie Zhou, Yun-Jung Choi, Jin-Hoi Kim
Tubastatin A (Tub-A), a highly selective histone deacetylase 6 (HDAC6) inhibitor, has been widely used as a cytotoxic anticancer agent, or for the treatment of patients with asthma. However, the potential toxicity of Tub-A on oocyte maturation and asymmetric division is still unclear. Therefore, the present study was designed to examine the effect and potential regulatory role of Tub-A on the meiotic maturation of oocytes. We observed that Tub-A treatment induced an increased level of the acetylation of α-tubulin, and a failure of spindle migration and actin cap formation...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811336/catastrophic-unbalanced-genome-rearrangements-cause-somatic-loss-of-berry-color-in-grapevine
#4
Pablo Carbonell-Bejerano, Carolina Royo, Rafael Torres-Pérez, Jérôme Grimplet, Lucie Fernandez, Jose M Franco-Zorrilla, Diego Lijavetzky, Elisa Baroja, Juana Martínez, Enrique García-Escudero, Javier Ibáñez, José M Martínez-Zapater
Grape color somatic variants that can be used to develop new grapevine cultivars occasionally appear associated to deletion events of uncertain origin. To understand the mutational mechanisms generating somatic structural variation in grapevine, we compared the Tempranillo Blanco (TB) white berry somatic variant to its black berry ancestor, Tempranillo Tinto. Whole-genome sequencing (WGS) uncovered a catastrophic genome rearrangement in TB that caused the hemizygous deletion of 313 genes, including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28810832/genome-wide-analysis-of-basic-helix-loop-helix-bhlh-transcription-factors-in-brachypodium-distachyon
#5
Xin Niu, Yuxiang Guan, Shoukun Chen, Haifeng Li
BACKGROUND: As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS: A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28809790/genome-wide-organization-and-expression-profiling-of-the-sbp-box-gene-family-in-chinese-jujube-ziziphus-jujuba-mill
#6
Shuang Song, Heying Zhou, Songbai Sheng, Ming Cao, Yingyue Li, Xiaoming Pang
Transcription factors play vital roles in the developmental processes of plants. The SQUAMOSA promoter binding protein (SBP) genes encode a family of plant-specific transcription factors and plays many crucial roles in plant development. In this study, 16 SBP-box gene family members were identified in Ziziphus jujuba Mill. Dongzao (Dongzao), which were distributed over 8 chromosomes. They were classified into seven groups according to their phylogenetic relationships with other SBP-box gene families. Within each group, genes shared similar exon-intron structures and motif locations...
August 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28809762/elucidation-of-novel-chromosomal-abnormalities-in-pancreatic-cancer-conventional-and-molecular-cytogenetic-characterization-of-16-pancreatic-cell-lines
#7
David Shabsovich, Carlos A Tirado
Pancreatic carcinoma is a major cause of cancer-related death in the United States, with a five-year survival rate of approximately 5%. Cytogenetic analysis has identified clinically significant chromosomal abnormalities in numerous malignancies, but it is not utilized in the clinical management of pancreatic carcinoma. We performed conventional and molecular cytogenetic analysis of 16 pancreatic carcinoma cell lines using Giemsa banding and DNA-based fluorescence in situ hybridization (FISH). Conventional cytogenetic analysis revealed a diversity of recurrent and clonal numerical and structural abnormalities in all cell lines analyzed, many of which occurred at loci of genes implicated in pancreatic or related cancers...
2017: Journal of the Association of Genetic Technologists
https://www.readbyqxmd.com/read/28809041/complex-malformations-involving-the-fetal-body-wall-definition-and-classification-issues
#8
Julia Bijok, Diana Massalska, Anna Kucińska-Chahwan, Anna Posiewka, Alicja Ilnicka, Grzegorz Jakiel, Tomasz Roszkowski
OBJECTIVE: To analyse the sonographic features, cytogenetic results and pregnancy outcomes in complex malformations involving the body wall in a large cohort of fetuses with regard to different definitions proposed in the literature. METHOD: A retrospective study on 96 fetuses with complex malformations comprising ventral wall, craniofacial structures, limbs and umbilical cord that were evaluated between 1997 and 2015. RESULTS: The most common sonographic finding was an extensive ventral wall defect (95...
August 14, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28808972/chromosome-conformation-capture-for-research-on-innate-antiviral-immunity
#9
Yoon Jung Kim, Tae Hoon Kim
Chromosome conformation capture (3C) technology has revolutionized our knowledge on chromatin folding and nuclear organization. This cis-loop detection approach can be used to identify candidate regulatory elements interacting with target gene of interest. This chapter introduces the application of 3C technique to investigate a dynamic alteration in the chromosome folding structure or genomic architecture resulting from interaction changes between the enhancer and its target gene. Innate antiviral immunity is one of the well-known gene induction systems, involving rapid first-line response to virus or pathogen to trigger gene expression changes in order to protect cells and to limit further infection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808044/germline-mutation-contribution-to-chromosomal-instability
#10
REVIEW
Sock Hoai Chan, Joanne Ngeow
Genomic instability is a feature of cancer that fuels oncogenesis through increased frequency of genetic disruption, leading to loss of genomic integrity and promoting clonal evolution as well as tumor transformation. A form of genomic instability prevalent across cancer types is chromosomal instability, which involves karyotypic changes including chromosome copy number alterations as well as gross structural abnormalities such as transversions and translocations. Defects in cellular mechanisms that are in place to govern fidelity of chromosomal segregation, DNA repair and ultimately genomic integrity are known to contribute to chromosomal instability...
September 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28806978/transcriptome-sequencing-in-pediatric-acute-lymphoblastic-leukemia-identifies-fusion-genes-associated-with-distinct-dna-methylation-profiles
#11
Yanara Marincevic-Zuniga, Johan Dahlberg, Sara Nilsson, Amanda Raine, Sara Nystedt, Carl Mårten Lindqvist, Eva C Berglund, Jonas Abrahamsson, Lucia Cavelier, Erik Forestier, Mats Heyman, Gudmar Lönnerholm, Jessica Nordlund, Ann-Christine Syvänen
BACKGROUND: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes...
August 14, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28805829/lineage-specific-dynamic-and-pre-established-enhancer-promoter-contacts-cooperate-in-terminal-differentiation
#12
Adam J Rubin, Brook C Barajas, Mayra Furlan-Magaril, Vanessa Lopez-Pajares, Maxwell R Mumbach, Imani Howard, Daniel S Kim, Lisa D Boxer, Jonathan Cairns, Mikhail Spivakov, Steven W Wingett, Minyi Shi, Zhixin Zhao, William J Greenleaf, Anshul Kundaje, Michael Snyder, Howard Y Chang, Peter Fraser, Paul A Khavari
Chromosome conformation is an important feature of metazoan gene regulation; however, enhancer-promoter contact remodeling during cellular differentiation remains poorly understood. To address this, genome-wide promoter capture Hi-C (CHi-C) was performed during epidermal differentiation. Two classes of enhancer-promoter contacts associated with differentiation-induced genes were identified. The first class ('gained') increased in contact strength during differentiation in concert with enhancer acquisition of the H3K27ac activation mark...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28805618/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of-mosaicism-for-a-small-supernumerary-marker-chromosome-derived-from-chromosome-21q11-2-q21-1-and-a-literature-review
#13
Chih-Ping Chen, Ming Chen, Chia-Hsun Wu, Chen-Ju Lin, Schu-Rern Chern, Peih-Shan Wu, Yen-Ni Chen, Shin-Wen Chen, Shun-Ping Chang, Li-Feng Chen, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis and molecular cytogenetic characterization of mosaicism for a small supernumerary marker chromosome (sSMC) derived from chromosome 21q11.2-q21.1, and we review the literature of an sSMC(21) with a duplication of 21q11.2-q21.1. CASE REPORT: A 40-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XX,+mar [18]/46,XX [4]. The parental karyotypes were normal...
August 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28803847/psychotic-symptoms-influence-the-development-of-anterior-cingulate-bold-variability-in-22q11-2-deletion-syndrome
#14
Daniela Zöller, Maria Carmela Padula, Corrado Sandini, Maude Schneider, Elisa Scariati, Dimitri Van De Ville, Marie Schaer, Stephan Eliez
Chromosome 22q11.2 deletion syndrome (22q11DS) is a neurodevelopmental disorder associated with a broad phenotype of clinical, cognitive and psychiatric features. Due to the very high prevalence of schizophrenia (30-40%), the investigation of psychotic symptoms in the syndrome is promising to reveal biomarkers for the development of psychosis, also in the general population. Since schizophrenia is seen as a disorder of the dynamic interactions between brain networks, we here investigated brain dynamics, assessed by the variability of blood oxygenation level dependent (BOLD) signals, in patients with psychotic symptoms...
August 10, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28802249/high-resolution-mapping-of-chromatin-conformation-in-cardiac-myocytes-reveals-structural-remodeling-of-the-epigenome-in-heart-failure
#15
Manuel Rosa-Garrido, Douglas J Chapski, Anthony D Schmitt, Todd H Kimball, Elaheh Karbassi, Emma Monte, Enrique Balderas, Matteo Pellegrini, Tsai-Ting Shih, Elizabeth Soehalim, David A Liem, Peipei Ping, Niels J Galjart, Shuxun Ren, Yibin Wang, Bing Ren, Thomas M Vondriska
Background -Cardiovascular disease is associated with epigenomic changes in the heart, however the endogenous structure of cardiac myocyte chromatin has never been determined. Methods -To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype...
August 11, 2017: Circulation
https://www.readbyqxmd.com/read/28801756/segregation-distortion-and-genome-wide-digenic-interactions-affect-transmission-of-introgressed-chromatin-from-wild-cotton-species
#16
Rahul Chandnani, Baohua Wang, Xavier Draye, Lisa K Rainville, Susan Auckland, Zhimin Zhuang, Edward L Lubbers, O Lloyd May, Peng W Chee, Andrew H Paterson
This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species...
August 11, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28801671/the-cpg-sites-of-the-cbx3-ubiquitous-chromatin-opening-element-are-critical-structural-determinants-for-the-anti-silencing-function
#17
Jessica Kunkiel, Natascha Gödecke, Mania Ackermann, Dirk Hoffmann, Axel Schambach, Nico Lachmann, Dagmar Wirth, Thomas Moritz
Suppression of therapeutic transgene expression from retroviral gene therapy vectors by epigenetic defence mechanisms represents a problem that is particularly encountered in pluripotent stem cells (PSCs) and their differentiated progeny. Transgene expression in these cells, however, can be stabilised by CpG-rich ubiquitous chromatin opening elements (UCOEs). In this context we recently demonstrated profound anti-silencing properties for the small (679 bp) CBX3-UCO element and we now confirmed this observation in the context of the defined murine chromosomal loci ROSA26 and TIGRE...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800607/rna-sequencing-based-transcriptome-and-biochemical-analyses-of-steroidal-saponin-pathway-in-a-complete-set-of-allium-fistulosum-a-cepa-monosomic-addition-lines
#18
Mostafa Abdelrahman, Magdi El-Sayed, Shusei Sato, Hideki Hirakawa, Shin-Ichi Ito, Keisuke Tanaka, Yoko Mine, Nobuo Sugiyama, Minoru Suzuki, Naoki Yamauchi, Masayoshi Shigyo
The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium's defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A...
2017: PloS One
https://www.readbyqxmd.com/read/28800583/the-nucleoid-protein-dps-binds-genomic-dna-of-escherichia-coli-in-a-non-random-manner
#19
S S Antipov, M N Tutukina, E V Preobrazhenskaya, F A Kondrashov, M V Patrushev, S V Toshchakov, I Dominova, U S Shvyreva, V V Vrublevskaya, O S Morenkov, N A Sukharicheva, V V Panyukov, O N Ozoline
Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity...
2017: PloS One
https://www.readbyqxmd.com/read/28799037/three-dimensional-hdlive-imaging-of-an-umbilical-cord-cyst
#20
Eisuke Inubashiri, Naomi Nishiyama, Sayuri Tatedo, Hiina Minami, Atushi Saitou, Yukio Watanabe, Masaki Sugawara
Umbilical cord cysts (UCC) are a rare congenital malformation. Previous reports have suggested that the second- and third-trimester UCC may be associated with other structural anomalies or chromosomal abnormalities. Therefore, high-quality imaging is clinically important for the antenatal diagnosis of UCC and to conduct a precise anatomical survey of intrauterine abnormalities. There have been few reports of antenatal diagnosis of UCC with the conventional two- and three-dimensional ultrasonography. In this report, we demonstrate the novel visual depiction of UCC in utero with three-dimensional HDlive imaging, which helps substantially with prenatal diagnosis...
August 10, 2017: Journal of Medical Ultrasonics
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