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Chromosome pairing

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https://www.readbyqxmd.com/read/28453634/recent-sex-chromosome-divergence-despite-ancient-dioecy-in-the-willow-salix-viminalis
#1
Pascal Pucholt, Alison E Wright, Lei Liu Conze, Judith E Mank, Sofia Berlin
Sex chromosomes can evolve when recombination is halted between a pair of chromosomes, and this can lead to degeneration of the sex-limited chromosome. In the early stages of differentiation sex chromosomes are homomorphic, and even though homomorphic sex chromosomes are very common throughout animals and plants, we know little about the evolutionary forces shaping these types of sex chromosomes. We used DNA- and RNA-Seq data from females and males to explore the sex chromosomes in the female heterogametic willow, Salix viminalis, a species with ancient dioecy but with homomorphic sex chromosomes...
April 27, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28442247/regional-enrichment-analyses-on-genetic-profiles-for-schizophrenia-and-bipolar-disorder
#2
Jingyu Liu, Jiayu Chen, Nora I Perrone-Bizzozero, Jessica A Turner, Vince D Calhoun
Both schizophrenia (SZ) and bipolar disorder (BD) are highly heritable psychiatric disorders. The significant genomic risk loci are of great importance but with no guarantee of known functional impact and they cannot totally explain the genetic inheritance. In this study we present regional enrichment analyses across the genome, aiming to strike a balance between individual risk loci and integrated regional effects. Chromosomes were partitioned into 2 million base-pair regions (indicated by an underscore sign in the cytogenetic bands) on which enrichment tests are performed...
April 22, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28437173/the-karyotype-of-microsternarchus-aff-bilineatus-a-first-case-of-y-chromosome-degeneration-in-gymnotiformes
#3
Jéssica Almeida Batista, Adauto Lima Cardoso, Susana Suely Rodrigues Milhomem Paixão, Jonathan Stuart Ready, Julio Cesar Pieczarka, Cleusa Yoshiko Nagamachi
Various species and lineages that until recently were identified as Microsternarchus bilineatus (Hypopomidae, Gymnotiformes) have a widespread distribution in the Amazon and Orinoco river basins and across the Guiana shield. Recent molecular studies show five distinct lineages for Microsternarchus from different localities. These results suggest that this previously monotypic genus actually consists of more than one species. Here, we describe the karyotype of M. aff. bilineatus from the Cururutuia River (Bragança, Pará, Brazil)...
March 6, 2017: Zebrafish
https://www.readbyqxmd.com/read/28435477/acrodermatitis-enteropathica-in-a-pair-of-twins
#4
Abdullatif Al Rashed, Mohja Al Shehri, Feroze Kaliyadan
BACKGROUND: Acrodermatitis enteropathica (AE) is a rare autosomal recessive metabolic disorder. First described by Brandt in 1936 and was named by Danbolt. A mutation in the SLC39A4 gene on chromosome 8 q24.3 is responsible for this disorder, which encodes zinc transporter Zip4. The diagnosis is made by the clinical presentation and histopathology and laboratory tests. In this case, we reported a twin presented with a typical rash and low zinc level. To our knowledge, very few cases reported as a twin with typical acrodermatitis enteropathica presentation...
December 31, 2016: Journal of Dermatological Case Reports
https://www.readbyqxmd.com/read/28435001/hi-c-2-0-an-optimized-hi-c-procedure-for-high-resolution-genome-wide-mapping-of-chromosome-conformation
#5
Houda Belaghzal, Job Dekker, Johan H Gibcus
Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28432294/genome-wide-identification-characterization-of-the-mads-box-gene-family-in-chinese-jujube-and-their-involvement-in-flower-development
#6
Liman Zhang, Jin Zhao, Chunfang Feng, Mengjun Liu, Jiurui Wang, Yafei Hu
MADS-box genes encode transcription factors that are involved in plant development control (particularly in floral organogenesis) and signal transduction pathways, though a comprehensive analysis of MADS-box family proteins in Chinese jujube (Ziziphus jujuba Mill.) is still missing. Here, we report a genome-wide analysis of the MADS-box gene family in Chinese jujube. Based on phylogenetic analyses, 52 jujube MADS-box genes were classified into 25 MIKC(C)-type, 3 MIKC(*)-type, 16 Mα, 5 Mβ and 3 Mγ genes. 37 genes were randomly distributed across all 12 putative chromosomes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431907/telomere-shortening-during-aging-attenuation-by-antioxidants-and-anti-inflammatory-agents
#7
REVIEW
Kedar N Prasad, Meixia Wu, Stephen C Bondy
Telomeres are a repeated sequence -of bases found at the ends of chromosomes. In humans, this sequence is TTAGGG, which is repeated over 2000 times. Telomeres protect the ends chromosomes from fusion with nearby chromosomes, and allow effective replication of DNA. Each time a cell divides, 25-200 base pairs are lost from the terminal sequence of chromosomes. By becoming truncated during cell division, telomeres protect essential genes from being shortened and thus inactivated. In addition, telomeres are sensitive to inflammation and oxidative stress, which can further promote telomere shortening...
April 18, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28431355/genome-wide-identification-and-analysis-of-the-populus-trichocarpa-tify-gene-family
#8
Yue Wang, Feng Pan, Danmei Chen, Wenyuan Chu, Huanlong Liu, Yan Xiang
The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome...
April 13, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#9
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28430019/characterization-of-rph24-a-gene-conferring-adult-plant-resistance-to-puccinia-hordei-in-barley
#10
Laura A Ziems, Lee T Hickey, Gregory J Platz, Jerome D Franckowiak, Peter M Dracatos, Davinder Singh, Robert F Park
We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers...
April 21, 2017: Phytopathology
https://www.readbyqxmd.com/read/28428799/a-novel-cytoplasmic-male-sterility-in-brassica-napus-inap-cms-with-carpelloid-stamens-via-protoplast-fusion-with-chinese-woad
#11
Lei Kang, Pengfei Li, Aifan Wang, Xianhong Ge, Zaiyun Li
A novel cytoplasmic male sterility (CMS) in Brassica napus (inap CMS) was selected from the somatic hybrid with Isatis indigotica (Chinese woad) by recurrent backcrossing. The male sterility was caused by the conversion of tetradynamous stamens into carpelloid structures with stigmatoid tissues at their tips and ovule-like tissues in the margins, and the two shorter stamens into filaments without anthers. The feminized development of the stamens resulted in the complete lack of pollen grains, which was stable in different years and environments...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28426986/schr%C3%A3-dinger-s-code-script-not-a-genetic-cipher-but-a-code-of-development
#12
A E Walsby, M J S Hodge
In his book What is Life? Erwin Schrödinger coined the term 'code-script', thought by some to be the first published suggestion of a hereditary code and perhaps a forerunner of the genetic code. The etymology of 'code' suggests three meanings relevant to 'code-script which we distinguish as 'cipher-code', 'word-code' and 'rule-code'. Cipher-codes and word-codes entail translation of one set of characters into another. The genetic code comprises not one but two cipher-codes: the first is the DNA 'base-pairing cipher'; the second is the 'nucleotide-amino-acid cipher', which involves the translation of DNA base sequences into amino-acid sequences...
April 17, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/28424414/integrated-analysis-of-promoter-methylation-and-expression-of-telomere-related-genes-in-breast-cancer
#13
Jianfu Heng, Fan Zhang, Xinwu Guo, Lili Tang, Limin Peng, Xipeng Luo, Xunxun Xu, Shouman Wang, Lizhong Dai, Jun Wang
Telomeres at the ends of eukaryotic chromosomes play a critical role in tumorgenesis. Using microfluidic PCR and next-generation bisulfite sequencing technology, we investigated the promoter methylation of 29 telomere related genes in paired tumor and normal tissues from 184 breast cancer patients. The expression of significantly differentially methylated genes was quantified using qPCR method.We observed that the average methylation level of the 29 telomere related genes was significant higher in tumor than that in normal tissues (P = 4...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423373/distribution-of-interstitial-telomeric-sequences-in-primates-and-the-pygmy-tree-shrew-scandentia
#14
Sofia Mazzoleni, Odessa Schillaci, Luca Sineo, Francesca Dumas
It has been hypothesized that interstitial telomeric sequences (ITSs), i.e., repeated telomeric DNA sequences found at intrachromosomal sites in many vertebrates, could be correlated to chromosomal rearrangements and plasticity. To test this hypothesis, we hybridized a telomeric PNA probe through FISH on representative species of 2 primate infraorders, Strepsirrhini (Lemur catta, Otolemur garnettii, Nycticebus coucang) and Catarrhini (Erythrocebus patas, Cercopithecus petaurista, Chlorocebus aethiops, Colobus guereza), as well as on 1 species of the order Scandentia, Tupaia minor, used as an outgroup for primates in phylogenetic reconstructions...
April 20, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28420610/the-diversity-of-dna-fragment-editing-by-crispr-cas9-in-highly-homologous-or-repetitive-sequences
#15
Wang Leyang, Huang Haiyan, Wu Qiang
In complex genomes, there are a large number of duplicated genes in the coding regions and many more repetitive sequences in the non-coding regions. Repetitive sequences can exert great impacts on the heredity and evolution of the organisms, as well as their genome 3D architecture and transcriptional regulation. The high homology nature of repetitive sequences renders their editing by CRISPR/Cas9 very complex. At diploid or polyploid situations, such repetitive sequences could be edited differently on each chromosome or chromatid...
April 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28417911/genome-wide-analyses-of-the-soybean-f-box-gene-family-in-response-to-salt-stress
#16
Qi Jia, Zhi-Xia Xiao, Fuk-Ling Wong, Song Sun, Kang-Jing Liang, Hon-Ming Lam
The F-box family is one of the largest gene families in plants that regulate diverse life processes, including salt responses. However, the knowledge of the soybean F-box genes and their roles in salt tolerance remains limited. Here, we conducted a genome-wide survey of the soybean F-box family, and their expression analysis in response to salinity via in silico analysis of online RNA-sequencing (RNA-seq) data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) to predict their potential functions...
April 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28413152/loss-of-pten-expression-is-associated-with-high-microrna-24-level-and-poor-prognosis-in-patients-with-tongue-squamous-cell-carcinoma
#17
Jingzhu Zhao, Jiadong Chi, Ming Gao, Jingtai Zhi, Yigong Li, Xiangqian Zheng
PURPOSE: The aim of this study was to detect the relationship between phosphatase and tensin homolog deletion on chromosome 10 (PTEN) and microRNA 24 (miR-24) and correlate PTEN expression with important clinical parameters of patients with tongue squamous cell carcinoma (TSCC). MATERIALS AND METHODS: In this retrospective case series, all TSCC patients treated at Tianjin Medical University Cancer Institute and Hospital between March 2005 and October 2011 were retrospectively reviewed...
March 23, 2017: Journal of Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/28412934/karyotype-diversity-and-chromosomal-organization-of-repetitive-dna-in-tityus-obscurus-scorpiones-buthidae
#18
Bruno Rafael Ribeiro de Almeida, Susana Suely Rodrigues Milhomem-Paixão, Renata Coelho Rodrigues Noronha, Cleusa Yoshiko Nagamachi, Marlyson Jeremias Rodrigues da Costa, Pedro Pereira de Oliveira Pardal, Johne Souza Coelho, Julio Cesar Pieczarka
BACKGROUND: Holocentric chromosomes occur in approximately 750 species of eukaryotes. Among them, the genus Tityus (Scorpiones, Buthidae) has a labile karyotype that shows complex multivalent associations during male meiosis. Thus, taking advantage of the excellent model provided by the Buthidae scorpions, here we analyzed the chromosomal distribution of several repetitive DNA classes on the holocentric chromosomes of different populations of the species Tityus obscurus Gervais, 1843, highlighting their involvement in the karyotypic differences found among them...
April 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28411125/hypersociability-in-the-angelman-syndrome-mouse-model
#19
David C Stoppel, Matthew P Anderson
Deletions and reciprocal triplications of the human chromosomal 15q11-13 region cause two distinct neurodevelopmental disorders. Maternally-derived deletions or inactivating mutations of UBE3A, a 15q11-13 gene expressed exclusively from the maternal allele in neurons, cause Angelman syndrome, characterized by intellectual disability, motor deficits, seizures, and a characteristic increased social smiling, laughing, and eye contact. Conversely, maternally-derived triplications of 15q11-13 cause a behavioral disorder on the autism spectrum with clinical features that include decreased sociability that we recently reconstituted in mice with Ube3a alone...
April 11, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/28410362/joint-assessment-of-donor-and-recipient-htert-gene-polymorphism-provides-additional-information-for-early-kidney-transplantation-outcomes
#20
Karolina Kłoda, Artur Mierzecki, Leszek Domański, Ewa Borowiecka, Krzysztof Safranow, Andrzej Ciechanowicz, Kazimierz Ciechanowski
BACKGROUND There are several genes and genetic loci affecting telomere length, including hTERT gene and BICD1 gene as well as polymorphisms within chromosome 18. It has been demonstrated that the age of the donor is a negative factor associated with long-term kidney allograft function, and that post-transplant complications accelerate transplanted organ aging, thus contributing to estimated glomerular filtration rate (eGFR) decreases. The aim of this study was a joint assessment of donors' and recipients' hTERT and BICD1 genes as well as chromosome 18 polymorphisms with regard to early kidney transplantation outcomes...
April 14, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
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