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https://www.readbyqxmd.com/read/28822625/landscaping-crossover-interference-across-a-genome
#1
REVIEW
Lidan Sun, Jing Wang, Mengmeng Sang, Libo Jiang, Bingyu Zhao, Tangran Cheng, Qixiang Zhang, Rongling Wu
The evolutionary success of eukaryotic organisms crucially depends on the capacity to produce genetic diversity through reciprocal exchanges of each chromosome pair, or crossovers (COs), during meiosis. It has been recognized that COs arise more evenly across a given chromosome than at random. This phenomenon, termed CO interference, occurs pervasively in eukaryotes and may confer a selective advantage. We describe here a multipoint linkage analysis procedure for segregating families to quantify the strength of CO interference over the genome, and extend this procedure to illustrate the landscape of CO interference in natural populations...
August 16, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28821587/drift-induced-selection-between-male-and-female-heterogamety
#2
Carl Veller, Pavitra Muralidhar, George W A Constable, Martin A Nowak
Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads...
August 16, 2017: Genetics
https://www.readbyqxmd.com/read/28814267/sex-and-tissue-specific-gene-expression-patterns-identified-following-de-novo-transcriptomic-analysis-of-the-norway-lobster-nephrops-norvegicus
#3
Guiomar Rotllant, Tuan Viet Nguyen, Valerio Sbragaglia, Lifat Rahi, Kevin J Dudley, David Hurwood, Tomer Ventura, Joan B Company, Vincent Chand, Jacopo Aguzzi, Peter B Mather
BACKGROUND: The Norway lobster, Nephrops norvegicus, is economically important in European fisheries and is a key organism in local marine ecosystems. Despite multi-faceted scientific interest in this species, our current knowledge of genetic resources in this species remains very limited. Here, we generated a reference de novo transcriptome for N. norvegicus from multiple tissues in both sexes. Bioinformatic analyses were conducted to detect transcripts that were expressed exclusively in either males or females...
August 16, 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
#4
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/28809014/genomic-and-transcriptomic-analyses-of-avian-sex-chromosomes-and-sex-linked-genes
#5
Jilin Zhang, Jing Li, Qi Zhou
Sex chromosomes and sex-linked genes usually show unusual features comparing to the rest of the genome and thus are of particular interests to evolutionary and developmental biologists. Here we describe recently developed bioinformatic methods for identifying sex-linked sequences, in a genome without priori linkage information. Some are developed during our course of studying avian genomes. These methods require sequence data, either assembled draft genome or raw sequences derived from the heterogametic sex (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28807610/genome-sequencing-of-two-bacillus-anthracis-strains-a-virulent-strain-and-a-vaccinal-strain
#6
Franciele Maboni Siqueira, Samuel Paulo Cibulski, Fabiana Quoos Mayer, David Driemeier, Saulo Petinatti Pavarini, Agueda Palmira Castagna de Vargas
Bacillus anthracis strain SPV842_15 was isolated from bovine fetus, while B. anthracis strain Brazilian vaccinal was recovered from a commercial vaccine. We report here the genome sequences of both strains. The SPV842_15 genome is composed of a single circular chromosome with a length of 5,228,664 base pairs, and comprises 5911 coding sequences. In turn, the Brazilian vaccinal genome remains in 201 contigs with 5733 coding sequences. Both genomes have an overall C+G content of 35.4%, and 11 genes encoding the ribosomal RNAs (rRNAs) 5S, 16S and 23S...
July 31, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28798212/the-dna-triangle-and-its-application-to-learning-meiosis
#7
L Kate Wright, Christina M Catavero, Dina L Newman
Although instruction on meiosis is repeated many times during the undergraduate curriculum, many students show poor comprehension even as upper-level biology majors. We propose that the difficulty lies in the complexity of understanding DNA, which we explain through a new model, the DNA triangle The DNA triangle integrates three distinct scales at which one can think about DNA: chromosomal, molecular, and informational Through analysis of interview and survey data from biology faculty and students through the lens of the DNA triangle, we illustrate important differences in how novices and experts are able to explain the concepts of ploidy, homology, and mechanism of homologous pairing Similarly, analysis of passages from 16 different biology textbooks shows a large divide between introductory and advanced material, with introductory books omitting explanations of meiosis-linked concepts at the molecular level of DNA...
2017: CBE Life Sciences Education
https://www.readbyqxmd.com/read/28797117/analysis-of-the-impact-of-the-absence-of-rad51-strand-exchange-activity-in-arabidopsis-meiosis
#8
Gunjita Singh, Olivier Da Ines, Maria Eugenia Gallego, Charles I White
The ploidy of eukaryote gametes must be halved to avoid doubling of numbers of chromosomes with each generation and this is carried out by meiosis, a specialized cell division in which a single chromosomal replication phase is followed by two successive nuclear divisions. With some exceptions, programmed recombination ensures the proper pairing and distribution of homologous pairs of chromosomes in meiosis and recombination defects thus lead to sterility. Two highly related recombinases are required to catalyse the key strand-invasion step of meiotic recombination and it is the meiosis-specific DMC1 which is generally believed to catalyse the essential non-sister chromatid crossing-over, with RAD51 catalysing sister-chromatid and non-cross-over events...
2017: PloS One
https://www.readbyqxmd.com/read/28794186/hfq-links-translation-repression-to-stress-induced-mutagenesis-in-e-coli
#9
Jiandong Chen, Susan Gottesman
Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA-RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis...
August 9, 2017: Genes & Development
https://www.readbyqxmd.com/read/28793327/qtl-mapping-for-nine-drought-responsive-agronomic-traits-in-bread-wheat-under-irrigated-and-rain-fed-environments
#10
Vijay Gahlaut, Vandana Jaiswal, Bhudeva S Tyagi, Gyanendra Singh, Sindhu Sareen, Harindra S Balyan, Pushpendra Kumar Gupta
In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits...
2017: PloS One
https://www.readbyqxmd.com/read/28792998/validation-of-qf-pcr-for-prenatal-diagnoses-in-a-brazilian-population
#11
Renata Wendel de Moraes, Mario Henrique Burlacchini de Carvalho, Antonio Gomes de Amorim-Filho, Rossana Pulcineli Vieira Francisco, Renata Moscolini Romão, José Eduardo Levi, Marcelo Zugaib
OBJECTIVES: Quantitative fluorescence polymerase chain reaction (QF-PCR) is a rapid and reliable method for screening aneuploidies, but in Brazil, it is not used in public services. We investigated the accuracy of QF-PCR for the prenatal recognition of common aneuploidies and compared these results with cytogenetic results in our laboratory. METHOD: A ChromoQuant QF-PCR kit containing 24 primer pairs targeting loci on chromosomes 21, 13, 18, X and Y was employed to identify aneuploidies of the referred chromosomes...
July 2017: Clinics
https://www.readbyqxmd.com/read/28791037/adaptation-of-the-pivotal-differential-genome-pattern-for-the-induction-of-intergenomic-chromosome-recombination-in-hybrids-of-synthetic-amphidiploids-within-triticeae-tribe
#12
Michal T Kwiatek, Joanna Majka, Maciej Majka, Jolanta Belter, Halina Wisniewska
A pivotal-differential evolution pattern is when two allopolyploids share a common genome, which is called pivotal, and differ with respect to the other genome or genomes, called differential. This feature induces the intergenomic recombination between chromosomes of differential genomes, which can lead to speciation. Our study is a cytomolecular insight into this mechanism which was adapted for the induction of intergenomic chromosome recombination in hybrids of synthetic amphidiploids Aegilops biuncialis × S...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28774726/girardia-dorotocephala-transcriptome-sequence-assembly-and-validation-through-characterization-of-piwi-homologs-and-stem-cell-progeny-markers
#13
Eugene Matthew P Almazan, Sydney L Lesko, Michael P Markey, Labib Rouhana
Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities...
August 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28771935/parallel-stranded-dna-and-rna-duplexes-structural-features-and-potential-applications
#14
REVIEW
Marta Szabat, Ryszard Kierzek
Nowadays, decades after the discovery of the right-handed B-DNA, it is well known that nucleic acids have a great conformational flexibility, exhibiting a large polymorphism of their structures. In nature, DNA and RNA exist in an antiparallel orientation, stabilized by Watson-Crick base pairs. However, in some cases, nucleic acid fragments with specific nucleotide sequences can adopt a parallel orientation involving noncanonical base pairing. Interestingly, parallel-stranded duplexes have been found in specific chromosome regions...
August 3, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28771462/a-tetrad-of-chromatin-interactions-for-chromosome-pairing-in-x-inactivation
#15
Ivan Krivega, Ann Dean
No abstract text is available yet for this article.
August 3, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28770277/quantitative-pcr-an-alternative-approach-to-detect-common-copy-number-alterations-in-multiple-myeloma
#16
M C Chillón, C Jiménez, R García-Sanz, M Alcoceba, I Prieto, M García-Alvarez, A Antón, R Maldonado, M Hernández-Ruano, M González, N C Gutiérrez, M E Sarasquete
Chromosome 1q gains and 13q deletions are common cytogenetic aberrations in multiple myeloma (MM) that confer a poor prognosis. There are several techniques for the targeted study of these alterations, but interphase fluorescence in situ hybridization (FISH) is the current gold standard. The aim of the present study was to validate quantitative PCR (qPCR) as an alternative to FISH studies in CD138+-enriched plasma cells (PCs) from MM patients at diagnosis. We analyzed 1q gains and 13q deletions by qPCR in 57 and 60 MM patients, respectively...
August 2, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28770061/chromosomal-distribution-of-interstitial-telomeric-sequences-as-signs-of-evolution-through-chromosome-fusion-in-six-species-of-the-giant-water-bugs-hemiptera-belostoma
#17
Mónica G Chirino, Martina Dalíková, František R Marec, María J Bressa
Tandem arrays of TTAGG repeats show a highly conserved location at the telomeres across the phylogenetic tree of arthropods. In giant water bugs Belostoma, the chromosome number changed during speciation by fragmentation of the single ancestral X chromosome, resulting in a multiple sex chromosome system. Several autosome-autosome fusions and a fusion between the sex chromosome pair and an autosome pair resulted in the reduced number in several species. We mapped the distribution of telomeric sequences and interstitial telomeric sequences (ITSs) in Belostoma candidulum (2n = 12 + XY/XX; male/female), B...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28761808/machine-learning-classification-of-22q11-2-deletion-syndrome-a-diffusion-tensor-imaging-study
#18
Daniel S Tylee, Zora Kikinis, Thomas P Quinn, Kevin M Antshel, Wanda Fremont, Muhammad A Tahir, Anni Zhu, Xue Gong, Stephen J Glatt, Ioana L Coman, Martha E Shenton, Wendy R Kates, Nikos Makris
Chromosome 22q11.2 deletion syndrome (22q11.2DS) is a genetic neurodevelopmental syndrome that has been studied intensively in order to understand relationships between the genetic microdeletion, brain development, cognitive function, and the emergence of psychiatric symptoms. White matter microstructural abnormalities identified using diffusion tensor imaging methods have been reported to affect a variety of neuroanatomical tracts in 22q11.2DS. In the present study, we sought to combine two discovery-based approaches: (1) white matter query language was used to parcellate the brain's white matter into tracts connecting pairs of 34, bilateral cortical regions and (2) the diffusion imaging characteristics of the resulting tracts were analyzed using a machine-learning method called support vector machine in order to optimize the selection of a set of imaging features that maximally discriminated 22q11...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28761142/methylation-profile-of-a-satellite-dna-constituting-the-intercalary-g-c-rich-heterochromatin-of-the-cut-trough-shell-spisula-subtruncata-bivalvia-mactridae
#19
Daniel García-Souto, Brankica Mravinac, Eva Šatović, Miroslav Plohl, Paloma Morán, Juan J Pasantes
Tandemly repeated DNAs usually constitute significant portions of eukaryotic genomes. In bivalves, however, repetitive DNAs are habitually not widespread. In our search for abundant repetitive DNAs in trough shells, we discovered a novel satellite DNA, SSUsat, which constitutes at least 1.3% of the genome of Spisula subtruncata. As foreseen by the satellite DNA library hypothesis, we confirmed that this satellite DNA is also present in two other Mactridae species, showing a highly conserved nucleotide sequence together with a dramatic diminution in the number of repeats...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28760747/significant-synteny-and-co-localization-of-ecologically-relevant-quantitative-trait-loci-within-and-across-species-of-salmonid-fishes
#20
Arne Jacobs, Robyn Womack, Mel Chen, Karim Gharbi, Kathryn Elmer
The organization of functional regions within genomes has important implications for evolutionary potential. Considerable research effort has gone toward identifying the genomic basis of phenotypic traits of interest through quantitative trait loci (QTL) analyses. Less research has assessed the arrangement of QTL in the genome within and across species. To investigate the distribution, extent of co-localization, and the synteny of QTL for ecologically relevant traits, we used a comparative genomic mapping approach within and across a range of salmonid species...
July 31, 2017: Genetics
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