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https://www.readbyqxmd.com/read/28915793/the-cacao-criollo-genome-v2-0-an-improved-version-of-the-genome-for-genetic-and-functional-genomic-studies
#1
X Argout, G Martin, G Droc, O Fouet, K Labadie, E Rivals, J M Aury, C Lanaud
BACKGROUND: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. METHODS: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome...
September 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28915715/epigenetic-regulation-during-the-differentiation-of-stem-cells-to-germ-cells
#2
REVIEW
Yuan-Chao Sun, Yong-Yong Wang, Wei Ge, Shun-Feng Cheng, Paul W Dyce, Wei Shen
Gametogenesis is an essential process to ensure the transfer of genetic information from one generation to the next. It also provides a mechanism by which genetic evolution can take place. Although the genome of primordial germ cells (PGCs) is exactly the same with somatic cells within an organism, there are significant differences between their developments. For example, PGCs eventually undergo meiosis to become functional haploid gametes, and prior to that they undergo epigenetic imprinting which greatly alter their genetic regulation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915635/dysregulation-of-an-x-linked-primate-specific-epididymal-microrna-cluster-in-unexplained-asthenozoospermia
#3
Xingrong Qing, Jian Shi, Tingting Dong, Chunlin Wu, Lian Hu, Honggang Li
Asthenoszoopermia, characterized by reduced sperm motility, is one of the primary forms of male infertility. Whereas most cases were diagnosed into unexplained asthenozoospermia (UA) because the etiology cannot be identified. In animal models, epigenetic dysregulation in epididymis can impair sperm maturation and result in asthenozoospermia. However, researches of epididymal epigenetic regulation on humans are impeded by the difficulty in obtaining epididymal tissues. We previously identified cell-free seminal microRNAs predominately derived from epididymis in human ejaculate...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28914051/chromosome-centric-human-proteome-project-allies-with-developmental-biology-a-case-study-of-the-role-of-y-chromosome-genes-in-organ-development
#4
Anna Meyfour, Paria Pooyan, Sara Pahlavan, Mostafa Rezaei-Tavirani, Hamid Gourabi, Hossein Baharvand, Ghasem Hosseini Salekdeh
One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination...
September 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28913147/summary-of-2185-prenatal-invasive-procedures-in-a-single-center-a-retrospective-analysis
#5
Hüseyin Çağlayan Özcan, Mete Gürol Uğur, Seyhun Sucu, Aynur Mustafa, Neslihan Bayramoğlu Tepe, Özcan Balat
OBJECTIVE: To determine the frequency, indications, and outcomes of diagnostic invasive prenatal procedures (DIPP) performed in a university hospital. MATERIALS AND METHODS: This retrospective, observational study included 2185 cases of DIPP (chorionic villus sampling, amniocentesis, and cordocentesis) performed at the department of obstetrics and gynecology of a university hospital between 2010 and 2016. We included all DIPP cases performed between 11 and 24 weeks of gestation...
June 2017: Turk J Obstet Gynecol
https://www.readbyqxmd.com/read/28910456/identification-of-alk-rearrangements-in-malignant-peritoneal-mesothelioma
#6
Yin P Hung, Fei Dong, Jaclyn C Watkins, Valentina Nardi, Raphael Bueno, Paola Dal Cin, John J Godleski, Christopher P Crum, Lucian R Chirieac
Importance: Malignant peritoneal mesothelioma is a rare, aggressive tumor arising from the peritoneal lining, induced by asbestos, therapeutic radiation, or germline mutations. Nevertheless, the molecular features remain largely unknown. Objective: To investigate anaplastic lymphoma kinase (ALK) rearrangements in a large series of peritoneal mesothelioma and characterize the mutational landscape of these tumors. Design, Setting, and Participants: We studied 88 consecutive patients (39 men, 49 women; median age 61, range 17-84 years) with peritoneal mesotheliomas diagnosed at a single institution between 2005 and 2015...
September 14, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28904421/impact-of-preservation-conditions-on-fatty-acids-xanthan-gum-production-and-other-characteristics-of-xanthomonas-campestris-pv-mangiferaeindicae-ibsbf-2103
#7
Graciete S Silva, Denilson J Assis, Janice I Druzian, Maria B P P Oliveira, Paulo L L Ribeiro, Soraia M Cordeiro, Cleber A Schmidt
The conditions of storage, cultivation and maintenance of microbial cultures should preserve the microbiological homogeneity, phenotypic and genotypic characteristics to ensure better reproducibility of metabolic production. To evaluate the influence of the storage condition on the composition of cell fatty acids, genetic profile and biochemical characteristics of Xanthomonas campestris pv. mangiferaeindicae IBSBF 2103, as well as, to identify its relationship with the yielding and viscosity of the xanthan gum produced, this study monitored the strain preserved in two simple and widely used conditions, ultra-freezer (-80 °C) and refrigeration (3-8 °C) during 5 months...
September 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28904386/skewed-x-inactivation-in-lesch-nyhan-disease-carrier-females
#8
Rosa J Torres, Juan G Puig
X chromosome inactivation (XCI) ratios of normal females can range from a highly skewed ratio of 0:100 to a 50:50 ratio. In several X-linked disorders, female carriers present skewed X inactivation. Hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency is an X-linked disorder. Males are affected and present with the complete Lesch-Nyhan disease (LND) or with a partial phenotype (Lesch-Nyhan variant, LNV). Female carriers are usually asymptomatic. The aim of the present study was to analyze the XCI pattern of HPRT-deficiency carrier females...
September 14, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28904021/bap-exposure-causes-oocyte-meiotic-arrest-and-fertilization-failure-to-weaken-female-fertility
#9
Mianqun Zhang, Yilong Miao, Qian Chen, Meng Cai, Wenkang Dong, Xiaoxin Dai, Yajuan Lu, Changyin Zhou, Zhaokang Cui, Bo Xiong
Benzo[a]pyrene (BaP) is a ubiquitous environmental pollutant and carcinogen that is frequently found in particulate matter, with a diameter of ≤2.5 μm (PM2.5). It has been reported to interrupt the normal reproductive system, but the exact molecular basis has not been clearly defined. To understand the underlying mechanisms regarding how BaP exposure disrupts female fertility, we evaluated oocyte quality by assessing the critical regulators and events during oocyte meiotic maturation and fertilization. We found that BaP exposure compromised the mouse oocyte meiotic progression by disrupting normal spindle assembly, chromosome alignment, and kinetochore-microtubule attachment, consequently leading to the generation of aneuploid eggs...
September 13, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28903905/the-pathogenicity-of-genomic-genetic-variant-of-x-chromosomal-genes-in-males-with-intellectual-disability
#10
Ji-Ping Peng, Fang Liu, Hua Xie, Xiao-Li Chen
Intellectual Disability (ID, previously named mental retardation) is a group of common pediatric neurology disorders characterized by extensive genetic and phenotypic heterogeneity. About 25%-50% of ID was caused by genomic/genetic variants, in which genomic/genetic variants of X-chromosome are one of key pathogenic causation (25%-30%), resulting in X-linked ID (XLID). The epidemiological data showed that the male to female ratio is 1.3: 1 in ID patients. The prevalence of XLID in the whole ID population is 10%-15%, and this prevalence reaches 20%-25% in the male ID population...
June 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28903352/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#11
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28901819/dna-methylation-changes-in-human-lung-epithelia-cells-exposed-to-multi-walled-carbon-nanotubes
#12
Marta I Sierra, Laura Rubio, Gustavo F Bayón, Isabel Cobo, Pablo Menendez, Paula Morales, Cristina Mangas, Rocio G Urdinguio, Virginia Lopez, Adolfo Valdes, Gerard Vales, Ricard Marcos, Ramon Torrecillas, Agustin F Fernández, Mario F Fraga
Humans are increasingly exposed to nanoparticles and, although many of their physiological effects have been described, the molecular mechanisms underlying them are still largely unknown. The present study aimed to determine the possible role of certain epigenetic mechanisms in the cellular response of human lung epithelial cells that are triggered by long-term exposure to titanium dioxide nanoparticles (TiO2NPs) and multi-walled carbon nanotubes (MWCNTs). The results showed that exposure to TiO2NPs had only minor effects on genome-wide DNA methylation...
September 13, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/28901681/a-vigs-screen-identifies-immunity-in-the-arabidopsis-pla-1-accession-to-viruses-in-two-different-genera-of-the-geminiviridae
#13
Maria Ines Reyes, Miguel A Flores-Vergara, Orlene Guerra-Peraza, Cyprian Rajabu, Jigar Desai, Yokiko H Hiromoto-Ruiz, Joseph Ndunguru, Linda Hanley-Bowdoin, Susanne Kjemtrup, Jose T Ascencio-Ibáñez, Dominique Robertson
Geminiviruses are DNA viruses that cause severe crop losses in different parts of the world, and there is a need for genetic sources of resistance to help combat them. Arabidopsis has been used as a source for virus resistance genes that derive from alterations in essential host factors. We used a virus-induced gene silencing (VIGS) vector derived from the geminivirus Cabbage leaf curl virus (CaLCuV) to assess natural variation in virus-host interactions in 190 Arabidopsis accessions. Silencing of CH-42, encoding a protein needed to make chlorophyll, was used as a visible marker to discriminate asymptomatic accessions from those showing resistance...
September 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28900292/a-bayesian-test-for-hardy-weinberg-equilibrium-of-biallelic-x-chromosomal-markers
#14
X Puig, J Ginebra, J Graffelman
The X chromosome is a relatively large chromosome, harboring a lot of genetic information. Much of the statistical analysis of X-chromosomal information is complicated by the fact that males only have one copy. Recently, frequentist statistical tests for Hardy-Weinberg equilibrium have been proposed specifically for dealing with markers on the X chromosome. Bayesian test procedures for Hardy-Weinberg equilibrium for the autosomes have been described, but Bayesian work on the X chromosome in this context is lacking...
October 2017: Heredity
https://www.readbyqxmd.com/read/28900090/-method-for-the-molecular-cytogenetic-visualization-of-fragile-site-fraxa
#15
T S Bobokova, N A Lemskaya, I S Kolesnikova, D V Yudkin
Fragile X syndrome is one of the most common reasons for human hereditary mental retardation. It is associated with the expansion of CGG repeats in the 5'-untranslated region of the FMR1 gene, which results in the suppression of its expression and the development of the disease. At present, methods based on PCR and Southern blot analysis are used for diagnostics of the fragile X syndrome. The presence of a fragile site FRAXA on the X chromosome is typical for patients with this pathology. We developed a method of visualizing this site in cell cultures obtained from patients using the fluorescent in situ hybridization (FISH) and the combination of two probes...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28898323/-pontocerebellar-hypoplasia-secondary-to-cask-gene-deletion-case-report
#16
Lucía Rivas, Óscar Blanco, Cristina Torreira, Alfredo Repáraz, Cristina Melcón, Alfonso Amado
INTRODUCTION: Pontocerebellar hypoplasia (PCH) is a reduction of the size of the cerebellum and pons secondary to an alteration in its development, and can be caused by neurodegenerative diseases of genetic origin, of which there are known 10 subtypes (PCH 1-10), cortical malformations, metabolic and genetic diseases. OBJECTIVE: To present the case of a child with microcephaly, PCH and West syndrome, in which the genetic study allowed to make the diagnosis of a deletion on chromosome X...
2017: Revista Chilena de Pediatría
https://www.readbyqxmd.com/read/28895353/-circulating-long-noncoding-rnas-as-biomarkers-in-tumor-diagnosis
#17
Nan Jiang, Haihua Tian, Jinchang Pan, Zhaohui Gong
Long noncoding RNAs (lncRNAs) are involved in vital life processes of gene expression, epigenetic regulation and X-chromosome inactivation. lncRNAs are also closely associated with tumor initiation and progression. Moreover, lncRNAs may enter human circulation system in the form of microvesicle or exosome, or in combination with RNA binding protein. Interestingly, the circulating lncRNAs are widely existed in body fluids, such as blood and urine. We review the origin of circulating lncRNAs, and the detection methods as potential biomarkers...
June 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28894175/sexual-congruency-in-the-connectome-and-translatome-of-vta-dopamine-neurons
#18
Amanda S Chung, Samara M Miller, Yanjun Sun, Xiangmin Xu, Larry S Zweifel
The ventral tegmental area (VTA) dopamine system is important for reward, motivation, emotion, learning, and memory. Dysfunctions in the dopamine system are linked to multiple neurological and neuropsychiatric disorders, many of which present with sex differences. Little is known about the extent of heterogeneity in the basic organization of VTA dopamine neurons with regard to sex. Here, we characterized the cell-specific connectivity of VTA dopamine neurons, their mRNA translational profile, and basic electrophysiological characteristics in a common strain of mice...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28893788/genomic-and-molecular-characterization-of-clinical-isolates-of-enterobacteriaceae-harboring-mcr-1-in-colombia-2002-2016
#19
Sandra Yamile Saavedra, Lorena Diaz, Magdalena Wiesner, Adriana Correa, Stefany Alejandra Arévalo, Jinnethe Reyes, Andrea Melissa Hidalgo, Elsa de la Cadena, Marcela Perenguez, Lucy Angeline Montaño, Javier Ardila, Rafael Ríos, María Victoria Ovalle, Paula Díaz, Paola Porras, Maria V Villegas, Cesar A Arias, Mauricio Beltrán, Carolina Duarte
Polymyxins are last resort antimicrobial agents used to treat infections caused by carbapenem-resistant Enterobacteriaceae Due to the worldwide dissemination of polymyxin resistance in animal and human isolates, we aimed to characterize polymyxin resistance associated with the presence of mcr-1 in Enterobacteriaceae and nonfermenter Gram-negative bacilli, in isolates collected retrospectively in Colombia from 2002 to 2016. A total of 5,887 Gram-negative clinical isolates were studied and 513 were found to be resistant to the polymyxins...
September 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28892214/parental-decisions-following-prenatal-diagnosis-of-sex-chromosome-aneuploidy-in-hong-kong
#20
Po Lam So, Kwun Yue Yvonne Cheng, Kwan Yiu Cheuk, Wan Kam Chiu, Shui Lam Mak, Sau Lan Mok, Tsz Kin Lo, Wai Kuen Yung, Fai Man Lo, Hon Yin Brian Chung, Sik Yau Anita Kan, Chin Peng Lee, Hoi Yin Mary Tang
AIM: According to the published work, pregnancy termination rates due to prenatal diagnosis of fetal sex chromosome aneuploidies (SCA) vary widely. Some potentially modifiable and non-modifiable factors have been reported to be associated with parental decision. This study aimed to evaluate the rate of pregnancy termination for fetal SCA and the factors influencing parents' decisions in Hong Kong. METHODS: This was a 21-year retrospective cohort study of parents' decisions following prenatal diagnosis of SCA...
September 11, 2017: Journal of Obstetrics and Gynaecology Research
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