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Miten Jain, Hugh E Olsen, Daniel J Turner, David Stoddart, Kira V Bulazel, Benedict Paten, David Haussler, Huntington F Willard, Mark Akeson, Karen H Miga
The human genome reference sequence remains incomplete owing to the challenge of assembling long tracts of near-identical tandem repeats in centromeres. We implemented a nanopore sequencing strategy to generate high-quality reads that span hundreds of kilobases of highly repetitive DNA in a human Y chromosome centromere. Combining these data with short-read variant validation, we assembled and characterized the centromeric region of a human Y chromosome.
March 19, 2018: Nature Biotechnology
Sabrina Z Jan, Aldo Jongejan, Cindy M Korver, Saskia K M van Daalen, Ans M M van Pelt, Sjoerd Repping, Geert Hamer
To prevent chromosomal aberrations to be transmitted to the offspring, strict meiotic checkpoints are in place to remove aberrant spermatocytes. However, in about 1% of all males these checkpoints cause complete meiotic arrest leading to azoospermia and subsequent infertility. We here unravel two clearly distinct meiotic arrest mechanisms that act during the prophase of human male meiosis. Type I arrested spermatocytes display severe asynapsis of the homologous chromosomes, disturbed XY-body formation and increased expression of the Y-chromosome encoded gene ZFY and seem to activate a DNA damage pathway leading to induction of p63, possibly causing spermatocyte apoptosis...
March 14, 2018: Development
C Krausz, Francesca Cioppi, Antoni Riera-Escamilla
Male infertility affects about 7% of the general male population, and it is a multifactorial, polygenic pathological condition. Known genetic factors, accounting for about 20-25% of male factor infertility, are present in each etiological category: i) hypothalamic-pituitary axis dysfunction; ii) quantitative and qualitative alterations of spermatogenesis; iii) ductal obstruction/dysfunction. Areas covered: All routinely available genetic tests are described. Indication for testing for chromosomal anomalies and Y chromosome microdeletions is based on sperm count (severe oligozoospermia/azoospermia)...
March 15, 2018: Expert Review of Molecular Diagnostics
Thomas C A Royle, Dionne Sakhrani, Camilla F Speller, Virginia L Butler, Robert H Devlin, Aubrey Cannon, Dongya Y Yang
Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region's Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop)...
2018: PloS One
A A Makhrov, V S Artamonova, O V Kolmakova, M V Ponomareva
This article is devoted to presenting the hypothesis explaining the fact of a considerable prevalence of phenotypic males among the triploid pink salmon as well as the regular occurrence of intersexes, which were revealed by us. This hypothesis also explains the large proportion (in some cases) in pink salmon populations of the individuals whose genetic sex does not match the phenotypic sex. We assume that the genes encoding the factors that contribute to the transformation of individuals into males (but not the marker sequences of the Y chromosome) are present not only in the Y chromosome of pink salmon but also in the X chromosome, although in smaller quantities...
January 2018: Doklady. Biochemistry and Biophysics
Yali Xue
The Sahara was once fertile; a recent study identifies human Y-chromosomal lineages that flourished in this Green Sahara and their relation to present-day populations.
March 13, 2018: Genome Biology
F Mohammadpour Lashkari, M A Sadighi Gilani, A Ghaheri, M R Zamanian, P Borjian Boroujeni, A Mohseni Meybodi, M Sabbaghian
Disorders of sex development (DSD) are congenital abnormalities as an atypical development process in either gonadal or chromosomal structure. It is the cause of the abnormality in phenotype and characteristics. Chromosomal analysis plays an important role in the DSD determination. 45,X/46,XY mosaicism is a rare karyotype, and its prevalence is about 1.5 in 10,000 newborns. It affects the growth, hormonal balance, gonad development and histology. All data such as height, male general appearance, testis size and volume, external genitalia, spermogram and hormonal levels, testis pathology, Y chromosome microdeletion and karyotype, and assisted reproductive technology (ART) outcome were recorded based on patients profile and history...
March 12, 2018: Andrologia
Frank Tüttelmann, Christian Ruckert, Albrecht Röpke
Infertility is a common condition estimated to affect 10-15% of couples. The clinical causes are attributed in equal parts to the male and female partners. Diagnosing male infertility mostly relies on semen (and hormone) analysis, which results in classification into the two major phenotypes of oligo- and azoospermia. The clinical routine analyses have not changed over the last 20 years and comprise screening for chromosomal aberrations and Y‑chromosomal azoospermia factor deletions. These tests establish a causal genetic diagnosis in about 4% of unselected men in infertile couples and 20% of azoospermic men...
2018: Medizinische Genetik: Mitteilungsblatt des Berufsverbandes Medizinische Genetik E.V
Rulin Dai, Yuan Pan, Yan Fu, Qian Liu, Weifeng Han, Ruizhi Liu
OBJECTIVE: This study aimed to investigate the roles of male genetic factors, including Y chromosome microdeletions and chromosomal heteromorphism, in recurrent pregnancy loss (RPL) in Northeast China. STUDY DESIGN: We evaluated 1072 male patients from Northeast China whose wives had a history of two or more consecutive miscarriages. We also selected 971 infertile and 200 fertile men as control groups. Semen analysis was carried out by computer-assisted sperm analysis...
March 1, 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
Arwin Ralf, Diego Montiel González, Kaiyin Zhong, Manfred Kayser
Next generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data it now contains many thousands. The complexity of both, Y tree and NGS data provide challenges for haplogroup assignment. For effective analysis and interpretation of Y-chromosome NGS data, we present Yleaf, a publically available, automated, user-friendly software for high-resolution Y-chromosome haplogroup inference independently of library and sequencing methods...
March 6, 2018: Molecular Biology and Evolution
Dan Xue, Dong-Hua Cao, Kai Mu, Yuan Lv, Jun Yang
Turner syndrome, characterized by the presence of a monosomy X cell line, is a common chromosomal disorder. Patients with Turner syndrome are usually phenotypically female, and male cases are rarely reported. Here, we report a fetus with a mosaic karyotype: mos 45,X/46,X,del(Y)(q11.21). The fetus was initially misdiagnosed as female with Turner syndrome by both noninvasive prenatal testing and cytogenetic analysis of amniotic fluid and was subsequently found to have male anatomy by antenatal ultrasonography at 24 weeks gestational age...
March 8, 2018: Journal of Obstetrics and Gynaecology Research
Mariana N Machado, Flavia Mazzoli-Rocha, Natália V Casquilho, Tatiana Maron-Gutierrez, Victor H Ortenzi, Marcelo M Morales, Rodrigo S Fortunato, Walter A Zin
Murine papain-induced emphysema is a model that reproduces many of the features found in patients. Bone marrow-derived mononuclear cells (BMMC) have already been used to repair the alveolar epithelium in respiratory diseases, but not in the papain model. Thus, we hypothesized that BMMC could prevent the pathophysiological processes in papain-induced experimental emphysema. Female BALB/c mice received intratracheal instillation of 50 μL of saline (S groups) or papain (P groups, 10 IU/50 μl of saline) on days 1 and 7 of the experimental protocol...
2018: Frontiers in Physiology
Marcia Manterola, Taylor M Brown, Min Young Oh, Corey Garyn, Bryan J Gonzalez, Debra J Wolgemuth
The double bromodomain and extra-terminal domain (BET) proteins are critical epigenetic readers that bind to acetylated histones in chromatin and regulate transcriptional activity and modulate changes in chromatin structure and organization. The testis-specific BET member, BRDT, is essential for the normal progression of spermatogenesis as mutations in the Brdt gene result in complete male sterility. Although BRDT is expressed in both spermatocytes and spermatids, loss of the first bromodomain of BRDT leads to severe defects in spermiogenesis without overtly compromising meiosis...
March 2018: PLoS Genetics
Yong Sheng Zhang, Ying Chun Du, Li Rong Sun, Xu Hai Wang, Shuai Bing Liu, Ji Feng Xi, Chao Cheng Li, Rui Wen Ying, Song Jiang, Xiang Zu Wang, Hong Shen, Bin Jia
The mammalian Y chromosome plays a critical role in spermatogenesis. However, the exact functions of each gene on the Y chromosome have not been completely elucidated, due, in part, to difficulties in gene targeting analysis of the Y chromosome. The zinc finger protein, Y-linked (ZFY) gene was first proposed to be a sex determination factor, although its function in spermatogenesis has recently been elucidated. Nevertheless, ZFY gene targeting analysis has not been performed to date. In the present study, RNA interference (RNAi) was used to generate ZFY-interrupted Hu sheep by injecting short hairpin RNA (shRNA) into round spermatids...
March 6, 2018: Reproduction, Fertility, and Development
Selma Feldman Witchel
Normal sex development depends on the precise spatio-temporal sequence and coordination of mutually antagonistic activating and repressing factors. These factors regulate the commitment of the unipotential gonad into the binary pathways governing normal sex development. Typically, the presence of the SRY gene on the Y chromosome triggers the cascade of molecular events that lead to male sex development. Disorders of sex development comprise a heterogeneous group of congenital conditions associated with atypical development of internal and external genitalia...
November 22, 2017: Best Practice & Research. Clinical Obstetrics & Gynaecology
José R Sandoval, Daniela R Lacerda, Marilza S Jota, Ronald Elward, Oscar Acosta, Donaldo Pinedo, Pierina Danos, Cinthia Cuellar, Susana Revollo, Fabricio R Santos, Ricardo Fujita
This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries...
March 3, 2018: Molecular Genetics and Genomics: MGG
Ming Hu, Guixian Guo, Qiang Huang, Chuanfang Cheng, Ruqin Xu, Aiqun Li, Ningning Liu, Shiming Liu
Stem cell therapy can be used to repair and regenerate damaged hearts tissue; nevertheless, the low survival rate of transplanted cells limits their therapeutic efficacy. Recently, it has been proposed that exosomes regulate multiple cellular processes by mediating cell survival and communication among cells. The following study investigates whether injured cardiomyocytes-derived exosomes (cardiac exosomes) affect the survival of transplanted bone marrow mesenchymal stem cells (BMSCs) in infarcted heart. To mimic the harsh microenvironment in infarcted heart that the cardiomyocytes or transplanted BMSCs encounter in vivo, cardiomyocytes conditioned medium and cardiac exosomes collected from H2 O2 -treated cardiomyocytes culture medium were cultured with BMSCs under oxidative stress in vitro...
March 2, 2018: Cell Death & Disease
C Phillips, K Butler Gettings, J L King, D Ballard, M Bodner, L Borsuk, W Parson
The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels...
February 21, 2018: Forensic Science International. Genetics
Maximilian Schmid, Karen White, Renee Stokowski, Danielle Miller, Patrick E Bogard, Venu Valmeekam, Eric Wang
OBJECTIVES: Various methods of fetal fraction measurement have been employed in conjunction with different approaches to cfDNA testing for fetal aneuploidy. In this study we evaluate the accuracy and reproducibility of fetal fraction measurement using polymorphic assays that are incorporated into test design as part the Harmony Prenatal Test® and confirm that the single nucleotide polymorphisms (SNPs) selected for and used in these assays can be applied broadly to all patient populations...
February 26, 2018: Ultrasound in Obstetrics & Gynecology
Lara Olivieri, Debora Mazzarelli, Barbara Bertoglio, Danilo De Angelis, Carlo Previderè, Pierangela Grignani, Annalisa Cappella, Silvano Presciuttini, Caterina Bertuglia, Paola Di Simone, Nicolò Polizzi, Agata Iadicicco, Vittorio Piscitelli, Cristina Cattaneo
Every year thousands of migrants die during the endeavour to reach the Italian coasts, making the Mediterranean the theatre of one of the greatest tragedies of mankind. Over 60% of these victims is buried unidentified: one of the reasons behind this is related to the specific difficulties and lack of strategies concerning AM and PM data collection. The present article describes how Italy is trying to face the problem of migrant identification, thanks to the collaboration between government, the Italian national police and universities...
February 6, 2018: Forensic Science International
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