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JOURNAL ARTICLE
Man Xu, Nan Yang, Jiang Pan, Qiang Hua, Chun-Xiu Li, Jian-He Xu
Squalene is a high-value antioxidant with many commercial applications. The use of microbial cell factories to produce squalene as an alternative to plant and animal extracts could meet increasing market demand. Yarrowia lipolytica is an excellent host for squalene production due to its high levels of acetyl-CoA and a hydrophobic environment. However, the need for precise and complicated gene editing has hindered the industrialization of this strain. Herein, the rapid construction of a strain with high squalene production was achieved by enhancing the homologous recombination efficiency in Y...
April 18, 2024: Journal of Agricultural and Food Chemistry
#42
REVIEW
Nurul Nadia Mohamad Zamberi, Asmaa Y Abuhamad, Teck Yew Low, M Aiman Mohtar, Saiful Effendi Syafruddin
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing is evolving into an essential tool in the field of biological and medical research. Notably, the development of catalytically deactivated Cas9 (dCas9) enzyme has substantially broadened its traditional boundaries in gene editing or perturbation. The conjugation of dCas9 with various molecular effectors allows precise control over transcriptional processes, epigenetic modifications, visualization of chromosomal dynamics, and several other applications...
April 2024: CRISPR Journal
#43
JOURNAL ARTICLE
Bin Li, Weiyao Xiong, Wu Zuo, Yuanyuan Shi, Teng Wang, Lingling Chang, Yueheng Wu, Heng Ma, Qian Bian, Alex C Y Chang
Telomeres, TTAGGGn DNA repeat sequences located at the ends of eukaryotic chromosomes, play a pivotal role in aging and are targets of DNA damage response. Although we and others have demonstrated presence of short telomeres in genetic cardiomyopathic and heart failure cardiomyocytes, little is known about the role of telomere lengths in cardiomyocyte. Here, we demonstrate that in heart failure patient cardiomyocytes, telomeres are shortened compared to healthy controls. We generated isogenic human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) with short telomeres (sTL-CMs) and normal telomeres (nTL-CMs) as model...
April 18, 2024: Nucleic Acids Research
#44
JOURNAL ARTICLE
Lajos Gergely, Vanda Repiská, Daniel Böhmer, Miroslav Korbeľ, Zuzana Václavová, Liam McCullough, Katarína Melišová, Petra Priščáková
BACKGROUND: Abortion and fetal death are common in fetuses with holoprosencephaly, so genetic examinations often have to be made in a post-mortem setting. The efficiency of the conventional karyotyping using cultured fibroblasts in these situations is limited due to frequent culture failure. In the current study, archived cases of holoprosencephaly, where post-mortem genetic evaluation was requested and sufficient frozen material was available, were reevaluated using the quantitative fluorescence polymerase chain reaction (QF-PCR) technique...
April 2024: Birth Defects Research
#45
JOURNAL ARTICLE
Robert Dagostino, Assaf Gottlieb
BACKGROUND: Deciphering gene regulation is essential for understanding the underlying mechanisms of healthy and disease states. While the regulatory networks formed by transcription factors (TFs) and their target genes has been mostly studied with relation to cis effects such as in TF binding sites, we focused on trans effects of TFs on the expression of their transcribed genes and their potential mechanisms. RESULTS: We provide a comprehensive tissue-specific atlas, spanning 49 tissues of TF variations affecting gene expression through computational models considering two potential mechanisms, including combinatorial regulation by the expression of the TFs, and by genetic variants within the TF...
April 17, 2024: BMC Genomics
#46
JOURNAL ARTICLE
Han Wei, Zhang Qing-Zhen, Yang Jing, Zhou Zhe
With the increasing number of complex forensic cases in recent years, it's more important to combine the different types of genetic markers such as short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (InDels), and microhaplotypes (MHs) to provide more genetic information. In this study, we selected totally 201 genetic markers, including 24 autosomes STRs (A-STRs), 24 Y chromosome STRs (Y-STRs), 110 A-SNPs, 24 Y-SNPs, 9 A-InDels, 1 Y-InDel, 8 MHs, and Amelogenin to establish the HID_AM Panel v1...
April 20, 2024: Yi Chuan, Hereditas
#47
REVIEW
Yue Li, Ruishuang Ma, Xia Hao
Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) represents the initial tumor suppressor gene identified to possess phosphatase activity, governing various cellular processes including cell cycle regulation, migration, metabolic pathways, autophagy, oxidative stress response, and cellular senescence. Current evidence suggests that PTEN is critical for stem cell maintenance, self-renewal, migration, lineage commitment, and differentiation. Based on the latest available evidence, we provide a comprehensive overview of the mechanisms by which PTEN regulates activities of different stem cell populations and influences neurological disorders, encompassing autism, stroke, spinal cord injury, traumatic brain injury, Alzheimer's disease and Parkinson's disease...
April 16, 2024: Cell Death & Disease
#48
JOURNAL ARTICLE
Xiao-Bo Wang, Hong-Wei Lu, Qing-You Liu, A-Lun Li, Hong-Ling Zhou, Yong Zhang, Tian-Qi Zhu, Jue Ruan
BACKGROUND: Most currently available reference genomes lack the sequence map of sex-limited (such as Y and W) chromosomes, which results in incomplete assemblies that hinder further research on sex chromosomes. Recent advancements in long-read sequencing and population sequencing have provided the opportunity to assemble sex-limited chromosomes without the traditional complicated experimental efforts. FINDINGS: We introduce the first computational method, Sorting long Reads of Y or other sex-limited chromosome (SRY), which achieves improved assembly results compared to flow sorting...
January 2, 2024: GigaScience
#49
JOURNAL ARTICLE
Kai-Xiong Qing, Amy C Y Lo, Siduo Lu, You Zhou, Dan Yang, Di Yang
The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and the subsequent damage caused by tissue reperfusion. Some research indicated that the retinal injury induced by ischemia-reperfusion (I/R) was related to reperfusion time.In this study, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model group and at different reperfusion time (24h, 72h, and 7d) with the aid of whole transcriptome sequencing technology, and the trend changes in time-varying mRNA, lncRNA, circRNA were obtained by chronological analysis...
April 15, 2024: BMC Genomics
#50
JOURNAL ARTICLE
Jianhai Chen, Yangying Jia, Jie Zhong, Kun Zhang, Hongzheng Dai, Guanglin He, Fuping Li, Li Zeng, Chuanzhu Fan, Huayan Xu
BACKGROUND: As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. METHODS: In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men...
April 15, 2024: Journal of Medical Genetics
#51
JOURNAL ARTICLE
Cui Chen, Junyi Jiang, Qin Yang, Xiaojing Cheng, Guiling Wang
This study aims to investigate the association between chromosomal polymorphisms and abnormalities in male reproductive health. Within the period from January 2018 to December 2022, a cohort of 10,827 males seeking fertility services at our reproductive center was selected for inclusion in this study. Peripheral blood chromosomal karyotype analysis was conducted for each participant to identify carriers of chromosomal polymorphisms, who were subsequently categorized into a polymorphism group. Additionally, a control group was constituted by randomly selecting 1,630 patients exhibiting normal chromosomal karyotypes...
April 15, 2024: Reproductive Sciences
#52
JOURNAL ARTICLE
Somayeh Alinaghi, Marzieh Mohseni, Zohreh Fattahi, Maryam Beheshtian, Fatemeh Ghodratpour, Farzane Zare Ashrafi, Sanaz Arzhangi, Khadijeh Jalalvand, Reza Najafipour, Hamid Reza Khorram Khorshid, Kimia Kahrizi, Hossein Najmabadi
BACKGROUND: The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies. METHODS: The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit...
February 1, 2024: Archives of Iranian Medicine
#53
JOURNAL ARTICLE
Jiashuo Zhang, Xuebo Li, Liangliang Li, Anqi Chen, Suhua Zhang
The goal of the following study is to clarify whether the skeletal remains over 70 years old from missing persons and their alleged relatives shared identical Y-STR loci. Nowadays, advances in ancient DNA extraction techniques and approaches of using multiple different Y-STRs have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Given the ages and conditions of the skeletal remains, ancient DNA extraction methods can be used to maximize the probability of DNA recovery...
June 2024: Forensic Sciences Research
#54
Aleksandra Greshnova, Karol Pál, Juan Francisco Iturralde Martinez, Stefan Canzar, Kateryna D Makova
Y chromosomes of great apes harbor A mpliconic G enes (YAGs)-multi-copy gene families ( BPY2 , CDY , DAZ , HSFY , PRY , RBMY , TSPY , VCY , and XKRY ) that encode proteins important for spermatogenesis. Previous work assembled YAG transcripts based on their targeted sequencing but not using reference genome assemblies, potentially resulting in an incomplete transcript repertoire. Here we used the recently produced gapless telomere-to-telomere (T2T) Y chromosome assemblies of great ape species (bonobo, chimpanzee, human, gorilla, Bornean orangutan, and Sumatran orangutan) and analyzed RNA data from whole-testis samples for the same species...
April 3, 2024: bioRxiv
#55
JOURNAL ARTICLE
Nayla Y León, Thanh Nha Uyen Le, Andrew Garvie, Lee H Wong, Stefan Bagheri-Fam, Vincent R Harley
ATR-X (alpha thalassemia, mental retardation, X-linked) syndrome features genital and testicular abnormalities including atypical genitalia and small testes with few seminiferous tubules. Our mouse model recapitulated the testicular defects when Atrx was deleted in Sertoli cells (Sc Atrx KO) which displayed G2/M arrest and apoptosis. Here, we investigated the mechanisms underlying these defects. In control mice, Sertoli cells contain a single novel "GATA4 PML nuclear body (NB)" that contained the transcription factor GATA4, ATRX, DAXX, HP1α, and PH3 and co-localized with the Y chromosome short arm (Yp)...
May 17, 2024: IScience
#56
JOURNAL ARTICLE
Kaitlyn J Nielson, Ross Rowsey, Surendra Dasari, William R Sukov, Benjamin R Kipp, Aditya Raghunathan, Rumeal D Whaley, Kingsley Ebare, Melissa L Stanton, Jordan P Reynolds, Vidit Sharma, R Houston Thompson, Stephen A Boorjian, Bradley C Leibovich, Loren Herrera Hernandez, Rafael E Jimenez, John C Cheville, Sounak Gupta
Mucinous tubular and spindle cell carcinoma (MTSCC) shows significant overlap with papillary renal cell carcinoma (PRCC), and harbor recurrent copy-number alterations (CNA). We evaluated 16 RCC with features suggestive of MTSCC using chromosomal microarrays. The cohort was comprised of 8 females and males, each, with an age range of 33-79 years (median, 59), and a tumor size range of 3.4-15.5 cm (median, 5.0). Half the tumors were high-grade (8/16, 50%) with features such as necrosis, marked cytologic atypia, and sarcomatoid differentiation, and 5/16 (31%) were high stage (≥pT3a)...
April 12, 2024: Human Pathology
#57
JOURNAL ARTICLE
Bianca Sacchi, Zoë Humphries, Jana Kružlicová, Markéta Bodláková, Cassandre Pyne, Baharul Choudhury, Yunchen Gong, Václav Bačovský, Roman Hobza, Spencer C H Barrett, Stephen I Wright
Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10MYA) and neo (<200,000 years) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup R...
April 12, 2024: Molecular Biology and Evolution
#58
JOURNAL ARTICLE
Rupin Shah, Amarnath Rambhatla, Widi Atmoko, Marlon Martinez, Imad Ziouziou, Priyank Kothari, Nicholas Tadros, Nguyen Ho Vinh Phuoc, Parviz Kavoussi, Ahmed Harraz, Gianmaria Salvio, Murat Gul, Taha Hamoda, Tuncay Toprak, Ponco Birowo, Edmund Ko, Mohamed Arafa, Ramy Abou Ghayda, Vilvapathy Senguttuvan Karthikeyan, Ramadan Saleh, Giorgio Ivan Russo, Germar-Michael Pinggera, Eric Chung, Missy Savira, Giovanni M Colpi, Wael Zohdy, Edoardo Pescatori, Hyun Jun Park, Shinichiro Fukuhara, Akira Tsujimura, Cesar Rojas-Cruz, Angelo Marino, Siu King Mak, Edouard Amar, Wael Ibrahim, Puneet Sindhwani, Naif Alhathal, Gian Maria Busetto, Manaf Al Hashimi, Ahmed El-Sakka, Asci Ramazan, Fotios Dimitriadis, Massimiliano Timpano, Davor Jezek, Baris Altay, Daniel Suslik Zylbersztejn, Michael Yc Wong, Du Geon Moon, Christine Wyns, Safar Gamidov, Hamed Akhavizadegan, Alessandro Franceschelli, Kaan Aydos, Vinh Nguyen Quang, Shedeed Ashour, Adel Al Dayel, Mohamed S Al-Marhoon, Sava Micic, Saleh Binsaleh, Alayman Hussein, Haitham Elbardisi, Taymour Mostafa, Emad Taha, Jonathan Ramsay, Athanasios Zachariou, Islam Fathy Soliman Abdelrahman, Osvaldo Rajmil, Arif Kalkanli, Juan Manuel Corral Molina, Kadir Bocu, Gede Wirya Kusuma Duarsa, Gokhan Ceker, Ege Can Serefoglu, Fahmi Bahar, Nazim Gherabi, Shinnosuke Kuroda, Abderrazak Bouzouita, Ahmet Gudeloglu, Erman Ceyhan, Mohamed Saeed Mohamed Hasan, Muhammad Ujudud Musa, Ahmad Motawi, Cho Chak-Lam, Hisanori Taniguchi, Christopher Chee Kong Ho, Jesus Fernando Solorzano Vazquez, Shingai Mutambirwa, Nur Dokuzeylul Gungor, Marion Bendayan, Carlo Giulioni, Aykut Baser, Marco Falcone, Luca Boeri, Gideon Blecher, Alireza Kheradmand, Tamilselvi Sethupathy, Ricky Adriansjah, Nima Narimani, Charalampos Konstantinidis, Tuan Thanh Nguyen, Andrian Japari, Parisa Dolati, Keerti Singh, Cevahir Ozer, Selcuk Sarikaya, Nadia Sheibak, Ndagijimana Jean Bosco, Mehmet Serkan Özkent, Sang Thanh Le, Ioannis Sokolakis, Darren Katz, Ryan Smith, Manh Nguyen Truong, Tan V Le, Zhongwei Huang, Muslim Dogan Deger, Umut Arslan, Gokhan Calik, Giorgio Franco, Ayman Rashed, Oguzhan Kahraman, Sotiris Andreadakis, Rosadi Putra, Giancarlo Balercia, Kareim Khalafalla, Rossella Cannarella, Anh Ðăng Tuân, Amr El Meliegy, Birute Zilaitiene, Marlene Lizbeth Zamora Ramirez, Filippo Giacone, Aldo E Calogero, Konstantinos Makarounis, Sunil Jindal, Bac Nguyen Hoai, Ravi Banthia, Marcelo Rodriguez Peña, Dharani Moorthy, Aram Adamyan, Deniz Kulaksiz, Hussein Kandil, Nikolaos Sofikitis, Ciro Salzano, Andreas Jungwirth, Surendra Reddy Banka, Tiago Cesar Mierzwa, Tahsin Turunç, Divyanu Jain, Armen Avoyan, Pietro Salacone, Ateş Kadıoğlu, Chirag Gupta, Haocheng Lin, Iman Shamohammadi, Nasser Mogharabian, Trenton Barrett, Yavuz Onur Danacıoğlu, Andrea Crafa, Salima Daoud, Vineet Malhotra, Abdulmalik Almardawi, Osama Mohamed Selim, Mohamad Moussa, Saeid Haghdani, Mesut Berkan Duran, Yannic Kunz, Mirko Preto, Elena Eugeni, Thang Nguyen, Ahmed Rashad Elshahid, Seso Sulijaya Suyono, Dyandra Parikesit, Essam Nada, Eduardo Gutiérrez Orozco, Florence Boitrelle, Nguyen Thi Minh Trang, Mounir Jamali, Raju Nair, Mikhail Ruzaev, Franco Gadda, Charalampos Thomas, Raphael Henrique Ferreira, Umit Gul, Serena Maruccia, Ajay Kanbur, Ella Kinzikeeva, Saad Abumelha, Nguyen Quang, Raghavender Kosgi, Fatih Gokalp, Mohammad Ayodhia Soebadi, Gustavo Marquesine Paul, Hesamoddin Sajadi, Deepak Gupte, Rafael F Ambar, Emrullah Sogutdelen, Karun Singla, Ari Basurkano, Shannon Hee Kyung Kim, Mohammad Ali Sadighi Gilani, Koichi Nagao, Sakti Ronggowardhana Brodjonegoro, Andri Rezano, Mohamed Elkhouly, Rossella Mazzilli, Hasan M A Farsi, Hung Nguyen Ba, Hamed Alali, Dimitrios Kafetzis, Tran Quang Tien Long, Sami Alsaid, Hoang Bao Ngoc Cuong, Knigavko Oleksandr, Akhmad Mustafa, Herik Acosta, Hrishikesh Pai, Bahadır Şahin, Eko Arianto, Colin Teo, Sanjay Prakash Jayaprakash, Rinaldo Indra Rachman, Mustafa Gurkan Yenice, Omar Sefrioui, Smit Paghdar, Shivam Priyadarshi, Marko Tanic, Noor Kareem Alfatlawy, Fikri Rizaldi, Ranjit B Vishwakarma, George Kanakis, Dinesh Thomas Cherian, Joe Lee, Raisa Galstyan, Hakan Keskin, Jana Wurzacher, Doddy Hami Seno, Bambang S Noegroho, Ria Margiana, Qaisar Javed, Fabrizio Castiglioni, Raman Tanwar, Ana Puigvert, Coşkun Kaya, Medianto Purnomo, Chadi Yazbeck, Azwar Amir, Edson Borges, Marina Bellavia, Isaac Ardianson Deswanto, Vinod K V, Giovanni Liguori, Dang Hoang Minh, Kashif Siddiqi, Fulvio Colombo, Armand Zini, Niket Patel, Selahittin Çayan, Ula Al-Kawaz, Maged Ragab, Charalampos Konstantinidis, Guadalupe Hernández Hebrard, Ivan Hoffmann, Ozan Efesoy, Barış Saylam, Ashok Agarwal
PURPOSE: Non-obstructive azoospermia (NOA) represents the persistent absence of sperm in ejaculate without obstruction, stemming from diverse disease processes. This survey explores global practices in NOA diagnosis, comparing them with guidelines and offering expert recommendations. MATERIALS AND METHODS: A 56-item questionnaire survey on NOA diagnosis and management was conducted globally from July to September 2022. This paper focuses on part 1, evaluating NOA diagnosis...
April 3, 2024: World Journal of Men's Health
#59
JOURNAL ARTICLE
Christoph Nössing, Paula Herek, Shahrokh F Shariat, Walter Berger, Bernhard Englinger
PURPOSE OF REVIEW: Bladder cancer incidence is on the rise, and until recently, there has been little to no change in treatment regimens over the last 40 years. Hence, it is imperative to work on strategies and approaches to untangle the complexity of intra and inter-tumour heterogeneity of bladder cancer with the aim of improving patient-specific care and treatment outcomes. The focus of this review is therefore to highlight novel targets, advances, and therapy approaches for bladder cancer patients...
April 11, 2024: Current Opinion in Urology
#60
JOURNAL ARTICLE
Crystal M Tomlin, Sitaram Rajaraman, Jeanne Theresa Sebesta, Anne-Cathrine Scheen, Mika Bendiksby, Yee Wen Low, Jarkko Salojärvi, Todd P Michael, Victor A Albert, Charlotte Lindqvist
Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i...
April 10, 2024: Nature Communications
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