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JOURNAL ARTICLE
Mélissa Poncet, Maureen Féménia, Clémence Pierre, Mathieu Charles, Aurélien Capitan, Arnaud Boulling, Dominique Rocha
Mitochondrial DNA sequences are frequently transferred into the nuclear genome, generating nuclear mitochondrial DNA sequences (NUMTs). Here, we analysed, for the first time, NUMTs in the domestic yak genome. We obtained 499 alignment matches covering 340.2 kbp of the yak nuclear genome. After a merging step, we identified 167 NUMT regions with a total length of ~ 503 kbp, representing 0.02% of the nuclear genome. We discovered copies of all mitochondrial regions and found that most NUMT regions are intergenic or intronic and mostly untranscribed...
May 3, 2024: Scientific Reports
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JOURNAL ARTICLE
Dhoha Ghorbel, Imen Amouri, Nahed Khemekhem, Sourour Neji, Houaida Trabelsi, Moez Elloumi, Hayet Sellami, Fattouma Makni, Ali Ayadi, Ines Hadrich
This study aimed to investigate azole resistance mechanisms in Aspergillus flavus, which involve cyp 51A and cyp 51B genes. Real-time Reverse Transcriptase qPCR method was applied to determine the overexpression of cyp 51A and cyp 51B genes for 34 A. flavus isolates. PCR sequencing of these two genes was used to detect the presence of gene mutations. Susceptibility test found sensitivity to voriconazole (VOR) in all strains. 14.7% and 8.8% of isolates were resistant to itraconazole (IT) and posaconazole (POS), respectively, with a cross-resistance in 5...
May 3, 2024: Polish Journal of Microbiology
#23
JOURNAL ARTICLE
Nilabja Roy Chowdhury, Vyacheslav Gurevich, Meir Shamay
Kaposi's sarcoma-associated herpesvirus (KSHV) belongs to the gamma-herpesvirus family and is a well-known human oncogenic virus. In infected cells, the viral genome of 165 kbp is circular DNA wrapped in chromatin. The tight control of gene expression is critical for latency, the transition into the lytic phase, and the development of viral-associated malignancies. Distal cis -regulatory elements, such as enhancers and silencers, can regulate gene expression in a position- and orientation-independent manner...
May 2, 2024: Journal of Virology
#24
JOURNAL ARTICLE
Dara Bakhtiar, Igor Vorechovsky
Eukaryotic DNA codes not only for proteins but contains a wealth of information required for accurate splicing of messenger RNA precursors and inclusion of constitutively or alternatively spliced exons in mature transcripts. This 'auxiliary' splicing code has been characterized as exonic splicing enhancers and silencers (ESE and ESS). The exact interplay between protein and splicing codes is, however, poorly understood. Here, we show that exons encoding copper-coordinating amino acids in human cuproproteins lack ESEs and/or have an excess of ESSs, yet RNA sequencing and expressed sequence tags data show that they are more efficiently included in mature transcripts by the splicing machinery than average exons...
May 1, 2024: Metallomics: Integrated Biometal Science
#25
JOURNAL ARTICLE
Joshua N Brehm, Joseph A Sorg
Historically, mutagenesis in the non-model enteropathogenic bacterium Clostridioides difficile has been challenging. Developing a versatile and reliable method of generating targeted mutations in C. difficile is important to further our understanding of its pathogenesis. Some of the most common targeted mutagenesis systems rely on allelic exchange mediated by either uracil auxotrophy combined with a toxic uracil precursor, a toxin / anti-toxin system, group II introns, or CRISPR/Cas mutagenesis. However, each of these methods suffers from its own issues...
April 29, 2024: Anaerobe
#26
JOURNAL ARTICLE
Young Gi Min, Sung-Yeoun Lee, Ehyun Lim, Mi-Young Park, Dong-Ho Kim, Ja Min Byun, Youngil Koh, Junshik Hong, Dong-Yeop Shin, Sung-Soo Yoon, Jung-Joon Sung, Seog Bae Oh, Inho Kim
Bortezomib-induced neuropathic pain (BINP) poses a challenge in multiple myeloma (MM) treatment. Genetic factors play a key role in BINP susceptibility, but research has predominantly focused on Caucasian populations. This research explored novel genetic risk loci and pathways associated with BINP development in Korean MM patients, while evaluating reproducibility of variants from Caucasians. Clinical data and buffy coat samples from 185 MM patients on bortezomib were collected. The cohort was split into discovery and validation cohorts through random stratification of clinical risk factors for BINP...
April 29, 2024: Journal of Pain
#27
Djurdja Djordjevic, Issa Alawneh, Kimberly Amburgey, Kyoko E Yuki, Lianna G Kyriakopoulou, Vilma Navickiene, Jim Stavropoulos, Grace Yoon, James J Dowling, Hernan Gonorazky
LAMA2-related muscular dystrophy is caused by pathogenic variants of the alpha2 subunit of Laminin. This common form of muscular dystrophy is characterized by elevated CK >1000IU/L, dystrophic changes on muscle biopsy, complete or partial absence of merosin staining, and both central and peripheral nervous system involvement. Advancements in genomic testing using NGS and wider application of RNA sequencing has expanded our knowledge of novel non-coding pathogenic variants in LAMA2. RNA sequencing is an increasingly utilized technique to directly analyze the transcriptome, through creation of a complementary DNA (cDNA) from the transcript within a tissue sample...
April 5, 2024: Neuromuscular Disorders: NMD
#28
JOURNAL ARTICLE
Fadi I Musfee, Goo Jun, Laura E Mitchell, Han Chen, Dongchuan Guo, Siddharth K Prakash, Shaunak Sanjay Adkar, Megan L Grove, Ryan Bohyun Choi, Derek Klarin, Eric Boerwinkle, Dianna M Milewicz
The male predominance in sporadic thoracic aortic aneurysm and dissection (TAD) suggests that the X chromosome contributes to TAD, but this has not been tested. We investigated whether X-linked variation-common (minor allele frequency [MAF] ≥0.01) and rare (MAF <0.01)-was associated with sporadic TAD in three cohorts of European descent (Discovery: 364 cases, 874 controls; Replication: 516 cases, 440,131 controls, and ARIC [Atherosclerosis Risk in Communities study]: 753 cases, 2247 controls). For analysis of common variants, we applied a sex-stratified logistic regression model followed by a meta-analysis of sex-specific odds ratios...
April 30, 2024: American Journal of Medical Genetics. Part A
#29
JOURNAL ARTICLE
Salima Benbarche, Jose Mario Bello Pineda, Laura Baquero Galvis, Jeetayu Biswas, Bo Liu, Eric Wang, Qian Zhang, Simon J Hogg, Kadeen Lyttle, Ariana Dahi, Alexander M Lewis, Martina Sarchi, Jahan Rahman, Nina Fox, Yuxi Ai, Sanjoy Mehta, Ralph Garippa, Juliana Ortiz-Pacheco, Zhuoning Li, Mara Monetti, Robert F Stanley, Sergei Doulatov, Robert K Bradley, Omar Abdel-Wahab
Mutations in the RNA splicing factor gene SF3B1 are common across hematologic and solid cancers and result in widespread alterations in splicing, yet there is currently no therapeutic means to correct this mis-splicing. Here, we utilize synthetic introns uniquely responsive to mutant SF3B1 to identify trans factors required for aberrant mutant SF3B1 splicing activity. This revealed the G-patch domain-containing protein GPATCH8 as required for mutant SF3B1-induced splicing alterations and impaired hematopoiesis...
April 21, 2024: Molecular Cell
#30
JOURNAL ARTICLE
Yu-Hua Xie, An Zhang, Han-Qing Zeng, Yun-Xing Cao
Hereditary protein C deficiency is a chromosomal genetic disease caused by mutations in the protein C gene,which can lead to venous thrombosis and is mostly related to mutations in exons 4-9 and intron 8.Fatal pulmonary embolism caused by mutations in the protein C gene is rare,and the treatment faces great challenges.This article reports a case of fatal pulmonary embolism caused by a frameshift mutation in exon 8 of the protein C gene and summarizes the treatment experience of combining extracorporeal membrane oxygenation (for respiratory and circulatory support) with interventional thrombectomy,providing a basis for the diagnosis and treatment of this disease...
April 2024: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
#31
JOURNAL ARTICLE
Christina Votsi, Marios Tomazou, Paschalis Nicolaou, Marios C Pantzaris, Giorgos Pitsas, Archontia Adamou, Kleopas A Kleopa, Eleni Zamba-Papanicolaou, Kyproula Christodoulou
BACKGROUND AND OBJECTIVES: The intronic biallelic AAGGG expansion in the replication factor C subunit 1 ( RFC1 ) gene was recently associated with a phenotype combining cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, as well as with late-onset ataxia. Following this discovery, studies in multiple populations extended the phenotypic and genotypic spectrum of this locus. Multiple benign and additional pathogenic configurations are currently known. Our main objectives were to study the prevalence of the pathogenic AAGGG expansion in the Cypriot population, to further characterize the RFC1 repeat locus allele distribution, and to search for possible novel repeat configurations...
June 2024: Neurology. Genetics
#32
JOURNAL ARTICLE
Sarah L Stenton, Melanie C O'Leary, Gabrielle Lemire, Grace E VanNoy, Stephanie DiTroia, Vijay S Ganesh, Emily Groopman, Emily O'Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael W Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O B Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S Podda, Aditya Rao, Ettore Rizzo, Vangala G Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E Brenner, Stephanie M Fullerton, Predrag Radivojac, Heidi L Rehm, Anne O'Donnell-Luria
BACKGROUND: A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting...
April 29, 2024: Human Genomics
#33
JOURNAL ARTICLE
Andrew T Nelson, Maria Elena Cicardi, Shashirekha S Markandaiah, John Ys Han, Nancy J Philp, Emily Welebob, Aaron R Haeusler, Piera Pasinelli, Giovanni Manfredi, Hibiki Kawamata, Davide Trotti
The most prevalent genetic cause of both amyotrophic lateral sclerosis and frontotemporal dementia is a (GGGGCC)n nucleotide repeat expansion (NRE) occurring in the first intron of the C9orf72 gene (C9). Brain glucose hypometabolism is consistently observed in C9-NRE carriers, even at pre-symptomatic stages, but its role in disease pathogenesis is unknown. Here, we show alterations in glucose metabolic pathways and ATP levels in the brains of asymptomatic C9-BAC mice. We find that, through activation of the GCN2 kinase, glucose hypometabolism drives the production of dipeptide repeat proteins (DPRs), impairs the survival of C9 patient-derived neurons, and triggers motor dysfunction in C9-BAC mice...
April 29, 2024: EMBO Reports
#34
JOURNAL ARTICLE
Marco Lombardo, Umberto Camellin, Raffaella Gioia, Sebastiano Serrao, Vincenzo Scorcia, Anna Maria Roszkowska, Giuseppe Lombardo, Matteo Bertelli, Maria Chiara Medori, Danilo Alunni Fegatelli, Annarita Vestri, Rita Mencucci, Domenico Schiano Lomoriello
OBJECTIVE: To report variants in 26 candidate genes and describe the clinical features of Italian patients with keratoconus (KC). SUBJECTS/METHODS: Sixty-four patients with a confirmed diagnosis of KC were enrolled in this genetic association study. Patients were classified into two study groups according to whether they had a confirmed diagnosis of progressive or stable KC. A purpose-developed Next Generation Sequencing (NGS) panel was used to identify and analyse the coding exons and flanking exon/intron boundaries of 26 genes known to be associated with KC and corneal dystrophies...
April 29, 2024: Eye
#35
JOURNAL ARTICLE
Jongyun Jung, Qing Wu
Recent studies suggest a shared genetic architecture between muscle and bone, yet the underlying molecular mechanisms remain elusive. This study aims to identify the functionally annotated genes with shared genetic architecture between muscle and bone using the most up-to-date genome-wide association study (GWAS) summary statistics from bone mineral density (BMD) and fracture-related genetic variants. We employed an advanced statistical functional mapping method to investigate shared genetic architecture between muscle and bone, focusing on genes highly expressed in muscle tissue...
2024: PloS One
#36
JOURNAL ARTICLE
Ziwei Sang, Xingwang Li, Hao Yan, Weishan Wang, Ying Wen
The availability of an alternative and efficient genetic editing technology is critical for fundamental research and strain improvement engineering of Streptomyces species, which are prolific producers of complex secondary metabolites with significant pharmaceutical activities. The mobile group II introns are retrotransposons that employ activities of catalytic intron RNAs and intron-encoded reverse transcriptase to precisely insert into DNA target sites through a mechanism known as retrohoming. We here developed a group II intron-based gene editing tool to achieve precise chromosomal gene insertion in Streptomyces...
May 2024: Microbial Biotechnology
#37
Wagner syndrome: Novel VCAN variant and prophylactic management with encircling band and retinopexy.
Ysé Borella, Claire-Marie Dhaenens, Olivier Grunewald, Georges Caputo
PURPOSE: Wagner syndrome is an autosomal genetic vitreoretinopathy characterized by chorioretinal atrophy, avascular vitreous veils, reduced visual acuity and early retinal detachment in advanced cases. Management of Wagner syndrome usually results in observation then management of occurring complications. OBSERVATIONS: We report the case of a 9-year-old girl presenting with supposed Wagner syndrome that we managed with prophylactic encircling band and retinopexy in both eyes...
June 2024: American Journal of Ophthalmology Case Reports
#38
JOURNAL ARTICLE
Hümeyra Yıldız Akkamış, Emir Can Kaya, Ahmet L Tek
BACKGROUND: Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily. OBJECTIVE: In this study, a novel family of Tourist-like MITE was characterized in wild soybean species Glycine falcata. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in G...
April 27, 2024: Genes & Genomics
#39
JOURNAL ARTICLE
Xiaohui Sun, Lili Zhang, Weihua Xu, Jianpeng Zheng, Meiling Yan, Ming Zhao, Xinyu Wang, Yan Yin
SPL (SQUAMOSA promoter binding protein-like), as one family of plant transcription factors, plays an important function in plant growth and development and in response to environmental stresses. Despite SPL gene families having been identified in various plant species, the understanding of this gene family in peanuts remains insufficient. In this study, thirty-eight genes ( AhSPL1 - AhSPL38 ) were identified and classified into seven groups based on a phylogenetic analysis. In addition, a thorough analysis indicated that the AhSPL genes experienced segmental duplications...
April 9, 2024: Plants (Basel, Switzerland)
#40
JOURNAL ARTICLE
Yue Liu, Xin Wang, Lei Ouyang, Ruonan Yao, Zhihui Wang, Yanping Kang, Liying Yan, Yuning Chen, Dongxin Huai, Qianqian Wang, Huifang Jiang, Yong Lei, Boshou Liao
Trehalose-6-phosphate phosphatase (TPP) is a pivotal enzyme in trehalose biosynthesis which plays an essential role in plant development and in the abiotic stress response. However, little is currently known about TPPs in groundnut. In the present study, a total of 16 AhTPP genes were identified, and can be divided into three phylogenetic subgroups. AhTPP members within the same subgroups generally displayed similar exon-intron structures and conserved motifs. Gene collinearity analysis revealed that segmental duplication was the primary factor driving the expansion of the AhTPP family...
April 9, 2024: Plants (Basel, Switzerland)
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