Computational protocol for analyzing whole-genome sequencing data from Staphylococcus aureus clinical isolates by Miquel Sánchez-Osuna, Ivan Erill, Oriol Gasch, Oscar Q. Pich

“…We describe steps for de novo assembly, functional annotation, and genetic characterization of chromosomal and extrachromosomal elements. This approach paves the way for an improved understanding of the interplay between virulence factors, resistome, strain type, and disease severity.For complete details on the use and execution of this protocol, please refer to Sánchez-Osuna et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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A Novel del(20q) in Aggressive Nodal Marginal Zone Lymphoma by Jason B. Kern, Deiter J. Duff, Jamie L. Odem, Magda Esebua, Lisa R. Smith, Donald Doll, Michael Wang

“…This is a case report of a previously undescribed 20q chromosomal deletion (del(20q)) in marginal zone lymphoma (MZL). …”
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A Review of Three Different Studies on Hidden Markov Models for Epigenetic Problems: A Computational Perspective by Kyung-Eun Lee, Hyun-Seok Park

“…Considering that epigenomic datasets are arranged over chromosomes, their analysis must account for spatial or temporal characteristics. …”
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RAS/RAF/MEK/ERK and PI3K/PTEN/AKT Signaling in Malignant Melanoma Progression and Therapy by Ichiro Yajima, Mayuko Y. Kumasaka, Nguyen Dinh Thang, Yuji Goto, Kozue Takeda, Osamu Yamanoshita, Machiko Iida, Nobutaka Ohgami, Haruka Tamura, Yoshiyuki Kawamoto, Masashi Kato

“…Melanomagenesis is initially triggered by environmental agents including ultraviolet (UV), which induces genetic/epigenetic alterations in the chromosomes of melanocytes. In human melanomas, the RAS/RAF/MEK/ERK (MAPK) and the PI3K/PTEN/AKT (AKT) signaling pathways are two major signaling pathways and are constitutively activated through genetic alterations. …”
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Simple Meets Single: The Application of CRISPR/Cas9 in Haploid Embryonic Stem Cells by Zixi Yin, Lingyi Chen

“…Mammalian haploid embryonic stem cells (haESCs) have only one set of chromosomes per cell, avoiding the issue of heterozygous recessive mutations in diploid cells. …”
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Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome? by Alfredo Focà, Maria Carla Liberto, Angela Quirino, Nadia Marascio, Emilia Zicca, Grazia Pavia

“…The human virome comprises viruses that infect host cells, virus-derived elements in our chromosomes, and viruses that infect other organisms, including bacteriophages and plant viruses. …”
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Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome by Yanmei Yang, Jinpeng Wang, Jianyong Di

“…From the statistical analysis of the molecular distances between duplicated genes, our study indicates that the whole genome duplication event occurred more than once in the genome evolution of soybean, which is often distributed near the ends of chromosomes.…”
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Genome-Wide Identification and Expression Analysis of the <i>GRF</i> and <i>GIF</i> Gene Families in <i>Prunus avium</i> by Hongxu Chen, Yangang Pei, Wanjia Tang, Hongfen Li, Yidi Huang, Yizhe Chu, Guanqiong Kou, Wenyi Niu, Runmei He, Ronggao Gong

“…Genome-wide analysis showed 13 <i>GRF</i> genes on eight chromosomes and three <i>GIF</i> genes on three chromosomes in <i>P. avium</i>, clustered into three and two branches, respectively. …”
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Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland by Anna Tumeo, Francesca McDonagh, Aneta Kovarova, Kate Ryan, Christina Clarke, Georgios Miliotis

“…Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to chromosomally identified blaNDM-5. Colistin resistance appeared associated with acquired mcr-1.1. …”
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Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program. by Allison E Ashley-Koch, Nathan A Kimbrel, Xue J Qin, Jennifer H Lindquist, Melanie E Garrett, Michelle F Dennis, Lauren P Hair, Jennifer E Huffman, Daniel A Jacobson, Ravi K Madduri, Hilary Coon, Anna R Docherty, Jooeun Kang, Niamh Mullins, Douglas M Ruderfer, VA Million Veteran Program (MVP), MVP Suicide Exemplar Workgroup, International Suicide Genetics Consortium, Philip D Harvey, Benjamin H McMahon, David W Oslin, Elizabeth R Hauser, Michael A Hauser, Jean C Beckham

“…European ancestry (EA) analysis identified GWS loci on chromosomes 6 and 9, as well as GWS gene associations in EXD3, DRD2, and DCC. …”
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Development of SacB-based counterselection for efficient allelic exchange in Fusobacterium nucleatum by Peng Zhou, Bibek G C, Bo Hu, Chenggang Wu

“…Post-counterselection with 5% sucrose, chromosomal plasmid loss occurred in all colonies, leading to gene alternations in half of the screened isolates. …”
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Genome-Wide Identification and Expression Analysis of the <i>CAMTA</i> Gene Family in Roses (<i>Rosa chinensis</i> Jacq.) by Wanyi Su, Yuzheng Deng, Xuejuan Pan, Ailing Li, Yongjie Zhu, Jitao Zhang, Siting Lu, Weibiao Liao

“…The results show that a total of five rose <i>CAMTA</i> genes were identified. Chromosomal localization shows that the <i>RcCAMTA</i> gene members were located on chromosomes 2, 4, and 7. …”
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Malignant Peripheral Nerve Sheath Tumor: MRI and CT Findings by K. O. Kragha

“…The diagnosis of MPNST is extremely difficult due to the lack of (1) conclusive immunohistochemistry or unique chromosomal anomaly, (2) universal distinctive histopathology, and (3) clinical criteria. …”
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Chimeric RNA in Cancer and Stem Cell Differentiation by Justin Elfman, Hui Li

“…Gene fusions are considered hallmarks of cancer which can be produced by chromosomal rearrangements. These DNA-level fusion events may result in the expression of chimeric RNAs; however, chimeric RNAs can be also produced by intergenic splicing events. …”
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Spatial Positioning of RET and H4 Following Radiation Exposure Leads to Tumor Development by Yuri E. Nikiforov

“…A high prevalence of chromosomal rearrangements involving the RET gene was found among these radiation-induced thyroid tumors [2,3]. …”
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Murine Leukemia Viruses: Objects and Organisms by Alan Rein

“…These are the Gag polyprotein, which is the structural protein of a retrovirus particle, the Pol protein, comprising the three retroviral enzymes—protease, which catalyzes the maturation of the particle, reverse transcriptase, which copies the viral RNA into DNA upon infection of a new host cell, and integrase, which inserts the DNA into the chromosomal DNA of the host cell, and the Env polyprotein, which induces the fusion of the viral membrane with that of the new host cell, initiating infection. …”
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Primary Synovial Sarcoma of the Scrotum by Nourah Al-Oudah, Sara Alanazi, Sarah Saad Alotaibi, Nayef Alzahrani

“…The cytogenetic testing showed a chromosomal translocation in the SS18 gene at 18q11.2, consistent with the diagnosis of primary synovial sarcoma. …”
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Protocol for genetic analysis of population-scale ultra-low-depth sequencing data by Jingyu Zeng, Linxuan Li, Ying Lin, Xianmei Lan, Xinyi Zhang, Yingying Wang, Mingzhi Liao, Xin Jin, Huanhuan Zhu

“…Summary: Non-invasive prenatal testing (NIPT) not only enables the detection of chromosomal anomalies in fetuses but also generates vast amounts of ultra-low-depth sequencing data, which can be leveraged for population genomic studies. …”
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A Case Report of a Patient with Turner Syndrome, Multiple Comorbidities, and Pustular Psoriasis: Correlation or Coincidence? by Andjela Egger, Andrea Maderal, Hadar Lev-Tov, Olivera Stojadinovic

“…Turner syndrome (TS) is one of the most common chromosomal abnormalities. Patients with TS are at an increased risk for the development of metabolic syndrome, hypertension (HTN), diabetes mellitus type II (DM2), hyperlipidemia (HLD), obesity, and cardiovascular disease. …”
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POLYMORPHISM AND INTERSPECIFIC VARIABILITY OF CYTOCHROME OXYDASE SUBUNIT I (COI) GENE NUCLEOTIDE SEQUENCE IN SIBLING SPECIES of A AND B Anopheles messeae AND An. beklemishevi (DIPT... by O. V. Vaulin, Yu. M. Novikov

“…It is concludedthat the COI polymorphism ofthe A andB Anopheles messeae species is common for them, as well as the chromosomal inversion polymorphism. It arose long before their divergence. …”
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