A significant part of horizontal gene transfer is facilitated by genomic islands. Haemophilus influenzae genomic island ICEHin1056 is an archetype of a genomic island that accounts for pandemic spread of antibiotics resistance. ICEHin1056 has modular structure and harbors modules involved in type IV secretion and integration. Previous studies have shown that ICEHin1056 encodes a functional type IV secretion system; however, other modules have not been characterized yet. Here we show that the module on the 5' extremity of ICEHin1056 consists of 15 genes that are well conserved in a number of related genomic islands. Furthermore by disrupting six genes of the investigated module of ICEHin1056 by site-specific mutagenesis we demonstrate that in addition to type IV secretion system module, the investigated module is also important for the successful conjugal transfer of ICEHin1056 from donor to recipient cells.
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http://dx.doi.org/10.1016/j.plasmid.2013.05.008 | DOI Listing |
Blood
January 2025
Umeå University, Department of Medical Biosciensces, Department of Clinical Microbiology, Umeå, Sweden.
Current intensive treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has substantial side-effects, highlighting a need for novel biomarkers to improve risk stratification. Canonical biomarkers such as genetics and immunophenotype are largely not used in pediatric T-ALL stratification. This study aimed to validate the prognostic relevance of DNA methylation CpG island methylator phenotype (CIMP) risk stratification in two pediatric T-ALL patient cohorts: the Nordic NOPHO ALL2008 T-ALL study cohort (n=192) and the Dutch DCOG ALL-10/ALL-11 validation cohorts (n=156).
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
Nullomers are short DNA sequences (11-18 base pairs) that are absent from a genome; however, they can emerge due to mutations. Here, we characterize all possible putative human nullomer-emerging single base pair mutations, population variants and disease-causing mutations. We find that the primary determinants of nullomer emergence in the human genome are the presence of CpG dinucleotides and methylated cytosines.
View Article and Find Full Text PDFBiotechnol J
January 2025
Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.
The implementation of site-specific integration (SSI) systems in Chinese hamster ovary (CHO) cells for the production of monoclonal antibodies (mAbs) can alleviate concerns associated with production instability and reduce cell line development timelines. SSI cell line performance is driven by the interaction between genomic integration location, clonal background, and the transgene expression cassette, requiring optimization of all three parameters to maximize productivity. Systematic comparison of these parameters has been hindered by SSI platforms involving low-throughput enrichment strategies, such as cell sorting.
View Article and Find Full Text PDFBMC Med Genomics
January 2025
Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania.
Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a formidable public scourge causing worldwide mild to severe life-threatening infections. The ability of this strain to swiftly spread, evolve, and acquire resistance genes and virulence factors such as pvl genes has further rendered this strain difficult to treat. Of concern, is a recently recognized ability to resist antiseptic/disinfectant agents used as an essential part of treatment and infection control practices.
View Article and Find Full Text PDFBMC Genomics
January 2025
Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
Background: Conserved non-coding sequences (CNS) are islands of non-coding sequences conserved across species and play an important role in regulating the spatiotemporal expression of genes. Identification of CNS provides valuable information about potentially functional genomic elements, regulatory regions, and helps to gain insights into the genetic basis of crop agronomic traits.
Results: Here, we comprehensively analyze CNS in maize, by comparing the genomes of maize inbred line B73 (Zea mays ssp.
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