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At least 289 records · Page 16Linked to original sources
PubMed2024

Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.

Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.

Humans↗
PubMed2003

Race, distributive justice and the promise of pharmacogenomics: ethical considerations.

Pharmacogenomics has emerged in the popular press as a key vehicle ushering in a new era of personalized medicine. Often described in utopian terms, gene-sequencing technology is predicted to result in the creation of a new line of therapeutics tailored to individual genetic signatures. In the absence of cost-effective, ubiquitous genome scanning tests, it may be more accurate to describe the next wave of genomic medicine as population-based rather than one focused on individual differences. Although the completion of the Human Genome Project seemed to confirm the fallacy of a genetic basis of 'race', the use of race in understanding human genetic variation has become a central focal point in the development of tools in genomic research in medicine. Despite the often repeated statement that humans share 99.9% of their genetic makeup, the growing number of privately and publicly funded cell repositories collecting DNA samples from racially identified populations reflects the increasing salience of the relationship between race and genes. Research on the ethical implications of identifying race in pharmacogenomics research has thus far, been fairly limited. As the field surges ahead, it is critical to examine the use of race in pharmacogenomics research and its attendant benefits and potential harm to individuals and groups.

Clinical Trials as Topic↗
PubMed1991

Structure, chromosomal localization and evolutionary conservation of the gene encoding human U1 snRNP-specific A protein.

Three specific proteins, called A, 70K and C, are present in the U1 small nuclear ribonucleoprotein (snRNP) particle, in addition to the common proteins. The human U1 snRNP-specific A protein is, apart from a proline-rich region, highly similar to the U2 snRNP-specific protein B". To examine the homologous regions at the genomic level, we isolated and characterized the human U1-A gene. The human U1-A protein appears to be encoded by a single-copy gene and its locus has been mapped to the q arm of chromosome 19. The gene, about 14-16 kb in length, consists of six exons. The regions homologous to the U2-B" gene are not limited to single exons and are mostly not confined by exon-exon junctions in the corresponding U1-A mRNA. However, the proline-rich region of U1-A, absent in U2-B", is encoded by a single exon, suggesting a specific function for this domain of U1-A. The region of the cap site and upstream sequences contain interesting similarities to the promoter region of other snRNP protein-encoding genes and several housekeeping genes, in particular the vertebrate ribosomal protein-encoding genes. Hybridization experiments with various vertebrate genomic DNAs revealed that U1-A sequences are evolutionarily conserved in all tested vertebrate genomes, except for chicken, duck and pigeon. The divergence of these avian genomes is probably typical for the class of birds.

Amino Acid Sequence↗
PubMed2004

Diversity Arrays Technology (DArT) for whole-genome profiling of barley.

Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised approximately 385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics.

Chromosome Mapping↗
PubMed2003

Bacteriophage SPP1 Chu is an alkaline exonuclease in the SynExo family of viral two-component recombinases.

Many DNA viruses concatemerize their genomes as a prerequisite to packaging into capsids. Concatemerization arises from either replication or homologous recombination. Replication is already the target of many antiviral drugs, and viral recombinases are an attractive target for drug design, particularly for combination therapy with replication inhibitors, due to their important supporting role in viral growth. To dissect the molecular mechanisms of viral recombination, we and others previously identified a family of viral nucleases that comprise one component of a conserved, two-component viral recombination system. The nuclease component is related to the exonuclease of phage lambda and is common to viruses with linear double-stranded DNA genomes. To test the idea that these viruses have a common strategy for recombination and genome concatemerization, we isolated the previously uncharacterized 34.1 gene from Bacillus subtilis phage SPP1, expressed it in Escherichia coli, purified the protein, and determined its enzymatic properties. Like lambda exonuclease, Chu (the product of 34.1) forms an oligomer, is a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, and shows a preference for 5'-phosphorylated DNA ends. A model for viral recombination, based on the phage lambda Red recombination system, is proposed.

5' Untranslated Regions↗
PubMed2004

Assessment of genetic testing and related counseling services: current research and future directions.

With the recent completion of the sequencing of the Human Genome, genetic testing will increasingly become available for a greater number of medical conditions, many of which are those that manifest in adulthood (e.g., various cancers, cardiovascular disease, diabetes) or for which little or no treatments are available (e.g., Alzheimer disease). Genetic services, defined here as those relating to genetic testing and counseling, will be with helping more individuals deal with medical information that affects their health directly, as opposed to affecting primarily the health of their offspring. This paper reviews the existing research in the genetic testing and counseling literature and presents an evaluation framework outlining the intended outcomes of genetic services. The purpose of this framework is to provide an overview of the potential outcomes of these services and highlight constructs for future research in this area. In addition, other issues that will affect the assessment of genetic services are raised, using examples from the existing literature. Ultimately, the goal of this paper is to highlight and suggest directions researchers can take to produce the information needed to guide genetic testing and counseling practice. Moreover, as genetic knowledge is increasingly applied towards the prevention and treatment of various common, chronic disease conditions, genetic information will have implications for providers outside of the traditional medical genetics realm, such as primary care providers and public health practitioners. A better understanding of the outcomes of genetic testing and counseling will provide a basis from which to ensure an appropriate application of genetic information by all those who eventually provide care and "genetic" services.

Decision Making↗
PubMed1994

Rapid and simple method for preparation of genomic DNA from easily obtainable clotted blood.

A method was developed for the preparation of genomic DNA from clotted blood that is usually discarded after extraction, for other laboratory tests. The method, which involves proteinase K digestion, salt/chloroform extraction and 90% ethanol precipitation of DNA from clotted blood, is rapid, simple, and easy because it does not impose an extra burden on the patient.

DNA↗
PubMed1989

A mouse linkage testing stock possessing multiple copies of the endogenous ecotropic murine leukemia virus genome.

A new linkage testing stock of the laboratory mouse has been constructed. The stock, designated MEV (multiple ecotropic provirus), was developed by inbreeding and selection beginning with the cross of strains C58/J and AKXD-14. Eleven different murine leukemia virus (MuLV) proviruses have been fixed in the MEV/1Ty strain. Nine of these can be uniquely identified by Southern blotting of PvuII-digested DNA and probing with a cloned fragment of the ecotropic viral genome. Two proviruses had been mapped previously to chromosome 7, while single proviruses had been mapped to chromosomes 2, 9, and 11. The mapping of six additional proviruses, derived from C58/J, to chromosomes 1, 3, 5, 10, 18, and 19 is described. Another C58/J provirus was mapped to chromosome 8 and proved to be identical to the previously mapped C58v-1 virus inducibility gene of strain C58/Lw. Three dominant visible markers, hammer-toe (Hm), steel (Sl), and caracul-J (CaJ), located on chromosomes 5, 10, and 15, respectively, have been introduced onto the MEV genetic background by repeated backcrosses to provide additional linkage markers. It is estimated that approximately 50% of the genome can be screened by scoring 50 fully informative gametes from a linkage cross of the MEV-Hm, -Sl, -CaJ stock for the combination of viral and visible markers. A strategy for efficiently mapping new recessive visible mutations by pooling tissues for DNA extraction from mutant homozygotes among F2 progeny is described. Ways of further improving the MEV stock are discussed. The location of the Myb proto-oncogene is defined relative to Sl and one of the C58/J proviruses on chromosome 10.

Animals↗
PubMed1993

Recombinant immunoblot and polymerase chain reaction testing in volunteer whole blood donors screened by a multi-antigen assay for hepatitis C virus antibodies.

The purpose of this study was to compare the results of supplementary testing of volunteer whole blood donors who had been screened by the first hepatitis C virus antibody assay licensed in the United States with results from donors screened by a newer, more sensitive, multi-antigen assay. In contrast to the earlier assay, the multi-antigen assay incorporates a recombinant hepatitis C virus antigen, c22-3, which is encoded by a structural region of the viral genome. Supplementary testing included a second-generation recombinant immunoblot assay and a highly sensitive polymerase chain reaction assay for evidence of hepatitis C virus genomic RNA. A comparison of supplementary test results reveals a higher percentage of donors screened by the newer assay to be indeterminate on recombinant immunoblot (34.4% vs. 6.4%, p < 0.05). Furthermore, polymerase chain reaction testing of donors with indeterminate blot results shows that 14 percent have evidence of viral RNA. For this reason, counseling of donors with indeterminate patterns on immunoblot must include informing them of the possibility that they are infected.

Antigens, Viral↗
PubMed2000

Selective binding of hepatitis C virus core protein to synthetic oligonucleotides corresponding to the 5' untranslated region of the viral genome.

Although it is assumed that hepatitis C virus (HCV) core protein binds with viral RNA to form a nucleocapsid, little is known about the resulting molecular interactions. We utilized surface plasmon resonance technology to study the structural basis of the affinity and the preference of the interaction between HCV core protein and oligonucleotides derived from the viral genome. Among the 10 oligonucleotides corresponding to the 5' untranslated region (5'UTR) of the tested HCV genome, the real-time analysis of sensorgrams indicated that the core protein binds most efficiently and stably to the 31-nucleotide-long sequence of the loop IIId domain, whose secondary structure is highly conserved not only among different HCV genotypes but also among pestiviruses. There also could be some interactions of the core protein with the loop I domain and the region of nt 23-41. The kinetic profiles, together with those obtained in experiments using single- and double-stranded polymeric oligonucleotides, suggest a multimerization of the core protein in solution. These newly characterized properties could provide a basis for understanding the pathway of the viral nucleocapsid assembly.

5' Untranslated Regions↗
PubMed1998

Large scale ENU screens in the mouse: genetics meets genomics.

The worldwide effort to completely sequence the human and mouse genome will be accomplished within the next years. The focus of current activities within the framework of human genome research is mainly on the assembly of high resolution genetic and physical maps and genomic sequencing. Cloning of new genes is getting more easy using those maps. Nevertheless, it is necessary to work on a systematic analysis of gene function. Results obtained from these efforts will be of enormous value for future biological and biomedical research. However, even the complete sequence will not in all cases reveal the molecular and cellular role of the different genes. Therefore, the next phase of the Human Genome Project will have at its core the functional analysis of genes. Those genes relevant for the diagnosis, prevention and therapy of human diseases are of particular interest. Looking at the history of life sciences, mutants have been the most important tool to obtain insight into the biological function of genes. The mouse is the model of choice for the study of inherited diseases in man. In order to meet the requirements for functional human genome analysis, we need a large number of mouse mutants similar to the collection of mutants available for other model organisms such as flys and worms. To fully apply the power of genetics, multiple alleles of the same gene such as hypomorphs or hypermorphs are required. Efficient production of mouse mutants showing specific phenotypes can be achieved by the use of ethylnitrosourea (ENU). ENU is the most powerful mutagen known and we currently see a renaissance of ENU mutagenesis. The application of ENU mutagenesis is reviewed and discussed in the context of a new era of functional genomics.

Animals↗
PubMed1997

Ovine-specific Y-chromosome RAPD-SCAR marker for embryo sexing.

An accurate, sensitive, and quick (approximately 3 h) method for determining the sex of ovine embryos was developed using polymerase chain reaction (PCR) primers derived from an ovine-specific Y-chromosome random amplified polymorphic DNA marker (UcdO43). The accuracy and sensitivity of the assay were first tested using genomic DNA from 10 males and 10 females of five different sheep breeds, and then tested using serial dilutions of male-in-female DNA. The assay was 100% accurate in confirming the sex of the individuals and the ovine male-specific fragment was detected in dilutions containing as little as 10 pg of male DNA in 50 ng of female DNA. The assay was also confirmed to be specific for the ovine Y-chromosome as bovine, caprine, porcine, murine, and human DNA did not amplify. The ovine embryo sexing method is a duplex PCR system that also includes ZFY/ZFX primers. ZFY/ZFX provide an internal positive control for amplification as well as a means to confirm the results obtained with the UcdO43 primers. All embryo sexing results (36/36) from our method were in agreement with the ZFY/ZFX assay results. However, while our method requires an internal control to detect PCR failure, it has the advantages of not requiring nested PCR or restriction endonuclease digestion of the PCR product, and concerns about cross-species contamination are eliminated.

Animals↗
PubMedDate not supplied

Health promotion in a changing world: preparing for the genomics revolution.

All health professionals must become actively engaged in preparing for the genomics revolution. Healthy lifestyles will continue to be of utmost importance, and we must maintain a balance between health promotion activities and genomic-based tests and therapies. We must understand the specific changes likely to occur as advances in genomics are developed and applied to medicine, as well as their ethical, social, and legal implications. We must develop new, Web-based systems and new educational models to most appropriately incorporate these changes into routine practice. Finally, we must offer timely, useful advice and guidance to the public as well as to policymakers in order to maintain realistic expectations and to ensure adequate and balanced funding for health promotion initiatives and research.

Confidentiality↗