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At least 1,603 records · Page 89Linked to original sources
PubMed2003

Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing.

Rice is an important crop and a model system for monocot genomics, and is a target for whole genome sequencing by the International Rice Genome Sequencing Project (IRGSP). The IRGSP is using a clone by clone approach to sequence rice based on minimum tiles of BAC or PAC clones. For chromosomes 10 and 3 we are using an integrated physical map based on two fingerprinted and end-sequenced BAC libraries to identifying a minimum tiling path of clones. In this study we constructed and tested two rice genomic libraries with an average insert size of 10 kb (10-kb library) to support the gap closure and finishing phases of the rice genome sequencing project. The HaeIII library contains 166,752 clones covering approximately 4.6x rice genome equivalents with an average insert size of 10.5 kb. The Sau3AI library contains 138,960 clones covering 4.2x genome equivalents with an average insert size of 11.6 kb. Both libraries were gridded in duplicate onto 11 high-density filters in a 5 x 5 pattern to facilitate screening by hybridization. The libraries contain an unbiased coverage of the rice genome with less than 5% contamination by clones containing organelle DNA or no insert. An efficient method was developed, consisting of pooled overgo hybridization, the selection of 10-kb gap spanning clones using end sequences, transposon sequencing and utilization of in silico draft sequence, to close relatively small gaps between sequenced BAC clones. Using this method we were able to close a majority of the gaps (up to approximately 50 kb) identified during the finishing phase of chromosome-10 sequencing. This method represents a useful way to close clone gaps and thus to complete the entire rice genome.

Chromosomes, Artificial, Bacterial↗
PubMed2001

The total laboratory solution: a new laboratory E-business model based on a vertical laboratory meta-network.

Major forces are now reshaping all businesses on a global basis, including the healthcare and clinical laboratory industries. One of the major forces at work is information technology (IT), which now provides the opportunity to create a new economic and business model for the clinical laboratory industry based on the creation of an integrated vertical meta-network, referred to here as the "total laboratory solution" (TLS). Participants at the most basic level of such a network would include a hospital-based laboratory, a reference laboratory, a laboratory information system/application service provider/laboratory portal vendor, an in vitro diagnostic manufacturer, and a pharmaceutical/biotechnology manufacturer. It is suggested that each of these participants would add value to the network primarily in its area of core competency. Subvariants of such a network have evolved over recent years, but a TLS comprising all or most of these participants does not exist at this time. Although the TLS, enabled by IT and closely akin to the various e-businesses that are now taking shape, offers many advantages from a theoretical perspective over the current laboratory business model, its success will depend largely on (a) market forces, (b) how the collaborative networks are organized and managed, and (c) whether the network can offer healthcare organizations higher quality testing services at lower cost. If the concept is successful, new demands will be placed on hospital-based laboratory professionals to shift the range of professional services that they offer toward clinical consulting, integration of laboratory information from multiple sources, and laboratory information management. These information management and integration tasks can only increase in complexity in the future as new genomic and proteomics testing modalities are developed and come on-line in clinical laboratories.

Chemistry, Clinical↗
PubMed1999

Value of the test for serum HCV-RNA in clinical practice.

The test to identify genomic RNA is the only tool currently available to directly evidence the presence of the hepatitis C virus (HCV) in infected subjects. In this review we examined the most commonly used qualitative and quantitative methods to detect HCV-RNA in serum or plasma, focusing particular attention on commercially available methods. Furthermore, we report the clinical conditions in which the viremia test is useful or even mandatory for the diagnosis of HCV infection, and comment on the usefulness of the test for monitoring patients in the course of antiviral therapy.

Journal Article↗
PubMed2026

Comparative genomic epidemiology of food- and patient-derived diarrheagenic Escherichia coli from sentinel surveillance in Southeast China.

Diarrheagenic Escherichia coli (DEC) remains an important foodborne pathogen, yet long-term comparative genomic surveillance data jointly characterizing food-derived and patient-derived isolates remain limited. This surveillance-based comparative study integrated antimicrobial susceptibility testing and whole-genome sequencing to characterize diarrheagenic Escherichia coli isolates recovered from food and patient sources in Lishui, Southeast China, during 2018-2025, with emphasis on occurrence, resistance profiles, genomic backgrounds, and plasmid replicon-associated features. Antimicrobial susceptibility testing was performed for 258 selected isolates, and whole-genome sequencing was conducted for a curated analytical subset of 204 isolates. The sequenced subset was used for diversity-oriented comparative genomic analysis rather than for unbiased prevalence estimation of the entire DEC collection. EAEC predominated in both sources, although food-associated occurrence was heterogeneous across categories, with the highest recovery rate observed in raw meat. Patient-derived isolates showed a broader overall resistance burden, whereas food-derived isolates retained substantial resistance to tetracycline, chloramphenicol, and florfenicol. Phylogenetic analysis showed partial overlap in genomic backgrounds between food-derived and patient-derived isolates, while representative resistance determinants displayed both broadly distributed and lineage-enriched patterns. Replicon-based plasmid profiling identified 42 plasmid types, including 12 detected in both sources, with IncF-related replicons predominating among these shared profiles. Several food-derived isolates carried multiple plasmid replicon types that were also observed in patient-derived isolates. Overall, food-derived and patient-derived DEC showed partial overlap in genomic backgrounds, resistance determinants, and replicon-defined plasmid profiles within this surveillance setting, while retaining source-associated heterogeneity. These findings should be interpreted as surveillance-based comparative evidence rather than as evidence of direct source attribution or transmission.

Humans↗
PubMed1992

Structure and organization of rhodophyte and chromophyte plastid genomes: implications for the ancestry of plastids.

Plastid genomes of two rhodophytes (Porphyra yezoensis and Griffithsia pacifica) and two chromophytes (Olisthodiscus luteus and Ochromonas danica) were compared with one another and with green plants in terms of overall structure, gene complement and organization. The rhodophyte genomes are moderately colinear in terms of gene organization, and are distinguished by three rearrangements that can most simply be explained by transpositions and a large (approximately 40 kb) inversion. Porphyra contains two loci for ppcBA and Griffithsia has two loci for rpoA. Although there is little similarity in gene organization between the rhodophytes and consensus green plant genome, certain gene clusters found in green plants appear to be conserved in the rhodophytes. The chromophytes Olisthodiscus and Ochromonas contain relatively large plastid inverted repeats that encode several photosynthetic genes in addition to the rRNA genes. With the exception of rbcS, the plastid gene complement in Olisthodiscus is similar to that of green plants, at least for the subset of genes tested. The Ochromonas genome, in contrast, appears unusual in that several of the green plant gene probes hybridizing to Olisthodiscus DNA did not detect similar sequences in Ochromonas DNA. Gene organization within the chromophytes is scrambled relative to each other and to green plants, despite the presence of putatively stabilizing inverted repeats. However, some gene clusters conserved in green plants and rhodophytes are also present in the chromophytes. Comparison of the entire rhodophyte, chromophyte and green plant plastid genomes suggests that despite differences in gene organization, there remain overall similarities in architecture, gene content, and gene sequences among in three lineages. These similarities are discussed with reference to the ancestry of the different plastid types.

Biological Evolution↗
PubMed2002

Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster.

BACKGROUND: We characterized RNA transcript levels for the whole Drosophila genome during normal aging. We compared age-dependent profiles from animals aged under full-nutrient conditions with profiles obtained from animals maintained on a low-calorie medium to determine if caloric restriction slows the aging process. Specific biological functions impacted by caloric restriction were identified using the Gene Ontology annotation. We used the global patterns of expression profiles to test if particular genomic regions contribute differentially to changes in transcript profiles with age and if global disregulation of gene expression occurs during aging. RESULTS: Whole-genome transcript profiles contained a statistically powerful genetic signature of normal aging. Nearly 23% of the genome changed in transcript representation with age. Caloric restriction was accompanied by a slowing of the progression of normal, age-related changes in transcript levels. Many genes, including those associated with stress response and oogenesis, showed age-dependent transcript representation. Caloric restriction resulted in the downregulation of genes primarily involved in cell growth, metabolism, and reproduction. We found no evidence that age-dependent changes in transcription level were confined to genes localized to specific regions of the genome and found no support for widespread disregulation of gene expression with age. CONCLUSIONS: Aging is characterized by highly dynamic changes in the expression of many genes, which provides a powerful molecular description of the normal aging process. Caloric restriction extends life span by slowing down the rate of normal aging. Transcription levels of genes from a wide variety of biological functions and processes are impacted by age and dietary conditions.

Aging↗
PubMed2004

Mapping disease-susceptibility genes in admixed populations using interval principal component tests.

Family-based association approach for mapping disease-susceptibility genes of complex human diseases is a topical issue in genetic epidemiology. It is well known that admixture between genetically differentiated populations can result in high levels of linkage disequilibrium at loci separated far apart. This property has been capitalized upon to reduce the burden of genotyping in a genomewide association scan. The authors describe a new approach for admixture mapping--the "interval principal component test" (IPCT). The genome is divided into a multitude of non-overlapping "intervals" (with interval length of 10-20 cM) and the information of the markers in the same interval is integrated using the principal component analysis. Monte-Carlo simulation shows that an interval-by-interval scan using IPCT has much better performances than a conventional marker-by-marker scan using the transmission/disequilibrium test (TDT).

Computer Simulation↗
PubMed2026

Genetic testing practices across European epilepsy centers: An ERN EpiCARE survey.

OBJECTIVE: Genetic testing plays an increasing role in the diagnostic pathway for rare and complex epilepsies. However, significant heterogeneity persists in access, implementation, and interpretation across Europe. This study aimed to assess genetic testing practices, accessibility, and challenges across expert epilepsy centers within the European Reference Network for Rare and Complex Epilepsies (ERN EpiCARE) and to identify key challenges and areas for harmonization. METHODS: A cross-sectional survey was developed by the ERN EpiCARE Clinical Genetics Working Group and distributed to 50 EpiCARE member centers across 27 European countries. The questionnaire collected quantitative and qualitative information on available genetic testing modalities, turnaround times, use of rapid testing, multidisciplinary team (MDT) organization, genetic counseling practices, and perceived challenges. Survey findings were complemented by a structured discussion held during the ERN EpiCARE General Assembly. RESULTS: Responses were received from 46 centers (51 responses). Most centers reported access to genetic testing, predominantly through in-house facilities. Whole-exome sequencing was available in 85% of centers, and gene panels were available in 78%. Whole-genome sequencing was available in 59% of centers, frequently restricted to research or performed externally. Turnaround times for standard genetic testing were most commonly between 1 and 6 months. Genetic testing strategies varied by epilepsy subtype, with gene panels most frequently used as first-tier testing, and exome sequencing preferentially applied in developmental and epileptic encephalopathies. Considerable heterogeneity was observed in MDT organization, access to genetic counseling, reimbursement, data-sharing and registry infrastructures. SIGNIFICANCE: Although genetic testing is widely available across ERN EpiCARE centers, substantial disparities persist in its organization, accessibility, and implementation. Addressing these gaps through strengthened multidisciplinary collaboration, harmonized diagnostic strategies, and enhanced European-level coordination will be essential to ensure equitable access to high-quality genetic care for individuals with epilepsy. PLAIN LANGUAGE SUMMARY: Genetic testing is increasingly integrated in the diagnostic pathway for rare and complex epilepsies and treatment decisions. An ERN EpiCARE survey assessed how genetic testing is implemented across specialist epilepsy centers in Europe and identified persistent organizational, financial, and clinical barriers. Although most centers had access to advanced genomic testing, important differences were identified in access, reimbursement, turnaround times, and multidisciplinary expertise. European collaboration and harmonized practices are needed to support equitable access to high-quality genetic care for people living with epilepsy.

European reference networks↗
PubMed2026

Experimental and genomic evidence clarifies the mycorrhizal helper role of a widespread bacterium in Bishop pine forests.

Whether a widespread bacterial strain of Paraburkholderia can enhance the physiological responses of ectomycorrhizal fungi (EcMF) and host Bishop pine seedling growth remains unclear. We developed a 'top-down meets bottom-up' approach that harmonized data from molecular field surveys, experimental forest soil manipulations, statistical interaction models, metabolomics studies, bacterial isolations, controlled growth chamber experiments, and comparative genomics analyses to test the direction and strength of Paraburkholderia-EcMF interactions on host seedling physiology and identify potential mechanisms that support these tripartite interactions. Paraburkholderia sp. D1E increased host root colonization of Suillus pungens - a keystone EcMF taxon for seedling establishment. Paraburkholderia-Suillus co-inoculations also often drove additive seedling growth responses (e.g. biomass and foliar chemistry) and generated nonadditive, positive effects on seedling shoot height. Genomic comparisons identified low chitin and high arabinitol utilization potential as distinguishing features of Paraburkholderia-EcMF symbioses. Our analyses provide experimental evidence, genomic resources, and cross-data validation that highlight potential mechanisms involved in a widespread bacteria-EcMF-tree interaction. Given the diversity of bacteria and fungi in the rhizosphere, however, this approach should continue to be applied to other species combinations to generalize interaction mechanisms among bacterial, fungal, and plant partners.

Paraburkholderia↗
PubMed2004

Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes.

We have performed the first genome-wide analysis of the Inverted Repeat (IR) structure in the human genome, using a novel and efficient software package called Inverted Repeats Finder (IRF). After masking of known repetitive elements, IRF detected 22,624 human IRs characterized by arm size from 25 bp to >100 kb with at least 75% identity, and spacer length up to 100 kb. This analysis required 6 h on a desktop PC. In all, 166 IRs had arm lengths >8 kb. From this set, IRs were excluded if they were in unfinished/unassembled regions of the genome, or clustered with other closely related IRs, yielding a set of 96 large IRs. Of these, 24 (25%) occurred on the X-chromosome, although it represents only approximately 5% of the genome. Of the X-chromosome IRs, 83.3% were >/=99% identical, compared with 28.8% of autosomal IRs. Eleven IRs from Chromosome X, one from Chromosome 11, and seven already described from Chromosome Y contain genes predominantly expressed in testis. PCR analysis of eight of these IRs correctly amplified the corresponding region in the human genome, and six were also confirmed in gorilla or chimpanzee genomes. Similarity dot-plots revealed that 22 IRs contained further secondary homologous structures partially categorized into three distinct patterns. The prevalence of large highly homologous IRs containing testes genes on the X- and Y-chromosomes suggests a possible role in male germ-line gene expression and/or maintaining sequence integrity by gene conversion.

Animals↗
PubMed2025

Separating direct, indirect and parent-of-origin genetic effects in the human population.

Here, we present a novel approach to estimate the degree to which the phenotypic effect of a DNA locus is attributable to four components: alleles in the child (direct genetic effects), alleles in the mother and the father (indirect genetic effects), or is dependent upon the parent from which it is inherited (parent-of-origin, PofO effects). Applying our model, JODIE, to 30,000 child-mother-father trios with phased DNA information from the Estonian Biobank (EstBB) and the Norwegian Mother, Father, Child Cohort (MoBa), we jointly estimate the phenotypic variance attributable to these four effects unbiased of assortative mating (AM) for height, body mass index (BMI) and childhood educational test score (EA). For all three traits, direct effects make the largest contribution to the genetic effect variance. But we find that parental indirect genetic effects make an equivalent combined contribution, and that there is a non-zero PofO effect variance for all traits. We calculate the heritability that would be obtained at the population-level in the absence of AM for common DNA loci, and show that the proportional contribution of direct effects to these heritability values can be calculated as 64.0% for EA in MoBa, 77.1% and 63.4% for height in MoBa and EstBB, and 81.2% and 88.0% for BMI in MoBa and EstBB. Additionally, using within-family genome-wide association testing, we identify 276 independently associated DNA regions that replicate across two additional biobanks, which all show a genotype-phenotype relationship that reflects an interplay of direct, indirect and PofO effects. Determining how direct, parental and PofO genetic effects combine across loci genome-wide to influence human phenotypic variation requires joint modeling of parental and child genotypes alongside the parental origin of loci and here, we make the first attempt to do this in the human population.

EstBB↗
PubMed1999

The Feasibility of Using Proteome Expression Profile for Genome Annotation.

By investigating into the expression data from ECO2DBASE (Edition 6),the feasibility of using proteome expression profile for genome annotation was tested. Based on our newly developed CRC (cellular role cluster) method,79 proteins extracted from ECO2DBASE were clustered into 4 CRCs. Function related proteins tend to be clustered into same CRC. Total 9 aminoacyl-tRNA synthetases were clustered into CRC2, whereas 4 heat-shock proteins into CRC3. These results indicate with enough proteome expression data and the efficient algorithm, proteome expression profile can provide very important information for genome annotation, while this kind of information is sequence-independent.

Journal Article↗
PubMed1988

The Great Island subgroup of tick-borne orbiviruses represents a single gene pool.

The geographical distribution of members of the Great Island (GI) subgroup in the Kemerovo serogroup of orbiviruses extends from the Arctic to the Sub-antarctic. To examine the gene pool size of this group, five topotypes whose origins ranged from Iceland in the northern hemisphere to Macquarie Island in the Southern Ocean were tested for their ability to reassort in vitro. All the isolates were distinguishable by plaque reduction neutralization tests, and their genome profile in polyacrylamide gels. They showed high frequency reassortment following dual infection of cell cultures with temperature-sensitive (ts) mutants and/or wild-type virus. Analysis of the dsRNA profile of the reassortants by PAGE confirmed the observation from reassortment assays that the Great Island subgroup constitutes a single gene pool. A seventh reassortment group was identified, distinct from the six groups previously described. The ts lesions for reassortment groups I, V and VII were considered to be in genome segments 9, 3 and 2, respectively. Segment 6 of GI virus (in contrast to segment 5 of Broadhaven and Wexford viruses) was shown to be the major genetic determinant of serotype specificity.

Animals↗
PubMed2006

Drosophila damaged DNA binding protein 1 contributes to genome stability in somatic cells.

The damaged DNA-binding protein (DDB) complex consists of a heterodimer of p127 (DDB1) and p48 (DDB2) subunits and is believed to have a role in nucleotide excision repair (NER). We used the GAL4-UAS targeted expression system to knock down DDB1 in wing imaginal discs of Drosophila. The knock-down was achieved in transgenic flies using over-expression of inverted repeat RNA of the D-DDB1 gene [UAS-D-DDB1(650)-dsRNA]. As a consequence of RNA interference (RNAi), the fly had a shrunken wing phenotype. The wing spot test showed induced genome instability in transgenic flies with RNAi knock-down of D-DDB1 in wing imaginal discs. When Drosophila larvae with RNAi knock-down of D-DDB1 in wing imaginal discs were treated with the chemical mutagen methyl methanesulfonate (MMS), the frequency of flies with a severely shrunken wing phenotype increased compared to non-treated transgenic flies. These results suggested that DDB1 plays a role in the response to DNA damaged with MMS and in genome stability in Drosophila somatic cells.

Animals↗
PubMed2003

Host-environment medicine: a primary care model for the age of genomics.

Rapid developments in genomic and proteomic testing promise to impact the way in which clinicians assess disease risk and drug selection in their patients. Because most diseases result from host-environment interactions, however, primary care providers will need to avoid the trap of biological determinism by examining the important role of environmental factors in their clinical assessments and interventions. This article discusses the application of host-environment concepts to recent developments in the areas of genomics and proteomics.

Antidepressive Agents, Tricyclic↗
PubMed1981

Characterization of AKR murine leukemia virus sequences in AKR mouse substrains and structure of integrated recombinant genomes in tumor tissues.

A specific cDNA probe of AKR murine leukemia virus (AKR-MLV) was prepared to detect AKR-MLV sequences in normal and tumor tissues in a variety of AKR mouse substrains. AKR strains contained up to six endogenous AKR-MLV genomes. All substrains tested had one AKR-MLV locus in common, and closely related substrains had several proviruses integrated in an identical site. Virus-induced tumors in the AKR/FuRdA and AKR/JS strains showed a reintegration pattern of AKR-MLV sequences unique for the individual animal, suggesting a monoclonal origin for the outgrown tumors. An analysis of tumor DNAs from the AKR/FuRdA and AKR/JS substrains with restriction enzymes cleaving within the proviral genome revealed a new EcoRI restriction site and BamHI restriction site not present in normal tissues. The positions of these sites corresponded both with cleavage sites of EcoRI and BamHI in integrated Moloney recombinants and with the structure of isolated AKR mink cell focus-forming viruses. All tumors analyzed to data contain nearly identical integrated recombinant genomes, suggesting a causal relationship between the formation of recombinants and the leukemogenic process.

AKR murine leukemia virus↗
PubMed2000

Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes.

We created a simulation based on experimental data from bacteriophage T7 that computes the developmental cycle of the wild-type phage and also of mutants that have an altered genome order. We used the simulation to compute the fitness of more than 10(5) mutants. We tested these computations by constructing and experimentally characterizing T7 mutants in which we repositioned gene 1, coding for T7 RNA polymerase. Computed protein synthesis rates for ectopic gene 1 strains were in moderate agreement with observed rates. Computed phage-doubling rates were close to observations for two of four strains, but significantly overestimated those of the other two. Computations indicate that the genome organization of wild-type T7 is nearly optimal for growth: only 2.8% of random genome permutations were computed to grow faster, the highest 31% faster, than wild type. Specific discrepancies between computations and observations suggest that a better understanding of the translation efficiency of individual mRNAs and the functions of qualitatively "nonessential" genes will be needed to improve the T7 simulation. In silico representations of biological systems can serve to assess and advance our understanding of the underlying biology. Iteration between computation, prediction, and observation should increase the rate at which biological hypotheses are formulated and tested.

Bacteriophage T7↗
PubMed1990

The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome.

To identify DNA polymorphisms that are abundant in the human genome and are detectable by polymerase chain reaction amplification of genomic DNA, we tested the hypothesis that the polydeoxyadenylate tract of the Alu family of repetitive elements is polymorphic among human chromosomes. We analyzed the 3' ends of three specific Alu sequences and found that two (in the adenosine deaminase gene and the beta-globin pseudogene) were polymorphic. This novel class of polymorphisms, termed AluVpA [Alu variable poly(A)] may represent one of the most useful and informative group of DNA markers in the human genome.

Alleles↗