Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “reference genome”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47Linked to original sources
PubMed2006

Herpes simplex virus type 1 DNA-packaging protein UL17 is required for efficient binding of UL25 to capsids.

Herpes simplex virus type 1 packages its DNA genome into a precursor capsid, referred to as the procapsid. Of the three capsid-associated DNA-packaging proteins, UL17, UL25, and UL6, only UL17 and UL6 appear to be components of the procapsid, with UL25 being added subsequently. To determine whether the association of UL17 or UL25 with capsids was dependent on the other two packaging proteins, B capsids, which lack viral DNA but retain the cleaved internal scaffold, were purified from nonpermissive cells infected with UL17, UL25, or UL6 null mutants and compared with wild-type (wt) B capsids. In the absence of UL17, the levels of UL25 in the mutant capsids were much lower than those in wt B capsids. These results suggest that UL17 is required for efficient incorporation of UL25 into B capsids. B capsids lacking UL25 contained about twofold-less UL17 than wt capsids, raising the possibilities that UL25 is important for stabilizing UL17 in capsids and that the two proteins interact in the capsid. The distribution of UL17 and UL25 on B capsids was examined using immunogold labeling. Both proteins appeared to bind to multiple sites on the capsid. The properties of the UL17 and UL25 proteins are consistent with the idea that the two proteins are important in stabilizing capsid-DNA structures rather than having a direct role in DNA packaging.

Animals↗
PubMed2023

Intra-Host Evolution Provides for the Continuous Emergence of SARS-CoV-2 Variants.

Variants of concern (VOC) in SARS-CoV-2 refer to viruses whose viral genomes differ from the ancestor virus by ≥3 single-nucleotide variants (SNVs) and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Still, too little is known regarding how frequently new viral variants emerge and under what circumstances. We report a study to determine the degree of SARS-CoV-2 sequence evolution in 94 patients and to estimate the frequency at which highly diverse variants emerge. Two cases accumulated ≥9 SNVs over a 2-week period and one case accumulated 23 SNVs over 3 weeks, including three nonsynonymous mutations in the spike protein (D138H, E554D, D614G). The remainder of the infected patients did not show signs of intra-host evolution. We estimate that in as much as 2% of hospitalized COVID-19 cases, variants with multiple mutations in the spike glycoprotein emerge in as little as 1 month of persistent intra-host virus replication. This suggests the continued local emergence of variants with multiple nonsynonymous SNVs, even in patients without overt immune deficiency. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of reinfection, and (iii) patients with diminished immune function may offer broad public health benefits. IMPORTANCE New SARS-CoV-2 variants can potentially disrupt ongoing public health measures and vaccine efforts. Still, little is known regarding how frequently new viral variants emerge and under what circumstances. Based on this study, we estimate that in hospitalized COVID-19 cases, variants with multiple mutations may emerge locally in as little as 1 month, even in patients without overt immune deficiency. Surveillance by sequencing for continuously shedding patients, patients suspected of reinfection, and patients with diminished immune function may offer broad public health benefits.

Humans↗
PubMed2004

Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with Minimal Mobile Elements.

BACKGROUND: There are four widely used experimental strains of N. gonorrhoeae, one of which has been sequenced and used as the basis for the construction of a multi-strain, mutli-species pan-neisserial microarray. Although the N. gonorrhoeae population structure is thought to be less diverse than N. meningitidis, there are some recognized gene-complement differences between strains, including the 59 genes of the Gonococcal Genetic Island. In this study we have investigated the three experimental strains that have not been sequenced to determine the extent and nature of their similarities and differences. RESULTS: Using the Pan-Neisseria microarray, three commonly used gonococcal laboratory experimental strains were investigated (F62, MS11, & FA19). Genes absent from these strains, but present in strain FA1090, were assessed as is possible with typical microarrays. Due to the design of this microarray, additional genes were also identified. Differences were associated with Minimal Mobile Elements (MMEs) or known divergences. Genomotyping indicates the presence of genes previously only described in meningococci and shows the presence of the complete Gonococcal Genetic Island in N. gonorrhoeae strain FA19. Five new neisserial genes were identified through microarray genomotyping and subsequent sequencing of two divergent MMEs in N. gonorrhoeae strain MS11 and four MMEs in N. gonorrhoeae strain FA19. No differences were identified between N. gonorrhoeae strains FA1090 and F62, indicating that these strains are very similar. CONCLUSION: This study shows extensive similarity between the experimental strains, associated with a varying number of strain-specific genes. This provides a framework for those working with these strains to refer to the available gonococcal genome sequence, and is the first detailed comparison of gene complements between gonococcal strains.

DNA Transposable Elements↗
PubMed2005

Intracellular localization of Crimean-Congo Hemorrhagic Fever (CCHF) virus glycoproteins.

BACKGROUND: Crimean-Congo Hemorrhagic Fever virus (CCHFV), a member of the genus Nairovirus, family Bunyaviridae, is a tick-borne pathogen causing severe disease in humans. To better understand the CCHFV life cycle and explore potential intervention strategies, we studied the biosynthesis and intracellular targeting of the glycoproteins, which are encoded by the M genome segment. RESULTS: Following determination of the complete genome sequence of the CCHFV reference strain IbAr10200, we generated expression plasmids for the individual expression of the glycoproteins GN and GC, using CMV- and chicken beta-actin-driven promoters. The cellular localization of recombinantly expressed CCHFV glycoproteins was compared to authentic glycoproteins expressed during virus infection using indirect immunofluorescence assays, subcellular fractionation/western blot assays and confocal microscopy. To further elucidate potential intracellular targeting/retention signals of the two glycoproteins, GFP-fusion proteins containing different parts of the CCHFV glycoprotein were analyzed for their intracellular targeting. The N-terminal glycoprotein GN localized to the Golgi complex, a process mediated by retention/targeting signal(s) in the cytoplasmic domain and ectodomain of this protein. In contrast, the C-terminal glycoprotein GC remained in the endoplasmic reticulum but could be rescued into the Golgi complex by co-expression of GN. CONCLUSION: The data are consistent with the intracellular targeting of most bunyavirus glycoproteins and support the general model for assembly and budding of bunyavirus particles in the Golgi compartment.

Animals↗
PubMed2026

Pilea: profiling bacterial growth dynamics from metagenomes with sketching.

BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging. RESULTS: We introduce Pilea ( https://github.com/xinehc/pilea ), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets. CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.

Bacteria↗
PubMed2007

Rate of evolution in brain-expressed genes in humans and other primates.

Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their brain-expressed genes. In this study, we carried out full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM) and then conducted three-way comparisons among (i) mouse, OWM, and human, and (ii) OWM, chimpanzee, and human. Although brain-expressed genes indeed appear to evolve more rapidly in species with more advanced brains (apes > OWM > mouse), a similar lineage effect is observable for most other genes. The broad inclusion of genes in the reference set to represent the genomic average is therefore critical to this type of analysis. Calibrated against the genomic average, the rate of evolution among brain-expressed genes is probably lower (or at most equal) in humans than in chimpanzee and OWM. Interestingly, the trend of slow evolution in coding sequence is no less pronounced among brain-specific genes, vis-à-vis brain-expressed genes in general. The human brain may thus differ from those of our close relatives in two opposite directions: (i) faster evolution in gene expression, and (ii) a likely slowdown in the evolution of protein sequences. Possible explanations and hypotheses are discussed.

Animals↗
PubMed2025

The structural features and immunological role of biomphalysins in the snail Biomphalaria glabrata.

Biomphalysins are β-Pore Forming Toxins (β-PFT) identified in the planorbid Biomphalaria glabrata that belong to the aerolysin-like protein family. Despite potentially diverse biochemical activities, very few eukaryotic aerolysin-related proteins have been extensively studied. Most of the data refers to their discovery in genomes or to transcriptional activity. The involvement of biomphalysins in the immune response of Biomphalaria glabrata has been studied previously, especially regarding biomphalysin 1, which can bind and kill Schistosoma mansoni mother sporocysts. However, the repartition of biomphalysin 1 protein in B. glabrata has yet to be defined. The transcriptional behavior of the 22 other biomphalysin genes following immune challenge also remains uncharacterized. Therefore, herein, we investigate for the first time the tissular distribution of biomphalysin 1 (and 2) in B. glabrata by histological and cytological analyses through immunofluorescence approaches, notably unveiling unexpected tissue location that are involved in biomphalysin 1 synthesis. Structural predictions of the 23 members of the family have been updated using predictions based on aminoacyl spatial pair representation (AlphaFold2), highlighting unique features of the small lobe. In addition, mass spectrometry-based proteomic data more precisely predicted the regions of post-translational cleavage of biomphalysin 1. Transcriptional activity of the biomphalysin genes was explored, after which the plasmatic presence of the biomphalysin proteins was investigated in naive and S. mansoni-infected snails. The ability of native biomphalysin 1 (and 2) to bind several cell types was also investigated and correlated with the lytic ability of plasma toward the exposed cells, highlighting the central role occupied by biomphalysin 1 (and 2) in the humoral immunity of B. glabrata.

Biomphalaria↗
PubMed1992

Detection of Campylobacter upsaliensis in diarrheic dogs and cats, using a selective medium with cefoperazone.

Using a newly formulated selective medium containing cefoperazone, we isolated 72 Campylobacter strains in fecal samples from 397 diarrheic dogs and cats. Of these, 39 were thermophilic catalase-negative Campylobacter species. We identified these Campylobacter strains by DNA:DNA hybridization, using digoxigenin-labeled total genomic DNA of 4 Campylobacter reference strains (C jejuni, C coli, C lari, and C upsaliensis) as a probe. The labeling was done with a commercially available kit. We could identify 66 of the 72 Campylobacter isolates to the species level with this method; identification with probes always agreed with conventional test results. Of the 66 identified strains, 33 were C upsaliensis and 33 were C jejuni. Six isolates could not be assigned to a known species with probes or conventional tests. On the basis of our findings, C upsaliensis is more resistant to cefoperazone than to cephalothin, thereby explaining the unexpected recovery of these campylobacters on cephalosporin-containing media.

Animals↗
PubMed2006

[MECP2 gene mutations in twenty-six cases with atypical Rett syndrome].

OBJECTIVE: Rett syndrome (RTT) is an X-linked progressive neurodeveopmental disorder that almost exclusively affects girls, and is one of the most common causes of mental retardation in females, with an estimated prevalence of approximately 1 in 10,000 - 15,000 female individuals. Mutations in X-linked methyl-CpG-binding protein 2 (MECP2) gene, located on chromosome Xq28, have been found to be a cause of RS. A lot of mutations have been reported to be related to RS recently. Mutations are found in 70% - 85% of patients with classical RTT and in less than 50% of patients with atypical RS. Up to now, RTT is diagnosed based on a consistent counseling for clinical features and the established diagnostic criteria. The present study aimed to investigate frequency and type of mutation of MECP2 gene and if hot spot of mutation exits in patients with atypical RTT and find out the relationship between genotype and phenotype. METHODS: A systematic analysis of the entire coding region of MECP2 in 26 unrelated patients with atypical RTT was performed by polymerase chain reaction (PCR) and direct sequencing. Genomic DNA was extracted using standard procedures from the peripheral blood leukocytes of each patient. PCR amplification products were checked by 2% agarose gel electrophoresis and were subsequently sequenced with ABI 3730 Automated DNA Sequencer with both the forward and reverse primers. Mutational analyses were performed using normal human genomic MECP2 sequence as a reference (GenBank accession NO.AF030876). RESULTS: Seven mutations were identified in 12 of 26 patients. Most of the mutations were missense mutation; c.397C > T (R133C) was found in 3 of 26 patients; c.473C > T (T158M) and c.916C > T (R306C) were found in 2 of 26 patients, respectively; c.397A > G (R133H) and c.1005G > A (R335C) were found in 1 of 26 patients, respectively. One base pair deletion mutation (806delG) resulting in frameshift was found in 2 of 26 patients, and 1 base pair transversion at splice accept-site (IVS3-2A > T). CONCLUSION: The results of this study indicated that c.397C > T (R133C), c.473C > T (T158M) and c.916C > T (R306C) were hot spot mutations in MECP2 gene of patients with atypical RTT. There was some relationship between genotype and phenotype.

Base Sequence↗
PubMed1990

Absence of papillomavirus in skin tumors induced in SENCAR mice by a two-stage carcinogenesis protocol.

SENCAR mice are unusually sensitive to induction of papillomas and squamous cell carcinomas by initiation with 7,12-dimethylbenzanthracene (DMBA) and promotion by 12-O-tetradecanoylphorbol-13-acetate (TPA). Tumors induced by this protocol were tested for the presence of papillomavirus by immunohistochemistry, Southern blot, reverse Southern blot and dot blot hybridization techniques. Papillomavirus antigens were not detected in any of 235 tumors or 142 non-tumor-bearing skin samples analyzed. Southern blots and dot blots, using a mixed probe of cloned rodent papillomavirus DNA from the multimammate rat, Mastomys natalensis, and the European harvest mouse, Micromys minutus, did not reveal the presence of either episomal or integrated papillomavirus genomes in total cellular DNA extracts from the tumors or non-tumor-bearing skin. To circumvent the possibility that insufficient cross-homology existed to detect a papillomavirus genome with the mixed probe used, DNAs extracted from six papillomas were labeled and each used to probe reference blots that contained 25 cloned papillomavirus genomes excised from their vectors. No evidence for the presence of a papillomavirus genome was detected by this method. Therefore, it is unlikely that papillomaviruses play a role in the induction of tumors in SENCAR mice by two-stage carcinogenesis protocols.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed2004

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics.

Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db.

Arabidopsis↗
PubMed2000

[Hepatitis C virus].

Hepatitis C virus (HCV) is a small enveloped virus whose genome is a RNA molecule encoding a polyprotein that is processed by cellular and viral proteases to produce the 3 structural proteins (the core protein C and the 2 envelope proteins E1 and E2) and the 6 nonstructural proteins (NS2, NS3, NS4A, NS4B, NS5A and NS5B). The HCV genome exhibits a significant genetic heterogeneity. HCV isolates can be divided into genetically distinct groups referred to as genotypes, whereas the population of HCV genomes, within an infected individual, is present as a group of heterogeneous but closely related sequences referred to as quasi-species. Studies of the molecular biology of HCV and of new vaccinal or therapeutic strategies are hampered by the lack of easy to use cellular culture systems and of animal models.

Animals↗
PubMed1991

A mutant of Sindbis virus with altered plaque morphology and a decreased ratio of 26 S:49 S RNA synthesis in mosquito cells.

When our stock of standard Sindbis virus (SVSTD) is assayed by plaque formation on Aedes albopictus mosquito cells, about 1-2% of the plaques appear much clearer and sharper than the majority of the plaques. One of these clear plaques was picked, grown into a viral stock (SVCP), and used to prepare viral cDNA. Making use of the infectious Sindbis virus plasmid, Toto 1101 (Rice et al., 1987), we mapped the causal mutation for the clear plaque phenotype to a region between nt 7334 and 7716, and by sequencing of the viral RNA identified a mutation at nucleotide 7592. This mutation lies in the junction region of the viral genome, specifically at nucleotide -6, with reference to the initiation site for 26 S RNA synthesis. In SVCP-infected mosquito cells, but not in SVCP-infected chick cells, the ratio of subgenomic 26 S to 49 S (genomic) RNA synthesis was decreased relative to that observed in SVSTD infected cells. In terms of amino acid coding, the SVCP mutation is silent.

Aedes↗
PubMed2001

Serological expression cloning and immunological evaluation of MTB48, a novel Mycobacterium tuberculosis antigen.

Improved diagnostics are needed for the detection of Mycobacterium tuberculosis, especially for patients with smear-negative disease. To address this problem, we have screened M. tuberculosis (H37Rv and Erdman strains) genomic expression libraries with pooled sera from patients with extrapulmonary disease and with sera from patients with elevated reactivity with M. tuberculosis lysate. Both serum pools were reactive with clones expressing a recombinant protein referred to here as MTB48. The genomic sequence of the resulting clones was identical to that of the M. tuberculosis H37Rv isolate and showed 99% identity to the Mycobacterium bovis and M. bovis BCG isolate sequences. The genomic location of this sequence is 826 bp upstream of a region containing the esat-6 gene that is deleted in the M. bovis BCG isolate. The mtb48 1,380-bp open reading frame encodes a predicted 47.6-kDa polypeptide with no known function. Southern and Western blot analyses indicate that this sequence is present in a single copy and is conserved in the M. tuberculosis and M. bovis isolates tested but not in other mycobacterial species tested, including Mycobacterium leprae and Mycobacterium avium. In addition, the native protein was detected in the cytoplasm, as was a processed form that was also shed into the medium during culture. Serological analysis of recombinant MTB48 and the M. tuberculosis 38-kDa antigen with a panel of patient and control sera indicates that the inclusion of recombinant MTB48 in a prototype serodiagnostic test increases assay sensitivity for M. tuberculosis infection when it is combined with other known immunodominant antigens, such as the 38-kDa antigen.

Amino Acid Sequence↗
PubMed2006

Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?

The phylogenetic profile method has been widely applied in the prediction of protein-protein interactions (PPIs). Studies often use all of the available complete genomes for this method. With more than 400 genomes complete and new ones on the horizon, it remains unclear how to select reference organisms for profile construction and then influence the PPI prediction. Here, we performed a systematic assessment of reference organism selection from 225 complete genomes with their evolutionary tree. Our results suggest that reference organisms should be selected from moderately and highly genetically distant organisms, from all three domains (Bacteria, Archaea, and Eukarya), and by their even distribution at the fifth hierarchical level in the evolutionary tree. Our study provides important guidance on the construction of phylogenetic profiles for PPI prediction and functional genomics, which has become challenging due to the large and increasing number of available candidate organisms.

Algorithms↗
PubMed1990

Enhanced resolution of DNA restriction fragments: a procedure by two-dimensional electrophoresis and double-labeling.

A probe-free method was developed to detect DNA rearrangement in bacteria based on the electrophoretic separation of twice-digested restriction fragments of genomic DNA into a two-dimensional (2-D) pattern. The first restriction enzyme digestion was done in solution, followed by electrophoresis of the restriction fragments in one dimension. A second restriction enzyme digestion was carried out in situ in the gel, followed by electrophoresis in a second dimension perpendicular to the first electrophoresis. The 2-D pattern provides for the resolution of 300-400 spots, which are defined and indexed by an "x,y" coordinate system with size markers. This approach has greatly increased the resolution power over conventional one-dimensional (1-D) electrophoresis. To study DNA rearrangement, a 2-D pattern from a test strain was compared with the 2-D pattern from a reference strain. After the first digestion, genomic DNA fragments from the test strain were labeled with 35S, while those from the reference strain were labeled with 35P. This was done to utilize the difference in the energy emission of 35S and 32P isotopes for autoradiography when two x-ray films were exposed simultaneously on top of the gel after the 2-D electrophoresis. The irradiation from the decay of 35S exposed only the lower film, whereas the irradiation from the decay of 32P exposed both the lower and upper films. Different DNA fragments existed in the test DNA compared with the reference DNA can be identified unambiguously by the differential two 2-D patterns produced on two films upon exposure to the 35S and 32P fragments in the same gel. An appropriate photographic procedure further simplified the process, allowing only the difference in DNA fragments between these two patterns to be shown in the map. We have utilized the difference map obtained from Escherichia coli strains HB101 and HB101 (lambda) genomic DNA to show the incorporation of one copy of phage lambda DNA without the use of a lambda DNA probe. This is the same test system that was used previously.

Bacteriophage lambda↗
PubMed2003

Elements for a theory of molecular evolution.

Biological evolution is known to be driven by the availability of genetic variants. Spontaneous genetic variation can be the result of a number of specific molecular mechanisms. These can be grouped into three qualitatively different natural strategies of generating genetic variations, namely local sequence changes, DNA rearrangement within the genome and horizontal gene transfer, which is referred to here as DNA acquisition. All of these strategies bring about alterations in the DNA sequences of the genome, thus corresponding to the molecular genetic definition of the term mutation. A detailed inspection of specific mechanisms of mutagenesis reveals on the one hand the impact of non-genetic internal and environmental factors, and on the other hand the specific involvement of gene products. The underlying so-called evolution genes can be classified into generators of genetic variations and into modulators of the frequency of genetic variation. These evolution genes are postulated to have themselves undergone biological evolution under the pressure of second-order selection. On the basis of a few selected examples of mutagenesis, elements for a theory of molecular evolution are collected without a claim for completeness. Philosophical dimensions as well as practical aspects of the advanced knowledge on specific molecular mechanisms involved in molecular evolution are also briefly discussed.

Evolution, Molecular↗