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At least 1,261 records · Page 70Linked to original sources
PubMed2026

Genomic characteristics and tracing analysis of an acute gastroenteritis outbreak associated with rotavirus C in a boarding high school.

BACKGROUND: Rotaviruses are major pathogens of childhood acute gastroenteritis, dominated by rotavirus A (RVA). Outbreaks caused by human rotavirus C (RVC) are rarely reported, and relevant genomic data remain scarce. This genomic investigation of an RVC outbreak improves our understanding of viral diversity and transmission dynamics. METHODS: We performed epidemiological surveys, nucleic acid testing and whole-genome sequencing (WGS) on specimens from a 2025 RVC-associated gastroenteritis outbreak at a Chinese boarding high school. Sequence alignment, phylogenetic and molecular tracing analyses were conducted to explore RVC evolution via point mutation, segment reassortment and genomic recombination. RESULTS: This typical point-source campus outbreak was linked to an indoor student gathering matching the incubation period of RVC. Thirteen RVC FX strains were recovered from 11 rectal swabs and two vomitus samples. Their viral protein (VP) 4 and VP7 sequences shared high homology with Russian reference strains, carrying distinct amino acid variations. No segment reassortment or recombination was detected in VP4/VP7 genes. CONCLUSIONS: Dense, closed campus settings facilitate RVC clustered transmission. Limitations included absent screening of asymptomatic canteen staff. Rapid nucleic acid testing enabled timely pathogen identification for outbreak control. Greater attention should be paid to the public health risk of RVC. These whole-genome sequencing data enrich resources for studying RVC evolution and vaccine development.

Acute gastroenteritis outbreak↗
PubMed1994

Neural networks for determining protein specificity and multiple alignment of binding sites.

We use a quantitative definition of specificity to develop a neural network for the identification of common protein binding sites in a collection of unaligned DNA fragments. We demonstrate the equivalence of the method to maximizing Information Content of the aligned sites when simple models of the binding energy and the genome are employed. The network method subsumes those simple models and is capable of working with more complicated ones. This is demonstrated using a Markov model of the E. coli genome and a sampling method to approximate the partition function. A variation of Gibbs' sampling aids in avoiding local minima.

Bacterial Proteins↗
PubMed2004

A local alignment metric for accelerating biosequence database search.

We introduce a metric for local sequence alignments that has utility for accelerating optimal alignment searches without loss of sensitivity. The metric's triangle inequality property permits identification of redundant database entries guaranteed to have optimal alignments to the query sequence that fall below a specified score threshold, thereby permitting comparisons to these entries to be skipped. We prove the existence of the metric for a variety of scoring systems, including the most commonly used ones, and show that a triangle inequality can be established as well for nucleotide-to-protein sequence comparisons. We discuss a database clustering and search strategy that takes advantage of the triangle inequality. The strategy permits moderate but significant acceleration of searches against the widely used "nr" protein database. It also provides a theoretically based method for database clustering in general and provides a standard against which to compare heuristic clustering strategies.

Algorithms↗
PubMed2002

Recombination in evolutionary genomics.

Recombination can be a dominant force in shaping genomes and associated phenotypes. To better understand the impact of recombination on genomic evolution, we need to be able to identify recombination in aligned sequences. We review bioinformatic approaches for detecting recombination and measuring recombination rates. We also examine the impact of recombination on the reconstruction of evolutionary histories and the estimation of population genetic parameters. Finally, we review the role of recombination in the evolutionary history of bacteria, viruses, and human mitochondria. We conclude by highlighting a number of areas for future development of tools to help quantify the role of recombination in genomic evolution.

Base Sequence↗
PubMed1990

The complete genome structure and synthesis of infectious RNA from clones of tomato bushy stunt virus.

The complete sequence of the genome of the cherry strain of tomato bushy stunt virus (TBSV), a member of the tombusvirus group, was determined. A full-length clone of the genome containing a bacteriophage T7 RNA polymerase promoter was assembled from partial cDNA clones. In vitro transcripts of the genome, either with or without a 5' cap structure, were highly infectious. In addition, a genomic clone modified to contain an EcoRI restriction site as a signature mutation was infectious. Five genes are encoded by the TBSV genome. The first ORF from the 5' terminus encodes a p33 protein as well as a p92 product translated by read-through of the amber terminator for p33. The capsid protein gene resides internally, and two ORFs for proteins of 19 and 22 kDa reside at the 3' terminus. These last three genes are expressed from two subgenomic RNAs. The genomic organization of TBSV agrees with previous models for tombusviruses. Computer alignments of TBSV proteins with those of two other tombusviruses suggest greater relatedness among the members of this group than previously reported.

Amino Acid Sequence↗
PubMed2001

Molecular characterisation of Banana mild mosaic virus, a new filamentous virus in Musa spp..

Banana mild mosaic virus (BanMMV) is a previously undescribed filamentous virus infecting Musa spp. The complete genome has been sequenced from PCR clones and consists of 7352 nucleotides, encoding five open reading frames (ORFs) of 205, 25.5, 12.4, 8.0 and 26.8 kDa, respectively. BanMMV was most closely related to fovea- and carlaviruses, based on phylogenetic analysis using a portion of the viral replicase. Analysis of other parts of the genome revealed similarities with fovea-, carla- and potexviruses, but the virus was not clearly aligned to any previously recognised genus.

3' Untranslated Regions↗
PubMed2003

PromoSer: A large-scale mammalian promoter and transcription start site identification service.

Proximal promoters have a major impact on transcriptional regulation. Studies of the sequence-based nature of this regulation usually require collection of proximal promoter sequences for large sets of co-regulated genes. We report a newly implemented web service that facilitates extraction of user specified regions around the transcription start site of all annotated human, mouse or rat genes. The transcription start sites have been identified computationally by considering alignments of a large number of partial and full-length mRNA sequences to genomic DNA, with provision for alternative promoters. The service is publicly available at http://biowulf.bu.edu/zlab/PromoSer/.

Animals↗
PubMed2006

Complete nucleotide sequence and affinities of the genomic RNA of Narcissus common latent virus (genus Carlavirus).

The complete sequence of an isolate of Narcissus common latent virus (NCLV) from Zhangzhou city, Fujian, China was determined from amplified fragments of purified viral RNA. Excluding the poly(A) tail, the genomic RNA of NCLV was 8539 nucleotides (nt) long and had the typical organization for a member of the genus Carlavirus. The most closely related species were Potato virus M, Hop latent virus and Aconitum latent virus, which had 58-59% nt identity to NCLV in their entire genomes. These relationships were confirmed by a phylogenetic analysis using a composite nucleotide alignment of all the open reading frames.

Base Sequence↗
PubMed2002

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.

We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus kandleri by using a whole direct genome sequencing approach. This approach is based on unlinking of genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and cycle sequencing directed by 2'-modified oligonucleotides (Fimers). Sequencing redundancy (3.3x) was sufficient to assemble the genome with less than one error per 40 kb. Using a combination of sequence database searches and coding potential prediction, 1,692 protein-coding genes and 39 genes for structural RNAs were identified. M. kandleri proteins show an unusually high content of negatively charged amino acids, which might be an adaptation to the high intracellular salinity. Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a very deep branch, close to the root of the archaeal tree. However, genome comparisons indicate that, in both trees constructed using concatenated alignments of ribosomal proteins and trees based on gene content, M. kandleri consistently groups with other archaeal methanogens. M. kandleri shares the set of genes implicated in methanogenesis and, in part, its operon organization with Methanococcus jannaschii and Methanothermobacter thermoautotrophicum. These findings indicate that archaeal methanogens are monophyletic. A distinctive feature of M. kandleri is the paucity of proteins involved in signaling and regulation of gene expression. Also, M. kandleri appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism.

Base Sequence↗
PubMed1988

Mitochondrial DNA rearrangements and transcriptional alterations in the male-sterile cytoplasm of Ogura radish.

Maternally inherited mutations, such as cytoplasmic male sterility, provide useful systems in which to study the function of plant mitochondrial genomes and also their interaction with nuclear genes. We have studied the organization and expression of the organelle genomes of the male-sterile cytoplasm of Ogura radish and compared them with those of normal radish to identify alterations that might be involved in cytoplasmic male sterility. The chloroplast DNAs of Ogura and normal radish are virtually indistinguishable, whereas their mitochondrial DNAs are highly rearranged. Alignment of a restriction map constructed for the 257-kilobase Ogura mitochondrial genome with that published for the 242-kilobase genome of normal radish reveals that the two mitochondrial DNAs differ in arrangement by at least 10 inversions. The transcriptional patterns of several known mitochondrial genes and of rearranged mitochondrial sequences were examined in three nuclear backgrounds. Altered transcripts were observed for three mitochondrial genes, atpA, atp6, and coxI. Rearrangements map near each of these genes and therefore may be responsible for their transcriptional alterations. Radish nuclear genes that restore fertility to the Ogura cytoplasm have no effect on the atp6 and coxI transcripts, but do influence the atpA transcriptional pattern.

DNA Restriction Enzymes↗
PubMed2002

Human caspase 12 has acquired deleterious mutations.

Caspase 12 has been cloned from rodent cells, in which it mediated apoptosis in response to endoplasmic reticulum stress. Based on experiments with murine cells it was suggested that this caspase plays a central role in the pathogenesis of Alzheimer's disease. By alignment of the murine caspase 12 cDNA with the human genome sequence we localized the human caspase 12 gene at a single locus within the caspase 1/ICE gene cluster on chromosome 11q22.3. RT-PCR and molecular cloning revealed that nine alternatively spliced transcripts of this gene are expressed. A frame shift mutation and a premature stop codon which is present in all splice variants preclude the expression of a full length protein. An additional loss-of-function mutation within the SHG box, a critical site in caspases, prohibits any proteins, if they are produced, from acting catalytically. Based on our data we conclude that functional caspase 12 is lost in humans and that it can therefore not play a role in Alzheimer's disease.

Alternative Splicing↗
PubMed1996

A third Ig light chain gene isotype in Xenopus laevis consists of six distinct VL families and is related to mammalian lambda genes.

Xenopus laevis is a unique model for studying the ontogenetic development of immune functions. A short primer PCR amplification method was employed to amplify fragments from Xenopus genomic DNA that are related to Ig light chains and TCR. One fragment was identified that appeared to represent a novel type of light chain and was used as a probe to recover the corresponding cDNA from a spleen cDNA library. We designate these light chains type III. Using an iterative screening procedure, six families of VL genes, two distinct JL and two distinct CL sequences, were identified. In a comparison of phylogenetically diverse light chains, the type III genes align with higher vertebrate lambda genes. Southern blot hybridization analyses with genomic DNA from different animals showed the VL and CL sequences to be both diverse and polymorphic. Intrafamily sequence comparisons of VL genes revealed additional diversity. Collectively, these studies confirm the existence of a third type of light chain gene in Xenopus, establish a high degree of genetic variation in the sequences encoding the light chain V regions, and provide the most significant evidence to date for the presence of a lambda-like light chain gene at the phylogenetic level of the amphibians.

Amino Acid Sequence↗
PubMed2006

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs.

The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.

Adenosine Triphosphatases↗
PubMed2002

Physical and genetic map of Epinotia aporema granulovirus genome.

The bean shoot borer, Epinotia aporema (Lep. Tortricidae), is an economically important pest of legume crops in South America. Recently, a granulovirus (EpapGV) was isolated from E. aporema larvae, and evaluated as a potential biological control agent. In order to generate a restriction map and to investigate the gene organisation of EpapGV genome, DNA isolated from occlusion bodies as well as a set of cloned genomic fragments were analysed using combinations of restriction endonucleases and Southern blot analyses that lead to a first version of the physical map. It was subsequently confirmed and refined by sequencing the termini of the cloned fragments and assessing their contiguity by comparing the sequences with databases to identify putative ORFs spanning neighbour fragments. This was also aided by PCR amplifications with primers that pointed outwards of the cloned viral DNA. The granulin gene was positioned on the physical map, cloned and sequenced. Its 747-nucleotide-long ORF encodes a predicted protein of 29 kDa and the core of the baculovirus very late promoter ATAAG was found 29 nucleotides upstream the initiation codon. In addition, 27 putative ORFs were located on the map and used to explore the genome organisation by GeneParityPlot against the fully sequenced granulovirus genomes. These data, taken together with the phylogenetic tree generated by alignment of the major occlusion proteins, indicate that EpapGV is closely related to CpGV, but has a distinct gene organisation.

Amino Acid Sequence↗
PubMed1994

Nuclear genes encoding chloroplast hemoglobins in the unicellular green alga Chlamydomonas eugametos.

When the green unicellular alga Chlamydomonas eugametos is grown under light/dark regimes, nuclear genes are periodically activated in response to the changes in light conditions. These genetic responses are dependent upon the activation of genes associated with photosynthesis (LI616 and LI637), nonphotosynthetic photoreceptors (LI410 and LI818) and the biological clock (LI818). We report here that the LI410 and LI637 genes are part of a small gene family encoding hemoglobins (Hbs) related to those from two unicellular eukaryotes, the ciliated protozoa Paramecium caudatum and Tetrahymena pyriformis, and from the cyanobacterium Nostoc commune. Investigations of the intracellular localization of C. eugametos Hbs by means of immunogold electron microscopy indicate that these proteins are predominantly located in the chloroplast, particularly in the pyrenoid and the thylakoid region. To our knowledge, this constitutes the first evidence for the presence of Hbs in chloroplasts. Alignment of the LI637 cDNA nucleotide sequence with its corresponding genomic sequence indicates that the LI637 gene contains three introns, the positions of which are compared with those in the Hb genes of plants, animals and the ciliate P. caudatum. Although the LI637 gene possesses a three-intron/four-exon pattern similar to that of plant leghemoglobin genes, introns are inserted at different positions. Similarly the position of the single intron in the P. caudatum gene differs from the intron sites in the LI637 gene. The latter observations argue against the current view that all eukaryotic Hbs have evolved from a common ancestor having a gene structure identical to that of plant or animal Hbs.

Amino Acid Sequence↗
PubMed1993

Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters.

The determination of long segments of DNA sequences encompassing the beta- and alpha-globin gene clusters has provided an unprecedented data base for analysis of genome evolution and regulation of gene clusters. A newly developed computer tool kit generates local alignments between such long sequences in a space-efficient manner, helps the user analyze the alignments effectively, and finds consistently aligning blocks of sequences in multiple pairwise comparisons. Such sequence analyses among the beta-like globin gene clusters of human, galago, rabbit, and mouse have revealed the general patterns of evolution of this gene cluster. Alignments in the flanking regions are very useful in assigning orthologous relationships. Investigation of such matches between the mouse and human beta-like globin gene clusters has led to a reassessment of some orthologous assignments in mouse and to a revision of the proposed pathway for evolution of this gene cluster. In general, the interspersed repetitive elements have inserted independently, presumably via a retrotransposition mechanism, in the different mammalian lineages. However, some examples of ancient L1 repeats are found, including one between the epsilon- and gamma-globin genes that appears to have been in the ancestral eutherian gene cluster. Prominent matching sequences are found in a long region 5' to the epsilon-globin gene, the locus control region (LCR) that is a positive regulator of the entire gene cluster. Three-way alignments among the human, goat, and rabbit sequences can extend for > or = 3 kb in part of the LCR (DNase hypersensitive site 3), indicating that the cis-acting components of this complex regulatory region cover a long segment of DNA. In contrast to the beta-like globin gene clusters, the alpha-like globin gene clusters of many mammals occur in very G+C-rich isochores and contain prominent CpG islands. The regions between the alpha-like globin genes are evolving faster than the intergenic regions of the beta-like globin gene clusters. The contrasts between the two gene clusters can be attributed to differences in DNA metabolism in the isochore. The proximal control elements of the rabbit alpha-globin gene are located both 5' to and within the gene. All of this region is part of a prominent CpG island that may be acting as an extended, enhancer-independent promoter. One can hypothesize that the analogue to the LCR in the alpha-globin gene cluster may interface with the distinctive alpha-globin promoter in ways different from the interaction between the beta LCR and the promoters of beta-like globin genes.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1992

Evolution of the salmonid mitochondrial control region.

To explore the evolutionary nature of the salmonid mitochondrial DNA (mtDNA) control region (D-loop) and its utility for inferring phylogenies, the entire region was sequenced from all eight species of anadromous Pacific salmon, genus Oncorhynchus; the Atlantic salmon, Salmo salar; and the Arctic grayling, Thymallus arcticus. A comparison of aligned sequences demonstrates that the generally conserved sequence elements that have been previously reported for other vertebrates are maintained in these primitive teleost fishes. Results reveal a significantly nonrandom distribution of nucleotide substitutions, insertions, and deletions that suggests that portions of the salmonid D-loop may be under differential selective constraints and that most of the control region of these fishes may evolve at a rate similar to that of the remainder of their mtDNA genomes. Maximum likelihood and Fitch parsimony analyses of 9 kb of aligned salmonid sequence data give evolutionary trees of identical topology. These results are consistent with previous molecular studies of a limited number of salmonid taxa and with more comprehensive, classical analyses of salmonid evolution. Predictions from these data, based on a molecular clock assumption for the mtDNA control region, are also consistent with fossil evidence that suggests that species of Oncorhynchus could be as old as the Middle Pliocene and would have thus given rise to the extant Pacific salmon prior to about 5 or 6 million years ago.

Animals↗
PubMed2005

Genomic classification using an information-based similarity index: application to the SARS coronavirus.

Measures of genetic distance based on alignment methods are confined to studying sequences that are conserved and identifiable in all organisms under study. A number of alignment-free techniques based on either statistical linguistics or information theory have been developed to overcome the limitations of alignment methods. We present a novel alignment-free approach to measuring the similarity among genetic sequences that incorporates elements from both word rank order-frequency statistics and information theory. We first validate this method on the human influenza A viral genomes as well as on the human mitochondrial DNA database. We then apply the method to study the origin of the SARS coronavirus. We find that the majority of the SARS genome is most closely related to group 1 coronaviruses, with smaller regions of matches to sequences from groups 2 and 3. The information based similarity index provides a new tool to measure the similarity between datasets based on their information content and may have a wide range of applications in the large-scale analysis of genomic databases.

Base Sequence↗