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PubMed2003

Transcriptome analysis of mouse stem cells and early embryos.

Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

Animals↗
PubMed2025

Genetic structure and demographic history of house mice in western Europe inferred using whole-genome sequences.

The western house mouse, Mus musculus domesticus, is a human commensal and an outstanding model organism for studying a wide variety of traits and diseases. However, we have few genomic resources for wild mice and only a rudimentary understanding of the demographic history of house mice in Europe. Here, we sequenced 59 whole genomes of mice collected from England, Scotland, Wales, Guernsey, northern France, Italy, Portugal and Spain. We combined this dataset with 24 previously published sequences from southern France, Germany and Iran and compared patterns of population structure and inferred demographic parameters for house mice in western Europe to patterns seen in humans. Principal component and phylogenetic analyses identified three genetic clusters in western European mice. Admixture and f-branch statistics identified historical gene flow between these genetic clusters. Demographic analyses suggest a shared history of population bottlenecks prior to 20 000 years ago. Estimated divergence times between populations of house mice from western Europe ranged from 1500 to 5500 years ago, in general agreement with the zooarchaeological record. These results correspond well with key aspects of contemporary human population structure and the history of migration in western Europe, highlighting the commensal relationship of this important genetic model.

Animals↗
PubMed2001

First pass annotation of promoters on human chromosome 22.

The publication of the first almost complete sequence of a human chromosome (chromosome 22) is a major milestone in human genomics. Together with the sequence, an excellent annotation of genes was published which certainly will serve as an information resource for numerous future projects. We noted that the annotation did not cover regulatory regions; in particular, no promoter annotation has been provided. Here we present an analysis of the complete published chromosome 22 sequence for promoters. A recent breakthrough in specific in silico prediction of promoter regions enabled us to attempt large-scale prediction of promoter regions on chromosome 22. Scanning of sequence databases revealed only 20 experimentally verified promoters, of which 10 were correctly predicted by our approach. Nearly 40% of our 465 predicted promoter regions are supported by the currently available gene annotation. Promoter finding also provides a biologically meaningful method for "chromosomal scaffolding", by which long genomic sequences can be divided into segments starting with a gene. As one example, the combination of promoter region prediction with exon/intron structure predictions greatly enhances the specificity of de novo gene finding. The present study demonstrates that it is possible to identify promoters in silico on the chromosomal level with sufficient reliability for experimental planning and indicates that a wealth of information about regulatory regions can be extracted from current large-scale (megabase) sequencing projects. Results are available on-line at http://genomatix.gsf.de/chr22/.

Algorithms↗
PubMed2003

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.

Rice is not only a major food staple for the world's population but it also is a model species for a major group of flowering plants, the monocotyledonous plants. Draft genomic sequence of two subspecies of rice, Oryza sativa spp. japonica and indica ssp. are publicly available. To provide the community with a resource to data-mine the rice genome, we have constructed an annotation resource for rice (http://www.tigr.org/tdb/e2k1/osa1/). In this resource, we have annotated the rice genome for gene content, identified motifs/domains within the predicted genes, constructed a rice repeat database, identified related sequences in other plant species, and identified syntenic sequences between rice and maize. All of the data is available through web-based interfaces, FTP downloads, and a Distributed Annotation System.

Chromosomes, Artificial↗
PubMed2003

Molecular characterization of the pig C3 gene and its association with complement activity.

The complement system catalyzes direct lysis of micro-organisms and modulates phagocytosis, inflammation, humoral and cellular immune responses. Since the complement protein C3 is the central component within all pathways of complement activation, C3 is a candidate gene for complement activity and also for improved protection against many pathogens. The pig C3 gene was sequenced, screened for polymorphisms, and analyzed for association with hemolytic complement activity of the alternative and classical pathway (AH(50), CH(50)). C3c serum levels and haptoglobin (HP) serum concentrations were measured before and after vaccination against Mycoplasma hyopneumoniae, Aujeszky virus, and porcine reproductive and respiratory syndrome virus in F2 animals of a pig resource population based on crossbreeding of Duroc and Berlin Miniature Pig. The genomic C3 sequence covers 444 bp of promoter region, 41 exons and 40 introns, as well as 881 bp of the 3'-flanking region. The cDNA codes for a 1,661-amino acid precursor C3. Five polymorphic sites were detected in the 5'-UTR, intron 13, exon 15, exon 30, and the 3'-UTR. Within the resource population two haplotypes were found to segregate. Analysis of variance applying a repeated measures model revealed a significant effect of the interaction of C3 genotype and time of measurement relative to immunization on CH(50), AH(50,)and C3c that is likely to be due to variation of C3 expression. In contrast, the time course of the HP acute-phase reaction is not associated with C3 genomic variation. The association of C3 with complement activity indicates the importance of C3 as a candidate gene for natural resistance to micro-organisms, although the causative polymorphism modulating the expression of C3 remains to be delineated.

Alleles↗
PubMed1991

PRENRL_3D: a computer program for an automatic creation of NRL_3D, protein sequence-structure database, from the Protein Data Bank.

Recently, we have developed a sequence-structure database of protein information, NRL_3D, that is extracted from the Protein Data Bank (PDB) of the Brookhaven National Laboratory. NRL_3D provides a vehicle for the retrieval of the three-dimensional coordinates of protein fragments as identified by sequence properties. These data are formulated to allow access by standard sequence analysis programs such as those provided by the Protein Identification Resource (PIR). Because the PDB is updated four times per year, semimanual construction of NRL_3D in coordination with these updates becomes a time-consuming and inefficient task. Hence, we have developed a computer program (PRENRL_3D) in the "C" computer language that automatically extracts NRL_3D from the PDB. Although the program was developed in a VAX/VMS environment, care was taken to ensure its portability to other computer systems. Customized versions of the NRL_3D database can be created from the PDB entry files using various options available in PRENRL_3D, such as selection of entries determined at high resolution and with low R-value. The program has been developed modularly and it contains a number of generalized procedures for manipulating various information in the PDB.

Amino Acid Sequence↗
PubMed2004

Genomes for medicine.

We have the human genome sequence. It is freely available, accurate and nearly complete. But is the genome ready for medicine? The new resource is already changing genetic research strategies to find information of medical value. Now we need high-quality annotation of all the functionally important sequences and the variations within them that contribute to health and disease. To achieve this, we need more genome sequences, systematic experimental analyses, and extensive information on human phenotypes. Flexible and user-friendly access to well-annotated genomes will create an environment for innovation, and the potential for unlimited use of sequencing in biomedical research and practice.

Genetic Variation↗
PubMed2005

Gene discovery and expression profiling in porcine Peyer's patch.

Peyer's patches of the intestinal mucosa are essential for host defense and immune regulation in the enteric system. To better understand molecular mechanisms of Peyer's patch function, we have screened for differentially expressed genes specific to Peyer's patch. cDNA libraries were created from normal Peyer's patch, immune stimulated Peyer's patch, and pooled cDNA subtracted with fibroblast RNA. From the subtracted library, 3687 expressed sequence tags (ESTs), representing 2414 unique nucleotide sequences, were isolated, identified by BLAST searches against public databases, and spotted onto a microarray for gene expression profiling. Approximately 30% of these ESTs BLAST to genes of unknown function and 20% have no known homology in the public databases (novel genes). Of the novel genes, 70% are expressed in normal immune tissues by microarray analysis, suggesting that at least 371 of the unidentified EST sequences from the subtracted library are novel porcine genes and can now be further characterized to determine their function in the porcine Peyer's patch. We surmise that the products of these genes participate in biochemical and cellular functions related to the unique immunological and gastroenterological functions of the small intestine. The BLAST and gene ontology information for each of the subtracted library EST sequences, the normal and immune stimulated libraries, and the microarray are all valuable resources that will facilitate further examination of the biological function of porcine Peyer's patch tissue.

Animals↗
PubMed2005

A situational picture of HIV/AIDS and injection drug use in Vinnitsya, Ukraine.

BACKGROUND: New and explosive HIV epidemics are being witnessed in certain countries of Eastern Europe, including Ukraine, as well as a rapid and dramatic increase in the supply, use, and negative public health consequences of illicit drugs. A majority of registered HIV cases in Ukraine occur among injection drug users (IDUs), large numbers of whom report HIV risk behaviors such as needle sharing. The purpose of this study was to apply the World Health Organization's Rapid Assessment and Response on Injection Drug Use (IDU-RAR) guide to create a situational picture in the Vinnitsya Oblast, Ukraine, a region with very scarce information about the HIV/AIDS and injection drug use (IDU) epidemics. METHODS: The IDU-RAR uses a combination of qualitative data collection techniques commonly employed in social science and evaluation research to quickly depict the extent and nature of the given health problem and propose locally relevant recommendations for improvement. The investigators focused their assessment on the contextual factors, drug use, and intervention and policy components of the IDU-RAR. A combination of network and block sampling techniques was used. Data collection methods included direct observation, review of existing data, structured and unstructured interviews, and focus group discussions. Key informants and locations were visited until no new information was being generated. RESULTS: The number of registered HIV cases in Vinnitsya has increased from 3 (1987-1995) to 860 (1999-10/2004), 57 of whom have already died. Ten percent of annual admissions to the area's Regional Narcological Dispensary were for opiate disorders, and the number of registered IDUs rose by 20% from 1999 to 2000. The level of HIV/AIDS awareness is generally poor among the general population but high among high-risk populations. Both HIV/AIDS and injection drug use carry a strong stigma in the community, even among medical professionals. There was very little evidence of primary HIV/AIDS prevention efforts, and IDU prevention efforts focused on promotion of anti-drug messages in the schools. CONCLUSION: Given that Ukraine has sparse resources to be devoted to this problem, action recommendations should be prioritized, realistic, and initially targeted to persons in greatest need. The following action recommendations are prioritized by the following categories: First priority: Voluntary Counseling and Testing; Second Priority: Prevention and Education; and Third Priority: Harm Reduction and Treatment. They are provided in this sequence based on what response can realistically be implemented first with limited additional resources and can make the greatest immediate impact. The persons at greatest risk, HIV positive persons and IDUs, should be attended to first.

Journal Article↗
PubMed2025

How Have Massively Parallel Sequencing Technologies Furthered Our Understanding of Oncogenesis and Cancer Progression?

Massively parallel sequencing technologies have been a boon to many fields of biological science, including oncology. Cancer is an umbrella term for many diseases featuring abnormal cellular growth due to genetic and epigenetic aberrations. Advances in sequencing technology allow for interrogation of the DNA and RNA of cancer cells and other cells in the tumor microenvironment down to a single-base resolution. However, these strides come after a rich history of ground-breaking biological assays, like the discovery of the Philadelphia chromosome in the context of leukemia. Many specific genetic and epigenetic modifications have been implicated in oncogenesis, cancer progression, and response to treatment. Sequencing technologies have also helped to associate populations of bacteria in the microbiome to cancer development and prognosis. However, all this new information, especially when procured via high-throughput methods, comes at the cost of being more computationally and staff-resource intensive. There is also more risk to the privacy of the individuals with sequenced genomes. Notwithstanding, the overall benefit of sequencing technologies can greatly outweigh the risks with careful advancements and continued focus on the goal: helping those affected by cancer via precision medicine. Cancer biology has been and will continue to be elucidated by sequencing innovations in ways unimaginable without it.

Humans↗
PubMed2006

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.

Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes and gene products. To make this information available on an ongoing basis, the Saccharomyces Genome Database (SGD) (http://www.yeastgenome.org/) has created the Genome Snapshot (http://db.yeastgenome.org/cgi-bin/genomeSnapShot.pl). The Genome Snapshot summarizes the current state of knowledge about the genes and chromosomal features of S.cerevisiae. The information is organized into two categories: (i) number of each type of chromosomal feature annotated in the genome and (ii) number and distribution of genes annotated to Gene Ontology terms. Detailed lists are accessible through SGD's Advanced Search tool (http://db.yeastgenome.org/cgi-bin/search/featureSearch), and all the data presented on this page are available from the SGD ftp site (ftp://ftp.yeastgenome.org/yeast/).

Chromosomes, Fungal↗
PubMed1996

Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture.

A system called MAGPIE (Multipurpose Automated Genome Project Investigation Environment) has been designed and implemented to meet the challenges of automated whole genome analysis. The system initiates large numbers of remote and local transactions, each depending on evolving criteria and on changing remote and local conditions. Transactions are requested from different types of remote and local resources. The remote request load is fairly balanced with other community demands on server resources. Local decision modules monitor and obey user preferences and combine evidence from multiple sources to formulate credible hypotheses about sequence function. Consistency checks from multiple types of data are integrated into the ongoing local analysis. The system performs reliably on local UNIX workstations and communicates with remote resources through standard networking protocols.

Automation↗
PubMed1996

Distance education through the Internet: the GNA-VSNS biocomputing course.

A prototype course on biocomputing was delivered via international computer networks in early summer 1995. The course lasted 11 weeks, and was offered free of charge. It was organized by the BioComputing Division of the Virtual School of Natural Sciences, which is a member school of the Globewide Network Academy. It brought together 34 students and 7 instructors from all over the world, and covered the basics of sequence analysis. Five authors from Germany and USA prepared a hypertext book which was discussed in weekly study sessions that took place in a virtual classroom at the BioMOO electronic conferencing system. The course aimed at students with backgrounds in molecular biology, biomedicine or computer science, complementing and extending their skills with an interdisciplinary curriculum. Special emphasis was placed on the use of Internet resources, and the development of new teaching tools. The hypertext book includes direct links to sequence analysis and databank search services on the Internet. A tool for the interactive visualization of unit-cost pairwise sequence alignment was developed for the course. All course material will stay accessible at the World Wide Web address (Uniform Resource Locator) http://+www.techfak.uni-bielefeld.de/bcd/welcome .html. This paper describes the aims and organization of the course, and gives a preliminary account of this novel experience in distance education.

Computational Biology↗
PubMed1999

[Finding of new FCC1/HN antigenic expressed sequence tag(ESTs) of Plasmodium falciparum].

AIM: To sequence the strong positive clones obtained by immuno-screening of Plasmodium falciparum FCC1/HN lambda gt11 cDNA expression library, and to elucidate the antigenic expressed sequence tags through sequencing the cDNA insert of these positive clones, and new antigenic ESTs could serve as a resource to pursue their corresponding antigen genes. METHODS: cDNA inserts of positive lambda gt11 phage clones were amplified by PCR. The PCR products, after purification, were cloned into the M13 mp18 sequencing vector. Single-stranded M13 DNA was prepared and sequenced. Then the acquired sequences were compared in homologies with EMBL/GenBank database on the PC/GENE software system and searched in NCBI (National Center for Biotechnology Information) GenBank using BLAST (Basic Local Alignment Search Tool) commond. RESULTS: Sequence C03 was part of the known P. falciparum antigenic heat shock protein 70 (Pfhsp70) gene, while the other 5 sequences were new P. falciparum antigenic expressed sequence tags (ESTs). CONCLUSION: The 5 new antigenic ESTs generated could serve as the breaking through points in our efforts to find out new P. falciparum antigen genes.

Animals↗
PubMed2004

Male chacma baboons (Papio hamadryas ursinus) discriminate loud call contests between rivals of different relative ranks.

Males in multi-male groups of chacma baboons (Papio hamadryas ursinus) in Botswana compete for positions in a linear dominance hierarchy. Previous research suggests that males treat different categories of rivals differently; competitive displays between males of similar rank are more frequent and intense than those between disparately ranked males. Here we test whether males also respond differently to male-male interactions in which they are not directly involved, using playbacks of the loud 'wahoo' calls exchanged between competing males in aggressive displays. We played paired sequences of vocal contests between two adjacently ranked and two disparately ranked males to ten subjects, half ranking below the signalers in the call sequences and half above. Subjects who ranked above the two signalers showed stronger responses than lower-ranking subjects. Higher-ranking subjects also responded more strongly to sequences involving disparately ranked, as opposed to adjacently ranked opponents, suggesting that they recognized those individuals' relative ranks. Strong responses to sequences between disparately ranked opponents might have occurred either because such contests typically involve resources of high fitness value (defense of meat, estrous females or infants vulnerable to infanticide) or because they indicate a sudden change in one contestant's condition. In contrast, subjects who ranked lower than the signalers responded equally strongly to both types of sequences. These subjects may have been able to distinguish between the two categories of opponents but did not respond differently to them because they had little to lose or gain by a rank reversal between males that already ranked higher than they did.

Acoustic Stimulation↗
PubMed2004

A physical map of the chicken genome.

Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.

Animals↗
PubMed2026

Meta2DB: curated shotgun metagenomic feature sets and metadata for health state prediction.

SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health. AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.

Metadata↗
PubMed2004

Molecular characterization of tgd057, a novel gene from Toxoplasma gondii.

The expressed sequence tag (EST) effort in Toxoplasma gondii has generated a substantial amount of gene information. To exploit this valuable resource, we chose to study tgd057, a novel gene identified by a large number of ESTs that otherwise show no significant match to known sequences in the database. Northern analysis showed that tgd057 is transcribed in this tachyzoite. The complete cDNA sequence of tgd057 is 1169 bp in length. Sequence analysis revealed that tgd057 possibly adopts two polyadenylation sites, utilizes the fourth in-frame ATG for translation initiation, and codes for a secretory protein. The longest open reading frame for the tgd057 gene was cloned and expressed as a recombinant protein (rd57) in Escherichia coli. Western analysis revealed that serum against rd57 recognized a molecule of ~21 kDa in the tachyzoite protein extract. This suggests that the tgd057 gene is expressed in vivo in the parasite.

Amino Acid Sequence↗