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PubMed2002

Protein structure resources.

The Protein Data Bank (PDB) is the primary source of macromolecular structure data for a worldwide community of users. A subset of those users then process these data to derive secondary information which is also available on the WWW. This process includes validation, some form of reductionism, via sequence or structure, or visualization. The result, a set of further web-accessible resources on protein structure and functional classification, links to primary genomic information, protein-protein and protein-ligand interactions, protein dynamics and protein-modeling resources. This paper reports on these processes and a subset of the web resources that result.

Crystallography, X-Ray↗
PubMed1991

Cloning of Amb a I (antigen E), the major allergen family of short ragweed pollen.

To determine the structure of Amb a I (previously called antigen E), the major allergen from short ragweed, cDNA from pollen was cloned into lambda gt11 and lambda gt10. One of the three distinct clones isolated from the lambda gt11 library by screening with anti-denatured Amb a I antibodies was used to screen both libraries for other Amb a I sequences. Multiple clones were isolated and sequenced and proved to be highly homologous but nonidentical. The clones could be divided into three groups based on sequence similarity, and in accordance with the International Union of Immunological Societies-approved nomenclature (Marsh, D. G., Goodfriend, L., King, T. P., Lowenstein, H., and Platts-Mills, T. A. E. (1986) Bull. WHO 64, 767-770) they have been designated Amb a I.1, Amb a I.2, and Amb a I.3. Clones within a group have greater than 99% identity, and similarity among groups is 85-90% at the nucleotide level. The amino acid sequence of four peptides (isolated from antigen E obtained from the Research Resources Branch of the National Institutes of Health) containing 132 amino acids was identical to one of the clones (Amb a I.1). The presence of multiple naturally occurring isoelectric forms of Amb a I was demonstrated by two-dimensional gel electrophoresis and Western blotting. Southern blot analysis demonstrates the presence of multiple Amb a I-related sequences in the ragweed genome. Amb a I is therefore not a single molecule but rather a family of closely related proteins.

Allergens↗
PubMed1990

Purification of a calcium binding protein (rat SPARC) from primary Sertoli cell-enriched culture medium.

A protein with an apparent Mr of 43,000 was purified from Sertoli cell-enriched culture medium by sequential anion-exchange, gel permeation, C4 reversed-phase, and diphenyl reversed-phase HPLC. N-Terminal sequence analysis of this protein revealed a sequence of NH2-XPQTEAAEEMVAEETVV for the first 17 amino acids. Comparison of this sequence with existing protein data base maintained at the Protein Identification Resource revealed that it shares extensive identity with a previously described protein secreted by mouse embryo parietal endoderm, SPARC, which is equivalent to a protein secreted by a basement-membrane-producing tumor, BM-40; and a bone protein, osteonectin. This protein also possesses similar in vitro biological activity of SPARC in which it binds Ca2+. The possible physiological significance of this protein was discussed.

Amino Acid Sequence↗
PubMed2025

JG2: an updated version of the Japanese population-specific reference genome.

Here we present the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously used in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a substantial advancement over the collapsed assembly-based JG1, with improvements including a greater number of identified variants (3,115,695 variants, of which 298,644 had an allele frequency (AF) of 1.0 in the 3.5KJPNv2 AF panel) and a higher N50 value (152,668,378 bp). These enhancements provide researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website ( https://jmorp.megabank.tohoku.ac.jp/ ).

Journal Article↗
PubMed2004

cpnDB: a chaperonin sequence database.

Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms. Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers. Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea. The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera. As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage. We built cpnDB from open source tools and it is available at http://cpndb.cbr.nrc.ca.

Animals↗
PubMed2001

Implications of the human genome for understanding human biology and medicine.

Clinical researchers, practicing physicians, patients, and the general public now live in a world in which the 2.9 billion nucleotide codes of the human genome are available as a resource for scientific discovery. Some of the findings from the sequencing of the human genome were expected, confirming knowledge presaged by many decades of research in both human and comparative genetics. Other findings are unexpected in their scientific and philosophical implications. In either case, the availability of the human genome is likely to have significant implications, first for clinical research and then for the practice of medicine. This article provides our reflections on what the new genomic knowledge might mean for the future of medicine and how the new knowledge relates to what we knew in the era before the availability of the genome sequence. In addition, practicing physicians in many communities are traditionally also ambassadors of science, called on to translate arcane data or the complex ramifications of biology into a language understood by the public at large. This article also may be useful for physicians who serve in this capacity in their communities. We address the following issues: the number of protein-coding genes in the human genome and certain classes of noncoding repeat elements in the genome; features of genome evolution, including large-scale duplications; an overview of the predicted protein set to highlight prominent differences between the human genome and other sequenced eukaryotic genomes; and DNA variation in the human genome. In addition, we show how this information lays the foundations for ongoing and future endeavors that will revolutionize biomedical research and our understanding of human health.

Clinical Medicine↗
PubMed2002

Molecular sexing of monomorphic endangered Ara birds.

Survival of most endangered birds may depend on breeding programs where sex identification plays an important role. Molecular sexing has shown to be a rapid and safe procedure. In this work we established sex identification of monomorphic endangered Ara birds using a chromosome W-linked DNA marker, the Chromo-helicase-DNA-Binding 1 (CHD) gene. Most birds have two CHD sex-linked genes, one W-linked (CHD-W) and one Z-linked (CHD-Z). These markers were characterized from Ara militaris and gender sex was determined by PCR and restriction analyzes. The procedure here reported was successfully applied to five different species of the genus Ara and confirmed the validity of the technique. To our knowledge, this is the first report of molecular sexing of the Ara species. This molecular sexing is currently been used in breeding programs of Ara birds.

Animals↗
PubMed1999

On the origins of congenic MATalpha and MATa strains of the pathogenic yeast Cryptococcus neoformans.

The basidiomycetous yeast Cryptococcus neoformans infects humans and causes a meningoencephalitis that is uniformly fatal if untreated. The organism has a defined sexual cycle involving mating of haploid MATa and MATalpha strains, gene disruption by transformation and homologous recombination is now readily accomplished, and robust animal models for infection have been well established. In addition, a pair of congenic MATalpha and MATa haploid strains have been constructed that permit detailed studies on physiology and virulence by classical genetic approaches. These strains represent a valuable resource for further studies in this organism, and the genomic sequence of one of these strains, JEC21 (=B-4500), was recently chosen to be sequenced by an international consortium. Because of the importance of these strains for genetic studies in C. neoformans and the fact that the genomic sequence of one of these strains is in progress, we review here how these congenic strains were originally constructed.

Animals↗
PubMed2001

Channel catfish follicle-stimulating hormone and luteinizing hormone: complementary DNA cloning and expression during ovulation.

Gonadotropins are important regulators of reproduction. To develop molecular resources for production of recombinant gonadotropins, we have cloned and sequenced complementary DNA encoding the channel catfish (Ictalurus punctatus) follicle-stimulating hormone (FSH) and luteinizing hormone (LH), which encode 132 and 140 amino acid proteins, respectively. The deduced amino acid sequences of the catfish FSH and LH are highly conserved with those cloned from other teleosts. Both the FSH and the LH were highly induced during ovulation after injection of carp pituitary extract. Taken together with our previous findings of enhanced expression of growth hormone and other pituitary hormones, this research suggests that a hormonal cocktail may be needed for more efficient manipulation of catfish reproduction. The availability of the catfish FSH and LH cDNAs provides the opportunity for production of immunologically or biologically active recombinant gonadotropins for the study of catfish reproductive physiology and the manipulation of artificial spawning for aquaculture.

Journal Article↗
PubMed2026

Comprehensive analysis of synonymous codon usage bias and evolutionary dynamics in the chloroplast genomes of eight Coptis species.

Coptis is a medically important genus renowned for producing valuable isoquinoline alkaloids. Although its chloroplast genomes encode key components for photosynthesis and plastid gene expression, the evolutionary constraints acting on their coding sequences and synonymous codon usage remain poorly resolved. Here, we combined a transparent taxon-level sampling strategy with comparative analyses of chloroplast CDSs from eight Coptis taxa. We quantified nucleotide composition, relative synonymous codon usage, effective number of codons, neutrality and PR2 patterns, and correspondence analysis, and then integrated these results with a core-CDS distance analysis and gene-wise pairwise dN/dS estimates. The chloroplast genomes showed a conserved AT-rich composition, especially at the third codon position (GC3 approximately 30.3-30.8%), with a consistent GC1 > GC2 > GC3 trend. Thirty preferred codons were detected, 28 ending in A/T, and eleven optimal codons were shared across the genus. The core-CDS distance analysis recovered a close relationship between C. chinensis and C. chinensis var. brevisepala, whereas most coding genes showed dN/dS values below one, consistent with pervasive purifying constraint. Across 48 consistently filtered CDSs, GC3s was negatively associated with mean dN (Spearman rho = -0.404, P = 0.00439) and CAI was positively associated with mean dN (rho = 0.303, P = 0.0361), whereas the remaining associations were not significant (all P > = 0.0972). These results extend codon-usage analysis by linking synonymous-site composition to coding-sequence evolution within Coptis, while providing a hypothesis-generating resource for future plastid engineering studies.

Genome, Chloroplast↗
PubMed2004

Medaka genomics: a bridge between mutant phenotype and gene function.

Recent advances in medaka genetics have proven that the medakafish is an excellent model system for developmental and evolutionary biology studies and that it can complement similar studies in zebrafish. Large-scale mutagenesis projects are now being conducted by several groups in Japan and are delivering a vastly expanded pool of medaka mutant stocks. This growing availability of genomic resources will greatly accelerate progress in moving from mutant phenotypes to the elucidation of gene function. This phenotype-driven approach can be expected to lead to the identification and characterization of novel genes and pathways in vertebrate genomes. This review discusses the current state of medaka genomic resources, the state of medaka gene mapping and medaka genome sequencing projects.

Animals↗
PubMed2006

Lotus japonicus as a platform for legume research.

The major role of 'model plants' is to provide knowledge and technologies obtained in related systems to researchers studying crop plants. Lotus japonicus was chosen as a model system first for legume genetics and then for legume genomics. A large number of L. japonicus mutants that have alterations in legume-specific phenomena have been generated and phenotypically characterized, and genomics has drastically accelerated the molecular characterization of these mutants. Substantial resources of information and experimental materials, including genomic and cDNA sequences, corresponding DNA libraries and high-density linkage maps demonstrate that L. japonicus is an excellent model system. Transfer of knowledge from L. japonicus to other legumes, especially crop legumes, is a matter for urgent consideration.

Chromosome Mapping↗
PubMed1994

Teaching medical physics to general audiences.

By judiciously selecting topics and reading materials, one can teach a full semester course on medical physics appropriate for college students not majoring in the natural sciences. This interdisciplinary field offers an opportunity to teach a great deal of basic physics at the freshman level in the context of explaining modern medical technologies such as ultrasound imaging, laser surgery, and positron emission tomography. This article describes one such course which combines lectures, outside visitors, varied readings, and laboratories to convey a select subset of physical principles and quantitative problem-solving skills. These resources are also valuable for enriching the standard freshman physics sequence for premedical students.

Biophysics↗
PubMed2001

Isolation and characterization of a new ribosome inactivating protein, momorgrosvin, from seeds of the monk's fruit Momordica grosvenorii.

Momorgrosvin, a single-chained glycoprotein with a molecular weight of 27.7 kilodaltons and an isoelectric point of about 9 was isolated from the seeds of Momordica grosvenorii (Family Cucurbitaceae). The isolation procedure entailed acetone precipitation, affinity chromatography on Hi Trap Blue, cation exchange chromatography on Resource S and size exclusion chromatography on Superose 12. The sequence of the first eighteen N-terminal amino acid residues of momorgrosvin exhibited homology to those of RIPs from other Momordica species. Momorgrosvin inhibited protein synthesis in the rabbit reticulocyte lysate system with an IC50 of 0.3 nM and displayed RNA N-glycosidase activity giving rise to the diagnostic Endo's band at a concentration as low as 9 nM. The protein acted on tRNA to produce acid-soluble uv-absorbing species.

China↗
PubMed1994

Outcomes assessment in clinical settings: a consensus statement on principles and best practices in project management.

BACKGROUND: The focus of this article is on health-related outcomes particularly reducing symptoms and improving health status. Public policy, purchaser demand, quality assurance/quality improvement, clinical research, and the computerized medical record have all fed the increasing interest in outcomes. "Outcomes assessment" refers to the measurement, monitoring, and feedback of outcomes. In implementing outcomes assessment, the bulk of the work is concentrated in managing individual projects. From May 1992 through March 1993, under a grant from the Functional Outcomes Program of the New England Medical Center (Boston), the directors of five major health outcomes assessment programs held a series of meetings to share their experiences in implementation. Principles and recommended best practices for project management are provided here. Implementing an outcomes project: Making a commitment to begin includes identifying a condition or procedure to investigate, assembling a project team, and naming a coordinator. Designing a project entails defining its purpose and scope, developing the measurement instruments, and establishing a logistical protocol for data collection. Managing the data entails collecting the data, entering the data into a database, maintaining quality control over the data, and storing the data. Using the data entails analyzing the data, providing feedback and interpretation to clinicians, and linking outcomes to the clinical process. CASE STUDY: For a typical outcomes project--total hip replacement--the sequence of activities in the project and the staffing and resources needed are all described.

Data Collection↗
PubMed1999

Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): conservation implications of range discontinuity.

A nucleotide sequence analysis of the first internal transcribed spacer region (ITS-1) between the 5.8S and 18S ribosomal DNA genes (640 bp) and cytochrome c oxidase subunit I (COI) of mitochondrial DNA (mtDNA) (576 bp) was conducted for the freshwater bivalve Lasmigona subviridis and three congeners to determine the utility of these regions in identifying phylogeographic and phylogenetic structure. Sequence analysis of the ITS-1 region indicated a zone of discontinuity in the genetic population structure between a group of L. subviridis populations inhabiting the Susquehanna and Potomac Rivers and more southern populations. Moreover, haplotype patterns resulting from variation in the COI region suggested an absence of gene exchange between tributaries within two different river drainages, as well as between adjacent rivers systems. The authors recommend that the northern and southern populations, which are reproductively isolated and constitute evolutionarily significant lineages, be managed as separate conservation units. Results from the COI region suggest that, in some cases, unionid relocations should be avoided between tributaries of the same drainage because these populations may have been reproductively isolated for thousands of generations. Therefore, unionid bivalves distributed among discontinuous habitats (e.g. Atlantic slope drainages) potentially should be considered evolutionarily distinct. The DNA sequence divergences observed in the nuclear and mtDNA regions among the Lasmigona species were congruent, although the level of divergence in the COI region was up to three times greater. The genus Lasmigona, as represented by the four species surveyed in this study, may not be monophyletic.

Animals↗
PubMed2002

DiffTool: building, visualizing and querying protein clusters.

UNLABELLED: DiffTool is a resource to build and visualize protein clusters computed from a sequence database. The package provides a clustering tool to construct protein families according to sequence similarities and a web interface to query the corresponding clusters. A subtractive genome analysis tool selects protein families specific for a genome or a group of genomes. For each protein cluster, DiffTool includes access to sequences, coloured multiple alignments and phylogenetic trees. AVAILABILITY: A cluster database built from yeast and complete prokaryotic genomes is queryable at http://bioweb.pasteur.fr/seqanal/difftool. All the Perl sources are freely available to non-profit organizations upon request.

Cluster Analysis↗
PubMed2026

CERTOMICS: trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies.

SUMMARY: Adoptive cellular immunontherapies, such as chimeric antigen receptor (CAR) T cell therapy, have transformed cancer treatment, yet challenges such as resistance, relapse, and high costs limit their efficacy and accessibility. A comprehensive understanding of cellular heterogeneity and molecular profiles is essential to improve these therapies. Advanced single-cell multiomics technologies have the power to analyze the complex interactions between CAR-engineered cells, immune cells, and tumor cells. However, standardized single-cell multiomics computational pipelines specifically tailored to CAR-engineered cell products are lacking. Due to the synthetic nature of CAR transgenes, additional steps for reliable identification and characterization of CAR-positive cells are required but not included in existing data-processing workflows. To address this, we present CERTOMICS, a Nextflow-based, CAR-aware pipeline offering enhanced CERTainty in immunophenotyping and data interpretation, tailored for single-cell multiOMICSprofiling of adoptive cellular immunotherapies. The pipeline standardizes processing 10x Genomics single-cell multiomics data and integrates CAR-specific identification and quality control. Additionally, a curated repository of CAR construct sequences and annotation data is provided, serving as an extensible resource to support the analysis and development of CAR T cell therapies. AVAILABILITY AND IMPLEMENTATION: Detailed documentation of this pipeline, along with a resource on latest FDA-approved CAR therapies is available on our website: https://fraunhofer-izi.github.io/Living-Drugs-Wiki/. The data underlying this article are available on GitHub at https://github.com/fraunhofer-izi/CERTOMICS. The code is also published on Zenodo at https://doi.org/10.5281/zenodo.18709693.

Multiomics↗