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Origins and genetic nonvariability of the proteins which diffuse from maize pollen.

The major function of pollen is to deliver the sperm nuclei to the embryo sac. It does this by germinating and producing a pollen tube and thus provides a relatively simple developmental system for study. Mutants for many pollen functions are accessible, as it is a haploid cell. Mature pollen was fractionated into diffusible proteins, soluble proteins, and proteins insolubly associated with membrane or wall; these protein fractions have been quantified and cataloged by native and SDS polyacrylamide gel electrophoresis. Diffusible proteins are localized in the pollen grain wall whereas soluble proteins are cytoplasmic. The roles of haploid and diploid genomes in specifying these proteins is discussed. Pollen from maximally divergent maize lines was examined for quantitative and qualitative variation in the diffusible proteins. A surprising conservation was found for these proteins indicating some functional role which is, at present, unknown. Initial experiments on the incorporation of 35S-methionine into germinating pollen indicate that major representatives of the diffusible proteins are made within the pollen grain itself. They are presumably included in the pollen wall during development and diffuse out through the pore region. Studies with pollen mRNA and experiments on incorporation of 35S-methionine into developing anthers are underway and will identify the origin of these proteins. A knowledge of the basic developmental biology of maize pollen is a prerequisite to its judicious use as a monitor of environmental mutagens.

Diffusion↗

Further characterization of BC3H1 myogenic cells reveals lack of p53 activity and underexpression of several p53 regulated and extracellular matrix-associated gene products.

To catalog factors that may contribute to the completion of myogenesis, we have been looking for molecular differences between BC3H1 and C2C12 cells. Cells of the BC3H1 tumor line, though myogenic, are nonfusing, and withdraw from the cell cycle only reversibly, whereas cells of the C2C12 line fuse, differentiate terminally, and express several muscle-specific gene products that BC3H1 cells do not. Relative to C2C12 cells, BC3H1 cells underaccumulated cyclin-dependent kinase inhibitor p21 and underaccumulated transcripts for p21, GADD45, CDO, decorin, osteopontin, H19, fibronectin, and thrombospondin-1 (tsp-1). Levels of accumulation of H19, tsp-1, and larger isoforms of fibronectin messenger ribonucleic acid (mRNA) were found to increase in response to expression of myogenic regulatory factors as shown by their accumulation in differentiated myogenically converted 10T1/2 cells but not in 10T1/2 fibroblasts. BC3H1s accumulated a temperature-insensitive, geldanamycin-sensitive, misfolded form of p53 incapable of transactivating a p53 responsive reporter, consistent with underexpression of p21, GADD45, and tsp-1. BC3H1 and C2C12 cells were similar with respect to upregulation of p27 protein, downregulation of mitogen-activated protein kinase phosphatase-1 (MKP-1) protein, upregulation of retinoblastoma (Rb) mRNA, and nuclear localization of hypophosphorylated Rb. Cells of both lines expressed the muscle-specific 1b isoform of MEF2D. Although nonfusing in the short term, after more than 18 d in differentiation medium, some cultures of BC3H1 cells formed viable multinucleated cells in which the nuclei did not reinitiate synthesis of DNA in response to serum. Our findings suggest participation of tsp-1 and specific isoforms of fibronectin in myogenesis and suggest additional avenues of research in myogenesis and oncogenesis.

Animals↗

Why do professionals disagree? The case of hormone replacement therapy and coronary heart disease prevention.

Why have professionals disagreed about whether midlife women should be advised to use hormone replacement therapy (HRT) for prevention of coronary heart disease (CHD)? Because the evidence has been incomplete and could be interpreted differently by different professionals, the question with regard to HRT and CHD prevention thus is not "What does the evidence prove?" but rather is "What are the decision rules by which research can be evaluated and made sense of?" The present article attempts to clarify the problem by cataloging dimensions along which professionals differ. These dimensions include the weight to be given to epidemiological vs. clinical trial data; whether a conclusion has already been drawn based on available evidence; whether a theoretical rationale exists; whether a professional is oriented to clinical work or research; and whether data is distorted.

Consensus↗

The vertical file enters the electronic age.

Vertical files are revered institutions in many libraries. The reference staff at the Spencer S. Eccles Health Sciences Library at the University of Utah automated their vertical file and made the information in it accessible via the Library's Integrated Library System. Medical Subject Headings (MeSH) were applied to vertical files and simple records leading to them were entered in the Library's online catalog. Electronic access to the vertical file increases the availability of concepts too new to be in medical books and permits the Library to meet the needs of lay patrons searching for basic information on popular health care topics.

Academic Medical Centers↗

Sources of information on postgraduate medical training programs--update.

This is an update of an earlier article listing directories, journal articles, and general books that aid the librarian, resident, or medical student in finding information on residency and fellowship programs. The article also gives suggestions for building a file of program catalogs related to residencies, fellowships, and clerkships and related materials.

Education, Medical↗

A metastrategy for World-Wide Web information retrieval in clinical medicine.

The metastrategy for World-Wide Web information retrieval was presented as an integrated approach to end-user searching in clinical medicine, although its application may be made to any search for WWW information. Certain distinctions, such as between anticipated and unanticipated clinical information needs and between WWW catalogs for retrieving Web sites and WWW databases for retrieving Web pages, were made. These distinctions are important in the end-user strategy because they help maximize the productivity of the WWW for clinicians.

Clinical Medicine↗

An educational program in the medical uses of computers for rural physicians.

The Medical College of Ohio and three rural hospitals co-sponsored three educational programs in the medical applications of computers for rural physicians in Northwest Ohio. The College's Outreach Librarian played a major role in the programs. These programs were significant and possibly unique because of the comprehensiveness of the material presented and their focus on training rural physicians. Topics covered in the programs included: basic computer skills; online catalogs; online databases; CD-ROMs; the World Wide Web; and e-mail.

Area Health Education Centers↗

Providing patients with written medication information.

OBJECTIVE: To review the literature and provide recommendations for the development and dissemination of written medication information to patients and their care providers. DATA SOURCES: A MEDLINE search (1966-1997) of the English-language literature was performed to identify articles pertaining to the development or use of written medication information. A search of the Internet was conducted by using Yahoo as the guide and "medication information" as the search term. Additional resources were obtained through texts, bibliographies, and catalogs from medical publishers. DATA EXTRACTION: Reports documenting the creation and use of written medication information systems were reviewed, as well as studies of readability and reading skills assessment. Examples of materials available for purchase by laypeople and healthcare providers were also examined. DATA SYNTHESIS: Current statistics support the widespread availability of written medication information for patients and care providers. The goal set forth by the Food and Drug Administration of having 75% of patients receive written information by the year 2000 appears achievable. However, there are still many issues to address. Content is not standardized, and materials are frequently written at reading levels higher than that of the average patient. The development and use of resources requiring only minimal reading skills and an increase in the availability of materials written in Spanish are needed. CONCLUSIONS: Written medication information provides a useful addition to counseling by healthcare professionals. A wide variety of prepared materials is available, as well as resources for those interested in developing tools for a specific patient, population, or setting. Healthcare professionals should be aware of the limitations of some resources. Content and readability must be appropriate for the intended audience for these tools to serve a useful role in patient education.

Counseling↗

Enamel matrix protein interactions.

UNLABELLED: The recognized structural proteins of the enamel matrix are amelogenin, ameloblastin, and enamelin. While a large volume of data exists showing that amelogenin self-assembles into multimeric units referred to as nanospheres, other reports of enamel matrix protein-protein interactions are scant. We believe that each of these enamel matrix proteins must interact with other organic components of ameloblasts and the enamel matrix. Likely protein partners would include integral membrane proteins and additional secreted proteins. INTRODUCTION: The purpose of this study was to identify and catalog additional proteins that play a significant role in enamel formation. MATERIALS AND METHODS: We used the yeast two-hybrid assay to identify protein partners for amelogenin, ameloblastin, and enamelin. Once identified, RT-PCR was used to assess gene transcription of these newly identified and potential "enamel" proteins in ameloblast-like LS8 cells. RESULTS: In the context of this yeast assay, we identified a number of secreted proteins and integral membrane proteins that interact with amelogenin, ameloblastin, and enamelin. Additionally, proteins whose functions range from the inhibition of soft tissue mineralization, calcium ion transport, and phosphorylation events have been identified as protein partners to these enamel matrix proteins. For each protein identified using this screening strategy, future studies are planned to confirm this physiological relationship to biomineralization in vivo. CONCLUSION: Identifying integral membrane proteins of the secretory surface of ameloblast cells (Tomes' processes) and additional enamel matrix proteins, based on their abilities to interact with the most abundant enamel matrix proteins, will better define the molecular mechanisms of enamel formation at its most rudimentary level.

Ameloblasts↗

A skeletal gene database.

Systematic organization of documented data coupled with ready accessibility is of great value to research. Catalogs and databases are created specifically to meet this purpose. The Skeletal Gene Database evolves as part of the Skeletal Genome Anatomy Project (SGAP), an ongoing multi-institute collaborative effort, to study the functional genome of bone and other skeletal tissues. The primary objective of the Skeletal Gene Database is to create a contemporary list of skeletal-related genes, offering the following information for each gene: gene name, protein name, cellular function, disease(s) caused by mutation of the corresponding gene, chromosomal location, LocusLink number, gene size, exon/intron numbers, messenger RNA (mRNA) coding region size, protein size/molecular weight, Online Mendelian Inheritance in Man (OMIM) number of the gene, UniGene assignment, and PubMed reference. The database includes genes already known and published in the literature as well as novel genes not yet characterized but known to be expressed in skeletal tissue. It will be posted on the web for easy access and swift referencing. The data will be updated in tempo with current and future research, thereby providing an invaluable service to the scientific community interested in obtaining information on bone-related genes.

Bone and Bones↗

Low-coherence tandem interferometer for measurement of group refractive index without knowledge of the thickness of the test sample.

A new low-coherence interferometric technique is proposed for measuring the group refractive indices of dispersive samples with high accuracy. A tandem configuration of interferometers is used to compensate for the asymmetrical distortion of interferograms that results from the broad spectrum of the light source. The group refractive index can be measured without knowledge of the geometrical thickness of the sample under test. The proposed technique can successfully measure even a thick sample. Computer calculations have shown the effectiveness of the proposed technique, which was verified by preliminary experiments; the difference between the experimental result and the catalog data was 7 x 10(-4).

Journal Article↗

Textpresso: an ontology-based information retrieval and extraction system for biological literature.

We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org.

Abstracting and Indexing↗

Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets.

Cytokinesis involves temporally and spatially coordinated action of the cell cycle and cytoskeletal and membrane systems to achieve separation of daughter cells. To dissect cytokinesis mechanisms it would be useful to have a complete catalog of the proteins involved, and small molecule tools for specifically inhibiting them with tight temporal control. Finding active small molecules by cell-based screening entails the difficult step of identifying their targets. We performed parallel chemical genetic and genome-wide RNA interference screens in Drosophila cells, identifying 50 small molecule inhibitors of cytokinesis and 214 genes important for cytokinesis, including a new protein in the Aurora B pathway (Borr). By comparing small molecule and RNAi phenotypes, we identified a small molecule that inhibits the Aurora B kinase pathway. Our protein list provides a starting point for systematic dissection of cytokinesis, a direction that will be greatly facilitated by also having diverse small molecule inhibitors, which we have identified. Dissection of the Aurora B pathway, where we found a new gene and a specific small molecule inhibitor, should benefit particularly. Our study shows that parallel RNA interference and small molecule screening is a generally useful approach to identifying active small molecules and their target pathways.

Animals↗

Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.

Microbiomes influence diverse ecosystems, and viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, host identification for these viruses remains challenging due to the limitations in scaling cultivation-based approaches and the uncertain reliability and relative low resolution of in silico predictions - particularly for understudied viral taxa. Towards this, Hi-C proximity ligation uses sequenced, cross-linked virus and host genomic fragments to infer virus-host linkages and has now been applied in at least 10 studies. However, its accuracy remains unknown. Here we assess Hi-C performance in recovering virus-host interactions using synthetic communities (SynComs) composed of four marine bacterial strains and nine phages with known interactions and then apply optimized bioinformatic protocols to natural soil samples. In SynComs, standard Hi-C sample preparations and analyses showed poor normalized contact score performance (26% specificity, 100% sensitivity, incorrect matches up to class level) that could be dramatically improved by Z-score filtering (Z ≥ 0.5, 99% specificity), though at reduced sensitivity (62% down from 100%). Detection limits were established as reproducibility was poor below minimal phage abundances of 105 PFU/mL. Applying optimized bioinformatic protocols to natural soil samples, we compared virus-host linkages inferred from proximity-ligated Hi-C sequencing with predictions generated by in silico homology-based and machine learning-based bioinformatic approaches. Prior to Z-score thresholding, agreement was relatively high at the phylum to family levels (72%), but not at the genus (43%) or species (15%) levels. Z-score thresholding reduced sensitivity (only 34% of predictions were retained), with only modest improvements in congruence with bioinformatic methods (48% or 18% at genus or species levels, respectively). Regardless, this led to 79 genus-level-congruent virus-host linkages and 293 new ones revealed by Hi-C alone, i.e., providing many new virus-host interactions to explore in already well-studied climate-critical soils. Overall, these findings provide empirical benchmarks and methodological guidelines to improve the accuracy and reliability of Hi-C for virus-host linkage studies in complex microbial communities.

Benchmarking↗

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

Many alternative splicing events are regulated by pentameric and hexameric intronic sequences that serve as binding sites for splicing regulatory factors. We hypothesized that intronic elements that regulate alternative splicing are under selective pressure for evolutionary conservation. Using a Wobble Aware Bulk Aligner genomic alignment of Caenorhabditis elegans and Caenorhabditis briggsae, we identified 147 alternatively spliced cassette exons that exhibit short regions of high nucleotide conservation in the introns flanking the alternative exon. In vivo experiments on the alternatively spliced let-2 gene confirm that these conserved regions can be important for alternative splicing regulation. Conserved intronic element sequences were collected into a dataset and the occurrence of each pentamer and hexamer motif was counted. We compared the frequency of pentamers and hexamers in the conserved intronic elements to a dataset of all C. elegans intron sequences in order to identify short intronic motifs that are more likely to be associated with alternative splicing. High-scoring motifs were examined for upstream or downstream preferences in introns surrounding alternative exons. Many of the high-scoring nematode pentamer and hexamer motifs correspond to known mammalian splicing regulatory sequences, such as (T)GCATG, indicating that the mechanism of alternative splicing regulation is well conserved in metazoans. A comparison of the analysis of the conserved intronic elements, and analysis of the entire introns flanking these same exons, reveals that focusing on intronic conservation can increase the sensitivity of detecting putative splicing regulatory motifs. This approach also identified novel sequences whose role in splicing is under investigation and has allowed us to take a step forward in defining a catalog of splicing regulatory elements for an organism. In vivo experiments confirm that one novel high-scoring sequence from our analysis, (T)CTATC, is important for alternative splicing regulation of the unc-52 gene.

Alternative Splicing↗

Integrating AlphaFold2 models and clinical data to improve the assessment of Short Linear Motifs (SLiMs) and their variants' pathogenicity.

Short Linear Motifs (SLiMs) are protein functionally relevant regions that mediate reversible protein-protein interactions. Variants that disrupt SLiMs can lead to numerous Mendelian diseases. Although various bioinformatic tools have been developed to identify SLiMs, most suffer from low specificity. In our previous work, we demonstrated that integrating sequence variant information with structural analysis can enhance the prediction of true functional SLiMs while simultaneously generating tolerance matrices that indicate whether each of the 19 possible single amino acid substitutions (SASs) is tolerated. However, the scarcity of representative crystallographic structures of SLiM-receptor complexes posed a significant limitation. In this study, we demonstrate that these interactions can be modeled using AlphaFold2 (AF2) to generate high-quality structures that serve as input for our MotSASi method. These AF2-derived structures show robust performance, both in reproducing known structures deposited in the Protein Data Bank (PDB) and in reflecting the deleterious effects of known sequence variants. This updated version of MotSASi expands the repertoire of high-confidence predicted SLiMs and provides a comprehensive catalog of variants located within SLiMs, along with their respective deleteriousness assessments. When compared to AlphaMissense, MotSASi demonstrates superior performance in predicting variant deleteriousness. By contributing to the accurate identification and interpretation of variants, this work aligns with ACMG/AMP standards and aims to improve diagnostic rates in clinical genomics.

Humans↗

A high-resolution map of segmental DNA copy number variation in the mouse genome.

Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.

Animals↗

Meta-evolutionary exome analysis identifies novel type 2 diabetes mellitus genes in the UK Biobank and all of us.

Type 2 diabetes mellitus (T2DM) risk is heavily influenced by genetics, yet current association tests have explained only parts of its heritability. We developed MEVA (Meta-Evolutionary Action), a meta-analytic framework that integrates three complementary methods-EAML, Sigma-Diff, and GeneEMBED-to assess the functional burden of protein-coding variants using evolutionary data. MEVA was applied to exome data from 28,115 T2DM cases and 28,115 controls in the UK Biobank (UKB), identifying 101 genes (p&#x2009;<&#x2009;1e-5). MEVA outperformed its component methods, each of which substantially outperformed a conventional burden test (MAGMA), in recovering known T2DM genes (AUROC&#x2009;=&#x2009;0.925) and maintaining robustness in progressively smaller cohorts (AUROC&#x2009;=&#x2009;0.917). MEVA showed significant enrichment for T2DM-related loci (p&#x2009;=&#x2009;6.8e-10, p&#x2009;=&#x2009;2.0e-34), protein interactions (z&#x2009;=&#x2009;4.6, z&#x2009;=&#x2009;4.2), pathways (p&#x2009;=&#x2009;1.3e-6, z&#x2009;=&#x2009;2.0), phenotypes (p&#x2009;=&#x2009;1.3e-21, z&#x2009;=&#x2009;9.1), and literature mentions (z&#x2009;=&#x2009;7.2). Replication in 16,915 T2DM cases and 16,915 controls from All of Us (AoU) yielded 99 genes (p&#x2009;<&#x2009;1e-5), 23 of which were also recovered in the UKB cohort - far exceeding random chance. These included established genes (SLC30A8, WFS1, HNF1A) and less-characterized candidates (NRIP1, ADAM30, CALCOCO2, TUBB1, ZFP36L2, WDR90). Notably, NRIP1 loss-of-function variants were associated with increased T2DM risk in both the UKB (OR = 1.09, FDR&#x2009;=&#x2009;5.4e-4) and AoU (OR = 1.09, FDR&#x2009;=&#x2009;0.046), and TUBB1 and CALCOCO2 gain-of-function variants showed consistent risk effects (FDR&#x2009;<&#x2009;0.05). Pathway analyses revealed convergence on endoplasmic reticulum chaperone complexes (FDR&#x2009;=&#x2009;0.02) and Hippo signaling (FDR&#x2009;=&#x2009;8.5e-4). Finally, all 177 candidate genes were functionally prioritized using ten orthogonal criteria to guide experimental follow-up. These results demonstrate that combining complementary, impact-aware association tests increases sensitivity, improves replication, and expands the catalog of genetic risk factors for T2DM.

Humans↗