Disease model curation improvements at Mouse Genome Informatics

Optimal curation of human diseases requires an ontology or structured vocabulary that contains terms familiar to end users, is robust enough to support multiple levels of annotation granularity, is limited to disease terms and is stable enough to avoid extensive reannotation following updates. At Mouse Genome Informatics (MGI), we currently use disease terms from Online Mendelian Inheritance in Man (OMIM) to curate mouse models of human disease. While OMIM provides highly detailed disease records that are familiar to many in the medical community, it lacks structure to support multilevel annotation. To improve disease annotation at MGI, we evaluated the merged Medical Subject Headings (MeSH) and OMIM disease vocabulary created by the Comparative Toxicogenomics Database (CTD) project. Overlaying MeSH onto OMIM provides hierarchical access to broad disease terms, a feature missing from the OMIM. We created an extended version of the vocabulary to meet the genetic disease-specific curation needs at MGI. Here we describe our evaluation of the CTD application, the extensions made by MGI and discuss the strengths and weaknesses of this approach.

Database URL:http://www.informatics.jax.org/

Genetic and environmental pathways to complex diseases

BACKGROUND

Pathogenesis of complex diseases involves the integration of genetic and environmental factors over time, making it particularly difficult to tease apart relationships between phenotype, genotype, and environmental factors using traditional experimental approaches.

RESULTS

Using gene-centered databases, we have developed a network of complex diseases and environmental factors through the identification of key molecular pathways associated with both genetic and environmental contributions. Comparison with known chemical disease relationships and analysis of transcriptional regulation from gene expression datasets for several environmental factors and phenotypes clustered in a metabolic syndrome and neuropsychiatric subnetwork supports our network hypotheses. This analysis identifies natural and synthetic retinoids, antipsychotic medications, Omega 3 fatty acids, and pyrethroid pesticides as potential environmental modulators of metabolic syndrome phenotypes through PPAR and adipocytokine signaling and organophosphate pesticides as potential environmental modulators of neuropsychiatric phenotypes.

CONCLUSION

Identification of key regulatory pathways that integrate genetic and environmental modulators define disease associated targets that will allow for efficient screening of large numbers of environmental factors, screening that could set priorities for further research and guide public health decisions.

The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study

Background

The etiology of many chronic diseases involves interactions between environmental factors and genes that modulate physiological processes. Understanding interactions between environmental chemicals and genes/proteins may provide insights into the mechanisms of chemical actions, disease susceptibility, toxicity, and therapeutic drug interactions. The Comparative Toxicogenomics Database (CTD; ) provides these insights by curating and integrating data describing relationships between chemicals, genes/proteins, and human diseases. To illustrate the scope and application of CTD, we present an analysis of curated data for the chemical arsenic. Arsenic represents a major global environmental health threat and is associated with many diseases. The mechanisms by which arsenic modulates these diseases are not well understood.

Methods

Curated interactions between arsenic compounds and genes were downloaded using export and batch query tools at CTD. The list of genes was analyzed for molecular interactions, Gene Ontology (GO) terms, KEGG pathway annotations, and inferred disease relationships.

Results

CTD contains curated data from the published literature describing 2,738 molecular interactions between 21 different arsenic compounds and 1,456 genes and proteins. Analysis of these genes and proteins provide insight into the biological functions and molecular networks that are affected by exposure to arsenic, including stress response, apoptosis, cell cycle, and specific protein signaling pathways. Integrating arsenic-gene data with gene-disease data yields a list of diseases that may be associated with arsenic exposure and genes that may explain this association.

Conclusion

CTD data integration and curation strategies yield insight into the actions of environmental chemicals and provide a basis for developing hypotheses about the molecular mechanisms underlying the etiology of environmental diseases. While many reports describe the molecular response to arsenic, CTD integrates these data with additional curated data sets that facilitate construction of chemical-gene-disease networks and provide the groundwork for investigating the molecular basis of arsenic-associated diseases or toxicity. The analysis reported here is extensible to any environmental chemical or therapeutic drug.

Effects of amino acid substitutions in and around the arginine-glycine-aspartic acid (RGD) sequence on fertilization and parthenogenetic development in mature bovine oocytes

Integrins have been shown to be involved in the process of fertilization and many integrin-ligand interactions are mediated through the recognition of an arginine-glycine-aspartic acid (RGD) sequence. Despite the fact the RGD domain is a principal player in determining the functional characteristics of an adhesive protein, increasing evidence has accumulated implicating the amino acids flanking the RGD sequence in determining the functional properties of the RGD-containing protein. A set of linear peptides in which the amino acid sequence in and around the RGD tri-peptide was modified was synthesized to better understand the specificity of the RGD-receptor interaction. Mature oocytes were fertilized in vitro in the presence of RGD-containing and RGD-modified peptides. Both the RGD-containing and RGD-modified peptides impaired the ability of sperm to fertilize bovine oocytes, illustrated by a reduction in cleavage. The linear modified RGD containing peptides were also examined for their ability to induce parthenogenetic development with the objective of providing a linear RGD peptide with greater biological activity than the one (GRGDSPK) used previously (Campbell et al., 2000). The data demonstrate the specificity of the receptor for the RGD sequence, further implicate the involvement of integrins in the process of bovine fertilization, and illustrate the importance of the amino acids surrounding the RGD sequence in determining the binding and functional properties of RGD-containing peptides. The data support the findings that a linear RGD peptide can block fertilization and that amino acids around the RGD sequence have an impact on the biological activity of the receptor.

Multiple-event study of bioretention for treatment of urban storm water runoff

Bioretention is a novel best management practice for urban storm water, employed to minimize the impact of urban runoff during storm events. Bioretention consists of porous media layers that can remove pollutants from infiltrating runoff via mechanisms that include adsorption, precipitation, and filtration. However, the effectiveness of bioretention in treating repetitive inputs of runoff has not been investigated. In this study, a bioretention test column was set up and experiments proceeded once every week for a total of 12 tests. Through all 12 repetitions, the infiltration rate remained constant (0.35 cm/min). All 12 tests demonstrated excellent removal efficiency for TSS, oil/grease, and lead (99%). For total phosphorus, the removal efficiency was about 47% the system removal efficiency ranged from 2.3% to 23%. Effluent nitrate concentration became higher than the influent concentration during the first 28 days and removal efficiency ranged from 9% to 20% afterward. Some degree of denitrification was apparently proceeding in the bioretention system. Overall, the top mulch layer filtered most of TSS in the runoff and prevented the bioretention media from clogging during 12 repetitions. Runoff quality was improved by the bioretention column.

The yeast recombinational repair protein Rad59 interacts with Rad52 and stimulates single-strand annealing

The yeast RAD52 gene is essential for homology-dependent repair of DNA double-strand breaks. In vitro, Rad52 binds to single- and double-stranded DNA and promotes annealing of complementary single-stranded DNA. Genetic studies indicate that the Rad52 and Rad59 proteins act in the same recombination pathway either as a complex or through overlapping functions. Here we demonstrate physical interaction between Rad52 and Rad59 using the yeast two-hybrid system and co-immunoprecipitation from yeast extracts. Purified Rad59 efficiently anneals complementary oligonucleotides and is able to overcome the inhibition to annealing imposed by replication protein A (RPA). Although Rad59 has strand-annealing activity by itself in vitro, this activity is insufficient to promote strand annealing in vivo in the absence of Rad52. The rfa1-D288Y allele partially suppresses the in vivo strand-annealing defect of rad52 mutants, but this is independent of RAD59. These results suggest that in vivo Rad59 is unable to compete with RPA for single-stranded DNA and therefore is unable to promote single-strand annealing. Instead, Rad59 appears to augment the activity of Rad52 in strand annealing.

Competitive photocatalytic oxidation of Cu(II)--EDTA and Cd(II)--EDTA with illuminated TiO2

Competitive photocatalytic oxidation (PCO) of mixtures of Cu(II)-EDTA and Cd(II)-EDTA was studied with variation of molar ratio of these two complexes (1 x 10(-4):0, 8 x 10(-5): 2 x 10(-5), 5 x 10-5:5 x 10(-5), 2 x 10-5:8 x 10(-5), 0:1 x 10(-4) M) and in the pH range of 4-8. PCO rates for each compound can be described using a combined aqueous + adsorbed pathway: -dC/dt = k1Caq(1+ k2Caq)+ kadsCads. This expression is valid under both noncompetitive and competitive conditions. Differences in rates under competition result from differences in the partitioning of the two species between the TiO2 surface and the aqueous phase. Total initial complex degradation rates (rTT), obtained by summation of the total destruction rates for Cu(II)-EDTA and Cd(II)-EDTA, were relatively constant at pH 4 and 5 for all ratios. At these pH values, contribution of adsorbed pathways to rTT was important, and rates were similar to those of the aqueous phase pathways. From pH 6 to 8, the degree of adsorption, and thus the adsorbed pathway rate, diminished. Through the adsorbed pathway, no difference in rate constants was found between Cu(II)-EDTA and Cd(II)-EDTA; Cd(II)-EDTA is somewhat more reactive through the aqueous phase pathway.

Loading estimates of lead, copper, cadmium, and zinc in urban runoff from specific sources

Urban stormwater runoff is being recognized as a substantial source of pollutants to receiving waters. A number of investigators have found significant levels of metals in runoff from urban areas, especially in highway runoff. As an initiatory study, this work estimates lead, copper, cadmium, and zinc loadings from various sources in a developed area utilizing information available in the literature, in conjunction with controlled experimental and sampling investigations. Specific sources examined include building siding and roofs; automobile brakes, tires, and oil leakage; and wet and dry atmospheric deposition. Important sources identified are building siding for all four metals, vehicle brake emissions for copper and tire wear for zinc. Atmospheric deposition is an important source for cadmium, copper, and lead. Loadings and source distributions depend on building and automobile density assumptions and the type of materials present in the area examined. Identified important sources are targeted for future comprehensive mechanistic studies. Improved information on the metal release and distributions from the specific sources, along with detailed characterization of watershed areas will allow refinements in the predictions.

Removal of Cu(II) and Cd(II) from aqueous solution by seafood processing waste sludge

Dried waste slurry generated in seafood processing factories has been shown to be an effective adsorbent for the removal of heavy metals from dilute solutions. Characterization of the sludge surface with scanning electron microscope and X-ray microanalyzer were carried out to evaluate the components on the sludge surface that are related to the adsorption of metal ions. Aluminum and calcium, as well as organic carbon are distributed on the surface of sludge. Alkalimetric titration was used to characterize the surface acidity of the sludge sample. The surface acidity constants, pKa1s and pKa2s, were 5.80 and 9.55, respectively. Batch as well as dynamic adsorption studies were conducted with 10(-5) to 5 x 10(-3) M Cu(II) and Cd(II). A surface complexation model with the diffuse layer model successfully predicted Cu(II) and Cd(II) removals in single metal solutions. Predictions of sorption in binary-adsorbate systems based on single-adsorbate data fits represented competitive sorption data reasonably well over a wide range of conditions. The breakthrough capacity found from column studies was different for each metal ion and the data reflect the order of metal affinity for the adsorbent material very well.

Cadmium adsorption on aluminum oxide in the presence of polyacrylic acid

Adsorption of metals from aqueous solution onto oxide and other surfaces is known to affect trace metal transport in many natural and engineered systems. It is therefore important to understand whether dissolved metal inputs will be easily bound to particles or will be strongly complexed in solution and transported with the water phase. The effect of poly(acrylic acid) (PAA), representing a model compound for natural organic matter, on the adsorption of Cd(II) onto gamma-Al2O3 was determined using batch adsorption experiments over a pH range from 4 to 10. Initially, interactions among the individual components were evaluated. Cadmium adsorption onto alumina showed a typical S-shaped metal adsorption curve. PAA adsorption onto gamma-Al2O3 decreased with increase in pH. The affinity of PAA for Cd2+ increased strongly with pH. In ternary systems, the presence of PAA resulted in an enhancement of Cd(II) adsorption below pH 6, apparently due to ternary surface complex formation. Above pH 6, a decrease in cadmium adsorption onto gamma-Al2O3 was observed resulting from an increase in the concentration of soluble Cd-PAA complexes. Overall, results indicate that the presence of natural organic matter could have a significant impact on the distribution and mobility of cadmium in the environment. Simple surface complexation modeling was insufficient to describe behavior in the ternary systems due to the complexity of the PAA polymer.

Laboratory study of biological retention for urban stormwater management

Urban stormwater runoff contains a broad range of pollutants that are transported to natural water systems. A practice known as biological retention (bioretention) has been suggested to manage stormwater runoff from small, developed areas. Bioretention facilities consist of porous soil, a topping layer of hardwood mulch, and a variety of different plant species. A detailed study of the characteristics and performance of bioretention systems for the removal of several heavy metals (copper, lead, and zinc) and nutrients (phosphorus, total Kjeldahl nitrogen [TKN], ammonium, and nitrate) from a synthetic urban stormwater runoff was completed using batch and column adsorption studies along with pilot-scale laboratory systems. The roles of the soil, mulch, and plants in the removal of heavy metals and nutrients were evaluated to estimate the treatment capacity of laboratory bioretention systems. Reductions in concentrations of all metals were excellent (> 90%) with specific metal removals of 15 to 145 mg/m2 per event. Moderate reductions of TKN, ammonium, and phosphorus levels were found (60 to 80%). Little nitrate was removed, and nitrate production was noted in several cases. The importance of the mulch layer in metal removal was identified. Overall results support the use of bioretention as a stormwater best management practice and indicate the need for further research and development.

Mutations in noncoding regions of the proteolipid protein gene in Pelizaeus-Merzbacher disease

BACKGROUND

Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive dysmyelinating disorder of the CNS. Duplications or point mutations in exons of the proteolipid protein (PLP) gene are found in most patients.

OBJECTIVE

To describe five patients with PMD who have mutations in noncoding regions of the PLP gene.

METHODS

Quantitative multiplex PCR and Southern blot analyses were used to detect duplication of the PLP gene, and DNA sequence analysis, including exon-intron borders, was used to detect mutation of the PLP gene.

RESULTS

Duplication of the PLP gene was ruled out, and mutations were identified in noncoding regions of five patients in four families with PMD. In two brothers with a severe form of PMD, a G to T transversion at IVS6+3 was detected. This mutation resulted in skipping of exon 6 in the PLP mRNA of cultured fibroblasts. A patient who developed nystagmus at 16 months and progressive spastic ataxia at 18 months was found to have a 19-base pair (bp) deletion of a G-rich region near the 5' end of intron 3 of the PLP gene. A patient with a T to C transition at IVS3+2 and a patient with an A to G transition at IVS3+4 have the classic form of PMD. These, like the 19-bp deletion, are in intron 3, which is involved in PLP/DM20 alternative splice site selection.

CONCLUSIONS

Mutations in introns of the PLP gene, even at positions that are not 100% conserved at splice sites, are an important cause of PMD.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

A novel allele of RAD52 that causes severe DNA repair and recombination deficiencies only in the absence of RAD51 or RAD59

With the use of an intrachromosomal inverted repeat as a recombination reporter, we have shown that mitotic recombination is dependent on the RAD52 gene, but reduced only fivefold by mutation of RAD51. RAD59, a component of the RAD51-independent pathway, was identified previously by screening for mutations that reduced inverted-repeat recombination in a rad51 strain. Here we describe a rad52 mutation, rad52R70K, that also reduced recombination synergistically in a rad51 background. The phenotype of the rad52R70K strain, which includes weak gamma-ray sensitivity, a fourfold reduction in the rate of inverted-repeat recombination, elevated allelic recombination, sporulation proficiency, and a reduction in the efficiency of mating-type switching and single-strand annealing, was similar to that observed for deletion of the RAD59 gene. However, rad52R70K rad59 double mutants showed synergistic defects in ionizing radiation resistance, sporulation, and mating-type switching. These results suggest that Rad52 and Rad59 have partially overlapping functions and that Rad59 can substitute for this function of Rad52 in a RAD51 rad52R70K strain.

Competitive Adsorption of Cu(II)-EDTA and Cd(II)-EDTA onto TiO2

Cu(II), EDTA, Cu(II)-EDTA, Cd(II)-EDTA, and Cu(II)/Cd(II) and Cu(II)-EDTA/Cd(II)-EDTA competitive adsorption onto TiO2 has been studied with variation of pH and concentration. For Cu(II) and EDTA, typical cationic and anionic types of adsorption are noted, respectively. Ligand-type adsorption is found for Cu(II)-EDTA and Cd(II)-EDTA under both single and competitive conditions. Surface complexation modeling considered inner-sphere complexation and the diffuse layer model employing MINTEQA2; surface complexes used include Ti-(OH2)O-Cu+, Ti-(OH)EDTAH-22, Ti-(OH)EDTA-Cu-2, and Ti-(OH)EDTA-Cd-2. Experimental and model predictions suggest no competitive adsorption between Cu(II) and Cd(II) at 5 x 10(-5) M. On the other hand, adsorption data and model predictions indicate that Cd(II)-EDTA adsorption is favored over that of Cu(II)-EDTA with some competition for adsorption sites. Cd(II)-EDTA adsorption was only slightly affected by the presence of Cu(II)-EDTA; however, Cu(II)-EDTA adsorption was strongly influenced by the presence of Cd(II)-EDTA, especially as the molar ratio of Cd(II)-EDTA/Cu(II)-EDTA increased. A modified surface complexation constant for Cd(II)-EDTA is required to explain the competitive data, suggesting surface site heterogeneity. Copyright 1999 Academic Press.

A novel technique for rapid automated genotyping of DNA polymorphisms in the mouse

The ability to rapidly and reliably genotype mice is an important concern. Traditional methods employ labour intensive and time consuming techniques such as test crossing, gel electrophoresis or nucleic acid hybridization. Here we show that a new molecular biology workstation, the WAVE DNA Fragment Analysis System, can easily resolve polymerase chain reaction (PCR) products that have small differences in their lengths. Analysis is fully automated and takes less than 7 min per sample. Approximately 200 samples can be analysed per day with only minutes of hands-on time after completion of the PCR. Genotyping with the WAVE DNA Fragment Analysis System is a fast and efficient method with minimal manual intervention.

Targeted disruption of Hoxd-10 affects mouse hindlimb development

Targeted disruption of the Hoxd-10 gene, a 5′ member of the mouse HoxD linkage group, produces mice with hindlimb-specific defects in gait and adduction. To determine the underlying causes of this locomotor defect, mutant mice were examined for skeletal, muscular and neural abnormalities. Mutant mice exhibit alterations in the vertebral column and in the bones of the hindlimb. Sacral vertebrae beginning at the level of S2 exhibit homeotic transformations to adopt the morphology of the next most anterior vertebra. In the hindlimb, there is an anterior shift in the position of the patella, an occasional production of an anterior sesamoid bone, and an outward rotation of the lower part of the leg, all of which contribute to the defects in locomotion. No major alterations in hindlimb musculature were observed, but defects in the nervous system were evident. There was a decrease in the number of spinal segments projecting nerve fibers through the sacral plexus to innervate the musculature of the hindlimb. Deletion of a hindlimb nerve was seen in some animals, and a shift was evident in the position of the lumbar lateral motor column. These observations suggest a role for the Hoxd-10 gene in establishing regional identity within the spinal cord and imply that patterning of the spinal cord may have intrinsic components and is not completely imposed by the surrounding mesoderm.

Adsorption of Pb(II), NTA, and Pb(II)-NTA onto TiO2

Nitrilotriacetic acid (NTA) is extensively used in different industries because of its excellent chelating properties. Introduction of NTA into the natural environment is a concern because of mobilization of heavy metal species that may be otherwise bound to natural particulate matter. The present study investigates the adsorption behavior of Pb(II) and NTA, both as individual species and as complex species onto titanium dioxide. This adsorption information is important in considering the TiO2-assisted photocatalytic treatment of these metal-organic complexes. Pb(II) shows a typical cationic type of adsorption behavior, whereas NTA demonstrates an anionic type of adsorption trend. Results from stoichiometric ternary systems show a gradual increase in Pb(II) adsorption and a decrease in NTA removal with an increase in pH. However, for the cases of Pb(II) > NTA, increased NTA adsorption as compared to pure NTA systems was noted even at higher pH. Model predictions employing MINTEQA2 software followed the experimental trends. Experimental and model results from ternary systems suggest adsorption of free Pb(II) and NTA, as well as ternary Ti-NTA-Pb(II) and Ti-O-Pb(II)-NTA2- species. The cationic-type complexation, i.e., Ti-O-Pb(II)-NTA2-, was essential for the successful NTA adsorption modeling, especially at higher pH and for Pb > NTA systems, where significant NTA adsorption was noted even at very high pH values. Most of the previous metal-ligand adsorption studies did not consider such a surface complexation. However, the present results indicate that any groundwater transport modeling of such pollutants will require the inclusion of cationic-type surface complexation, in addition to other surface species. Copyright 1997 Academic Press. Copyright 1997Academic Press

Influence of elastic nonlinearity on arterial anastomotic compliance

This study illustrates how the highly nonlinear elastic behavior of artery wall material can cause unusual structural characteristics that do not occur with a linear-elastic material. An example mathematical model of an end-to-end anastomosis successfully predicts the experimentally observed area of elevated elastic compliance, called the "Para-anastomotic Hypercompliant Zone" (PHZ). The elastic hypercompliance is shown to occur because the anastomosis locally restricts the arterial diameter, thus forcing the adjacent material to remain in a lower strain, and correspondingly a lower stiffness, part of its non-linear stress-strain curve. Elevated elastic compliance can be avoided by locally matching both the arterial diameter and the elastic compliance within the physiological pressure range.

Targeting the vulnerable in emergency situations: who is vulnerable?

BACKGROUND

Emergencies such as wars and natural disasters increase the vulnerability of affected populations and expose these populations to risks such as disease, violence, and hunger. Emergency public health interventions aim to mitigate these effects by providing basic minimum requirements, reducing vulnerability, and reducing exposure to risk. Targeted services are generally aimed at children under 5. Mortality rates among young children are higher than the crude mortality rate (CMR) among the whole population in emergency settings, so attention is focused on this age group. However, even under normal conditions mortality is higher in young children. This analysis compared the relative risk of death for young children with that for older children and adults under normal conditions and in emergency settings.

METHODS

Mortality data from refugee camps set up in response to three different emergencies were examined. Baseline mortality rates in the refugees' countries of origin were calculated from published data. Relative risks between normal and emergency conditions were calculated and compared.

FINDINGS

Mortality rates were higher among children under 5 than among older children and adults both under normal circumstances and in the emergency setting in camps in Tanzania, Uganda, and Zaire. However, the relative risk for under-5 versus over-5 mortality was smaller under emergency conditions than under normal circumstances. Thus, children over 5 and adults are disproportionately more affected by exposure to emergency risks than are younger children.

INTERPRETATION

If the objective of intervention, to reduce mortality, is to be achieved, the population over the age of 5 cannot be ignored. Emergency public health needs to develop specific tools to investigate risk in other age groups (as well as children under 5), to identify causes, and to design programmes to address such needs.

A mutational analysis of the 5' HoxD genes: dissection of genetic interactions during limb development in the mouse

Using gene targeting in mice, we have undertaken a systematic mutational analysis of the homeobox-containing 5' HoxD genes. In particular, we have characterized the limb defects observed in mice with independent targeted disruptions of hoxd-12 and hoxd-13. Animals defective for hoxd-12 are viable, fertile, and appear outwardly normal yet have minor autopodal defects in the forelimb which include a reduction in the bone length of metacarpals and phalanges, and a malformation of the distal carpal bone d4. The limb phenotypes observed in hoxd-13 mutant mice are more extensive, including strong reductions in length, complete absences, or improper segmentations of many metacarpal and phalangeal bones. Additionally, the d4 carpal bone is not properly formed and often produces an extra rudimentary digit. To examine the genetic interactions between the 5' HoxD genes, we bred these mutant strains with each other and with our previously characterized hoxd-11 mouse to produce a series of trans-heterozygotes. Skeletal analyses of these mice reveal that these genes interact in the formation of the vertebrate limb, since the trans-heterozygotes display phenotypes not present in the individual heterozygotes, including more severe carpal, metacarpal and phalangeal defects. Some of these phenotypes appear to be accounted for by a delay in the ossification events in the autopod, which lead to either the failure of fusion or the elimination of cartilaginous elements. Characteristically, these mutations lead to the overall truncation of digits II and V on the forelimb. Additionally, some trans-animals show the growth of an extra postaxial digit VI, which is composed of a bony element resembling a phalange. The results demonstrate that these genes interact in the formation of the limb. In addition to the previously characterized paralogous interactions, a multitude of interactions between Hox genes is used to finely sculpt the forelimb. The 5' Hox genes could therefore act as a major permissive genetic milieu that has been exploited by evolutionary adaptation to form the tetrapod limbs.

A mutational analysis of the 5′ HoxD genes: dissection of genetic interactions during limb development in the mouse

Using gene targeting in mice, we have undertaken a systematic mutational analysis of the homeobox-containing 5′ HoxD genes. In particular, we have characterized the limb defects observed in mice with independent targeted disruptions of hoxd-12 and hoxd-13. Animals defective for hoxd-12 are viable, fertile, and appear outwardly normal yet have minor autopodal defects in the forelimb which include a reduction in the bone length of metacarpals and phalanges, and a malformation of the distal carpal bone d4. The limb phenotypes observed in hoxd-13 mutant mice are more extensive, including strong reductions in length, complete absences, or improper segmentations of many metacarpal and phalangeal bones. Additionally, the d4 carpal bone is not properly formed and often produces an extra rudimentary digit. To examine the genetic interactions between the 5′ HoxD genes, we bred these mutant strains with each other and with our previously characterized hoxd-11 mouse to produce a series of trans-heterozygotes. Skeletal analyses of these mice reveal that these genes interact in the formation of the vertebrate limb, since the trans-heterozygotes display phenotypes not present in the individual heterozygotes, including more severe carpal, metacarpal and phalangeal defects. Some of these phenotypes appear to be accounted for by a delay in the ossification events in the autopod, which lead to either the failure of fusion or the elimination of cartilaginous elements. Characteristically, these mutations lead to the overall truncation of digits II and V on the forelimb. Additionally, some trans-animals show the growth of an extra postaxial digit VI, which is composed of a bony element resembling a phalange. The results demonstrate that these genes interact in the formation of the limb. In addition to the previously characterized paralogous interactions, a multitude of interactions between Hox genes is used to finely sculpt the forelimb. The 5′ Hox genes could therefore act as a major permissive genetic milieu that has been exploited by evolutionary adaptation to form the tetrapod limbs.

Absence of radius and ulna in mice lacking hoxa-11 and hoxd-11

Mice with targeted disruptions in Hox genes have been generated to evaluate the role of the Hox complex in determining the mammalian body plan. This complex of 38 genes encodes transcription factors that specify regional information along the embryonic axes. Early in vertebrate evolution an ancestral complex shared with invertebrates was duplicated twice to give rise to the four linkage groups (Hox A, B, C and D). As a consequence, corresponding genes on the separate linkage groups, called paralogues, are most closely related to each other. Based on sequence similarities, the Hox genes have been subdivided into 13 paralogous groups. The five most 5' groups (Hox 9-13) pattern the posterior region of the vertebrate embryo and the appendicular skeleton. Mice with individual mutations in the paralogous genes hoxa-11 and hoxd-11 have been described. By breeding these two strains together we have generated double mutants which have dramatic phenotypes not apparent in mice homozygous for the individual mutations. The radius and the ulna of the forelimb are almost entirely eliminated, the axial skeleton shows homeotic transformations, and there are severe kidney defects not present in either single mutant. The limb and axial phenotypes are quantitative: as more mutant alleles are added to the genotype, the phenotype becomes progressively more severe. The appendicular skeleton defects suggest that paralogous Hox genes function together to specify limb outgrowth and patterning along the proximodistal axis.

Axial homeosis and appendicular skeleton defects in mice with a targeted disruption of hoxd-11

Using gene targeting, we have created mice with a disruption in the homeobox-containing gene hoxd-11. Homozygous mutants are viable and the only outwardly apparent abnormality is male infertility. Skeletons of mutant mice show a homeotic transformation that repatterns the sacrum such that each vertebra adopts the structure of the next most anterior vertebra. Defects are also seen in the bones of the limb, including regional malformations at the distal end of the forelimb affecting the length and structure of phalanges and metacarpals, inappropriate fusions between wrist bones, and defects at the most distal end in the long bones of the radius and ulna. The phenotypes show both incomplete penetrance and variable expressivity. In contrast to the defects observed in the vertebral column, the phenotypes in the appendicular skeleton do not resemble homeotic transformations, but rather regional malformations in the shapes, length and segmentation of bones. Our results are discussed in the context of two other recent gene targeting studies involving the paralogous gene hoxa-11 and another member of the Hox D locus, hoxd-13. The position of these limb deformities reflects the temporal and structural colinearity of the Hox genes, such that inactivation of 3′ genes has a more proximal phenotypic boundary (affecting both the zeugopod and autopod of the limb) than that of the more 5′ genes (affecting only the autopod). Taken together, these observations suggest an important role for Hox genes in controlling localized growth of those cells that contribute to forming the appendicular skeleton.

Modulation of interleukin 2 high affinity binding to human T cells by a pyrimidodiazepine insect metabolite

An insect metabolite containing the little known pyrimido[4,5-b][1,4]diazepine ring system has been found to act as an effective mimic of tetrahydrobiopterin in its ability to modulate the affinity of interleukin 2 (IL-2) for its receptors on human T cells. Semi-empirical molecular orbital calculations reveal that while tetrahydrobiopterin has considerable flexibility, the pyrimidodiazepine has rather few conformational options and offers a useful model for exploring the nature of the pterin binding site.

The functional basis of minor histocompatibility loci

This work addresses the functional basis of classical minor histocompatibility (H) loci. We focus on the H-3 locus, which is actually a complex genetic unit to which the phenotypic trait of tissue rejection, genes whose products stimulate specific subsets of T cells, and Ir genes have been mapped. To clarify how these genes relate to one another and to the trait of tissue rejection, strains of intra-H-3 recombinant mice were produced and analyzed. These mice allowed us to selectively elicit immune responses to Ag (referred to as type I Ag) that stimulate MHC class I-restricted CTL, or Ag (referred to as type II Ag) that stimulate MHC class II-restricted Th. The splitting of H-3 in this manner resulted in a dramatic diminution of the skin allograft response, and with rare exception, an elimination of the CTL response after spleen cell immunization. A selective response to type I Ag resulted in slow, incomplete skin allograft rejection that demonstrated both CD4+ cell-dependent and -independent components. A selective response to the type II Ag failed to result in allograft rejection. The type II Ag did, however, act as an Ir gene that determined whether responses to type I Ag could occur. Altogether, the results indicate that the trait of tissue rejection associated with H-3 is a consequence of the strongly synergistic effects of Th-CTL collaboration induced by products of type I and type II genes. Moreover, the results suggest a genetic explanation for some of the Ir gene effects associated with H-3.

The functional basis of minor histocompatibility loci

This work addresses the functional basis of classical minor histocompatibility (H) loci. We focus on the H-3 locus, which is actually a complex genetic unit to which the phenotypic trait of tissue rejection, genes whose products stimulate specific subsets of T cells, and Ir genes have been mapped. To clarify how these genes relate to one another and to the trait of tissue rejection, strains of intra-H-3 recombinant mice were produced and analyzed. These mice allowed us to selectively elicit immune responses to Ag (referred to as type I Ag) that stimulate MHC class I-restricted CTL, or Ag (referred to as type II Ag) that stimulate MHC class II-restricted Th. The splitting of H-3 in this manner resulted in a dramatic diminution of the skin allograft response, and with rare exception, an elimination of the CTL response after spleen cell immunization. A selective response to type I Ag resulted in slow, incomplete skin allograft rejection that demonstrated both CD4+ cell-dependent and -independent components. A selective response to the type II Ag failed to result in allograft rejection. The type II Ag did, however, act as an Ir gene that determined whether responses to type I Ag could occur. Altogether, the results indicate that the trait of tissue rejection associated with H-3 is a consequence of the strongly synergistic effects of Th-CTL collaboration induced by products of type I and type II genes. Moreover, the results suggest a genetic explanation for some of the Ir gene effects associated with H-3.

Experience with a planned exposure program for the control of enzootic transmissible gastroenteritis in swine

Oral inoculation of pregnant sows and gilts with a homogenate of pig intestines containing live, virulent transmissible gastroenteritis (TGE) virus was associated with significant (P < 0.01) reduction of mortality in nursery pigs in a herd affected with enzootic TGE. The mortality of weaned pigs from April through June 1981, when sows were not vaccinated or inoculated, was 9.3%. Mortality of weanling pigs from July through December 1981 was 5.7% (P < 0.01), and stayed consistently between 2.6 and 4.8% from 1982 through 1990. After beginning the exposure program, there were no clinical signs attributable to TGE in the farrowing house or nursery until 1986, when recrudescence of TGE was evident in the nursery. Although the source of the virus could not be substantiated, recrudescence suggested that TGE virus would not be eradicated as long as exposure was continued. The most plausible explanation for the decrease in the incidence of diarrhea and mortality in the nursery pigs after initiation of the planned exposure program is that a higher, longer lasting amount of lactogenic immunity was provided to suckling pigs. Presumably over time, this resulted in less TGE virus carryover into the nursery by weanling pigs, thereby reducing and confining the environmental challenge to the nursery. Strict all-in, all-out pig movement in the nursery with thorough cleaning and disinfecting presumably further reduced the environmental challenge.

The genetic origin of minor histocompatibility antigens

The purpose of this study was to elucidate the genetic origin of minor histocompatibility (H) antigens. Toward this end common inbred mouse strains, distinct subspecies, and species of the subgenus Mus were examined for expression of various minor H antigens. These antigens were encoded by the classical minor H loci H-3 and H-4 or by newly identified minor H antigens detected as a consequence of mutation. Both minor H antigens that stimulate MHC class I-restricted cytotoxic T cells (Tc) and antigens that stimulate MHC class II-restricted helper T cells (Th) were monitored. The results suggested that strains of distinct ancestry commonly express identical or cross-reactive antigens. Moreover, a correlation between the lack of expression of minor H antigens and ancestral heritage was observed. To address whether the antigens found on unrelated strains were allelic with the sensitizing minor H antigens or a consequence of antigen cross-reactivity, classical genetic segregation analysis was carried out. Even in distinct subspecies and species, the minor H antigens always mapped to the site of the appropriate minor H locus. Together the results suggest: 1) minor H antigen sequences are evolutionarily stable in that their pace of antigenic change is slow enough to predate subspeciation and speciation; 2) the minor H antigens originated in the inbred strains as a consequence of a rare polymorphism or loss mutation carried in a founder mouse stock that caused the mouse to perceive the wild-type protein as foreign; 3) there is a remarkable lack of antigenic cross-reactivity between the defined minor H antigens and other gene products.

Structural requirements for the modulatory effect of 6-substituted pterins on interleukin 2 receptor binding

(6R)-5,6,7,8-Tetrahydrobiopterin is produced by stimulated human T lymphocytes, and is known to affect various aspects of interleukin-2-directed T cell proliferation. Using an increased apparent affinity of interleukin 2 receptor to interleukin 2 as a measure of activity, this study explores whether other 6-substituted pterins might have the same effect, and what structural features are necessary for activity. Of the compounds tested, only the T-lymphocyte-derived (6R)-5,6,7,8-tetrahydrobiopterin was active. The diastereomeric (6S)-5,6,7,8-tetrahydrobiopterin was inactive, as were 7,8-dihydrobiopterin, sepiapterin, 5,6,7,8-tetrahydroneopterin, 6,7-dimethyl-5,6,7,8-tetrahydropterin and 6-hydroxymethylpterin. 7,8-Dihydroneopterin and neopterin were also found to be inactive. It follows that neither of these compounds participates in the feedback modulation of IL-2 receptor affinity, although both of them can be detected upon IFN-gamma stimulation of human monocytes/macrophages. A computer-based molecular modelling study of (6R)-5,6,7,8-tetrahydrobiopterin and (6R)-5,6,7,8-tetrahydroneopterin revealed substantial differences in overall shape between the two molecules, with certain features figuring prominently in the low-energy conformers of (6R)-5,6,7,8-tetrahydrobiopterin.

Complexity at the mouse minor histocompatibility locus H-4

The fine immunogenetics of the chromosome 7 mouse minor histocompatibility (H) locus H-4 was investigated. Both class I major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL) and class II MHC-restricted "helper" T cells (TH) specifically reactive with H-4 antigens were isolated as clones and were used as genetic probes for classical backcross segregation analysis. Results of a four point cross indicated that the H-4 locus was actually comprised of two genes, that have been designated H-46 and H-47. The former encodes antigens recognized by the TH and the latter encodes antigens recognized by the CTL. Moreover, these two genes could be separated from the gene pink-eyed dilution (p) which was found to be "sandwiched" between them. The functional significance of a minor H congenic strain differing by both TH-defined H-46 and CTL-defined H-47 was addressed using F1 complementation tests. Such studies indicated that immune responses against H-46 antigens was required for generation of H-47-specific CTL. Altogether, these results suggest selective presentation of different minor H gene products by class I or class II MHC proteins and that the minor H "locus" H-4 may have necessarily included both TH and CTL-defined genes because of requisite TH-CTL collaboration.

Responses against antigens encoded by the H-3 histocompatibility locus: antigens stimulating class I MHC- and class II MHC-restricted T cells are encoded by separate genes

The purpose of this work was to study the genetic basis of histocompatibility antigens encoded by the mouse minor histocompatibility (H) locus H-3. Both class I major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL) and class II MHC-restricted helper T cells (TH) specific for antigens encoded by genes within the H-3 locus were isolated and analyzed. Typing a number of mouse strains for expression of antigens recognized by these TH and CTL suggested that there was a different strain distribution pattern of expression of the antigens recognized by TH compared with those recognized by CTL. Separation of the genes whose products stimulate TH from those whose products stimulate CTL was suggested by: (1) analysis of the strain B10.FS(92NX)/Grf that has undergone recombination within the H-3 region; (2) genetic segregation studies of (B10.UW-H-3b/Sn x C57BL/10Sn)F2 mice; and (3) F1 complementation studies in which CTL specific for products of the TH-defined gene(s) could not be detected, even in the absence of immune responses to products of the CTL-defined genes. Taken together, these data suggest that in addition to two genes (B2m and Cd-1) within the H-3 region whose products typically stimulate class I MHC-restricted CTL, there is at least one additional gene whose product selectively stimulates class II MHC-restricted TH. This new gene is located telomeric from the CTL-defined genes and between the loci we and un on chromosome 2. These data demonstrate a novel degree of complexity of the H-3 "locus" and suggest selective presentation of minor H gene products in the context of class I or class II MHC proteins.

Homospermic versus heterospermic insemination of zona-free hamster eggs to assess fertility of fluorochrome-labeled acrosome-reacted bull spermatozoa

Fresh spermatozoa from six bulls, with fertility ranging from 64% to 78%, (based upon 59-day nonreturn rates for 159,448 cows inseminated) were mixed with zona-free hamster eggs in 15 heterospermic pair inseminations. Five of the bulls were used in homospermic insemination studies. Prior to incubation, spermatozoa from each bull were labeled with contrasting fluorescent stains pretested for effects on spermatozoa. Equal numbers of spermatozoa were mixed and treated with liposomes of dilauroylphosphatidylcholine to induce the acrosome reaction. Spermatozoa from split ejaculates within a male competed against each other equally in the hamster egg test, indicating that the staining procedure did not affect egg penetration rates. Bulls differed in their egg penetration rates when their sperm were inseminated either homospermically or heterospermically, but the differences in the homospermic inseminations were not significantly correlated with sire fertility. The number and percentage of sperm which penetrated eggs, and the number of eggs penetrated in the heterospermic competitive tests were highly correlated with fertility (r greater than or equal to 0.86). Therefore, egg penetration rates from heterospermic inseminations appear to be valuable indicators of fertility and much more sensitive predictors than results from homospermic inseminations.

Relationship of sire fertility to acrosome-reacted and motile spermatozoa after treatment with liposomes

The relationship between bull non-return rate and percent acrosome-reacted and percent motile sperm treated with 24.8, 34.8, and 44.8 microM dilauroylphosphatidylcholine liposomes was examined. Frozen-thawed spermatozoa from six bulls, with fertility ranging from 64 to 78%, were incubated at 39 degrees C with the liposomes for 0, 7, and 15 min. Bulls differed in percentages of motile sperm, and this decreased over time, especially at the highest concentration of lipids (44.8 microM). Bulls differed initially in their percentage of sperm with intact acrosomes and in their linear rate of increase in percent acrosome-reacted sperm. At 24.8 microM of lipid the rate of increase was nearly linear, whereas at higher concentrations the maximum acrosome reaction was approached during short incubations. The variables 1) decline in percent motile sperm and 2) increase in percent acrosome-reacted sperm, used singly, predicted fertility most accurately when measured on sperm treated with 44.8 and 24.8 microM of lipids, respectively. However, the highest relationship (R2 greater than or equal to .97) was established by combining the acrosome and motility measurements of sperm exposed to 34.8 microM of lipids. Thus, potential fertility of bulls may be predicted by application of this assay to frozen-thawed semen.

Slime production by bovine milk Staphylococcus aureus and identification of coagulase-negative staphylococcal isolates

Staphylococcus aureus isolates from bovine milk were assessed for capsule or slime production. When pure S. aureus cultures in milk were inoculated directly into serum-soft agar constituted with a modified staphylococcus 110 medium, 100% of the isolates grew with diffuse colony morphology. Diffuse colony morphology was rapidly lost on subculture and was more rapidly lost in brain heart infusion-serum-soft agar. No evidence was seen for encapsulation in India ink preparations or by the clumping factor test. It was concluded that freshly isolated S. aureus strains produce slime, not true capsules. During examination of the 84 milk samples that grew staphylococci in addition to S. aureus (27.4%), a significant number of coagulase-negative staphylococcal species were encountered and identified by conventional tests as S. simulans (41.7%), S. xylosus (11.9%), S. epidermidis (3.6%), S. saprophyticus (3.6%), S. hyicus (2.9%), S. cohnii (1.2%), S. haemolyticus (1.2%), and S. warneri (1.2%). Five isolates (6.0%) were not identified. Attempts were also made to identify the isolates by the API Staph-Ident system, which gave an overall accuracy of 45.2%. The susceptibilities of the isolates to a variety of antibiotics were determined, and they appeared to be less resistant than human clinical isolates.

Project HITE (health individualization and teacher education): a health curriculum for 3-, 4- and 5-year olds

South Carolina has been a national leader in such health problems as cardiovascular disease, syphillis and gonorrhea. Since many of the problems could be attributed to poor health habits, education of the state's residents seemed in order. The education/re-education of inaccessible adults with firmly established health habits--poor or otherwise--was not feasible, but the education of impressionable, readily accessible three-, four- and five-year olds was possible. Through a grant from the federal government, an individualized health curriculum that could accommodate the differences of the learners and include vital health content was developed. This project of developing and distributing the health curriculum to teachers of young children was called Project HITE (Health Individualization and Teacher Education).