Germline TCR-A restriction of immunoglobulin E responses to allergen

 Immunoglobulin E responses to known environmental antigens (allergens) may serve as a general model to investigate germline genetic restriction of the immune response. We have previously shown genetic linkage between IgE responses to major allergens and the T-cell receptor (TCR) A/D locus, but not to TCR-B, implying that elements in TCR A/D restrict the ability to react to specific antigens. We now show, in two sets of subjects from the same population, a strong allelic association between a VA8.1 polymorphism (VA8.1 ^* 2) and reactivity to Der p II, a major antigenic component of the house dust mite Dermatophagoides pteronyssinus. Association was also seen between Der p II IgE titres and HLA-DRB1 ^* 1501 alleles. Reactivity to Der p II was confined to subjects who were positive for VA8.1 ^* 2 and HLA-DRB1 ^* 1501, demonstrating germline HLA-DR and TCR-A interaction in restricting the response to exogenous antigen. Received: 28 January 1997 / Revised: 28 February 1997     

Chromosomal Localization of the Human Urothelial “Tetraspan” Gene, UPK1B, to 3q13.3–q21 and Detection of aTaqI Polymorphism

The TI1/UPK1b gene codes for a protein of the “tetraspan” family and is expressed as a differentiation product of the mammalian urothelium. A partial genomic clone of the human homologue of the TI1/UPK1b gene was isolated and used as probe to localize the human gene to chromosome 3q13.3–q21 byin situhybridization. Using the same probe, aTaqI restriction fragment length polymorphism, with 29% heterozygosity, was identified by Southern analysis.     

On the stabilization by fixation of configurational states in beef heart mitochondria

The energized configuration of the cristal membrane of beef heart mitochondria can be maintained only as long as oxygen is available for electron transfer. When the oxygen supply is exhausted, the membrane undergoes a transition to the nonenergized configuration. Since the exhaustion of the available oxygen supply is complete in 5–20 sec, it is impossible to apply the method of sedimenting the mitochondria prior to fixation for studying the energized configurational states of mitochondria. The direct addition of glutaraldehyde followed by osmium tetroxide to the mitochondrial suspension is the most effective way of freezing the configurational state of the cristal membrane. Fixation with glutaraldehyde appears to be complete within 1–2 sec even at 0°. Osmium tetroxide alone can also freeze the energized configuration by fixation but the concentration of the fixative is critical. The problem of capturing the configurational state applies not only to energized transitions (nonenergized to energized) but also to nonenergized transitions (orthodox to aggregated). The freezing by fixation of the cristal membrane in the aggregated configuration is best accomplished by the sequential use of glutaraldehyde and osmium tetroxide. When the levels of glutaraldehyde and osmium tetroxide are respectively too low or too high, the mitochondrion will undergo a transition from the aggregated to the orthodox configuration before fixation is complete. Light-scattering studies provide an independent method for monitoring configurational changes in mitochondria; these light-scattering measurements confirm that the conditions for fixation which lead to stabilization of the energized state as judged by electron microscopy, also show maintenance of configuration as judged by absence of light-scattering changes after the fixatives are introduced. Reagents used in negative staining will induce the geometrical form of the energized configuration of the mitochondrion even under nonenergizing conditions. These reagents are thus unsuitable for use in studies of configurational transitions in mitochondria.     

A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility

The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by nuclear magnetic resonance spectroscopy. Three types of β‐(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di‐ and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated, and free energy maps of the φ – ψ space and hydrogen‐bonding patterns were obtained. The glycosidic linkage between Glc‐Glc or Glc‐Man (C‐type) was the stiffest with mainly one probable conformation; the linkage from Man‐Man or Man‐Glc (M‐type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl‐units (X‐type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of the function of hemicelluloses both in the cell wall and in technical products.     

Life‐history tradeoffs revealed by seasonal declines in reproductive traits of Arctic‐breeding shorebirds

Seasonal declines in breeding performance are widespread in wild animals, resulting from temporal changes in environmental conditions or from individual variation. Seasonal declines might drive selection for early breeding, with implications for other stages of the annual cycle. Alternatively, selection on the phenology of nonbreeding stages could constrain timing of the breeding season and lead to seasonal changes in reproductive performance. We studied 25 taxa of migratory shorebirds (including five subspecies) at 16 arctic sites in Russia, Alaska, and Canada. We investigated seasonal changes in four reproductive traits, and developed a novel Bayesian risk‐partitioning model of daily nest survival to examine seasonal trends in two causes of nest failure. We found strong seasonal declines in reproductive traits for a subset of species. The probability of laying a full four‐egg clutch declined by 8–78% in 12 of 25 taxa tested, daily nest survival rates declined by 1–12% in eight of 22 taxa, incubation duration declined by 2.0–2.5% in two of seven taxa, and mean egg volume declined by 5% in one of 15 taxa. Temporal changes were not fully explained by individual variation. Across all species, the proportion of failed nests that were depredated declined over the season from 0.98 to 0.60, while the proportion abandoned increased from 0.01 to 0.35 and drove the seasonal declines in nest survival. An increase in abandonment of late nests is consistent with a life‐history tradeoff whereby either adult mortality increased or adults deserted the breeding attempt to maximize adult survival. In turn, seasonal declines in clutch size and incubation duration might be adaptive to hasten hatching of later nests. In other species of shorebirds, we found no seasonal patterns in breeding performance, suggesting that some species are not subject to selective pressure for early breeding.     

Long‐term nutrient addition alters arthropod community composition but does not increase total biomass or abundance

A simple bottom–up hypothesis predicts that plant responses to nutrient addition should determine the response of consumers: more productive and less diverse plant communities, the usual result of long‐term nutrient addition, should support greater consumer abundances and biomass and less consumer diversity. We tested this hypothesis for the response of an aboveground arthropod community to an uncommonly long‐term (24‐year) nutrient addition experiment in moist acidic tundra in arctic Alaska. This experiment altered plant community composition, decreased plant diversity and increased plant production and biomass as a deciduous shrub, Betula nana, became dominant. Consistent with strong effects on the plant community, nutrient addition altered arthropod community composition, primarily through changes to herbivore taxa in the canopy‐dwelling arthropod assemblage and detritivore taxa in the ground assemblage. Surprisingly, however, the loss of more than half of plant species was accompanied by negligible changes to diversity (rarefied richness) of arthropod taxa (which were primarily identified to family). Similarly, although long‐term nutrient addition in this system roughly doubles plant production and biomass, arthropod abundance was either unchanged or decreased by nutrient addition, and total arthropod biomass was unaffected. Our findings differ markedly from the handful of terrestrial studies that have found bottom‐up diversity cascades and productivity responses by consumers to nutrient addition. This is probably because unlike grasslands and salt marshes (where such studies have historically been conducted), this arctic tundra community becomes less palatable, rather than more so, after many years of nutrient addition due to increased dominance of B. nana. Additionally, by displacing insulating mosses and increasing the cover of shrubs that cool and shade the canopy microenvironment, fertilization may displace arthropods keenly attuned to microclimate. These results indicate that terrestrial arthropod assemblages may be more constrained by producer traits (i.e. palatability, structure) than they are by total primary production or producer diversity.     

Comparative Genomics of Cultured and Uncultured Strains Suggests Genes Essential for Free-Living Growth of Liberibacter

The full genomes of two uncultured plant pathogenic Liberibacter, Ca. Liberibacter asiaticus and Ca. Liberibacter solanacearum, are publicly available. Recently, the larger genome of a closely related cultured strain, Liberibacter crescens BT-1, was described. To gain insights into our current inability to culture most Liberibacter, a comparative genomics analysis was done based on the RAST, KEGG, and manual annotations of these three organisms. In addition, pathogenicity genes were examined in all three bacteria. Key deficiencies were identified in Ca. L. asiaticus and Ca. L. solanacearum that might suggest why these organisms have not yet been cultured. Over 100 genes involved in amino acid and vitamin synthesis were annotated exclusively in L. crescens BT-1. However, none of these deficiencies are limiting in the rich media used to date. Other genes exclusive to L. crescens BT-1 include those involved in cell division, the stringent response regulatory pathway, and multiple two component regulatory systems. These results indicate that L. crescens is capable of growth under a much wider range of conditions than the uncultured Liberibacter strains. No outstanding differences were noted in pathogenicity-associated systems, suggesting that L. crescens BT-1 may be a plant pathogen on an as yet unidentified host.     

Addition of superoxide dismutase mimics during cooling process prevents oxidative stress and improves semen quality parameters in frozen/thawed ram spermatozoa

High levels of reactive oxygen species (ROS), which may be related to reduced semen quality, are detected during semen cryopreservation in some species. The objectives of this study were to measure the oxidative stress during ram semen cryopreservation and to evaluate the effect of adding 2 antioxidant mimics of superoxide dismutase (Tempo and Tempol) during the cooling process on sperm motility, viability, acrosomal integrity, capacitation status, ROS levels, and lipid peroxidation in frozen and/or thawed ram spermatozoa. Measuring of ROS levels during the cooling process at 35, 25, 15, and 5 °C and after freezing and/or thawing showed a directly proportional increase (P < 0.05) when temperatures were lowering. Adding antioxidants at 10 °C confered a higher motility and sperm viability after cryopreservation in comparison with adding at 35 °C or at 35 °C/5 °C. After freezing and/or thawing, sperm motility was significantly higher (P < 0.05) in Tempo and Tempol 1 mM than that in control group. Percentage of capacitated spermatozoa was lower (P < 0.05) in Tempo and Tempol 1 mM in comparison with that in control group. In addition, ROS levels and lipid peroxidation in group Tempo 1 mM were lower (P < 0.05) than those in control group. These results demonstrate that ram spermatozoa are exposed to oxidative stress during the cooling process, specifically when maintained at 5 °C and that lipid peroxidation induced by high levels of ROS decreases sperm motility and induces premature sperm capacitation. In contrast, the addition of Tempo or Tempol at 0.5 to 1 mM during the cooling process (10 °C) protects ram spermatozoa from oxidative stress.     

The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease

Congenital heart disease (CHD) is the most common congenital malformation, with evidence of a strong genetic component. We analyzed data from 223 consecutively ascertained families, each consisting of at least one child affected by a conotruncal defect (CNT) or hypoplastic left heart disease (HLHS) and both parents. The NimbleGen HD2-2.1 comparative genomic hybridization platform was used to identify de novo and rare inherited copy number variants (CNVs). Excluding 10 cases with 22q11.2 DiGeorge deletions, we validated de novo CNVs in 8 % of 148 probands with CNTs, 12.7 % of 71 probands with HLHS and none in 4 probands with both. Only 2 % of control families showed a de novo CNV. We also identified a group of ultra-rare inherited CNVs that occurred de novo in our sample, contained a candidate gene for CHD, recurred in our sample or were present in an affected sibling. We confirmed the contribution to CHD of copy number changes in genes such as GATA4 and NODAL and identified several genes in novel recurrent CNVs that may point to novel CHD candidate loci. We also found CNVs previously associated with highly variable phenotypes and reduced penetrance, such as dup 1q21.1, dup 16p13.11, dup 15q11.2-13, dup 22q11.2, and del 2q23.1. We found that the presence of extra-cardiac anomalies was not related to the frequency of CNVs, and that there was no significant difference in CNV frequency or specificity between the probands with CNT and HLHS. In agreement with other series, we identified likely causal CNVs in 5.6 % of our total sample, half of which were de novo.