Computational sequence analysis of matrix metalloproteinases

Matrix metalloproteinases (MMP) play a cardinal role in the breakdown of extracellular matrix involved in a variety of biological and pathological processes. Research on MMPs has classified and characterized these enzymes according to their matrix substrate specificity, gene and protein domain structure, and regulation of activity and expression. However, the discovery of new MMPs has introduced a need for a more comprehensive and systematic method of classification and quantitative comparison of known and newly discovered members. This study compiles a sequence alignment, constructs a dendrogram, and calculates physical data and homology percentage assignments in order to obtain further insight into MMP structure-function relationships. Thorough analysis of MMP primary sequence domains, physical data patterns, and statistical analysis of sequence homology yields higher resolution in the similarities and differences that group MMP members.     

Zinc status does not affect aluminum deposition in tissues of rats

To examine whether zinc deficiency would increase the toxicity of dietary aluminum, weanling, male Sprague-Dawley rats were fed purified diets containing either 2 or 30 mg Zn/kg diet, with or without 500 mg Al/kg diet for 28 d. Individually pair-fed rats were fed the 30 mg Zn/kg diet with or without added aluminum to control for inanition secondary to zinc deficiency. Rats fed the 2 μg Zn/kg diet showed evidence of zinc deficiency, including anorexia, growth retardation, and depressed concentrations of zinc in tibias and livers. Zinc deficiency did not significantly increase the concentrations of aluminum in the tibias, livers, kidneys, or regions of the brain examined (cerebrum, cerebellum, midbrain, and hippocampus). Inclusion of aluminum in the diet did not alter aluminum concentrations in the various tissues. Under the conditions of this study, zinc deficiency did not result in greater sensitivity to dietary aluminum exposure.     

Spontaneous methylation of hemoglobin by S-adenosylmethionine by a specific and saturable mechanism

The methyl group from S-adenosylmethionine (AdoMet) is transferred into hemoglobin without any evident involvement of an enzyme. There are multiple sites for incorporation of the methyl group into hemoglobin, since both and chains are methylated. The methyl linkages formed in hemoglobin are stable at both alkaline and acidicpH, and the reaction occurs optimally at slightly below neutralpH. Only a small fraction (2%) of hemoglobin tetramers are methylated under the conditions tested. Acid hydrolysis of [³H-methyl]-labeled hemoglobin and determination of phenylisothiocynate derivatives yields N-methyl lysine, which accounts for about one-half of the incorporated [³H-methyl] radioactivity. Other amino acids are methylated as well, with much of the remaining radioactivity being distributed among one or more of the side chains of histidine, cysteine, and arginine. Methyl group transfer to hemoglobin from AdoMet is slow and inefficient (k _cat/K _m5×10^–2), but the reaction velocity tends toward a plateau with increasing AdoMet concentration in a manner suggesting that saturable binding of AdoMet onto hemoglobin is involved in methyl transfer. The velocity of hemoglobin methylation is inhibited by S-adenosylhomocysteine, the known end-product inhibitor of methyltransferases, a further indication that methyl group transfer involves binding and catalysis by a specific site (or sites) in the hemoglobin molecule. These observations may help to explain the known existence of methylated hemoglobins in erythrocyte.     

Multiple DNA Variant Association Analysis: Application to the Insulin Gene Region in Type 1 Diabetes

Association and linkage studies have shown that at least one of the genetic factors involved in susceptibility to insulin-dependent diabetes mellitus (IDDM) is contained within a 4.1-kb region of the insulin gene. Sequence analysis has led to the identification of 10 DNA variants in this region that are associated with increased risk for IDDM. These variants are in strong linkage disequilibrium with each other, and previous studies have failed to distinguish between the variant(s) that cause increased susceptibility to IDDM and others that are associated with the disease because of linkage disequilibrium. To address this problem, we have undertaken a large population study of French diabetics and controls and have analyzed genotype patterns for several of the variant sites simultaneously. This has led to the identification of a subset consisting of four variants (−2733AC, −23HphI, −365VNTR, and +1140AC), at least one of which appears to be directly implicated in disease susceptibility. The multiple-DNA-variant association-analysis approach that is applied here to the problem of identifying potential susceptibility variants in IDDM is likely to be important in studies of many other multifactorial diseases.     

Use of Genetic and Physical Mapping to Locate the Spinal Muscular Atrophy Locus between Two New Highly Polymorphic DNA Markers

The gene for autosomal recessive forms of spinal muscular atrophy (SMA) has recently been mapped to chromosome 5ql3, within a 4-cM region between the blocks D5S465/D5S125 and MAP-1B/D5S112. We identified two new highly polymorphic microsatellite DNA markers—namely, AFM265wf5 (D5S629) and AFM281yh9 (D5S637)—which are the closest markers to the SMA locus. Multilocus analysis by the location-score method was used to establish the best estimate of the SMA gene location. Our data suggest that the most likely location for SMA is between locus D5S629 and the block D5S637/D5S351/MAP-1B/D5S112/D5S357. Genetic analysis of inbred SMA families, based on homozygosity by descent and physical mapping using mega-YACs, gave additional information for the loci order as follows: cen–D5S6–D5S125/D5S465–D5S435–D5S629–SMA–D5S637–D5S351–MAP–1B/D5S112–D5S357–D5S39–tel. These data give the direction for bidirectional walking in order to clone this interval and isolate the SMA gene.     

Morphological variability of geographically distinct populations of the estuarine copepod Acartia Tonsa

Variations in the number of spines on the left and right posterior dorsal and posterior margins of the prosome as well as the length of the prosome of Acartia tonsa from three estuaries, the upper western side of the Chesapeake Bay, Montauk Bay near the eastern end of Long Island Sound and the coast of Peru were determined. The length of the prosome and number of spines in each of the four locations were used as an indication of morphological similarity between the populations.     

Amphetamine Promotes Neostriatal Ascorbate Release via a Nigro-Thalamo-Cortico-Neostriatal Loop

Abstract: In the neostriatum, amphetamine and other dopamine agonists elevate the extracellular level of ascorbate, which is known to modulate neostriatal function. Although both D₁ and D₂ receptors have been linked to neostriatal ascorbate release, ample evidence suggests it is controlled by areas outside the neostriatum. The present series of experiments used selective lesions and intracerebral drug infusions to probe the involvement of the ventromedial thalamus and substantia nigra pars reticulata. Our results implicate both of these sites in amphetamine-induced increases in the release of neostriatal ascorbate. Thus, whereas unilateral electrolytic lesions of the substantia nigra pars reticulata completely abolished the ability of systemic amphetamine (2.5 mg/kg) to increase extracellular ascorbate in ipsilateral neostriatum, intranigral infusions of this drug (10 and 30 µg/µl) elevated neostriatal ascorbate release. This infusion effect, moreover, was blocked by electrolytic lesions of the ipsilateral ventromedial thalamus, which receives input from the substantia nigra pars reticulata and projects to the cerebral cortex. These results, combined with previous evidence implicating cortical projections to neostriatum as the source of extracellular ascorbate, suggest that neostriatal ascorbate release is regulated, at least in part, by a nigro-thalamo-cortico-neostriatal pathway.     

Effects of omnivorous shrimp in a montane tropical stream: sediment removal,disturbance of sessile invertebrates and enhancement of understory algal biomass

Freshwater shrimp dominate the faunal biomass of many headwater tropical streams: however, their role in community organization is unclear. Enclosure/exclosure experiments in a montane Puerto Rican stream examined direct and indirect effects of two dominant taxa of atyid (Atyidae) shrimp, Atya lanipes Holthuis and Xiphocaris elongata Guerin-Meneville. Both shrimp taxa caused significant reductions in sediment cover on rock substrata, reducing sedimentation and enhancing algal biovolume on clay tiles in cages. When tiles incubated in shrimp exclosures for 2 wks were placed outside of cages, atyid shrimp removed 100% of the sediment cover within a 30 min observation period. Atyid shrimp appear to play an important role in stream recovery after high discharge events by rapidly removing sediments and detritus deposited on benthic substrata in pools. We evaluated the mechanism by which A. lanipes influences algae and benthic insects by comparing patterns of algal biomass, taxonomic composition, and insect abundance between shrimp-exclusion and shrimp-presence treatments both with and without manual sediment removal. The shrimp exclusion treatment without manual sediment removal bad significantly lower algal biomass and greater sedimentation than all other treatments. The treatment in which shrimp were excluded but sediment was manually removed, however, accrued almost the same algal biovolume as the shrimp enclosure treatment, supporting the hypothesis that sediment removal enhances the biovolume of understory algal taxa. Algal community composition was similar between stream bottom bedrock exposed to natural densities of shrimp and all experimental treatments for both Atya and Xiphocaris: a diatom community strongly dominated (78–95%) by the adnate taxon, Achnanthes lanceolata Breb ex. Kutz. Atyid shrimp are important in determining the distribution and abundance of benthic insects through both direct and indirect effects. Sessile, retreat-building chironomid larvae (Chironomidae: Diptera) are negatively affected by both A. lanipes and X. elongata, through direct removal by foraging activities and/or indirectly through depression of sediment resources available to larvae for the construction of retreats. In constrast, the mobile grazer, Cloeodes maculipes (Baetidae: Ephemeroptera) was not adversely affected and atyid shrimp have the potential to exert positive indirect effects on this taxon by facilitating its exploitation of algal resources and/or through enhancement of understory algal food resources through sediment removal.