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PubMed2004

Structural brain variation and general intelligence.

Total brain volume accounts for about 16% of the variance in general intelligence scores (IQ), but how volumes of specific regions-of-interest (ROIs) relate to IQ is not known. We used voxel-based morphometry (VBM) in two independent samples to identify substantial gray matter (GM) correlates of IQ. Based on statistical conjunction of both samples (N = 47; P < 0.05 corrected for multiple comparisons), more gray matter is associated with higher IQ in discrete Brodmann areas (BA) including frontal (BA 10, 46, 9), temporal (BA 21, 37, 22, 42), parietal (BA 43 and 3), and occipital (BA 19) lobes and near BA 39 for white matter (WM). These results underscore the distributed neural basis of intelligence and suggest a developmental course for volume--IQ relationships in adulthood.

Adult↗
PubMed2003

Primary structure and variation of the T-cell receptor delta-chain from a marsupial, Macropus eugenii.

Although gammadelta T-cells form only a small portion of circulating T-cells in mice and humans, they are more frequent in many other types of mammals and this has lead to speculation regarding their roles and the evolutionary significance of their relative abundance. Moreover, whilst clear homologues of four types of T-cell receptor (TCR) chains (alpha, beta, delta and gamma) have been identified in vertebrates as distantly related as eutherian mammals and cartilaginous fish, there are still many gaps in our knowledge of these TCR components from various taxa. Such knowledge would further illuminate the evolution and function of these receptors and of gammadelta T-cells. Here, we report the molecular cloning of a TCR-delta chain cDNA from the tammar wallaby (Macropus eugenii) which represents the first component of the gammadelta TCR to be characterised from a marsupial. A PCR-based survey of variable (V) segment usage in tammar wallaby mammary-associated lymph node indicated that, although gammadelta T-cells may be sparse in this type of tissue, this species has at least three subfamilies of V genes that have been broadly conserved across vertebrate evolution. Two V subfamilies found in the tammar wallaby were relatively similar and may have diverged more recently, an event that probably occurred at some point in the marsupial lineage.

Amino Acid Sequence↗
PubMed1987

The normal variation in structure and composition of canine hip articular cartilage proteoglycans.

The composition of the weight bearing portion of the femoral head articular cartilage from both sides of greyhounds 11-32 months of age was studied with regard to variability of proteoglycans. Extractability of proteoglycans was very similar for all samples. Other parameters, i.e. contents of proteoglycans in the cartilage, hyaluronic acid content of the proteoglycan fraction, as well as contents of keratan sulfate and chondroitin sulfate, size of proteoglycans and ability of proteoglycans to aggregate with hyaluronic acid, were similar in samples from the right and left side of each dog. The variability from one dog to another was large and not related to age. The data show that in experimental studies of joint disease the contralateral joint can be used as a control to a treated joint, while the large interindividual variability makes comparison difficult between individuals.

Aging↗
PubMed2002

The middle ear of gekkonoid lizards: interspecific variation of structure in relation to body size and to auditory sensitivity.

Wishing to assess the effects of the dimensions of the middle ear on the auditory sensitivity of gekkonoid lizards, we measured middle ear components in preserved geckos, which in life had yielded 'cochlear microphonics' audiograms. We examined two to seven specimens of 14 species. The measures of middle ear elements varied relative to head or body length similarly within species and among species. The areas of the external ear opening, tympanic membrane, and columellar footplate, and the ratio between the last two ('hydraulic lever'), were correlated with animal length. The hydraulic and mechanical (extracolumellar) lever ratios appeared to complement each other, the former being emphasized in large animals, the latter in small animals. The apparent auditory sensitivity correlated with the sizes of the animal, head and external ear opening, and negatively (insignificantly) correlated with the mechanical lever ratio. The correlation of sensitivity with the hydraulic lever was insignificant, perhaps due to a 'tympanic membrane lever' (catenary effect). The most sensitive frequency negatively correlated with the area of the external ear opening, the area of the tympanic membrane, and with the level of greatest sensitivity. It was positively correlated with the relative length of the cartilaginous portion of the ossicular chain. However, the number of hair cells in the basilar papilla, too, is known to correlate with animal size. Moreover, the least sensitive species were not only the smallest species, they were also the species known to lack a zone of unidirectional hair cells in the basilar papilla. Hence the apparent sensitivity hypothetically depends on both middle ear dimensions and summation of inner ear output. This hypothesis requires verification by other methods.

Animals↗
PubMed1997

Anatomic variation of structural properties of periacetabular bone as a function of age. A quantitative computed tomography study.

The shape of the acetabulum, the volume of the periacetabular bone, and its density for 125 patients with a wide age range have been quantified using quantitative computed tomography. The goals were to study the relationship between geometric and densitometric properties and provide normative data for finite-element analysis. Significant correlations were found between acetabular diameter and (1) depth, (2) cancellous periacetabular bone density, and (3) periacetabular total bone volume. Only changes in densitometric properties significantly correlated with age. Sphericity of the acetabulum did not increase with age. Variability in bone morphology and density was found for both male and female groups. Surgeons using purely geometric measures to quantify the integrity of acetabular bone should be aware of their limitations when selecting hardware for total hip arthroplasty.

Acetabulum↗
PubMed2002

Ultrastructural morphogenesis of dimorphic arcuate infection (gun) cells of Haptoglossa erumpens an obligate parasite of Bunonema nematodes.

Haptoglossa is a genus of biflagellate organisms that has been placed in the oomycetes and is characterised by producing unique infective gun cells, which usually infect by physically rupturing the nematode cuticle. Haptoglossa erumpens is a parasite of Bunonema nematodes that produces arcuate infection cells and aplanospores that are discharged following the swelling and rupture of the thallus wall and distended host cuticle. Recent isolations of H. erumpens have revealed that the germinating aplanospores develop into two similar-sized but morphologically distinct infection cells. The uni-nucleate, convexly arcuate, gun cells were observed to fire in response to host nematodes, producing a cylindrical sporidium inside the host body. These gun cells had an apical missile chamber containing a needle with a unique arrangement of investing cones. Unlike previously described gun cells, the tube tail did not wind around the nucleus but continued into the basal vacuole where it terminated. The second type of infection cell was a concavely arcuate, bi-nucleate, cell that had an unusually large and elongate annulus component in the missile chamber. These modified bi-nucleate gun cells were never observed to fire in response to contact with Bunomena nematodes. The patterns of morphological and structural variations in these infection structures in this genus are reviewed in the light of these findings.

Animals↗
PubMed2001

Strain-based sequence variations and structure analysis of murine prostate specific spermine binding protein using mass spectrometry.

Mouse spermine binding protein (SBP) has been characterized using mass spectrometry, including its localization within the prostate, sequence verification, and its posttranslational modifications. MALDI (matrix-assisted laser desorption/ionization) mass spectrometry was employed for localization of proteins expressed by different lobes of the mouse prostate obtained after tissue blotting on a polyethylene membrane. The mass spectra showed complex protein profiles that were different for each lobe of the prostate. The prostate-specific spermine binding protein (SBP), primarily identified by its in-source decay fragment ion signals, was found predominantly expressed by the ventral lobe of the prostate. The MALDI in-source decay measurements combined with nanoESI (nanoelectrospay ionization) MS/MS measurements obtained after specific proteolysis of SBP, allowed the exact positioning of a single N-linked carbohydrate group, and the identification of a pyroglutamate residue at the sequence N-terminus. The N-linked carbohydrate component was further investigated and the general pattern of the N-linked carbohydrate identified. The presence of a disulfide bridge between cysteine78 and cysteine124 was also established. The full sequence characterization of SBP showed several strain-based sequence differences when compared to the published gene sequence.

Amino Acid Sequence↗
PubMed2006

Characterization of human saposins by NMR spectroscopy.

Saposins are lipid-binding and membrane-perturbing glycoproteins of the mammalian lysosomes involved in sphingolipid and membrane digestion. Although the four human saposins (Saps), A-D, are sequence-related, they are responsible for the activation of different steps in the cascade of lysosomal glycosphingolipid degradation. Saposin activity is maximal under acidic conditions, and the pH dependence of lipid and membrane binding has been assigned to conformational variability. We have employed solution NMR spectroscopy to all four (15)N-labeled human saposins at both neutral and acidic pH. Using backbone NOEs and residual dipolar couplings, the "saposin fold" comprising five alpha-helices was confirmed for Sap-A, Sap-C, and Sap-D. Structural variations within these proteins are in the order of variations between the known structures of Sap-C and NK-lysin. In contrast, Sap-B yielded spectra of very poor quality, presumably due to conformational heterogeneity and molecular association. Sap-D exists in a slow dynamic equilibrium of two conformational states with yet unknown function. At pH 4.0, where all saposins are highly unstable, Sap-C undergoes a transition to a specific dimeric state, which is likely to resemble the structure recently found in both Sap-C in a detergent environment and crystals of Sap-B.

Amino Acid Sequence↗
PubMed1999

NMR characterization of the metallo-beta-lactamase from Bacteroides fragilis and its interaction with a tight-binding inhibitor: role of an active-site loop.

Understanding the structure and dynamics of the enzymes that mediate antibiotic resistance of pathogenic bacteria will allow us to take steps to combat this increasingly serious public health hazard. Complete backbone NMR resonance assignments have been made for the broad-specificity metallo-beta-lactamase CcrA from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. Chemical shift indices show that the secondary structure of the CcrA molecule in solution is very similar to that in published crystal structures. A loop adjacent to the two-zinc catalytic site exhibits significant structural variation in the published structures, but appears from the NMR experiments to be a regular beta-hairpin. Backbone heteronuclear NOE measurements indicate that this region has slightly greater flexibility on a picosecond to nanosecond time scale than the molecule as a whole. The loop appears to have an important role in the binding of substrates and inhibitors. Binding of the inhibitor 3-[2'-(S)-benzyl-3'-mercaptopropanoyl]-4-(S)-carboxy-5, 5-dimethylthiazolidine causes a marked increase in the stability of the protein toward unfolding and aggregation, and causes changes in the NMR resonance frequencies of residues close to the active (zinc-binding) site, including the beta-hairpin loop. There is a small but significant increase in the heteronuclear NOE for this loop upon inhibitor binding, indicative of a decrease in flexibility. In particular, the NOE of the indole ring of tryptophan 49, at the tip of the beta-hairpin loop, changes from a low value characteristic of a random coil chain to a significantly higher value, close to that observed for the backbone amides in this region of the protein. These results strongly suggest that the hairpin loop participates in the binding of substrate and in the shielding of the zinc sites from solvent. The broad specificity of the CcrA metallo-beta-lactamase may in fact reside in the plasticity of this part of the protein, which allows it to accommodate and bind tightly to substrates of a variety of shapes and sizes.

Bacterial Proteins↗
PubMed2003

Dioxo-bridged dinuclear manganese(III) and -(IV) complexes of pyridyl donor tripod ligands: combined effects of steric substitution and chelate ring size variations on structural, spectroscopic, and electrochemical properties.

The syntheses and structural, spectral, and electrochemical characterization of the dioxo-bridged dinuclear Mn(III) complexes [LMn(mo-O)(2)MnL](ClO(4))(2), of the tripodal ligands tris(6-methyl-2-pyridylmethyl)amine (L(1)) and bis(6-methyl-2-pyridylmethyl)(2-(2-pyridyl)ethyl)amine (L(2)), and the Mn(II) complex of bis(2-(2-pyridyl)ethyl)(6-methyl-2-pyridylmethyl)amine (L(3)) are described. Addition of aqueous H(2)O(2) to methanol solutions of the Mn(II) complexes of L(1) and L(2) produced green solutions in a fast reaction from which subsequently precipitated brown solids of the dioxo-bridged dinuclear complexes 1 and 2, respectively, which have the general formula [LMn(III)(mu-O)(2)Mn(III)L](ClO(4))(2). Addition of 30% aqueous H(2)O(2) to the methanol solution of the Mn(II) complex of L(3) ([Mn(II)L(3)(CH(3)CN)(H(2)O)](ClO(4))(2) (3)) showed a very sluggish change gradually precipitating an insoluble black gummy solid, but no dioxo-bridged manganese complex is produced. By contrast, the Mn(II) complex of the ligand bis(2-(2-pyridyl)ethyl)(2-pyridylmethyl)amine (L(3a)) has been reported to react with aqueous H(2)O(2) to form the dioxo-bridged Mn(III)Mn(IV) complex. In cyclic voltammetric experiments in acetonitrile solution, complex 1 shows two reversible peaks at E(1/2) = 0.87 and 1.70 V (vs Ag/AgCl) assigned to the Mn(III)(2) <--> Mn(III)Mn(IV) and the Mn(III)Mn(IV) <--> Mn(IV)(2) processes, respectively. Complex 2 also shows two reversible peaks, one at E(1/2) = 0.78 V and a second peak at E(1/2) = 1.58 V (vs Ag/AgCl) assigned to the Mn(III)(2) <--> Mn(III)Mn(IV) and Mn(III)Mn(IV) <--> Mn(IV)(2) redox processes, respectively. These potentials are the highest so far observed for the dioxo-bridged dinuclear manganese complexes of the type of tripodal ligands used here. The bulk electrolytic oxidation of complexes 1 and 2, at a controlled anodic potential of 1.98 V (vs Ag/AgCl), produced the green Mn(IV)(2) complexes that have been spectrally characterized. The Mn(II) complex of L(3) shows a quasi reversible peak at an anodic potential of E(p,a) of 1.96 V (vs Ag/AgCl) assigned to the oxidation Mn(II) to Mn(III) complex. It is about 0.17 V higher than the E(p,a) of the Mn(II) complex of L(3a). The higher oxidation potential is attributable to the steric effect of the methyl substituent at the 6-position of the pyridyl donor of L(3).

Journal Article↗
PubMed2004

The structure of variation and its influence on the estimation of status: indicators of condition of lakes in the Northeast, U.S.A.

One goal of regional-scale sample surveys is to estimate the status of a resource of interest from a statistically drawn representative sample of that resource. An expression of status is the frequency distribution of indicator scores capturing variability of attributes of interest. However, extraneous variability interferes with the status description by introducing bias into the frequency distributions. To examine this issue, we used data from a regional survey of lakes in the Northeast U.S. collected by the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP). We employ a components of variance model to identify sources of extraneous variance pertinent to status descriptions of physical, chemical, and biological attributes of the population of lakes in the NE. We summarize the relative magnitude of four components of variance (lake-to-lake, year, interaction, and residual) for each indicator and illustrate how extraneous variance biases the status descriptions. We describe a procedure that removes this bias from the status descriptions to produce unbiased estimates and introduce a novel method for estimating the 'cost' of removing the bias (expressed as either increased sampling uncertainty or additional samples needed to achieve the target precision in the absence of bias). We compare the relative magnitude of the four variance components across the array of indicators, finding in general that conservative chemical indicators are least affected by extraneous variance, followed by some nonconservative indicators, with nutrient indicators most affected by extraneous variance. Intermediate were trophic condition indicators (including sediment diatoms), fish species richness and individuals indicators, and zooplankton taxa richness and individuals indicators. We found no clear patterns in the relative magnitude of variance components as a function of several methods of aggregating fish and zooplankton indicators (e.g., level of taxonomy, or species richness vs. numbers of individuals).

Analysis of Variance↗
PubMed2002

Structure of variation in enzyme activity in natural Drosophila melanogaster populations.

Enzyme activity variation was assessed in several isofemale lines originating from two Hungarian Drosophila melanogaster populations. Samples from each population were taken from from two villages; 8-9 isofemale lines were established from each village. The activities of ADH, alphaGPDH, IDH and 6PGDH were determined in the adults (in the F1 generation) and in the larvae (in the F3 generation) as well. Enzyme activities were measured on starch gel after electrophoresis. The activity of the enzyme was detected in a single individual and it was also possible to determine its genotype. The results showed that most of the variation occurred within sites for all four enzymes. This within site variation was more or less equally partitioned into within and between isofemale line (family) components. A smaller portion of variation was attributable to the differences between the populations. Nevertheless, adult alphaGPDH, and larval IDH and 6PGDH activities exhibited significant differences between the two populations. Variation in larval activities of all enzymes was higher than that of the adults, but 6PGDH had considerably higher variation in the adults. The greater variation in larval activities probably reflected the greater environmental variation in the microhabitat of the larvae compared to that of the adults. Larval activities of the investigated enzymes showed much stronger correlation than adult activities. The correlation pattern in the adults differed greatly between the two populations.

Animals↗
PubMed1982

Structure and variation of human alpha 1-antitrypsin.

The sequence of alpha 1-antitrypsin is in keeping with its role as a tissue scavenger of leukocyte elastase. Two abnormal variants commonly present in Europeans cause a deficiency that predisposes them to a progressive loss of lung elasticity. The nature of the reactive centre helps explain why cigarette smoking greatly accelerates the onset and severity of this degenerative process to give the disease emphysema.

Amino Acid Sequence↗
PubMed1993

Sequence-dependent reactivity of linear DNA to chemical cleavage by Cu(II):thiol combinations including cysteine or glutathione.

The chemical cleavage of linear DNA by Cu(II):thiol combinations was investigated using end-labelled double-stranded restriction fragments. Single-strand cleavage of the target DNA occurred with apparent sequence preference, but there appeared to be no apparent consensus sequence for such preferentially cleaved sites based on studies of three different restriction fragments. For any given restriction fragment, the observed Cu(II):thiol DNA-cleavage sequence preference was found to be independent of the nature of the thiol used. Cleavage of 3'-end-labelled DNA generated fragments bearing 5'-phosphoryl termini, and cleavage of 5'-end-labelled DNA gave rise to fragments bearing 3'-phosphoryl and 3'-'phosphatase-inert' termini in equal proportions. No appreciable amounts of fragments bearing 3'- or 5'-hydroxy termini were detected. This pattern of cleavage products is similar to that observed using the hydroxyl-radical-generating systems, 60Co gamma-irradiation or methidium propyl EDTA:Fe(II), but is dissimilar to that found with the Cu(II):phenanthroline or bleomycin systems. Cu(II):thiol cleavage of DNA fragments containing inserts of repeated dinucleotide sequence showed alternating patterns of relative cleavage intensities within the insert-sequence regions which were not seen in the sequences flanking the insert sequence. The assembled experimental data indicate that a reaction product of the Cu(II):thiol interaction, probably the hydroxyl radical, causes DNA cleavage. The Cu(II):thiol interaction may occur free in solution or via a copper species which is bound non-specifically to DNA. The observed low sequence-dependence of the cleavage reaction probably reflects the nature of the DNA structure itself, the Cu(II):thiol system serving as a structural probe of sequence-dependent structural variations in the DNA structure.

Base Sequence↗
PubMed1998

Site-directed mutations in the vnd/NK-2 homeodomain. Basis of variations in structure and sequence-specific DNA binding.

Secondary structures, DNA binding properties, and thermal denaturation behavior of six site-directed mutant homeodomains encoded by the vnd/NK-2 gene from Drosophila melanogaster are described. Three single site H52R, Y54M, and T56W mutations, two double site H52R/T56W and Y54M/T56W mutations, and one triple site H52R/Y54M/T56W mutation were investigated. These positions were chosen based on their variability across homeodomains displaying differences in secondary structure and DNA binding specificity. Multidimensional NMR, electrophoretic mobility shift assays, and circular dichroism spectropolarimetry studies were carried out on recombinant 80-amino acid residue proteins containing the homeodomain. Position 56, but more importantly position 56 in combination with position 52, plays an important role in determining the length of the recognition helix. The H52R mutation alone does not affect the length of this helix but does increase the thermal stability. Introduction of site mutations at positions 52 and 56 in vnd/NK-2 does not modify their high affinity binding to the 18-base pair DNA fragment containing the vnd/NK-2 consensus binding sequence, CAAGTG. Site mutations involving position 54 (Y54M, Y54M/T56W, and H52R/Y54M/T56W) all show a decrease of 1 order of magnitude in their binding affinity. The roles in structure and sequence specificity of individual atom-atom interactions are described.

Amino Acid Sequence↗
PubMed1987

Gene conversion variations generate structurally distinct pilin polypeptides in Neisseria gonorrhoeae.

Pilus+ to pilus- phenotype change occurs in Neisseria gonorrhoeae through gene conversion of the gonococcus' complete, expressed pilin gene by nucleotides homologous to the pilS1 copy 5 partial pilin gene; assembly missense pilin is synthesized but pili are not. Reversion to pilus+ occurs by a subsequent recombinational event that replaces the complete pilin gene's pilS1 copy 5-like sequence with nucleotides from a different partial gene to effect expression of an orthodox (i.e., pilus producing) pilin. Sibling pilus+ revertants of common parentage can carry different sequences in their expressed pilin genes because they have undergone nonidentical gene conversion events such as recombinations with sequences from different partial genes, or recombinations with different length nucleotide stretches of the same partial gene; either can yield structurally and antigenically variant pilin polypeptides.

Amino Acid Sequence↗