Testing an inference of function from structure: Snake vertebrae do the twist

The zygapophyses and zygosphene–zygantrum articulations of snake vertebrae are hypothesized to restrict or eliminate vertebral torsion. This hypothesis is apparently based solely on the inference of function from structure, despite the limitations of such inferences, as well as contradictory observations and measurements. In this study, I observed and measured axial torsion in gopher snakes, Pituophis melanoleucus. To examine the structural basis of axial torsion, I measured the vertebral articulation angles along the body and the insertion angles of five epaxial muscles. To examine torsion in a natural behavior, I digitized video images and measured the degree of apparent axial torsion during terrestrial lateral undulation. Finally, I measured the mechanical capacity of the vertebral joints for actual torsion over intervals of 10 vertebrae in fresh, skinned segments of the trunk. Vertebral articulation angles vary up to 30° and are associated with variation in torsional capacity along the trunk. The freely crawling P. melanoleucus twisted up to 2.19° per vertebra, which produced substantial overall torsion when added over several vertebrae. The vertebral joints are mechanically capable of torsion up to 2.89° per joint. Therefore, despite the mechanical restriction imposed by the complex articulations, vertebral torsion occurs in snakes and appears to be functionally important in several natural behaviors. Even in cases in which mechanical function appears to be narrowly constrained by morphology, specific functions should not be inferred solely from structural analyses. J. Morphol. 241:217–225, 1999. © 1999 Wiley‐Liss, Inc.     

Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints

Introductory biochemistry texts often note that the fold of a protein is completely defined when the dihedral angles phi and psi are known for each amino acid. This assertion was examined with torsion angle dynamics and simulated annealing (TAD/SA) calculations of protein G using only dihedral angle restraints. When all dihedral angles were restrained to within 1 degrees of the values of the X-ray structure, the TAD/SA structures gave a backbone root mean square deviation to the target of 4 A. Factors that contributed to divergence from the correct solution include deviations of peptide bonds from planarity, internal conflicts resulting from the nonuniform energies of different phi, psi combinations, and relaxation to extended conformations in the absence of long-range constraints. Simulations including hydrogen-bond restraints showed that even a few long-range contacts constrain the fold better than a complete set of accurate dihedral restraints. A procedure is described for TAD/SA calculations using hydrogen-bond restraints, idealized dihedral restraints for residues in regular secondary structures, and "hydrophobic distance restraints" derived from the positions of hydrophobic residues in the amino acid sequence. The hydrogen-bond restraints are treated as inviolable, whereas violated hydrophobic restraints are removed following reduction of restraint upper bounds from 2 to 1 times the predicted radius of gyration. The strategy was tested with simulated restraints from X-ray structures of proteins from different fold classes and NMR data for cold shock protein A that included only backbone chemical shifts and hydrogen bonds obtained from a long-range HNCO experiment.     

The sperm roller: a modified testicular duct linked to giant sperm transport within the male reproductive tract

The male reproductive tracts of Drosophila display considerable variation in the relative size of their components, notably of the testes, but there are few structural differences between species. Here we report a remarkable coiled structure separating the testes from the seminal vesicles in the giant sperm species Drosophila bifurca. This evolutionary novelty, known as the 'sperm roller', seems to be an exaggeration in the size of the testicular duct as revealed by light and electron microscopic observations. It consists of a tubular monocellular epithelium lying on the basal laminae and muscle and conjunctive cells. The lumen of the roller contains crypts. The apical membrane of the epithelial cells presents numerous long microvilli protruding into the lumen. The sperm roller structure is probably involved in managing sperm during their transit through the male genital tract, because sperm are seen in bundles at the base of the testis, whereas they are singly rolled up by the time they enter the seminal vesicles. The hypercoiling of the individual spermatozoon within the roller probably occurs as the result of an osmotic process produced by features of the epithelial wall and the dramatically increased exchange surface. This is the first report of a specialized device of this type in Drosophila or, more generally, in insects.     

Ginkgo biloba supplement abates lead-induced endothelial and testicular dysfunction in Wistar rats via up-regulation of Bcl-2 protein expression,pituitary-testicular hormones and down-regulation of oxido-inflammatory reactions

BackgroundApoptotic and oxido-inflammatory pathways have been found to be up-regulated in lead acetate poisoning which has been associated to endothelial and testicular dysfunctions. It is yet uncertain, nevertheless, if treatment with Ginkgo biloba supplements (GBS), a flavonoid-rich natural product can lessen the adverse effects of lead on endothelial and testicular functions. This study investigated the impact of Ginkgo biloba supplementation on lead-induced endothelial and testicular dysfunctions.MethodsThe animals were treated with GBS (50 mg/kg and 100 mg/kg orally) for 14 days following oral exposure to lead acetate (25 mg/kg) for 14 days. After euthanasia, blood samples, epididymal sperm, testes, and aorta were collected. The quantities of the hormones (testosterone, follicle stimulating hormone (FSH) and luteinizing hormone (LH), as well as the anti-apoptotic, oxidative, nitrergic, inflammatory markers, were then determined using immunohistochemistry, ELISA, and conventional biochemical methods.ResultsGBS reduced lead-induced oxidative stress by increasing the levels of the antioxidant enzymes catalase (CAT), glutathione (GSH), and superoxide dismutase (SOD), while lowering malondialdehyde (MDA) in endothelium and testicular cells. Normal testicular weight was restored by GBS which also decreased endothelial endothelin-I and increased nitrite levels. TNF-α and IL-6 were decreased while Bcl-2 protein expression was enhanced. Lead-induced alterations in reproductive hormones (FSH, LH, and testosterone) were also restored to normal.ConclusionAccording to our result, using Ginkgo biloba supplement prevented lead from causing endothelial and testicular dysfunction by raising pituitary-testicular hormone levels, boosting Bcl-2 protein expression and lowering oxidative and inflammatory stress in the endothelium and testes.     

The phylogeny and ontogeny of humeral torsion

In a series of specimens extending from fossil material through recent vertebrates including man there occurs a gradual phylogenetic increase in the degree of humeral torsion. A further (ontogenetic) torsion is superimposed upon the phylogenetic one in man which increases from birth until the proximal epiphysial cartilage of the humerus disappears and bony fusion occurs. There is a distinct correlation between the calculated strength of humeral rotator muscles inserting above and below the proximal epiphysis; this suggests that they provide the forces involved in the production of humeral torsion. It is shown that ontogenetic or secondary torsion occurs proximally and not along the shaft of the bone. Differences in the degree of humeral torsion in either sex of adult Whites and Negroes are given and discussed.     

Torsional Movements in the Ameba,Chaos carolinensis,Suggest a Helical Cytoskeletal Organization*†

SYNOPSIS. Centrifugation for 30–40 seconds at 8,000 g has been used to render monopodial specimens of the large free-living ameba. Chaos carolinensis. These monopodial amebae exhibit obvious torsional movements in the tail. In many cases the posterior ectoplasm assumes the form of a screw with helical ridges forming in place of the more common straight dorsal fins. This finding prompted a re-examination of normal polypodial C. carolinensis, and a majority of these were found also to exhibit torsional movement in the tail and in retracting pseudopodia. These movements suggest that the cytoskeleton of Chaos may have a helical component in its organization.     

Numerous severely twisted N-acetylglucosamine conformations found in the protein databank

Taking advantage of the known planarity of the N-acetyl group of N-acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N-acetyl group was often found in the less favorable cis conformation (12% of the cases). It was also found severely twisted in numerous instances, especially in structures with a resolution poorer than 1.9 Å determined between 2000 and 2015. Though the automated PDB-REDO procedure has proved able to improve nearly 85% of the structural models deposited to the PDB, and does prove able to cure most severely twisted conformations of the N-acetyl group, it fails to correct its high rate of cis conformations. More generally, for structures with a resolution poorer than 1.6 Å, it produces N-acetylglucosamine models in slightly poorer agreement with experimental data, as measured using real-space correlation coefficients. Significant improvements are thus still needed, at least as far as this carbohydrate structure is concerned.     

One-bond and two-bond J couplings help annotate protein secondary-structure motifs: J-coupling indexing applied to human endoplasmic reticulum protein ERp18

NMR coupling constants, both direct one‐bond (¹J) and geminal two‐bond (²J), are employed to analyze the protein secondary structure of human oxidized ERp18. Coupling constants collected and evaluated for the 18 kDa protein comprise 1268 values of ¹J_CαHα, ¹J_CαCβ, ¹J_CαC′, ¹J_C′N′, ¹J_N′Cα, ¹J_N′HN, ²J_CαN′, ²J_HNCα, ²J_C′HN, and ²J_HαC′. Comparison with ¹J and ²J data from reference proteins and pattern analysis on a per‐residue basis permitted main‐chain φ,ψ torsion‐angle combinations of many of the 149 amino‐acid residues in ERp18 to be narrowed to particular secondary‐structure motifs. J‐coupling indexing is here being developed on statistical criteria and used to devise a ternary grid for interpreting patterns of relative values of J. To account for the influence of the varying substituent pattern in different amino‐acid sidechains, a table of residue‐type specific threshold values was compiled for discriminating small, medium, and large categories of J. For the 15‐residue insertion that distinguishes the ERp18 fold from that of thioredoxin, the J‐coupling data hint at a succession of five isolated Type‐I β turns at progressively shorter sequence intervals, in agreement with the crystal structure. Proteins 2011. © 2010 Wiley‐Liss, Inc.     

Male rats with the testicular feminization mutation of the androgen receptor display elevated anxiety-related behavior and corticosterone response to mild stress

Testosterone influences the hypothalamic–pituitary–adrenal axis, anxiety-related behavior, and sensorimotor gating in rodents, but little is known about the role of the androgen receptor (AR) in mediating these influences. We compared levels of the stress hormone corticosterone at baseline and following exposure to a novel object in an open field in wild type (wt) male and female rats, and male rats with the testicular feminization mutation (Tfm) of the AR, which disables its function. Basal corticosterone was equivalent in all groups, but exposure to a novel object in an open field elicited a greater increase in corticosterone in Tfm males and wt females than in wt males. Tfm males also showed increased behavioral indices of anxiety compared to wt males and females in the test. Analysis of the immediate early gene c-Fos expression after exposure to a novel object revealed greater activation in Tfm males than wt males in some regions (medial preoptic area) and lesser activation in others (dentate gyrus, posterodorsal medial amygdala). No differences were found in a measure of sensorimotor gating (prepulse inhibition of the acoustic startle response), although Tfm males had an increased acoustic startle response compared to wt males and females. These findings demonstrate that ARs play a role in regulating anxiety-related behaviors, as well as corticosterone responses and neural activation following exposure to a mild stressor in rats.     

Food availability during migratory stopover affects testis growth and reproductive behaviour in a migratory passerine

Long-distance migratory passerines initiate testicular recrudescence during spring migration to meet the demands of timely reproduction upon immediate arrival on the breeding grounds. The degree of testicular development is known to depend on environmental factors like stopover habitat quality; reproductive performance may be strongly impacted by testicular maturation upon arrival on the breeding grounds. We investigated the effect of stopover food availability on subsequent reproductive performance in garden warblers (Sylvia borin). Spring migration was simulated by repeated food deprivation and re-feeding to imitate the alternation of flight and stopover periods. During the two final stopover periods, males were either kept under ad libitum food (ad libitum males) or under limited food conditions (limited males). After simulated arrival in the breeding area, manipulation of previous stopover food availability resulted in significantly slower testicular recrudescence (p < 0.001) and decreased plasma testosterone (p < 0.01) in limited males compared to ad libitum males. Body mass change was not significantly different between the two groups (p = 0.38). Limited males also exhibited reduced performance in reproductive behaviours employed in territorial and sexual contexts. Limited males had a longer ‘freezing’ interval (p < 0.05) and decreased activity (p < 0.01) when challenged with a live male decoy. In direct confrontation between limited and ad libitum males in the presence of a female, limited males exhibited significantly fewer behavioural traits in sexual context, i.e. directed to the female (p < 0.001). Therefore, we suggest that conditions encountered during previous migratory stopover may affect subsequent annual reproductive success by influencing key reproductive behaviours.