Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method

The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in three‐dimensional space and characterizes it by curvature κ and torsion τ as a function of arc length s, was applied on 77 proteins to determine all secondary structural units via specific κ(s) and τ(s) patterns. A total of 533 α‐helices and 644 β‐strands were recognized by APSA, whereas DSSP gives 536 and 651 units, respectively. Kinks and distortions were quantified and the boundaries (entry and exit) of secondary structures were classified. Similarity between proteins can be easily quantified using APSA, as was demonstrated for the roll architecture of proteins ubiquitin and spinach ferridoxin. A twenty‐by‐twenty comparison of all α domains showed that the curvature‐torsion patterns generated by APSA provide an accurate and meaningful similarity measurement for secondary, super secondary, and tertiary protein structure. APSA is shown to accurately reflect the conformation of the backbone effectively reducing three‐dimensional structure information to two‐dimensional representations that are easy to interpret and understand. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Impact of fine or large needle aspiration on the dog's testis: in vitro ultrasonographic, bacteriological, gross anatomy and histological assessment

Despite its extensive use for evaluation of spermatogenesis and assisted reproduction, the safety and consequences of fine (FNA) and large needle aspiration (LNA) to the testicular parenchyma and its normal function have not been established. This study was performed in order to accurately assess, by serial in vitro ultrasonographic, bacteriologic, gross anatomic and histological examinations, the type and extent of the effect of FNA or LNA on the dog's testis. Twenty three sexually mature, 1 to 2 years old, healthy laboratory Beagles were randomly assigned to 2 groups: (1) 5 dogs without testicular aspiration (control group) and (2) 18 dogs in which one of their testes was aspirated using a 23 G butterfly needle and the other using a 19 G butterfly needle (experimental group). Two dogs at a time were castrated 10 minutes, 60 minutes, 2, 14, 29, 63, 76, 90 or 180 days post-aspiration. The control group was also castrated 2, 29, 63, 90 or 180 days after the beginning of the experiment. Following castration, in vitro ultrasonographic, gross anatomic, cytological examinations of epididymal sperm, bacteriologic and histological examinations of the testes were performed. Following testicular FNA and LNA bacteriologic, gross anatomic, histologic, epididymal sperm findings and the in vitro ultrasonographic appearance of the testis were normal, except of intratesticular haemorrhage, detected the first days post-aspiration, and degeneration of less than 1.5% of the seminiferous tubules. Within the parameters of this experiment, testicular FNA and LNA have no ill effect on the canine testis and therefore, both FNA and LNA should be considered safe.     

Restoration of spermatogenesis after transplantation of c-Kit positive testicular cells in the fowl

Transplantation of male germ line cells into sterilized recipients has been used in mammals for conventional breeding as well as for transgenesis. We have previously adapted this approach for the domestic chicken and we present now an improvement of the germ cell transplantation technique by using an enriched subpopulation of c-Kit-positive spermatogonia as donor cells. Dispersed c-Kit positive testicular cells from 16 to 17 week-old pubertal donors were transplanted by injection directly into the testes of recipient males sterilized by repeated gamma irradiation. We describe the repopulation of the recipient's testes with c-Kit positive donor testicular cells, which resulted in the production of functional heterologous spermatozoa.Using manual semen collection, the first sperm production in the recipient males was observed about nine weeks after the transplantation. The full reproduction cycle was accomplished by artificial insemination of hens and hatching of chickens.     

Long term testicular ischemia-reperfusion injury-induced apoptosis: Involvement of survivin down-regulation

Testicular torsion is associated with damage to the testicular tissue as a result of ischemia-reperfusion injury (IRI) and induction of apoptosis leading to progressive damage to spermatogenesis. Survivin is suggested to be an important regulator in the control of the mitochondrial apoptotic pathway, although its role in torsion-induced IRI is unknown. Therefore, we sought to evaluate testicular survivin expression after long term IRI induced by testicular torsion. Survivin expression was measured by real-time PCR in 6-12 month old New Zealand white rabbits divided into three groups (4 animals/group): group (A) sham control, group (B) ischemia alone for 60 min and group (C) ischemia for 60 min followed by reperfusion for 6 months. Germ cell apoptosis was evaluated by TUNEL assay, Bax/Bcl-2 ratio and DNA fragmentation. The Johnsen score was used to assess testicular morphological damage, while lipid peroxidation was used as an indicator for oxidative stress. Survivin expression was detected in all testicular tissue samples. The rate of survivin expression after IRI was significantly higher (p < 0.05) compared with ischemic only and sham control testes. Its expression in IRI samples was inversely correlated with the significant increase (p < 0.05) in apoptosis, oxidative levels and spermatogenic damage. In conclusion, down-regulation of testicular survivin expression after long term IRI to the testis and its association with apoptosis induction suggests its involvement in the regulation of this apoptotic pathway. These findings also identify survivin as a potential new target for the prevention of germ cell death during testicular torsion.     

Testicular atrophy, zinc concentration, and angiotensin-converting enzyme activity in the testes of vitamin a-deficient rats

Angiotensin-converting enzyme (ACE) as a part of the renin angiotensin system (RES) regulates blood pressure and fluid and electrolyte homeostasis, and the enzyme is considered to have a function in reproduction. Reduced enzyme activities have been observed in atrophied testes as a results of zinc and pituitary deficiencies. Vitamin A deficiency causes atrophy of testes. The present study was conducted on three groups of male, 3-wk-old, Wistar rats. After 54 d of the experimental period, testicular weights of the vitamin A-deficient rats (Agroup, allowed free access to vitamin Adeficient diet) was significantly lower than its pair-fed, PF (given restricted amount control diet) and A+ (allowed free access to control diet) groups. Zinc concentrations and both soluble and particulate ACE activities in the testes of vitamin A-deficient rats (Agroup) were significantly lower than the other two groups. No significant differences were observed regarding zinc concentration, particulate ACE, and total ACE activities in the testes of PF and A+ groups. Vitamin A deficiency did not significantly affect the enzyme activity in the lung. From the observations of the present study, we speculate that testicular atrophy in vitamin A deficiency may have resulted from lower zinc concentration and decreased ACE activity in that organ.     

Potential energy functions: from consistent force fields to spectroscopically determined polarizable force fields

We review our methodology for producing physically accurate potential energy functions, particularly relevant in the context of Lifson's goal of including frequency agreement as one of the criteria of a self-consistent force field. Our spectroscopically determined force field (SDFF) procedure guarantees such agreement by imposing it as an initial constraint on parameter optimization, and accomplishes this by an analytical transformation of ab initio "data" into the energy function format. After describing the elements of the SDFF protocol, we indicate its implementation to date and then discuss recent advances in our representation of the force field, in particular those required to produce an SDFF for the peptide group.     

Tightly winding structure of sequential model peptide for repeated helical region in Samia cynthia ricini silk fibroin studied with solid-state NMR

There are many kinds of silks from silkworms and spiders with different structures and properties, and thus, silks are suitable to study the structure-property relationship of fibrous proteins. Silk fibroin from a wild silkworm, Samia cynthia ricini, mainly consists of the repeated similar sequences by about 100 times where there are alternative appearances of the polyalanine (Ala)(12-13) region and the Gly-rich region. In this paper, a sequential model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical sequence of the silk fibroin, was synthesized, and the atomic-level conformations of Gly residues at the N- and C-terminal ends of the polyalanine region were determined as well as that of the central Ala residue using (13)C 2D spin diffusion solid-state nuclear magnetic resonance (NMR) under off-magic angle spinning. In the model peptide with alpha-helical conformation, the torsion angle of the central Ala residue, the 19th Ala, was determined to be (phi, psi) = (-60 degrees, -50 degrees ), which was a typical alpha-helical structure, but the torsion angles of two Gly residues, the 12th and 25th Gly residues, which are located at the N- and C-terminal ends of the polyalanine region, were determined to be (phi, psi) = (-70 degrees, -30 degrees ) and (phi, psi) = (-70 degrees, -20 degrees ), respectively. Thus, it was observed that the turns at both ends of polyalanine with alpha-helix conformation in the model peptide are tightly wound.     

Functional significance of cortical bone distribution in anthropoid mandibles: an in vitro assessment of bone strain under combined loads

Local variation in cortical bone thickness in the postcanine mandibular corpus appears to be stereotypical among anthropoids. Specifically, at sections under the molars, lingually situated cortical bone is typically thinner than that along the lateral aspect. This pattern applies despite phylogenetic, dietary, and allometric differences among the anthropoids sampled to date. Demes et al. (Food Acquisition and Processing in Primates [1984] New York: Plenum Press, p. 369-390) employed a theoretical analysis of mastication in Gorilla and Homo to argue that this pattern could be explained with reference to biomechanical stresses. Specifically, they proposed that the combined effects of torsion and direct shear on the working-side corpus create a condition in which net stresses and strains are reduced along the lingual cortical plate. Demonstration of this effect would suggest a functional linkage between localized differences in bone mass and strain gradients in the facial skeleton. We conducted an empirical evaluation of the effects of the combined loads of torsion and direct shear in vitro on a sample of formalin-fixed human mandibles. Rosette strain gages were affixed to the lateral and medial aspects of the corpus in each specimen, and surface strains were recorded separately under controlled torsional and occlusal loads, and under simultaneous application of these loads. The hypothesis that lingual strains are reduced under combined twisting and occlusal loads was generally supported; however, we observed reduction in surface strains at some sites along the lateral aspect of the corpus under these combined loads as well. These unexpected findings are attributable to unanticipated loading conditions imposed by occlusal forces, which result from sources of stress in addition to direct shear. These experiments provide provisional support for the hypothesis that superposed sources of bone strain produce large strain gradients between buccal and lingual aspects of the mandibular corpus, and that local variation in bone mass may be associated with these gradients.     

Comparison of urinary creatine with other biomarkers for detection of cadmium induced testicular damage

In this study, biomarkers of testicular damage were compared. In particular, urinary creatine was evaluated as a non-invasive marker of damage. Male rats were exposed to various doses of cadmium chloride, an established testicular toxicant. Pathological damage, testes weights, urinary creatine and creatinine, serum LDH-C4 and serum testosterone were determined. Cadmium chloride caused dose-dependent damage to the testes undetectable at the lowest dose (0.75 mg kg-1) but apparent at a dose of 1.125 mg kg-1. Urinary creatine was significantly raised after doses of 1.125 mg kg-1 and above 24-48 hr after dosing, and at the highest dose within 24 hr after dosing. Testes weight and serum testosterone were significantly decreased, and LDH-C4 significantly increased, at the highest dose (3.0 mg kg-l). Therefore urinary creatine was the most sensitive marker of acute cadmium-induced testicular damage and dysfunction.