The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths andweaknesses that need to be highlighted.We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.

Lower limb and associated injuries in frontal-impact road traffic collisions.

Objectives: To study the relationship between severity of injury of the lower limb and severity of injury of the head, thoracic, and abdominal regions in frontal-impact road traffic collisions. Methods: Consecutive hospitalised trauma patients who were involved in a frontal road traffic collision were prospectively studied over 18 months. Patients with at least one Abbreviated Injury Scale (AIS) ≥3 or AIS 2 injuries within two AIS body regions were included. Patients were divided into two groups depending on the severity of injury to the head, chest or abdomen. Low severity group had an AIS < 2 and high severity group had an AIS ≥ 2. Backward likelihood logistic regression models were used to define significant factors affecting the severity of head, chest or abdominal injuries. Results: Eighty-five patients were studied. The backward likelihood logistic regression model defining independent factors affecting severity of head injuries was highly significant (p=0.01, nagelkerke r square = 0.1) severity of lower limb injuries was the only significant factor (p=0.013) having a negative correlation with head injury (Odds ratio of 0.64 (95% CI: 0.45-0.91). Conclusion: Occupants who sustain a greater severity of injury to the lower limb in a frontal-impact collision are likely to be spared from a greater severity of head injury.

Early and late effects of Ibuprofen on mouse sperm parameters, chromatin condensation, and DNA integrity in mice

Background: There are few studies indicating the detrimental effects of ibuprofen on sperm fertility potential and DNA integrity. Objective: To determine the effects of Ibuprofen on sperm parameters, chromatin condensation and DNA integrity of mice. Materials and Methods: In this experimental study, 36 adult male mice with average weight 37 gr were divided into three groups, including control (group I, n=12), normal dosage of ibuprofen (group II, n=12) and high dosage (group III, n=12). Ibuprofen with different doses was dissolved in daily water of animals. After 35, 70 and 105 days, the cauda epididymis of mice were cut and incubated in Ham’s F10 media. Sperm samples were analyzed for parameters (motility, morphology and count), DNA integrity (SCD test) and chromatin condensation (chromomycin A3 and Aniline blue staining). Results: After 35 days, in addition to above mentioned sperm parameters, all of the treated mice showed statistically significant increase in spermatozoa with immature chromatin (P<0.05). However, after 70 days, the rate of sperm DNA fragmentation assessed by SCD was increased in group II (66.5±0.7) and the percentage of immature spermatozoa (AB+ and CMA3+) was higher in group III (77.5±0.7 and 49.5±6.3 respectively) than other groups. After 105 days, the AB+ spermatozoa were increased in both normal dose and high dose groups. Conclusion: Ibuprofen may cause a significant reduction in sperm parameters and sperm chromatin/DNA integrity in mice. It should be noted that these deleterious effects are dose-dependent and can be seen in early and late stage of drug treatments.