CoagVDb: a comprehensive database for coagulation factors and their associated SAPs

The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure–function relationship and disease genotype–phenotype correlation.

Electronic supplementary material

The online version of this article (doi:10.1186/s40659-015-0028-5) contains supplementary material, which is available to authorized users.     

Rural life, lower socioeconomic status and parasitic infections

This study was conducted both to assess the prevalence of parasitic infections in two neighboring villages of Manisa province in Turkey, with different socioeconomic levels and investigate the influences of some individual and environmental factors on these infections. A total of 100 school children were enrolled and their cellophane tape and stool samples were examined for parasites. Pediculus capitis infestation was diagnosed by visual inspection of the hair. Although the prevalences of both intestinal parasitosis and pediculosis were high in both villages, there was a statistically significant difference for pediculosis, but not for intestinal parasitosis. Lack of social security and father's regular job were found to be highly correlated with all parasitic infections. Pediculosis was more common in younger children, girls and those in crowded families. These results indicate not only the high prevalence of parasitic infections, but also the urgent need for the improvement of basic health services and infrastructure in the rural areas, crowded with poorer immigrant population.     

Evaluating germinability of eight desert halophytes under long-term seed storage: Implications for conservation

Ex situ conservation in seed banks is a potential complementary conservation strategy for native plant species.It is well established that ex situ seed banking of native wild plants prolongs seed viability and thereby preserves genetic and species diversity for future use.We evaluated ex situ storage potential of eight halophytic species from deserts in the United Arab Emirates(UAE)by studying seed germination.Specifically,we examined the germinability of freshly collected seeds and seeds stored for three years in a seed bank.We also examined the effect of light conditions on fresh and stored seed germination.Fresh seeds of seven of the eight species tested had a higher germination rates under 12/12 h light/dark fluctuations than did those exposed to total darkness.Storage reduced light sensitivity in Halocnemum strobilaceum,Suaeda aegyptiaca,Salsola drummondii and Salsola imbricata,but increased the requirement for light in Arthrocnemum macrostachyum.In Anabasis setifera,storage decreased germination percentage when there was a 12-hour light/dark fluctuation,but increased germination rate when exposed to the dark treatment.Storage significantly reduced germination in both the light/dark and dark treatments in Suaeda vermiculata and S.aegyptiaca.Germination speed also responded differently to storage;whereas Timson's index significantly increased in A.macrostachyum and H.strobilaceum,it significantly decreased for S.drummondii,S.aegyptiaca and S.vermiculata.Germination of these species at a range of temperatures requires further testing;additionally,we strongly suggest that these laboratory findings be complemented by field studies.     

In vitro and in vivo bio-assay of phytobiocidal effect of plant extracts on Alternaria solani causing agent of early blight disease in tomato

The efficacy of six locally available plants extract was evaluated for their phytobiocidal effect on Alternaria solani the causal agent of early blight (EB) disease of tomato and was compared with commercial fungicide mancozeb under in vitro and in vivo conditions. Under in vitro conditions, Eucalyptus globus and Datura alba were found to be ineffective, while the remaining plants extract (Allium sativum, Curcuma longa, Melia azedarach, Zingiber officinale) significantly reduced A. solani growth on PDA. Increasing concentrations of A. sativum (0–25%) were found negatively correlated with growth of A. solani on PDA. Among the tested plants, A. sativum extract at 20% concentration was found most effective against A. solani witnessed by both in vitro and in vivo experiments result. It reduced EB disease up to 75.11% over positive control. Similarly, among the different plants extract, maximum plant height (76.25 cm), fruit size (57.50 cm³) and yield (511.30 g) were observed in A. sativum sprayed treatments (20%), beside mancozeb and negative control. Upon phytochemical analysis of these extracts, flavonoids, alkaloids, saponins, tannins, terpenoids, glycosides and steroids were detected. Present study showed that 20% concentration of garlic extract has the potential to reduce EB disease severity, while having no noticeable phytotoxicity.     

Molecular dynamics-based analyses of the structural instability and secondary structure of the fibrinogen gamma chain protein with the D356V mutation

Mutations in the fibrinogen gamma chain (FGG) gene have been associated with various disorders, such as dysfibrinogenemia, thrombophilia, and hypofibrinogenemia. A literature survey showed that a residue exchange in fibrinogen Milano I from γ Asp to Val at position 330 impairs fibrin polymerization. The D356V (D330V) mutation located in the C-terminus was predicted to be highly deleterious and to affect the function of the protein. The pathogenicity of the altered gene and changes in protein functions were predicted using in silico methods, such as SIFT, PolyPhen 2, I-Mutant 3.0, Align GV–GD, PhD–SNP, and SNPs&GO. The secondary structure of the mutant protein was unwound by the end of the 50-ns simulation period, and a structural change in the helix-turn transition of the alpha-helical (352–356) region residues was observed. Moreover, a change in the length of the helical region was visualized in the mutant trajectory file, indicating the local transient unfolding of the protein. The obtained computational results suggest that the substitution of the neutral amino acid valine for the acidic amino acid aspartic acid at position 356 results in an unwound conformation within 50 ns, which might contribute to defective polymerization. Our analysis also provides insights into the effect of the conformational change in the D356V (D330V) mutant on protein structure and function.     

Effects of operating parameters on performances of nitrification and denitrification processes

Nitrification and denitrification of synthetic wastewater was studied by using two reactors in series. An activated sludge unit was used for nitrification followed by a downflow biofilter (packed column) for denitrification. A glucose solution was fed to the denitrification column to supply carbon source. Effects of important process variables such as sludge age, hydraulic residence time and feed ammonium concentration on system's performance were investigated. Effluent ammonium-nitrogen (NH4-N) concentration decreased with increasing sludge age and hydraulic residence time and remained constant for sludge age and hydraulic residence times greater than 12 d and 15 h, respectively. Feed ammonium-nitrogen concentration above 200 mg/l resulted in significant levels of NH4-N in the effluent at Š_c = 15 d and Š_H = 12 h in nitrification. Performance of denitrification stage was not satisfactory for feed NO₃-N concentrations above 150 mg N/l resulting in significant effluent NO₃-N levels at hydraulic residence time of Š_H = 6 h.