The thioredoxin gene family in rice: genome-wide identification and expression profiling under different biotic and abiotic treatments

Thioredoxin (TRX) is a multi-functional redox protein. Genome-wide survey and expression profiles of different stresses were observed. Conserved amino acid residues and phylogeny construction using the OsTRX conserved domain sequence suggest that the TRX gene family can be classified broadly into six subfamilies in rice. We compared potential gene birth-and-death events in the OsTRX genes. The Ka/Ks ratio is a measure to explore the mechanism and 3 evolutionary stages of the OsTRX genes divergence after duplication. We used 270 TRX genes from monocots and eudicots for synteny analysis. Furthermore, we investigated expression profiles of this gene family under 5 biotic and 3 abiotic stresses. Several genes were differentially expressed with high levels of expression and exhibited subfunctionalization and neofunctionalization after the duplication event response to different stresses, which provides novel reference for the cloning of the most promising candidate genes from OsTRX gene family for further functional analysis.     

Catalase and Lipid Peroxidation Values in Serum of Tunisian Patients with Pemphigus Vulgaris and Foliaceus

Pemphigus is an autoimmune disorder resulting from the interaction between autoantibodies and desmoglein. Oxidative stress seems to be responsible for the onset/aggravation of many human diseases. Actually, it is considered as one of the several factors for the etiopathogenesis of pemphigus. The present study aims to evaluate the oxidative state in the sera of pemphigus vulgaris and pemphigus foliaceus patients by assessing lipid peroxidation, proteins oxidation, and antioxidant enzyme activity. This study included 36 pemphigus vulgaris and 42 pemphigus foliaceus patients as well as a group of controls consisting of 78 healthy volunteers. Malondialdehyde levels (p?<?0.001) and catalase activity (p?<?0.001) are higher in both groups of patients than in the control group. The two groups of patients showed a nonsignificant decrease in the thiol groups compared with the healthy one. A nonsignificant difference was shown between pemphigus vulgaris and pemphigus foliaceus patients, except for the catalase which shows an increase in the pemphigus vulgaris group. We have also found significant correlations between serum oxidative stress marker levels and serum anti-desmoglein antibody levels in the two pemphigus groups. These findings underline the implication of oxidative stress in the physiopathology of pemphigus by the increase in the autoantibodies?? reactivity.     

Screening and structural evaluation of deleterious Non-Synonymous SNPs of ePHA2 gene involved in susceptibility to cataract formation

Age-related cataract is clinically and genetically heterogeneous disorder affecting the ocular lens, and the leading cause of vision loss and blindness worldwide. Here we screened nonsynonymous single nucleotide polymorphisms (nsSNPs) of a novel gene, EPHA2 responsible for age related cataracts. The SNPs were retrieved from dbSNP. Using I-Mutant, protein stability change was calculated. The potentially functional nsSNPs and their effect on protein was predicted by PolyPhen and SIFT respectively. FASTSNP was used for functional analysis and estimation of risk score. The functional impact on the EPHA2 protein was evaluated by using SWISSPDB viewer and NOMAD-Ref server. Our analysis revealed 16 SNPs as nonsynonymous out of which 6 nsSNPs, namely rs11543934, rs2291806, rs1058371, rs1058370, rs79100278 and rs113882203 were found to be least stable by I-Mutant 2.0 with DDG value of > -1.0. nsSNPs, namely rs35903225, rs2291806, rs1058372, rs1058370, rs79100278 and rs113882203 showed a highly deleterious tolerance index score of 0.00 by SIFT server. Four nsSNPs namely rs11543934, rs2291806, rs1058370 and rs113882203 were found to be probably damaging with PSIC score of ≥ 2. 0 by Polyp hen server. Three nsSNPs namely, rs11543934, rs2291806 and rs1058370 were found to be highly polymorphic with a risk score of 3-4 with a possible effect of Non-conservative change and splicing regulation by FASTSNP. The total energy and RMSD value was higher for the mutant-type structure compared to the native type structure. We concluded that the nsSNP namely rs2291806 as the potential functional polymorphic that is likely to have functional impact on the EPHA2 gene.     

Effect of Bavistin,Cotoran and Curacron on Egyptian soil fungi

Tests were conducted to determine the effects of the fungicide Bavistin (Carbendazim), the herbicide Cotoran (Fluometuron) and the insecticide Curacron on Egyptian soil fungi when applied at the recommended field dose, and four and eightfold field doses. Bavistin when added to the soil induced a regular significant inhibition of the total count of fungi by the 3 doses after 5 and 40 days and by the higher doses after 80 days. The response ofAspergillus to this fungicide was almost similar to that of the total count. Cotoran was of no significant effect on the total count of fungi after 2 days at all doses, but after 5 days the herbicide was significantly depressive at the medium and the high doses. After 80 days the effect changed into significant promotion at the field dose only. Curacron was significantly toxic to the total count of soil fungi, after the shorter and longer periods at the 3 doses.     

Effect of Bavistin,Cotoran and Curacron on Egyptian soil fungi

Tests were conducted to determine the effects of the fungicide Bavistin (Carbendazim), the herbicide Cotoran (Fluometuron) and the insecticide Curacron on Egyptian soil fungi when applied at the recommended field dose, and four and eightfold field doses.Bavistin when added to the soil induced a regular significant inhibition of the total count of fungi by the 3 doses after 5 and 40 days and by the higher doses after 80 days. The response ofAspergillus to this fungicide was almost similar to that of the total count.Cotoran was of no significant effect on the total count of fungi after 2 days at all doses, but after 5 days the herbicide was significantly depressive at the medium and the high doses. After 80 days the effect changed into significant promotion at the field dose only.Curacron was significantly toxic to the total count of soil fungi, after the shorter and longer periods at the 3 doses.     

Optimizing coffee cultivation and its impact on economic growth and export earnings of the producing countries: The case of Saudi Arabia

Coffee is one of the historical socioeconomic crops. It has received an increasing attention at the global level, due to its positive interlinkage with the economic growth and on the gross domestic product for most of the producing countries, particularly, developing and least developed countries. Saudi Arabia is one of the coffee producing countries that has a relative comparative advantage of coffee cultivation. Yet, coffee cultivation has not received as much attention in Saudi Arabia as that of producing countries around the world. This study aims to assess the current state of coffee cultivation in Saudi Arabia and to investigate the potential to optimize coffee cultivation in Saudi Arabia that maximizes the net national economic return and export earnings, given limitation of cultivated areas, local market activities, and international trade activities. The study statistically analyzed primary data collected from around (65) coffee farms and traders in the study regions at the south and southwest Saudi Arabia, and optimized coffee cultivation in Saudi Arabia using LINGO optimization software. Empirical results of the study revealed the great potential of Saudi Arabia to expand coffee cultivation at south and southwest regions to meet the escalating local demand and to increase its share at the world market up to 2%. Optimization of coffee cultivation in Saudi Arabia showed a high potential to meet the local demand for coffee by producing 80.07 thousand tons grown over 2861.78 hectares and to generate a net return equivalent to $395.72 million a year, which is equivalent to $138.28 thousand per hectare and $4.94 thousand per ton of coffee. Optimizing coffee cultivation will play a substantial role to increase market share of Saudi Arabia to about 1–2% of the world market by increasing its export volume, respectively, to about 69.66 and 112.56 thousand tons, the national net economic return by about $395.86 and $395.95 million a year, and the export earnings of coffee by about $219.43–354.57 million a year, which in turns, will serve the national strategic trend to diversify the economic base and lower the dependency of incomes generated from oil exportation.     

Antimicrobial activity of some plant extracts against bacterial strains causing food poisoning diseases

Prevention of food spoilage and food poisoning pathogens is usually achieved by use of chemical preservatives which have negative impacts including: human health hazards of the chemical applications, chemical residues in food & feed chains and acquisition of microbial resistance to the used chemicals. Because of such concerns, the necessity to find a potentially effective, healthy safer and natural alternative preservatives is increased. Within these texts, Plant extracts have been used to control food poisoning diseases and preserve foodstuff. Antimicrobial activity of five plant extracts were investigated against Bacillus cereus, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Salmonella typhi using agar disc diffusion technique. Ethanolic extracts of Punica granatum, Syzygium aromaticum, Zingiber officinales and Thymus vulgaris were potentially effective with variable efficiency against the tested bacterial strains at concentration of 10 mg/ml while extract of Cuminum cyminum was only effective against S. aureus respectively. P. granatum and S. aromaticum ethanolic extracts were the most effective plant extracts and showed bacteriostatic and bactericidal activities against the highly susceptible strains of food borne pathogenic bacteria (S. aureus and P. aeruginosa) with MIC's ranged from 2.5 to 5.0 mg/ml and MBC of 5.0 and 10 mg/ml except P. aeruginosa which was less sensitive and its MBC reached to 12.5 mg/ml of S. aromaticum respectively. These plant extracts which proved to be potentially effective can be used as natural alternative preventives to control food poisoning diseases and preserve food stuff avoiding healthy hazards of chemically antimicrobial agent applications.     

Turner syndrome female with a small ring X chromosome lacking the XIST, an unexpectedly mild phenotype and an atypical association with alopecia universalis

Rearranged X chromosome in Turner syndrome (TS) are generally well tolerated but in cases of ring X chromosomes and of X/autosome translocations the incidence of mental retardation and other congenital abnormalities can be significantly higher. These abnormal phenotypes can be ascribed to failed or partial X inactivation. Here, we report a 10-year-old female who was referred for a cytogenetic analysis because she developed an alopecia universalis. The patient, of normal intelligence, had been found to have traits of TS, especially short stature. A first cytogenetic analysis showed a no mosaic 45,X karyotype. Since, the risk of developing gonadoblastoma in TS patients with mosaicism for a Y derivative chromosome and because association of alopecia universalis and TS is uncommon, fluorescence in situ hybridization (FISH) was performed to search for a second cell population. Our patient was found to have a mosaic 45,X/46,X,+r. FISH analysis using sex chromosome probes permitted us to identify the very small marker as a ring X chromosome, detected in 90% of cells. The ring appeared to be formed almost totally of alphoid sequences with breakpoints in the juxtacentromeric region. The r(X) does not include the XIST locus and may, therefore, not be subject to X-inactivation. Unexpectedly mild phenotype in our patient and its association with alopecia universalis will be discussed.     

BACTIBASE second release: a database and tool platform for bacteriocin characterization

Background  

BACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins.     

Monocyte-derived dendritic cells induce a house dust mite-specific Th2 allergic inflammation in the lung of humanized SCID mice: involvement of CCR7

In rodents, airway dendritic cells (DCs) capture inhaled Ag, undergo maturation, and migrate to the draining mediastinal lymph nodes (MLN) to initiate the Ag-specific T cell response. However, the role of human DCs in the pathogenesis of the Th2 cell-mediated disease asthma remains to be clarified. Here, by using SCID mice engrafted with T cells from either house dust mite (HDM)-allergic patients or healthy donors, we show that DCs pulsed with Der p 1, one of the major allergens of HDM, and injected intratracheally into naive animals migrated into the MLN. In the MLN, Der p 1-pulsed DCs from allergic patients induced the proliferation of IL-4-producing CD4(+) T cells, whereas those from healthy donors induced IFN-gamma-secreting cells. In reconstituted human PBMC-reconstituted SCID mice primed with pulsed DCs from allergic patients, repeated exposure to aerosols of HDM induced 1) a strong pulmonary inflammatory reaction rich in T cells and eosinophils, 2) an increase in IL-4 and IL-5 production in the lung lavage fluid, and 3) increased IgE production compared with that in mice primed with unpulsed DCs. All these effects were reduced following in vivo neutralization of the CCR7 ligand secondary lymphoid tissue chemokine. These data in human PBMC-reconstituted SCID mice show that monocyte-derived DCs might play a key role in the pathogenesis of the pulmonary allergic response by inducing Th2 effector function following migration to the MLN.