CentiServer: A Comprehensive Resource,Web-Based Application and R Package for Centrality Analysis

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/     

Highly Heterogeneous Probiotic Lactobacillus Species in Healthy Iranians with Low Functional Activities

Background

Lactic acid bacteria (LAB) have been considered as potentially probiotic organisms due to their potential human health properties. This study aimed to evaluate both in vitro and in vivo, the potential probiotic properties of Lactobacillus species isolated from fecal samples of healthy humans in Iran.

Methods and Results

A total of 470 LAB were initially isolated from 53 healthy individual and characterized to species level. Of these, 88 (86%) were Lactobacillus species. Biochemical and genetic fingerprinting with Phene-Plate system (PhP-LB) and RAPD-PCR showed that the isolates were highly diverse consisted of 67(76.1%) and 75 (85.2%) single types (STs) and a diversity indices of 0.994 and 0.997, respectively. These strains were tested for production of adhesion to Caco-2 cells, antibacterial activity, production of B12, anti-proliferative effect and interleukin-8 induction on gut epithelial cell lines and antibiotic resistance against 9 commonly used antibiotics. Strains showing the characteristics consistent with probiotic strains, were further tested for their anti-inflammatory effect in mouse colitis model. Only one L. brevis; one L. rhamnosus and two L. plantarum were shown to have significant probiotic properties. These strains showed shortening the length of colon compared to dextran sulfate sodium and disease activity index (DAI) was also significantly reduced in mouse.

Conclusion

Low number of LAB with potential probiotic activity as well as high diversity of lactobacilli species was evident in Iranian population. It also suggest that specific strains of L. plantarum, L. brevis and L. rhamnosus with anti-inflammatory effect in mouse model of colitis could be used as a potential probiotic candidate in inflammatory bowel disease to decrease the disease activity index.     

Compatibility and interaction between Bacillus thuringiensis and certain insecticides: perspective in management of Tuta absoluta (Lepidoptera: Gelechiidae)

Bacillus thuringiensis var. kurstaki (Berliner) (Bt) has been suggested as a biological control agent for Tuta absoluta (Meyrick). The objective of this study was to determine the interaction between abamectin, azadirachtin, indoxacarb, chlorantraniliprole, dichlorvos and metaflumizone with Bt. Effect of recommended doses of the chemical insecticides on colonisation of Bt was also investigated in culture medium. Except for metaflumizone, none of the chemicals tested reduced the colonisation of Bt compared with control. Interaction between Bt and the chemical insecticides on 2nd-instar larvae was also assessed. In interaction tests, Bt was applied at LC₅₀ level, 0, 12, 24 or 36 h after treating the larvae with LC₁₀ or LC₂₅ of the chemical insecticides. An antagonistic effect was observed in all treatments where Bt was applied immediately after the chemical insecticide. Also, antagonism was observed when treatment with Bt was done 12 h after azadirachtin and metaflumizone applications. Applying Bt 12 and 24 h after treatment with LC₂₅ of chlorantraniliprole, dichlorvos and abamectin resulted in synergism. But, synergism with LC₁₀ of dichlorvos and abamectin was observed only after 12 h. Additive effect was observed in the rest of the time and concentration combinations. Based on the results obtained, simultaneous use of the chemical insecticides tested and Bt is not recommended for T. absoluta control; and an appropriate time interval should be taken into consideration accordingly.     

Demystifying computer science for molecular ecologists

In this age of data‐driven science and high‐throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long‐standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373–389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context‐specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade‐offs that are not obvious to the uninitiated.     

Fatty acid composition,antioxidant and antibacterial properties of the microwave aqueous extract of three varieties of Labisia pumila Benth

Background

The present study was conducted in order to evaluate the fatty acid profile, anti-oxidant and anti-bacterial activities from the microwave aqueous extract of the leaves of three different varieties of Labisia pumila Benth.

Results

The chemical analysis of the extract showed that fatty acids (palmitic, palmitoleic, stearic, oleic, linoleic and α-linolenic) acid as the main components in three varieties of L. pumila leaves. Furthermore, the obtained results of the anti-oxidant revealed that L. pumila var. alata contained higher anti-oxidative activities compared to var. pumila and var. lanceolata. However, these values were lower than the tested anti-oxidant standards. On the other hand, the aqueous leaf extracts in all three varieties of L. pumila were also found to inhibit a variable degree of antibacterial activities against eight bacteria (four Gram-positive and four Gram-negative bacteria).

Conclusions

In this study, it was observed the leaves of three varieties of L. pumila exhibited variable patterns of fatty acids and the microwave aqueous extraction possess anti-oxidant and anti-bacterial activities.     

The association between two genetic polymorphisms in ITGB3 and increase risk of venous thromboembolism in cancer patients in Eastern Province of Saudi Arabia

Venous thromboembolism (VTE) is one of the major complications in most cancer patients leading to poor prognosis and short survival. Several common clinical risk factors coexist in cancer patients are used as risk predictive biomarkers to help in the management and prevention of VTE. These include cancer site and stage, chemotherapy regimen and elevated biological markers. However, Genetic polymorphisms in genes controlling coagulation and fibrinolysis are significantly associated with VTE if detected, then they might be more sensitive individual predictive biomarkers for VTE risk assessment. This study was conducted to evaluate the association between ITGB3 rs3809865 and rs5918 with VTE risk as well as monitor the effect of VTE on overall survival of these cancer patients. In this retrospective case-control study, 195 cancer patients’ formalin-fixed paraffin embedded tissue (FFPE) samples were collected (controls n = 157, case n = 38) using the stored data through Jan 2010 to Sep 2018 from King Fahad Specialist Hospital in Dammam. Samples were genotyped using TaqMan genotyping assay, then logistic regression analysis and Chi-square were used to predict the association between risk factors and VTE. Survival Comparison was tested by the log-rank test. Genetic polymorphisms in ITGB3 (rs3809865 and rs5918) found not to be associated with VTE increasing risk in cancer patients (p>0.05). While the advanced stage was potentially increasing the risk of VTE events (OR 5.1 CI 2.01–12.9p = 0.001). Patients with VTE showed a poor overall survival reflected by the median survival rate of only three years compared to seven years for cancer patients without VTE. This study highlighted the potential influence of VTE on prognosis and survival of cancer patients and raised the importance of exploring risk predictive biomarkers in our population. This will improve the risk prediction biomarkers leading to implementing safe and effective thrombosis prophylaxis strategies.     

Male infertility is not liked with HSF1, HSF2 and UBE2I gene polymorphisms among Indian subjects

We analysed the polymorphisms at rs78202224 (C/A) for HSF1 gene, rs139496713 (C/T) and rs45504694 (C/A) for HSF2 gene and rs116868327 (G/A) for UBE2I gene in 547 infertile cases (non-obstructive azoospermia = 464, asthenozoospermia = 83) and 419 proven fertile controls of similar age group and ethnicity. SNP genotyping was done using AgenaMassARRY platform (Agena Bioscience, CA). Common, heterozygous, rare genotypes and allelic frequencies were analysed using dominant, recessive and co-dominant models. Data shows no significant association between HSF1, HSF2 polymorphisms and male infertility. However, under dominant (GG vs GA+AA) and co-dominanat (GG vs GA) model, polymorphism at the rs116868327 (G/A) locus in UBE2I gene was found to be linked with asthenozoospermia in males with a significant odd-ratio of 6.91 (confidence interval at 95% was 1.52-31.46; p=0.017). Moreover, frequency of rare allele was higher (2.4%) compared to controls (0.4%). Thus, this data showed a significant risk of developing asthenozoospermic condition in males (Odds ratio= 6.75; Confidence interval at 95%= 1.50-30.49; P= 0.018]. Hence, more number of genotyping studies along with the functional assay in multiple cohorts is needed to validate potential variants associated with male infertility.     

Rejuvenation of Sequoia sempervirens by Repeated Grafting of Shoot Tips onto Juvenile Rootstocks in Vitro: Model for Phase Reversal of Trees

Repeated grafting of 1.5-centimeter long shoot tips from an adult Sequoia sempervirens tree onto fresh, rooted juvenile stem cuttings in vitro resulted in progressive restoration of juvenile traits. After four successive grafts, stem cuttings of previously adult shoots rooted as well, branched as profusely, and grew with as much or more vigor as those of seedling shoots. Reassays disclosed retention for 3 years of rooting competence at similar levels as originally restored. Adventitious shoot formation was remanifested and callus development was depressed in stem segments from the repeatedly grafted adult. The reversion was associated with appearance and disappearance of distinctive leaf proteins. Neither gibberellic acid nor N⁶-beneyladenine as nutrient supplements duplicated the graft effects.     

Cell-mediated cytotoxicity can be regulated by p53 tumor suppressor gene activity in vitro

Summary— The wild-type human p53 tumor suppressor gene was tested for its ability to modulate cytotoxic activity of in vitro activated peripheral blood lymphocytes. Peripheral blood mononuclear cells (PBMCs) were stimulated by phytohemagglutinin (PHA), interferon α2b (IFNα2b), interleukin 2 (IL-2) or their combinations to induce cytotoxicity. This stimulation significantly increased the percentage of cells expressing p53, which was at its maximum when induced by IL-2 combined with IFNα2b. The role of p53 in the modulation of different aspects of cytotoxic activity of these cells was analyzed by studying the effects of p53 abrogation by antisense oligonucleotide (p53 AS) treatment in comparison with p53 sense or scrambled (missense) oligonucleotide (p53 S or p53 MS) treatment. We show that p53 plays a key role through induction of apoptosis in target cells (tumor necrosis factor pathway) rather than through osmolytic degeneration (perforin pathway) which is only slightly increased by p53 abrogation. Meanwhile, in vitro abrogation of p53 expression in PBL was found to be accompanied by an increase of CD8+ lymphocytes and an important increase of the CD56 ‘bright’ NK cell sub-population.