Cost-Effective Production and Optimization of Alkaline Xylanase by Indigenous Bacillus mojavensis AG137 Fermented on Agricultural Waste

A xylanase producer Bacillus mojavensis strain, called AG137, isolated from cotton farm (Kashan-Iran). The optimal xylanase activity reached at 55°C & pH 9.0. Enzyme yield was studied using a medium with different agricultural wastes as inducers. Xylanase production of about 249.308 IU/mL was achieved at pH 8 and 37°C, within 48 h submerged fermentation in enzyme production medium supplemented with 2% (w/v) oat bran as an optimum carbon source. A mixture of 1% (w/v) yeast extract and 1% (w/v) tryptone as optimum nitrogen sources, agitation speed 200 rpm, and inoculum size 2% (v/v) were the optimums for maximum production. Accordingly, xylanase yield from 194.68 IU/mL under non-optimized fermentation condition enhanced to 302.466 IU/mL in optimized condition. Screened xylanase is thermostable, presenting 70% stability at 60°C during 30 min. Further enzyme incubation in higher temperature caused a decrease in the residual enzyme activity, yet it retained 68%–50% of its activity after 1 hour from 45°C to 55°C. Besides, it is stable in pH 9 and 10, maintaining over 70% of its activity for 2 h. The enzyme also could preserve 71% and 63% of its initial activity after 3 hours of pre-incubation in the same alkaline condition. Produced xylanase therefore was introduced as an alkaline-active and stable one, displaying suitable thermostability feature, confirmed by HPLC analysis. Hence, all xylanase properties highlight its promising uses in industrial scale

Cancer driver gene detection in transcriptional regulatory networks using the structure analysis of weighted regulatory interactions

Identification of genes that initiate cell anomalies and cause cancer in humans is among the important fields in the oncology researches. The mutation and development of anomalies in these genes are then transferred to other genes in the cell and therefore disrupt the normal functionality of the cell. These genes are known as cancer driver genes (CDGs). Various methods have been proposed for predicting CDGs, most of which based on genomic data and based on computational methods. Therefore, some researchers have developed novel bioinformatics approaches. In this study, we propose an algorithm, which is able to calculate the effectiveness and strength of each gene and rank them by using the gene regulatory networks and the stochastic analysis of regulatory linking structures between genes. To do so, firstly we constructed the regulatory network using gene expression data and the list of regulatory interactions. Then, using biological and topological features of the network, we weighted the regulatory interactions. After that, the obtained regulatory interactions weight was used in interaction structure analysis process. Interaction analysis was achieved using two separate Markov chains on the bipartite graph obtained from the main graph of the gene network. To do so, the stochastic approach for link-structure analysis has been implemented. The proposed algorithm categorizes higher-ranked genes as driver genes. The efficiency of the proposed algorithm, regarding the F-measure value and number of identified driver genes, was compared with 23 other computational and network-based methods

The innate immune response during acute urinary tract infections; an overview

The components of immune system are specific (adaptive immunity) and non-specific (innate immunity). Regardless of antigenic properties, the non-specific components function either as eliminators or barriers of wide range of pathogens. A person is born with innate immunity as the natural resistances, which has three kinds; anatomic mechanical and biochemical factors. The resistances are provided by innate immunity via various chemical, cellular and physical approaches. The colonization, entry and spread of microorganisms can be prevented by innate immunity. Two main sub-divided types of adaptive immunity are humeral and cellular. Active immunity resulting from the development of antibodies in response to the presence of an antigen is a long-term and acquired immunity. This review article summarizes some important potential mechanisms in innate immune system. The host renal tract which has been investigated from many aspects of the pathogenesis of urinary tract infection (UTI) are still poorly defined and require a better understanding of the pathophysiology immune system

Production of Vitamins B3, B6 and B9 by Lactobacillus Isolated from Traditional Yogurt Samples from 3 Cities in Iran, Winter 2016

Background and Objective: B-group vitamins have important roles in many aspects of cellular metabolism and humans cannot synthesize them. So, they should be obtained from external resources. This project provides a new insight into assessing the production of vitamins B3, B6 and B9 by Lactobacillus, isolated from traditional yogurt samples from 3 different cities of Iran; Golpayegan, Sanandaj and Tehran (Damavand).Material and Methods: Following 72 h of anaerobic culture of the Lactic acid bacteria at 37°C in 5% CO2, some Lactobacillus species from traditional yogurt samples were isolated and characterized both morphologically and biochemically. Isolates were identified following 16S rRNA PCR-amplification and sequencing. Including Lactobacillus (L.) ozensis strain Gon2-7, L. acidophilus strain KU, L. helveticus strain D76, L. helveticus strain Dpc 4571, L. fermentum strain 1, L. rossiae strain DSM15814T, L. casei strain NCDO, L. delbrueckii strain ATCC 11842, L. crispatus strain MRS 54.4, L. delbrueckii strain SB3 and L. paracasei subsp. tolerans JCM1171 (T). The sequence of L. paracasei subsp. tolerans JCM1171 (T) was submitted to the NCBI. The ability to produce B-group vitamins was evaluated by high performance liquid chromatography. Lactobacillus strains and amount of vitamin B3, B6 and B9 production were analyzed by Analysis of Variance test.Results and Conclusion: Eleven isolates of Lactobacillus species from traditional yogurt samples were identified. Optimal conditions for Lactobacillus growth were pH 5-6 and temperatures 37-40°C. The isolates produced vitamins B3, B6 and B9. L. paracasei subsp. tolerance JCM 1171 (T) showed the highest amount of produced vitamins (p≤0.01) consist of vitamin B6 (1566.17 µg ml-1) and B9 (1279.72 µg ml-1). L. acidophilus strain KU showed the highest production of vitamin B3 (522.7 µg ml-1). L. fermentum produced the highest amount of vitamin B2. These strains are a natural and cost efficient source of vitamin. The Lactobacillus strains isolated in this research particularly, L. paracasei, could be applied in improving new fermented products, fortified with B-group vitamin that could be applied as substitution for enriching and supplementation with the controversial synthetic vitamins. Conflict of interest: The authors declare that there is no conflict of interest

Comparison of three primer pairs included: novel primers IS711, universal primers B4 - B5 and 16SrRNA in the diagnosis of human brucellosis in suspected patients in Iran

The genus Brucella is a worldwide distributed intracellular bacteria, which infects animals and human. Currently, this zoonosis has been diagnosed by microbiological and serological laboratory tests. Different PCR protocols with various primer pairs and different target genes have been published for the detection of Brucella, but only a few of these primers have been used in human samples. This study aimed to evaluate and compare the sensitivity and specificity of three primer pairs in the PCR technique, each of which separately amplifies three different regions in the Brucella genome, to determine which are more comfortable for the detecting of Brucella DNA in human clinical samples. 49 clinical serum samples were isolated from suspected patients in different cities in Iran from October 2017 to July 2018. The suspected patients with brucellosis-compatible symptoms were checked. These primers amplified 3 distinctive fragments in BCSP 31 gene (B4/B5), Designed IS711 primers, and a sequence of 16SrRNA of Brucella melitensis. The results showed that the B4/B5 primer pair had the highest sensitivity and specificity for the detection of both positive and negative samples (100%). The designed IS711 primer pair detected 94% of samples, whereas the 16SrRNA primer pair was the least sensitivity, being able to detect only 30.64% of samples. The specificity of 3 techniques was 100%. The B4/B5 primers were able to detect the smallest number of bacteria 0.05 CFU/reaction whereas IS711 was able to detect 2 CFU/reaction and 16SrRNA was able to detect 2×105 CFU/reaction. &nbsp

ICLab: A Global, Longitudinal Internet Censorship Measurement Platform

Researchers have studied Internet censorship for nearly as long as attempts to censor contents have taken place. Most studies have however been limited to a short period of time and/or a few countries; the few exceptions have traded off detail for breadth of coverage. Collecting enough data for a comprehensive, global, longitudinal perspective remains challenging. In this work, we present ICLab, an Internet measurement platform specialized for censorship research. It achieves a new balance between breadth of coverage and detail of measurements, by using commercial VPNs as vantage points distributed around the world. ICLab has been operated continuously since late 2016. It can currently detect DNS manipulation and TCP packet injection, and overt "block pages" however they are delivered. ICLab records and archives raw observations in detail, making retrospective analysis with new techniques possible. At every stage of processing, ICLab seeks to minimize false positives and manual validation. Within 53,906,532 measurements of individual web pages, collected by ICLab in 2017 and 2018, we observe blocking of 3,602 unique URLs in 60 countries. Using this data, we compare how different blocking techniques are deployed in different regions and/or against different types of content. Our longitudinal monitoring pinpoints changes in censorship in India and Turkey concurrent with political shifts, and our clustering techniques discover 48 previously unknown block pages. ICLab's broad and detailed measurements also expose other forms of network interference, such as surveillance and malware injection.Comment: To appear in Proceedings of the 41st IEEE Symposium on Security and Privacy (Oakland 2020). San Francisco, CA. May 202

An Integrated Model of Project Scheduling and Material Ordering: A Hybrid Simulated Annealing and Genetic Algorithm

This study aims to deal with a more realistic combined problem of project scheduling and material ordering. The goal is to minimize the total material holding and ordering costs by determining the starting time of activities along with material ordering schedules subject to some constraints. The problem is first mathematically modelled. Then a hybrid simulated annealing and genetic algorithm is proposed tosolve it. In addition, some experiments are designed and the Taguchi method is employed to both tune the parameters of the proposed algorithm and to evaluate its performance. The results of the performance analysis show the efficiency of the proposed methodology

Epidemiological, Clinical and Laboratory characteristics of acute disseminated encephalomyelitis in children: a retrospective study

We aimed to study the precipitating factors, demographic data, clinical and radiological manifestations, electroencephalography and laboratory findings, as well as association with infections, immunization and incidence of relapse of acute disseminated encephalomyelitis (ADEM) in children admitted to Mofid Children Hospital, Tehran, Iran from Mar 2013 to Mar 2016.Materials & MethodsA 3-yr retrospective review of 29 children with definite final diagnosis of ADEM in Mofid Hospital in Tehran, Iran was performed. The diagnosis was based on specified criteria, including a presumed acute demyelinating process with no history of unexplained neurological symptoms and at least one demyelinating lesion shown on magnetic resonance imaging without evidence of previous destructive white matter lesions.ResultsOverall, 29 children diagnosed as ADEM were studied in terms of demographic characteristics, clinical manifestations and laboratory findings in two groups according to their recurrence. The mean age of the patients with recurrence was less than those without it were. It was more common in females but the difference was not statistically meaningful. There was no relationship between the season of the first episode of the disease and the recurrence incidence. Moreover, the relationship between viral infections and recurrence was statistically non-meaningful. No relationship between the recurrence of ADEM and clinical manifestations, radiological and laboratory findings was found.ConclusionThe reason for high rate of recurrence in our patients may be related to the younger age of children in our study.

Thermoacidophilic bacteria isolated from Sarcheshmeh low-grade copper ore in chalcopyrite bioleaching from mineral tailing

This research has focused on isolating and identifying different thermoacidophilic bacteria from a Sarcheshmeh low-grade copper ore and evaluating their ability of copper bioleaching from the mineral tailing. After the isolation of the bacteria, molecular identification was carried out based on the 16S rRNA gene sequences and drawing the phylogenetic tree. Then, the effect of the pH, pulp density, and composition of the media on the copper bioleaching was determined using the identified bacteria. The isolated strain (Strain SCM1) belonged to Delftia acidovorans with a 95.73% of identity. The optimal condition for the copper bioleaching was reported in a medium consisting of sulfur (10 g/L), glucose (10 g/L), yeast extract (2 g/L), and mineral tailing (5% wt/vol) at the pH of 2.00 at 50°C. Under this condition, the highest amount of copper (83%) was bioleached. It proves that the lately isolated strain can be effectively employed in the copper bioleaching process

In Vitro Assessment of the Anti-Proliferative and Anti-Viability Effects of Salivary Gland Extracts from Hyalomma ticks (Acari: Ixodidae) on Human Colorectal Cancer Cells

Background: The saliva and salivary glands of ticks possess a wide range of immuno-pharmacologically active mole­cules that effectively modulate the activity of enzymes, antibodies, and amines that have a role in different biological processes. Derived components from saliva and salivary glands of hard ticks Ixodidae have been characterized as poten­tial natural sources for discovering promising anti-cancer drug candidates. Methods: The anti-cancer activity of salivary gland extracts (SGEs) from Hyalomma anatolicum, Hyalomma drome­darii, Hyalomma marginatum, and Hyalomma schulzei was assessed. MTT assays and flow cytometry were done on the HT-29 colorectal cancer cell line to evaluate the anti-viability and proliferative inhibition. Results: Based on the MTT assay results, the SGEs from Hy. dromedarii had the highest and lowest substantial anti-viability effects on the HT-29 cancer cell and human foreskin fibroblast (HFF) normal cell, respectively. The cytometric assessment revealed a significant increase in the apoptosis and necrosis ratio of the HT-29 cancer cells after treatment with Hy. dromedarii SGEs. Conclusion: The results demonstrated that Hy. dromedarii SGEs have significant anti-proliferative, anti-viability, and apoptotic potential. The result of this study suggests that Hy. dromedarii SGEs is an appropriate candidate for further investigations to identify and purify the mechanisms and molecules involved in the anti-cancer activity of the SGEs