Progress in Biological Sciences
Volume:6 Issue: 2, Summer and Autumn 2016

The Profile Hidden Markov Model (PHMM) can be poor at capturing dependency between observations because of the statistical assumptions it makes. To overcome this limitation, the dependency between residues in a multiple sequence alignment (MSA) which is the representative of a PHMM can be combined with the PHMM. Based on the fact that sequences appearing in the final MSA are written based on their similarity; the one-by-one dependency between corresponding amino acids of two current sequences can be append to PHMM. This perspective makes it possible to consider a generalization of PHMM. For estimating the parameters of generalized PHMM (emission and transition probabilities), we introduce new forward and backward algorithms. The performance of generalized PHMM is discussed by applying it to the twenty protein families in Pfam database. Results show that the generalized PHMM significantly increases the accuracy of ordinary PHMM.

Automated data analysis and pattern recognition techniques are the requirements of biological and proteomics research studies. The analysis of proteins consists of some stages among which the analysis of two dimensional electrophoresis (2-DE) images is crucial. The aim of image capturing is to generate a Photostat that can be used in future works such as image comparison. The researchers introduced a new method for matching two 2-DE gel images. In this method, a neighborhood circular region is defined to obtain information about spots’ neighbors. In the present paper, the information obtained by this region is reordered into a matrix as a descriptor of the neighbors of each spot. The matrix is then used in matching the spots between two images. All conducted tests to evaluate the method’s performance showed the power of the method in spot matching, even when the number of candidate matching spots in the second images increased. The proposed method provides a robust automatic comparison idea in gel images matching. Despite its low speed, its accuracy is excellent. The Novelty of the present study is the use of matrices as neighborhood descriptor. This idea is applicable in any other similar domain.

Amylase is one of the most widely used enzymes in the industry. Cold environments are the most ubiquitous environments in the world that have been occupied by cold tolerant microorganisms. The enzymes of these microorganisms have a wide range of applications in various areas of biotechnology. The aim of this study was to isolate cold-active amylase producing bacteria. A total of 64 cold-tolerant bacteria producing amylase were isolated from Binaloud Mountain soil, Iran. An isolate (Pedobacter sp. BTR84) registered under accession number KM459538 with the highest enzyme productivity was selected for production optimization. The production of amylase was evaluated via One-factor-at-a-timemethod and RSM (Response Surface Methodology). The enzyme production was optimized at 20°C, pH 9, starch 2% (w/v), and inoculation level 3% (v/v) by One-factor-at-a-timemethod. Then, in order to investigate the interaction between these variables and determine the final optimal conditions, optimization was carried out through the response surface methodology (RSM). Four variables were evaluated at three levels using the Box-Behnken design. Starch concentration and inoculation level variables had a significant effect on amylase production (p

In this study, the feasibility of cruxrhodopsin (CR) production as a multifunctional nanoparticle was investigated and optimized by Halorculasp. IRU1, a novel halophile Archaea isolated from Urmia Lake, Iran in batch experiments. In this case, Taguchi method was used for effect measurement of three important factors (petrochemical wastewater, yeast extract and KH2PO4) on CR production. Results illustrated that the petrochemical wastewater concentration was the meaningful factor in CR synthesis. The optimum factor levels for petrochemical wastewater concentration, yeast extract and KH2PO4 were 2% (w/v), 0.2% (w/v) and 0.004% (w/v), respectively. Also, under these conditions, the predicted value for CR production was about 44.24%. Therefore, this investigation demonstrated that Haloarcula sp. IRU1 has a high potential for synthesis of CR from petrochemical wastewater.

Radiation resistant bacteria have adopted a variety of ingenious strategies for survival under the high dose of radiation, for example through their pigments. In the present study, two ultraviolet-C (UVC) radiation tolerant bacteria, named NM1 and NM3 strains, were isolated from the industrial waste and soil that identified by the molecular analysis. Survival assay of irradiated bacteria was performed by plate counting and flow cytometry (by a fluorescent dye, Rhodamin 123). Also, hydrogen peroxide tolerance of the isolated strains was analyzed by turbidimetric microplate technique. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and EC50 values in reducing power were measured to evaluate antioxidant activity and reductive power of their methanol extracted pigments. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the NM1 and NM3 strains belonged to Microbacterium esteraromaticum and Dietzia schimae with 99% identity, respectively. Both of them showed much high resistance to 15 and 20 J/cm2 UVC irradiation (254nm). Visible spectra of their methanolic extracted pigments were considered identical with λmax at 413, 439 and 468nm for Microbacterium NM1 and λmax at 451nm for Dietzia NM3. EC50 values in reducing power were 35.26 and 36.13 µg/ml for pigments of NM1 and NM3 strains, respectively. Whereas scavenging abilities of DPPH radicals were 3.42 and 1.58 mg/ml for pigments of NM1 and NM3 strains, respectively. Based on the results, the pigments of isolated UVC tolerant bacteria displayed strong antioxidant activity. These bacteria may be a good source for antioxidative-related functional foods and the pharmaceutical industry.

Naphthalene is an ubiquitous pollutant of the environment and the biodegradation of this pollutant has been receiving constant scientific consideration. The aim of this study was to isolate and identify bacteria that could degrade naphthalene from three regions of the Gol Gohar Mine at Sirjan, Iran. In this study, the total naphthalene degrading bacteria were quantified with the most probable number (MPN) and the colony forming unit (CFU) methods. The results showed that most of the bacteria communities capable of degrading naphthalene aggregated in the (WG) site. Among 22 isolated bacteria, seven strains were selected for their ability to grow at higher concentrations of naphthalene (300 and 400 mg/l) and biochemical characteristics. Finally, two strains named isolates 72N and 79N were selected for analysis of the 16S rRNA sequences. Strain 72N was identified as Pseudomonas fluorescens AHB72N and strain 79N was shown to be related to Pseudomonas gessardii AHB79N. The results of biodegradation tests showed that these two strains could degrade 600 mg/l naphthalene in 7 days. The results indicated that strain 79N showed higher potential for removing naphthalene than strain 72N. Practical application of bacterial strains for the degradation of naphthalene from the industrial zones opens interesting prospects. The results of this study provide useful information in evaluating naphthalene degraders isolated from wastewater and industrial sites.

The worldwide dissemination of multi drug resistant Acinetobacter baumannii strains has caused serious concern and high rate of mortality in recent decades that originate from limited effective antibiotics in the treatment of A. baumannii infections. Myxobacteria are Gram-negative bacteria that are important for their complex lifestyle and production of novel structurally secondary metabolites with diverse bioactivities. In this study, a total of 60 myxobacterial strains were purified by culturing and investigation of 130 soil samples. Secondary metabolite extracts of the selected strains were screened for antibacterial activity against multi-drug resistant (MDR) Acinetobacter baumannii. The most potent extracts derived from Stigmatella sp. UTMC 4081, Stigmatella sp. UTMC 4072, and Archangium sp. UTMC 4070 which were investigated by recording percentage of growth inhibition, MIC, MBC, and IC50 values. The results showed that the MIC value of extract No. 4072 was 2.5 μg/ml and its MBC value against A. baumannii recorded as 5 μg/ml. Extract No. 4081 was known to be active with MIC of 2.5 μg/ml and MBC of 10 μg/ml. In addition, MIC and MBC values of extract No. 4070 were found to be 10 and 25 μg/ml, respectively. Myxobacterial extracts showed no toxicity against Artemia salina. This study demonstrated the importance of myxobacterial metabolites as promising antimicrobial agents against multi drug resistant A. baumannii

The extensive use of heavy metals and nanoparticles (NPs) has led to their release into the environment that might have negative impacts on both organisms and the environment. In this study, the molecular responses of wheat seedlings to silver nitrate and silver nanoparticles (AgNPs) were assessed by transcript accumulation analysis of genes coding for products potentially involved in heavy metal tolerance. A quantitative Real-time PCR experiment was performed with MAPK (Mitogen-activated protein kinase) and thioredoxin genes using RNA isolated from wheat shoots treated for 0, 2, 6, 12 and 24 h with AgNO3 and AgNPs at 100 mg-1L concentration. Results indicated that stressful conditions led to the antioxidant responses of wheat seedlings that could be reflected as changes in MAPK and thioredoxin gene transcripts. The genes expression patterns were slightly different. The expression of these genes in response to both treatments was high at the beginning of the stress and was decreased with time. Our results showed the effects of AgNO3 treatment were faster than AgNPs. We found that wheat seedlings might develop different strategies to cope with AgNO3 and AgNPs toxicity with change in the expression of MAPK and thioredoxin heavy metal-related genes.

DNA size markers (ladder) are essential tools in molecular biology, genetics and biotechnology. In this study, a simple and cost-effective method for laboratory production of DNA ladders is introduced. For this purpose, different sizes of 100 to 2000 bp DNA segments were designed using PCR technique. For producing 14 different gene fragments as DNA molecular weight markers, recombinant plasmid pET28a containing α-amylase gene as a DNA source and one forward and 14 reverse primers were used. The gene fragments containing 100 to 400bp segments with a distance of 50 bp and 400 to 1600 bp segments with a distance of 200 bp as well as 1600 to 2000 bp segments with the distance of 400 bp were generated in a single run of PCR. The present technique could prove to be simple, time saving, inexpensive and good quality approach as compared to the usual DNA ladder preparation procedures. Also, according to the same conditions for designed primers there is a possibility of producing other marker sizes by choosing different types of forward and reverse primers. The PCR product mixture could be directly loaded onto the agarose gel and used as a molecular weight marker without further purification because that was as reliable and uniform as markers from commercial sources. Finally, this marker can be useful for most of molecular biology laboratory techniques.

The composition of hydro-distilled essential oils of Phlomis anisodonta Boiss. subsp. occidentalis Jamzad in vegetative, flowering and post flowering stages were investigated using GC and GC-MS, leading to identification of 41, 26 and 23 compounds, respectively. In all three samples, sesquiterpenes were the main components. In vegetative stage the main components of the oil were germacrene-D (14.3%), bicyclogermacrene (12.4%) and α-pinene (6.8%); in flowering stage, germacrene-D (52.6%) and β-caryophyllene (15.9%); and in fruiting stage, germacrene-D (27.9%), bicyclogermacrene (17.6%), caryophyllene oxide (14.7%) and β-caryophyllene (11.3%). The samples were also subjected to screening for their possible antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and β-carotene-linoleic acid assays. In the first experiment, the free radical scavenging activity of polar subfraction of methanol extract in fruiting stage was superior to all other extracts (IC50= 41±0.4 μg/ml). When using linoleic acid system, oxidation of the linoleic acid was effectively inhibited by the non-polar subfraction of methanol extract in different stages. The results of this study show that the composition of essential oils varies considerably both in different parts of the plants and at different stages of development. When using the plants for medicinal purposes, it is important to be aware of the effective developmental phase, i.e. when the most effective components reach their peak volume, as well as the most useful parts.

An efficient protocol is suggested for in vitro culture of five Phalaenopsis hybrids obtained by hand-cross-pollination of three commercial hybrids Calgary, Ankara, and Kendall. Four nutrient media- namely half-strength Murashige and Skoog, Knudson, Phytamax containing activated charcoal, and Mitra– once supplemented (with coconut water, peptone, or both), and once without any supplement were considered as the experimental and control groups of the study which were then compared and evaluated for seed germination and protocorm formation. All of the seeds of hybrids H and N were germinated on half-strength Murashige and Skoog medium supplemented with peptone. To evaluate plant regeneration rate, three different media including half-strength Murashige and Skoog, Viking-Ship containing 2.75gr/L NPK (10-20-30), and Hyponex containing [1gr/L NPK (20-20-20)혊 NPK (6.5-6-19)] were compared. The maximum number of healthy plantlets, roots per plantlet, and leaves per plantlet were induced in the half-strength Murashige and Skoog medium. Around 93% of the plants produced in vitro were able to establish ex vitro. The obtained results showed that, the use of the half-strength Murashige and Skoog medium is well suited for the mass propagation of Phalaenopsis.