فهرست مطالب

Progress in Biological Sciences - Volume:4 Issue: 1, 2014
  • Volume:4 Issue: 1, 2014
  • تاریخ انتشار: 1393/03/15
  • تعداد عناوین: 10
  • Mohammad Ali Malboobi, Katayoun Zamani, Tahmineh Lohrasebi, Mohammad Reza Sarikhani, Ali Samaian, Mohammad Sadegh Sabet Pages 1-32
    Phosphorus (P) is one of the most vital elements for all living organisms which acts as aconstituent of essential biomolecules such as nucleic acids, phospholipids, and phosphosugars, and as a major contributor to almost all metabolic reactions including photosynthesis, respiration, and energy delivery. It is one of the most needed nutrients for plant growth and development. Despite high levels of P in the soil, plants absorb it only in the soluble inorganic form of free phosphate ion (Pi) which is scarce in soil. Therefore, there has been a large demand for Pi fertilizers to secure crop yields, yet its deposition in soil and gradual run-off into water reservoirs lead to chains of events that cause irreversible damages to ecosystems. Researches, including genome-wide data analyses, have revealed interesting molecular aspects of plant adaptive strategies to deal with low Pi concentrations in soil. These include the higher expression of acid phosphatases and Pi transporters as well as the secretion of organic acids in the rhizosphere that maintain cellular Pi homeostasis in order to keep metabolic reactionsrunning. Describing the cycle of Pi exchange between physical and biological worlds, the extent to which current agricultural practices are disturbing the cycle, the necessity of introducing lessdestructive methods of providing Pi, and alternative measures and solutions for sustainable agriculture will be discussed in this review.
    Keywords: biofertilizer, fertilizer, phosphatase, phosphate, phosphate rock, phosphatesolubilizing microorganism
  • Sedigheh Asad, Seyed Mohammad Mehdi Dastgheib, Mohammad Ali Amoozegar Pages 33-42
    Halophilic and halotolerant microorganisms are good candidates for decolorization of azo dyes which are routinely used in the dyeing process in textile industries. In this paper, theoptimization of biological decolorization of synthetic dye solutions containing Remazol Black B by the previously isolated halophilic bacterium Halomonas sp. D2 is investigated. In a primary investigation using a one-factor–at-a-time method, temperature, initial pH of the solution, and concentrations of glucose, yeast extract, and sodium chloride were chosen for optimizing dye removal using the Taguchi method. Based on the statistical analysis of the results, the most significant parameter by far was the yeast extract concentration which accounted for 72.67% of the total effect, followed by pH (11.84%) and the NaCl concentration (8.90%). The optimized conditions for dye removal were predicted to be a temperature of 35°C, an initial pH of 10, glucose concentration of 1% (w/v), yeast extract concentration of 1% (w/v), and sodium chloride of 10% (w/v). Under these conditions, 95% decolorization was achieved in confirming experiments.
    Keywords: azo dye, Halophilic bacteria, decolorization, media optimization, Taguchi method
  • Samaneh Saadat, Zhaleh Safikhani, Kambiz Badie, Mehdi Sadeghi Pages 43-52
    Given the importance of transcriptome analysis in various biological studies and considering the vast amount of whole transcriptome sequencing data, it seems necessary to develop an algorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequences are generated using de Bruijn graph with different k-mer lengths. Then, the eclectic mixtures of sequences are gathered in order to form the final sequences. Lastly, the contiguous sequences are clustered and the isoform groups are provided. This proposed algorithm is capable of generating long contiguous sequences and accurately clustering them into isoform groups.To evaluate our algorithm, we applied it to a simulated RNA-seq dataset of rat transcriptome and a real RNA-seq experiment of the loricaria gr. cataphracta transcriptome. The correctness of the assembled contigs was more than 95%, and our algorithm was able to reconstruct over 70% of the transcripts at more than 80% of the transcripts’ lengths. This study demonstrates thatapplying a sophisticated merging method improves transcriptome assembly. The source code isavailable upon request by contacting the corresponding author by email.
    Keywords: De novo, next generation sequencing, RNA, seq, transcriptome assembly
  • Mohammad Ali Tajick, Hamideh Seid Mohammad Khani, Valiollah Babaeizad Pages 53-61
    Microorganisms are important components of soil. Some soil filamentous fungi such asPenicilium produce many bioactive small molecules, or secondary metabolites, that range from beneficial bioactive compounds to harmful toxins. In this study, the metabolites of three penicillium species (P. goditanum, P. moldavicum and P. corylophilum) were extracted by adding ethyl acetate to liquid cultures. The metabolites were determined using gas chromatography and mass spectrometry. The results obtained from the GC-MS analysis showed that Penicillium species are sources of bioactive compounds. We have identified different groups of compounds, such as alkaloids, alkenes, sesquiterpens, fatty acids, and essential oils. Among them, 1,3,8-p-Menthatriene, 2-methylenecyclohexane, anthracene, neoisolongifolene, [14] annulene and thioxanthene in P. goditanum, isocyclocitral, coumarin-6-ol and 2, 4, 6 Trimethoxystyrene in P. moldavicum as well as asarone in P. corylophilum were major compounds. Moreover, several compounds, such as oxalic acid, dibenzothiophene, hexadecanoic acid, and alkane hydrocarbons, were identified in all species.
    Keywords: biological compounds, fungi, GC, MS
  • Behnaz Hajiuon Pages 63-73
    Electromagnetic waves can damage sex organs and cause hormonal disorders, and garlic isknown to reduce risk factors for various diseases. The aim of this study was to investigate the probable effects of mobile phone radiation and the consumption of garlic on testosterone levels and testicular changes. Five groups of rats were used: control, sham (exposed to 900 MHz wavelength), experimental group 1 (receiving garlic extract), and experimental groups 2 and 3 (receiving both extract and microwaves). After a month, the rats were weighed and their serum testosterone levels were measured. The testes were also removed, weighed, and their probable histological changes were studied.The mean body weight in the sham group showed a significant decrease, whereas an increase was seen in experimental group 3 compared with the sham (P<0.05). Mean plasma testosterone levels in experimental groups 2 and 3 were decreased. Similarly, a decrease was seen in the number of Leydig cells in the testes of experimental groups. Although microwaves can cause weight loss, the presence of allicin and vitamins A and B in garlic can compensate for some of this weight loss. Microwaves and garlic extract are reflected both in the number of Leydig cells and in serum testosterone concentration. These changes might be attributed to the induction of heat, non-specificstresses, and apoptosis. However, some of these overlapping effects are synergistic and others are antagonistic; thus, garlic consumption is not always beneficial in reducing the deleterious effects of cell phones.
    Keywords: De electromagnetic wave, garlic, mobile phone, Testis, testosterone
  • Ahmad Ali Pourbabaee, Atefeh Etemadikhah Pages 73-83
    This study investigated biodegradation of dibenzothiophene (DBT) in marsh soil spiked bywhite-rot fungus Phanerochaete chrysosporium. Soil samples were spiked with 100 ppm DBT and incubated at 30°C in a dark chamber for 30 days. Samples were evaluated for pH, Mnperoxidase activity, sulfate ion concentration and growth during the tests. Results showed maximum levels of pH, Mn-peroxidase and sulfate concentrations at 8.19, 66 U L-1 and 31.21 mg kg-1 respectively. Colony forming unit assay determinations for contaminated soil samples showed that the fungus was able to grow and use dibenzothiophene as a source of carbon and energy. GC analysis of contaminated samples compared to control samples, demonstrated degradation of DBT by Phanerochaete chrysosporium. There was no significantly improved effect on degradation when the treatment was performed in presence of soil micro flora. The system attained a high rate of DBT degradation at approximately 83.34%, the 30 day test operation under optimal conditions. After 20 days, the sulfate ion concentration in soil samples had almost doubled.
    Keywords: biodegradation, dibenzothiophene, Phanerochaete chrysosporium, soil
  • Hossein Kishani Farahani, Ahmad Ashouri, Seyed Hossein Goldansaz, Martin S. Shapiro, Akbar Golshani, Pouria Abrun Pages 85-94
    Learning ability and memory duration are two inseparable factors which can increase theefficiency of a living organism during its lifetime. Trichgramma brassice Bezdenko (Hym.:Trichogrammatidae) is a biological control agent widely used against different pest species.This research was conducted to study the olfactory associative learning ability and memory duration of T. brassicae under laboratory conditions. According to our results, T. brassicae showed olfactory learning ability in response to conditioned odors, and this learned olfactory stimuli lasted for 20 hours. In a second experiment, the effects of frequent experiences on the memory duration of females were studied. A direct relationship between frequent experiences and memory duration was observed. When exposed to a conditioned odor, wasps’ memory duration increased in response to the number of experiences. Memory was observed at 28 h after one extra conditioning. The duration of the associative memory lasted 42 hours when 2 extra experiences were given, 50 hours after 3 experiences, and 58 hours after 4 extra conditioning experiences. Our results showed that T. brassicae can associate new odors to host existence, and they will show increased memory duration after multiple experiences.
    Keywords: associative learning, memory duration, olfactory, Trichogramma brassicae
  • Ardeshir Hesampour, Omid Ranaei, Mohammad Ali Malboobi, Javad Harati, Nooshin Mohandesi Pages 95-109
    Phytic acid is the dominant form of phosphorous in plant seeds. However, phytic acid cannot be utilized by animals and causes them serious phosphate deficiency. Utilization of phytase as an animal feed additive can affect liberation of phosphor and its mineral availability. In this study, heterologous expression of the A. niger phyA gene was investigated in the methylotrophic yeasts P. pastoris and H.polymorpha and its expressed active recombinant phytase biochemical and biophysical properties were studies and compared to native A.niger phytase. The phyA gene sequence of A.niger was designed and expression of synthetic genes was highly successfully in active form in both yeast hosts. Size of the secreted recombinant phytases, due to heavy glycosylation, varied from 50 to 65 KDa. Expressed extracellular recombinant phytase samples were purified and biochemical tests on properties demonstrated that both recombinant phytase samples had similar pH profiles with pH optima determinations of pH 2.5, pH.5.5 as acidphosphatase and optimum temperature of 60 and 50 °C respectively in P. pastoris and H.polymorpha. This study concludes that recombinant P. pastoris and H. polymorpha phytases could fulfil a series of predefined industrial quality criteria for application as animal feed supplement.
    Keywords: phytase, Pichia pastoris, Hansenula polymorpha
  • Javad Hamedi, Reyhaneh Papiran, Hamid Moghimi Pages 111-119
    Cardaria draba is an important, troublesome weed in the sustainable production of wheat. In the first step of this study, 100 actinomycete isolates were purified from soil samples collected from the rhizosphere and phyllosphere of plants in different provinces of Iran. All isolates were subjected to primary screening by assaying the fermentation broth of the sterile surfaces of C. draba leaves. Considerable herbicidal activity was observed for four isolates. During secondary screening and assaying of the extracted culture medium with ethyl acetate, two isolates, Streptomyces sp. UTMC 2102 and Streptomyces sp. UTMC 2104, were selected as superior phytotoxin-producing isolates in the biological control of C. draba. Leaf necrosis was observed in 500 and 1000 μg/ml and ≥100 μg/ml dilutions for isolates UTMC 2102 and UTMC 2104, respectively. Phylogenic identification confirmed that the 16S rRNA gene has 100% similarity to Streptomycin anulatus for the isolate Streptomyces sp. UTMC 2102 and 100% similarity to Streptomyces vinaceusdrappus for the isolate Streptomyces sp. UTMC 2104. These results suggest that the S. anulatus and S. vinaceusdrappus isolates can be used in the biological control of C. draba in wheat fields.
    Keywords: actinomycetes, biological control, Cardaria draba, phytotoxin
  • Masomeh Ebrahimi, Hamidreza Vaziri, Mohammad Hadi Bahadori, Farzam Ajamian Pages 121-129
    Infertility can be caused by an unexplained reduction in semen quality in males who present as normal on physical examination and endocrine testing. There is some evidence that aberrant metabolism of micronutrients such as choline may play a causative role in male factor infertility. Choline is a crucial factor in the regulation of sperm membrane structure and motility, and this nutrient plays an important role in the maturing and fertilizing capacity of spermatozoa. In the present study, we explored the contribution of the choline dehydrogenase gene polymorphism located in the codon 78 (CHDH +432G>T), one of the basic enzymes of choline metabolism, to idiopathic male infertility. In this study, 50 infertile men and 50 fertile men of the Guilan population were selected. Genomic DNA was extracted from peripheral blood. Genotypes were determined by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). Statistical analysis was performed using MedCalc software (v12.1.4.0). A significant difference was observed between patients and healthy subjects in the distribution of G and T alleles. The prevalence of genotype frequencies of CHDH +432 GG, GT, and TT were 28%, 50%, and 22%, respectively, in patients, while in healthy subjects they were 52%, 36%, and 12%, respectively. In other words, there was a significant difference in the genotype distribution of CHDH +432G>T in patients compared with controls (Ρ<0.05). This finding suggests a possible influence of this gene polymorphism on idiopathic male infertility.
    Keywords: Choline dehydrogenase, gene polymorphism, infertility