@article { author = {Malboobi, Mohammad Ali and Zamani, Katayoun and Lohrasebi, Tahmineh and Sarikhani, Mohammad Reza and Samaian, Ali and Sabet, Mohammad Sadegh}, title = {Phosphate: the Silent Challenge}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {1-32}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50302}, abstract = {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 anddevelopment. Despite high levels of P in the soil, plants absorb it only in the soluble inorganicform of free phosphate ion (Pi) which is scarce in soil. Therefore, there has been a large demandfor Pi fertilizers to secure crop yields, yet its deposition in soil and gradual run-off into waterreservoirs lead to chains of events that cause irreversible damages to ecosystems. Researches,including genome-wide data analyses, have revealed interesting molecular aspects of plantadaptive strategies to deal with low Pi concentrations in soil. These include the higherexpression of acid phosphatases and Pi transporters as well as the secretion of organic acids inthe rhizosphere that maintain cellular Pi homeostasis in order to keep metabolic reactionsrunning. Describing the cycle of Pi exchange between physical and biological worlds, the extentto which current agricultural practices are disturbing the cycle, the necessity of introducing lessdestructivemethods of providing Pi, and alternative measures and solutions for sustainableagriculture will be discussed in this review.}, keywords = {Biofertilizer,Fertilizer,phosphatase,Phosphate,phosphate rock,phosphatesolubilizing microorganism}, url = {https://pbiosci.ut.ac.ir/article_50302.html}, eprint = {https://pbiosci.ut.ac.ir/article_50302_f00ef4afa7a7da7c2e26aa1c64f3a027.pdf} } @article { author = {Asad, Sedigheh and Dastgheib, Seyed Mohammad Mehdi and Amoozegar, Mohammad Ali}, title = {Optimization for decolorization of azo dye Remazol Black B by a Halomonas strain using the Taguchi approach}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {33-42}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50304}, abstract = {Halophilic and halotolerant microorganisms are good candidates for decolorization of azo dyeswhich are routinely used in the dyeing process in textile industries. In this paper, theoptimization of biological decolorization of synthetic dye solutions containing Remazol Black Bby the previously isolated halophilic bacterium Halomonas sp. D2 is investigated. In a primaryinvestigation using a one-factor–at-a-time method, temperature, initial pH of the solution, andconcentrations of glucose, yeast extract, and sodium chloride were chosen for optimizing dyeremoval using the Taguchi method. Based on the statistical analysis of the results, the mostsignificant parameter by far was the yeast extract concentration which accounted for 72.67% ofthe total effect, followed by pH (11.84%) and the NaCl concentration (8.90%). The optimizedconditions 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 sodiumchloride of 10% (w/v). Under these conditions, 95% decolorization was achieved in confirmingexperiments.}, keywords = {azo dye,Halophilic bacteria,decolorization,media optimization,Taguchi Method}, url = {https://pbiosci.ut.ac.ir/article_50304.html}, eprint = {https://pbiosci.ut.ac.ir/article_50304_d0382e46e6f5dfc257b55c7f7fb12bbc.pdf} } @article { author = {Saadat, Samaneh and Safikhani, Zhaleh and Badie, Kambiz and Sadeghi, Mehdi}, title = {Clustering of Short Read Sequences for de novo Transcriptome Assembly}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {43-52}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50305}, abstract = {Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with different k-mer lengths. Then, the eclectic mixtures ofsequences are gathered in order to form the final sequences. Lastly, the contiguous sequencesare clustered and the isoform groups are provided. This proposed algorithm is capable ofgenerating long contiguous sequences and accurately clustering them into isoform groups.Toevaluate our algorithm, we applied it to a simulated RNA-seq dataset of rat transcriptome and areal RNA-seq experiment of the loricaria gr. cataphracta transcriptome. The correctness of theassembled contigs was more than 95%, and our algorithm was able to reconstruct over 70% ofthe 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}, url = {https://pbiosci.ut.ac.ir/article_50305.html}, eprint = {https://pbiosci.ut.ac.ir/article_50305_0020397eff8270749dd28d95054cf66e.pdf} } @article { author = {Tajick, Mohammad Ali and Seid Mohammad Khani, Hamideh and Babaeizad, Valiollah}, title = {Identification of biological secondary metabolites in three Penicillium species, P. goditanum, P. moldavicum, and P. corylophilum}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {53-61}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50303}, abstract = {Microorganisms are important components of soil. Some soil filamentous fungi such asPenicilium produce many bioactive small molecules, or secondary metabolites, that range frombeneficial bioactive compounds to harmful toxins. In this study, the metabolites of threepenicillium species (P. goditanum, P. moldavicum and P. corylophilum) were extracted byadding ethyl acetate to liquid cultures. The metabolites were determined using gaschromatography and mass spectrometry. The results obtained from the GC-MS analysis showedthat Penicillium species are sources of bioactive compounds. We have identified differentgroups 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 majorcompounds. Moreover, several compounds, such as oxalic acid, dibenzothiophene,hexadecanoic acid, and alkane hydrocarbons, were identified in all species.}, keywords = {biological compounds,fungi,GC-MS}, url = {https://pbiosci.ut.ac.ir/article_50303.html}, eprint = {https://pbiosci.ut.ac.ir/article_50303_863334ac0882b73c159f8d0c09ab5f54.pdf} } @article { author = {Hajiuon, Behnaz}, title = {Effects of cell phone radiation on testosterone levels and testicular changes in rats treated with garlic (Allium sativum L.) hydroalcoholic extract}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {63-73}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50306}, abstract = {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 theprobable effects of mobile phone radiation and the consumption of garlic on testosterone levelsand testicular changes. Five groups of rats were used: control, sham (exposed to 900 MHzwavelength), 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 serumtestosterone levels were measured. The testes were also removed, weighed, and theirprobable histological changes were studied.The mean body weight in the sham groupshowed a significant decrease, whereas an increase was seen in experimental group 3 comparedwith the sham (P<0.05). Mean plasma testosterone levels in experimental groups 2 and 3 weredecreased. Similarly, a decrease was seen in the number of Leydig cells in the testes ofexperimental groups. Although microwaves can cause weight loss, the presence of allicinand vitamins A and B in garlic can compensate for some of this weight loss. Microwaves andgarlic extract are reflected both in the number of Leydig cells and in serum testosteroneconcentration. These changes might be attributed to the induction of heat, non-specificstresses, and apoptosis. However, some of these overlapping effects are synergistic and othersare antagonistic; thus, garlic consumption is not always beneficial in reducing the deleteriouseffects of cell phones.}, keywords = {De electromagnetic wave,Garlic,Mobile Phone,testis,Testosterone}, url = {https://pbiosci.ut.ac.ir/article_50306.html}, eprint = {https://pbiosci.ut.ac.ir/article_50306_42f28ca1fe751b63fc3da41feab4821d.pdf} } @article { author = {Pourbabaee, Ahmad Ali and Etemadikhah, Atefeh}, title = {Biological Removal of Dibenzothiophene from Soil and Changes to soil Sulfate by White-Rot Fungus Phanerochaete chrysosporium}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {75-85}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50307}, abstract = {This study investigated biodegradation of dibenzothiophene (DBT) in marsh soil spiked bywhite-rot fungus Phanerochaete chrysosporium. Soil samples were spiked with 100 ppm DBTand incubated at 30°C in a dark chamber for 30 days. Samples were evaluated for pH, Mnperoxidaseactivity, sulfate ion concentration and growth during the tests. Results showedmaximum levels of pH, Mn-peroxidase and sulfate concentrations at 8.19, 66 U L-1 and 31.21mg kg-1 respectively. Colony forming unit assay determinations for contaminated soil samplesshowed that the fungus was able to grow and use dibenzothiophene as a source of carbon andenergy. GC analysis of contaminated samples compared to control samples, demonstrateddegradation of DBT by Phanerochaete chrysosporium. There was no significantly improvedeffect on degradation when the treatment was performed in presence of soil micro flora. Thesystem attained a high rate of DBT degradation at approximately 83.34%, the 30 day testoperation under optimal conditions. After 20 days, the sulfate ion concentration in soil sampleshad almost doubled.}, keywords = {biodegradation,dibenzothiophene,Phanerochaete chrysosporium,soil}, url = {https://pbiosci.ut.ac.ir/article_50307.html}, eprint = {https://pbiosci.ut.ac.ir/article_50307_4dd48f26c4e4419d1a6bf9724562b4e4.pdf} } @article { author = {Kishani Farahani, Hossein and Ashouri, Ahmad and Goldansaz, Seyed Hossein and Shapiro, Martin S. and Golshani, Akbar and Abrun, Pouria}, title = {Associative learning and memory duration of Trichogramma brassicae}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {87-96}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50308}, abstract = {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 memoryduration of T. brassicae under laboratory conditions. According to our results, T. brassicaeshowed olfactory learning ability in response to conditioned odors, and this learned olfactorystimuli lasted for 20 hours. In a second experiment, the effects of frequent experiences on thememory duration of females were studied. A direct relationship between frequent experiencesand memory duration was observed. When exposed to a conditioned odor, wasps’ memoryduration increased in response to the number of experiences. Memory was observed at 28 hafter one extra conditioning. The duration of the associative memory lasted 42 hours when 2extra experiences were given, 50 hours after 3 experiences, and 58 hours after 4 extraconditioning experiences. Our results showed that T. brassicae can associate new odors to hostexistence, and they will show increased memory duration after multiple experiences. }, keywords = {associative learning,memory duration,olfactory,Trichogramma brassicae}, url = {https://pbiosci.ut.ac.ir/article_50308.html}, eprint = {https://pbiosci.ut.ac.ir/article_50308_fd17584a33570a27921d2ce3bf49c80a.pdf} } @article { author = {Hesampour, Ardeshir and Ranaei, Omid and Malboobi, Mohammad Ali and Harati, Javad and Mohandesi, Nooshin}, title = {Comparison of biochemical properties of recombinant phytase expression in the favorable methylotrophic platforms of Pichia pastoris and Hansenula polymorpha}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {97-111}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50309}, abstract = {Phytic acid is the dominant form of phosphorous in plant seeds. However, phytic acid cannot beutilized by animals and causes them serious phosphate deficiency. Utilization of phytase as ananimal 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 yeastsP. pastoris and H.polymorpha and its expressed active recombinant phytase biochemical andbiophysical properties were studies and compared to native A.niger phytase. The phyA genesequence of A.niger was designed and expression of synthetic genes was highly successfully inactive form in both yeast hosts. Size of the secreted recombinant phytases, due to heavyglycosylation, varied from 50 to 65 KDa. Expressed extracellular recombinant phytase sampleswere purified and biochemical tests on properties demonstrated that both recombinant phytasesamples 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 aseries of predefined industrial quality criteria for application as animal feed supplement.}, keywords = {Phytase,Pichia pastoris,Hansenula polymorpha}, url = {https://pbiosci.ut.ac.ir/article_50309.html}, eprint = {https://pbiosci.ut.ac.ir/article_50309_263167ce92c004b31958caa197a3bad7.pdf} } @article { author = {Hamedi, Javad and Papiran, Reyhaneh and Moghimi, Hamid}, title = {Isolation and screening of phytotoxin-producing actinomycetes for biological control of Cardaria draba}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {113-121}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50310}, abstract = {Cardaria draba is an important, troublesome weed in the sustainable production of wheat. Inthe first step of this study, 100 actinomycete isolates were purified from soil samples collectedfrom the rhizosphere and phyllosphere of plants in different provinces of Iran. All isolates weresubjected 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 secondaryscreening and assaying of the extracted culture medium with ethyl acetate, two isolates,Streptomyces sp. UTMC 2102 and Streptomyces sp. UTMC 2104, were selected as superiorphytotoxin-producing isolates in the biological control of C. draba. Leaf necrosis was observedin 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% similarityto Streptomycin anulatus for the isolate Streptomyces sp. UTMC 2102 and 100% similarity toStreptomyces vinaceusdrappus for the isolate Streptomyces sp. UTMC 2104. These resultssuggest that the S. anulatus and S. vinaceusdrappus isolates can be used in the biological controlof C. draba in wheat fields. }, keywords = {actinomycetes,biological control,Cardaria draba,phytotoxin}, url = {https://pbiosci.ut.ac.ir/article_50310.html}, eprint = {https://pbiosci.ut.ac.ir/article_50310_26d3bbeaaa497bc2f81764b0cbdc9982.pdf} } @article { author = {Ebrahimi, Masomeh and Vaziri, Hamidreza and Bahadori, Mohammad Hadi and Ajamian, Farzam}, title = {Genetic Variation of Choline Dehydrogenase Gene in Idiopathic Male Infertility}, journal = {Progress in Biological Sciences}, volume = {4}, number = {1}, pages = {123-131}, year = {2014}, publisher = {University of Tehran Press}, issn = {1016-1058}, eissn = {2228-7833}, doi = {10.22059/pbs.2014.50311}, abstract = {Infertility can be caused by an unexplained reduction in semen quality in males who present asnormal on physical examination and endocrine testing. There is some evidence that aberrantmetabolism of micronutrients such as choline may play a causative role in male factorinfertility. Choline is a crucial factor in the regulation of sperm membrane structure andmotility, and this nutrient plays an important role in the maturing and fertilizing capacity ofspermatozoa. In the present study, we explored the contribution of the choline dehydrogenasegene polymorphism located in the codon 78 (CHDH +432G>T), one of the basic enzymes ofcholine metabolism, to idiopathic male infertility. In this study, 50 infertile men and 50 fertilemen of the Guilan population were selected. Genomic DNA was extracted from peripheralblood. Genotypes were determined by polymerase chain reaction (PCR) and restrictionfragment length polymorphism (RFLP). Statistical analysis was performed using MedCalcsoftware (v12.1.4.0). A significant difference was observed between patients and healthysubjects in the distribution of G and T alleles. The prevalence of genotype frequencies ofCHDH +432 GG, GT, and TT were 28%, 50%, and 22%, respectively, in patients, while inhealthy subjects they were 52%, 36%, and 12%, respectively. In other words, there was asignificant difference in the genotype distribution of CHDH +432G>T in patients comparedwith controls (Ρ<0.05). This finding suggests a possible influence of this gene polymorphism onidiopathic male infertility. }, keywords = {Choline dehydrogenase,gene polymorphism,infertility}, url = {https://pbiosci.ut.ac.ir/article_50311.html}, eprint = {https://pbiosci.ut.ac.ir/article_50311_57e7b4a72a3b8d2bedc0265ea7168c13.pdf} }