Progress in Biological Sciences最新文献_第9页

APPRAISAL OF THE ENTIRE MITOCHONDRIAL GENOME FOR DNA BARCODING IN BIRDS 鸟类线粒体全基因组DNA条形码鉴定

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52297

Leila Nourani, M. Aliabadian

{"title":"APPRAISAL OF THE ENTIRE MITOCHONDRIAL GENOME FOR DNA BARCODING IN BIRDS","authors":"Leila Nourani, M. Aliabadian","doi":"10.22059/PBS.2014.52297","DOIUrl":"https://doi.org/10.22059/PBS.2014.52297","url":null,"abstract":"DNA barcoding based on a standardized region of 648 base pairs of mitochondrial DNAsequences from Cytochrome C Oxidase 1 (COX1) is proposed for animal species identification.Recent studies suggested that DNA barcoding has been effective for identifying 94% of birdspecies. The proposed threshold of 10 times the average intraspecific variation could be used forthe identification and delimitation of new species. As a different part of the mitochondrial DNAevolves at various mutation rates, they show a variety of capabilities to distinguish taxa tospecies level. In order to compare the efficiency of protein-coding genes (PCGs) in birds, thecomplete genome of 310 birds, including 12 mitochondrial genes (except ND6) and barcodingthe region of COX1, were examined. We concentrated on the intra- and inter-specific variationsand the degree of mutational saturation as criteria for our evaluations. Some genes like ATP8,ND2 and ND5 showed the greatest divergence in intra- and inter-specific variations. Theoverlap between intra- and inter-specific variability for all genes is still troublesome. Our resultsmay have been influenced by the sample size because our data were not representative of allbird species. More additional taxa may shed light more on DNA barcoding candidate genes.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"18 1","pages":"167-178"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85000909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Genetic worth and stability of selection indices in rice (Oryza sativa L.) 水稻选择指标的遗传价值与稳定性

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52296

M. Fotokian, K. Agahi

{"title":"Genetic worth and stability of selection indices in rice (Oryza sativa L.)","authors":"M. Fotokian, K. Agahi","doi":"10.22059/PBS.2014.52296","DOIUrl":"https://doi.org/10.22059/PBS.2014.52296","url":null,"abstract":"Improvement of one trait on its own will affect the performance of other traits because of genotypic correlations between traits. Index selection is one of the tools used by plant breeders to overcome this problem. The purpose of this paper is to evaluate selection indices developed for improving grain yield in rice (Oryza sativa L.). Forty-nine rice genotypes were cultivated at Tonekabon Rice Research Station, Iran, in 2009 and 2010. Selection indices were developed based on phenotypic and genotypic correlations, path coefficients, broad-sense heritability of traits and stepwise multiple linear regression coefficients. Assessment of indices revealed that the stability decreased concurrently with increase in the genetic worth, and hence an inverse association existed between stability and genetic worth of indices. The results also suggested that selection for TP, GW, GP and GL and against PH using their multiple linear regression parameters as economic weights was an effective criterion for improving grain yield in rice genotypes. On the other hand, the most stable indices were those that were developed based on heritability of traits as well as genotypic path coefficients.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"1 1","pages":"153-166"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79975148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Re-assessment of subspecific taxa in Astragalus section Anthylloidei (Fabaceae) based on molecular evidence 基于分子证据的黄芪科花楸属亚特异分类群的再评价

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52301

K. N. Safar, S. K. Osaloo, A. Maasoumi

{"title":"Re-assessment of subspecific taxa in Astragalus section Anthylloidei (Fabaceae) based on molecular evidence","authors":"K. N. Safar, S. K. Osaloo, A. Maasoumi","doi":"10.22059/PBS.2014.52301","DOIUrl":"https://doi.org/10.22059/PBS.2014.52301","url":null,"abstract":"The taxonomic and phylogenetic status of several taxa previously recognized as subspecies in Astragalus sect. Anthylloidei is re-assessed based on DNA sequences and morphological features. We focused on Astragalus ebenoides (subsp. ebenoides and subsp. naghadehensis), Astragalus murinus (subsp. murins and subsp. bornmuelleri), Astragalus remotiflorus (subsp. remotiflorus and subsp. melanogramma), Astragalus nigrohirsutus (=Astragalus remotiflorus subsp. nigrohirsutus), Astragalus submitis (=Astragalus submitis subsp. submitis) and Astragalus yushensis (=Astragalus submitis subsp. maassoumii). A total of 15 accessions representing 14 ingroups and one outgroup were analysed for nrDNA ITS and plastid DNA, rpl32 gene and rpl32-trnL(UAG) intergenic spacer. Phylogenetic trees were constructed using neighbour joining, Bayesian and maximum parsimony methods. The phylogenetic analyses of both datasets revealed that the subspecies described formerly under each of the studied species are distinct and should be elevated to specific rank. The nucleotide sequence variations observed among different subspecies, along with morphological characters, provided appropriate criteria in setting the species boundaries. The new combinations and a diagnostic key to the studied species are provided.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"180 1","pages":"219-234"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78036013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Optimization for decolorization of azo dye Remazol Black B by a Halomonas strain using the Taguchi approach 田口法优化盐单胞菌对偶氮染料Remazol Black B的脱色效果

Progress in Biological Sciences Pub Date : 2014-05-01 DOI: 10.22059/PBS.2014.50304

S. Asad, S. Dastgheib, M. A. Amoozegar

引用次数: 5

Isolation and screening of phytotoxin-producing actinomycetes for biological control of Cardaria draba 产植物毒素放线菌的分离与筛选及其生物防治研究

Progress in Biological Sciences Pub Date : 2014-05-01 DOI: 10.22059/PBS.2014.50310

J. Hamedi, Reyhaneh Papiran, H. Moghimi

{"title":"Isolation and screening of phytotoxin-producing actinomycetes for biological control of Cardaria draba","authors":"J. Hamedi, Reyhaneh Papiran, H. Moghimi","doi":"10.22059/PBS.2014.50310","DOIUrl":"https://doi.org/10.22059/PBS.2014.50310","url":null,"abstract":"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.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"127 1","pages":"113-121"},"PeriodicalIF":0.0,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89783374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Genetic Variation of Choline Dehydrogenase Gene in Idiopathic Male Infertility 特发性男性不育症中胆碱脱氢酶基因的遗传变异

Progress in Biological Sciences Pub Date : 2014-05-01 DOI: 10.22059/PBS.2014.50311

Marzieh Ebrahimi, H. Vaziri, M. Bahadori, F. Ajamian

{"title":"Genetic Variation of Choline Dehydrogenase Gene in Idiopathic Male Infertility","authors":"Marzieh Ebrahimi, H. Vaziri, M. Bahadori, F. Ajamian","doi":"10.22059/PBS.2014.50311","DOIUrl":"https://doi.org/10.22059/PBS.2014.50311","url":null,"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.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"119 1","pages":"123-131"},"PeriodicalIF":0.0,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73634534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Associative learning and memory duration of Trichogramma brassicae 芸苔赤眼蜂的联想学习和记忆持续时间

Progress in Biological Sciences Pub Date : 2014-05-01 DOI: 10.22059/PBS.2014.50308

H. K. Farahani, A. Ashouri, S. H. Goldansaz, M. Shapiro, Akbar Golshani, Pouria Abrun

{"title":"Associative learning and memory duration of Trichogramma brassicae","authors":"H. K. Farahani, A. Ashouri, S. H. Goldansaz, M. Shapiro, Akbar Golshani, Pouria Abrun","doi":"10.22059/PBS.2014.50308","DOIUrl":"https://doi.org/10.22059/PBS.2014.50308","url":null,"abstract":"Learning ability and memory duration are two inseparable factors which can increase the efficiency 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.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"116 1","pages":"87-96"},"PeriodicalIF":0.0,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76685103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

COMPARISON OF BIOCHEMICAL PROPERTIES OF RECOMBINANT PHYTASE EXPRESSION IN THE FAVORABLE METHYLOTROPHIC PLATFORMS OF PICHIA PASTORIS AND HANSENULA POLYMORPHA 重组植酸酶在毕赤酵母和多形羊草有利甲基化营养平台上表达的生化特性比较

Progress in Biological Sciences Pub Date : 2014-05-01 DOI: 10.22059/PBS.2014.50309

Ardeshir Hesampour, Omid Ranaei, M. Malboobi, J. Harati, N. Mohandesi

{"title":"COMPARISON OF BIOCHEMICAL PROPERTIES OF RECOMBINANT PHYTASE EXPRESSION IN THE FAVORABLE METHYLOTROPHIC PLATFORMS OF PICHIA PASTORIS AND HANSENULA POLYMORPHA","authors":"Ardeshir Hesampour, Omid Ranaei, M. Malboobi, J. Harati, N. Mohandesi","doi":"10.22059/PBS.2014.50309","DOIUrl":"https://doi.org/10.22059/PBS.2014.50309","url":null,"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.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"19 1","pages":"97-111"},"PeriodicalIF":0.0,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85934428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Effects of cell phone radiation on testosterone levels and testicular changes in rats treated with garlic (Allium sativum L.) hydroalcoholic extract 手机辐射对大蒜(Allium sativum L.)水酒精提取物治疗大鼠睾丸激素水平和睾丸变化的影响

Progress in Biological Sciences Pub Date : 2014-05-01 DOI: 10.22059/PBS.2014.50306

B. Hajiuon

{"title":"Effects of cell phone radiation on testosterone levels and testicular changes in rats treated with garlic (Allium sativum L.) hydroalcoholic extract","authors":"B. Hajiuon","doi":"10.22059/PBS.2014.50306","DOIUrl":"https://doi.org/10.22059/PBS.2014.50306","url":null,"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.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"11 1","pages":"63-73"},"PeriodicalIF":0.0,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80390552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Clustering of Short Read Sequences for de novo Transcriptome Assembly 用于从头转录组组装的短读序列聚类

Progress in Biological Sciences Pub Date : 2014-05-01 DOI: 10.22059/PBS.2014.50305

Samaneh Saadat, Z. Safikhani, K. Badie, M. Sadeghi

{"title":"Clustering of Short Read Sequences for de novo Transcriptome Assembly","authors":"Samaneh Saadat, Z. Safikhani, K. Badie, M. Sadeghi","doi":"10.22059/PBS.2014.50305","DOIUrl":"https://doi.org/10.22059/PBS.2014.50305","url":null,"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.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"114 1","pages":"43-52"},"PeriodicalIF":0.0,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77969480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0