Genetics of Aquatic Organisms最新文献_第2页

Molecular Phylogenetic Analysis of Nemoura flexuosa Aubert, 1949 Based on Cytochrome Oxidase C Subunit-I Gene from Türkiye 基于细胞色素氧化酶C亚基- i基因的1949年弯叶线虫分子系统发育分析

Genetics of Aquatic Organisms Pub Date : 2023-01-19 DOI: 10.4194/ga565

Famil Yusufoglu, F. Uçkan

{"title":"Molecular Phylogenetic Analysis of Nemoura flexuosa Aubert, 1949 Based on Cytochrome Oxidase C Subunit-I Gene from Türkiye","authors":"Famil Yusufoglu, F. Uçkan","doi":"10.4194/ga565","DOIUrl":"https://doi.org/10.4194/ga565","url":null,"abstract":"Plecoptera species are valuable both as freshwater indicators and as key role in the food chain of river ecosystems. Moreover, they constitute an order with a high speciation capacity. Therefore, identification at the species level by morphological analysis leads to reliability problems. Studies on the phylogeny of Nemoura flexuosa which belongs to this order are scarce in the literature. Samples were collected from Kocaeli-Türkiye and then morphological and phylogenetic descriptions of the specimens were made. The Cytochrome Oxidase C Subunit-I gene region in mitochondrial DNA was amplified and sequenced. Molecular analyses revealed that the samples belong to the N. flexuosa species. Phylogenetic analyses were carried out by comparing the gene sequences of N. flexuosa haplotypes in Europe with gene sequences of the same basepair length and with the gene sequence of Amphinemura borealis which was used as an outgroup. The two phylogenetic trees were consistent and the collected specimens were evolutionarily closer to the OK316196.1, OK316261.1, OK316397.1, MZ608304.1, KY261370.1 and JX905853.1 haplotype. The presence of N. flexuosa in Kocaeli and the phylogenetic status of the Türkiye haplotype were reported. Clarifying the phylogenetic status of ecologically important species provides basic information for biosecurity studies for possible future conservation and control programs.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47916354","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

First Identification DNA Barcoding of Bronze Featherback Fish, Notopterus notopterus (Pallas, 1769) (Osteoglossiformes: Notopteridae), in Brantas River, East Java, Indonesia 印度尼西亚东爪哇布兰塔斯河青铜羽背鱼，Notopterus Notopterus (Pallas, 1769)(骨舌目:Notopteridae)首次鉴定DNA条形码

Genetics of Aquatic Organisms Pub Date : 2023-01-03 DOI: 10.4194/ga549

Amatul Firdausy Khansa, Hutama Satria Farizky, M. B. Santanumurti, M. Jamal, Lalu M Iqbal Sani, H. Madduppa, P. D. Wulansari

引用次数: 1

In Silico Structural Analysis, Classification, and Functional Annotation of an Uncharacterized Protein from an Aquatic Fungus Lindgomyces ingoldianus 水生真菌lingdgomyces ingoldianus的结构分析、分类和功能注释

Genetics of Aquatic Organisms Pub Date : 2022-12-06 DOI: 10.4194/ga527

Jayzon G. Bitacura, Mudjekeewis D. Santos

{"title":"In Silico Structural Analysis, Classification, and Functional Annotation of an Uncharacterized Protein from an Aquatic Fungus Lindgomyces ingoldianus","authors":"Jayzon G. Bitacura, Mudjekeewis D. Santos","doi":"10.4194/ga527","DOIUrl":"https://doi.org/10.4194/ga527","url":null,"abstract":"An uncharacterized protein from Lindgomyces ingoldianus was initially annotated to contain various domains with promising biotechnological applications. Thus, this study was conducted to determine the structural characteristics, classification, and potential function of this protein through in silico methods. Results revealed that this protein has a neutral charge and is unstable and non-polar. It is predicted to have a signal peptide, glycoside hydrolase family 114 (GH114) domain, low complexity region, and fungal type cellulose-binding domain (fCBD) or type 1 carbohydrate-binding module (CBM1) region. Structural characterization and phylogenetic analysis revealed that this protein is an endo-α-1,4-polygalactosaminidase enzyme. This protein was also predicted to contain 36 active sites and is extracellularly secreted. Molecular docking analysis showed that it could bind galactosaminogalactan (GAG), a key virulence factor for Aspergillus fumigatus chronic infections. The binding of this protein to GAG was much better than Ega3, which could be attributed to the presence of the fCBD region that is unique to this protein. It is hypothesized that the fCBD domain helps in carbohydrate recognition and holds them in place for maximum catalysis in the GH114 domain. Finally, this protein is found to be related to its orthologue from the plant pathogenic fungus Zopfia rhizophila.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44607615","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

Isolation and Identification of Tersakan Stream (Amasya, Suluova TÜRKİYE) Cyanobacteria and Investigation of the Presence of the Microcystin-LR Tersakan Stream（Amasya，Suluova TÜRKïYE）蓝藻的分离鉴定和微囊藻毒素LR的存在

Genetics of Aquatic Organisms Pub Date : 2022-12-05 DOI: 10.4194/ga538

E. Çelikoğlu, Meral Yilmaz Cankilic, Onder Idil

{"title":"Isolation and Identification of Tersakan Stream (Amasya, Suluova TÜRKİYE) Cyanobacteria and Investigation of the Presence of the Microcystin-LR","authors":"E. Çelikoğlu, Meral Yilmaz Cankilic, Onder Idil","doi":"10.4194/ga538","DOIUrl":"https://doi.org/10.4194/ga538","url":null,"abstract":"Cyanobacteria are a concern worldwide due to their blooms and the toxins they produce. The aim of this study is to reveal the cyanobacterial diversity of Tersakan Stream and toxin analysis. For these purpose, water samples were taken from Tersakan Stream in 2018 and cyanobacterial diversity was determined by culture-dependent and independent methods. PCR amplification of microcystin genes (McyB and McyE) and Microcystin-LR (L:Leucine, R: Arginine) (MC-LR) analysis in water sample was performed. While 10 different Cyanobacteria were identified by light microscopy examination and 16S rRNA + ITS sequence, less diversity was revealed by culture-independent methods. Sequences of the isolates were associated with Pseudanabaena lonchoides, Leptolyngbya sp, Toxifilum sp, Cylindrospermum moravicum, Nostoc sp, Oscillatoria sp, Synechocystis sp, Synechococcus sp, Cyanobacterium aponinum and Cyanobium sp. Culture-independent sequences were associated with Microcytis sp, Nostoc sp, Cyanobium sp, Dolichospermum sp, Anabaena sp, Leptolyngbya sp and Uncultured cyanobacterium. Microcystin analysis was performed by both molecular and analytical methods. PCR results of McyB and McyE genes supported the HPLC-DAD analysis result. 0.467 μg L-1 microcystin LR was detected in Tersakan Stream by HPLC-DAD analysis. Although the microcystin concentration is low, Tersakan Stream is an important area to be monitored with its eutrophic character and cyanobacterial diversity.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49327440","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

The Effect of Benzo[a]pyrene on Xenobiotic Metabolizing Cytochrome P4501A (CYP1A) Expression in Spotted Scat, Scatophagus argus (Linnaeus, 1766) 苯并[a]芘对斑点刀疤外源代谢细胞色素P4501A（CYP1A）表达的影响（Linnaeus，1766）

Genetics of Aquatic Organisms Pub Date : 2022-10-06 DOI: 10.4194/ga496

A. Shadi, A. Ghasemi

引用次数: 0

Molecular Diversity of Far-Eastern Trematodes of the Genus Crepidsotomum (Allocreadiidae) by Means of Nuclear 28S rRNA and Mitochondrial COI Gene Sequences 利用核28S rRNA和线粒体COI基因序列研究灰蝶属远东银耳的分子多样性

Genetics of Aquatic Organisms Pub Date : 2022-08-04 DOI: 10.4194/ga510

D. Atopkin

引用次数: 0

Heat-shock Protein 70: Sequence and Expression Analysis in African Catfish Clarias gariepinus after Bacterial Infection and Stress Exposures 细菌感染和应激暴露后非洲鲶鱼热休克蛋白70的序列和表达分析

Genetics of Aquatic Organisms Pub Date : 2022-06-13 DOI: 10.4194/ga509

H. Nasrullah, Likhawan Layinatuzzain, Dinar Tri Soelistiyowati, W. Widanarni, A. Alimuddin

{"title":"Heat-shock Protein 70: Sequence and Expression Analysis in African Catfish Clarias gariepinus after Bacterial Infection and Stress Exposures","authors":"H. Nasrullah, Likhawan Layinatuzzain, Dinar Tri Soelistiyowati, W. Widanarni, A. Alimuddin","doi":"10.4194/ga509","DOIUrl":"https://doi.org/10.4194/ga509","url":null,"abstract":"Heat-shock protein 70 (HSP70) is a member of the Heat-shock protein family that plays an important role in cellular homeostasis against various stressors in fish. This research aimed to identify the full length of cDNA sequence HSP70 in African catfish C. gariepinus and assessed its mRNA expression under various tissues and stress conditions. The cDNA was cloned and amplified using the polymerase chain reaction (PCR) followed by bi-directional sequencing. The mRNA expression was quantified using the real-time PCR (qPCR) method. A full-length ORF of C. gariepinus HSP70 cDNA was 1932 bp long, encoded 643 amino acids. Three signature sequences of the HSP70 family were detected in the predicted amino acid sequence. The C. gariepinus HSP70 showed the highest similarity in nucleotide and amino acid sequence (>90%) to HSP70 from other Siluriformes catfish species. The HSP70 mRNA was expressed in all tested tissues, with the highest expression found in the liver and spleen, followed by the intestine, heart, head-kidney, and gill. The C. gariepinus HSP70 expression was significantly induced generally after 6 hours of bacterial infection, transportation, heat shock, and high nitrite exposure. The results indicated that the HSP70 gene could serve as an early stress biomarker in C. gariepinus","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46295981","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

Analysis of Genetic Diversity in Wild and Domesticated Stocks of the Tropical Abalone Haliotis asinina by Microsatellite Polymorphism 应用微卫星多态性分析热带鲍野生和驯化种群的遗传多样性

Genetics of Aquatic Organisms Pub Date : 2022-06-02 DOI: 10.4194/ga501

P. Praipue, S. Klinbunga, Sirikan Prasertlux, Sirithorn Janpoom, Puttawan Rongmung, Ornchuda Ratdee, Wanwipa Ittarat, Phimsucha Boonphimpapha, P. Jarayabhand, B. Khamnamtong

{"title":"Analysis of Genetic Diversity in Wild and Domesticated Stocks of the Tropical Abalone Haliotis asinina by Microsatellite Polymorphism","authors":"P. Praipue, S. Klinbunga, Sirikan Prasertlux, Sirithorn Janpoom, Puttawan Rongmung, Ornchuda Ratdee, Wanwipa Ittarat, Phimsucha Boonphimpapha, P. Jarayabhand, B. Khamnamtong","doi":"10.4194/ga501","DOIUrl":"https://doi.org/10.4194/ga501","url":null,"abstract":"The basic information on genetic diversity of wild and hatchery-propagated stocks of tropical abalone, Haliotis asinina is important for the construction of a breeding scheme leading to the sustainable culturing activity of this species. In this study, 2,876 expressed sequence tags (ESTs) were in silico analyzed and 178 EST sequences contained microsatellite motifs. Four loci (DW455, DW503, PHe177, and PT102) of type I and two loci (Haμ9 and Haμ10) of type II microsatellites were applied for genetic diversity studies. The mean number of alleles per locus and observed heterogeneity in wild populations were 4.167 and 0.483, and 4.833 and 0.528 for CAME (east coast) and TRGW (west coast) while those of hatchery-propagated samples were 3.000 and 0.708, 4.500 and 0.479, 5.167 and 0.524, and 6.333 and 0.527 for PHIH (2nd generation, G2; Philippines), SAMH (G1), SMaRT-TRGH (G8) and SMaRT-SICH (G8), respectively. The numbers of alleles, observed heterozygosity and effective population sizes suggested no severe reduction of genetic diversity in our breeding program of H. asinina. However, reduced Ne was observed in the cultured stocks from the Philippines (PHIH). FST-statistics and the exact test between pairs of samples revealed significant genetic differences between all pairwise comparisons of samples in this study.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41246551","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

Isolation and Expression Analysis of cAMP-Dependent Protein Kinase and Adenylyl Cyclase-Associated Protein 1-like cDNAs in the Giant Tiger Shrimp Penaeus monodon 对虾camp依赖性蛋白激酶和腺苷酸环化酶相关蛋白1样cdna的分离与表达分析

Genetics of Aquatic Organisms Pub Date : 2022-03-24 DOI: 10.4194/ga480

S. Klinbunga, Kanchana Sittikankaew, Sirikan Prasertlux, Sirithorn Janpoom, Puttawan Rongmung, Wanwipa Ittarat, Phimsucha Boonpimpapha, B. Khamnamtong

{"title":"Isolation and Expression Analysis of cAMP-Dependent Protein Kinase and Adenylyl Cyclase-Associated Protein 1-like cDNAs in the Giant Tiger Shrimp Penaeus monodon","authors":"S. Klinbunga, Kanchana Sittikankaew, Sirikan Prasertlux, Sirithorn Janpoom, Puttawan Rongmung, Wanwipa Ittarat, Phimsucha Boonpimpapha, B. Khamnamtong","doi":"10.4194/ga480","DOIUrl":"https://doi.org/10.4194/ga480","url":null,"abstract":"Characterization of genes exhibiting differential expression profiles during ovarian development is important for understanding reproductive maturation of the giant tiger shrimp (Penaeus monodon). Here, the partial cDNAs of P. monodon cAMP-dependent protein kinase, catalytic subunit 1 (PmPkaC1) and adenylyl cyclase-associated protein 1-like (PmCap1-l) were studied. They were more preferentially expressed in ovaries than testes of cultured juveniles and wild broodstock. PmPkaC1 mRNA in ovaries of non-ablated broodstock was significantly increased during vitellogenesis (P<0.05). However, unilateral eyestalk ablation (the removal of one eyestalk) resulted in a significant reduction of its expression (P<0.05). PmCap1-l was not differentially expressed during ovarian development in wild non-ablated broodstock. It was up-regulated in mature ovaries following eyestalk ablation (P<0.05). The PmCap1-l transcript in each ovarian stage of the former was significantly lower than that of the latter (P<0.05). The levels of ovarian PmPkaC1 and vitellogenin 1 (PmVtg1) treated in vitro with 17-20β-DHP (0.1, 1.0 and 10.0 μg/ml for 24 h) was not significantly different from the control (P>0.05). Nevertheless, the expression of PmCap1-l was increased in ovaries treated with 0.1 and 10 μg/ml 17-20β-DHP at 24 hours post treatment (hpt, P<0.05).","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42862829","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

An In-silico Approach for Identifying Phytochemical Inhibitors Against Nervous Necrosis Virus (NNV) in Asian Sea Bass by Targeting Capsid Protein 以衣壳蛋白为靶点鉴定亚洲鲈鱼神经坏死病毒（NNV）植物化学抑制剂的计算机方法

Genetics of Aquatic Organisms Pub Date : 2022-03-15 DOI: 10.4194/ga487

Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Sarower Mahfuj

{"title":"An In-silico Approach for Identifying Phytochemical Inhibitors Against Nervous Necrosis Virus (NNV) in Asian Sea Bass by Targeting Capsid Protein","authors":"Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Sarower Mahfuj","doi":"10.4194/ga487","DOIUrl":"https://doi.org/10.4194/ga487","url":null,"abstract":"Nervous necrosis virus (NNV) is a devastating infectious pathogen for fish species with 100% mortality. To date, no specific drugs or vaccines have been developed that can prevent infections in aquaculture caused by NNV. It has been found that the NNV utilizes capsid protein to enter into the host cell in Asian sea bass and cause disease. In this study, we evaluated the inhibitory potential of Allium sativum compounds that have been reported to show antiviral activity against various pathogens. The capsid protein was modeled and the binding affinity of all the compounds was calculated with the docking approach and top 2 (PubChem CID: 122130381 and CID 12303662) inhibitory compounds were selected for further ADMET properties and DFT analysis. Both the geometry optimization and redocking of the two inhibitory compounds (PubChem CID: 122130381 and CID 12303662) showed a strong binding affinity of -8.2 and -8.0 kcal/mol, respectively with the capsid protein. The molecular dynamic simulation approach further validated the capsid protein – CID: 122130381 and capsid protein- CID 12303662 complex stability. In conclusion, this study deduces that these Allium sativum phytochemicals might act as significant inhibitors of the NNV in sea bass, which can be further validated experimentally.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42607322","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