Transcriptome generation and analysis from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758) through normalized cDNA library

Catfishes are commercially important fish for both the fisheries and aquaculture industry. Clarias batrachus, an Indian catfish species is economically important owing to its high demand. A normalized cDNA library was constructed from spleen of the Indian catfish to identify genes associated with immune function. One thousand nine hundred thirty seven ESTs were submitted to the GenBank with an average read length of approximately 700 bp. Clustering analysis of ESTs yielded 1,698 unique sequences, including 184 contigs and 1,514 singletons. Significant homology to known genes was found by homology searches against data in GenBank in 576 (34 %) ESTs, including similarity to functionally annotated unigenes for 158 ESTs. Additionally, 433 ESTs revealed similarity to unigenes and ESTs in the dbEST but the remaining 658 EST sequences (39 %) did not match any sequence in GenBank. Of a total of 1,698 ESTs generated, 65 ESTs were found to be associated with immune functions. Gene Ontology and KEGG pathway analyses of C. batrachus ESTs collectively revealed a preponderance of immune relevant pathways apart from the presence of pathways involved in protein processing, localization, folding and protein degradation. This study constitutes first EST analysis of lymphoid organ in aquaculturally important Indian catfish species and could pave the way for further research of immune-related genes and functional genomics in this catfish.     

Biochemical analysis of glucocorticoid-induced inhibition of IgE-mediated histamine release from mouse mast cells

Pretreatment of mouse mast cells with 10(-7) to 10(-6) M dexamethasone (DM) during overnight sensitization with mouse IgE antibody resulted in inhibition of antigen-induced histamine release and degranulation. The inhibition of both degranulation and histamine release increased linearly with the duration of the treatment; maximal inhibition was obtained after approximately 16 hr with DM. The addition of DM to sensitized mast cells immediately before antigen challenge did not affect the antigen-induced histamine release. DM interacted directly with mast cells by binding to DM-specific cytoplasmic receptors. The treatment of mast cells with DM did not affect the binding of IgE to mast cells or intracellular cAMP levels. Bridging of cell-bound IgE anti-DNP antibody on mouse mast cells either by multivalent DNP-HSA or by anti-IgE induced phospholipid methylation at the plasma membrane and Ca++ influx into the cells. Pretreatment of mast cells with DM inhibited the antigen-induced phospholipid methylation and Ca++ uptake but failed to affect histamine release by Ca++ ionophore A23187. The results suggest that DM treatment inhibits histamine release by the inhibition of the early stage of biochemical processes leading to opening Ca++ channels but does not affect the process distal to Ca++ influx or the binding of IgE molecules to IgE receptors.     

Chromosome analysis of walking catfish,Clarias magur (Teleostei,Siluriformes, Clariidae), using staining,FISH with 18S, 5S and BAC probes

The chromosomal characteristics of Clarias magur were examined using conventional (Giemsa-staining, Ag-impregnation and CMA₃ + DAPI fluorescence) and molecular/ FISH (18S & 5S rDNA probes + one BAC DNA probe) cytogenetic tools. The diploid chromosome number was 50 and the karyotype consisted of 14 metacentric, 20 sub-metacentric, 8 sub-telocentric, 8 acrocentric chromosomes with 84 chromosome arms without any heteromorphic pair. The C-heterochromatic blocks were located on centromeric position of 13 pairs of chromosomes. The NOR sites, visualized by AgNO₃- and CMA₃- staining, were situated at p arms of chromosome pair No. 21, which also corresponded to 18S rDNA site visualized by FISH. The FISH signal of ICF_001_D19 clone probe was observed on 18th chromosome pair. The findings of the present study on C. magur provided valuable markers for the chromosome identification and locations of genes of the BAC clone on the chromosome will lead to the construction of physical map of genome of this species.     

Kinetic characterization and regulation of purified glutamine synthetase from brain of Clarias batrachus.

Glutamine synthetase (GS) from brain of Clarias batrachus is purified to about 42-fold and characterized at optimum pH and temperature with respect to its kinetic parameters. Values for apparent Michaelis constant of the enzyme for L-glutamine, hydroxylamine and ADP are 50, 62.5 and 0.833 mM respectively. The very low apparent Km for ADP may be specially related to the expression of GS action under high energy bond and also be evidenced by the requirement of enzyme for a high ionic strength of the ADP. The study is extended by examining the effect of various amino acids and metabolites on GS activity in order to gain further understanding of the changes in kinetics and regulation. It reveals that whereas uridine monophosphate and glutamate act competitively with respect to L-glutamine, carbamylphosphate and asparagine act non-competitively. GS activity is markedly inhibited by leucine, aspartic acid and AMP but not by lysine. ATP and methionine sulfoximine behaved as potent inhibitors of the enzyme in vitro. It is suggested that the teleostean GS has most of the properties similar to those reported for mammalian and avian glutamine synthetases. However, it is proposed that kinetic regulation of this enzyme may play a significant role in ammonia detoxication and rate of formation of glutamine-derived neurotransmitters in fish brain.     

四个大豆栽培种的花序转录组分析

针对大豆落花落荚问题,选取花器官脱落性质存在差异的4份大豆(Glycine max)花序样品进行了RNA提取、转录组测序和分析。共获得原始数据20 GB,其中有效数据14.87 GB。结果表明,多荚与少荚品种花序转录水平差异主要集中在物质代谢、胁迫应答(GLYMA02g03301、GLYMA02G03230等)、刺激应答、病害抗性等方面,与脱落直接相关的基因表达上并无显著差异,表明参与上述生理过程的相关基因表达的差异与不同品种大豆落花落荚性质上的差异具有一定相关性。该结果系统地了解了不同品种大豆在花期花序部分的转录组特征与差异,分析了相关表达差异对于大豆落花落荚的影响,同时丰富了大豆转录组数据信息。     

Mg2+ inhibition of Na2+-stimulated Ca2+ release from brain mitochondria

Magnesium has been shown to modulate the Na+-stimulated release of Ca2+ (Na/Ca exchange) from brain mitochondria. The presence of 5 mM MgCl2 extramitochondrially inhibits the Na/Ca exchange as much as 70%. Additionally, Na+-stimulated Ca2+ release is enhanced by the presence of divalent chelators, this stimulation also being inhibited by the addition of excess Mg2+. The inhibitory effect of Mg2+ and the enhancement by chelating agents were both reversible. Heart mitochondria exhibit a similar enhancement of Na/Ca exchange by chelators and inhibition by MgCl2, though not as pronounced.     

革胡子鲶生长激素cDNA克隆与蛋白质结构分析

从革胡子鲶(Clarias lazera(Burchell))的脑垂体组织中提取总RNA, 应用RT-PCR方法, 扩增得到了革胡子鲶生长激素(Growth hormone, GH)基因cDNA的开放阅读框(Open reading frame, ORF)序列。ORF全长为603 nt, 编码由22个信号肽氨基酸和178个成熟肽氨基酸共同组成的生长激素前体蛋白。序列同源比较结果表明, 研究中得到的革胡子鲶生长激素氨基酸序列与GenBank中已报道的其他6种鲶形目鱼类的氨基酸序列同源性高达95.8%。二级结构预测分析结果表明, 革胡子鲶生长激素蛋白中含有a 螺旋、b 折叠和b 转角以及无规卷曲等二级结构, 以a 螺旋为主, 是典型的a 型结构蛋白质。此外, 抗原性分析表明, 在氨基酸序列中的4个区域均可形成优势抗原表位, 其结构特点非常适合改造成为重组生长激素疫苗或单克隆抗体制剂加以开发利用。     

Kinetic studies of catechol-o-methyltransferase from the brain of the African catfish,Clarias gariepinus

• 1.1. Optimum in vitro conditions, and kinetics of the enzyme catechol-O-methyltransferase from the brain of the male African catfish were studied.
• 2.2. A saturated level for S-adenosylmethionine, as methyldonor, and magnesium as cofactor was reached at 5 μM and 10 mM, respectively.
• 3.3. The addition of ascorbic acid, as an antioxidant, and tranylcypromine, as a MAO inhibitor, was not necessary, during incubations with fore-brain homogenates.
• 4.4. Kinetic analysis of the methylation of catecholestrone, catecholestradiol and dopamine showed K_m values of 1.2, 0.6 and 0.5 μM, respectively.
• 5.5. The affinity of the catecholsubstrates for the enzyme catechol-O-methyltransferase is much higher in the brain of the African catfish than in tissues of mammals.

     

Y chromosome DNA haplotyping suggests that most European and Asian men are descended from one of two males

Three hypervariable Y chromosome DNA loci have been analyzed in human males. The haplotypes defined allow paternal lineages to be identified. Most of these lineages fall into two groups. This indicates that the ancestry of a large proportion of the men studied can be traced back to one of two males.     

Development and characterization of genic SSR markers from low depth genome sequence of <Emphasis Type="Italic">Clarias batrachus</Emphasis> (magur)

Indian magur (Clarias batrachus) is an important freshwater catfish, which is listed as endangered under A3cde + 4acde ver. 3.1 categories by the IUCN (2015) due to decreasing population trend. Microsatellites or short sequence repeats (SSRs) tagged to genes have been utilized as gene marker. In the present study, 31,814 SSRs of C. batrachus (magur) were identified using microsatellite identification tool programme from the next generation sequencing data generated on Roche 454 and Ion Torrent platforms. A bioinformatics pipeline, with stringent criteria resulted in selection of 1672 microsatellite loci falling in the genic region. Initially, a total of 30 loci were selected for primer development; and of these 14 were successfully amplified and five were found to be polymorphic in 30 individuals of C. batrachus (magur). The observed as well as expected heterozygosity ranged from 0.038 to 0.526 and 0.434 to 0.784, respectively, and the number of observed alleles ranged from three to five. The study reported the application of next generation sequencing technologies for rapid development of microsatellite loci in Indian catfish species, C. batrachus (magur).     

Comparative analysis of milt quality and steroid levels in blood and seminal fluid of Persian sturgeon males, Acipenser persicus during final maturation induced by hormonal treatment

Steroids both in seminal fluid (SF) and blood serum (BS) as well as the milt quality (sperm motility and sperm production) were investigated during final maturation of Persian sturgeon. The BS levels of testosterone (T), 11-Ketotestosterone (11-KT), progesterone (P), 17α,20β,21-trihydroxy-4-pregnen-3-one (20βS), cortisol (C) and 17α,hydroxyprogesterone (OHP) elevated after pituitary preparation (PP) treatment and then decreased during stripping period for spermiating males. Such elevations did not occur for non-spermiating individuals and steroids remained in basal levels after PP treatment until the end of stripping period. For both groups (spermiating and non-spermiating fish), the BS levels of 17α,20β-dihydroxy-4-pregnen-3-one (DHP) did not show significant changes during experiment. During stripping period, the values of all tested steroids were significantly lower in SF than in BS of spermiating males. SF levels of 20βS and 11-KT showed a decreasing trend and the other steroids were unchanged during this period. Significant positive correlations were found between the values of 20βs and 11-KT in BS with their levels in SF. Also, BS and SF levels of 20βs and 11-KT were positively correlated with sperm motility characteristics (percentage and duration of motility) and sperm production (sperm density and milt volume), respectively. The results showed the probable involvement of 20βs, P, OHP, T, 11-KT and C in final maturation of Persian sturgeon, especially 20βs and 11-KT had good correlations with qualitative parameters of milt. The lower levels of steroids in SF than those in BS might also be essential for viability of Persian sturgeon spermatozoa. Probably, there are mechanisms that stabilize the concentrations of a number of hormones in the SF.     

Extraction and analysis of carotenoids from the New Zealand sea urchin Evechinus chloroticus gonads

Sea urchin gonad (roe) is a highly valued food in Japan and North America. Gonad price is strongly influenced by quality, with appearance, especially colour being a major determinant. Previous attempts to extract a carotenoid profile from the New Zealand sea urchin species Evechinus chloroticus have been challenging due to the large amount of lipid present in the gonad. A carotenoid extraction and high performance liquid chromatography (HPLC) analysis method was developed to reduce lipid contamination by incorporating a saponification and lipid cold precipitation in the extraction procedure. This method enabled greater carotenoid purity and enhanced analysis by HPLC. Echinenone was found to be the main carotenoid present in all E. chloroticus gonads. Dark coloured gonads contained higher levels of fucoxanthin/fucoxanthinol, β-carotene and xanthophylls such as astaxanthin and canthaxanthin. This information on the modification and deposition of carotenoids will help in the development of diets to enhance gonad colour.