Purification and characterization of tributyltin-binding protein type 2 from plasma of Japanese flounder, Paralichthys olivaceus

We used gel filtration chromatography, anion-exchange chromatography and polyacrylamide gel electrophoresis to purify tributyltin-binding protein type 2 (TBT-bp 2) from plasma of Japanese flounder (Paralichthys olivaceus) injected intraperitoneally with TBT (5.0 mg/kg body weight). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the molecular mass of TBT-bp 2 was approximately 48 kDa, and isoelectric focusing-polyacrylamide gel electrophoresis indicated that the isoelectric point was approximately 3.0. TBT-bp 2 contained 40% N-glycan. The complete cDNA nucleotide sequence and the genome sequence of TBT-bp 2 were determined by means of rapid amplification of cDNA ends of liver tissue of Japanese flounder and a genome-walking technique, respectively. The 216 amino acid sequence of TBT-bp 2 showed 47% identity to the sequences of puffer fish (Takifugu pardalis) saxitoxin- and tetrodotoxin-binding protein but only 27% similarity to the sequence of TBT-bp 1. Analysis of the motif sequence of the amino acid sequence and the structure of the gene encoding TBT-bp 2 suggested that this protein belongs to the lipocalin superfamily.     

Purification and characterization of mosquitocidal Bacillus sphaericus BinA protein

Certain strains of Bacillus sphaericus produce a highly toxic mosquito-larvicidal binary toxin during sporulation. The binary toxin is composed of toxic BinA (41.9 kDa) and receptor binding BinB (51.4 kDa) polypeptides and is active against vectors of filariasis, encephalitis and malaria. The toxin has been tested with limited use for the control of vector mosquitoes for more than two decades. The binA gene from a local ISPC-8 strain of B. sphaericus that is highly toxic to Culex and Anopheles mosquito species was cloned into pET16b and expressed in Escherichia coli. The purified BinA protein differs by one amino acid (R197 M) from BinA of the highest toxicity strains 1593/2362/C3-41. Majority of the expressed protein was observed in inclusion bodies. BinA inclusions alone from E. coli did not show toxic activity, like reported previously. However, the active form of BinA could be purified to homogeneity from the soluble fraction of E. coli cell lysate, grown at reduced temperature after isopropyl β-d-thiogalactopyranoside induction. The purified BinA protein with and without poly-histidine tag showed LC₅₀ dose of 82.3 and 66.9 ng ml⁻¹, respectively, at 48 h against Culex quinquefasciatus larvae. The secondary structure of BinA is expected to be mainly β strands as estimated using far-UV circular dichroism. The estimates matched well with the secondary structure predictions using amino acid sequence. This is the first report of large-scale purification and accurate toxicity estimation of soluble B. sphaericus BinA. This can help in design and synthesis of improved bacterial insecticide.     

Identification, characterization and expression of a novel cytokine M17 homologue (MSH) in fish

Members of the interleukin 6 (IL6)-cytokine subfamily of proteins are involved in numerous physiological processes including cellular development, inflammatory function, and acute phase and immune responses. Previously, a cytokine-like gene named M17, which is closely associated with the IL6 subfamily, has been identified in fish with no apparent orthologue in higher vertebrates. Here, we cloned a novel cDNA from Japanese flounder, Paralichthys olivaceus, which had significant identity but exhibited contrasting expression with fish M17s, named here as M17 Homologue (MSH). With subsequent in silico search and full annotation of the M17 orthologue in zebrafish (Danio rerio), MSH orthologues in tiger puffer (Takifugu rubripes), green spotted pufferfish (Tetraodon nigroviridis) and stickleback (Gastorosteus aculeatus), as well as structural, synteny comparisons and phylogenetic analysis with known IL6-cytokines, we determined the novelty of the fish MSH. Japanese flounder MSH was observed to be highly expressed in immune-related tissues and are induced by immune stimulants, lipopolysaccharide (LPS), polyI:C and peptidoglycan (PG) in vitro suggesting that it is involved in fish immunity particularly against viral and bacterial agents, a functional feature exhibited by previously reported fish cytokines.     

Purification,characterization, and molecular cloning of chitinases from the stomach of the threeline grunt Parapristipoma trilineatum

Two chitinase isozymes, PtChiA and PtChiB, were purified from the stomach of the threeline grunt, Parapristipoma trilineatum. The molecular masses of PtChiA and PtChiB were estimated to be 50 and 60 kDa by SDS-PAGE, respectively. Both chitinases were stable at pH 3.0–6.0 (acidic) and showed the optimum pH toward both short and long substrates in the acidic region (pH 2.5–5.0). PtChiA and PtChiB preferentially degraded the second and third glycosidic bonds from the non-reducing end of N-acetylchitooligosaccharides, respectively. PtChiA and PtChiB exhibited wide substrate specificities toward crystalline chitin. Moreover, 2 cDNAs encoding PtChiA and PtChiB, PtChi-1 and PtChi-2, respectively, were cloned. The deduced amino acid sequences of both chitinase cDNAs comprised N-terminal signal peptides, glycoside hydrolase 18 catalytic domains, linker regions, and C-terminal chitin-binding domains. Phylogenetic tree analysis of vertebrate chitinases revealed that fish stomach chitinases including PtChi-1 and PtChi-2 form unique chitinase groups, acidic fish chitinase-1 (AFCase-1) and acidic fish chitinase-2 (AFCase-2), which differ from the acidic mammalian chitinase (AMCase) group. The present results suggest that fish have a chitin-degrading enzymatic system in which 2 different chitinases, AFCase-1 and AFCase-2, with different degradation patterns are expressed in the stomach.     

Complete mitochondrial genome of Odontobutis haifengensis (Perciformes,Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis

Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016 bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.     

Purification and characterization of Xanthomonas campestris pv. glycines exopolysaccharide

The exopolysaccharides (EPS) of virulent and avirulent strains of Xanthomonas campestris pv. glycines, causal agent of bacterial pustule disease of soybean, and one strain of the soybean non-pathogen X. c. pv. campestris were isolated, purified, and their compositions compared. EPS produced by X. c. pv. glycines in a completely defined medium appears to be identical to the well-characterized EPS produced by X. c. pv. campestris (commonly referred to as xanthan gum). The EPS of all strains was composed of the carbohydrates glucose, mannose and glucuronic acid with acetyl and pyruvyl substituents present. Permethylation analyses indicated EPS preparations had identical hexose substitution patterns. Avirulent strains of X. c. pv. glycines produced as much or more acidic EPS as did virulent strains in vitro. None of the EPS preparations were active as elicitors of the soybean pterocarpanoid phytoalexin glyceollin as determined by a soybean cotyledon bioassay.     

Purification,characterization and immunostimulatory activity of polysaccharide from Cipangopaludina chinensis

In this study, we investigated the purification, preliminary characterization and immunostimulatory activity in vivo of polysaccharide from Cipangopaludina chinensis (CCPS). Firstly, crude CCPS was prepared by hot water extraction. And the crude CCPS was sequentially purified by chromatography of DEAE-52 and Sephadex G-100, resulting in two purified fractions of CCPS-1 and CCPS-2. We found the two fractions were homogeneous heteropolysaccharides mainly composed of rhamnose and glucose with the average molecular weight of 226 and 235 kDa, respectively. CCPS-2 was quite different from CCPS-1. It had much higher content of uronic acid and sulfuric radical. For immunostimulatory activity in vivo, crude CCPS could significantly increase the thymus and spleen indices, enhance the macrophage function, and increase the level of serum hemolysin in cyclophosphamide-treated mice, suggesting CCPS had a potent immunostimulatory activity and could be explored as a potential natural immunomodulatory agent     

Purification and characterization of a wound-inducible thaumatin-like protein from the latex of Carica papaya

A 22.137 kDa protein constituent of fresh latex was isolated both from the latex of regularly damaged papaya trees and from a commercially available papain preparation. The protein was purified up to apparent homogeneity and was shown to be absent in the latex of papaya trees that had never been previously mechanically injured. This suggests that the protein belongs to pathogenesis-related protein family, as expected for several other protein constituents of papaya latex. The protein was identified as a thaumatin-like protein (class 5 of the pathogenesis-related proteins) on the basis of its partial amino acid sequence. By sequence analysis of the Carica genome, three different forms of thaumatin-like protein were identified, where the latex constituent belongs to a well-known form, allowing the molecular modeling of its spatial structure. The papaya latex thaumatin-like protein was further characterized. The protein appears to be stable in the pH interval from 2 to 10 and resistant to chemical denaturation by guanidium chloride, with a of 15.2 kcal/mol and to proteolysis by the four papaya cysteine proteinases. The physiological role of this protein is discussed.     

Purification and characterization of mononocardomycoloylglycerol from Nocardia rhodochrous

A component of the acetone-soluble lipids of Nocordia rhodochrous grown on glycerol, was purified by column chromatography on silicic acid and characterized by infrared, nuclear magnetic resonance spectroscopy, optical rotation measurement and product identification after alkaline hydrolysis. Glycerol was the sole water-soluble component and nocardomycolic acids with chain lengths ranging from C₄₀ to C₄₄ were the constituent fatty acids identified. On the basis of the evidence obtained, the substance isolated from N. rhodochrous is identified as a mixture of mononocardomycoloylglycerols in which nocardomycolic acids are bound to one of the primary hydroxyl groups of the glycerol molecule.     

Purification and characterization of basic glucosyltransferase from Streptococcus mutans serotype c

Streptococcus mutans Ingbritt (serotype c) was found to secrete basic glucosyltranserase (sucrose: 1,6-α-^D-glucan 3-α- and 6-α- glucosyltransferase). The enzyme preparation obtained by ethanol fractionation, DEAE Bio-Gel A chromatography, chromatofocusing and preparative isoelectric focusing was composed of three isozymes with slightly different isoelectric points (pI 8.1–8.4). The molecular weight was estimated to be 151 000 by SDS-polyacrylamide gel electrophoresis. The specific activity of the enzyme was 9.8 IU per mg of protein and the optimum pH was 6.5. The enzyme was activated 2.4-fold by commercial dextran T10, and had K_m values of 7.1 μM for the dextran and 4.3 mM for sucrose. Glucan was de novo synthesized from sucrose by the enzyme and found to be 1,6- α-D-glucan with 17.7% of 1,3,6-branching structure by a gas-liquid chromatography-mass spectroscopy.     

Characterization,expression and localization of valosin-containing protein in ovaries of the giant tiger shrimp Penaeus monodon

Valosin-containing protein (VCP), a member of the ATPase-associated with diverse cellular activity (AAA) family, was identified from the giant tiger shrimp (Penaeus monodon). The full-length cDNA of the PmVCP mRNA consisted of 2724 bp containing an ORF of 2367 bp corresponding to a deduced polypeptide of 788 amino acids. The deduced PmVCP protein contained two putative Cdc48 domains (positions 17–103, E-value = 2.00e− 36 and 120–186, E-value = 3.60e− 11) and two putative AAA domains (positions 232–368, E-value = 3.67e− 24 and 505–644, E-value = 3.73e− 25). PmVCP mRNA expression in ovaries was greater than that in testes in both juveniles and broodstock. PmVCP was significantly up-regulated in stages II and IV ovaries in intact wild broodstock (P < 0.05) but it was not differentially expressed during ovarian development in eyestalk-ablated broodstock (P > 0.05). The expression level of PmVCP mRNA in ovaries of 14-month-old shrimp was not affected by progesterone injection (0.1 μg/g body weight, P > 0.05). In contrast, exogenous 5-HT administration (50 μg/g body weight) resulted in an increase of PmVCP mRNA in ovaries of 18-month-old shrimp at 6 and 24 h post-injection (hpi) (P < 0.05). The rPmCdc48-VCP protein and its polyclonal antibody were successfully produced. Cellular localization revealed that PmVCP was localized in the ooplasm of previtellogenic oocytes. Subsequently, it was translocated into the germinal vesicle of vitellogenic oocytes. Interestingly, PmVCP was found in nucleo-cytoplasmic compartments, in the cytoskeletal architecture and in the plasma membrane of mature oocytes in both intact and eyestalk-ablated broodstock.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of obscure puffer (Takifugu obscurus) and cross-species amplification

Obscure puffer (Takifugu obscurus) is an anadromous fish species in China. Here, we reported 10 polymorphic microsatellite loci isolated from a dinucleotide-enriched genomic library of T. obscurus. The number of alleles, observed and expected heterozygosity per locus in 30 individuals ranged from four to 10, from 0.57 to 0.86 and from 0.68 to 0.90, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium between pairs of loci was found. Cross-species amplification of these microsatellite loci in additional three fish species was performed. These polymorphic microsatellite loci would be useful for investigating genetic population structure and construction of genetic linkage map in T. obscurus.     

Purification and characterization of uricase,a nitrogen-regulated enzyme,from Neurospora crassa

Uricase, a purine catabolic enzyme, is controlled by induction and by nitrogen catabolite repression in Neurospora. Uricase was purified nearly 1000-fold to homogeneity. Only a single protein band could be detected in analytical gels of the pure enzyme, and the protein band in each case corresponded exactly to the position of in situ staining for enzyme activity. The molecular weight of native uricase was estimated to be 123,000 ± 7000. The enzyme is a tetramer composed of identical or similar-sized subunits. The K_m value of uricase for uric acid was estimated to be 4.2 × 10^?5, m. Oxonic acid was shown to be a competitive inhibitor of uricase, with a K_i value of 6.7 × 10^?7, m. Uricase is a stable enzyme and is not subject to feedback inhibition by ammonia, glutamate, or glutamine in Neurospora. The regulation of uricase appears to occur primarily at the biosynthesis level. Uricase appears to be a metalloenzyme with no essential sulfhydryl groups.     

Effects of different land use patterns on nifH genetic diversity of soil nitrogen-fixing microbial communities in Leymus Chinensis steppe

Biological nitrogen fixation through prokaryotic microbe is an important source of nitrogen been input into many natural ecosystems. In this study the active diazotrophic community was investigated in the three treatments of mowed, grazed and enclosed Leymus chinensis steppes in Hulunbeier grassland of Inner Mongolia by using approaches of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) and sequence analysis. The community structure and diversity of the bacterial groups from the different samples was further analyzed by using different techniques, such as statistical analysis and diversity index evaluation of the band patterns etc. The results showed that grazing activity significantly reduced the number of species and quantities of nitrogen-fixing microorganisms, as well as the nifH gene diversity. However, enclosed plots had the lowest diversity of nifH gene. While the highest one found in mowing plots. A total of 30 sequences representing 25 different sequence types were recovered from the DGGE gels after phylogenetic constructions. The results also revealed that most sequences were coming from Alphaproteobacteria of Proteobacteria, and characterized by sequences of members of Rhodobacter, Bradyrhizobium, Mesorhizobium, Rhodopseudomonas, Xanthomonas, Azospirillum, Gluconacetobacter, Methylobacterium and Methylocystis. Symbiotic nitrogen-fixers existed in grazing, mowing and enclosed plots accounted for 21.4%, 47.3% and 31.3% respectively in their dominant nitrogen-fixing bacteria. The result of principal components analysis showed that the influence of different land use patterns on nitrogen-fixing microbial communities composition can be ordered as grazing plots > enclosed plots > mowing plots. Nitrogen-fixing microbial communities in L. chinensis steppe were significantly (P < 0.05) influenced by the levels of nitrate nitrogen, total phosphorus, available phosphorus contents and pH value when canonical correspondence analysis was employed to identify relationship between nifH gene and soil physicochemical factors under different land use patterns. The result obtained from correlation analysis showed that there was a significant (P < 0.05) negative relationship between the nitrate nitrogen and the total phosphorus content, furthermore, the available phosphorus content was strongly correlated (P < 0.01) with the pH value.     

Purification, characterization, and cDNA cloning of a novel soluble saxitoxin and tetrodotoxin binding protein from plasma of the puffer fish, Fugu pardalis.

Some species of puffer fish have been reported to possess both of tetrodotoxin and saxitoxin, which share one binding site on sodium channels. We purified a novel soluble glycoprotein that binds to these toxins from plasma of the puffer fish, Fugu pardalis, and named puffer fish saxitoxin and tetrodotoxin binding protein (PSTBP). PSTBP possessed a binding capacity of 10.6 +/- 0.97 nmol x mg(-1) protein and a K(d) of 14.6 +/- 0.33 nm for [(3)H]saxitoxin in equilibrium binding assays. [(3)H]Saxitoxin (10 nm) binding to PSTBPs was half-inhibited by the presence of tetrodotoxin and saxitoxin at 12 microm and 8.5 nm, respectively. From the results of gel filtration chromatography (200 kDa) and SDS/PAGE (104 kDa), PSTBP was suggested to consist of noncovalently linked dimers of a single subunit. PSTBP was completely deglycosylated by glycopeptidase F, producing a single band at 42 kDa. Two highly homologous cDNAs to each other coding PSTBP (PSTBP1 and PSTBP2, the predicted amino-acid identity 93%), were obtained from a cDNA library of F. pardalis liver. These proteins consisted to two tandemly repeated homologous domains. The predicted amino-acid sequences of PSTBP1 and 2 were not homologous to that of saxiphilin, a reported saxitoxin binding protein, or sodium channels, but their N-terminus sequences were homologous to that of the reported tetrodotoxin binding protein from plasma of Fugu niphobles, which has not been fully characterized. The partially homologous cDNA sequences to PSTBP1 and 2 were also found in expressed sequence tag clones of nontoxic flounders liver. Presumably, PSTBP is involved in accumulation and/or excretion of toxins in puffer fish.     

中缅树鼩UCP2 cDNA核心片段的序列分析

解偶联蛋白2(UCP2)是近年新发现的一种解偶联蛋白,具有多种生物学活性,相关研究表明,UCP2可以抑制某些细胞(如免疫细胞等)线粒体活性氧的过量生成.本研究通过设计简并引物进行RT-PCR从中缅树鼩(Tupaia belangeri肝中获得UCP2基因cDNA核心序列.该片段长745 bp,推测氨基酸序列为248个氨基酸.结构功能分析发现,此段氨基酸序列具有2个线粒体内膜载体蛋白特征结构、5个跨膜α-螺旋结构域、1个嘌呤结合区域(PNBD)以及3个解耦联蛋白质的特征序列.中缅树鼩UCP2氨基酸序列与普氏野马(Equus caballus)、小家鼠(Mus musculus)、家犬(Canis lupus familiaris)、人(Homo sapiens)、褐家鼠(Rattus norvegicus)、豚鼠(Cavia porcellus)、苏门达腊猩猩(Pongo abelii)、加卡利 安鼠(Phodopus sungorus)和马铁菊头蝠(Rhinolophus ferrumequinum)UCP2进行比较,氨基酸同源性均在90％以上.同时,本研究通过MEGA5构建系统树,对UCP2分子进化特征进行了一定的探讨.     

Species delimitation in the European species of Clavulina (Cantharellales, Basidiomycota) inferred from phylogenetic analyses of ITS region and morphological data

The identification of the conventionally accepted species of Clavulina (Cantharellales, Basidiomycota) in Europe (Clavulina amethystina, Clavulina cinerea, Clavulina cristata, and Clavulina rugosa) is often difficult and many specimens are not straightforwardly assignable to any of those four species, which is why some authors have questioned their identity. In order to assess the status of those species, a morphological examination was combined with the molecular analysis of the ITS region. The same six major clades were obtained in the Bayesian and parsimony phylogenetic analyses, and all six clades were well-supported at least by one of the analyses. Morphological characters, such as the overall branching pattern, the presence and intensity of grey colour, the cristation of the apices, and basidiospore size and shape were to various extents correlated with the phylogenetic signal obtained from the ITS region. The congruence between the molecular analyses and morphology, rather than geographical origin, suggests the existence of several species that can be delimited using a combined phylogenetic and morphological species recognition. The analyses revealed that C. cristata and C. rugosa are well-delimited species. In contrast, more than one taxa could be subsumed under the names C. amethystina and C. cinerea, the taxonomical complexity of which is discussed. The ITS region is proved to be adequate to separate phylogenetic species of Clavulina.