Length Nucleotide Sequence Research Articles

Integrative Analysis of Vibrio Cholerae Genomic Data for Understanding its Pathogenicity and Evolution

Cholera remains a significant global health threat, with substantial mortality rates, yet limited information exists on the pathogenicity, genomic data, and evolutionary relationships of Vibrio cholerae. This study presents a comprehensive genomic analysis of ten V. cholerae strains, examining nucleotide sequence length, virulence factors, pathogenicity islands, and mobile genetic elements. Using tools like NCBI, VFDV, ISLANDviewer, VRprofile, and CLUSTAL OMEGA, the analysis revealed notable variation in nucleotide sequence lengths, with the Amazonia strain and P16 strain showing the highest numbers. Virulence factor analysis identified that some strains, such as Amazonia and C1, possess significantly more virulence factors than others, contributing to cholera pathogenesis. Pathogenicity island analysis showed variability, with some strains like P16 and Amazonia containing more islands, while others, such as strain 0395-B, have fewer, underscoring their role in disease causation. Mobile genetic elements were identified in nine of the ten strains, facilitating the spread of crucial traits across bacterial populations. Evolutionary analysis indicated that all strains share a common ancestor, with Amazonia and strain 1 showing the greatest evolutionary distance from other strains. Additionally, sequence similarity analysis revealed that regions with 80-100% similarity are conserved, while those with less than 80% similarity are non-conserved. These findings offer valuable insights into the genetic diversity, virulence, and evolutionary relationships among V. cholerae strains, contributing to a deeper understanding of cholera pathogenesis and potential avenues for intervention.

Superstatistics Applied to Cucurbitaceae DNA Sequences.

The short and long statistical correlations are essential in the genomic sequence. Such correlations are long-range for introns, whereas, for exons, these are short. In this study, we employed superstatistics to investigate correlations and fluctuations in the distribution of nucleotide sequence lengths of the Cucurbitaceae family. We established a time series for exon sizes to probe these correlations and fluctuations. We used data from the National Center for Biotechnology Information (NCBI) gene database to extract the temporal evolution of exon sizes, measured in terms of the number of base pairs (bp). To assess the model's viability, we utilized a timescale extraction method to determine the statistical properties of our time series, including the local distribution and fluctuations, which provide the exon size distributions based on the q-Gamma and inverse q-Gamma distributions. From the Bayesian statistics standpoint, both distributions are excellent for capturing the correlations and fluctuations from the data.

Identification of watermelon H3K4 and H3K27 genes and their expression profiles during watermelon fruit development.

The ClaH3K4s and ClaH3K27s gene families are subfamilies of the SET family, each with a highly conserved SET structure domain and a PHD structural domain. Both participate in histone protein methylation, which affects the chromosome structure and gene expression, and is essential for fruit growth and development. In order to demonstrate the structure and expression characteristics of ClaH3K4s and ClaH3K27s in watermelon, members of the watermelon H3K4 and H3K27 gene families were identified, and their chromosomal localization, gene structure, and protein structural domains were analyzed. The phylogeny and covariance of the gene families with other species were subsequently determined, and the expression profiles were obtained by performing RNA-Seq and qRT-PCR. The watermelon genome had five H3K4 genes with 3207-8043bp nucleotide sequence lengths and four H3K27 genes with a 1107-5499bp nucleotide sequence. Synteny analysis revealed the close relationship between watermelon and cucumber, with the majority of members displaying a one-to-one covariance. Approximately half of the 'Hua-Jing 13 watermelon' ClaH3K4s and ClaH3K27s genes were expressed more in the late fruit development stages, while the changes were minimal for the remaining half. H3K4-2 expression was observed to be slightly greater on day 21 compared to other periods. Moreover, ClaH3K27-1 and ClaH3K27-2 were hardly expressed throughout the developing period, and ClaH3K27-4 exhibited the highest expression. These results serve as a basis for further functional characterization of the H3K4 and H3K27 genes in the fruit development of watermelon.

Morpho-molecular variability of different isolates of Ustilagonoidea virens causing false smut of rice

Spore balls of false smut of rice caused by Ustilagonoidea virens were collected from different major rice belts of eastern part of India. Ten isolates from ten different locations were collected and isolated in the laboratory for their, cultural, morphological and molecular characterization. Potato sucrose agar media was used for their cultural studies and observation on colony diameter, colour and sporulation were made. Spores of all the isolates were observed under scanning electron microscope (SEM) and light microscope for spore size, spine length and colour. Differences in colony characters were observed where the highest mycelial growth was observed in isolate Uv2 with 5.33 cm colony diameter and lowest mycelial growth was observed in Uv9 (3.70 cm). Most of the isolates produced white and circular colony. Spores of all the isolates observed under a light microscope appeared to be olive green in colour, however, a significant variation in spore size and spike length under SEM was observed. Spores size and spike length of different isolates ranged between 4.533 μm to 6.169 μm and 362.567 nm to 799.533 nm, respectively. For genetic identification and variability, DNAs of isolates were amplified using ITS1 and ITS 4 primers. The length of nucleotide sequences of different isolates varied from 583 to 606 bp. Phylogenetic analysis revealed genetic variation among the isolates, dividing them into two major groups.

Identification of Panax spp. in the Northern Vietnam based on ITS-rDNA sequence analysis

In order to accurately identify ginseng species (Panax spp.) that grow naturally in some Northern provinces of Vietnam, we collected 30 natural ginseng samples and used nuclear genetic region (ITS-rDNA) for current analysis. The success rate for nuclear genomic region PCR (ITS-rDNA) amplification is 100%. The bidirectional sequence read success rate obtained from the PCR product was 100%, with a nucleotide sequence length of 588 bp. Based on the analysis of ITS-rDNA region results, the samples of ginseng species from Tuyen Quang and Cao Bang provinces have a close relationship with Panax notoginseng (MLBS = 100%), while the samples of ginseng species from Ha Giang and Yen Bai provinces have a close relationship with P. stipuleanatus (MLBS = 99%). As the results, the ginseng samples from Tuyen Quang and Cao Bang provinces were identified as Panax notoginseng and the ginseng samples from Ha Giang and Yen Bai provinces were identified as Panax stipuleanatus. The obtained result also recorded new distribution areas of P. notoginseng in Tuyen Quang and Cao Bang provinces. Furthermore, we successfully registered the nuclear nucleotide sequences of these two Panax species on GenBank with 24 codes (from OM190408 to OM190410, from OM213014 to OM213030, and from OK376138 to OK376141).

Comparative HIV-1 Phylogenies Characterized by PR/RT, Pol and Near-Full-Length Genome Sequences.

In an effort to evaluate the accuracy of HIV-1 phylogenies based on genomes of increasing length, we developed a comprehensive near-full-length HIV-1 genome RT–PCR assay and performed a comparative evaluation via phylogenetic analyses. To this end, we conducted comparative analyses of HIV-1 phylogenies derived based on HIV-1 PR/RT (2253–3359 in the HXB2 genome) and pol region (2253–5250 in the HXB2 genome) sequences isolated from 134 HIV-1-infected patients in Cyprus (2017–2019). The HIV-1 genotypic subtypes determined using six subtyping tools (REGA 3.0, COMET 2.3, jpHMM, SCUEAL, Stanford, and Geno2pheno) were compared to investigate the discrepancies generated among different tools. To evaluate the accuracy of defined HIV-1 phylogenies, the samples exhibiting at least one discrepant subtyping result among different subtyping tools in both PR/RT and pol regions or only in the pol region (n = 38) were selected for near-full-length HIV-1 genome (790–8795 in HXB2 genome) sequencing using a newly developed RT–PCR/sequencing assay. The obtained sequences were employed for HIV-1 genotypic subtype determination and subjected to comparative phylogenetic-based analyses. It was observed that 39.6% of the 134 samples presented discrepancies in the PR/RT region, while 28.4% presented discrepancies in the pol region. REGA 3.0 produced the fewest discrepancies collectively in both regions and was selected for subsequent subtyping and comparative phylogenetic analyses of near-full-length HIV-1 genome sequences. The analyses of near-full-length HIV-1 genome sequences identified 68.4% of the 38 ‘discrepant samples’ (n = 26) as belonging to uncharacterized recombinant HIV-1 strains, while 21.1% were circulating recombinant forms (CRFs) (n = 8) and 10.5% belonged to pure group M subtypes (n = 4). The findings demonstrated a significant reduction of 11.2% in discrepancies when pol region sequences were used compared to PR/RT region sequences, indicating that increased nucleotide sequence lengths are directly correlated with more consistent subtype classification. The results also revealed that if the discrepancy in pol region subtyping results persists, then there is a high likelihood (89.5%) that the query sequence is a recombinant HIV-1 strain, 68.4% of which belong to uncharacterized recombinant HIV-1 strains. The results of this study showed that REGA 3.0 presented the best performance in subtyping recombinant HIV-1 strains, while Stanford performed better in defining phylogenies of pure group M subtypes. The study highlights that, especially in populations with polyphyletic HIV-1 epidemics resulting in a high prevalence of recombinant HIV-1 strains, neither PR/RT nor pol region sequences are reliable for the determination of HIV-1 genotypic subtypes in samples showing discrepancies among different subtyping tools, and only near-full-length or full-length HIV-1 genome sequences are sufficiently accurate.

Transcriptome-wide characterization, evolutionary analysis, and expression pattern analysis of the NF-Y transcription factor gene family and salt stress response in Panax ginseng

Jilin ginseng (Panax ginseng C. A. Meyer) has a long history of medicinal use worldwide. The quality of ginseng is governed by a variety of internal and external factors. Nuclear factor Y (NF-Y), an important transcription factor in eukaryotes, plays a crucial role in the plant response to abiotic stresses by binding to a specific promoter, the CCAAT box. However, the NF-Y gene family has not been reported in Panax ginseng. In this study, 115 PgNF-Y transcripts with 40 gene IDs were identified from the Jilin ginseng transcriptome database. These genes were classified into the PgNF-YA (13), PgNF-YB (14), and PgNF-YC (13) subgroups according to their subunit types, and their nucleotide sequence lengths, structural domain information, and amino acid sequence lengths were analyzed. The phylogenetic analysis showed that the 79 PgNF-Y transcripts with complete ORFs were divided into three subfamilies, NF-YA, NF-YB, and NF-YC. PgNF-Y was annotated to eight subclasses under three major functions (BP, MF, and CC) by GO annotation, indicating that these transcripts perform different functions in ginseng growth and development. Expression pattern analysis of the roots of 42 farm cultivars, 14 different tissues of 4-year-old ginseng plants, and the roots of 4 different-ages of ginseng plants showed that PgNF-Y gene expression differed across lineages and had spatiotemporal specificity. Coexpression network analysis showed that PgNF-Ys acted synergistically with each other in Jilin ginseng. In addition, the analysis of the response of PgNF-YB09, PgNF-YC02, and PgNF-YC07-04 genes to salt stress treatment was investigated by fluorescence quantitative PCR. The expression of these genes increased after salt stress treatment, indicating that they may be involved in the regulation of the response to salt stresses in ginseng. These results provide important functional genetic resources for the improvement and gene breeding of ginseng in the future.Conclusions: This study fills a knowledge gap regarding the NF-Y gene family in ginseng, provides systematic theoretical support for subsequent research on PgNF-Y genes, and provides data resources for resistance to salt stress in ginseng.

Morphological description and DNA barcoding study of Paramignya trimera collected in Khanh Hoa, Vietnam

Paramignya trimera is a valuable traditional medicinal plant, typically distributing in Khanh Hoa, Vietnam. In recent years, P. trimera has been exploited to treat liver diseases such as hepatitis, cirrhosis and liver cancers. The recorded during the investigation, in Khanh Hoa currently appears a number of species with similar phenotypes known collectively as P. trimera and appeared some morphology with differences in leaf morphology and thorns. Therefore, this study was carried out for identification, breeding and propagation conservation.This study has been described, characterized morphological characteristics and analyzed DNA barcodes based on ITS, matK and rbcL gene markers. About the morphology, P. trimera is distinguished from other species of the genus Paramignya with the following characteristics: elongated, single leaf, leaf-shaped lobe end, leaf veins shaped like a feather. Petiole with big, pointed and straight spines. Corolla 3, 6 stamens, upper election, with three sepals and two ovule leaves, the seed has a seed coat. The analysis of DNA barcodes shows that the results combination of the analysis of the three regions of ITS, matK and rbcL can be used to determine the genetic relationship between five samples of P. trimera. The nucleotide sequence lengths of the samples for the three regions of the ITS, matK and rbcL genes are 850 bp, 850 bp and 500 bp, respectively. On the basis of phenotypic tree analysis, the samples (X1, X2, X3, X4, X5) have the same evolutionary origin in ITS, matK and rbcL. Base on to identified the five morphological forms of P. trimera distributed in Khanh Hoa as the same species and expanded the distribution area as well as in-depth research on P. trimera morphologies in Khanh Hoa, Vietnam.

Structural, molecular hybridization and network based identification of miR-373-3p and miR-520e-3p as regulators of NR4A2 human gene involved in neurodegeneration

MicroRNAs (miRNAs) are short non-coding RNAs with a 22 nucleotide sequence length and docks to the 3′UTR/5’UTR of the gene to regulate their mRNA translation to play a vital role in neurodegenerative diseases. The Nuclear Receptor gene (NR4A2), a transcription factor, and a steroid-thyroid hormone retinoid receptor is involved in neural development, memory formation, dopaminergic neurotransmission, and cellular protection from inflammatory damage. Therefore, recognizing the miRNAs is essential to efficiently target the 3′UTR/5’UTR of the NR4A2 gene and regulate neurodegeneration. Highly stabilized top miRNA-mRNA hybridized structures, their homologs, and identification of the best structures based on their least free energy were evaluated using in silico techniques. The miR-gene, gene-gene network analysis, miR-disease association, and transcription factor binding sites were also investigated. Results suggest top 166 miRNAs targeting the NR4A2 mRNA, but with a total of 10 miRNAs bindings with 100% seed sequence identity (both at 3’ and 5’UTR) at the same position on the NR4A2 mRNA region. The miR-373-3p and miR-520e-3p are considered the best candidate miRNAs hybridizing with high efficiency at both 3’ and 5’UTR of NR4A2 mRNA. This could be due to the most significant seed sequence length complementary, supplementary pairing, and absence of non-canonical base pairs. Furthermore, the miR-gene network, target gene-gene interaction analysis, and miR-disease association provide an understanding of the molecular, cellular, and biological processes involved in various pathways regulated by four transcription factors (PPARG, ZNF740, NRF1, and RREB1). Therefore, miR-373-3p, 520e-3p, and four transcription factors can regulate the NR4A2 gene involved in the neurodegenerative process.

Identification of Streptomyces spp. from garbage dump soils in Surabaya, Indonesia.

Background and Aim:Streptomyces is a well-known agent of secondary metabolite production. This study aimed to identify Streptomyces spp. from garbage dump soils in Surabaya based on the 16S rRNA gene sequence. Moreover, the structure of new chemical compounds used for treating infectious diseases in humans, animals, and plants was elucidated.Materials and Methods:We isolated Streptomyces spp. from garbage dump soils in Surabaya. In this study, all isolates were characterized according to phenotype, and they were also confirmed by 16S rRNA gene sequence analysis using real-time polymerase chain reaction. Multiple sequence alignment and molecular phylogeny analyses were conducted using the MEGA 5.0 software, and then the TREE VIEW program was used to display the phylogenetic tree. The level of DNA similarity was also evaluated using the basic local alignment search tool (BLAST) program and then compared with nucleotide sequences stored in the GenBank database using National Center for Biotechnology Information BLAST.Results:The eight Streptomyces spp. showed different nucleotide sequence lengths in gel electrophoresis and photography, which is in accordance with the results observed in the phylogenetic tree. New types of Streptomyces spp., Sp-C, Sp-D, Sp-Ep, Sp-G, and Sp-I, were found from the waste heap in Surabaya. Of these, Sp-Ep was very closely related to Streptomyces indonesiasis and Streptomyces nashvillensis. Sp-F was identified as Streptomyces levis strain NRRL B-24299, and Sp-C was identified as Synodontis filamentosus. Sp-D was related to Sida javensis and Staphylococcus roseus. Sp-G was related to Streptomyces roseoviridis strain NBRC 12911 and Streptomyces thermocarboxydovorans strain AT52. Sp-I was related to Streptomyces cangkringensis and Streptomyces asiaticus. Finally, Sp-A was related to Sansevieria laurentii strain LMG 19959.Conclusion:Based on the phylogenetic tree, new strains of Streptomyces isolate, namely, Sp-D, Sp-Ep, Sp-G, and Sp-I, were found in the garbage dump soils of Surabaya. This new strain can produce antibiotics to be used as an alternative to antibiotics; however, further research is needed to confirm the activity.

Biocontrol Potential of Four Indigenous Entomopathogenic Nematodes From Kenya

Globally, vegetable production including tomato is constrained by pests and diseases. The tomato leafminer, Tuta absoluta (Meyrick.), is a major pest of tomato, mainly managed using chemical pesticides. There is a need for integrated pest management (IPM), approaches that are human and environmentally friendly. The study aimed at molecular identification and virulence evaluation of four entomopathogenic nematodes (EPNs) against T. absoluta larvae. The DNA was extracted, sequenced, and phylogeny analyzed. The EPNs virulence was evaluated using the insect baiting technique at different nematode concentrations (0-Control, 100, 150, 200, and 250 infective juveniles/ml of distilled water). Larval mortality data were collected for five days. Molecular identification resulted in nucleotide sequence lengths of 877-895 base pairs (bp). All the isolates were found to be Steinernema species of EPNs. The % similarity of the isolates and their close relatives ranged between 82-100%. The isolates closely matched Steinernema spp. AY230184 (Sri Lanka); AY230186 (Kenya), JN651414 (Ethiopia), and MW151701 (Kenya). The sequences were deposited to Genbank as Steinernema sp. Isolate Kalro 75 (MW150871), Steinernema sp. Isolate Kalro S86 (MW150872), Steinernema sp. isolate Kalro97 (MW150873) and Steinernema sp. Isolate KalroR52 (MW150874). All the EPN isolates were virulent against T. absoluta. Isolate Kalro R52 and Kalro S86 recorded the highest mortality of 76±7.5%; 72±15.0% respectively in the 48 h. There was a significant difference (P < 0.001), between all the isolates and the Control. The four EPNs were virulent and have bio-control potential against, T. absoluta. Research on their virulence against T. absoluta in the field is recommended.

In silico Characterization of the Structure of Genes and Proteins related to β-carotene Degradation in Musa acuminata ‘DH-Pahang’ and Musa balbisiana ‘Pisang Klutuk Wulung’

β-carotene is an important nutritious content in banana. However, its lifetime depends on the enzymes controlling its conversion into strigolactone. To understand the involved enzymes’ activity, which are β-carotene isomerase (D27), carotenoid cleavage dioxygenase 7 (CCD7), and CCD8, would be the key to manipulate the rate of β-carotene degradation. In this research, we characterized the structure of genes and proteins of the D27, CCD7, and CCD8 from Musa acuminata ‘DH-Pahang’ and Musa balbisiana ‘Pisang Klutuk Wulung’ (PKW). We aligned the corresponding sequence of genes from both species to determine similarity and intron/exon positions. We also identified domains and motifs in the sequences of putative proteins of D27, CCD7, and CCD8. We found that D27, CCD7, and CCD8 genes in DH-Pahang and PKW comprise of various nucleotide sequence length, putative proteins, and numbers and length of exons and introns. However, the putative proteins possess the same domains: DUF4033 (domain of unknown function) in D27 and RPE65 (retinal pigment epithelium) in CCD7 and CCD8. Phylogenetic trees showed that D27, CCD7, and CCD8 proteins from DH-Pahang and PKW are conserved and clustered in the same clades with the same proteins of monocot plants. Hence, the results could be useful for future research in optimizing β-carotene content in banana.

Non-coding Regions of Mitochondrial DNA and the cox1 Gene Reveal Genetic Variability Among Local Belarusian Populations of the Causative Agent of Cercarial Dermatitis, Bird Schistosome Trichobilharzia szidati (Digenea: Schistosomatidae).

The cercariae of avian blood flukes Trichobilharzia szidati (Digenea, Schistosomatidae) are known to cause cercarial allergic dermatitis ("swimmer's itch") in humans. Global epidemics can have significant impacts on local tourism-related economies in recreational areas. Little is known about the genetic polymorphism of the parasite population, or about the variability of the non-coding regions of mitochondrial DNA (mtDNA) and the possibility of using this as a genetic marker. The T. szidati cercariae were collected over 7years from 33 naturally infected Lymnaea stagnalis snails from five sites at two neighboring lakes in Belarus. We investigated the variability of the short (SNR) and long (LNR) non-coding regions of mt DNA and the genetic diversity within the 1125-bp sequences of the gene for subunit 1 of cytochrome c oxidase (cox1). In the SNR sequences, we found only length variability caused by changes in the number of bases in the mononucleotide tracts T6-T8. LNR demonstrates high variability in nucleotide sequence length (182-260bp) depending on the presence of two long deletions of 59 and 78 nucleotides. Both mitochondrial loci (LNR and cox1) are characterized by high haplotype diversity (H = 0.922 and H = 1.0, respectively); the nucleotide diversity is significantly higher for LNR (π = 1.926 ± 0.443) compared to cox1 (π = 0.704 ± 0.059). Phylogenetic reconstructions based on the variability of each of the loci (LNR and cox1) and their concatenated sequences revealed their shallow structure and the absence of a correlation between the distribution of single-nucleotide polymorphisms and the geographic origin of parasites from two Belarusian lakes. We identified at last four weakly sublineages in the phylogenetic pattern of T. szidati. The carriers of each deletion have specific patterns for each of the two loci and form their own phylogeographic sublineages. An association between two fixed LNR substitutions and a fixed non-synonymous substitution in cox1 was found in four representatives of one lineage that had a short deletion in the LNR. This study clarified the phylogeographic structure of the Belarusian population of T. szidati. Our data provide the basis for the use two mt markers in large-scale population studies of the parasite, as well as for studying the molecular evolution of coding and non-coding mtDNA in trematodes.

Genetic diversity of porcine circovirus

This article is dedicated to the species diversity of porcine Circovirus that has been the causative agent of a disease caused by Porcine Circovirus widespread in pig farms of the Russian Federation and worldwide. The disease caused by porcine circovirus type II (PCV2) has various clinical signs accompanied by a number of syndromes as Postweaning multisystem wasting syndrome (SPMD), piglet dermatitis and nephropathy (SDNP), lymphoid, respiratory and reproductive dysfunctions and lesions in the central nervous system and gastrointestinal tract. The historical information in the review reflects the stages of porcine circovirus study, its first discovery, isolation in porcine kidney cell culture and identification of new nucleotide sequences of the virus. The presented data demonstrate the genetic differences of the viral genome, as well as the divergence in the clinics depending on the level of pathogenicity of the strains. Data of the previously unknown genotypes of Circovirus the study of their genetic sequences and the features of their distribution are presented in the article. The data on the genetic organization of porcine circovirus, its structure, virion size and nucleotide sequence length are illuminated in the article. Information was collected on the number of reading frames in the genomes of different types of circovirus, the sizes of capsid and replicative proteins, as well as their functions and influence on immune responses in the host organism, are given. It has been noted that an increase in the number of genotypes directly depends on the mutation of the capsid proteins of the circovirus. The data of phylogenetic analysis of porcine circovirus type 2 has been analyzed and in accordance with six genotypes of the virus has been identified (PCV-2a, PCV-2b, PCV-2c, PCV-2d, PCV-2e and PCV-2f). The prevalence of genotypes in the territory of the Russian Federation is provided. According to the retrospective analysis shifts in the genotypes of the virus with an increase in the virulence of the strains has been detected. It became possible to trace the distribution of genotypes across the territories of different countries, as well as to determine the prevailing types of porcine circovirus characteristic of these geographic areas as a result of the study.

Identification of Single Nucleotide Polymorphisms and Analysis of Linkage Disequilibrium in Different Bamboo Species Using the Candidate Gene Approach

Bamboos are one of the most beautiful and useful plants on Earth. The genetic background and population structure of bamboos are well known, which helps accelerate the process of artificial domestication of bamboo. Partial sequences of six genes involved in nitrogen use efficiency in 32 different bamboo species were analyzed for occurrence of single nucleotide polymorphisms (SNPs). The nucleotide diversity θw and total nucleotide polymorphisms πT of the sequenced DNA regions was 0.05137 and 0.03332, respectively. Both πnonsyn /πsyn and Ka/Ks values were 0.1. Estimation and analysis of linkage disequilibrium of five genes revealed that with the increase in nucleotide sequence length, the degree of SNP linkage disequilibrium decreased rapidly. We inferred the population genetic structure of 32 bamboo species based on the SNP loci of six genes with frequencies >18%. 32 bamboo species were divided into five categories, which indicated that the combined population of all bamboo species had obvious multivariate characteristics and was heterogeneous; red (Group 1) and green (Group 2) were the main groups.

먹장어 유래의 카텝신 B 유전자 클로닝, 발현 및 효소학적 활성 측정

Hagfish belongs to cyclostomata which has different characteristics from teleost and chondrichthyes. So, they are considered to have important taxonomic position. They are consumed as food and their skin can be used for leather. Cathepsin B is an enzyme classified as cysteine protease and papain family. Also, it can act as endopeptidase. It is involved in the process to degrade proteins in lysosome. In this research, we identified nucleotide and amino acid sequence of cathepsin B in Eptatretus burgeri. The nucleotide sequence length of EbCtsB is 1694 bp including 5’-UTR (107 bp), ORF (1002 bp), and 3’-UTR (585 bp). ORF encode 333 AA (amino acid sequences) which molecular weight is 36.8 kDa. And we purified recombinant EbCtsB and conducted activity assay using diverse pH condition, substrates, inhibitors, metal ions, and detergents. Z-RR-AMC considered as good substrate of EbCtsB have optimal activity at pH 7.5. Antipain is the best inhibitor of EbCtsB. Also, ZnSO₄, CuSO₄, and HgCl₂ can decrease the activity of EbCtsB. MgSO₄ and CaCl₂ can increase its activity. In the presence of SDS, the activity of EbCtsB is decreased.

Molecular characterization of an indigenous minor carp Bangana dero (Cyprinidae: Labeoninae) of Manipur and its relationship with Labeonin fishes of North East India based on mitochondrial 16SrRNA gene sequences

Bangana dero is an economically important indigenous cyprinid fish of Manipur, India having maximum standard length of 40cm. For the taxonomic placement of this species among the Labeonin fishes, molecular characterization is conducted by using mitochondrial 16SrRNA gene sequences. Partial sequences of mito. 16SrRNA gene of fifteen cyprinid species of the sub-family Labeoninae were downloaded from NCBI Genbank. The analysed nucleotide sequence lengths were 538 bp. In a total of 811 characters, 194 were conserved sites (monomorphic) and 347 were variable sites (polymorphic) and out of 347 variable sites, 73 were parsimony informative sites and 274 singleton sites. The nucleotide frequencies are 31.4% (A), 22.57% (T), 24.00% (C) and 21.96% (G). The transition/transversion bias (R) is 2.51. The overall mean distance is 0.083. The dendogram constructed by Neighbour-Joining tree have three clusters which can indicate the taxonomic positions of Bangana dero .

An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus

Ribosome biogenesis and turnover are processes necessary for cell viability and proliferation, and many kinds of proteins are known to regulate these processes. However, many questions still remain, especially in the Archaea. Generally, several ribonucleases are required to process precursor rRNAs to their mature forms, and to degrade rRNAs for quality control. Here, we found that FAU-1, which is known to be an RNA binding protein, possesses an RNase activity against precursor 5S rRNA derived from P. furiosus and T. kodakarensis in the order Thermococcales in vitro. An in vitro analysis revealed that UA sequences in the upstream of 5S rRNA were preferentially degraded by addition of FAU-1. Moreover, a fau-1 gene deletion mutant of T. kodakarensis showed a delay of exponential phase, reduction of maximum cell number and significant changes in the nucleotide sequence lengths of its 5S, 16S, and 23S rRNAs in early exponential phase. Our results suggest that FAU-1 is a potential RNase involved in rRNA stability through maturation and/or degradation processes.

Multigene characterization of aster yellows phytoplasmas infecting grapevine in South Africa

The genetic diversity of aster yellows phytoplasmas in grapevine collected in two locations in South Africa (Vredendal and Robertson) was investigated by the use of multilocus analysis of gene sequences amplified by polymerase chain reaction. Based on results from restriction fragment length polymorphism profiling and nucleotide sequence alignments of 16S rRNA, rp, amp, groEL and secY genes in comparison with aster yellows strains from Italy and reference aster yellows strains, four lineages have been detected in samples from South Africa.

Comparative Evolution of S7 Intron 1 and Ribosomal Internal Transcribed Spacer in Coilia nasus (Clupeiformes: Engraulidae)

Coilia nasus is widely distributed in the Yangtze River, the coastal waters of China, Korea and the Ariake Sound of Japan. Several ecotypes exist and this provides a useful model for the study of comparative diversity between molecular markers. Here we analyze and compare the nucleotide sequences between single-copy ribosomal protein S7 gene intron 1 (rpS7) and multiple-copy ribosomal internal transcribed spacer 1 (ITS1) in this species to compare the phylogenetic signal of the two nuclear genes. Nucleotide substitutions among the two gene sequences and partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) gene were also analyzed. A total of 115 clones for rpS7 and 122 clones for ITS1 were obtained from 37 specimens. The nucleotide sequence length is 741 to 743 bp for rpS7 and 334 to 348 bp for ITS1. Intra- and inter-specimen variation in rpS7 results from nucleotide substitution, while such variation in ITS1 is mainly due to different numbers of short base repeats. The content of G + C is lower in rpS7 (43.5%) than in ITS1 (68.2%). Our results indicate that the proportion of the sequence variable sites is higher in rpS7 (61) than in ITS1 (23); the informative parsimony of rpS7 is evidently higher than that of ITS1 (26 vs. 2); the overall ratio between transitions and transversions in ITS1 is slightly lower than in rpS7, but remarkably lower than in COI. These results suggest that rpS7 is more suitable than ITS1 as a marker for genetic divergence of this group. Furthermore, gene flow is observed between the different geographic populations of C. nasus from the phylogeny of this species based on rpS7, showing that rpS7 has more evolutionary characteristics for understanding the processes of genomic evolution at the intraspecific level.