• Title/Summary/Keyword: Gene arrangement

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Morphological, Phylogenetic and Biological Characteristics of Ectropis obliqua Single-Nucleocapsid Nucleopolyhedrovirus

  • Ma Xiu-cui;Xu Hai-Jun;Tang Mei-Jun;Xiao Qiang;Hong Jian;Zhang Chuan-Xi
    • Journal of Microbiology
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    • v.44 no.1
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    • pp.77-82
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    • 2006
  • The tea looper caterpillar, Ectropis obliqua, is one of the major pests of tea bushes. E. obliqua single-nucleocapsid nucleopolyhedrovirus (EcobSNPV) has been used as a commercial pesticide for biocontrol of this insect. However only limited genetic analysis for this important virus has been done up to now. EcobSNPV was characterized in this study. Electron microscopy analysis of the occlusion body showed polyhedra of 0.7 to $1.7\;{\mu}m$ in diameter containing a single nucleocapsid per envelope of the virion. A 15.5 kb genomic fragment containing EcoRI-L, EcoRI-N and HindIII-F fragments, was sequenced. Analysis of the sequence revealed that the fragment contained eleven potential open reading frames (ORFs): lef-1, egt, 38.7k, rrl, polyhedrin, orfl629, pk-1, hoar and homologues to Spodoptera exigua multicapsid NPV (SeMNPV) ORFs 15, 28, and 29. Gene arrangement and phylogeny analysis suggest that EcobSNPV is closely related to the previously described Group II NPV. Bioassays on lethal concentration $(LC_{50}\;and\;LC_{90})$ and lethal time $(LT_{50}\;and\;LT({90})$ were conducted to test the susceptibility of E. obliqua larvae to the virus.

Taxonomic Revision of Notohymena gangwonensis (Protozoa: Ciliophora), with Notes on Its Cortical Granules and Scanning Electron Micrographs

  • Moon, Ji Hye;Kim, Kang-San;Chae, Kyu Seok;Min, Gi-Sik;Jung, Jae-Ho
    • Animal Systematics, Evolution and Diversity
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    • v.36 no.2
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    • pp.113-122
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    • 2020
  • From a moss sample, we isolated and identified Notohymena gangwonensis Kim et al., 2019 based on morphological and molecular data. The moss and type population has completely identical 18S rRNA (nuclear small subunit ribosomal RNA) gene sequences and both are highly similar in morphological and morphometric attributes, except for the diameter and arrangement of the cortical granules. Thus, we reexamined the type materials(i.e., micrographs and gDNA) and resulted in finding mistakes made by the authors of the species. Based on these data and supporting materials newly obtained (i.e., internal transcribed spacer [ITS] 1, ITS2, 5.8S, and partial 28S rDNA sequences, and scanning electron micrographs), we provide improved diagnosis of the species to clarify its identity. In addition, a key for Notohymena species is provided.

Cloning of p-Hydroxybenzoate Degradation Genes and the Overexpression of Protocatechuate 4,5-Dioxygenase from Pseudomonas sp. K82

  • Yoon, Young-Ho;Park, Soon-Ho;Leem, Sun-Hee;Kim, Seung-Il
    • Journal of Microbiology and Biotechnology
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    • v.16 no.12
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    • pp.1995-1999
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    • 2006
  • Pseudomonas sp. K82 cultured in p-hydroxybenzoate induces protocatechuate 4,5-dioxygenase (PCD 4,5) for p-hydroxybenzoate degradation. In this study, a 6.0-kbp EcoR1 fragment containing p-hydroxybenzoate degradation genes was cloned from the genome of Pseudomonas sp. K82. Sequence analysis identified four genes, namely, pcaD, pcaA, pcaB, and pcaC genes known to be involved in p-hydroxybenzoate degradation. Two putative 4-hydroxyphenylpyruvate dioxygenases and one putative oxidoreductase were closely located by the p-hydroxybenzoate degradation genes. The gene arrangement and sequences of these p-hydroxybenzoate degradation genes were similar to those of Comamonas testosteroni and Pseudomonas ochraceae. PcaAB (PCD4,5) was overexpressed in the expression vector pGEX-4T-3, purified using a GST column, and confirmed to have protocatechuate 4,5-dioxygenase activity. The N-terminal amino acid sequences of overexpressed PCD4,5 were identical with those of purified PCD4,5 from Pseudomonas sp. K82.

Altered Gene Expression in Cerulein-Stimulated Pancreatic Acinar Cells: Pathologic Mechanism of Acute Pancreatitis

  • Yu, Ji-Hoon;Lim, Joo-Weon;Kim, Hye-Young
    • The Korean Journal of Physiology and Pharmacology
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    • v.13 no.6
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    • pp.409-416
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    • 2009
  • Acute pancreatitis is a multifactorial disease associated with the premature activation of digestive enzymes. The genes expressed in pancreatic acinar cells determine the severity of the disease. The present study determined the differentially expressed genes in pancreatic acinar cells treated with cerulein as an in vitro model of acute pancreatitis. Pancreatic acinar AR42J cells were stimulated with $10^{-8}$ M cerulein for 4 h, and genes with altered expression were identified using a cDNA microarray for 4,000 rat genes and validated by real-time PCR. These genes showed a 2.5-fold or higher increase with cerulein: lithostatin, guanylate cyclase, myosin light chain kinase 2, cathepsin C, progestin-induced protein, and pancreatic trypsin 2. Stathin 1 and ribosomal protein S13 showed a 2.5-fold or higher decreases in expression. Real-time PCR analysis showed time-dependent alterations of these genes. Using commercially available antibodies specific for guanylate cyclase, myosin light chain kinase 2, and cathepsin C, a time-dependent increase in these proteins were observed by Western blotting. Thus, disturbances in proliferation, differentiation, cytoskeleton arrangement, enzyme activity, and secretion may be underlying mechanisms of acute pancreatitis.

The nonconserved N-terminus of protein phosphatases 1 influences its active site

  • Xie, XiuJie;Huang, Wei;Xue, ChengZhe;Wei, Qun
    • BMB Reports
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    • v.41 no.12
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    • pp.881-885
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    • 2008
  • Protein phosphatase 1 consists of a secondary structure arrangement, conserved in the serine/threonine protein phosphatase gene family, flanked by nonconserved N-terminal and C-terminal domains. The deletion mutant of PP1 with the 8 nonconserved N-terminal residues removed was designated PP1-(9-330). PP1-(9-330) had a higher activity and affinity than PP1 when assayed against four different substrates, and it also demonstrated a 6-fold higher sensitivity to the inhibitor okadaic acid. This suggested that the N-terminal domain suppresed the activity of PP1 and interfered with its inhibition by okadaic acid. The ANS fluorescence intensity of PP1-(9-330) was greater than that of PP1, which implies that the hydrophobic groove running from active site in the truncated PP1 was more hydrophobic than in PP1. Our findings provide evidence that the nonconserved N-terminus of PP1 functions as an important regulatory domain that influences the active site and its pertinent properties.

The Complete Mitochondrial Genome of the Fourhorn Sculpin Triglopsis quadricornis (Perciformes, Cottidae) from Sirius Passet, North Greenland

  • Kim, Bo-Mi;Kihm, Ji-Hoon;Park, Tae-Yoon S.
    • Ocean and Polar Research
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    • v.43 no.4
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    • pp.371-374
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    • 2021
  • Triglopsis quadricornis Linnaeus, 1758 (Cottidae) is distributed in the Atlantic and Arctic and has four unique bony protuberances on its head. Here, we report the complete, circular, and annotated mitochondrial genome of T. quadricornis. The complete T. quadricornis mitochondrion was sequenced by high-throughput Illumina HiSeq platform. The sequences are 16,736 bp in size and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, a control region, and large and small ribosomal subunits. The overall genomic structure of T. quadricornis mitochondrion was conserved with the gene arrangement of Megalocottus and Myoxocephalus species, and phylogenetic analysis supports their sister relationships. Most PCGs consist of TAA or TAG as a termination codon, whereas COII, ND4, and CYTB have T-- as a stop codon. This complete mitochondrial DNA information of T. quadricornis will provide an essential genomic resource to elucidate the phylogenetic relationship and evolutionary history of the family Cottidae.

Complete mitochondrial genome of freshwater goby Rhinogobius cliffordpopei (Perciformes, Gobiidae): genome characterization and phylogenetic analysis

  • Zhong, Liqiang;Wang, Minghua;Li, Daming;Tang, Shengkai;Zhang, Tongqing;Bian, Wenji;Chen, Xiaohui
    • Genes and Genomics
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    • v.40 no.11
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    • pp.1137-1148
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    • 2018
  • Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the complete mitochondrial genome of R. cliffordpopei was determined, which was 16,511 bp in length with A+T content of 51.1%, consisting of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the R. cliffordpopei complete mtDNA were identical to most of other teleosts. Phylogenetic analyses placed R. cliffordpopei in a well-supported monophyletic cluster with other Rhinogobius fish. But the phylogenetic relationship between genus Rhinogobius and Tridentiger remained to be resolved.

Complete mitochondrial genome of Nyctalus aviator and phylogenetic analysis of the family Vespertilionidae

  • Lee, Seon-Mi;Lee, Mu-Yeong;Kim, Sun-sook;Kim, Hee-Jong;Jeon, Hye Sook;An, Junghwa
    • Journal of Species Research
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    • v.8 no.3
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    • pp.313-317
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    • 2019
  • Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).

Genetic Analysis of Quantitative Characters of Rice (Oryza sativa L.) by Diallel Cross (이면교배(二面交配)에 의한 수도량적(水稻量的) 형질(形質)의 유전분석(遺傳分析)에 관(關)한 연구(硏究))

  • Jo, Jae-seong
    • Korean Journal of Agricultural Science
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    • v.4 no.2
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    • pp.254-282
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    • 1977
  • To obtain information on the inheritance of the quantitative characters related with the vegetative and reproductive growth of rice, the $F_1$ seeds were obtained in 1974 from the all possible combinations of the diallel crosses among five leading rice varieties : Nongbaek, Tongil, Palgueng, Mangyeong and Gimmaze. The $F_1$'s including reciprocals and parents were grown under the standard cultivation method at Chungnam Provincial Office of Rural Development in 1975. The arrangement of experimental plots was randomized block design with 3 replications and 12 characters were used for the analysis. Analytical procedure for genetic components was followed the Griffing's and Hayman's methods and the results obtained are summarized as follows. 1. In all $F_1$'s of Tongil crosses, the longer duration to heading was due to dominant effect of Tongil and each $F_1$ showed high heterosis in delaying the heading time. It was assumed that non-allelic gene action besides dominant gene effect might be involed in days to heading character. However, in all $F_1$'s from the crosses among parents excluding Tongil the shorter duration was due to dominant gene action and the degree of dominance was partial, since dominance effects were not greater than the additive effect. The non-allelic gene interaction was not significant. Considering the results mentioned above, it was regarded that there were two kinds of Significantly different genetic systems in the days to heading. 2. The rate of heterosis was significantly different depending upon the parents used in the crosses. For instance, the $F_1$'s from Togil cross showed high rate of heterosis in longer culm. Compared to short culm, longer culm was due to recesive gene action and short culm was due to recesive gene action. The dominant gene effect was greater than the additive gene effect in culm length. The narrow sense of heretability was very low and the maternal effects as well as reciprocal effects were significantly recognized. 3. The lenght of the of the uppermost internode of each $F_1$ plant was a little lorger than these of respective parental means or same as those of parents having long internodes, indicating partial dominance in the direction of lengthening the uppermost internodes. The additive gene effects on the uppermost internode was greater than the dominance gene effect. The narrow as well as broad sense of heritabilities for the character of the uppermost internode were very high. There were significant maternal and reciprocal effect in the uppermost internode. 4. The gene action for the flag leaf angle was rather dominance in a way of getting narrower angle. However, in the Palgueng combinations, heterosis of $F_1$ was observed in both narrow and wide angles of the flag leaf. The dominant effects were greater than the additive effects on the flag leaf angle. There were observed also a great deal of non-allelic gene interacticn on the inheritance of the flag leaf angle. 5. Even though the dominant gene action on the length and width of flag leaf was effective in increasing the length or width of the flag leaf, there were found various degrees of hetercsis depending upon the cross combination. Over-dominant gene effect were observed in the inheritance of length of the flag leaf, while additive gene effects was found in the inheritance of the width of the flag leaf. High degree of heretabilities, either narrow or broad sense, were found in both length and width of the flag leaf. No maternal and reciprocal effect were found in both characters. 6. When Tongil was used as one parent in the cross, the length of panicle of $F_1$'s was remarkedly longer than that of parents. In other cross comination, the length of panicle of $F_1$'s was close to the parental mean values. Rather greater dominent gene effect than additive gene effect was observed in the inheritance of panicle length and the dominant gene was effective in increasing the panicle length. 7. The effect of dominant genes was effective in increasing the number of panicles. The degree of heterosis was largely dependent on the cross combination. The effect of dominant gene in the inheritance of panicle number was a little greater than that of additive genes, and the inheritance of panicle number was assumed to be due to complete dominant gene effects. Significantly high maternal and reciprocal effects were found in the character studied. 8. There were minus and plus values of heterosis in the kernel number per panicle depending upon the cross combination. The mean dominant effect was effective in increasing the kernel number per panicle, the degree of dominant effect varied with cross combination. The dominant gene effect and non-allelic gene interaction were found in the inheritance of the kernel number per panicle. 9. Genetic studies were impossible for the maturing ratio, because of environmental effects such as hazards delaying heads. The dominant gene effect was responsible for improving the maturing ratio in all the cross combinations excluding Tongil 10. The heavier 1000 grain weight was due to dominant gene effects. The additive gene effects were greater than the dominant gene effect in the 1000 grain weight, indicating that partial dominance was responsible for increasing the 1000 grain weight. The heritabilites, either narrow or broad sense of, were high for the grain weight and maternal or reciprocal effects were not recognized. 11. When Tongil was used as parent, the straw weight was showing high heterosis in the direction of increasing the weight. But in other crosses, the straw weight of $F_1$'s was lower than those of parental mean values. The direction of dominant gene effect was plus or minus depending upon the cross combinations. The degree of dominance was also depending on the cross combination, and apparently high nonallelic gene interaction was observed.

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The embryological studies on the interspecific hybrid of ginseng plant (Panax ginseng x P. Quiuquefolium) with special references to the seed abortion (인삼의 종간잡종 Panax ginseng x P Quinquefoilium의 발생학적 연구 특히 결실불능의 원인에 관하여)

  • Jong-Kyu Hwang
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.5 no.1
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    • pp.69-86
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    • 1969
  • On the growing of the interspecific hybrid ginseng plant, the phenomena of hybrid vigoures are observed in the root, stem, and leaf, but it can not produce seeds favorably since the ovary is abortive in most cases in interspecific hybrid plants. The present investigation was undertaken in an attempt to elucidate the embryological dses of the seed failure in the interspecific hybrid of ginseng (Panax Ginseng ${\times}$ P. Quinque folium). And the results obtained may be summarized as follows. 1). The vegetative growth of the interspecific hybrid ginseng plant is normal or rather vigorous, but the generative growth is extremely obstructed. 2). Even though the generative growth is interrupted the normal development of ovary tissue of flower can be shown until the stage prior to meiosis. 3). The division of the male gameto-genetic cell and the female gameto-genetic cell are exceedingly irregular and some of them are constricted prior to meiosis. 4). At meiosis in the microspore mother cell of the interspecific hybrid, abnormal division is observed in that the univalent chromosome and chromosome bridge occure. And in most cases, metaphasic configuration is principally presented as 23 II+2I, though rarely 22II+4I is also found. 5). Through the process of microspore and pollen formation of F1, the various developmental phases occur even in an anther loclus. 6). Macro, micro and empty pollen grains occur and the functional pollen is very rare. 7). After the megaspore mother cell stage, the rate of ovule development is, on the whole, delayed but the ovary wall enlargement is nearly normal. 8). Degenerating phenomena of ovules occur from the megaspore mother cell stage to 8-nucleate embryo sac stage, and their beginning time of constricting shape is variously different. 9). The megaspore arrangement in the parent is principally of the linear type, though rarely the intermediate type is also observed, whereas various types, viz, linear, intermediate, Tshape, and I shape can be observed in hybrid. 10). After meiosis, three or five megaspore are some times counted. 11). Charazal end megaspore is generally functional in the parents, whereas, in F1, very rarely one of the center megaspores (the second of the third megaspore) grows as an embryo sac mother cell. 12). In accordance with the extent of irregularity or abnormality in meiosis, division of embryo sac nuclei and embryo sac formation cause more nucellus tissue to remain within th, embryo sac. 13). Even if one reached the stage of embryo sac formation, the embryo sac nuclei are always precarious and they can not be disposed to theil proper, respective position. 14). Within the embryo sac, which is lacking the endospermcell, the 4-celled proembryo, linear arrangement, is observed. 15). Through the above respects, the cause of sterile or seed failure of interspecific hybrid would be presumably as follows, By interspecific crossing gene reassortments takes place and the gene system influences the metabolism by the interference of certain enzyme as media. In the F1 plant, the quantity and quality of chemicals produced by the enzyme system and reaction system are entirely different from the case of the parents. Generally, in order to grow, form, and develop naw parts it is necessary to change the materials and energy with reasonable balance, whereas in the F1 plant the metabolic process becomes abnormal or irregular because of the breakdown of the balancing. Thus the changing of the gene-reaction system causes the alteration of the environmental condition of the gameto-genetic cells in the anther and ovule; the produced chemicals cause changes of oxidatio-reduction potential, PH value, protein denaturation and the polarity, etc. Then, the abnormal tissue growing in the ovule and emdryo sac, inhibition of normal development and storage of some chemicals, especially inhibitor, finally lead to sterility or seed failure. Inconclusion, we may presume that the first cause of sterile or seed abortion in interspecific hybrids is the gene reassortment, and the second is the irregularity of the metabolic system, storage of chemicals, especially inhibitor, the growth of abnormal tissue and the change of the polarity etc, and they finally lead to sexual defect, sterility and seed failure.

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