• Title/Summary/Keyword: pseudo-gene

Search Result 29, Processing Time 0.021 seconds

Complete genome sequence of Neisseria sp. KEM232 isolated from a human smooth surface caries (사람 평활면 치아우식에서 분리한 Neisseria sp. KEM232 균주의 유전체 서열 분석)

  • Kim, Eun Mi;Seong, Chi Nam
    • Korean Journal of Microbiology
    • /
    • v.54 no.1
    • /
    • pp.81-83
    • /
    • 2018
  • We sequenced the genome of the Neisseria sp. KEM232 isolated from the smooth surface caries of human cavity of a 7-year old male in Republic of Korea by using the standard dilution plating technique. The genome comprises a single circular 2,371,912 bp chromosome with a G + C content of 58.5%, 2,210 protein-coding genes, 108 pseudo genes, 51 RNA genes, and one CRISPR array. Based on the 16S rRNA gene sequence similarity and average nucleotide identity, the strain KEM232 is most closely related to Neisseria baciliformis.

An Algorithm for Spot Addressing in Microarray using Regular Grid Structure Searching (균일 격자 구조 탐색을 이용한 마이크로어레이 반점 주소 결정 알고리즘)

  • 진희정;조환규
    • Journal of KIISE:Computer Systems and Theory
    • /
    • v.31 no.9
    • /
    • pp.514-526
    • /
    • 2004
  • Microarray is a new technique for gene expression experiment, which has gained biologist's attention for recent years. This technology enables us to obtain hundreds and thousands of expression of gene or genotype at once using microarray Since it requires manual work to analyze patterns of gene expression, we want to develop an effective and automated tools to analyze microarray image. However it is difficult to analyze DNA chip images automatically due to several problems such as the variation of spot position, the irregularity of spot shape and size, and sample contamination. Especially, one of the most difficult problems in microarray analysis is the block and spot addressing, which is performed by manual or semi automated work in all the commercial tools. In this paper we propose a new algorithm to address the position of spot and block using a new concept of regular structure grid searching. In our algorithm, first we construct maximal I-regular sequences from the set of input points. Secondly we calculate the rotational angle and unit distance. Finally, we construct I-regularity graph by allowing pseudo points and then we compute the spot/block address using this graph. Experiment results showed that our algorithm is highly robust and reliable. Supplement information is available on http://jade.cs.pusan.ac.kr/~autogrid.

Draft genome sequence of a bacterial plant pathogen Erwinia pyrifoliae strain EpK1/15 isolated from an apple twig showing black shoot blight (가지검은마름병 병징을 보이는 사과나무 가지에서 분리한 식물병원세균인 Erwinia pyrifoliae EpK1/15 균주의 유전체 해독)

  • Lee, Gyu Min;Oh, Eom-Ji;Ko, Seyoung;Park, Jungkum;Park, Duck Hwan;Kim, Donghyuk;Oh, Chang-Sik
    • Korean Journal of Microbiology
    • /
    • v.54 no.1
    • /
    • pp.69-70
    • /
    • 2018
  • Erwinia pyrifoliae is a Gram-negative bacterium causing black shoot blight in apple and Asian pear trees. E. pyrifoliae strain EpK1/15 was isolated in 2014 from an apple twig from the Pocheon, Gyeonggi-do, South Korea. In this study, we report the draft genome sequence of E. pyrifoliae EpK1/15 using PacBio RS II platform. The draft genome is comprised of a circular chromosome with 4,027,225 bp and 53.4% G + C content and a plasmid with 48,456 bp and 50.3% G + C content. The draft genome includes 3,798 protein-coding genes, 22 rRNA genes, 77 tRNA genes, 13 non-coding RNA genes, and 231 pseudo genes.

Successful Embolization in the Patient with Hemoptysis Due to Right Inferior Phrenic Artery-pulmonary Artery Anastomosis and Pseudoaneurysm (우하횡경막동맥-폐동맥 문합부위의 가성동맥류로 인한 객혈로 색전술 후 성공한 예)

  • Park, Hyun Woong;Lee, Go Eun;Park, Yong Sung;Son, Ji Woong;Choi, Eu Gene;Na, Moon Jun;Kwon, Sun Jung
    • Tuberculosis and Respiratory Diseases
    • /
    • v.66 no.4
    • /
    • pp.319-323
    • /
    • 2009
  • The primary cause of hemoptysis is the bronchial artery. However, it should be noted that pulmonary artery and other vessels can cause hemoptysis. If the source of the bleeding is not determined after embolization, other evaluations are needed. Systemic-pulmonary anastomosis and pulmonary artery pseudo-aneurysm are rare vascular abnormalities with varying etiologies. An accurate and rapid diagnosis is needed in hemoptysis, since the cause may be life-threatening. We report a case of a 77-years-old man with persistent hemoptysis due to the right inferior phrenic artery - pulmonary artery anastomosis and pseudoaneurysm. After the embolization of the inferior phrenic artery, the hemoptysis was successfully treated.

Integrative Comparison of Burrows-Wheeler Transform-Based Mapping Algorithm with de Bruijn Graph for Identification of Lung/Liver Cancer-Specific Gene

  • Ajaykumar, Atul;Yang, Jung Jin
    • Journal of Microbiology and Biotechnology
    • /
    • v.32 no.2
    • /
    • pp.149-159
    • /
    • 2022
  • Cancers of the lung and liver are the top 10 leading causes of cancer death worldwide. Thus, it is essential to identify the genes specifically expressed in these two cancer types to develop new therapeutics. Although many messenger RNA (mRNA) sequencing data related to these cancer cells are available due to the advancement of next-generation sequencing (NGS) technologies, optimized data processing methods need to be developed to identify the novel cancer-specific genes. Here, we conducted an analytical comparison between Bowtie2, a Burrows-Wheeler transform-based alignment tool, and Kallisto, which adopts pseudo alignment based on a transcriptome de Bruijn graph using mRNA sequencing data on normal cells and lung/liver cancer tissues. Before using cancer data, simulated mRNA sequencing reads were generated, and the high Transcripts Per Million (TPM) values were compared. mRNA sequencing reads data on lung/liver cancer cells were also extracted and quantified. While Kallisto could directly give the output in TPM values, Bowtie2 provided the counts. Thus, TPM values were calculated by processing the Sequence Alignment Map (SAM) file in R using package Rsubread and subsequently in python. The analysis of the simulated sequencing data revealed that Kallisto could detect more transcripts and had a higher overlap over Bowtie2. The evaluation of these two data processing methods using the known lung cancer biomarkers concludes that in standard settings without any dedicated quality control, Kallisto is more effective at producing faster and more accurate results than Bowtie2. Such conclusions were also drawn and confirmed with the known biomarkers specific to liver cancer.

Feasibility of Coculture Method for Production of Chimeric Mice Using J1 Embryonic Stem Cells

  • Shin Hye-Jun;Park Sung-Sik;Kim Sun-Uk;Cho Sang-Mi;Han Ying-Hao;Kim Hyun-Sun;Kim Sang-Geun;Lee Dong-Seok;Yu Dae-Yeul
    • Biomedical Science Letters
    • /
    • v.10 no.4
    • /
    • pp.391-395
    • /
    • 2004
  • The demand for the production of gene-defective mice from embryonic stem (ES) cells is increasing to clarify decisive gene function in vivo. Although blastocyst injection is widely used to generate ES cell-mediated knockout mice, coculture method has been alternatively used because of several advantages, such as low cost and simple procedure. Thus, this experiment was designed to demonstrate the feasibility of the coculture method using J1 ES cells, which are known to be efficient for blastocyst injection. Eight-cell embryos were harvested from 2.5 days post-coitum (dpc), denuded with acid tyrode's solution, and transferred onto trypsinized J1 ES cells. Aggregation was carried out following two typical methods, which are simple coculture method and aggregation in groove prepared by aggregation needle. Successfully aggregated-embryos were developed to blastocysts for 24 h and transferred into uterus of pseudo-pregnant foster mother. Chimeric offspring was judged by coat pigmentation. In this study, we could obtain chimeric mice from all the two aggregation methods, but the chimera production efficiencies in coculture using groove were three times higher at least than those in the other group. In conclusion, these observations suggest that coculture method should be available for production of knockout mice from J1 ES cells. Presently, the germ-line transmission rates of the chimeras produced from the two methods are under investigation.

  • PDF

A Case Report of Novel Mutation in GNPTAB in Two Siblings with Mucolipidosis Type III Alpha/beta (GNPTAB 유전자에서 새로운 돌연변이가 확인된 뮤코지방증 III형 남매)

  • Kim, Min-Sun;Park, Esther;Song, Ari;Im, Minji;Park, Hyung-Doo;Cho, Sung Yoon;Jin, Dong-Kyu
    • Journal of The Korean Society of Inherited Metabolic disease
    • /
    • v.18 no.3
    • /
    • pp.99-106
    • /
    • 2018
  • Mucolipidosis type III (pseudo-Hurler polydystrophy) is a mucolipids degrading disorder caused by a mutation in the GNPTAB gene and is inherited by autosomal recessive. It is diagnosed by examining highly concentrated mucolipids in blood and the diagnosis can be confirmed by genetic testing. Mucolipidosis type III is a rare and progressive metabolic disorder. Its initial signs and symptoms usually occur around 3 years of age. Clinical manifestations of the disease include slow growth, joint stiffness, arthralgia, skeletal abnormalities, heart valve abnormalities, recurrent respiratory infection, distinctive facial features, and mild intellectual disability. Here, we are presenting two siblings of mucolipidosis type III, a 4-year-old female and a 2 years and 7 months old male with features of delayed growth and coarse face. The diagnosis was confirmed by [c.2715+1G>A(p.Glu906Leufs*4), c.2544del(p.Glu849Lysfs*22)] mutation in targeted gene panel sequencing. In this case, c.2544del is a heterozygote newly identified mutation in mucolipidosis type III and was not found in the control group including the genome aggregation database. And it is interpreted as a pathogenic variant considering the association with phenotype. Here, we report a Korean mucolipidosis type III patients with novel mutations in GNPTAB gene who have been treated since early childhood. Owing to recent development of molecular genetic techniques, it was possible to make early diagnosis and treatment with pamidronate was initiated appropriately in case 1. In addition to these supportive therapies, efforts must be made to develop fundamental treatment for patients with early diagnosis of mucolipidosis.

  • PDF

Complete genome sequence of Celluosilyticum lentocellum WCF-2 isolated from cow dung (소 분변에서 분리된 Celluosilyticum lentocellum WCF-2의 유전체 염기서열 분석)

  • Heo, Jun;You, Jaehong;Park, InCheol;Han, Byeong-Hak;Kwon, Soon-Wo;Ahn, Jae-Hyung
    • Korean Journal of Microbiology
    • /
    • v.55 no.3
    • /
    • pp.313-315
    • /
    • 2019
  • An anaerobic bacterial strain WCF-2 was isolated from cow dung in finding cellulose-degrading bacteria for use as silage additives. Strain WCF-2 showed a higher cellulolytic activity than Cellulosilyticum lentocellum DSM $5427^T$, the closest relative of strain WCF-2 (98.2% of 16S rRNA gene sequence similarity). We sequenced the complete genome of strain WCF-2 and compared it with that of C. lentocellum DSM $5427^T$. The OrthoANI value between the two strains was 97.9% thus strain WCF-2 was identified as C. lentocellum. The genome size of strain WCF-2 was 4,779,774 bp with a G + C content of 34.4%, 4,154 coding genes (CDS), 54 pseudo genes, and 142 RNA genes. Strain WCF-2 harbored seven cellulase genes, five of which showed low similarities with those of C. lentocellum DSM $5427^T$.

Variation of Genus Ilex in Korea and their Ornamental Values (Ilex속(屬) 수목(樹木)의 유전변이(遺傳變異)의 분석(分析)과 조경학적(造景學的) 이용가치(利用價値)의 조사(調査) 연구(硏究))

  • Yim, Kyong Bin
    • Journal of Korean Society of Forest Science
    • /
    • v.42 no.1
    • /
    • pp.1-38
    • /
    • 1979
  • The woody species of Genus Ilex which are endemic to Korea are distributed on limited area due to solely temperature factor. There is some differences according to species, however in general, the evergreen Ilex are found along southern coastal area of Korean Peninsula and near islands where the cold index does not exceed $-5^{\circ}C$. But Ilex macropoda and the variety, only deciduous ones, are grown in temperate zone of the peninsula and some islands. The list of Ilex species of Korea are as follows. Ilex cornuta Lindley et Pax., I. crenata Thunb. var. microphylla Max., I. crenata Thunb., I. rotunda Thunb., I. macropoda Miq., I. macropoda Miq. var. pseudo-macropoda Loensner, I. integra Thunb. The author surveyed the populations of Ilex species as many as possible and data of some characters such as leaf shape, spine, fruit shape, stomata density, sex ratio in natural communities, etc. are collected. Almost all the Ilex species in Korea show sporadic distribution. This means quite small sized populations isolate distantly each other eliminating the change of gene exchange in between. Particularly Ilex conuta and I. crenata show the morphological differentiation among populations as well as significant individual variation within a population. These were true with such characteristics, leaf shape, leaf dimension, leaf margin, fruit shape, spine, and stomata density. The founded are that the fruit length and the stomata density counted on the beneath surface of leaves of Ilex cornuta increased with the decrease of latitude. These are naturally closely related with the cold index values. The table shown below indicates the correlation between mean stomata density per $0.3642mm^2$ and cold index values. These relation however were not observed on Ilex crenata. The most dominated natured in relation to individual variation were outline of leaf, the number of marginal spine, the shape of leaf cross section and the degree of luster of the upper leaf surface. As shown in photos 5~7, these variations are agreed at a glance. There are reports that the development of marginal spines in some Ilex species is associated with the juvenility and topophysis. In present study, these two factors were neglected because of the intended sampling procedure. Of Ilex rotunda, population difference with the characteristics of leaf length is recognized but not for leaf width, petiole length, and fruit size. However, individual variations within a population were significantly large. In case of Ilex integra, only individual differences within population were calculated statistically for such characteristics as leaf length, leaf width, and petiole length. As to natural population, the sex ratio was 1:2 (female to male) for Ilex cornuta, and 1:1 for Ilex crenata. The tendency of more male than female in I. cornuta was agreed to other observations. Preparing the tip cutting of length 10cm, and treating with IBA, then attaching earth ball to the cut end, very successful rooting percentages were obtained. Asexual propagation has the advantages of maintaining the heterozygosity of existing varieties and overcoming the difficulties of delayed seed germination frequently encountered with Ilex species. Considering a great deal of variation in morphological traits, a good possibility of selection breeding for decorative and ornamental purposes exists. At present, these evergreen Ilex are ignored by local people as nuisance weedy shrubs. So the proper protection measures should promptly be taken.

  • PDF