• Journal for History of Mathematics
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• v.33 no.3
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• pp.167-177
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• 2020

Cooperative behavior may seem contrary to the notion of natural selection and adaptation, but is widely observed in nature, from the genetic level to the organism. The origin and persistence of cooperative behavior has long been a mystery to scientists studying evolution and ecology. One of the important research topics in the field of evolutionary ecology and behavioral ecology is to find out why cooperation is maintained over time. In this paper we take a historical overview of mathematical models representing cooperative relationships from the perspective of mathematical biology, which studies population dynamics between interacting biological groups, and analyze the mathematical characteristics and meanings of these cooperative models.

• Fisheries and Aquatic Sciences
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• v.15 no.1
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• pp.63-67
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• 2012

A comparative study of bile acid components from four lamprey species revealed that mature male chestnut lamprey Ichthyomyzon castaneus can produce 3 keto petromyzonol sulfate (3kPZS) while mature males of Pacific lamprey Lampetra tridentata, river lamprey Lampetra fluviatilis and American brook lamprey Lethenteron appendix produce petromyzonol sulfate (PZS). Identification of 3kPZS from a group of ancient lamprey species and of PZS from recently derived species led to a speculation that differentiation of bile acid biosynthetic systems has taken place during the course of evolution. Further studies on the biological functions of different bile acids in the adult lampreys are required to understand the evolution of chemical communication in lampreys.

• BMB Reports
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• v.52 no.8
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• pp.475-481
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• 2019

The evolution of genome editing technology based on CRISPR (clustered regularly interspaced short palindromic repeats) system has led to a paradigm shift in biological research. CRISPR/Cas9-guide RNA complexes enable rapid and efficient genome editing in mammalian cells. This system induces double-stranded DNA breaks (DSBs) at target sites and most DNA breakages induce mutations as small insertions or deletions (indels) by non-homologous end joining (NHEJ) repair pathway. However, for more precise correction as knock-in or replacement of DNA base pairs, using the homology-directed repair (HDR) pathway is essential. Until now, many trials have greatly enhanced knock-in or substitution efficiency by increasing HDR efficiency, or newly developed methods such as Base Editors (BEs). However, accuracy remains unsatisfactory. In this review, we summarize studies to overcome the limitations of HDR using the CRISPR system and discuss future direction.

• Journal of Life Science
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• v.11 no.1
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• pp.39-41
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• 2001

Cytohesin family has been thought to participate in inside-outside signaling linking growth factor receptor stimulation of PI 3-kinase to cell adhesion and stimulate nucleotide exchange of ARF through its Sec7 domain. The genomic structure of the cytohesin family was analyzed by BLAST search using cDNA and genomic DNA sequences from the GeneBank database. The cytohesin-2 was encoded by 12 exons. while the cytohesin-4 was encoded by 13 exons. The Sec7 and PH domains were not encoded by separate exons. In an analysis of retroviral integration, those two families did not contain any retroviral elements in introns or exons. The phylogenetic tree calculated by the neighbor-joining method suggests that the cytohesin-1 family was closely related to cytohesin-3 (ARNO3) family. These date could be of great use in further studies for resolving the exact function and evolution of the cytohesin family.

• Animal Systematics, Evolution and Diversity
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• v.28 no.2
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• pp.117-125
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• 2012

Many members of xanthid crabs have the black coloured fingers and are found easily in the intertidal or subtidal zone. Three xanthids, $Danielea$ $noelensis$ (Ward, 1934), $Etisus$ $anaglyptus$ H. Milne Edwards, 1834, and $Gaillardiellus$ $rueppelli$ (Krauss, 1843), are newly reported from Korean waters as a result of continuous taxonomic studies on crabs. Of these, the present specimen of $D.$ $noelensis$ has rather projecting angle on the antero-external border of the merus of the third maxilliped differed from that of the original description. The genus $Danielea$ Ng and Clark, 2003 and the genus $Etisus$ H. Milne Edwards, 1834 are also reported first time from Korean fauna. Their descriptions are provided with illustrations. Korean Xanthoidea now consists of 28 species belonging to 24 genera.

• Journal of Life Science
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• v.11 no.2
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• pp.81-82
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• 2001

The human ribosomal protein 54 genes, RPS4X and RPS4Y are located on the X and Y chromosomes. They have been postulated as candidate for Turner syndrome which was characterized by gonadal dysgenesis, short stature, and various external and internal anomalies. Using the BLAST search program, we identified sixteen RPS4 pseudogenes from the human genome and analyzed them phylogenetically. The RPS4-C12-1, C12-2, and C12-3 pseudogenes from chromosome 12 have been evolved independently during hominid evolution. The RPS4X gene from X chromosome it closely related to the RPS4-C12-2 from chromosome 12 and RPS4-C5 from chromosome 5, whereas the RPS4Y gene is very closely related to RPS4-C16 from chromosome 16. The exact mapping of the RPS4 pseudogene family was peformed, indicating that the RPS4 pseudogene family was mapped on human chromosomes 1, 2, 5, 6, 8, 10, 11, 12, 13, 16, 18, 19 and 20. Taken together, the precise chromosomal localization and phylegenetic relationship of the RPS4 pseudo-genes could be of great use in further study for understanding the Turner syndrome.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1696-1701
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• 2010

The ${\alpha}$-amylases activity was improved by random mutagenesis and screening. A region comprising residues from the position 34-281 was randomly mutated in B. licheniformis ${\alpha}$-amylase (AmyL), and the library with mutations ranging from low, medium, and high frequencies was generated. The library was screened using an effective liquid-phase screening method to isolate mutants with an altered pH profile. The sequencing of improved variants indicated 2-5 amino acid changes. Among them, mutant TP8H5 showed an altered pH profile as compared with that of wild type. The sequencing of variant TP8H5 indicated 2 amino acid changes, Ile157Ser and Trp193Arg, which were located in the solvent accessible flexible loop region in domain B.

• Animal Systematics, Evolution and Diversity
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• v.25 no.3
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• pp.301-308
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• 2009

Three Loxodes ciliates collected from estuarine littoral, wetland and small pond in Korea, were identified as Loxodes kahli Dragesco and Njin$acute{e}$, 1971, L. magnus Stokes, 1887 and L. vorax Stokes, 1885. The descriptions for these species based on living and protargol impregnated specimens were given. Morphometry, illustrations and microphotographs were also provided. Diagnoses of three species are as follows. Loxodes kahli; size in vivo $160-300{\times}40-70\;{\mu}m$; oral area with reddish to brownish pigments; 6-11 macronuclei arranged linearly; 5-9 micronuclei located near macronuclei; 4-12 M$\ddot{u}$ller's vesicles; somatic kineties on right 18-20 and left 2 in number. L. magnus: size in vivo $250-470{\times}87-15\;{\mu}m$; body colored dark brown; 5-13 macronuclei; 8-13 micronuclei; 8-18 M$\ddot{u}$ller's vesicles; somatic kineties on right 23-26 and left 2 in number. L. vorax: size in vivo $70-160{\times}20-35\;{\mu}m$; oral area with brownish pigments; 2 macronuclei; 1 micronucleus located between macronuclei; 2-4 M$\ddot{u}$ller's vesicles; somatic kineties on right 18-20 and left 2 in number.

• Animal Systematics, Evolution and Diversity
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• no.nspc5
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• pp.13-28
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• 2005

A taxonomic survey was carried out to see the decapod fauna of Jindo Island and its adjacent islet, Korea in June 2004. The 35 species in 13 families were identified in this study and of which 12 species of caridean shrimps in three families, one thalassinidean species, two anomuran species in one family, and two crab species in two families were newly added to the decapod faun3 of the study area. With the previously known 58 species in the Jindo Island and its adjacent islets, a total of 75 species are listed with some brief remarks. Distribution patterns of species are also discussed based on the composition of geographical distribution forms.

• Genomics & Informatics
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• v.19 no.3
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• pp.27.1-27.4
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• 2021

Due to the rapid evolution of high-throughput technologies, a tremendous amount of data is being produced in the biological domain, which poses a challenging task for information extraction and natural language understanding. Biological named entity recognition (NER) and named entity normalisation (NEN) are two common tasks aiming at identifying and linking biologically important entities such as genes or gene products mentioned in the literature to biological databases. In this paper, we present an updated version of OryzaGP, a gene and protein dataset for rice species created to help natural language processing (NLP) tools in processing NER and NEN tasks. To create the dataset, we selected more than 15,000 abstracts associated with articles previously curated for rice genes. We developed four dictionaries of gene and protein names associated with database identifiers. We used these dictionaries to annotate the dataset. We also annotated the dataset using pretrained NLP models. Finally, we analysed the annotation results and discussed how to improve OryzaGP.