• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.12
• /
• pp.1980-1990
• /
• 2018

Objective: The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome Methods: Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. Results: Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. Conclusion: The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.

• Journal of Animal Reproduction and Biotechnology
• /
• v.36 no.1
• /
• pp.35-44
• /
• 2021

A pregnancy diagnosis is an important standard for control of livestock's reproduction in paricular dairy cattle. High reproductive performance in dairy animals is a essential condition to realize of high life-time production. Pregnancy diagnosis is crucial to shortening the calving interval by enabling the farmer to identify open animals so as to treat or re-breed them at the earliest opportunity. MicroRNAs are short RNA molecules which are critically involved in regulating gene expression during both health and disease. This study is sought to establish the feasible of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from 12 non-pregnant cows ("open" cows: samples were collected before insemination (non-pregnant state) and after pregnancy check at the indicated time points) on weeks 0, 4, 8, 12 and 16. Using small RNA sequencing we identified a total of 115 miRNAs that were differentially expressed weeks 16 relative to non-pregnancy ("open" cows). Weeks 8, 12 and 16 of pregnancy commonly showed a distinct increase in circulating levels of miR-221 and miR-320a. Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with pregnancy in cattle. Their application in the field of reproductive biology has opened up opportunities for research communities to look for pregnancy biomarker molecules in dairy cattle.

• Mycobiology
• /
• v.44 no.3
• /
• pp.121-130
• /
• 2016

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade.

• ETRI Journal
• /
• v.37 no.2
• /
• pp.212-221
• /
• 2015

As the amount of re-sequencing genome data grows, minimizing the execution time of an analysis is required. For this purpose, recent computing systems have been adopting both high-performance coprocessors and host processors. However, there are few applications that efficiently utilize these heterogeneous computing resources. This problem equally refers to the work of single nucleotide polymorphism (SNP) detection, which is one of the bottlenecks in genome data processing. In this paper, we propose a method for speeding up an SNP detection by enhancing the utilization of heterogeneous computing resources often used in recent high-performance computing systems. Through the measurement of workload in the detection procedure, we divide the SNP detection into several task groups suitable for each computing resource. These task groups are scheduled using a window overlapping method. As a result, we improved upon the speedup achieved by previous open source applications by a magnitude of 10.

• The Korean Journal of Malacology
• /
• v.30 no.3
• /
• pp.197-210
• /
• 2014

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.

• Phonetics and Speech Sciences
• /
• v.6 no.3
• /
• pp.121-130
• /
• 2014

This study investigates the acoustic property of aspiration realized in English voiceless stops of /Cr/ and /sCr/ clusters. VOT is measured from stops in these clusters produced by two groups; one from native speakers of English and the other from Korean native speakers. Aspiration of stops in different types of clusters is compared to various phonological factors such as location of stress, syllable type, and position in word. Pursuing the idea that phonetic realization is correlated with phonological representation, attempts are made to account for the gradient nature of aspiration of stops on the basis of syllable structure at the phonetic level, which may vary in the wake of resyllabification. Voiceless stops in /Cr/ and /sCr/ clusters are further compared to results obtained in the previous study on /sC/ cluster. Variations in aspiration are also characterized in terms of segmental precedence relation of stops in the clusters, namely, post-[s], pre-[r], or both.

• The Plant Pathology Journal
• /
• v.31 no.1
• /
• pp.41-49
• /
• 2015

Sweet cherry is an important fruit crop with increasing economical value in Turkey and the world. A number of viruses cause diseases and economical losses in sweet cherry. Prune dwarf virus (PDV), is one of the most common viruses of stone fruits including sweet cherry in the world. In this study, PDV was detected from 316 of 521 sweet cherry samples collected from 142 orchards in 10 districts of Isparta province of Turkey by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). The presence of PDV in ELISA positive samples was confirmed in 37 isolates by reverse transcription- polymerase chain reaction (RT-PCR) method. A genomic region of 862 bp containing the coat protein (CP) gene of PDV was re-amplified from 21 selected isolates by RT-PCR. Amplified DNA fragments of these isolates were purified and sequenced for molecular characterization and determining genetic diversity of PDV. Sequence comparisons showed 84-99% to 81-100% sequence identity at nucleotide and amino acid level, respectively, of the CP genes of PDV isolates from Isparta and other parts of the world. Phylogenetic analyses of the CP genes of PDV isolates from different geographical origins and diverse hosts revealed that PDV isolates formed different phylogenetic groups. While isolates were not grouped solely based on their geographical origins or hosts, some association between phylogenetic groups and geographical origins or hosts were observed.

• The Korean Journal of Zoology
• /
• v.35 no.1
• /
• pp.80-86
• /
• 1992

The nucleotide sequences of 185 rRNAs of the five Korean decapods were partially determined by the direct sequencing method using the reverse transcriptase. ne average GC content of five species was 51.1% which is higher than that of yeast(45.0%) and lower than those of frog (53.0%) and rat (55.6%). This result follows the general patterns of the GC content in the nucleotides of the nucleic acid shown among the various phylogenetic groups. The average ratio of transrional/transversional nucleotide substitution of pairwise comparison among six species (including Anemia salina) was 1.200 $\pm$ 0.310 when whole region alas examined. However, the ratio showed some differences when the conservative regions and variable regions frere separatelv examined. The molecular phylogenies of the five species were constructed by using two different tree making methods. In general the results support the previously reported molecular phylogeny of the decapod crustaceans. However, our results indicate thats in the analysis of the sequence dat3, the UPGMA clustering method of the distance matrix method should be carefully employed after considering the rate of nucneotide substitution in the different regions of the molecule.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.7 no.5
• /
• pp.919-925
• /
• 2006

Mobile IPv6 generates the loss of packets and out of sequencing when hand off, In this paper, We propose a improved hand off techniques using the mobility pattern of mobile nodes. As making group by presetting the moving range of mobile nodes, and putting buffer server in the group, the packet loss and out of packet sequence can be reduced. The proposed method prevents the out of packet sequence in If level which can be happened in the stable state, minimizes the packet re-send in TCP level. In the simulation, the proposed hand off techniques transmits packets efficiently by using the mobility pattern of mobile nodes.

• Archives of Pharmacal Research
• /
• v.18 no.2
• /
• pp.113-117
• /
• 1995

We re-cloned mouse ${\delt}-Opioid$receptor from NG108-15 cells using RT-PCR, and confirmed it by restriction analysis and by sequencing the beginning and end part of the amplified DNA. When transiently expressed in COS-7 cells, cloned ${\delt}-Opioid$ receptor showed saturable and specific binding to $[^3H]$naloxone with very similar binding parameters to originally reported ones. To make antibodies specific for the ${\delt}-Opioid$ receptor, the carboxy tail of the receptor, which is unique to the ${\delt}-Opioid$ receptor compared with other opioid receptors, was expressed in bacteria as a ufsion proteinwith glutathione S-transferase. Purified fusion protein selective for ${\delt}-Opioid$ receptor when tested by western blotting using membrane proteins prepared from transfected COS-7 cells. Cloned ${\delt}-Opioid$ receptor andl antibodies specific for ${\delt}-Opioid$ receptor are going to be valuable tools for studying pharmacological actions of the ${\delt}-Opioid$ receptor and morphine dependence.