• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• Parasites, Hosts and Diseases
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• v.48 no.2
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• pp.151-155
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• 2010

Allergen extracts from dust mites and cockroaches commonly found in Korean homes were used to evaluate their enzymatic activity as they are believed to influence allergenicity. Allergen extracts were prepared from 3 dust mite species (Dermatophagoides farinae, D. pteronyssinus, and Tyrophagus putrescentiae) and 3 cockroach species (Blattella germanica, Periplaneta americana, and P. fuliginosa) maintained in the Korea National Arthropods of Medical Importance Resource Bank. Proteins were extracted in PBS after homogenization using liquid nitrogen. The activities of various enzymes were investigated using the API Zym system. No significant difference in phosphatase, lipase, or glycosidase activity was observed among the 6 allergen extracts, but much difference was observed in protease activity. Protease activity was assessed in more detail by gelatin zymography and the EnzChek assay. Extract from T. putrescentiae showed the highest protease activity, followed by those of the cockroach extracts. Extracts from D. farinae and D. pteronyssinus showed only weak protease activity. Gelatinolytic activity was detected mainly in a 30-kDa protein in D. farinae, a 28-kDa protein in D. pteronyssinus, a > 26-kDa protein in T. putrescentiae, a > 20-kDa protein in B. germanica, and a > 23-kDa protein in P. americana and P. fuliginosa. The information on various enzymatic activities obtained in this study may be useful for future studies. In particular, the strong protease activity found in cockroach extracts could contribute to sensitization to cockroach allergens, which is known to be associated with the development of asthma.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.8
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• pp.1097-1102
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• 2008

Paraoxonase-1 (PON1), like lipoprotein lipase (LPL), plays a key role in the metabolism and physiology of mammalian growth. The objectives of this study were to estimate the allele and genotype frequencies at the PON1/EcoRV and PON1/AluI loci in three genetic groups of beef cattle and to determine associations between these polymorphisms and growth and carcass traits. Genotyping was performed on 30 Angus, 32 Hereford and 26 Simmental. The association analysis was carried out using the GLM procedure of SAS 9.1 and the least squares means of the genotypes were compared by the Tukey's test. Animals with AG genotype at the PON1/EcoRV locus had higher weight at the time of entry into the fattening corrals ($329.97{\pm}6.08kg$) and close to the time of slaughter ($577.56{\pm}8.32kg$) and net meat weight ($275.89{\pm}4.05kg$) and fitted tenderness ($3.10{\pm}0.19kg$) (p<0.05). Animals with AA genotype at the PON1/AluI locus had higher weight at the time of entry ($333.37{\pm}8.93kg$) and slaughter ($576.82{\pm}13.18kg$) and net meat weight ($275.49{\pm}6.43kg$) and average daily gain ($0.68{\pm}0.02kg/d$) (p<0.05). The meat color score was also significantly higher (p<0.05). Between genotypes and breeds, there were significant differences observed except for TBW, REMG, MBS, REA and MCS. As a metabolism gene, genotypes of the SNPs of PON1 gene might be reflecting BFT directly, such as $A_eA_eG_aG_a$ genotype in this experiment.