• Industrial Engineering and Management Systems
• /
• v.16 no.1
• /
• pp.64-79
• /
• 2017

Identifying disease genes from human genome is a critical task in biomedical research. Important biological features to distinguish the disease genes from the non-disease genes have been mainly selected based on traditional feature selection approaches. However, the traditional feature selection approaches unnecessarily consider many unimportant biological features. As a result, although some of the existing classification techniques have been applied to disease gene identification, the prediction performance was not satisfactory. A small set of the most important biological features can enhance the accuracy of disease gene identification, as well as provide potentially useful knowledge for biologists or clinicians, who can further investigate the selected biological features as well as the potential disease genes. In this paper, we propose a new stepwise random forests (SRF) approach for biological feature selection and disease gene identification. The SRF approach consists of two stages. In the first stage, only important biological features are iteratively selected in a forward selection manner based on one-dimensional random forest regression, where the updated residual vector is considered as the current response vector. We can then determine a small set of important biological features. In the second stage, random forests classification with regard to the selected biological features is applied to identify disease genes. Our extensive experiments show that the proposed SRF approach outperforms the existing feature selection and classification techniques in terms of biological feature selection and disease gene identification.

• Journal of Biosystems Engineering
• /
• v.43 no.1
• /
• pp.59-71
• /
• 2018

Purpose: Cellulose nanocrystals (CNCs) are natural polymers that have been promoted as a next generation of new, sustainable materials. CNCs are invaluable as reinforcing materials for composites because they can impart improved mechanical, chemical, and thermal properties and they are biodegradable. The purpose of this review is to provide researchers with information that can assist in the application of CNCs extracted from waste agricultural byproducts (e.g. rice husks, corncobs, pineapple leaves). Methods & Results: This paper presents the unique characteristics of CNCs based on agricultural byproducts, and lists processing methods for manufacturing CNCs from agricultural byproducts. Various mechanical treatments (microfluidization and homogenization) and chemical treatments (alkali treatment, bleaching and hydrolysis) can be performed in order to generate nanocellulose. CNC-based composite properties and various applications are also discussed. Conclusions: CNC-based composites from agricultural byproducts can be combined to meet end-use applications such as sensors, batteries, films, food packaging, and 3D printing by utilizing their properties. The review discusses applications in food engineering, biological engineering, and cellulose-based hydrogels.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.12
• /
• pp.2119-2128
• /
• 2017

Citrinin (CIT) is a toxic secondary metabolite produced by fungi belonging to the Penicillium, Aspergillus, and Monascus spp. This toxin has been detected in many agricultural products. In this study, a strain Y3 with the ability to eliminate CIT was screened and identified as Cryptococcus podzolicus, based on the sequence analysis of the internal transcribed spacer region. Neither uptake of CIT by cells nor adsorption by cell wall was involved in CIT elimination by Cryptococcus podzolicus Y3. The extracellular metabolites of Cryptococcus podzolicus Y3 stimulated by CIT or not showed no degradation for CIT. It indicated that CIT elimination was attributed to the degradation of intracellular enzyme(s). The degradation of CIT by C. podzolicus Y3 was dependent on the type of media, yeast concentration, temperature, pH, and initial concentration of CIT. Most of the CIT was degraded by C. podzolicus Y3 in NYDB medium at 42 h but not in PDB medium. The degradation rate of CIT was the highest (94%) when the concentration of C. podzolicus Y3 was $1{\times}10^8cells/ml$. The quantity of CIT degradation was highest at $28^{\circ}C$, and there was no degradation observed at 3$5^{\circ}C$. The study also showed that acidic condition (pH 4.0) was the most favorable for CIT degradation by C. podzolicus Y3. The degradation rate of CIT increased to 98% as the concentration of CIT was increased to $20{\mu}g/ml$. The toxicity of CIT degradation product(s) toward HEK293 was much lower than that of CIT.

• Korean Chemical Engineering Research
• /
• v.52 no.4
• /
• pp.407-412
• /
• 2014

Lactulose is well known for functional component in the food and pharmaceutical field and utilized in a wide variety of foods as a bifidus factor or functional ingredient for intestinal regulation. Lactulose synthesis can be classified into chemical and biological methods. In chemical methods, lactulose is synthesized by alkaline isomerization, but it has many disadvantages such as including product purification, lactulose degradation, side reactions and waste management. Therefore, the enzymatic synthesis methods were recently studied to solve these problems. ${\beta}$-galactosidase is a important enzyme in the dairy industry, because of the production of lactose-hydrolyzed products. Also, ${\beta}$-galactosidases can be utilized to synthesize lactulose from lactose by a trans-galactosylation reaction, using fructose as a galactosyl acceptor. However, the synthesis of lactulose from lactose is economically not suitable due to high levels of lactose price. This review summarizes the current state of lactulose production by chemical and biological processes.

• Journal of the Korean Electrochemical Society
• /
• v.19 no.3
• /
• pp.87-94
• /
• 2016

In order to improve performances of submicrometer-sized Si negative electrode which shows larger volumetric change than nano-sized Si, composite binders are introduced by blending between poly(phenanthrenequinone) (PPQ) conductive polymer binder and poly(acrylic acid) (PAA) having good adhesion strength due to its carboxyl functional group. Blending between PPQ and PAA shows an effect that the adhesion strength of the Si electrode with the composite conductive binder is greatly improved after blending and this makes its better stable cycle performance. Blending ratios between PPQ and PAA in this work are 2:1, 1:1, 1:2 (by weight) and the best capacity retention at 50th cycle is observed in the electrode with the blending ratio 2:1 (named QA21). This is because that PPQ plays a role of conductive carbon among the Si particles or between Si particles and Cu current collector and PAA binds effectively the particles and the current collector. According to this synergetic effect, the internal resistance of the Si electrode with the blending ratio 2:1 is the smallest value. In addition, the Si electrode with PPQ-PAA composite binder shows the better stable cycle performance than the electrode with conventional super-P conductive carbon (20 wt.%).

• KSBB Journal
• /
• v.20 no.3
• /
• pp.233-237
• /
• 2005

In order to investigate the feasibility of 30K protein from silkworm (Bombyx mori) hemolymph (SH) on the proliferation of human cells, a simple separating procedure by anion-exchange chromatography system with Q-Sepharose fast flow gel was established. The 30K protein was eluted with an optimized condition of 0.16 M sodium chloride in 20 mM tris buffer (pH 9.0). The separated 30K protein at three concentrations of 0.04, 0.12, and 0.4 mg/ml was added to the culture medium with various human cells, such as chondrocytes, periosteum-derived cells, and MRC-5 cells, and their growth rates were measured. The cell growth rate at protein concentration of 0.4 mg/ml was always higher than that without 30K protein in all human cells tested, suggesting that the 30K protein has positive effect on the increase of the life span of human cells.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.9
• /
• pp.1377-1383
• /
• 2006

Among 46 Acinetobacter baumannii isolates collected in 2004, two imipenem-resistant isolates were obtained from clinical specimens taken from patients hospitalized in Busan, Republic of Korea. Two carbapenemase-producing isolates were further investigated to determine the mechanism of resistance. These isolates were analyzed by antibiotic susceptibility testing, microbiological tests of carbapenemase activity, determination of pI, transconjugation test, enterobacterial repetitive consensus (ERIC)-PCR, and DNA sequencing. Two cases of infection by A. baumannii producing the IMP-1 ${\beta}$-lactamase were detected. The isolates were characterized by a modified cloverleaf synergy test and EDTA-disk synergy test. Isoelectric focusing of crude bacterial extracts revealed nitrocefin-positive bands with a pI value of 9.0. PCR amplification and characterization of the amplicons by direct sequencing indicated that the isolates carried a $bla_{IMP-l}$ determinant. The isolates were characterized by a multidrug resistance phenotype, including penicillins, extended-spectrum cephalosporins, carbapenems, and aminoglycosides. These results indicate that the observed imipenem resistance of two Korean A. baumannii isolates was due to the spread of an IMP-1-producing clone. Our microbiological test of carbapenemase activity is simple to screen class B metallo-${\beta}$-lactamase-producing clinical isolates to determine their clinical impact and to prevent further spread. This study shows that the $bla_{IMP-l}$ resistance determinant, which is emerging in Korea, may become an emerging therapeutic problem, since clinicians are advised not to use extended-spectrum cephalosporins, imipenem, and aminoglycosides. This observation emphasizes the importance of having effective control measures in Asian hospitals, such as early detection of colonized patients, isolation procedures, and a judicious use of antibiotics.

• Journal of Veterinary Science
• /
• v.22 no.4
• /
• pp.43.1-43.10
• /
• 2021

Background: The H5 avian influenza viruses (AIVs) of clade 2.3.4.4 circulate in wild and domestic birds worldwide. In 2017, nine strains of H5N6 AIVs were isolated from aquatic poultry in Xinjiang, Northwest China. Objectives: This study aimed to analyze the origin, reassortment, and mutations of the AIV isolates. Methods: AIVs were isolated from oropharyngeal and cloacal swabs of poultry. Identification was accomplished by inoculating isolates into embryonated chicken eggs and performing hemagglutination tests and reverse transcription polymerase chain reaction (RT-PCR). The viral genomes were amplified with RT-PCR and then sequenced. The sequence alignment, phylogenetic, and molecular characteristic analyses were performed by using bioinformatic software. Results: Nine isolates originated from the same ancestor. The viral HA gene belonged to clade 2.3.4.4B, while the NA gene had a close phylogenetic relationship with the 2.3.4.4C H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated from shoveler ducks in Ningxia in 2015. The NP gene was grouped into an independent subcluster within the 2.3.4.4B H5N8 AIVs, and the remaining six genes all had close phylogenetic relationships with the 2.3.4.4B H5N8 HPAIVs isolated from the wild birds in China, Egypt, Uganda, Cameroon, and India in 2016-2017, Multiple basic amino acid residues associated with HPAIVs were located adjacent to the cleavage site of the HA protein. The nine isolates comprised reassortant 2.3.4.4B HPAIVs originating from 2.3.4.4B H5N8 and 2.3.4.4C H5N6 viruses in wild birds. Conclusions: These results suggest that the Northern Tianshan Mountain wetlands in Xinjiang may have a key role in AIVs disseminating from Central China to the Eurasian continent and East African.

• Genes and Genomics
• /
• v.40 no.11
• /
• pp.1169-1180
• /
• 2018

Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (TST complex) comprises twenty cave-adapted taxa, which mainly occur in the anchialine environment. Anchialine habitats may undergo drastic environmental fluctuations, including spatial and temporal changes in salinity, temperature, and dissolved oxygen content. Previous studies of crustaceans from anchialine caves suggest that they have possessed morphological, behavioral, and physiological adaptations to cope with the extreme conditions, similar to other cave-dwelling crustaceans. However, the genetic basis has not been thoroughly explored in crustaceans from anchialine habitats, which can experience hypoxic regimes. To test whether the TST shrimp-complex hypoxia adaptations matched adaptive evolution of mitochondrial OXPHOS genes. The 13 OXPHOS genes from mitochondrial genomes of 98 shrimps and 1 outgroup were examined. For each of these genes was investigated and compared to orthologous sequences using both gene (i.e. branch-site and Datamonkey) and protein (i.e. TreeSAAP) level approaches. Positive selection was detected in 11 of the 13 candidate genes, and the radical amino acid changes sites scattered throughout the entire TST complex phylogeny. Additionally, a series of parallel/convergent amino acid substitutions were identified in mitochondrial OXPHOS genes of TST complex shrimps, which reflect functional convergence or similar genetic mechanisms of cave adaptation. The extensive occurrence of positive selection is suggestive of their essential role in adaptation to hypoxic anchialine environment, and further implying that TST complex shrimps might have acquired a finely capacity for energy metabolism. These results provided some new insights into the genetic basis of anchialine hypoxia adaptation.

• Animal Bioscience
• /
• v.35 no.2_spc
• /
• pp.332-346
• /
• 2022

Shortage of protein feed resources is the major challenge to the world farm animal industry. Insects are known as an alternative protein source for poultry. A wide range of insects are available for use in poultry diets. Insect larvae thrive in manure, and organic waste, and produce antimicrobial peptides to protect themselves from microbial infections, and additionally these peptides might also be functional in poultry feed. The feed containing antimicrobial peptides can improve the growth performance, nutrient digestibility, intestinal health, and immune function in poultry. Insect meal contains a higher amount of essential amino acids compared to conventional feedstuffs. Black soldier fly, mealworm, housefly, cricket/Grasshopper/Locust (Orthoptera), silkworm, and earthworm are the commonly used insect meals in broiler and laying hen diets. This paper summarizes the nutrient profiles of the insect meals and reviews their efficacy when included in poultry diets. Due to the differences in insect meal products, and breeds of poultry, inconsistent results were noticed among studies. The main challenge for proper utilization, and the promising prospect of insect meal in poultry diet are also addressed in the paper. To fully exploit insect meal as an alternative protein resource, and exert their functional effects, modes of action need to be understood. With the emergence of more accurate and reliable studies, insect meals will undoubtedly play more important role in poultry feed industry.