• Molecules and Cells
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• v.39 no.5
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• pp.382-388
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• 2016

Inherited peripheral neuropathies (IPN), which are a group of clinically and genetically heterogeneous peripheral nerve disorders including Charcot-Marie-Tooth disease (CMT), exhibit progressive degeneration of muscles in the extremities and loss of sensory function. Over 70 genes have been reported as genetic causatives and the number is still growing. We prepared a targeted gene panel for IPN diagnosis based on next generation sequencing (NGS). The gene panel was designed to detect mutations in 73 genes reported to be genetic causes of IPN or related peripheral neuropathies, and to detect duplication of the chromosome 17p12 region, the major genetic cause of CMT1A. We applied the gene panel to 115 samples from 63 non-CMT1A families, and isolated 15 pathogenic or likelypathogenic mutations in eight genes from 25 patients (17 families). Of them, eight mutations were unreported variants. Of particular interest, this study revealed several very rare mutations in the SPTLC2, DCTN1, and MARS genes. In addition, the effectiveness of the detection of CMT1A was confirmed by comparing five 17p12-nonduplicated controls and 15 CMT1A cases. In conclusion, we developed a gene panel for one step genetic diagnosis of IPN. It seems that its time- and cost-effectiveness are superior to previous tiered-genetic diagnosis algorithms, and it could be applied as a genetic diagnostic system for inherited peripheral neuropathies.

• Journal of the Korea Institute of Building Construction
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• v.13 no.5
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• pp.491-497
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• 2013

The objective of the present study is to establish a straightforward mixture proportioning procedure for structural lightweight aggregate concrete (LWAC), and evaluate the selection range of the targeted dry density of concrete against the designed concrete compressive strength. In developing this procedure, mathematical models were formulated based on a nonlinear regression analysis over 347 data sets and two boundary conditions of the absolute volume and dry density of concrete. The proposed procedure demonstrated the appropriate water-to-cement ratio and dry density of concrete to achieve the designed strength decrease with the increase in volumetric ratio of coarse aggregates. This trend was more significant in all-LWAC than in sand-LWAC. Overall, the selection range of the dry density of LWAC exists within a certain range according to the designed strength, which can be obtained using the proposed procedure.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1529-1540
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• 2011

Silencing of a specific gene using RNAi (RNA interference) is a valuable tool for functional analysis of a target gene. However, information on RNAi for analysis of gene function in farm animals is relatively nil. In the present study, we have validated the interfering effects of siRNA (small interfering RNA) using both quantitative and qualitative gene silencing in buffalo granulosa cells. Qualitative gene knockdown was validated using a fluorescent vector, enhanced green fluorescence protein (EGFP) and fluorescently labeled siRNA (Cy3) duplex. While quantitatively, siRNA targeted against the luciferase and CYP19 mRNA was used to validate the technique. CYP19 gene, a candidate fertility gene, was selected as a model to demonstrate the technique optimization. However, to sustain the expression of CYP19 gene in culture conditions using serum is difficult because granulosa cells have the tendency to luteinize in presence of serum. Therefore, serum free culture conditions were optimized for transfection and were found to be more suitable for the maintenance of CYP19 gene transcripts in comparison to culture conditions with serum. Decline in fluorescence intensity of green fluorescent protein (EGFP) was observed following co-transfection with plasmid generating siRNA targeted against EGFP gene. Quantitative decrease in luminescence was seen when co-transfected with siRNA against the luciferase gene. A significant suppressive effect on the mRNA levels of CYP19 gene at 100 nM siRNA concentration was observed. Also, measurement of estradiol levels using ELISA (enzyme-linked immunosorbent assay) showed a significant decline in comparison to control. In conclusion, the present study validated gene silencing using RNAi in cultured buffalo granulosa cells which can be used as an effective tool for functional analysis of target genes.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.11
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• pp.4507-4511
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• 2014

Background: Breast cancer is a heterogeneous disease comprising of distinct biological subtypes with many targeted prognostic biomarkers having therapeutic implications. However, no specific targeted therapy for triple negative breast cancer has been discovered to date and hence further research is needed. Aim: The aim and objectives of the present study were to examine the prevalence of triple negative breast cancer (TNBC) in North-East India and to compare the clinicopathological parameters in two study groups defined by immunohistochemistry (IHC) - "TNBC" and "Others". Materials and Methods: We carried out a retrospective study in a cohort of 972 patients diagnosed with invasive breast carcinoma in the Department of Pathology, Dr. B. Borooah Cancer Institute, a Regional Cancer Centre for treatment and research, Guwahati, for a period of 3 years and 10 months from January 2010 to October 2013. Based on IHC findings, patients were divided into two groups - "TNBC" and "Others". All relevant clinicopathological parameters were compared in both. TNBC were defined as those that were estrogen receptor (ER), progesterone receptor (PR), and HER2/neu negative while those positive for any of these markers were defined as "Others". Results: In this study, out of total 972 cases 31.9% (310 cases) were defined as TNBC and 662 cases (68.1%) as "Others" based on IHC markers. Compared to the "Others" category, TNBC presented at an early age (mean 40 years), were associated with high grade large tumours and high rate of node positivity, IDC NOS being the most common histological subtype in TNBC. Conclusions: TNBC accounts for a significant portion of breast cancers in this part of India and commonly present at younger age and tend to be large high grade tumours.

• Journal of Genetic Medicine
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• v.16 no.2
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• pp.62-66
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• 2019

Harlequin ichthyosis (HI, OMIM #242500) is one of the most severe skin diseases among the autosomal recessive congenital ichthyoses, with high morbidity and mortality, particularly in newborns. Clinically, it is characterized by a typical appearance of generalized, thick, yellowish, hyperkeratotic plates with deep erythematous fissures on the skin. Herein, we present the case of a newborn girl with HI that was genetically confirmed by targeted gene panel analysis. The premature baby was encased in an opaque white membrane with erosion covering the skin of the entire body except the lips, with her hands and feet restricted by the membrane. Humidification, emollient, and retinoic acid treatment were started; the thick ichthyosis gradually peeled off and the underlying skin was only covered with thin scales. Targeted gene panel analysis using next-generation sequencing and validation with Sanger sequencing and quantitative polymerase chain reaction analyses confirmed compound heterozygous mutations of the ABCA12 gene (p.N1380S and a partial gene deletion encompassing exon 9). The parents were carriers for each of the identified mutations. Early recognition of the genetic etiology of congenital ichthyosis can, thus, facilitate genetic counseling for patients and their families.

• Genomics & Informatics
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• v.17 no.4
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• pp.42.1-42.6
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• 2019

Robust identification of genetic alterations is important for the diagnosis and subsequent treatment of tumors. Screening for genetic alterations using tumor tissue samples may lead to biased interpretations because of the heterogeneous nature of the tumor mass. Liquid biopsy has been suggested as an attractive tool for the non-invasive follow-up of cancer treatment outcomes. In this study, we aimed to verify whether the mutations identified in primary tumor tissue samples could be consistently detected in plasma cell-free DNA (cfDNA) by digital polymerase chain reaction (dPCR). We first examined the genetic alteration profiles of three colorectal cancer (CRC) tissue samples by targeted next-generation sequencing (NGS) and identified 11 non-silent amino acid changes across six cancer-related genes (APC, KRAS, TP53, TERT, ARIDIA, and BRCA1). All three samples had KRAS mutations (G12V, G12C, and G13D), which were well-known driver events. Therefore, we examined the KRAS mutations by dPCR. When we examined the three KRAS mutations by dPCR using tumor tissue samples, all of them were consistently detected and the variant allele frequencies (VAFs) of the mutations were almost identical between targeted NGS and dPCR. When we examined the KRAS mutations using the plasma cfDNA of the three CRC patients by dPCR, all three mutations were consistently identified. However, the VAFs were lower (range, 0.166% to 2.638%) than those obtained using the CRC tissue samples. In conclusion, we confirmed that the KRAS mutations identified from CRC tumor tissue samples were consistently detected in the plasma cfDNA of the three CRC patients by dPCR.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.3
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• pp.413-418
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• 2016

Myostatin (MSTN) is a secreted growth factor expressed in skeletal muscle and adipose tissue that negatively regulates skeletal muscle mass. Gene knockout of MSTN can result in increasing muscle mass in sheep. The objectives were to investigate whether myostatin gene can be edited in sheep by transcription activator-like effector nucleases (TALENs) in tandem with single-stranded DNA oligonucleotides (ssODNs). We designed a pair of TALENs to target a highly conserved sequence in the coding region of the sheep MSTN gene. The activity of the TALENs was verified by using luciferase single-strand annealing reporter assay in HEK 293T cell line. Co-transfection of TALENs and ssODNs oligonucleotides induced precise gene editing of myostatin gene in sheep primary fibroblasts. MSTN gene-edited cells were successfully used as nuclear donors for generating cloned embryos. TALENs combined with ssDNA oligonucleotides provide a useful approach for precise gene modification in livestock animals.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.85.1-85
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• 2003

In most ascomycetes, a single mating type locus, MAT, with two alternate forms (MAT1-1 and MAT1-2) called idiomorphs, controls mating ability. In heterothallic ascomycetes these alternate idiomorphs reside in different nuclei. In contrast, most homothallic ascomycetes carry both MAT1-1 and MAT1-2 in a single nucleus, usually closely linked. An example of the latter is Gibberella zeae, a producer of mycotoxins such as trichothecene and zearalenone that threaten human and animal health. We asked if G. zeae could be made strictly heterothallic by manipulation of MAT. Targeted gene replacement was used to differentially delete MAT1-1 or MAT1-2 from a wild type haploid MAT1-1 MAT1-2 strain, resulting in MAT1-1；mat1-2, mat1-1；MAT1-2 strains that were self-sterile, yet able to cross to wild type testers and more importantly, to each other. These results indicated that differential deletion of MAT idiomorphs eliminates selfing ability of G. zeae, but the ability to outcross is retained. To our knowledge, this is the first report of complete conversion of fungal reproductive strategy from homothallic to heterothallic by targeted manipulation of MAT. Practically, this approach opens the door to simple and efficient procedures for obtaining sexual recombinants of G. zeae that will be useful for genetic analyses of mycotoxin production and other traits, such as ability to cause disease.

• Journal of Digital Convergence
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• v.13 no.6
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• pp.29-37
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• 2015

Entering the convergence education era, the emergence of smart devices removed the constraint of time and space for study, so if we use smart devices appropriately for education, it will strengthen students' abilities and cultivate creative human resource. Therefore the current study analyzed the general application condition of the smart devices through surveys targeted to students and proposed a measure in applying the smart device as an educational information. In relation to information application, a test was proceeded after carrying out education targeted to experiment group students by naming the group information search, communication, cooperation, sharing, report generation, data storage, online assessment and project management activity. Through the test and survey analysis, it was discovered that the experiment group students displayed higher self-efficacy and ability in applying the smart device as information compared to the control group.

• Journal of the Korea Institute of Building Construction
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• v.18 no.4
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• pp.329-335
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• 2018

The objective of this study is to develop a mortar mixture with high workability and adhesive strength for section jacketing in seismic strengthening technology of existing concrete structures. To achieve targeted requirements of the mortars (initial flow exceeding 200 mm, compressive strength of 30MPa, and adhesive strength exceeding 1MPa), step-by-step tests were conducted under the variation of the following mixture parameters: water-to-binder ratio, sand-to-binder ratio, polymer-to-binder ratio, dosage of viscosity agent, and content of ultra-rapid-hardening cement. The adhesive strength of the mortars was also estimated with respect to the various surface treatment states of existing concrete. Based on the test results, the mortar mixture with the polymer-to-binder ratio of 10% and the content of ultra-rapid-hardening cement of 5% can be recommended for the section jacketing materials. The recommended mortar mixture satisfied the targeted requirements as follows: initial flow of 220 mm, high-early strength gain, 28-day compressive strength of 35MPa, and adhesive strength exceeding 1.2MPa.