• Asian Pacific Journal of Cancer Prevention
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• v.15 no.21
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• pp.9495-9498
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• 2014

Background: The difference in prognosis of adult and childhood acute lymphoblastic leukemia (ALL) can be attributed largely to variation in cytogenetic abnormalities with age groups. Cytogenetic analysis in acute leukemia is now routinely used to assist patient management, particularly in terms of diagnosis, disease monitoring, prognosis and risk stratification. Knowing about cytogenetic profile at the time of diagnosis is important in order to take critical decisions in management of the patients. Aim and Objectives: To determine the frequency of cytogenetic abnormalities in Pakistani adult patients with ALL in order to have insights regarding behavior of the disease. Materials and Methods: A retrospective analysis of all the cases of ALL (${\geq}15$years old) diagnosed at Aga Khan University from January 2006 to June 2014 was performed. Phenotype (B/T lineage) was confirmed in all cases by flow cytometry. Cytogenetic analysis was made for all cases using the trypsin-Giemsa banding technique. Karyotypes were interpreted using the International System for Human Cytogenetic Nomenclature (ISCN) criteria. Results: A total of 166 patients were diagnosed as ALL during the study period, of which 151 samples successfully yielded metaphase chromosomes. The male to female ratio was 3.4:1. The majority (n=120, 72.3%) had a B-cell phenotype. A normal karyotype was present in 51% (n=77) of the cases whereas 49% (n=74) had an abnormal karyotype. Of the abnormal cases, 10% showed Philadelphia chromosome; t(9;22)(q34;q11.2). Other poor prognostic cytogenetic subgroups were t(4;11)(q21;q23), hypodiploidy (35-45 chromosomes) and complex karyotype. Hyperdiploidy (47-57 chromosomes) occurred in 6.6%; all of whom were younger than 30 years. Conclusions: This study showed a relatively low prevalence of Philadelphia chromosome in Pakistani adults with ALL with an increase in frequency with age (p=0.003). The cumulative prevalence of Philadelphianegative poor cytogenetic aberrations in different age groups was not significant (p=0.6).

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.23-23
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• 2017

Rice (Oryza sativa L.) is the world's most important cereal crop. In crop plant, chlorophyll content and leaf senescence could affect grain filling and yield. We analyzed a QTL associated with chlorophyll content and delayed leaf senescence using high chlorophyll near isogenic line (HC-NIL). HC-NIL derived from a cross between Oryza sativa cv. Hwaseong as a recurrent parent and wild species O. grandiglumis as a donor parent showed higher chlorophyll content than Hwaseong. To identify QTL associated with chlorophyll content, 58 $F_3$ and 38 $F_4$ lines were developed from a cross between HC-NIL and Hwaseong. For QTL analysis, simple sequence repeat (SSR) markers were used for genotyping and one-way ANOVA was conducted. A QTL for chlorophyll content (qCC2) was detected in chromosome 2 and explained 24.63% of phenotypic variation. The senescence effect of the qCC2 was examined in dark-induced incubation (DII). Detached leaves from Hwaseong and HC-NIL were incubated on 3mM MES buffer (pH 5.8) at $27^{\circ}C$ under complete dark condition. After 3 days of incubation, the Hwaseong leaves turned yellow, but the HC-NIL leaves were green. HC-NIL has higher chlorophyll content with delayed senescence than Hwaseong. These results indicated that qCC2 is associated with stay-green phenotype. To know whether the qCC2 is responsible for leaf functionality, ion leakage test and Fv/Fm measurement were performed. Both experiment results showed that differences were observed between Hwaseong and HC-NIL but it was not statistically significant. These results might suggest that the qCC2 is possibly related to chlorophyll content and non-functional stay-green phenotype.

• Asian-Australasian Journal of Animal Sciences
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• v.5 no.2
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• pp.285-294
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• 1992

Biochemical polymorphisms of sow's milk proteins, $\beta$-casein ($\beta$-CN), $\beta$-lactoglobulin ($\beta$-LG), post-lactoglobulin (post-LG), $\alpha$-lactalbumin ($\alpha$-LA) and X-protein, as genetic markers for major pig breeds (Landrace, Yorkshire, Duroc, Hampshire and cross bred) in Korea were determined by starch gel electrophoresis. Phenotype and gene frequencies at all marker loci were estimated and genetic differences among breed populations were analyzed. Three $\beta$-CN phenotypes (AA, AB and BB) controlled by two codominant alleles (${\beta}-CN^A$ and ${\beta}-CN^B$), four $\beta$-LG phenotypes (AA, AC, $AC^{\pm}$ and CC) controlled by two codominant alleles (${\beta}-LG^A$ and ${\beta}-LG^C$) and ten X-protein phenotypes (AA, BB, CC, DD, AB, AC, AD, BC, BD and CD) controlled by four codominant alleles ($X^A,\;X^B,\;X^C\;and\;X^D$) were identified. In addition, a genetically controlled polymorphism of post-LG was found for the first time in sow's milk protein. Three different phenotypes (AA, AB and BB) were designated $post-LG^A$ and $post-LG^B$. Of the five marker loci examined, $\alpha$-LA locus was observed to lack any individual variation in all breeds studied. All populations were in Hardy-Weinberg equilibrium for all loci. There were marked breed differences for phenotype and gene frequencies in the post-LG and X-protein marker loci. However, there were little differences between breeds in the gene frequencies at the $\beta$-CN and $\beta$-LG marker loci.

• Biomolecules & Therapeutics
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• v.10 no.3
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• pp.193-199
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• 2002

The arylamine N-acetyltransferases (NATs) are a family of enzymes that N-acetylate mylhydrazines and arylamines through transfer of an acetyl group from acetyl coenzyme A. This activity was found to vary among individuals as a Mendalian trait and the basis of the genetic differences in human NAT activity is one of the best of the genetic studied examples of pharmacogenetic variation. The classical N-acetylation polymorphism is regulated at the NAT2 locus, which segregates individuals into rapid, intermediate, and slow acetylator phenotypes. In this study, the relationship between NAT2 activity phenotype using HPLC:UV assay for the determination of dapsone and monoacetyldapsone in plasma and NAT2 genotype by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) was investigated in the F2 hybrid (Fischer 344 vs Wistar-Kyoto) rats. Three Common mutant alleles at the NAT2 gene locus have been identified in the F2 generation progeny of Fischer 344 rats as raid acetylator and Wistar-Kyoto rats as slow acetylator segregated into three modes (low, intermediates, and high) with simple Mendelian inheritance. The metabolic activity of NAT2 of the intermediate and rapid acetylators is significant1y greater than slow acetylator, but the metabolic activity of rapid acetylator is not significantly different from Intermediate type. Therefore, we could observe that complete trimodal NAT2 genotypic alleles and incomplete trimodal NAT2 metabolic phenotypic distribution in tile F2 hybrid rats. These observations suggest that the relationships between NAT2 genotype and metabolic phenotype exists and F2 hybrid (Fischer 344: Wistar-Kyoto) animal models about NAT2 polymorphism might be applied in the toxicity and pharmacogenetic studies of arylamine drugs and carcinogens.

• Plant Biotechnology Reports
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• v.5 no.3
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• pp.273-281
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• 2011

Diverse epigenetic phenotypes are frequently found during research on transgenic plants. To understand the factors underlying such diversity, hundreds of independent 35S-GFP transgenic N. benthamiana plants were analyzed. The diverse GFP-expression phenotypes of the transgenic plants were classified into three major types based on the GFP expression patterns and their response to 35S-GFP agroinfiltration: steady-green, silenced and non-uniform phenotype. The non-uniform phenotype was further sub-divided into five minor phenotypes: variegated, red-dropped, on-silencing, partitioned and misty, according to the distribution of GFP expression on the leaves. Many of transgenic plants continuously generated diverse phenotypes over several generations despite the transgene identity. Such epigenetic GFP phenotyping was found to be the result of spontaneous transgene silencing mediated by either or both of post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). This finding was verified by the detection of 21- and 24-nt small interfering RNA (siRNA) molecules, and DNA methylation in the transgenic plants that showed repeated epigenetic variation. Agroinfiltration demonstrated that irregular distribution of GFP on a leaf was the result of erratic transgene silencing, and the technique also proved to be a rapid and effective method for selecting fully silenced plants within 3 days. Furthermore, two novel phenotypes described are potential materials for in-depth investigations into the genes and mechanisms responsible for spontaneous transgene silencing.

• Genomics & Informatics
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• v.14 no.4
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• pp.211-215
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• 2016

The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs.

• Plant Biotechnology Reports
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• v.5 no.2
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• pp.187-195
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• 2011

The gesneriaceous perennial plant Titanotrichum oldhamii has beautiful foliage and attractive bright yellow flowers. However, breeding of T. oldhamii by conventional sexual hybridization may be difficult because sexual reproduction of this species is very rare. In the present study, plant regeneration systems via both direct and indirect formation of adventitious shoots from leaf explants were established as the first step toward breeding T. oldhamii by using biotechnological techniques. Adventitious shoots were formed efficiently on medium containing $0.1mg\;l^{-1}$ benzyladenine. Histological observation showed that shoot formation on this medium occurred directly from leaf epidermal cells without callus formation. On the other hand, leaf explants formed calluses on medium containing $0.1mg\;l^{-1}$ 2,4-dichlorophenoxyacetic acid. The calluses could be maintained by monthly subculturing to fresh medium of the same composition. When the calluses were transferred to plant growth regulator-free medium, they formed adventitious shoots. Directly and indirectly formed shoots rooted well on medium containing $0.1mg\;l^{-1}$ indole-3-butyric acid. Plantlets thus obtained were successfully acclimatized and grew vigorously in the greenhouse. Flow cytometry analysis indicated that no variation in the ploidy level was observed in plants regenerated via direct shoot formation, whereas chromosome doubling occurred in several plants regenerated via indirect shoot formation. Regenerated plants with the same ploidy level as the mother plants showed almost the same phenotype as the mother plants, whereas chromosome-doubled plants showed apparent morphological alterations: they had small and crispate flowers, and round and deep green leaves.

• Horticultural Science & Technology
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• v.32 no.3
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• pp.366-374
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• 2014

The study was conducted to investigate the possibility that epigenetic DNA methylation causes tree phenotypic variation in autotetraploids through evaluating the phenotypic variation and DNA methylation in autotetraploids occurred spontaneously from diploid trifoliate orange. Chromosome analysis confirmed that fourteen trifoliate orange trees of selected by flow cytometry were tetraploids (2n = 4X = 36) without any aneuploids. Chromomycin A3 staining determined that these trees were all autotetraploid with doubled chromosome set. Tree phenotypes, such as tree height and width, branching number, length, and angle, internode length, and leaf characteristics, varied in the autotetraploids. Chlorophyll indices were diverse in the autotetraploids, but photosynthetic rates were not significantly different. In addition, a wide range of variation was observed in stomatal density and guard cell length. Analysis of global cytosine DNA methylation showed that there was a variation of the methylation level in autotetraploids. More than half of 14 autotetraploids had at least 2 times higher methylation level than diploid trifoliate orange. The results indicate that tree phenotypic variation in autotetraploids might be related to global DNA methylation for reducing gene redundancy.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.3
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• pp.311-317
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• 2015

Phenotypic characterization and body biometric in 13 traits (height at withers, body length, chest girth, paunch girth, ear length, tail length, length of tail up to switch, face length, face width, horn length, circumference of horn at base, distances between pin bone and hip bone) were recorded in 233 adult Gojri buffaloes from Punjab and Himachal Pradesh states of India. Traits were analysed by using varimax rotated principal component analysis (PCA) with Kaiser Normalization to explain body conformation. PCA revealed four components which explained about 70.9% of the total variation. First component described the general body conformation and explained 31.5% of total variation. It was represented by significant positive high loading of height at wither, body length, heart girth, face length and face width. The communality ranged from 0.83 (hip bone distance) to 0.45 (horn length) and unique factors ranged from 0.16 to 0.55 for all these 13 different biometric traits. Present study suggests that first principal component can be used in the evaluation and comparison of body conformation in buffaloes and thus provides an opportunity to distinguish between early and late maturing to adult, based on a small group of biometric traits to explain body conformation in adult buffaloes.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.3863-3868
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• 2012

In this study mitochondrial D-Loop variations in Iranian prostate cancer and benign prostatic hyperplasia (BPH) patients were investigated. Tumour samples and corresponding non-cancerous prostate tissue from 40 prostate cancer patients and 40 age-matched BPH patients were collected. The entire mtD-loop region (16024-576) was amplified using the PCR method and products were gel-purified and subjected to direct nucleotide sequencing. A total of 129 variations were found, the most frequent being 263A${\rightarrow}$G and 310T${\rightarrow}$C among both BPH and prostate cancer patients. Variation of 309 C${\rightarrow}$T was significantly more frequent in prostate cancer patients (P value<0.05). Four novel variations were observed on comparison with the MITOMAP database. Novel variations were np16154delT, np366G${\rightarrow}$A, np389G${\rightarrow}$A and 56insT. There was no correspondence between the different variations and the age of subjects. Considering that D-loop variations were frequent in both BPH and prostate cancer patients in our study, the fact that both groups had high average age can be a possible contributing factor. D-loop polymorphisms and microsatellite instability can influence cell physiology and result in a benign or malignant phenotype. Significantly higher frequency of 309 C${\rightarrow}$T variation in cancer patients is a notable finding and must be a focus of attention in future studies.