Search results for: deletion polymorphism

Authors: Ayse Ozge Demir, Nihat Mert

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In this research, Kilis and Honamli goats are used, which are specific local genetic resources of Turkey. The herds were independent, but they had similar care and nutrition circumstances. From each breed 30 samples were taken, in all 120 samples were collected. Erytrocyte, all blood and serum samples were used for hemoglobine (Hb), glutathione (GSH) and Tf with Cp analysis, respectively. In the analysis of this samples, Hb and Tf bands were determined by electrophoresis. However, Cp and GSH levels were analyzed by the spectrophotometer. Three Hb phenotypes (AA, BB, AB) and Six Tf phenotypes (AA, AB, AC, BB, BC, CC) were determined in this study. In addition, both the observed and the expected values of polymorphic characteristic for 2 characters were presented according to the Hardy-Weinberg Equilibrium (HWE). Cp levels were detected as 0.822 ± 0.055 mg/dl and 1.793 ± 0.109 mg/dl in Kilis and Honamli herds, respectively. GSH levels were detected as, 42,486 ± 1,034 mg/dl and 33.515 ± 0.345 mg/dl in these breeds, respectively,. On the other hand, the high and low GSH levels (GSHH and GSHh) of herds were presented.

Keywords: electrophoresis, gene resource, goat, spectrophotometer

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Authors: Apurva Singh, S. P. Jaiswar, Apala Priyadarshini, Akancha Pandey

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Objective: The aim of this study is to find the association of PON1 gene polymorphism with pesticides In RPL subjects. Background: Recurrent pregnancy loss (RPL) is defined as three or more sequential abortions before the 20th week of gestation. Pesticides and its derivatives (organochlorine and organophosphate) are proposed to accommodate a ruler chemical for RPL in the sub-humid region of India. The paraoxonase-1 enzyme (PON1) plays an important role in the toxicity of some organophosphate pesticides, with low PON1 activity being associated with higher pesticide sensitivity Methodology: This is a case-control study done in Department of Obstetrics & Gynaecology & Department of Biochemistry, K.G.M.U, Lucknow, India. The subjects were enrolled after fulfilling the inclusion & exclusion criteria. Inclusion criteria: Cases- Subject having two or more spontaneous abortions & Control- Healthy female having one or more alive child was selected. Exclusion criteria: Cases & Control- Subject having the following disease will be excluded from the study Diabetes mellitus, Hypertension, Tuberculosis, Immunocompromised patients, any endocrine disorder and genital, colon or breast cancer any other malignancies. Blood samples were collected in EDTA tubes from cases & healthy control women & genomic DNA was extracted by phenol-chloroform method. The estimation of pesticides residue from blood was done by HPLC. Biochemical estimation was also performed. Genotyping of PON1 gene polymorphism was performed by RFLP. Statistical analysis of the data was performed using the SPSS16.3 software. Results: A sum of total 14 pesticides (12 organochlorine and 2 organophosphate) selected on the basis of their persistent nature and consumption rate. The significant level of pesticide (ppb) estimated by the Mann whiney test and it was found to be significant at higher level of β-HCH (p:0.04), γ-HCH (p:0.001), δ-HCH (p: 0.002), chloropyrifos (p:0.001), pp-DDD (p:0.001) and fenvalrate (p: 0.001) in case group compare to its control. The level of antioxidant enzymes were found to be significantly decreased among the cases. Wild homozygous TT was more frequent and prevalent among control groups. However, heterozygous group (Tt) was more in cases than control groups (CI-0.3-1.3) (p=0.06). Conclusion: Higher levels of pesticides with endocrine disrupting potential in cases indicate the possible role of these compounds as one of the causes of recurrent pregnancy loss. Possibly, increased pesticide level appears to indicate increased levels of oxidative damage that has been associated with the possible cause of Recurrent Miscarriage, it may reflect indirect evidence of toxicity rather than the direct cause. Since both factors are reported to increase risk, individuals with higher levels of these 'Toxic compounds' especially in 'high-risk genotypes' might be more susceptible to recurrent pregnancy loss.

Keywords: paraoxonase, pesticides, PON1, RPL

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Authors: Vijay Kumar Kutala, Addepalli Pavani, M. Amresh Rao, Naushad Sm

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In this study, we evaluated the impact of CYP2C9*2 and CYP2C9*3 variants on binding and hydroxylation of warfarin. In silico data revealed that warfarin forms two hydrogen bonds with protein backbone i.e. I205 and S209, one hydrogen bond with protein side chain i.e. T301 and stacking interaction with F100 in CYP2C9*1. In CYP2C9*2 and CYP2C9*3 variants, two hydrogen bonds with protein backbone are disrupted. In double variant, all the hydrogen bonds are disrupted. The distances between C7 of S-warfarin and Fe-O in CYP2C9*1, CYP2C9*2, CYP2C9*3 and CYP2C9*2/*3 were 5.81A°, 7.02A°, 7.43° and 10.07°, respectively. The glide scores (Kcal/mol) were -7.698, -7.380, -6.821 and -6.986, respectively. Increase in warfarin/7-hydroxy warfarin ratio was observed with increase in variant alleles. To conclude, CYP2C9*2 and CYP2C9*3 variants result in disruption of hydrogen bonding interactions with warfarin and longer distance between C7 and Fe-O thus impairing warfarin 7-hydroxylation due to lower binding affinity of warfarin.

Keywords: warfarin, CYP2C9 polymorphism, personalized medicine, in Silico

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Authors: Jana Kisková, Dana Gabriková

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Monoamine oxidase A gene (MAOA) is suggested to be a candidate gene implicated in many neuropsychiatric disorders, including autism spectrum disorder (ASD). This meta-analytic review evaluates the relationship between ASD and MAOA markers such as 30 bp variable number tandem repeats in the promoter region (uVNTR) and single nucleotide polymorphisms (SNPs) by using findings from recently published studies. It seems that in Caucasian males, the risk of developing ASD increase with the presence of 4-repeat allele in the promoter region of MAOA gene whereas no differences were found between autistic patients and controls in Egyptian, West Bengal and Korean population. Some studies point to the importance specific haplotype groups of SNPs and interaction of MAOA with others genes (e.g. FOXP2 or SRY). The results of existing studies are insufficient and further research is needed.

Keywords: autism spectrum disorder, MAOA, uVNTR, single nucleotide polymorphism

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Authors: Chao Wu

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Thioredoxin reductase 2 is a mitochondrial enzyme that belongs to the cellular defense against oxidative stress. We deleted mitochondrial Txnrd2 in a KrasG12D-driven pancreatic tumor model. Despite an initial increase in precursor lesions, tumor incidence decreased significantly. We isolated cancer cell lines from these genetically engineered mice and observed an impaired proliferation and colony formation. Reactive Oxygen Species, as determined by DCF fluorescence, were increased. We detected a higher mitochondrial copy number in Txnrd2-deficient cells (KTP). However, measurement of mitochondrial bioenergetics showed no impairment of mitochondrial function and comparable O₂-consumption and extracellular acidification rates. In addition, the mitochondrial complex composition was affected in Txnrd2 deleted cell lines. To gain better insight into the role of Txnrd2, we deleted Txnrd2 in clones from parental KrasG12D cell lines using Crispr/Cas9 technology. The deletion was confirmed by western blot and activity assay. Interestingly, and in line with previous RNA expression analysis, we saw changes in EMT markers in Txnrd2 deleted cell lines and control cell lines. This might help us explain the reduced tumor incidence in KrasG12D; Txnrd2∆panc mice.

Keywords: PDAC, TXNRD2, epithelial-to-mesenchymal-transition, ROS

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Authors: Fhajema Kunso

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People who live in the same region and who seemed to speak the same language still vary in some aspects of their language. The variation may occur in terms of pronunciation, lexicon, morphology, and syntax. This qualitative study described the phonological, morphological, and lexical variations of the Maguindanaon language among the ten Maguindanao municipalities. Purposive sampling, in-depth interviews, focus group discussion, and sorting and classifying of words according to phonological and morphological as well as lexical structures in data analysis were employed. The variations occurred through phonemic changes and other phonological processes and morphological processes. Phonological processes consisted of vowel lengthening and deletion while morphological processes included affixation, borrowing, and coinage. In the phonological variation, it was observed that there were phonemic changes in one dialect to another. For example, there was a change of phoneme /r/ to /l/. The phoneme /r/ was most likely to occur in Kabuntalan like /biru/, /kurIt/, and /kɘmɅr/ whereas in the rest of the dialects these were /bilu/, /kuIɪt/, and /kɘmɅl/ respectively. Morphologically, the affixation was the main way to know the tenses. For example, the root sarig (expect) when inserted with im becomes simarig, i.e. s + im + arig = simarig (expected). Lexical variation also existed in the Maguindanaon language. Results revealed that the variation in phonology, morphology, and lexicon were observed to be associated primarily on geographic distribution.

Keywords: applied linguistics, language, lexicon, Maguindanao, morphology, Philippines, phonology, processes, qualitative, variation

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Authors: Elly Usman, S. Dante, Diah Purnamasari

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Type 2 diabetes mellitus ( T2DM ) is a syndrome characterized by a state of increased blood sugar levels due to chronic disorders of insulin secretion by pancreatic beta cells and insulin action or a combination of both. The organic cation transporter 1, encoded by the SLC22A1 gene, responsible for the uptake of the antihyperglycemic drug, metformin, in the hepatocyte. We assessed whether a genetic variation in the SLC22A1 gene was associated with the glucose - lowering effect of metformin. Method case study research design. Samples are children with type 2 diabetes mellitus who meet the inclusion criteria. The results proportions SLC22A1 gene polymorphisms in children with diabetes mellitus type 2 amounted to 52.04 % at position 400T/C, there is one heterozygous and one at position 595T/C Conclusion The presence of SLC22A1 gene polymorphisms in children with diabetes mellitus type 2.

Keywords: diabetes Mellitus type 2, metformin, organic cation transporter 1, pharmacogenomics

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Authors: K. Ali, M. F. Qamar, M. A. Zaman, M. Younus, I. Khan, S. Ehtisham-ul-Haque, R. Tamkeen, M. I. Rashid, Q. Ali

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This study centers on molecular identification of Haemonchus contortus and isolation of Benz-imidazoles (BZ) resistant strains. Different abattoirs’ of two geographic regions of Punjab (Pakistan) were frequently visited for the collection of worms. Out of 1500 (n=1500) samples that were morphologically confirmed as H. contortus, 30 worms were subjected to molecular procedures for isolation of resistant strains. Resistant worms (n=8) were further subjected to DNA gene sequencing. Bio edit sequence alignment editor software was used to detect the possible mutation, deletion, replacement of nucleotides. Genetic diversity was noticed and genetic variation existing in β-tubulin isotype 1 of the H. contortus population of small ruminants of different regions considered in this study. H. contortus showed three different type of genetic sequences. 75%, 37.5%, 25% and 12.5% of the studied samples showed 100% query cover and identity with isolates and clones of China, UK, Australia and other countries, respectively. Interestingly the neighbor countries such as India and Iran haven’t many similarities with the Pakistani isolates. Thus, it suggests that population density of same genetic makeup H. contortus is scattered worldwide rather than clustering in a single region.

Keywords: Haemonchus contortus, Benzimidazole resistant, β-tubulin-1 gene, abattoirs

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Authors: Bimrisha Mali

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The present study investigates the type of errors English as a second language (ESL) learners produce using the definite article ‘the’. The participants were provided a questionnaire on the learner's ability test. The questionnaire consists of three cloze tests and two free composition tests. Each participant's response was received in the form of written data. A total of 78 participants from three government schools participated in the study. The participants are high-school students from Rural Assam. Assam is a north-eastern state of India. Their age ranged between 14-15. The medium of instruction and the communication among the students take place in the local language, i.e., Assamese. Pit Corder’s steps for conducting error analysis have been followed for the analysis procedure. Four types of errors were found (1) deletion of the definite article, (2) use of the definite article as modifiers as adjectives, (3) incorrect use of the definite article with singular proper nouns, (4) substitution of the definite article by the indefinite article ‘a’. Classifiers in Assamese that express definiteness is used with nouns, adjectives, and numerals. It is found that native language (L1) transfer plays a pivotal role in the learners’ errors. The analysis reveals the learners' inability to acquire the semantic connotation of definiteness in English due to native language (L1) interference.

Keywords: definite article error, l1 transfer, error analysis, ESL

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Authors: Mir Hussain Nawaz, Lyudmila Nedyalkova, Haizhong Zhu, Wael M. Rabeh

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In this study, we aim to biochemically and structurally characterize the interactions of human HK2 with the mitochondria in addition to the role of its N-terminal domain in catalysis and stability of the full-length enzyme. Here, we solved the crystal structure of human HK2 in complex with glucose and glucose-6-phosphate (PDB code: 2NZT), where it is a homodimer with catalytically active N- and C-terminal domains linked by a seven-turn α-helix. Different from the inactive N-terminal domains of isozymes 1 and 3, the N- domain of HK2 not only capable to catalyze a reaction but it is responsible for the thermodynamic stabilizes of the full-length enzyme. Deletion of first α-helix of the N-domain that binds to the mitochondria altered the stability and catalytic activity of the full-length HK2. In addition, we found the linker helix between the N- and C-terminal domains to play an important role in controlling the catalytic activity of the N-terminal domain. HK2 is a major step in the regulation of glucose metabolism in cancer making it an ideal target for the development of new anticancer therapeutics. Characterizing the structural and molecular mechanisms of human HK2 and its role in cancer metabolism will accelerate the design and development of new cancer therapeutics that are safe and cancer specific.

Keywords: cancer metabolism, enzymology, drug discovery, protein stability

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Authors: Yasser M. Saad, Heba El-Sebaie Abd El-Sadek

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Some Metapenaeus monoceros cox1 gene fragments were isolated, purified, sequenced, and comparatively analyzed with some other Crustacean Cox1 gene sequences (obtained from National Center for Biotechnology Information). This work was designed for testing the efficiency of this system in reconstruction of phylogenetic relations among some Crustacean species belonging to four genera (Metapenaeus, Artemia, Daphnia and Calanus). The single nucleotide polymorphism and haplotype diversity were calculated for all estimated mt-DNA fragments. The genetic distance values were 0.292, 0.015, 0.151, and 0.09 within Metapenaeus species, Calanus species, Artemia species, and Daphnia species, respectively. The reconstructed phylogenetic tree is clustered into some unique clades. Cytochrome oxidase subunit 1 gene (cox1) was a powerful system in reconstruction of phylogenetic relations among evaluated crustacean species.

Keywords: crustaceans, genetics, Cox1, phylogeny

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Authors: Atefeh Esmailnejad, Gholamreza Nikbakht Brujeni

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Major histocompatibility complex (MHC) is one of the best characterized genetic regions associated with immune responses and controlling disease resistance in chicken. Association of the MHC with a wide range of immune responses makes it a valuable predictive factor for the disease pathogenesis and outcome. In this study, the association of MHC with cell-mediated immune responses was analyzed in commercial broiler chicken. The tandem repeat LEI0258 was applied to investigate the MHC polymorphism. Cell-mediated immune response was evaluated by peripheral blood lymphocyte proliferation assay using MTT method. Association study revealed a significant influence of MHC alleles on cellular immune responses in this population. Alleles 385 and 448 bp were associated with elevated cell-mediated immunity. Haplotypes associated with improved immune responses could be considered as candidate markers for disease resistance and applied to breeding strategies.

Keywords: MHC, cell-mediated immunity, broiler, chicken

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene

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Authors: Mehrnoosh Pirhayati

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Translation can be affected by different meta-textual factors of target context such as ideology, politics, and culture. So, the rule of fidelity, or being faithful to the source text, can be ignored by the translator. On the other hand, critical discourse analysis, derived from applied linguistics, is entered into the field of translation studies and used by scholars for revealing hidden deviations and possible roots of manipulations. This study focused on the famous Persian translation of the bestseller book, “A**hole No More,” written by XavierCrement 1990, performed by Mahmud Farjami to comparatively and critically analyze it with its corresponding English original book. The researcher applied Pirhayati’s model and framework of translation criticism at the textual and semiotic levels for this qualitative study. It should be noted that Kress and Van Leeuwen’s semiotic model, along with Machin’s model of typographical analysis, was also used at the semiotic level. The results of the comparisons and analyses indicate thatthis Persian translation of the book is affected by the factors of ideology and economics and reveal that the Islamic attitude causes the translator to employ some strategies such as substitution and deletion. Those who may benefit from this research are translation trainers, students of translation studies, critics, and scholars.

Keywords: farjami (2013), Ideology, manipulation, pirhayati's (2013) model of translation criticism, Xavier crement (1990)

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Authors: Yun-Hsuan Chang, Chih-Chun Huang, Ru-Band Lu

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Dopamine, metabolized to 3,4-dihydroxyphenylacetic acid (DOPAC) by aldehyde dehydrogenase 2 (ALDH2), ALDH2*1/*1, and ALDH2*1/*2+ALDH*2/*2 equally carried in Han Chinese. The relationship between dopamine metabolic enzyme and cognitive performance in bipolar II disorder comorbid with anxiety disorder (AD) remains unclear. This study proposed to explore the association between ALDH2 polymorphisms, anxiety comorbidity in bipolar II disorder. One hundred and ninety-seven BPII with or without AD comorbidity were recruited and compared with 130 Health controls (HC). A polymerase chain reaction and restriction fragment length polymorphism analysis was used to determine genotypes for ALDH2, and neuropsychological battery was performed. Two factor analyses with AD comorbidity and ALDH2 showed a significant main effect of ALDH2 on attention and marginally significant interaction between AD and ALDH2 memory performance. The ALDH2 polymorphisms may play a different role in the neuropsychological performance on varied neuropsychological performance in BPII comorbid with and without AD.

Keywords: anxiety disorder, bipolar II disorder, comorbidity, genetic

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Authors: Gordon Wong

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This paper shows how the task of disk defragmentation can be handled by modern operating systems in a transparent, automated, efficient, and confined way through user's file-access patterns. Since files tend to gradually fragment from time to time through file creation, deletion, growth, and shrinking, the problem gets even worse when a disk becomes so fragmented that file accesses cannot be made reasonably efficient without performing the operation of defragmentation for the "entire" disk, which is done manually by the user by launching the disk defragmentation utility program normally bundled with the operating system. In this paper, we argue that the disk defragmentation problem described can be solved without having to manually use the utility program to defragment the entire disk. The argument is based on the observation that system users tend to access certain files in a particular time interval like the way observed for programs exhibiting temporal locality of memory references during their execution. The task of disk defragmentation can be initiated and acted upon for those files contained in the current file-access locality detected and identified by the operating system. The paper also discusses how to use the locality of file references approach to quantitatively measure and determine the locality of user's file access patterns on which the task of disk defragmentation is based.

Keywords: operating systems, disk defragmentation, locality of file accesses, system performance

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Authors: Huanhuan Zhao, Bryony J. James

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The relationship between the non-fat solid ratio and bloom formation in untempered chocolate was investigated using two types of chocolate: model chocolate made of varying cocoa powder ratios (46, 49.5 and 53%) and cocoa butter, and commercial Lindt chocolate with varying cocoa content (70, 85 and 90%). X-ray diffraction and colour measurement techniques were used to examine the polymorphism of cocoa butter and the surface whiteness index (WI), respectively. The polymorphic transformation of cocoa butter was highly correlated with the changes of WI during 30 days of storage since it led to the redistribution of fat within the chocolate matrix and resulted in a bloomed surface. The change in WI indicated a similar bloom rate in the chocolates, but the model chocolates with a higher cocoa powder ratio had more pronounced total bloom. This is due to a higher ratio of non-fat solid particles on the surface resulting in microscopic changes in morphology. The ratio of non-fat solids is an important factor in determining the extent of bloom but not the bloom rate.

Keywords: untempered chocolate, microstructure of bloom, polymorphic transformation, surface whiteness

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Authors: B. Falah, N. E. Abakouy

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Due to its high computational cost, mutation testing has been neglected by researchers. Recently, many cost and mutants’ reduction techniques have been developed, improved, and experimented, but few of them has relied the possibility of reducing the cost of mutation testing on the program type of the application under test. This paper is a comparative study between four operators’ selection techniques (mutants sampling, class level operators, method level operators, and all operators’ selection) based on the program code type of each application under test. It aims at finding an alternative approach to reveal the effect of code type on mutation testing score. The result of our experiment shows that the program code type can affect the mutation score and that the programs using polymorphism are best suited to be tested with mutation testing.

Keywords: equivalent mutant, killed mutant, mutation score, mutation testing, program code type, software testing

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Authors: Zi-Han Li, Lu Fang, Liang Wu, Dong-Yuan Chang, Manyuan Dong, Liang Ji, Qi Zhang, Ming-Hui Zhao, Sydney C. W. Tang, Lemin Zheng, Min Chen

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Uncoupling of mitochondrial respiration by chemical uncouplers has proven effective in ameliorating obesity, insulin resistance, and hyperglycemia, which were risk factors for diabetic nephropathy (DN). Recently, we found that ANXA1 could improve mitochondrial function to mitigate DN progression. However, the underlying mechanism is not fully clear yet. Here, we identified uncoupling protein 1 (UCP1), an inner membrane protein of mitochondria, as a key to mitochondrial homeostasis improved by ANXA1. Specifically, ANXA1 attenuated mitochondrial dysfunction via appropriately upregulating UCP1 by stabilizing its transcription factor GATA binding protein 3 (GATA3) by combining it with thioredoxin. Moreover, specific overexpression of UCP1 in the renal cortex rescued renal injuries in diabetic Anxa1-KO mice. UCP1 deletion aggravated renal injuries in HFD/STZ-induced diabetic mice. Mechanistically, UCP1 reduced mitochondrial fission through the aristaless-related homeobox (ARX)/cardiolipin synthase 1 (CRLS1) pathway. Therapeutically, CL316243, a UCP1 agonist, could attenuate established DN in db/db mice. This work established an alternative principle to harness the power of uncouplers for the treatment of DN.

Keywords: diabetic nephropathy, uncoupling protein 1, mitochondrial homeostasis, cardiolipin metabolism

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Authors: Zi-Han Li, Lu Fang, Liang Wu, Dong-Yuan Chang, Manyuan Dong, Liang Ji, Qi Zhang, Ming-Hui Zhao, Sydney C.W. Tang, Lemin Zheng, Min Chen

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Uncoupling of mitochondrial respiration by chemical uncouplers has proven effective in ameliorating obesity, insulin resistance, and hyperglycemia, which were risk factors for diabetic nephropathy (DN). Recently, it was found that annexin A1(ANXA1) could improve mitochondrial function to mitigate DN progression. However, the underlying mechanism is not fully clear yet. Here, it was identified that uncoupling protein 1 (UCP1), an inner membrane protein of mitochondria, as a key to mitochondrial homeostasis improved by ANXA1. Specifically, ANXA1 attenuated mitochondrial dysfunction via appropriately upregulating UCP1 by stabilizing its transcription factor GATA binding protein 3 (GATA3) through combining with thioredoxin. Moreover, specific overexpression of UCP1 in renal cortex rescued renal injuries in diabetic Anxa1-KO mice. UCP1 deletion aggravated renal injuries in HFD/STZ-induced diabetic mice. Mechanistically, UCP1 reduced mitochondrial fission through the aristaless-related homeobox (ARX)/cardiolipin synthase 1 (CRLS1) pathway. Therapeutically, CL316243, a UCP1 agonist, could attenuate established DN in db/db mice. This work established a novel principle to harness the power of uncouplers for the treatment of DN.

Keywords: diabetic nephropathy, uncoupling protein 1, mitochondrial homeostasis, cardiolipin metabolism

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Authors: Byeong-Uk Lim, Young-Ran Song, Sang-Ho Baik

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This study aimed to develop yeast starters for scientific alcohol production and systematic quality control of whisky. A total of 389 yeast strains were isolated from traditional Korean fermentation starter (nuruk) and rice wine (makgeolli), and ten strains were finally selected for their high alcohol productivities, in which their alcohol productions were above 17.3% (v/v) during 10 days under two steps of glucose feeding condition (30% and then 15%, w/v). By 18s rDNA sequence analysis, all strains were identified as Saccharomyces cerevisiae (SC), and they can grow well under 50% (w/v) glucose and 10% (v/v) ethanol conditions. Furthermore, the capability of ten different SC strains to ferment rice wine for whisky was studied. Rice wine was fermented with only steamed rice, water, and two types of enzymes (glucoamylase and α-amylase) during 14 days at 25 °C, and then their oenological properties have been determined. As the results, the fermented rice wines indicated the final pH range of 4.24-4.38 and acidity range of 0.12-0.18. The highest ethanol production of 20.2% (v/v) was found in the fermentation with a SC-156 strain, whereas SC-92 (16.8%) and SC-119 (16.4%) showed significantly lowest ethanol productions. In addition, the residual sugar contents showed negative correlation with alcohol contents. Moreover, this study focused on nucleotide polymorphisms in the MSN2 and MSN4 genes to investigate the cause of the defective stress responses in yeast. Consequently, it was also confirmed that the deletion of the N termini of Msn4p from identified point mutations in SC-63, SC-95, SC-156, SC-158, and SC-160 strains.

Keywords: yeast, high-alcohol, whisky, rice wine

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Authors: M. Nakkuntod, S. Srinarang, K.W. Hilu

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Water lily (Nymphaea L.) is the largest genus of Nymphaeaceae. This family is composed of six genera (Nuphar, Ondinea, Euryale, Victoria, Barclaya, Nymphaea). Its members are nearly worldwide in tropical and temperate regions. The classification of some species in Nymphaea is ambiguous due to high variation in leaf and flower parts such as leaf margin, stamen appendage. Therefore, the phylogenetic relationships based on 18S rDNA were constructed to delimit this genus. DNAs of 52 specimens belonging to water lily family were extracted using modified conventional method containing cetyltrimethyl ammonium bromide (CTAB). The results showed that the amplified fragment is about 1600 base pairs in size. After analysis, the aligned sequences presented 9.36% for variable characters comprising 2.66% of parsimonious informative sites and 6.70% of singleton sites. Moreover, there are 6 regions of 1-2 base(s) for insertion/deletion. The phylogenetic trees based on maximum parsimony and maximum likelihood with high bootstrap support indicated that genus Nymphaea was a paraphyletic group because of Ondinea, Victoria and Euryale disruption. Within genus Nymphaea, subgenus Nymphaea is a basal lineage group which cooperated with Euryale and Victoria. The other four subgenera, namely Lotos, Hydrocallis, Brachyceras and Anecphya were included the same large clade which Ondinea was placed within Anecphya clade due to geographical sharing.

Keywords: nrDNA, phylogeny, taxonomy, waterlily

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Authors: H. Imad, Q. Cheah, J. Mohammad, O. Aamera

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The aim of this study is twofold. One is to determine the genetic structure of Iraq population and the second objective of the study was to evaluate the importance of these loci for forensic genetic purposes. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. Twenty STR loci and Amelogenin including D3S1358, D13S317, PentaE, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D2S1338, D5S818, D6S1043, D12S391, D19S433, and Amelogenin amplified by using power plex21® kit. PCR products detected by genetic analyzer 3730xL then data analyzed by PowerStatsV1.2. Based on the allelic frequencies, several statistical parameters of genetic and forensic efficiency have been estimated. This includes the homozygosity and heterozygosity, effective number of alleles (n), the polymorphism information content (PIC), the power of discrimination (DP), and the power of exclusion (PE). The power of discrimination values for all tested loci was from 75% to 96% therefore, those loci can be safely used to establish a DNA-based database for Iraq population.

Keywords: autosomal STR, genetic variation, Middle and South of Iraq, statistical parameters

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Authors: Sanaa Bardaweel

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Inorganic polyphosphate (poly P) is present in all living forms tested to date, from each of the three kingdoms of life. Studied mainly in prokaryotes, poly P and its associated enzymes are vital in diverse basic metabolism, in at least some structural functions and, notably, in stress responses. These plentiful and unrelated roles for poly P are probably the consequence of its presence in life-forms early in evolution. The genomes of many bacterial species, including pathogens, encode a homologue of a major poly P synthetic enzyme, poly P kinase 1 (PPK1). Genetic deletion of ppk1 results in reduced poly P levels and loss of pathogens virulence towards protozoa and animals. Thus far, no PPK1 homologue has been identified in higher-order eukaryotes and, therefore, PPK1 represents a novel target for chemotherapy. The idea of the current study is to purify the PPK1 from Escherichia coli to homogeneity in order to study the effect of active site point mutations on PPK1 catalysis via the application of site-directed mutagenesis strategy. The knowledge obtained about the active site of PPK1 will be utilized to characterize the catalytic and kinetic mechanism of PPK1 with model substrates. Comprehensive understanding of the enzyme kinetic mechanism and catalysis will be used to design and screen a library of synthetic compounds for potential discovery of selective PPK1-inhibitors.

Keywords: antimicobial, Escherichia coli, inorganic polyphosphate, PPK1-inhibitors

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Authors: Daniel Fundi Murithi

Abstract:

Missing data is a real bane in many surveys. To overcome the problems caused by missing data, partial deletion, and single imputation methods, among others, have been proposed. However, problems such as discarding usable data and inaccuracy in reproducing known population parameters and standard errors are associated with them. For regression and stochastic imputation, it is assumed that there is a variable with complete cases to be used as a predictor in estimating missing values in the other variable, and the relationship between the two variables is linear, which might not be realistic in practice. In this project, we estimate population total in presence of missing values in two-phase sampling. Instead of regression or stochastic models, non-parametric model based regression model is used in imputing missing values. Empirical study showed that nonparametric model-based regression imputation is better in reproducing variance of population total estimate obtained when there were no missing values compared to mean, median, regression, and stochastic imputation methods. Although regression and stochastic imputation were better than nonparametric model-based imputation in reproducing population total estimates obtained when there were no missing values in one of the sample sizes considered, nonparametric model-based imputation may be used when the relationship between outcome and predictor variables is not linear.

Keywords: finite population total, missing data, model-based imputation, two-phase sampling

Procedia PDF Downloads 104

Authors: Kaouther Jaouadi, Jihene Bettaieb, Amira Bennour, Ghassen Kharroubi, Sadok Salem, Afif Ben Salah

Abstract:

In Tunisia, chronic cutaneous leishmaniasis due to Leishmania (L) tropica is an important health problem. Its spreading has not been fully elucidated. Information on sandfly vectors, as well as their associated Leishmania species, is of paramount importance since vector dispersion is one of the major factors responsible for pathogen dissemination. In total, 650 sandflies were captured between June and August 2015 using sticky paper traps in the governorate of Sidi Bouzid, a classical focus of L. major in the Central-West of Tunisia. Polymerase chain reaction-restriction fragment length polymorphism analysis of the internal transcribed spacer 1 and sequencing were used for Leishmania detection and identification. Ninety-seven unfed females were tested for the presence of Leishmania parasite DNA. Six Phlebotomus sergenti were found positive for L. tropica. This finding enhances the understanding of the cycle extension of L. tropica outside its original focus of Tataouine in the South-East of the country.

Keywords: cutaneous leishmaniasis, Leishmania tropica, sandflies, Tunisia

Procedia PDF Downloads 124

Authors: Chinmayee Choudhury

Abstract:

Human Melanocortin 4 Receptor (HMC4R) is one of the most potential drug targets for the treatment of obesity which controls the appetite. A deletion of the residues 88-92 in HMC4R is sometimes the cause of severe obesity in the humans. In this study, two homology models are constructed for the normal as well as mutated HMC4Rs and some phytochemicals present in Green Tea, Honey and Cinnamon have been docked to them to study their differential binding to the normal and mutated HMC4R as compared to the natural agonist α- MSH. Two homology models have been constructed for the normal as well as mutated HMC4Rs using the Modeller9v7. Some of the phytochemicals present in Green Tea, Honey, and Cinnamon, which have appetite suppressant activities are constructed, minimized and docked to these normal and mutated HMC4R models using ArgusLab 4.0.1. The mode of binding of the phytochemicals with the Normal and Mutated HMC4Rs have been compared. Further, the mode of binding of these phytochemicals with that of the natural agonist α- Melanocyte Stimulating Hormone(α-MSH) to both normal and mutated HMC4Rs have also been studied. It is observed that the phytochemicals Kaempherol, Epigallocatechin-3-gallate (EGCG) present in Green Tea and Honey, Isorhamnetin, Chlorogenic acid, Chrysin, Galangin, Pinocambrin present in Honey, Cinnamaldehyde, Cinnamyl acetate and Cinnamyl alcohol present in Cinnamon have capacity to form more stable complexes with the Mutated HMC4R as compared to α- MSH. So they may be potential agonists of HMC4R to suppress the appetite.

Keywords: HMC4R, α-MSH, docking, photochemical, appetite suppressant, homology modelling

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Authors: Prachi Sharma, Mukesh Kumar Rana

Abstract:

In the present study, the simple sequence repeat(SSR) markers have been used in analysis of genetic diversity of 37 genotypes of Triticum aestivum. The DNA was extracted using cTAB method. The DNA was quantified using the fluorimeter. The annealing temperatures for 27 primer pairs were standardized using gradient PCR, out of which 16 primers gave satisfactory amplification at temperature ranging from 50-62⁰ C. Out of 16 polymorphic SSR markers only 10 SSR primer pairs were used in the study generating 34 reproducible amplicons among 37 genotypes out of which 30 were polymorphic. Primer pairs Xgwm533, Xgwm 160, Xgwm 408, Xgwm 120, Xgwm 186, Xgwm 261 produced maximum percent of polymorphic bands (100%). The bands ranged on an average of 3.4 bands per primer. The genetic relationship was determined using Jaccard pair wise similarity co-efficient and UPGMA cluster analysis with NTSYS Pc.2 software. The values of similarity index range from 0-1. The similarity coefficient ranged from 0.13 to 0.97. A minimum genetic similarity (0.13) was observed between VL 804 and HPW 288, meaning they are only 13% similar. More number of available SSR markers can be useful for supporting the genetic diversity analysis in the above wheat genotypes.

Keywords: wheat, genetic diversity, microsatellite, polymorphism

Procedia PDF Downloads 581

Authors: Ilian Badjakov, Ivayla Dincheva, Violeta Kondakova, Rossitza Batchvarova

Abstract:

In this study, we present our initial results on the assessment of genetic diversity among wild Bulgarian berry accessions (Rubus idaeus L. Fragaria Vesca L., Vaccinium vitis-idaea L., Vaccinium myrtillus L.) using Random Amplified Polymorphic DNA (RAPDs) markers. Leaves and fruits were collected from two natural habitats - the Balkan Mountain and the Mountain of Orpheus - Rhodope Mountain. All accessions were screened for their polymorphism using five RAPD primers. The phylogenetic distances calculated from RAPD data ranged from 0.29 to 0.82 thus indicating that a high level of gene diversity is present in the selected genotypes. In order to characterize further the structure and grouping of berry accessions, a dendrogram deriving from UPGMA cluster analysis based on the genetic similarity (GS) coefficient matrix was designed. RAPD analysis provided to be efficient for discrimination of accessions within the same species with similar morphological characters

Keywords: Bulgarian wild berries, genetic diversity, RAPD, UPGMA

Procedia PDF Downloads 277

Authors: Huseyi̇n Das, Bülent Tarim, Sunay Demi̇r, Nurçi̇n Küçükkent, Sevi̇l Cengi̇z, Engi̇n Tülek, Veci̇hi̇ Aksakal

Abstract:

Atak-S laying hens are a high-performance strain obtained by crossing of the Rhode Island Red (RIR) X the Barred Plymouth Rock (BR) and are being produced in the Ankara Poultry Research Institute since 1997. Phenotypic and genetic improving studies are continued for this strain. In this study, 2 from IGF and 1 from IGFBP2, totally 3 different SNP polymorphisms were examined in 200 Atak-S chickens. Genotypes of SNPs were compared using ANOVA to body weight and egg number thorough 32 weeks of age, body weight at sexual maturity, age at sexual maturity and also egg quality traits such as egg shell breaking strength, shell thickness, Haugh unit, albumen index, yolk index, shape index. Only IGF(a) locus was in agreement with Hardy-Weinberg equilibrium, while, the other loci were not. As a result of the performance comparisons to the 3 SNP loci, it was determined that there has a significant association (P<0.05) between only TC genotypes of the IGF(b) locus and body weight at 32 weeks of age, but there was not any association to the other traits.

Keywords: Atak-S, Igf, Igfbp2, single nucleotide polymorphism

Procedia PDF Downloads 340