Search results for: phenotypic & genotypic markers

Authors: Hani Belhadj, Daoud Harzallah, Seddik Khennouf, Saliha Dahamna, Mouloud Ghadbane

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In this study, Lactobacillus strains isolated from pollen were identified by means of phenotypic and genotypic methods, At pH 2, most strains proved to be acid resistants, with losses in cell viability ranging from 0.77 to 4.04 Log orders. In addition, at pH 3 all strains could grew and resist the acidic conditions, with losses in cell viability ranging from 0.40 to 3.61 Log orders. It seems that, 0.3% and 0.5% of bile salts does not affect greatly the survival of most strains, excluding Lactobacillus sp. BH1398. Survival ranged from 81.0±3.5 to 93.5±3.9%. In contrast, in the presence of 1.0% bile salts, survival of five strains was decreased by more than 50%. Lactobacillus fermentum BH1509 was considered the most tolerant strain (77.5% for 1% bile) followed by Lactobacillus plantarum BH1541 (59.9% for 1% bile). Furthermore, all strains were resistant to colistine, clindamycine, chloramphenicol, and ciprofloxacine, but most of the strains were susceptible to Peniciline, Oxacillin, Oxytetracyclin, and Amoxicillin. Functionally interesting Lactobacillus isolates may be used in the future as probiotic cultures for manufacturing fermented foods and as bioactive delivery systems.

Keywords: probiotics, lactobacillus, pollen, bile, acid tolerance

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Authors: Gohar Rahman, Rabia Saad Ullah

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This research aims to examine the use of discourse markers within the dominion of political speeches, differentiating between genders. The analysis centers on twelve speakers, comprising six males and six females. Speeches selected include commencement, victory, state union addresses, campaigns, and presidential speeches. Halliday and Hasan's cohesion framework, specifically discourse markers, is utilized as a theoretical framework. Data is quantitatively analyzed using AntConc to identify marker frequency. The findings are presented through Excel's tables and graphs, suggesting differences in discourse marker preferences between genders. The findings suggest a divergence in the preferences for discourse markers between males and females. However, asserting that females utilize discourse markers more frequently due to the increased use of filler words, face threat mitigation, and polite speech would be an exaggeration. The disparity in frequency is not substantial, suggesting that males and females exhibit varying language inclinations to some degree.

Keywords: discourse markers, political discourse, gender, speeches, language

Procedia PDF Downloads 38

Authors: Hilda Freimuth

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This study examined the interactional resources of self-mentions and engagement markers in twenty official IELTS reading exam passages to determine the passages’ similarity to academic research papers. Although the findings revealed a variation ranging from zero to 22 instances for any given passage, the study found the average number of markers (5.5) per passage in line with those found on research papers. This finding confirms that the IELTS exam’s reading passages mirror the academic nature of research papers in this regard.

Keywords: IELTS exam, IELTS reading, interpersonal resources, self-mentions, engagement markers

Procedia PDF Downloads 81

Authors: Mohammad Muhebbullah Ibne Hoque, Zheng Jun, Wang Guoying

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Salinity stress is one of the most important abiotic factors contributing to crop growth and yield loss. Exploring the genetic basis is necessary to develop maize varieties with salinity tolerance. In order to discover the inherent basis for salinity tolerance traits in maize, 121 polymorphic SSR markers were used to analyze 163 F2 individuals derived from a single cross of inbred line B73 (a salt susceptible inbred line) and CZ-7 (a salt tolerant inbred line). A linkage map was constructed and the map covered 1195.2 cM of maize genome with an average distance of 9.88 cM between marker loci. Ten salt tolerance traits at seedling stage were evaluated for QTL analysis in maize seedlings. A total of 41 QTLs associated with seedling shoot and root traits were detected, with 16 and 25 QTLs under non-salinity and salinity condition, respectively. And only 4 major stable QTLs were detected in two environments. The detected QTLs were distributed on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, and chromosome 10. Phenotypic variability for the identified QTLs for all the traits was in the range from 6.27 to 21.97%. Fourteen QTLs with more than 10% contributions were observed. Our results and the markers associated with the major QTL detected in this study have the potential application for genetic improvement of salt tolerance in maize through marker-assisted selection.

Keywords: salt tolerance, seedling stage, root shoot traits, quantitative trait loci, simple sequence repeat, maize

Procedia PDF Downloads 279

Authors: Muhammad Tanveer Altaf, Mehmet Bedir, Waqas Liaqat, Gönül Cömertpay, Volkan Çatalkaya, Celaluddin Barutçular, Nergiz Çoban, Ibrahim Cerit, Muhammad Azhar Nadeem, Tolga Karaköy, Faheem Shehzad Baloch

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Food production needs to be almost double by 2050 in order to feed around 9 billion people around the Globe. Plant production mostly relies on fertilizers, which also have one of the main roles in environmental pollution. In addition to this, climatic conditions are unpredictable, and the earth is expected to face severe drought conditions in the future. Therefore, water and fertilizers, especially nitrogen are considered as main constraints for future food security. To face these challenges, developing integrative approaches for germplasm characterization and selecting the resilient genotypes performing under limiting conditions is very crucial for effective breeding to meet the food requirement under climatic change scenarios. This study is part of the European Research Area Network (ERANET) project for the characterization of the diversity panel of 172 sorghum accessions and six hybrids as control cultivars under limiting (+N/-H2O, -N/+H2O) and non-limiting conditions (+N+H2O). This study was planned to characterize the sorghum diversity in relation to resource Use Efficiency (RUE), with special attention on harnessing the interaction between genotype and environment (GxE) from a physiological and agronomic perspective. Experiments were conducted at Adana, a Mediterranean climate, with augmented design, and data on various agronomic and physiological parameters were recorded. Plentiful diversity was observed in the sorghum diversity panel and significant variations were seen among the limiting water and nitrogen conditions in comparison with the control experiment. Potential genotypes with the best performance are identified under limiting conditions. Whole genome resequencing was performed for whole germplasm under investigation for diversity analysis. GWAS analysis will be performed using genotypic and phenotypic data and linked markers will be identified. The results of this study will show the adaptation and improvement of sorghum under climate change conditions for future food security.

Keywords: germplasm, sorghum, drought, nitrogen, resources use efficiency, sequencing

Procedia PDF Downloads 53

Authors: A. H. Shaikat, M. B. Hossain, S. K. M. A. Islam, M. M. Hassan, S. A. Khan, A. K. M. Saifuddin, M. N. Islam, M. A. Hoque

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A total of eighteen (18) sex reversed chickens with unusual phenotypic characteristics of male birds were identified over 2000 Hyline layer chickens at Motaher Poultry Farm, Ramu, Cox’s Bazar. Chickens were subdivided into two groups (case = 18, control = 20) based on the appearance of sex-reversed secondary sexual characteristics. Phenotypic traits of studied chickens were measured with farm management details. Hormone assay using ELISA, autopsy followed by gross examination of viscera was performed. The study found higher body weight (gm) (1579.3; 95% CI: 1561.7-1596.8), comb length (cm) (12.2; 11.5-12.8), comb width (cm) (7.9; 7.7-8.2), wattle length (cm) (4.9; 4.8-5.1) distinct spur, and shortened pubic bones distance, suggesting decrease oviposition in sex-reversed chickens. Testosterone concentration (ng/ml) (8.5; 6.4-10.6) was significantly higher (p<0.001) along with decrease estrogen (pg/ml) (5.1; 4.9-5.5) and progesterone concentration (pg/ml) (310.9; 289.4-332.5) in sex-reversed chickens. Mass abdominal fat deposition with atrophied ovary was found upon exploration of viscera.

Keywords: ovary, phenotypic traits, sex hormone, sex reversal

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Authors: Shu-Yu Hsu, Chen-Chien Hsu, Wei-Yen Wang

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Color segmentation is a basic and simple way for recognizing the visual markers in a robotic tracking system. In this paper, we propose a new method for color segmentation by incorporating differential evolution algorithm and connected component labeling to autonomously preset the HSV threshold of visual markers. To evaluate the effectiveness of the proposed algorithm, a ROBOTIS OP2 humanoid robot is used to conduct the experiment, where five most commonly used color including red, purple, blue, yellow, and green in visual markers are given for comparisons.

Keywords: color segmentation, differential evolution, connected component labeling, humanoid robot

Procedia PDF Downloads 578

Authors: Saimir Heta, Ilma Robo, Nevila Alliu, Tea Meta

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Background: Plasma levels of inflammatory markers are the expression of the infectious wastes of existing periodontitis, as well as of existing inflammation everywhere in the body. Materials and Methods: The study consists of the clinical part of the measurement of inflammatory markers of 23 patients diagnosed with chronic periodontitis and the recording of parental periodontal parameters of patient periodontal status: hemorrhage index and probe values, before and 7-10 days after non-surgical periodontal treatment. Results: The level of fibrinogen drops according to the categorization of disease progression, active and passive, with the biggest % (18%-30%) at the fluctuation 10-20 mg/d. Fluctuations in fibrinogen level according to the age of patients in the range 0-10 mg/dL under 40 years and over 40 years was 13%-26%, in the range 10-20 mg/dL was 26%-22%, in the 20-40 mg/dL was 9%-4%. Conclusions: Non-surgical periodontal treatment significantly reduces the level of non-inflammatory markers in the blood. Oral health significantly reduces the potential source for periodontal bacteria, with the potential of promoting thromboembolism, through interaction between thrombocytes.

Keywords: chronic periodontitis, atherosclerosis, risk factor, inflammatory markers

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Authors: Siwapech Silapaprayoon, Januluk Khanobdee, Sompid Samipak

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Chili peppers are the fruits of Capsicum pepper plants well known for their fiery burning sensation on the tongue after consumption. They are members of the Solanaceae or common nightshade family along with potato, tomato and eggplant. Thai cuisine has gained popularity for its distinct flavors due to usages of various spices and its heat from the addition of chili pepper. Though being used in little quantity for each dish, chili pepper holds a special place in Thai cuisine. There are many varieties of chili peppers in Thailand, and thirty accessions were collected at Rajamangala University of Technology Lanna, Lampang, Thailand. To effectively manage any germplasm it is essential to know the diversity and relationships among members. Thirty-six Inter Simple Sequence Repeat (ISSRs) DNA markers were used to analyze the germplasm. Total of 335 polymorphic bands was obtained giving the average of 9.3 alleles per marker. Unweighted pair-group mean arithmetic method (UPGMA) clustering of data using NTSYS-pc software indicated that the accessions showed varied levels of genetic similarity ranging from 0.57-1.00 similarity coefficient index indicating significant levels of variation. At SM coefficient of 0.81, the germplasm was separated into four groups. Phenotypic variation was discussed in context of phylogenetic tree clustering.

Keywords: diversity, germplasm, Chili pepper, ISSR

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Authors: Mohammad Sadegh Khavarinejad

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In this study, genetic diversity of 10 bread wheat genotypes by SSR and RAPD markers was evaluated. 11 primers were used included 6 RAPD primers and 5 SSR primers. RAPDs and SSRs could find 33 and 17 polymorphism respectively. In RAPDs, primers UBC 350 and UBC 109 and in SSRs, Primers Xgwm 469-6D and Xgwm120-2B showed genetic diversity among genotypes more than others.

Keywords: wheat, molecular markers, SSR, RAPD

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Authors: Ashraf M. Ward, Ruban S. Yu

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Data consisting of 2757 records from tow Holstein herds made between 2000 and 2010 were used to examine environmental factors affecting age at first calving (AFC) and calving intervals (CI) and consequently estimate genetic and phenotypic parameters and trends. The overall means and standard errors for AFC and CI were 39.4 ± 7.2 months and 487.5 ± 151.6 days respectively. The respective heritability estimates were 0.091 ± 0.05 and 0.044 ± 0.032, while the repeatability estimate for CI was 0.096 ± 0.001. The genetic trends for CI and AFC were -0.6 d/yr and -0.01 mo/yr respectively and were both significant (P < 0.001), indicating a decrease in mean breeding value over the study period. Phenotypic trends were -0.31 mo/yr and -0.35 d/yr for AFC and CI respectively though non-significant (P > 0.05). The low heritability for CI and AFC indicated that temporary environmental influences were much greater than genetic influences or permanent environmental influences on these traits.

Keywords: Holstein, reproductive, genetic parameters, heritability

Procedia PDF Downloads 696

Authors: S. Ibrahim, U. B. Abubakar, S. Danbirni, A. Usman, F. M. Ballah, C. A. Kudi, L. Lawson, G. H. Abdulrazak, I. A. Abdulkadir

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Performing culture and characterization of mycobacteria in low resource settings like Nigeria is a very difficult task to undertake because of the very few and limited laboratories carrying out such an experiment; this is a largely due to stringent and laborious nature of the tests. Hence, a rapid, simple and accurate test for characterization is needed. The “SD BIOLINE TB Ag MPT 64 Rapid ®” is a simple and rapid immunochromatographic test used in differentiating Mycobacteria into Mycobacterium tuberculosis (NTM). The 100 sputa were obtained from patients suspected to be infected with tuberculosis and presented themselves to hospitals for check-up and treatment were involved in the study. The samples were cultured in a class III Biosafety cabinet and level III biosafety practices were followed. Forty isolates were obtained from the cultured sputa, and there were identified as Acid-fast bacilli (AFB) using Zeihl-Neelsen acid-fast stain. All the isolates (AFB positive) were then subjected to the SD BIOLINE Analyses. A total of 31 (77.5%) were characterized as MTBC, while nine (22.5%) were NTM. The total turnaround time for the rapid assay was just 30 minutes as compared to a few days of phenotypic and genotypic method. It was simple, rapid and reliable test to differentiate MTBC from NTM.

Keywords: culture, mycobacteria, non tuberculous mycobacterium, SD Bioline

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Authors: Hamid Mustafa, Huson J. Heather, Kim Eiusoo, McClure Matt, Khalid Javed, Talat Nasser Pasha, Afzal Ali1, Adeela Ajmal, Tad Sonstegard

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Genetic differences associated with speciation, breed formation or local adaptation can help to preserve and effective utilization of animals in selection programs. Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among ten Pakistani indigenous cattle breeds. In total, 25 individuals from three cattle populations, including Achi (n=08), Bhagnari (n=04) and Cholistani (n=13) were genotyped for 777, 962 single nucleotide polymorphism (SNP) markers. Population structure was examined using the linkage model in the program STRUCTURE. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. We further searched for spatial patterns of genetic diversity among these breeds under the recently developed spatial principal component analysis framework. Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time.

Keywords: Pakistan, cattle, genetic diversity, population structure

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Authors: Ibrahim Sani

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This paper examines the use of English discourse markers with the aim of investigating their communicative functions on Facebook as used by UMYUK members of academic staff. The paper uses the qualitative approach and relevance theory by Sperber and Wilson (1995) to highlight and examine DMs in different communicative contexts. In the course of data collection, five (5) academic staff from the five faculties of the university who are already Facebook friends of the researcher are used as the participants with their consent. The paper examines the communicative functions of English DMs among UMYUK academic staff on Facebook and reveals a number of communicative functions used in different contexts. One of the major findings indicates that 'contrastive markers' such as 'but', 'however', 'although' etc. are the dominant communicative functions employed by UMYUK academic staff on Facebook with 42% occurrence; it also shows that a single DM can function differently in the same linguistic environment.

Keywords: role, communicative, discourse markers, facebook, academic staff

Procedia PDF Downloads 140

Authors: Michael Josef Schwerer

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Background: The identification of unknown victims from mass disasters, violent crimes, or terrorist attacks is frequently facilitated through information from missing persons lists, portrait photos, old or recent pictures showing unique characteristics of a person such as scars or tattoos, or simply reference samples from blood relatives for DNA analysis. In contrast, the identification or at least the characterization of an unknown perpetrator from criminal or terrorist actions remains challenging, particularly in the absence of material or data for comparison, such as fingerprints, which had been previously stored in criminal records. In scenarios that result in high levels of destruction of the perpetrator’s corpse, for instance, blast or fire events, the chance for a positive identification using standard techniques is further impaired. Objectives: This study shows the forensic genetic procedures in the Legal Medicine Service of the German Air Force for the identification of unknown individuals, including such cases in which reference samples are not available. Scenarios requiring such efforts predominantly involve aircraft crash investigations, which are routinely carried out by the German Air Force Centre of Aerospace Medicine as one of the Institution’s essential missions. Further, casework by military police or military intelligence is supported based on administrative cooperation. In the talk, data from study projects, as well as examples from real casework, will be demonstrated and discussed with the audience. Methods: Forensic genetic identification in our laboratories involves the analysis of Short Tandem Repeats and Single Nucleotide Polymorphisms in nuclear DNA along with mitochondrial DNA haplotyping. Extended DNA analysis involves phenotypic markers for skin, hair, and eye color together with the investigation of a person’s biogeographic ancestry. Assessment of the biological age of an individual employs CpG-island methylation analysis using bisulfite-converted DNA. Forensic Investigative Genealogy assessment allows the detection of an unknown person’s blood relatives in reference databases. Technically, end-point-PCR, real-time PCR, capillary electrophoresis, pyrosequencing as well as next generation sequencing using flow-cell-based and chip-based systems are used. Results and Discussion: Optimization of DNA extraction from various sources, including difficult matrixes like formalin-fixed, paraffin-embedded tissues, degraded specimens from decomposed bodies or from decedents exposed to blast or fire events, provides soil for successful PCR amplification and subsequent genetic profiling. For cases with extremely low yields of extracted DNA, whole genome preamplification protocols are successfully used, particularly regarding genetic phenotyping. Improved primer design for CpG-methylation analysis, together with validated sampling strategies for the analyzed substrates from, e.g., lymphocyte-rich organs, allows successful biological age estimation even in bodies with highly degraded tissue material. Conclusions: Successful identification of unknown individuals or at least their phenotypic characterization using pigmentation markers together with age-informative methylation profiles, possibly supplemented by family tree search employing Forensic Investigative Genealogy, can be provided in specialized laboratories. However, standard laboratory procedures must be adapted to work with difficult and highly degraded sample materials.

Keywords: identification, forensic genetics, phenotypic markers, CPG methylation, biological age estimation, forensic investigative genealogy

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Authors: Vladimir Ryabov, Mikhail Baryshevs, Mikhail Voskresenskey, Boris Popov

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The human prostate gland (PG) samples were obtained from patients who had undergone radical prostatectomy for prostate cancer (PC) and used to extract total RNA and prepare the prostate stromal cell cultures (PSCC) and patients-derived organoids (PDO). Growth of the cell cultures was accessed under microscopic evaluation in transmitted light and the marker expression by reverse polymerase chain reaction (RT-PCR), immunofluorescence, and immunoblotting. Some PCR products from prostate tissue, PSCC, and PDO were cloned and sequenced. We found that the cells of early and late passages of PSCC and corresponding PDO expressed luminal (androgen receptor, AR; cytokeratin 18, CK18) and basal (CK5, p63) epithelial markers, the production of which decreased or disappeared in late PSCC and PDO. The PSCC and PDO of early passages from cancer tissue additionally produced cancer markers AMACR, TMPRSS2-ERG, and Ezh2. The expression of TMPRSS2-ERG fusion transcripts was verified by cloning and sequencing the PCR products. The results obtained suggest that early passages of PSCC might be used as a pre-clinical model for the evaluation of early markers of prostate cancer.

Keywords: localized prostate cancer, prostate epithelial markers, prostate cancer markers, AMACR, TMPRSS2-ERG, prostate stromal cell cultures, PDO

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Authors: Begüm Terzi, Özlem Ateş Sönmezoğlu, Ahmet Yildirim

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Drought is the most important factor that limiting the production and productivity of wheat in the world. The yield of wheat, which is one of the most important crop in the world, reduced depend on drought. Researches to minimize effects of drought are one of the most important about breeding of drought resistant varieties. In recent years, benefiting from the drought resistance wild species and rapid advances in molecular biology studies, researches about drought have been accelerated and number of studies were made on molecular plant breeding which included the molecular mechanisms related to drought resistance. The aim of the present study was characterization of some bread wheat lines for drought tolerance which commonly cultivated in different location of Turkey. In this study, registered 9 bread wheat varieties which on the physiological tests about drought tolerance and 10 bread wheat line has been developed by Transitional Zone Agricultural Research Institute were used. SSR, STS, RAPD and SNP markers that associated with drought tolerance were used. The polymorphisms of the markers were determined by screening of two control varieties. For these purpose 40 molecular markers were used and 12 markers of them were polymorphic among the drought tolerance and the drought sensitive varieties. Control varieties were screened using polymorphic markers. All the DNAs on the genotypes will be searched for the presence of QTLs mapped to different chromosomes. Result of the research, the studied genotypes will be grouped according to drought tolerance and will be detected drought tolerance varieties by molecular markers. In addition, the results will be compared also with physiological tests. The drought tolerant wheat genotypes may be used in breeding studies related to drought stress.

Keywords: bread wheat, drought, molecular marker, Triticum aestivum

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Authors: Mehmet Demir Kaya, Engin Gökhan Kulan, Onur İleri, Süleyman Avcı

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Due to variation in seed size, shape and oil content of safflower cultivars, germination and emergence performance have been severely influenced by seed characteristics. This study aimed to determine genotypic variation among safflower genotypes for one thousand seed weight, oil content, germination and seed vigor using electrical conductivity (EC) and cold test. In the study, safflower lines ES37-5, ES38-4, ES43-11, ES55-14 and ES58-11 which were developed by single seed selection method, and Dinçer and Remzibey-05 were used as standard varieties. The genotypes were grown under rainfed conditions in Eskişehir, Turkey with four replications. The seeds of each genotype were subjected to standard germination and emergence test at 25°C for 10 days with four replications and 50 seeds per replicate. Electrical conductivity test was performed at 25°C for 24 h to assess the seed vigor. Also, cold test were applied to each safflower genotype at 10°C for 4 days and 25°C for 6 days. Results showed that oil content of the safflower genotypes were different. The highest oil content was determined in ES43-11 with 36.6% while the lowest was 25.9% in ES38-4. Higher germination and emergence rate were obtained from ES55-14 with 96.5% and 73.0%, respectively. There was no significant difference among the safflower genotypes for EC values. Cold test showed that ES43-11 and ES55-14 gave the maximum germination percentages. It was concluded that genotypic factors except for soil and climatic conditions play an important role for determining seed vigor because safflower genotypes grown at the same condition produced various seed vigor values.

Keywords: Carthamus tinctorius L., germination, emergence, cold test, electrical conductivity

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Authors: Y. Hajjam, I. T. Alami, S. M. Udupa, S. Cherkaoui

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Faba bean (Vicia faba L.) is an important food legume crop in Morocco. It is mainly used as human food and feed for animals. Faba bean also plays an important role in cereal-based cropping systems, when rotated with cereals it improves soil fertility by fixing N2 in root nodules mediated by Rhizobium. Both faba bean and its biological nitrogen fixation symbiotic bacterium Rhizobium are affected by different stresses such as: salinity, drought, pH, heavy metal, and the uptake of inorganic phosphate compounds. Therefore, the aim of the present study was to evaluate the phenotypic diversity among the faba bean rhizobial isolates and to select the tolerant strains that can fix N2 under environmental constraints for inoculation particularly for affected soils, in order to enhance the productivity of faba bean and to improve soil fertility. Result have shown that 62% of isolates were fast growing with the ability of producing acids compounds , while 38% of isolates are slow growing with production of alkalins. Moreover, 42.5% of these isolates were able to solubilize inorganic phosphate Ca3(PO4)2 and the index of solubilization was ranged from 2.1 to 3.0. The resistance to extreme pH, temperature, water stress heavy metals and antibiotics lead us to classify rhizobial isolates into different clusters. Finally, the authentication test under greenhouse conditions showed that 55% of the rhizobial isolates could induce nodule formation on faba bean (Vicia faba L.) under greenhouse experiment. This phenotypic characterization may contribute to improve legumes and non legumes crops especially in affected soils and also to increase agronomic yield in the dry areas.

Keywords: rhizobia, vicia faba, phenotypic characterization, nodule formation, environmental constraints

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Authors: Ognen Kostovski, Svetozar Antovic, Rubens Jovanovic, Irena Kostovska, Nikola Jankulovski

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Introduction:Colorectal carcinoma (CRC) is one of the most common malignancies in the world. The cancer stem cell (CSC) markers are associated with aggressive cancer types and poor prognosis. The aim of study was to determine whether the expression of colorectal cancer stem cell markers CD133 and CD44 could be significant in prediction of clinically aggressive form of CRC. Materials and methods: Our study included ninety patients (n=90) with CRC. Patients were divided into two subgroups: with metatstatic CRC and non-metastatic CRC. Tumor samples were analyzed with standard histopathological methods, than was performed immunohistochemical analysis with monoclonal antibodies against CD133 and CD44 stem cell markers. Results: High coexpression of CD133 and CD44 was observed in 71.4% of patients with metastatic disease, compared to 37.9% in patients without metastases. Discordant expression of both markers was found in 8% of the subgroup with metastatic CRC, and in 13.4% of the subgroup without metastatic CRC. Statistical analyses showed a significant association of increased expression of CD133 and CD44 with the disease stage, T - category and N - nodal status. With multiple regression analysis the stage of disease was designate as a factor with the greatest statistically significant influence on expression of CD133 (p <0.0001) and CD44 (p <0.0001). Conclusion: Our results suggest that the coexpression of CD133 and CD44 have an important role in prediction of clinically aggressive form of CRC. Both stem cell markers can be routinely implemented in standard pathohistological diagnostics and can be useful markers for pre-therapeutic oncology screening.

Keywords: colorectal carcinoma, stem cells, CD133+, CD44+

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Authors: Karen Louise Lacey, Dario Javier Pavon Vargas, Massimiliano Rinaldi, Luca Cattani, Sara Rainieri

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The effects of high-pressure processing (HPP) and thermal treatments (TT) on quality markers of strawberry nectar (12 °Brix, 3,3 pH) was studied before and after treatments. TT and HPP treatments ensured a 3-log aerobic bacteria inactivation. No significant difference was detected in terms of pH and °Brix. TT samples were less red (a* less positive) than all HPP treated samples, while all samples were less red than the control. Apparent viscosity was significantly increased in all the HPP treatments, at 10 1/s shear rate, control was 79.04±7.94 mPa•s and the 600 MPa-20 min treatment were 327.10±1.64 mPa•s. This work suggests that HPP treatments may maintain the quality markers of strawberry nectar better.

Keywords: HPP, strawberry nectar, colour , viscosity

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Authors: Zhao Yang Liu, Jing Tao

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The Asian long-horned beetle, Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae: Lamiinae), is a wood-borer and polyphagous xylophages native to Asia and killing healthy trees. As it causes serious danger to trees, the beetle has been paid close attention in the world. However, the genetic markers limited, especially microsatellite. In this study, 24 novel simple sequence repeat (SSR) molecular markers, a powerful tool for genetic diversity studies and linkage map construction, were developed and characterized from whole genome shotgun sequences. We developed SSR loci of 2 to 6 repeated and perfect units including 9895 points, the density of SSRs was found one SSR per 56.57 kb and the abundance of SSR was 0.02/kb, besides 140 types of repeats motifs were found. Half of the 48 pairs SSR primers (containing 4 di-, 7 tri-, 2 tetra- and 11 hexamers SSRs) we selected randomly from 1222 pairs of primers were polymorphism. The number of alleles for these markers in 48 individuals varied from 3 to 21 with an average of 7.71, the number of effective alleles ranged from 1.22 to 9.97 with an average of 3.54. Besides this, the polymorphic information content (PIC) ranged from 0.18 to 0.89 with a mean of 0.65, And Shannon's Information index (I) ranged from 0.46 to 2.62 with an average of 1.44. The results suggest that the method for screening of SSR in the whole genome is feasible and efficient. SSR markers developed in this study can be used for population genetic studies of A. glabripennis. Moreover, they may also be helpful for the development of microsatellites for other Coleoptera.

Keywords: SSR markers, Anoplophora glabripennis, genetic diversity, whole genome

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Authors: Rajendra K. Meena, Maneesh S. Bhandari, Santan Barthwal, Harish S. Ginwal

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Microsatellite markers are the most valuable tools for the characterization of plant genetic resources or population genetic analysis. Since it is codominant and allelic markers, utilizing them in polyploid species remained doubtful. In such cases, the microsatellite marker is usually analyzed by treating them as a dominant marker. In the current study, it has been showed that despite losing the advantage of co-dominance, microsatellite markers are still a powerful tool for genotyping of polyploid species because of availability of large number of reproducible alleles per locus. It has been studied by genotyping of 19 subpopulations of Dendrocalamus hamiltonii (hexaploid bamboo species) with 17 polymorphic simple sequence repeat (SSR) primer pairs. Among these, ten primers gave typical banding pattern of microsatellite marker as expected in diploid species, but rest 7 gave an unusual pattern, i.e., more than two bands per locus per genotype. In such case, genotyping data are generally analyzed by considering as dominant markers. In the current study, data were analyzed in both ways as dominant and co-dominant. All the 17 primers were first scored as nonallelic data and analyzed; later, the ten primers giving standard banding patterns were analyzed as allelic data and the results were compared. The UPGMA clustering and genetic structure showed that results obtained with both the data sets are very similar with slight variation, and therefore the SSR marker could be utilized to characterize polyploid species by considering them as a dominant marker. The study is highly useful to widen the scope for SSR markers applications and beneficial to the researchers dealing with polyploid species.

Keywords: microsatellite markers, Dendrocalamus hamiltonii, dominant and codominant, polyploids

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Authors: András Farkas, István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Cseh, Márta Molnár-Láng, Jaroslav Doležel

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Species of Aegilops played a central role in the evolution of wheat and are sources of traits related to yield quality and tolerance against biotic and abiotic stresses. These wild genes and alleles are desirable to use in crop improvement programs via introgressive hybridization. However, the success of chromosome mediated gene transfer to wheat are hampered by the pour knowledge on the genome structure of Aegilops relative to wheat and by the low number of cost-effective molecular markers specific for Aegilops chromosomes. The COS markers specific for genes conserved throughout evolution in both sequence and copy number between Triticeae/Aegilops taxa and define orthologous regions, thus enabling the comparison of regions on the chromosomes of related species. The present study compared individual chromosomes of Aegilops umbellulata (UU), Ae. comosa (MM), Ae. speltoides (SS) and Ae. caudata (CC) purified by flourescent labelling with oligonucleotid SSR repeats and biparametric flow cytometry with wheat by identifying orthologous chromosomal regions by COS markers. The linear order of bin-mapped COS markers along the wheat D chromosomes was identified by the use of chromosome-specific sequence data and virtual gene order. Syntenic regions of wheat identifying genome rearrangements differentiating the U, M, S or C genomes from the D genome of wheat were detected. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species and wheat will facilitate the targeted development of new markers specific for U, M, S and C genomic regions and will contribute to the understanding of molecular processes related to the evolution of Aegilops.

Keywords: Aegilops, cos-markers, flow-sorting, wheat

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Authors: Recep Kesli, Huseyin Bilgin, Yasar Unlu, Gokhan Gungor

Abstract:

Aim: The aim of this study was to compare diagnostic values of two different molecular-based tests (GenoType® HelicoDR ve Seeplex® H. pylori-ClaR- ACE Detection) in detection presence of the H. pylori from gastric biopsy specimens. In addition to this also was aimed to determine resistance ratios of H. pylori strains against to clarytromycine and quinolone isolated from gastric biopsy material cultures by using both the genotypic (GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection) and phenotypic (gradient strip, E-test) methods. Material and methods: A total of 266 patients who admitted to Konya Education and Research Hospital Department of Gastroenterology with dyspeptic complaints, between January 2011-June 2013, were included in the study. Microbiological and histopathological examinations of biopsy specimens taken from antrum and corpus regions were performed. The presence of H. pylori in all the biopsy samples was investigated by five differnt dignostic methods together: culture (C) (Portagerm pylori-PORT PYL, Pylori agar-PYL, GENbox microaer, bioMerieux, France), histology (H) (Giemsa, Hematoxylin and Eosin staining), rapid urease test (RUT) (CLOtest, Cimberly-Clark, USA), and two different molecular tests; GenoType® HelicoDR, Hain, Germany, based on DNA strip assay, and Seeplex ® H. pylori -ClaR- ACE Detection, Seegene, South Korea, based on multiplex PCR. Antimicrobial resistance of H. pylori isolates against clarithromycin and levofloxacin was determined by GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, and gradient strip (E-test, bioMerieux, France) methods. Culture positivity alone or positivities of both histology and RUT together was accepted as the gold standard for H. pylori positivity. Sensitivity and specificity rates of two molecular methods used in the study were calculated by taking the two gold standards previously mentioned. Results: A total of 266 patients between 16-83 years old who 144 (54.1 %) were female, 122 (45.9 %) were male were included in the study. 144 patients were found as culture positive, and 157 were H and RUT were positive together. 179 patients were found as positive with GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection together. Sensitivity and specificity rates of studied five different methods were found as follows: C were 80.9 % and 84.4 %, H + RUT were 88.2 % and 75.4 %, GenoType® HelicoDR were 100 % and 71.3 %, and Seeplex ® H. pylori -ClaR- ACE Detection were, 100 % and 71.3 %. A strong correlation was found between C and H+RUT, C and GenoType® HelicoDR, and C and Seeplex ® H. pylori -ClaR- ACE Detection (r:0.644 and p:0.000, r:0.757 and p:0.000, r:0.757 and p:0.000, respectively). Of all the isolated 144 H. pylori strains 24 (16.6 %) were detected as resistant to claritromycine, and 18 (12.5 %) were levofloxacin. Genotypic claritromycine resistance was detected only in 15 cases with GenoType® HelicoDR, and 6 cases with Seeplex ® H. pylori -ClaR- ACE Detection. Conclusion: In our study, it was concluded that; GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection was found as the most sensitive diagnostic methods when comparing all the investigated other ones (C, H, and RUT).

Keywords: Helicobacter pylori, GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, antimicrobial resistance

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Authors: Parmjit S. Panesar, Rupinder Kaur, Ram S. Singh

Abstract:

Enzymes are the biocatalysts which catalyze the biochemical processes and thus have a wide variety of applications in the industrial sector. β-Galactosidase (E.C. 3.2.1.23) also known as lactase, is one of the prime enzymes, which has significant potential in the dairy and food processing industries. It has the capability to catalyze both the hydrolytic reaction for the production of lactose hydrolyzed milk and transgalactosylation reaction for the synthesis of prebiotics such as lactulose and galactooligosaccharides. These prebiotics have various nutritional and technological benefits. Although, the enzyme is naturally present in almonds, peaches, apricots and other variety of fruits and animals, the extraction of enzyme from these sources increases the cost of enzyme. Therefore, focus has been shifted towards the production of low cost enzyme from the microorganisms such as bacteria, yeast and fungi. As compared to yeast and bacteria, fungal β-galactosidase is generally preferred as being extracellular and thermostable in nature. Keeping the above in view, the present study was carried out for the isolation of the β-galactosidase producing fungal strain from the food as well as the agricultural wastes. A total of more than 100 fungal cultures were examined for their potential in enzyme production. All the fungal strains were screened using X-gal and IPTG as inducers in the modified Czapek Dox Agar medium. Among the various isolated fungal strains, the strain exhibiting the highest enzyme activity was chosen for further phenotypic and genotypic characterization. The strain was identified as Rhizomucor pusillus on the basis of 5.8s RNA gene sequencing data.

Keywords: beta-galactosidase, enzyme, fungal, isolation

Procedia PDF Downloads 226

Authors: Hameed Alsamadany, Nader Aryamanesh, Guijun Yan

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Heat is one of the major abiotic stresses limiting wheat production worldwide. To identify heat tolerant genotypes, a newly designed system involving a large plastic box holding many layers of filter papers positioned vertically with wheat seeds sown in between for the ease of screening large number of wheat geno types was developed and used to study heat tolerance. A collection of 499 wheat geno types were screened under heat stress (35ºC) and non-stress (25ºC) conditions using the new method. Compared with those under non-stress conditions, a substantial and very significant reduction in seedling length (SL) under heat stress was observed with an average reduction of 11.7 cm (P<0.01). A damage index (DI) of each geno type based on SL under the two temperatures was calculated and used to rank the genotypes. Three hexaploid geno types of Triticum aestivum [Perenjori (DI= -0.09), Pakistan W 20B (-0.18) and SST16 (-0.28)], all growing better at 35ºC than at 25ºC were identified as extremely heat tolerant (EHT). Two hexaploid genotypes of T. aestivum [Synthetic wheat (0.93) and Stiletto (0.92)] and two tetraploid genotypes of T. turgidum ssp dicoccoides [G3211 (0.98) and G3100 (0.93)] were identified as extremely heat susceptible (EHS). Another 14 geno types were classified as heat tolerant (HT) and 478 as heat susceptible (HS). Extremely heat tolerant and heat susceptible geno types were used to develop re combinant inbreeding line populations for genetic studies. Four major QTLs, HTI4D, HTI3B.1, HTI3B.2 and HTI3A located on wheat chromosomes 4D, 3B (x2) and 3A, explaining up to 34.67 %, 28.93 %, 13.46% % and 11.34% phenotypic variation, respectively, were detected. The four QTLs together accounted for 88.40% of the total phenotypic variation. Random wheat geno types possessing the four heat tolerant alleles performed significantly better under the heat condition than those lacking the heat tolerant alleles indicating the importance of the four QTLs in conferring heat tolerance in wheat. Molecular markers are being developed for marker assisted breeding of heat tolerant wheat.

Keywords: bread wheat, heat tolerance, screening, RILs, QTL mapping, association analysis

Procedia PDF Downloads 524

Authors: Dina A. Selim, Eman Shawky, Rasha M. Abu El-Khair

Abstract:

In the current study, UPLC-MS/MS combined to chemometrics were applied on seven Sri Lankan tea grades; Orange Pekoe, Flowery Pekoe, Broken Orange Pekoe Fannings, Broken Orange Pekoe black tea, green tea, silver tips and golden tips white tea grades for their comprehensive metabolic profiling. Certain metabolites, namely, Theasensinin C and E, theaflavin and theacitrin appeared to be the main chemical markers of black tea type, catechin, epicatechin, epigallocatechin, methyl epigallocatechin were the main discriminatory markers of green tea type, while theanine, oolongotheanine and quercetin glycosides were the main chemical markers of white tea type. Theogalloflavin, epigallocatechin and flavonoid glycosides were the main down-accumulated metabolites while theaflavin gallate, and N-ethyl pyrrolidinone epicatechin were the chief up- accumulated metabolites between whole and broken black tea leave grades while puerin A and C and gallic acid was the main down- accumulated metabolites and N-ethyl pyrrolidinone epicatechin gallate was the main up-accumulated one between broken and fanning black tea grades.

Keywords: tea grading, Sri Lankan tea, chemometrics, metabolomics, chemical markers

Procedia PDF Downloads 106

Authors: Yash M. Gupta, Kittisak Buddhachat, Surin Peyachoknagul, Somjit Homchan

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The house cricket, Acheta domesticus is one of the commonly found species of field crickets. Although it is very commonly used as food and feed, the genomic information of house cricket is still missing for genetic investigation. DNA sequencing technology has evolved over the decades, and it has also revolutionized the molecular marker development for genetic analysis. In the present study, we have sequenced the whole genome of A. domesticus using illumina platform based HiSeq X Ten sequencing technology for searching simple sequence repeats (SSRs) in DNA to develop polymorphic microsatellite markers for population genetic analysis. A total of 112,157 SSRs with primer pairs were identified, 91 randomly selected SSRs used to check DNA amplification, of which nine primers were polymorphic. These microsatellite markers have shown cross-amplification with other three species of crickets which are Gryllus bimaculatus, Gryllus testaceus and Brachytrupes portentosus. These nine polymorphic microsatellite markers were used to check genetic variation for forty-five individuals of A. domesticus, Phitsanulok population, Thailand. For nine loci, the number of alleles was ranging from 5 to 15. The observed heterozygosity was ranged from 0.4091 to 0.7556. These microsatellite markers will facilitate population genetic analysis for future studies of A. domesticus populations. Moreover, the transferability of these SSR makers would also enable researchers to conduct genetic studies for other closely related species.

Keywords: cross-amplification, microsatellite markers, observed heterozygosity, population genetic, simple sequence repeats

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Authors: Akbar Nawaz Khan, Abdul Ghaffar, Muhammad Naeem Riaz

Abstract:

The study was conducted to investigate the phenotypic features, morphometry and production potentialities of indigenous naked neck chicken (NN) of Pakistan under intensive management condition. A total of 35 NN chicks were randomly selected, and the experiment was performed at Poultry and wildlife research section NARC Islamabad for a period of 22 weeks. The predominant plumage color was black and golden while skin color was observed white. The average shank length, leg length, thigh length, keel length, chest breadth, head width, wing space, wing length, body length, body girth, body height and pubic bone width in adult males and females were 69.19 ± 3.34mm, 117.93 ± 4.42mm, 117.93 ± 4.42mm, 90.87 ± 6.53mm, 95.03 ± 4.56mm, 49.77 ± 2.53mm, 30.63 ± 1.50cm, 27.24 ± 2.71cm, 18.88 ± 0.65cm, 17.77 ± 1.01cm, 25.96 ± 0.56cm, 47.81 ± 1.41cm and 35.69 ± 4.09mm respectively. The average age and live body weight of NN chicken at sexual maturity were recorded as 165.85 days and 1269.38 g. While hen-day egg production of NN was recorded as 45%. The present study was aimed to investigate the existence of polymorphism at IGF-I gene in indigenous naked neck chicken through PCR based Restriction Fragment Length Polymorphism. Based on restriction analysis using Hinf I restriction enzyme, three genotypes were detected designated as AA, AC, and CC. Restriction analysis of PCR amplified product showed the presence of DNA fragments of 622, 378, 244 and 191, (genotypes). The PCR-RFLP analysis is easy, cost effective method which permits the easy characterization of IGF-I gene. This showed the investigated IGF-I genes can serve as good molecular markers for marker assisted selection (MAS) concerning growth related traits in chicken.

Keywords: Desi chicken, naked neck, morphology, morphometry, production potential, egg traits, egg geometry, IGF-I, growth, PCR- RFLP, chicken

Procedia PDF Downloads 363