An improved multiplex PCR for diagnosis and differentiation of Mycoplasma hyopneumoniae and Mycoplasma hyorhinis

Barate, Abhijit K.,Lee, Hwi-Young,Jeong, Hye-Won,Truong, Lam Quang,Joo, Hong-Gu,Hahn, Tae-Wook The Korean Society of Veterinary Science 2012 大韓獸醫學會誌 Vol.52 No.1

A multiplex PCR was developed for the simultaneous detection and differentiation of Mycoplasma (M.) hyopneumoniae and M. hyorhinis in clinical samples. Improved sensitivity is advantage of this technique over the previously reported multiplex assay. It was capable of detecting as little as 125 fg genomic DNA from M. hyopneumoniae and 62.5 fg genomic DNA from M. hyorhinis. Application of this multiplex PCR method to field isolates showed that M. hyopneumoniae and M. hyorhinis were present in 29% (107 of 370) of lung specimens and no mycoplasmas were detected in 56% (208 of 370) of the slaughtered pigs' lungs. At the farm level, M. hyopneumoniae and M. hyorhinis were detected in 34 of 36 (94.4%) randomly selected farms. We conclude that this assay would prove itself a value tool for monitoring these mycoplasmal infections and both M. hyopneumoniae and M. hyorhinis have been widely spread in swine herds of Korea.

A micro-level perspective to fostering IDEAs in the classroom and beyond

Barat Somjit 한국마케팅과학회 2024 마케팅과학연구 Vol.34 No.1

Inclusion, Diversity, Equity, & Access (IDEA) spurs creativity, encourages ideas from people who have been historically ignored, and promotes an invigorating learning environment. Despite such benefits, we do precious little when it comes to practicing the same in our classrooms. Regrettably, our infrastructure and education system does not always provide enough opportunities for the younger generation to appreciate, understand and experience the significance of an inclusive society, preventing our students an opportunity to apply what they learn in the classroom for the betterment of marginalized and minoritized communities. Against such a backdrop, the author focuses on how faculty can enhance the classroom-level student-experience through a model that helps students’ understanding and appreciation of IDEA. The author believes that this research model not only plugs a significant gap in our attitude towards IDEA practice and implementation but will also spur educators and practitioners to consider adopting similar measures while designing their respective curricula.

Characteristics of Surface Urban Heat Island (SUHI) over the Gangetic Plain of Bihar, India

Archisman Barat,Sunny Kumar,Praveen Kumar,P. Parth Sarthi 한국기상학회 2018 Asia-Pacific Journal of Atmospheric Sciences Vol.54 No.2

The rapid urbanisation impacts on environment, climate, agriculture, water resources trigger several problems to human beings. The present study is carried out to estimate intensity and trend of Urban Heat Island (UHI) as Surface UHI (SUHI) over towns/cities of the Gangetic plain of the state of Bihar, India, in which urban areas show relatively greater Land Surface Temperature (LST) than its rural surroundings especially during night times. The LST data (2001-14) of Moderate Resolution Imaging Spectroradiometer (MODIS) is used for five major towns/cities of Bihar namely, Bhagalpur, Gaya, Patna, Purnea and Muzzaffarpur. Each city is classified into Urban, Suburban and Rural zones as per land cover of the area. During winter months (January, February, November and December), UHI is more intense over all towns/cities. Mann-Kendall Test is applied on Surface Urban Heat Island Intensity (SUHII) in which MK-Test Statistic (S) shows a significant increasing trend. This trend would alarm a risk to increase in air pollution, heat related biohazards, energy demand in the region. This study shows the need of urban greening and proper town planning over the considered areas to mitigate the changes.

Immunization with a Fusion Protein Composed of Mycoplasma hyopneumoniae p97 Adhesin r1repeat and Escherichia coli Heat-labileEnterotoxin B Subunit

Abhijit K Barate,Tae Wook Hahn 대한수의학회 2012 대한수의학회 학술대회발표집 Vol.2012 No.-

Genetic control of some plant growth characteristics of bread wheat (Triticum aestivum L.) under aluminum stress

Sara Farokhzadeh,Barat Ali Fakheri,Nafiseh Mahdinezhad,Sirous Tahmasebi,Abbas Mirsoleimani,C. Lynne McIntyre 한국유전학회 2020 Genes & Genomics Vol.42 No.3

Background Biomass yield is an important trait for wheat breeding programs. Enhancing the yield of the aerial components of wheat cultivars will be an integral part of future wheat improvement. Aluminum (Al) toxicity is one of the main factors limiting wheat growth and production in acid soils, which occur on up to 50% of the arable lands of the world especially in tropical and subtropical regions. Objective Our objective was to identify quantitative trait loci (QTL) of plant growth characteristics and yield in wheat. Methods A recombinant inbred line (RIL) population consisting of 167 lines, derived from a cross between SeriM82 and Babax were evaluated under two Al treatments (+ Al, 800 µM of Al; −Al, 0 µM of Al) in the field based on an alpha lattice design with two replications for two consecutive crop seasons. Results A total of 40 QTLs including nine putative and 31 suggestive QTLs were found for all traits using the composite interval mapping (CIM) method. By mixed model-based composite interval mapping (MCIM) method, 42 additive QTLs and nine pairs of epistatic effects were detected for studied traits, of which 20 additive and six pairs of epistatic QTLs showed significant QTL × environment interactions. Most of the detected QTLs across environments were stable, and the highest number of stable QTLs was related to A genome. Co-localization of QTL was found on linkage groups (LGs) 2B, 4B, 6A-a, and 7A (CIM method) and 2A-d, and 6A-a (MCIM method). Conclusion These results have implications for selection strategies in biomass yield and for increasing the yield of the aerial part of wheat following further evaluations in various genetic backgrounds and environments.

Phylogenetic relationships of Iranian Allium species using the matK (cpDNA gene) region

Hemadollah Zarei,Barat Ali Fakheri,Mohammad Reza Naghavi,Nafiseh Mahdinezhad (사)한국식물생명공학회 2020 JOURNAL OF PLANT BIOTECHNOLOGY Vol.47 No.1

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima’s D and -1.19 for Fu’s Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

Evaluating phylogenetic relationships in the Lilium family using the ITS marker

Sina Ghanbari,Barat Ali Fakheri,Mohammad Reza Naghavi,Nafiseh Mahdinezhad 한국식물생명공학회 2018 JOURNAL OF PLANT BIOTECHNOLOGY Vol.45 No.3

Lilium is a perennial bulbous plant belonging to the liriotypes genus. Our aim was to study the phylogenetic relationships of the Lilium family. Two varieties of Lilium ledebourii, 44 varieties of the gene bank, and one variety from the Tulipa family served as the out group. In order to study the diversity between lilium masses, ITS regions were used to design the marker. The results showed that the guanine base is the most abundant nucleotide. Relatively high conservation was observed in the ITS regions of the populations (0.653). Phylogenetic analysis showed that sargentiae and hybrid varieties are older than other varieties of the Lilium family. Also, the location of L. ledebourii varieties (Damash and Namin) was identified in a phylogenetic tree by using the ITS marker. Overall, our research showed that ITS molecular markers are very suitable for phylogenetic studies in the Lilium family.

Search for neutral MSSM Higgs bosons at LEP

Schael, S.,Barate, R.,Bruneli챔re, R.,De Bonis, I.,Decamp, D.,Goy, C.,J챕z챕quel, S.,Lees, J. P.,Martin, F.,Merle, E. SPRINGER 2006 The European physical journal. C, Particles and fi Vol.47 No.3

New protocol for the indirect regeneration of the Lilium ledebourii Bioss by using bulb explants

Sina Ghanbari,Barat Ali Fakheri,Mohammad Reza Naghavi,Nafiseh Mahdinezhad 한국식물생명공학회 2018 JOURNAL OF PLANT BIOTECHNOLOGY Vol.45 No.2

Lilium ledebourii Bioss is a wild species of Lilium, which grows naturally in some provinces of Iran. Previous studies on Lilium tissue culture have been linked to direct regeneration and a few studies have been conducted on indirect regeneration, which has been studied under bright conditions. In this study, for the first time in the world, all the stages of indirect regeneration (callus induction, shoot and root induction) have been studied under dark conditions. Callus formation and the regeneration levels of L. Ledebourii Bioss were examined for three replicates in an MS (Murashige and Skoog) medium with different hormonal compositions and by using a factorial experiment in the framework of a completely random plan. For callus initiation, 2,4-D and kinetin hormones were used in five and four levels, respectively, as auxin and cytokinin. Results showed that the highest percentage of the callus was found in 3 μM of 2,4-D and 0.5 μM of kinetin. In terms of callus wet weight, the highest amount was found in 3 μM of 2,4-D and 0.5 μM of kinetin. In addition, in terms of diameter, the highest amount was found in 3 μM of 2,4-D, and 0.5 μM of kinetin. In summary, the 2,4-D hormone had a major impact on the percentage of regeneration increase so that the best response was related to the composition of 3 μM of 2,4-D, and 0.1 μM of kinetin. This study contended that auxin and cytokinin can induce long shoots and roots through cell elongation in dark condition.

Evaluating phylogenetic relationships in the Lilium family using the ITS marker

Ghanbari, Sina,Fakheri, Barat Ali,Naghavi, Mohammad Reza,Mahdinezhad, Nafiseh The Korean Society of Plant Biotechnology 2018 식물생명공학회지 Vol.45 No.3

Lilium is a perennial bulbous plant belonging to the liriotypes genus. Our aim was to study the phylogenetic relationships of the Lilium family. Two varieties of Lilium ledebourii, 44 varieties of the gene bank, and one variety from the Tulipa family served as the out group. In order to study the diversity between lilium masses, ITS regions were used to design the marker. The results showed that the guanine base is the most abundant nucleotide. Relatively high conservation was observed in the ITS regions of the populations (0.653). Phylogenetic analysis showed that sargentiae and hybrid varieties are older than other varieties of the Lilium family. Also, the location of L. ledebourii varieties (Damash and Namin) was identified in a phylogenetic tree by using the ITS marker. Overall, our research showed that ITS molecular markers are very suitable for phylogenetic studies in the Lilium family.