Study of QTLs linked to awn length and their relationships with chloroplasts under control and saline environments in bread wheat

Bahram Masoudi,Mohsen Mardi,Eslam Majidi Hervan,Mohammad Reza Bihamta,Mohammad Reza Naghavi,Babak Nakhoda,Behnam Bakhshi,Mehrzad Ahmadi,Mohammad Taghi Tabatabaei,Mohamad Hossein Dehghani Firouzabadi 한국유전학회 2019 Genes & Genomics Vol.41 No.2

Introduction Some studies in wheat showed that awns may have a useful effect on yield, especially under drought stress. Up to this time few researches has identified the awn length QTLs with different effect in salinity stress. Objective The primary objective of this study was to examine the additive (a) and the epistatic (aa) QTLs involve in wheat awns length in control and saline environments. Methods A F7 RIL population consisting of 319 sister lines, derived from a cross between wheat cultivars Roshan and Falat (seri82), and the two parents were grown in two environments (control and Saline) based on an alpha lattice design with two replications in each environment. At flowering, awn length was measured for each line. For QTL analysis, the linkage map of the ‘‘Roshan × Falat’’ population was used, which included 748 markers including 719 DArT, 29 simple sequenced repeats (SSRs). Additive and pleiotropic QTLs were identified. In order to reveal the relationship between the identified QTL for awns length and the role of the gene or genes that it expresses, the awns length locus location and characteristics of its related CDS, gene, UTRs, ORF, exons and Introns were studied using ensemble plant (http://plant s.ensem bl.org/Triti cum_aesti vum). Furthermore, the promoter analysis has been done using NSITE-PL. Results We identified 6 additive QTLs for awn length by QTL Cartographer program using single-environment phenotypical values. Also, we detected three additive and two epistatic QTLs for awn length by the QTLNetwork program using multienvironment phenotypical values. Our results showed that none of the additive and epistatic QTLs had interactions with environment. One of the additive QTLs located on chromosome 4A was co-located with QTLs for number of sterile spikelet per spike in both environment and number of seed per spike in control environment. Coclusion Studies of the locus linked to the awns length QTL revealed the role of awn and its chloroplasts in grain filing during abiotic stress could be enhanced by over expression of some genes like GTP-Binding proteins which are enriched in chloroplasts encoded by genes included wPt-5730 locus.

Ki-67/MIB-1 as a Prognostic Marker in Cervical Cancer - a Systematic Review with Meta-Analysis

Piri, Reza,Ghaffari, Alireza,Gholami, Nasrin,Azami-Aghdash, Saber,PourAli-Akbar, Yasmin,Saleh, Parviz,Naghavi-Behzad, Mohammad Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.16

Background: In cervical cancer patients it has been reported that there in a significant Ki-67/MIB-1 expression is correlated with survival in cervical cancer patients. However, the prognostic value is still not well understood. Materials and Methods: In the present meta-analysis the prognostic value of Ki-67/MIB-1 with regard to overall survival (OS) and disease-free survival (DFS) in cervical cancer was investigated. The databases of PubMed, ISI Web of Science, Cochrane Central Register of Controlled Trials, EMBASE, Science Direct and Wiley Online Library were used to identify appropriate literature. Results: In order to explore the relationship between Ki-67/MIB-1 and cervical cancer, we have included 13 studies covering 894 patients in the current meta-analysis. The effect of Ki-67/MIB-1 on OS for pooled random effects HR estimate was 1.63 (95%confidence interval (CI) 1.09-2.45; P<0.05). The pooled HR for DFS was 1.26 (95%CI 0.58-2.73; P>0.05) and the subgroup analysis indicated Ki-67/MIB1 was associated with DFS (HR=3.67, 95%CI 2.65-5.09) in Asians. Conclusions: According to this meta-analysis, Ki-67/MIB-1 has prognostic value for OS in patients suffering from cervical cancer. For better evaluation of the prognostic role of Ki-67/MIB-1 on DFS, studies with larger numbers of patients are needed to validate present findings in the future.

Knowledge Production Status of Iranian Researchers in the Gastric Cancer Area: Based on the Medline Database

Ghojazadeh, Morteza,Naghavi-Behzad, Mohammad,Nasrolah-Zadeh, Raheleh,Bayat-Khajeh, Parvaneh,Piri, Reza,Mirnia, Keyvan,Azami-Aghdash, Saber Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.12

Background: Scientometrics is a useful method for management of financial and human resources and has been applied many times in medical sciences during recent years. The aim of this study was to investigate the status of science production by Iranian scientists in the gastric cancer field based on the Medline database. Materials and Methods: In this descriptive-cross sectional study Iranian science production concerning gastric cancer during 2000-2011 was investigated based on Medline. After two stages of searching, 121 articles were found, then we reviewed publication date, authors names, journal title, impact factor (IF), and cooperation coefficient between researchers. SPSS.19 was used for statistical analysis. Results: There was a significant increase in published articles about gastric cancer by Iranian researchers in Medline database during 2006-2011. Mean cooperation coefficient between researchers was $6.14{\pm}3.29$ person per article. Articles of this field were published in 19 countries and 56 journals. Those basex in Thailand, England, and America had the most published Iranian articles. Tehran University of Medical Sciences and Mohammadreza Zali had the most outstanding role in publishing scientific articles. Conclusions: According to results of this study, improving cooperation of researchers in conducting research and scientometric studies about other fields may have an important role in increasing both quality and quantity of published studies.

Biodiversity status of Tulipa (Liliaceae) in Iran inferred from molecular characterization

Davoud Asgari,Alireza Babaei,Mohammad Reza Naghavi,Mahmoud Kiani 한국원예학회 2020 Horticulture, Environment, and Biotechnology Vol.61 No.3

Here, we used data generated from amplifi ed fragment length polymorphism (AFLP) analysis to address the biodiversitystatus and taxonomic relationships among 47 wild accessions representing 9 species of the genus Tulipa in Iran. A high levelof genetic diversity within the genus was observed; the most distant taxa were T. humilis and T. schrenkii , while the highestdegree of similarity was found between T. montana and T. bifl ora . Twelve AFLP primer sets amplifi ed 342 fragments, ofwhich 304 were polymorphic (88.1%). The average number of polymorphic bands per AFLP primer pair was 28.5. A hierarchicalcluster analysis was carried out on the genetic profi le of the taxa, and the results mostly reconfi rmed the recognizedtaxonomy of the genus. However, we found evidence for recognition of a new subgenus for T. biebersteiniana .

Application of SSR Markers for Characterization of Genetic Diversity within Iranian Grapevine Cultivars (‘Askari’ and ‘Keshmeshi’)

Rahim Nikkhah,Ali Ebadi,Mohammad Reza Naghavi,Mauro Cresti,Monica Scali,Mehdi Hadadynejad 한국원예학회 2010 Horticulture, Environment, and Biotechnology Vol.51 No.1

The present study was designed to identify intra-varietal diversity via SSR markers within ‘Askari’ and ‘Keshmeshi’ (Vitis vinifera L.). These two semi-seedless grape cultivars are used as table grape and raisin. Some accessions of these cultivars are morphologically different. For instance, some accessions had big berries with big bunches and empty seeds, whereas others had small berries in small bunches with soft seed traces. In order to evaluate these differences at the genetic level, we selected 14 SSR loci to evaluate intra-cultivar diversity. In total, 42 accessions of ‘Askari’, 10 accessions of ‘Keshmeshi’ and one accession of Sultanina as a control were analysed, using a capillary electrophoresis fragment sizing system. Genetic analysis discriminated six accessions of ‘Askari’ (No. A3, A21, A31, A44, A46, and A114) which were different from other accessions. These accessions were also different in some morphological traits. Accessions no. A3 and no. A21 had soft seed traces with berries and bunches that were smaller than others. Other accessions had empty seeds. Accessions no. A44, A46 and A114 had big bunches, big berries and empty seeds. In accession no. A31 berry shape was approximately round vs. oval shape in other accessions. The remaining accessions (36 accessions) were identical in 14 SSR loci. In ‘Keshmeshi’ four different accessions (No. K6, K8, K15, and K27) were discriminated in genetic analysis. In accessions no. K6 and no. K8, the number of bunch and yield per vine was higher than other accessions. In accessions no. K15 and no. K27, berries and bunches were bigger than others and the number of seed traces were higher than other accessions. Other six accessions were identical in14 SSR loci. Cluster analysis of all three cultivars divided accessions to three groups (each cultivar in one group) at 0.67 similarity coefficient. Our study showed SSR markers can be useful for identifying of intra-cultivar diversity.

Motor learning and training strategy effect on motor control; Comparison between Taekwondo and Karate front kick (Ap Chagi and Mae Geri)

Hamidreza Barnamehei,Faezeh Khazaee,Mohammad Ali Safaei,Hadi Jabari,Neda Golfeshan,Mohammad Barnamehei,Ali Rezaei,Mohammad Reza Kharazi,Nader Naghavi 국제무예학회 2020 International Journal of Martial Arts Vol.6 No.-

The aims of the current study were first, to evaluate whether there were differences in the front kicking kinematics executed by professional Taekwondo and Karate athletics. Second, biomechanical evaluations aimed to determine the kinematic variables of effective front kicking performance between different training strategies. Sixteen elite Taekwondo and fourteen Karate athletics performed front kick. Kinematics and kinetics were recorded using a ten high-speed camera and two force plates. Taekwondo and karate groups present significant kinematic and repeatability differences, which significant differences observed in the range of motion, angular velocity, and peak values of lower limb angular positions and velocities. Although, the movement pattern of a front kick in group was similar. Based on our results, different training strategies for one movement (front kick) can change neuromuscular, motor control, and kicking efficacy. Analyzing this kind of research and comparison between two different groups that executes the same action with two different learning methods can improve the knowledge of athletics and coaches to better performance in training and learning strategies. In addition, this type of study of training strategy and motor control can reduce sports mistakes in coaching, particularly in the primary period of athletics training, and decrease injury probability.

Comparative Study of Dermatoscopic and Histopathologic Results in Facial Basal Cell Carcinoma and Melanocytic Nevi

Amirnia, Mehdi,Ranjkesh, Mohammad-Reza,Azimpouran, Mahzad,Karkon-Shayan, Farid,Alikhah, Hossein,Jafari-Asl, Mohammadali,Piri, Reza,Naghavi-Behzad, Mohammad Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.1

Background: Dermatoscopy can be applied to diagnose pigmented skin lesions. The aim of the present study was to compare dermatoscopic and histopathologic results in basal cell carcinoma (BCC) and melanocytic nevus of theface. Materials and Methods: In an analytical-descriptive study, 61 patients suspected of BCC or melanocytic nevi of face were randomly selected. The skin lesions of patients were evaluated with dermatoscopic method from February 2012 to February 2014 and results were compared with pathological features of samples. Results: In this study, mean age of patients was $49.5{\pm}18.9$. Some 25 (41%) were men and 36 (59%) were women. In 27 cases (44.3%) there was diagnosis of melanocytic nevus, in 28 cases (45.9%) diagnosis of BCC, and in 3 cases (4.9%) there was mixed diagnosis. The relationship between patients' gender and dermatoscopic diagnosis of the patients was statistically significant (P=0.001). For BCC the sensitivity and specificity of dermatoscopic method were 100% and 97% respectively and for melanocytic nevi 96.4% and 97%. Conclusions: Dermatoscopic study not only can be helpful in improving clinical diagnosis while guiding missed malignant lesions to pathologic evaluations, but also could be useful in evaluating further suspicious or recurrent cases.

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

Zarei, Hemadollah,Fakheri, Barat Ali,Naghavi, Mohammad Reza,Mahdinezhad, Nafiseh The Korean Society of Plant Biotechnology 2020 식물생명공학회지 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.

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.

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.