Search results for: gene modification

Authors: Ananthakrishna L. R., Ramesh D., Kumar Wodeyar, Kotresh A. M., Gururaj P. M.

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Malnad Gidda is the indigenous recognized cattle breed of Shivamogga District of Karnataka state, India is known for its disease resistance to many of the infectious diseases. There are 25 LRR (Leucine Rich Repeats) identified in bovine (Bos indicus) TLR9. The amino acid sequence of LRR is deduced to nucleotide sequence in BLASTx bioinformatic online tools. LRR2 to LRR10 are involved in pathogen recognition and binding in human TLR9 which showed a higher degree of nucleotide variations with respect to disease resistance to various pathogens. Hence, primers were designed to amplify the flanking sequences of LRR2 to LRR10, to discover the nucleotide variations if any, in Malnad Gidda breed of Cattle which is associated with disease resistance. The DNA isolated from peripheral blood mononuclear cells of ten Malnad Gidda cattle. A desired and specific amplification product of 0.8 kb was obtained at an annealing temperature of 56.6ᵒC. All the PCR products were sequenced on both sides by gene-specific primers. The sequences were compared with TLR9 sequence of cross breed cattle obtained from NCBI data bank. The sequence analysis between Malnad Gidda and crossbreed cattle revealed no nucleotide variations in the region LRR2 to LRR9 which shows the conserved in pathogen binding domain (LRR) of TLR9.

Keywords: leucine rich repeats, Malnad Gidda, cross breed, TLR9

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Authors: Miguel García-Ferrús, Ana González, María A. Ferrús

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The most demanded organic foods worldwide are those that are consumed fresh, such as fruits and vegetables. However, there is a knowledge gap about some aspects of organic food microbiological quality and safety. Organic fruits and vegetables are more exposed to pathogenic microorganisms due to surface contact with natural fertilizers such as animal manure, wastes and vermicompost used during farming. It has been suggested that some emergent pathogens, such as Helicobacter pylori or Arcobacter spp., could reach humans through the consumption of raw or minimally processed vegetables. Therefore, the objective of this work was to study the contamination of organic fresh green leafy vegetables by Arcobacter spp. and Helicobacter pylori. For this purpose, a total of 24 vegetable samples, 13 lettuce and 11 spinach were acquired from 10 different ecological supermarkets and greengroceries and analyzed by culture and PCR. Arcobacter spp. was detected in 5 samples (20%) by PCR, 4 spinach and one lettuce. One spinach sample was found to be also positive by culture. For H. pylori, the H. pylori VacA gene-specific band was detected in 12 vegetable samples (50%), 10 lettuces and 2 spinach. Isolation in the selective medium did not yield any positive result, possibly because of low contamination levels together with the presence of the organism in its viable but non-culturable form. Results showed significant levels of H. pylori and Arcobacter contamination in organic vegetables that are generally consumed raw, which seems to confirm that these foods can act as transmission vehicles to humans.

Keywords: Arcobacter sp., Helicobacter pylori, Organic Vegetables, Polymerase Chain Reaction (PCR)

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Authors: Rueyhung Weng, Chia-En Huang, Jung-Chi-Liao

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The transition zone (TZ) serves as a diffusion barrier to regulate the ins and outs of the proteins recruited to the primary cilia. TCTN2 is one of the TZ proteins and its mutation causes Joubert syndrome, a serious multi-organ disease. Despite its important medical relevance, the functions of TCTN2 remain elusive. Here we created a TCTN2 gene deleted retinal pigment epithelial cells (RPE1) using CRISPR/Cas9-based genome editing technique and used this knockout line to reveal roles of TCTN2. TCTN2 knockout RPE1 cells displayed a significantly reduced ciliogenesis or a shortened primary cilium length in the cilium-remaining population. Intraflagellar transport protein IFT88 aberrantly accumulated at the tip of TCTN2 deficient cells. Guanine nucleotide exchange factor Arl13B was mostly absent from the ciliary compartment, with a small population localizing at the ciliary tip. The deficient TZ was corroborated with the mislocalization of two other TZ proteins TMEM67 and MKS1. In addition, TCTN2 deficiency induced TZ impairment led to the suppression of Sonic hedgehog signaling in response to Smoothened (Smo) agonist. Together, depletion of TCTN2 destabilizes other TZ proteins and considerably alters the localization of key transport and signaling-associated proteins, including IFT88, Arl13B, and Smo.

Keywords: CRISPR/Cas9, primary cilia, Sonic hedgehog signaling, transition zone

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Authors: R. M. Srivastava, Subbanna A.R.N.S, Md Abbas Ahmad, S. P.More, Shivashankar, B. Kalyanbabu

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The similar morphology associated with high genetic variability poses problems in phylogenetic studies of Helicoverpa armigera (Hubner). To identify genetic variation of North Western Himalayan population’s, partial (Mid to terminal region) cytochrome c oxidase subunit I (COX-1) gene was amplified and sequenced for three populations collected from Pantnagar, Almora, and Chinyalisaur. The alignment of sequences with other two populations, Nagpur representing central India population and Anhui, China representing complete COX-1 sequence revealed unanimity in middle region with eleven single nucleotide polymorphisms (SNPs) in Nagpur populations. However, the consensus is missing when approaching towards terminal region, which is associated with 15 each SNPs and pair base substitutions in Chinyalisaur populations. In minimum evolution tree, all the five populations were majorly separated into two clades, one comprising of only Nagpur population and the other with rest. Amongst, North Western populations, Chinyalisaur one is promising by farming a separate clade. The pairwise genetic distance ranges from 0.025 to 0.192 with the maximum between H. armigera populations of Nagpur and Chinyalisaur. This genetic isolation of populations can be attributed to a key role of topological barriers of weather and mountain ranges and temporal barriers due to cropping patterns.

Keywords: cytochrome c oxidase subunit I, northwestern Himalayan population, Helicoverpa armigera (Noctuidae: Lepidoptera), phylogenetic relationship, genetic variation

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Authors: Mudassar Iqbal, Riaz Hussain, Khalid Mehmood, Farah Ali, Fazal Mahmood, Abdul Ghaffar

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Corynebacterium pseudotuberculosis is an important cause of caseous lymphadenitis (CL), a complex, chronic devastating and destructive disease of small ruminants. In present study, postmortem examination of Chinkara deer (n=25) was conducted in year 2014. Pus samples suggestive of CL were collected from the superficial lymph nodes, liver, spleen and lungs during necropsy and subjected to standard microbiological procedures for isolation and molecular analysis of bacterial pathogens. Pus samples collected from carcasses (25) presenting clinical lesions of C. pseudotuberculosis infection was identified in 19 (76%) carcasses on the basis of culture characteristics. The frequency of C. pseudotuberculosis bacterium was higher in older animals as compared to young animals. Grossly, multiple tubercles of variable size having caseous material were observed in liver, lungs, spleen and lymph nodes. Histopathologically, tissue sections from all the visceral organs were extensively plugged with abscess. In present study specific prolineiminopeptidase (PIP) gene of the C. pseudotuberculosis was amplified by the Polymerase chain reaction technique (PCR) in 17(25) cases. The efficient and reliable molecular analysis along with necropsy findings in present study can be used as valuable approach for diagnosis of caseous lymphadenitis in small ruminants.

Keywords: Chinkara deer, Corynebacterium pseudotuberculosis, Caseous lymphadenitis, PCR

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Authors: Yuchen Yang, Zhenming Wang, Jun Zhu, Ning Zhao

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An easy-to-implement and robust finite volume multi-resolution Weighted Essentially Non-Oscillatory (WENO) scheme is proposed on adaptive cartesian grids in this paper. Such a multi-resolution WENO scheme is combined with the ghost cell immersed boundary method (IBM) and wall-function technique to solve Navier-Stokes equations. Unlike the k-exact finite volume WENO schemes which involve large amounts of extra storage, repeatedly solving the matrix generated in a least-square method or the process of calculating optimal linear weights on adaptive cartesian grids, the present methodology only adds very small overhead and can be easily implemented in existing edge-based computational fluid dynamics (CFD) codes with minor modifications. Also, the linear weights of this adaptive finite volume multi-resolution WENO scheme can be any positive numbers on condition that their sum is one. It is a way of bypassing the calculation of the optimal linear weights and such a multi-resolution WENO scheme avoids dealing with the negative linear weights on adaptive cartesian grids. Some benchmark viscous problems are numerical solved to show the efficiency and good performance of this adaptive multi-resolution WENO scheme. Compared with a second-order edge-based method, the presented method can be implemented into an adaptive cartesian grid with slight modification for big Reynolds number problems.

Keywords: adaptive mesh refinement method, finite volume multi-resolution WENO scheme, immersed boundary method, wall-function technique.

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Authors: Ebtissam Saleh Al-Meghaiseeb, Abdulaziz Al Masood, Abdulrahman Al-Robayan, Reem Al-Amro, Misbahul Arfin, Abdulrahman Al Asmari

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Objective: The objective of this study was to evaluate the role of apolipoprotein E (APOE) polymorphism on the onset of inflammatory bowel disease (IBD) in Saudi patients. Methods: APOE gene was genotyped to evaluate the frequencies of the alleles and genotypes in Saudi subjects, including IBD patients (n=200) and matched controls (n=200), using APOE StripAssayTM kit (ViennaLab Labordiagnostika GmbH, Vienna, Austria). Results: The frequencies of alleles and genotypes of APOE differed in patients and controls. The APOE allele ε2 and ε4, genotype ε2/ε3 and ε2/ε4 were significantly higher in the IBD patients than the healthy controls. The frequencies of ε3 allele and ε3/ε3 genotype were higher in the control group as compared to patients. The higher prevalence of allele ε2 and ε4 allele in patients compared to that in controls suggested that ε2 and ε4 alleles may increase the risk of IBD. Results also indicated that APOE ε4 allele was associated with early age at onset of IBD. On the other hand, the decreased frequencies of ε3 allele and ε3/ε3 genotype in patients as compared to those in the controls suggested a protective effect of APOE ε3 for IBD susceptibility. In this study, the frequency distribution of APOE alleles and genotypes was not affected by the gender or type of IBD (familial or sporadic). Conclusion: This study indicates that APOE polymorphism plays a significant role in developing IBD and early age of onset in Saudi patients. However, further studies with large-size sample are warranted to confirm this relationship.

Keywords: APOE, polymorphism, IBD, saudis

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Authors: Sana Gul, Sheeba Murad, Aneela Javed

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Introduction: Human Papilloma Virus (HPV) is small DNA virus mostly infecting mucosa and cutaneous keratinocytes. So far, more than 200 Human papillomaviruses are known. HPV have been divided into high- and low-risk on the basis of their oncogenic potential. High risk HPV is considered to be the main etiological cause for cervical cancer. Objective: Current study was designed to screen the local cervical cancer patients from the twin cities of Pakistan for the occurance of high risk HPV. Methodology: A total of 67 formalin fixed paraffin-embedded samples of cervical cancer biopsies were obtained from the government hospitals in Islamabad and Rawalpindi. Cervical cancer biopsies were examined for the presence of HPV DNA. Polymerase chain reaction (PCR) was used for the amplification of a region in the HPV-L1 gene for the general detection of the Papilloma virus and for the genotype specific detection of high risk HPV 16 and 18 using the GP5/GP6 primers and genotype specific primers respectively. Results: HPV DNA was detected in 59 out of 67 samples analyzed. 30 samples showed the presence of HPV16 while 22 samples were positive for HPV 18 . HPV subtype could not be determined in 7 samples. Conclusion: Our results show a strong association between HPV infection and cervical cancer among women in twin cities of Pakistan. One way to minimize the disease burden in relation to HPV infection in Pakistani population is the use of prophylactic vaccines and routine screening. An early diagnosis of HPV infection will allow better health management to reduce the risk of developing cervical cancer.

Keywords: cervical cancer, Pakistan, human papillomavirus, HPV 16

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Authors: Mohd Adil, Rosina Khan, Danishuddin, Asad U. Khan

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The aim of this study was to evaluate the influence of the crude and active solvent fraction of Trachyspermum ammi on S. mutans cariogenicity, effect on expression of genes involved in biofilm formation and caries development in rats. GC–MS was carried out to identify the major components present in the crude and the active fraction of T. ammi. The crude extract and the solvent fraction exhibiting least MIC were selected for further experiments. Scanning electron microscopy was carried out to observe the effect of the extracts on S. mutans biofilm. Comparative gene expression analysis was carried out for nine selected genes. 2-Isopropyl-5-methyl-phenol was found as major compound in crude and the active fraction. Binding site of this compound within the proteins involved in biofilm formation was mapped with the help of docking studies. Real-time RT-PCR analyses revealed significant suppression of the genes involved in biofilm formation. All the test groups showed reduction in caries (smooth surface as well as sulcal surface caries) in rats. Moreover, it also provides new insight to understand the mechanism influencing biofilm formation in S. mutans. Furthermore, the data suggest the putative cariostatic properties of T. Ammi and hence can be used as an alternative medicine to prevent caries infection.

Keywords: bio-film, Streptococcus mutans, dental caries, bio-informatic

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Authors: Deepak Deshpande, Vikas Minchekar

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Day by day in modern India communal forces became stronger and stronger. Each and every caste group trying to show their strength through massive marches. Such kind of marches or ralliesruinous national integrity in India. To test this assumption present investigation has been carried out. This research was undertaken by using survey techniques. The study has been carried out in two phases. In the first stage, the students’ attitudes were collected while in the second phase the views of the members of the historical association were collected. The social dominance orientation scale and sources of social dominance inventory have been administered on 200 college students belonging to Maratha caste. Analyzed data revealed ahigh level of social dominance in Maratha caste students. Approximately, 80 percent students have reported that they have learned such dominance from the medieval history. The other sources disappear very less prominent. These results and present Indian social situation have been communicated with the members of the historical association of India. The majority members of this association agreed with this reality. The consensus also received on that Maratha caste person experiencing dominance due to the misinterpretation of the King Shivaji Empire; synchronize by politicians. The survey monkey app was used through electronic mail to collect the views on ‘The attitude towards the modification of curricula questionnaire’. The maximum number of members of the historical association agreed to employ to teach the medieval Indian history accordingly the secular perspectives.

Keywords: social dominance orientation, secular perceptive, national integrity, Maratha caste and medieval Indian history

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Authors: M. A. García, J. Vinolas, A. Hernando

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Steel is nowadays one of the most important structural materials because of its outstanding mechanical properties. Therefore, in order to look for a sustainable economic model and to optimize the use of extensive resources, new methods to monitor and prevent failure of steel-based facilities are required. The classical mechanical tests, as for instance building tasting, are invasive and destructive. Moreover, for facilities where the steel element is embedded, (as reinforced concrete) these techniques are directly non applicable. Hence, non-invasive monitoring techniques to prevent failure, without altering the structural properties of the elements are required. Among them, electromagnetic methods are particularly suitable for non-invasive inspection of the mechanical state of steel-based elements. The magnetoelastic coupling effects induce a modification of the electromagnetic properties of an element upon applied stress. Since most steels are ferromagnetic because of their large Fe content, it is possible to inspect their structure and state in a non-invasive way. We present here a distinct electromagnetic method for contactless evaluation of internal stress in steel-based elements. In particular, this method relies on measuring the magnetic induction between two coils with the steel specimen in between them. We found that the alteration of electromagnetic properties of the steel specimen induced by applied stress-induced changes in the induction allowed us to detect stress well below half of the elastic limit of the material. Hence, it represents an outstanding non-invasive method to prevent failure in steel-based facilities. We here describe the theoretical model, present experimental results to validate it and finally we show a practical application for detection of stress and inhomogeneities in train railways.

Keywords: magnetoelastic, magnetic induction, mechanical stress, steel

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Authors: Yayan Harry Yadi, L. Meily Kurniawidjaja

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Work activities for MMH (Manual Material Handling) in the storage of liquid catalyst raw material workstations in chemical industries identify high-risk MSDs (Musculoskeletal Disorders). Their work is often performed frequently requires an awkward body posture, twisting, bending because of physical space limited, cold, slippery, and limited tools for transfer container and weighing the liquid chemistry of the catalyst into the container. This study aims to develop an ergonomic work system design on the transfer and weighing process of liquid catalyst raw materials at the storage warehouse. A triangulation method through an interview, observation, and detail study team with assessing the level of risk work posture and complaints. Work postures were analyzed using the RULA method, through the support of CATIA software. The study concludes that ergonomic design can make reduce 3 levels of risk scores awkward posture. CATIA Software simulation provided a comprehensive solution for a better posture of manual material handling at task weigh. An addition of manual material handling tools such as adjustable conveyors, trolley and modification tools semi-mechanical weighing with techniques based on rule ergonomic design can reduce the hazard of chemical fluid spills.

Keywords: ergonomic design, MSDs, CATIA software, RULA, chemical industry

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Authors: Juan Jose Filgueira, Daniela Londono-Serna, Liliana Maria Hoyos

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Carnation (Dianthus caryophyllus) is one of the most important products of exportation in the floriculture industry worldwide. Fusariosis is the disease that causes the highest losses on farms, in particular the one produced by Fusarium oxysporum f.sp. dianthi, called vascular wilt. Gene identification and metabolic routes of the genes that participate in the building of the plant response to Fusarium are some of the current targets in the carnation breeding industry. The techniques for the identifying of resistant genes in the plants, is the analysis of the transcriptome obtained during the host-pathogen interaction. In this work, we report the cell transcriptome of different varieties of carnation that present differential response from Fusarium oxysporum f.sp. dianthi attack. The cells of the different hybrids produced in the outbreeding program were cultured in vitro and elicited with the parasite in a dual culture. The isolation and purification of mRNA was achieved by using affinity chromatography Oligo dT columns and the transcriptomes were obtained by using Illumina NGS techniques. A total of 85,669 unigenes were detected in all the transcriptomes analyzed and 31,000 annotations were found in databases, which correspond to 36.2%. The library construction of genic expression techniques used, allowed to recognize the variation in the expression of genes such as Germin-like protein, Glycosyl hydrolase family and Cinnamate 4-hydroxylase. These have been reported in this study for the first time as part of the response mechanism to the presence of Fusarium oxysporum.

Keywords: Carnation, Fusarium, vascular wilt, transcriptome

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Authors: B. Hekner, J. Myalski, P. Wrzesniowski

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This study presents aluminum matrix composites reinforced by glassy carbon (GC) and titanium (Ti). In the first step, the heterophase (GC+Ti), spatial form (similar to skeleton) of reinforcement was obtained via own method. The polyurethane foam (with spatial, open-cells structure) covered by suspension of Ti particles in phenolic resin was pyrolyzed. In the second step, the prepared heterogeneous foams were infiltrated by aluminium alloy. The manufactured composites are designated to industrial application, especially as a material used in tribological field. From this point of view, the glassy carbon was applied to stabilise a coefficient of friction on the required value 0.6 and reduce wear. Furthermore, the wear can be limited due to titanium phase application, which reveals high mechanical properties. Moreover, fabrication of thin titanium layer on the carbon skeleton leads to reduce contact between aluminium alloy and carbon and thus aluminium carbide phase creation. However, the main modification involves the manufacturing of reinforcement in the form of 3D, skeleton foam. This kind on reinforcement reveals a few important advantages compared to classical form of reinforcement-particles: possibility to control homogeneity of reinforcement phase in composite material; low-advanced technique of composite manufacturing- infiltration; possibility to application the reinforcement only in required places of material; strict control of phase composition; High quality of bonding between components of material. This research is founded by NCN in the UMO-2016/23/N/ST8/00994.

Keywords: metal matrix composites, MMC, glassy carbon, heterophase composites, tribological application

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Authors: Sonam Kumari

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Tuberculosis is the deadliest disease worldwide. Millions of people lose their lives every year due to this disease. It has turned lethal due to the erratic nature of its causative organism, Mycobacterium tuberculosis (Mtb). Mtb tends to enter into an inactive, dormant state and emerge to replicating state upon encountering favorable conditions. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes. Mtb has seven such proteins (WhiB1 to WhiB7). WhiB proteins are transcriptional regulators; they regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical parameters of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: mycobacterium tuberculosis, TB, whiB proteins, ITC

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Authors: Ceren Karaman, Onur Karaman

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The adsorption of Remazol Black B (RBB), an anionic dye, onto dried orange pulp (DOP) adsorbent prepared by only drying and by treating with cetyltrimetylammonium bromide (CTAB), a cationic surfactant, surface-modified orange pulp (SMOP) was studied in a stirred batch experiments system at 25°C. The adsorption of RBB on each adsorbent as a function of surfactant dosage, initial pH of the solution and initial dye concentration was investigated. The optimum amount of CTAB was found to be 25g/l. For RBB adsorption studies, while working pH value for the DOP adsorbent system was determined as 2.0, it was observed that this value shifted to 8.0 when the 25 g/l CTAB treated-orange pulp (SMOP) adsorbent was used. It was obtained that the adsorption rate and capacity increased to a certain value, and the adsorption efficiency decreased with increasing initial RBB concentration for both DOP and SMOP adsorbents at pH 2.0 and pH 8.0. While the highest adsorption capacity for DOP was determined as 62.4 mg/g at pH 2.0, and as 325.0 mg/g for SMOP at pH 8.0. As a result, it can be said that permanent cationic coating of the adsorbent surface by CTAB surfactant shifted the working pH from 2.0 to 8.0 and it increased the dye adsorption rate and capacity of orange pulp much more significantly at pH 8.0. The equilibrium RBB adsorption data on each adsorbent were best described by the Langmuir isotherm model. The adsorption kinetics of RBB on each adsorbent followed a pseudo-second-order model. Moreover, the intraparticle diffusion model was used to describe the kinetic data. It was found that diffusion is not the only rate controlling step. The adsorbent was characterized by the Brunauer–Emmett–Teller (BET) analysis, Fourier-transform-infrared (FTIR) spectroscopy, and scanning-electron-microscopy (SEM). The mechanism for the adsorption of RBB on the SMOP may include hydrophobic interaction, van der Waals interaction, stacking and electrostatic interaction.

Keywords: adsorption, Cetyltrimethylammonium Bromide (CTAB), orange pulp, Remazol Black B (RBB), surface modification

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Authors: Arati Inamdar, Siddharth Bhattacharyya, Kester Haye

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Collision tumors are rare entities characterized by neoplasms of two different cell populations with distinct separating boundaries. Such tumors could be benign, malignant, or a combination of both. The exact mechanism of origin for collision tumors is predicted to be tumor heterogeneity or concurrent occurrence of neoplasm in the same organ. We present two cases of plasmacytoma presenting as a collision tumor, one with a tumor of hematological origin and another with a non-hematological origin, namely Chronic Lymphocytic Leukemia and Adenocarcinoma of the colon, respectively. The immunohistochemical stains and flowcytometry analysis performed on the specimens aided incorrect diagnosis. Interestingly, neoplastic cells of plasmacytoma in the first case demonstrated strong cytokeratin along with weak Epithelial Specific Antigen/ Epithelial cell adhesion molecule Monoclonal Antibody (MOC31) positivity, indicating that the tumor may influence the microenvironment of the tumor in the vicinity. Furthermore, the next-generation sequencing studies performed on the specimen with plasmacytoma and chronic lymphocytic lymphoma demonstrated BReast CAncer gene (BRCA2) and Tumor Necrosis Factor Alpha Induced Protein 3 (TNFAIP3) as a disease associated variants suggestive of risk for multiple tumors including collision tumors. Our reports highlight the unique collision tumors involving plasmacytoma, which have never been reported previously, as well as provide necessary insights about the underline genetic aberrations and tumor heterogeneity through sequencing studies and allow clonality assessment for subsequent tumors.

Keywords: BRCA2, collision tumor, chronic lymphocytic leukemia, plasmacytoma

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Authors: Seyyed Mohammad Amin Mousavi Sagharchi, Alireza Mahmoudi Nasab, Tim Bakker

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Introduction: Mycobacterium tuberculosis (MTB) is the most intelligent bacterium that existed in the world to our best knowledge. This bacterium can cause tuberculosis (TB) which is responsible for its spread speed and murder of millions of people around the world. MTB has the practical function to escape from anti-tuberculosis drugs (AT), for this purpose, it handles some mutations in the main genes and creates new patterns for inhibited genes. Method and materials: Researchers have their best tries to safely isolate MTB from the sputum specimens of 35 patients in some hospitals in the Tehran province and detect MTB by culture on Löwenstein-Jensen (LJ) medium and microscopic examination. DNA was extracted from the established bacterial colony by enzymatic extraction method. It was amplified by the polymerase chain reaction (PCR) method, reverse hybridization, and evaluation for detection of resistance genes; generally, researchers apply GenoType MTBDRplus assay. Results: Investigations of results declare us that 21 of the isolated specimens (about 60%) have mutation in rpoB gene, which resisted to rifampicin (most prevalence), and 8 of them (about 22.8%) have mutation in katG or inhA genes which resisted to isoniazid. Also, 4 of them (about 11.4%) don't have any mutation, and 2 of them (about 5.7%) have mutation in every three genes, which makes them resistant to the two drugs mentioned above. Conclusion: Rifampicin and isoniazid are two essential AT that using in the first line of treatment. Resistance in rpoB, and katG, and inhA genes related to mentioned drugs lead to ineffective treatment.

Keywords: mycobacterium tuberculosis, tuberculosis, drug resistance, isoniazid, rifampicin

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Authors: Zia Ullah, Muhammad Asim, Shi Sujuan, Rayyan Khan, Aaqib Shaheen, LIU Haobao

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The plant-specific auxin efflux proteins PIN-FORMED (PIN) have been well depicted in many plant species for their essential roles in regulating the transport of auxins in several phases of plant growth. Little is known about the various functions of the PIN family genes in the Nicotiana tabacum (N. tabacum) species during plant growth. To define the expression pattern of the NtPIN1a gene under abiotic stresses and hormone treatment, transgenic tobacco with promoterNtPIN1a::GUS construct was employed. Comprehensive computational analyses of the NtPIN1a promoter confirmed the existence of common core promoter elements including CAAT-box, TATA-box, hormone, and abiotic stress-responsive elements such as ABRE, P-box, MYC, MYB, ARE, and GC-motifs. The transgenic plants with the promoter of NtPIN1a displayed a promising expression of β-glucuronidase (GUS) in germinating seeds, root tips, shoot-apex, and developing leaves under optimal conditions. While the differential expression of GUS in moderate salt, drought, low potassium stresses, and externally high auxin level at two different time points, suggested NtPIN1a played a key role in growth processes and the plants’ response to abiotic stresses. This analysis provides a foundation for more in-depth discoveries of the biological functions of NtPIN1a in Nicotiana species and this promoter may be employed in genetic engineering of other crops for enhanced stress tolerance.

Keywords: tobacco, nicotiana tabacum, pin, promoter, GUS, abiotic stresses, auxin

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Authors: Burcu Inal, Irfan Kandemir

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Sequences of mitochondrial cytochrome oxidase I (COI) gene of twenty-five Turkish and one Greek Myzus cerasi (Fabricus) (Hemiptera: Aphididae) in populations were collected from Prunus avium and Prunus cerasus. The partial coding region of COI studied is 605 bp for all the populations, from which 565 nucleotides were conserved, 40 were variable, 37 were singleton, and 3 sites were parsimony-informative. Four haplotypes were identified based on nucleotide substitutions, and the mean of intraspecific divergence was calculated to be 0.3%. Phylogenetic trees were constructed using Maximum Likelihood, Minimum Evolution, Neighbor-joining, and Unweighed Pair Group Method of Arithmetic Averages (UPGMA) and Myzus persicae (Sulzer) and Myzus borealis Ossiannilson were included as outgroups. The population of M. cerasi from Isparta diverged from the rest of the groups and formed a clade (Haplotype B) with Myzus borealis. The rest of the haplotype diversity includes Haplotype A and Haplotype C with individuals characterized as Myzus cerasi pruniavium and Haplotype D with Myzus cerasi cerasi. M. cerasi diverge into two subspecies and it must be reevaluated whether this pest is monophagous or oligophagous in terms of plant type dependence. The obligated endosymbiont Buchnera aphidicola was also found during this research, but no facultative symbionts could be found. It is expected further studies will be required for a complete barcoding and diversity of bacterial endosymbionts present.

Keywords: bacterial endosymbionts, barcoding, black cherry aphid, nucleotide diversity

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Authors: Hafsa Tahir, Sanaullah Iqbal

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Glactooligosaccharide (GOS) is a type of prebiotic which is mainly found in human milk. GOS belongs to those bacteria which stimulates the growth of beneficial bacteria in human intestines. The aim of the present study was to develop a value-added product by producing prebiotic (GOS) in buttermilk through trans galactosylation. Buttermilk is considered as an industrial waste which is discarded after the production of butter and cream. It contains protein, minerals, vitamins and a smaller amount of fat. Raw milk was pasteurized at 100º C for butter production and then trans galactosylation process was induced in the butter milk thus obtained to produce prebiotic GOS. Results showed that the enzyme (which was obtained from bacterial strain of Esecrshia coli and has a gene of Lactobacillus reuteri L103) concentration between 400-600µl/5ml can produce GOS in 30 minutes. Chemical analysis and sensory evaluation of plain and GOS containing buttermilk showed no remarkable difference in their composition. Furthermore, the shelf-life study showed that there was non-significant (P>0.05) difference in glass and pouch packaging of buttermilk. Buttermilk in pouch packaging maintained its stability for 6 days without the addition of preservatives. Therefore it is recommended that GOS enriched buttermilk which is generally considered as a processing waste in dairy manufacturing can be turned into a cost-effective nutritional functional food product. This will not only enhance the production efficiency of butter processing but also will create a new market opportunity for dairy manufacturers all over the world.

Keywords: buttermilk, galactooligosaccharide, shelf Life, transgalactosylation

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Authors: Subhasree Majumdar, Sovan Dey, Sayari Mukherjee, Sourav Dutta, Dalia Dasgupta Mandal

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Bacterial isolates from Planococcus genus are known for the production of yellowish orange pigment that belongs to the carotenoid family. These pigments are of immense pharmacological importance as antioxidant, anticancer, eye and liver protective agent, etc. The production of this pigment in a cost effective manner is a challenging task. The present study explored paper mill sludge (PMS), a solid lignocellulosic waste generated in large quantities from pulp and paper mill industry as a substrate for carotenoid pigment production by Planococcus sp. TRC1. PMS was compared in terms of efficacy with sugarcane bagasse, which is a highly explored substrate for valuable product generation via solid state fermentation. The results showed that both the biomasses yielded the highest carotenoid during 48 hours of incubation, 31.6 mg/gm and 42.1 mg/gm for PMS and bagasse respectively. Compositional alterations of both the biomasses showed reduction in lignin, hemicellulose and cellulose content by 41%, 15%, 1% for PMS and 38%, 25% and 6% for sugarcane bagasse after 72 hours of incubation. Structural changes in the biomasses were examined by FT-IR, FESEM, and XRD which further confirmed modification of solid biomasses by bacterial isolate. This study revealed the potential of PMS to act as cheap substrate for carotenoid pigment production by Planococcus sp. TRC1, as it showed a significant production in comparison to sugarcane bagasse which gave only 1.3 fold higher production than PMS. Delignification of PMS by TRC1 during pigment production is another important finding for the reuse of this waste from the paper industry.

Keywords: carotenoid, lignocellulosic, paper mill sludge, Planococcus sp. TRC1, solid state fermentation, sugarcane bagasse

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Authors: Abeer A. Q. Ahmed, Tracey McKay

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Biomass can provide a sustainable source for the production of high valued chemicals. Under the uncertain availability of fossil resources biomass could be the only available source for chemicals in future. Cellulose and hemicellulose can be hydrolyzed into their building blocks (hexsoses and pentoses) which can be converted later to the desired high valued chemicals. A cellulase- and xylanase- producing bacterial strain identified as Paenibacillus illinoisensis CX11 by 16S rRNA gene sequencing and phylogenetic analysis was found to have the ability to saccharify different lignocellulosic materials. Cellulase and xylanase activities were evaluated by 3,5-dinitro-salicylic acid (DNS) method using CMC and xylan as substrates. Results showed that P. illinoisensis CX11 have cellulase (2.63± 0.09 mg/ml) and xylanase (3.25 ± 0.2 mg/ml) activities. The ability of P. illinoisensis CX11 to saccharify lignocellulosic materials was tested using wheat straw (WS), wheat bran (WB), saw dust (SD), and corn stover (CS). DNS method was used to determine the amount of reducing sugars that were released from lignocellulosic materials. P. illinoisensis CX11 showed to have the ability to saccharify lignocellulosic materials and producing total reducing sugars as 2.34 ± 0.12, 2.51 ± 0.37, 1.86 ± 0.16, and 3.29 ± 0.20 mg/l from WS, WB, SD, and CS respectively. According to the author's knowledge, current findings are the first to report P. illinoisensis CX11 as a cellulase and xylanase producing species and that it has the ability to saccharify different lignocellulosic materials. This study presents P. illinoisensis CX11 that can be good source for cellulase and xylanase enzymes which could be introduced into lignocellulose bioconversion processes to produce high valued chemicals.

Keywords: cellulase, high valued chemicals, lignocellulosic materials, Paenibacillus illinoisensis CX11, Xylanase

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Authors: Muhammad Sohail Sajid, Qurat-ul-Ain, Zafar Iqbal, Muhammad Nisar Khan, Asma Kausar, Adil Ejaz

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Rickettsiosis, caused by a Spotted Fever Group Rickettsiae (SFGR), is considered as an emerging infectious disease from public and veterinary perspective. The present study reports distribution of SFGR in the host (buffalo and cattle) and vector (ticks) population determined through gene specific amplification through PCR targeting outer membrane protein (ompA). Tick and blood samples were collected using standard protocols through convenient sampling from district Faisalabad. Ticks were dissected to extract salivary glands (SG). Blood and tick SG pools were subjected to DNA extraction and amplification of ompA using PCR. Overall prevalence of SFGR was reported as 21.5% and 33.6 % from blood and ticks, respectively. Hyalomma anatolicum was more prevalent tick associated with SFGR as compared to Rhipicephalus sp. Higher prevalence of SFGR was reported in cattle (25%) population as compared to that of buffalo (17.07%). On seasonal basis, high SFGR prevalence was recorded during spring season (48.1%, 26.32%, 17.76%) as compared to winter (27.9%, 21.43%, 15.38%) in vector and host (cattle and buffalo respectively) population. Sequencing analysis indicated that rickettsial endo-symbionts were associated with ticks of the study area. These results provided baseline information about the prevalence of SFGR in vector and host population.

Keywords: Rickettsia, livestock, polymerase chain reaction, sequencing, ticks, vectors

Procedia PDF Downloads 258

Authors: Rudzani Manafe, Ezekiel Green

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Brucella, has many different virulence factors that act as a causative agent of brucellosis, depending on the environment and other factors, some factors may play a role more than others during infection and as a result, play a role in becoming a causative agent for pathogenesis. Brucella melitensis and Brucella abortus are considered to be pathogenic to humans. The genetic regularity of nine potential causes of virulence of two Brucella species in Eastern Cape livestock have been examined. A hundred and twenty isolates obtained from Molecular Pathogenesis and Molecular Epidemiology Research Group (MPMERG) were used for this study. All isolates were grown on Brucella agar medium. Nine primer pairs were used for the detection of virB2, virB5, vceC, btpA, btpB, prpA, betB, bpe275, and bspB virulence factors using Polymerase chain reaction (PCR). Approximately 100% was observed for genes BecC and BetB from B. arbotus. While the lowest gene observed was PrpA at 4.6% from B. arbotus. BetB was detected in 34.7%, while virB2 and prpA (0%) were not detected in B. melitensis. The results from this research suggest that most isolates of Brucella have virulence-related genes associated with disease pathogenesis. Finally, our findings showed that Brucella strains in the Eastern Cape Province are extremely virulent as virulence characteristics exist in most strains investigated.

Keywords: putative virulence genes, brucella, polymerase chain reaction, milk

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Authors: Long Wang, Yongjin Feng, Xiaofang Luo

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Tritium permeation through structural materials is a significant issue for fusion demonstration (DEMO) reactor blankets in terms of fuel cycle efficiency and radiological safety. Reduced activation ferritic (RAFM) steel CLF-1 is a prime candidate for the China’s CFETR blanket structural material, facing high permeability of hydrogen isotopes at reactor operational temperature. To confine tritium as much as possible in the reactor, surface modification of the steels including fabrication of tritium permeation barrier (TPB) attracts much attention. As a new alloy system, high entropy alloy (HEA) contains at least five principal elements, each of which ranges from 5 at% to 35 at%. This high mixing effect entitles HEA extraordinary comprehensive performance. So it is attractive to lead HEA into surface alloying for protective use. At present, studies on the hydrogen isotope permeability of HEA coatings is still insufficient and corresponding mechanism isn’t clear. In our study, we prepared three kinds of HEA coatings, including AlCrTaTiZr, (AlCrTaTiZr)N and (AlCrTaTiZr)O. After comprehensive characterization of SEM, XPS, AFM, XRD and TEM, the structure and composition of the HEA coatings were obtained. Deuterium permeation tests were conducted to evaluate the hydrogen isotope permeability of AlCrTaTiZr, (AlCrTaTiZr)N and (AlCrTaTiZr)O HEA coatings. Results proved that the (AlCrTaTiZr)N and (AlCrTaTiZr)O HEA coatings had better hydrogen isotope permeation resistance. Through analyzing and characterizing the hydrogen isotope permeation results of the corroded samples, an internal link between hydrogen isotope permeation behavior and structure of HEA coatings was established. The results provide valuable reference in engineering design of structural and TPB materials for future fusion device.

Keywords: high entropy alloy, hydrogen isotope permeability, tritium permeation barrier, fusion demonstration reactor

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Authors: Anton V. Bourdine, Vladimir A. Burdin, Oleg R. Delmukhametov

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This work presents a fast and simple method for the design of large core silica optical fibers with differential mode delay (DMD) management. Some results are reported concerned with refractive index profile optimization for 42 µm core 16-LP-mode optical fiber for next-generation optical networks. Here special refractive index profile form provides total DMD reducing over all mode staff under desired enhanced mode effective area. Method for the simulation of 'real manufactured' few-mode optical fiber (FMF) core geometry differing from the desired optimized structure by core non-symmetrical ellipticity and refractive index profile deviation including local fluctuations is proposed. Results of the following analysis of optimized FMF with inserted geometry distortions performed by earlier on developed modification of rigorous mixed finite-element method showed strong DMD degradation that requires additional higher-order mode management. In addition, this work also presents a method for design mode division multiplexer channel precision spatial positioning scheme at FMF core end that provides one of the potentiality solutions of described DMD degradation problem concerned with 'distorted' core geometry due to features of optical fiber manufacturing techniques.

Keywords: differential mode delay, few-mode optical fibers, nonlinear Shannon limit, optical fiber non-circularity, ‘real manufactured’ optical fiber core geometry simulation, refractive index profile optimization

Procedia PDF Downloads 146

Authors: Laurence G. Almoguera, Vitaliana U. Malamug, Armando N. Espino, Marvin M. Cinense

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The mangrove pens were modified to produce mud crab (Scylla serrata) and milkfish (Chanos chanos) in a polyculture system. The modification of mangrove pens was done by adding excavations inside the pen. The water quality parameters (dissolved oxygen, pH, salinity, and temperature) were monitored, the recovery and the production rate in each pen were evaluated. The experiment was conducted for a rearing period of 143 days in nine mangrove pens, each having an area of 32 m² with an average net enclosure height of 3 m from the soil surface. The three different pens constructed (existing design - with canal only, with 43% excavation by area, and 54% excavation by area) were designated as T₁, T₂, and T₃, respectively. All experimental units were stocked with 31 pieces of crablets (with 33.3 g average weight) and additional 130 pieces of milkfish fingerlings (with 0.11 g average weight) to the modified mangrove pens. The water quality parameters recorded in the pens were favorable for the growth and recovery of the mud crab and milkfish, except for dissolved oxygen (DO). It was found to be the reason for the total mortality of the stocked milkfish. For mud crab, the highest mean recovery was recorded in T₂ (34.41%), followed by T₃ (26.91%) and the lowest in T1 (21.50%). The production rate followed the same trend as the recovery, where T₂ (74.49 g/m²) obtained the highest, followed by T₃ (55 g/m2) and the lowest was in T₁ (34.87 g/m²). The statistical analysis revealed that the variations of the mud crab recovery were not significant, while in terms of production rate, modified mangrove pens were found to be more effective than the existing design. Due to the total mortality of the cultured milkfish, the current set-up of modified mangrove pens was found to be not suitable for the polyculture system of milkfish and mud crab production.

Keywords: aquasilviculture, milkfish, modified mangrove pen, mud crab, polyculture, production rate

Procedia PDF Downloads 182

Authors: Kamran Dastafkan, Chuan Zhao

Abstract:

Improving surface chemistry is a promising approach in addition to the rational alteration in the catalyst composition to advance water electrolysis. Here, we demonstrate an evident enhancement of oxygen evolution on an iron-nickel vanadate catalyst synthesized by a facile successive ionic adsorption and reaction method. The vanadate-modified catalyst demonstrates a highly efficient oxygen evolution in 1 M KOH by requiring low overpotentials of 274 and 310 mV for delivering large current densities of 100 and 400 mA cm⁻², respectively where vigorous gas bubble evolution occurs. Vanadate modification augments the OER activity from three aspects. (i) Both the electrochemical surface area (47.1 cm²) and intrinsic activity (318 mV to deliver 10 mA cm⁻² per unit ECSA) of the catalytic sites are improved. (ii) The amorphous and roughened nanoparticle-comprised catalyst film exhibits a high surface wettability and a low-gas bubble-adhesion, which is beneficial for the accelerated mass transport and gas bubble dissipation at large current densities. The gas bubble dissipation behavior is studied by operando dynamic specific resistance measurements where a significant change in the variation of the interfacial resistance during the OER is detected for the vanadate-modified catalyst. (iii) The introduced vanadate poly-oxo-anions with high charge density have electronic interplay with Fe and Ni catalytic centers. Raman study reveals the structural evolution of β-NiOOH and γ-FeOOH phases during the OER through the vanadate-active site synergistic interactions. Achievement of a high catalytic turnover of 0.12 s⁻¹ put the developed FeNi vanadate among the best recent catalysts for water oxidation.

Keywords: gas bubble dissipation, iron-nickel vanadate, low-gas bubble-adhesion catalyst, oxygen evolution reaction

Procedia PDF Downloads 120

Authors: Mst. Tuhina-Khatun, Mohamed Hanafi Musa, Mohd Rafii Yosup, Wong Mui Yun, Md. Aktar-Uz-Zaman, Mahbod Sahebi

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Rice is a staple crop of economic importance of most Asian people, and blast is the major constraints for its higher yield. Heritability of plants traits helps plant breeders to make an appropriate selection and to assess the magnitude of genetic improvement through hybridization. Diversity of crop plants is necessary to manage the continuing genetic erosion and address the issues of genetic conservation for successfully meet the future food requirements. Therefore, an experiment was conducted to estimate heritability and to determine the diversity of 27 blast resistant upland rice genotypes based on 18 quantitative traits using randomized complete block design. Heritability value was found to vary from 38 to 93%. The lowest heritability belonged to the character total number of tillers/plant (38%). In contrast, number of filled grains/panicle, and yield/plant (g) was recorded for their highest heritability value viz. 93 and 91% correspondingly. Cluster analysis based on 18 traits grouped 27 rice genotypes into six clusters. Cluster I was the biggest, which comprised 17 genotypes, accounted for about 62.96% of total population. The multivariate analysis suggested that the genotype ‘Chokoto 14’ could be hybridized with ‘IR 5533-55-1-11’ and ‘IR 5533-PP 854-1’ for broadening the gene pool of blast resistant upland rice germplasms for yield and other favorable characters.

Keywords: blast resistant, diversity analysis, heritability, upland rice

Procedia PDF Downloads 362