Isolation, characterisation and expression of Ty1-copia retrotransposons in Agave tequilana

Agave tequilana is native to Mexico and famous for its use in the production of alcoholic beverage tequila. Due to the growing demands of tequila it has been intensively cultivated through asexual means resulting in a narrow genetic variability. The crop is extremely prone to insects and diseases and a breeding programme for selection and conservation of the crop is required. However poorly understood classification of agave and limited availability of molecular data is a big hurdle in establishing a useful breeding programme. Retrotransposons are mobile genetic elements that can replicate through a copy and paste mechanism occupying large proportions of genomes in short periods of time. They can play a vital role in the organisation and evolution of plant genomes and retrotransposon based molecular markers can be used as powerful molecular tools. Retrotransposons can play a key role in understanding Agave tequilana genetics as well as its relationship with other agave species and cultivars. In the work described here Ty1-copia retrotransposon have been isolated and characterised, retrotransposon based molecular markers have been used to evaluate the asexual genetic diversity in different vegitatively propagated mother and daughter plants. The phylogenetic relationship of these sequences revealed that Ty1-copia retrotransposons are heterogeneous in nature and they might have been actively replicating in recent past. The copy number of Ty1- copia retreotransposon was also evaluated and it was found that a large proportion of agave genome is occupied by these elements. Ty1-copia retrotransposons were also found to be polymorphic in agave tissue culture lines suggesting that they might be activated under the effect of stressed conditions. The findings of this study will help in understanding the genetics of Agave tequilana, and will provide a basis for further research on retrotransposon mediated asexual genetic variability in agave and other clonally propagated plants in general. It will also help us understand the activity of retrotransposons in the genome of agave in unusual environmental conditions

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice (Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice ( Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection

Role of Potash Alum in Hepatitis C virus Transmission at Barber's Shop

Hepatitis C virus (HCV) is the main cause of severe liver disease, including hepatocellular carcinoma, cirrhosis and end stage liver disease. In Pakistan most of HCV positive patients have history of facial/armpit shaving from barbers. 79% of barbers are rubbing Potash Alum stone on facial shaving cuts. Dark blood spots are analyzed on Potash Alum stones being used at different barber shops. The aim of the study was to check the viability of hepatitis C virus on potash alum stone being used at barber shops. Blood samples from HCV positive patients were taken and treated with 0.1, 0.2, 0.3, 0.4 and 0.5 molar concentrations of Potash Alum for different periods of time. Blood was centrifuged to isolate the serum; HCV RNA was extracted from serum and subjected to first strand synthesis and PCR. PCR fragments were confirmed by sequencing. PCR amplification was observed in all the samples, treated with different concentrations of Potash Alum, indicated that the virus remains alive on Potash Alum stone for a long period of time. Potash Alum being used by barbers on facial shaving cuts has definite role in HCV transmission in Pakistani population. Therefore use of Potash Alum stone should be banned on facial shaving cuts at barber shops

Ty1-Copia retrotranposons are heterogeneous, extremely high copy number and are major players in the geonome organisation and evolution of Agave tequilana

Agave tequilana is native to Mexico and is famous for its use in the production of the alcoholic beverage tequila. The crop is extremely prone to insects and diseases, and a breeding programme for selection and conservation is required. Moreover, poorly understood classification of agave varieties and the limited availability of molecular data represent a big hurdle in its genetic research and improvement. Retrotransposons are mobile genetic elements that can occupy large proportions of plant genomes and play a vital role in their organisation and evolution. They can be used as genetic tools to address the challenges faced by A. tequilana. Ty1- Copia retrotransposons were isolated and characterised, and their copy number in the genome of A. tequilana was estimated. The phylogenetic analysis of isolated reverse transcriptase sequences showed that A. tequilana contains a large population of Ty1- Copia retrotransposons. They occur in the form of groups of closely related heterogeneous elements. The copy number estimates revealed that they are extremely abundant in A. tequilana. The characterisation of the Ty1-Copia population suggests that they are a major component of the agave genome and might have played a vital role in its genome organisation and evolution

PS-CARA Context-Aware Resource Allocation Scheme for Mobile Public Safety Networks

The fifth-generation (5G) communications systems are expecting to support users with diverse quality-of-service (QoS) requirements. Beside these requirements, the task with utmost importance is to support the emergency communication services during natural or man-made disasters. Most of the conventional base stations are not properly functional during a disaster situation, so deployment of emergency base stations such as mobile personal cell (mPC) is crucial. An mPC having moving capability can move in the disaster area to provide emergency communication services. However, mPC deployment causes severe co-channel interference to the users in its vicinity. The problem in the existing resource allocation schemes is its support for static environment, that does not fit well for mPC. So, a resource allocation scheme for mPC users is desired that can dynamically allocate resources based on users’ location and its connection establishment priority. In this paper, we propose a public safety users priority-based context-aware resource allocation (PS-CARA) scheme for users sum-rate maximization in disaster environment. Simulations results demonstrate that the proposed PS-CARA scheme can increase the user average and edge rate around 10.3% and 32.8% , respectively because of context information availability and by prioritizing the public safety users. The simulation results ensure that call blocking probability is also reduced considerably under the PS-CARA scheme

Ty1-Copia retrotranposons are heterogeneous, extremely high copy number and are major players in the geonome organisation and evolution of Agave tequilana

Agave tequilana is native to Mexico and is famous for its use in the production of the alcoholic beverage tequila. The crop is extremely prone to insects and diseases, and a breeding programme for selection and conservation is required. Moreover, poorly understood classification of agave varieties and the limited availability of molecular data represent a big hurdle in its genetic research and improvement. Retrotransposons are mobile genetic elements that can occupy large proportions of plant genomes and play a vital role in their organisation and evolution. They can be used as genetic tools to address the challenges faced by A. tequilana. Ty1- Copia retrotransposons were isolated and characterised, and their copy number in the genome of A. tequilana was estimated. The phylogenetic analysis of isolated reverse transcriptase sequences showed that A. tequilana contains a large population of Ty1- Copia retrotransposons. They occur in the form of groups of closely related heterogeneous elements. The copy number estimates revealed that they are extremely abundant in A. tequilana. The characterisation of the Ty1-Copia population suggests that they are a major component of the agave genome and might have played a vital role in its genome organisation and evolution

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice ( Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice (Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the *Corresponding author short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection