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As a multi-beneficial amendment, biochar is very useful to be applied for improving soil health and crop productivity. Therefore, this study was carried out to assess the influence of wood biochar and mineral nitrogen (N), phosphorus (P) and potassium (K) fertilisers viz, [(control; 100% NPK (120:90:60 kg ha−1); 75% NPK + 5 tonne biochar; 50% NPK + 10 tonne biochar; 25% NPK + 15 tonne biochar and 20 tonne biochar ha−1)] on wheat yield and soil properties under different management practices [(raised bed (more than 30 cm above the ground) and flat-bed)]. Split plot two factors randomised completed block (RCB) design with three replications were used where management practices were placed to main plot, while treatments were assigned to subplots. Maximum spike length, grain per spike, 1000 grain weight, grain and biological yield were obtained with application of 75% NPK + 5 tonne biochar ha−1 under both raised and flat-bed, which were statistically at par to 50% NPK + 10 tonne biochar ha−1. The grain and biological yield observed at 75% NPK + 5 tonne biochar and 50% NPK + 10 tonne biochar ha−1 were significantly higher than that of 20 tonne biochar ha−1. However, maximum soil organic matter, extractable P and K contents with slight increases in soil pH and EC was observed at 20 tonne biochar ha−1. Moreover, almost all agronomic parameters were significantly better in raised bed compared to flat-bed sowing. Hence, the present study suggested that 75% NPK + 5 tonne biochar ha−1 is suitable for improving wheat yield and soil properties. more...

Screening ethnobotanical plants is a pre-requisite to evaluating their therapeutic potential and can lead to the isolation of new bioactive compounds.To determine the antibacterial and antifungal therapeutic potential of Justicia adhatoda.The research team conducted an antimicrobial activity.The study was conducted in a bioscience lab at International Islamic University, Islamabad, Pakistan.Methanolic, ethanolic, and ethyl acetate crude extracts of Justicia adhatoda were prepared at concentrations of 1000, 500, and 100 µg/ml.The crude extracts were evaluated for in vitro antibacterial activity against Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli and for in vitro antifungal activity against Aspergillus flavus, Aspergillus niger, Candida albicans, and Fusarium oxysporum, indicating different zones of inhibition.The highest antibacterial activity was recorded in Justicia adhatoda-methanolic extract (16.33 ± 0.57 mm) and Justicia adhatoda-ethanolic extract (17 ± 1 mm) against Escherichia coli at 1000 μg/ml. Justicia adhatoda-ethyl acetate extract (13 ± 1 mm) showed a significant result as a zone of inhibition against Staphylococcus aureus at 1000 μg/ml. In the fungal strain culture, the highest antifungal activity was recorded in Justicia adhatoda-methanolic extract (15.66 ± 0.57 mm), Justicia adhatoda-ethanolic extract (14 ± 1 mm), and Justicia adhatoda-ethyl acetate extract (14.33 ± 1.15 mm) against the Aspergillus niger at 1000 μg/ml.The antimicrobial activities may be due to the strong occurrence of active compounds, i.e., saponins, tannins, alkaloids, steroids, phenols, and flavonoids. It has been concluded that Justicia adhatoda extracts are suitable candidates for the development of novel antibacterial compounds. more...

Biochar remediation efficiency could be enhanced through numerous treatments such as acids treatment. Still, there has little work done on H

Soil organic carbon plays considerable roles in binding soil particles together forming aggregates. Carbon (C) incorporated within these aggregates is thought to be microbially processed; thus, investigating changes in microbial activities i.e. dehydrogenase, urease, catalase and phosphatase enzymes may explain, to some extent, the dynamics and probably mechanisms responsible of formation of these aggregates. Since, soil water content (SWC) may take part in stimulating/lessening activities of organic matter decomposers; thus, this study aimed at investigating the effects of rice straw as a source of organic C in combination with variable SWC on bioaccumulation of C within different soil aggregate size fractions (2000-250, 250-53 and 53 μm) and hence formation of these aggregates. To achieve these objectives, a pot experiment was conducted for 90 days, including five water levels i.e. maintaining a water head 1 cm above the soil surface (W1), 100% of the saturation percentage, SP (W2), 80% of SP (W3), 65% of SP (W4) and 50% of SP (W5), beside of two rates of applied rice straw i.e. 0 and 15 g kg more...

The application of plant growth-promoting rhizobacteria (PGPR) could allow growers to reduce the use of synthetic fertilizers and increase the sustainability of crop production. Wheat is the main staple food crop of Pakistan, and few studies have reported on the impact of PGPR on wheat crops. To determine if PGPR can maintain wheat productivity with reduced fertilizer applications, we isolated bacteria from the rhizosphere of wheat grown in sandy loam. We selected 10 strains based on in vitro assays for traits associated with PGPR: ACC deaminase activity, siderophore productivity, P-solubilization, and productivity of indole acetic acid (IAA). Furthermore, the strains were tested in three experiments (using a growth-chamber, pots with an experimental area of 0.05 m2, and a field). Strains that possessed the four traits associated with PGPR increased the shoot length, root length, and fresh and dry weight of plants in the growth chamber study. Similarly, under the pot trial, maximum crop traits were observed under the consortium + half dose, while under field conditions maximum crop parameters were detected in the case of consortium 1 and consortium 2 along with half the recommended dose of fertilizer. This confirms that this consortium could provide growers with a sustainable approach to reduce synthetic fertilizer usage in wheat production. more...

Plant growth promoting rhizobacteria (PGPR) are capable to reduce the use of chemical fertilizers input cost of farmer. Keeping in view the study was designed to investigate and evaluate inoculation effect of indigenous rhizospheric bacteria on growth and yield of wheat (Triticum aestivum L.) under in vitro and in vivo conditions using different treatments. Ten potential strains were selected on the basis of their ACC deaminase activity, siderophore production, P-solubilization and production of indole acetic acid (IAA). Further these strains were tested in three different experiments (growth chamber, pot and field). We found significant increase in crop growth response to the inoculants in comparison with un-inoculated control. In pot and field trial we tested PGPR with recommended dose of inorganic fertilizers. The results of present study revealed that inoculation of bacterial strains with wheat seeds significantly increased plant growth and improved crop yield. Results of present study reveal that these strains could be employed in different combinations and can get higher yield in case of half recommended doses of inorganic fertilizers along with consortium of strains in comparison with sole application of recommended dose of fertilizer and with consortium of strains. These strains were further identified by 16Sr RNA gene sequencing, fatty acid profile and biolog. It can be concluded that inoculated bacteria have more potential and contributes in good crop quality, increased yield when they are applied in combination, thus have potential to minimize use of chemical fertilizers. more...

Summary Background The gold standard treatment for chronic hepatitis C virus (HCV) infection is pegylated interferon (PEG-IFN) in combination with ribavirin. Most patients treated with PEG-IFN achieve a sustained virological response (SVR). However host genetic factors play a vital role in the spontaneous and treatment-induced clearance of HCV infection from these infected patients. In the current study, polymorphisms of IL28B (rs8099917 and rs12979860) were analyzed and their association with the virological response to PEG-IFN alpha treatment was determined. Methods One hundred and fifty HCV genotype 3 patients were assessed to study the correlation of IL28B with a therapeutic regimen of PEG-IFN alpha plus ribavirin. Twenty patients were excluded due to a refusal to participate in the study and 25 patients failed to meet the inclusion criteria. Of the 105 patients recruited, 49 (46.7%) were male and 56 (53.3%) were female. In order to determine single nucleotide polymorphisms of rs8099917 and rs12979860, the sample was amplified by PCR and then IL28B typing was carried out by restriction fragment length polymorphism (RFLP) followed by standard sequencing. Results We found three types of genotype in rs8099917 of IL28B : wild-type TT in 60.0% of patients, heterozygous GT minor genotype in 36.2%, and GG in 3.8%. The frequency of the CC genotype of rs12979860 was 54.3%, CT was 37.1%, and TT was 8.6%. Overall, SVR was achieved in 68.6% of patients. A higher SVR was achieved for patients with the favorable genotype CC of rs12979860, with 84.2% as compared to 56.4% and 22.2% for minor genotype CT and TT, respectively ( p =0.0001). We did not find a significant association for SVR to antiviral treatment in patients with genotype TT (rs8099917) (71.9%, p =0.36). The rapid virological response (RVR) rate was significantly higher in patients with major genotype TT (88.9%, p =0.04). These results show that IL28B polymorphism is highly associated with SVR to therapy in the Pakistani population infected with HCV genotype 3. Conclusions HCV-infected patients carrying homozygous C/C have a higher chance of SVR. In addition, patients who carry T/T (rs8099917) have a higher chance of RVR. more...

Channel catfish has practically proven to be one of the species with virtually remarkable performance in fresh water pond culture. Due to better growth rate, good adaptation and acceptability towards artificial feed channel catfish was introduced to Pakistan. A study was conducted to see the role of dietary enzyme Laccasse supplementation in a diet (35% CP) on growth of fingerlings of channel catfish. For this purpose a six week nutrition study was conducted in Aquaria of Aquaculture and Fisheries program (NARC). Fish was fed a locally prepared (35% CP) diet incorporated with three different concentration of Laccasse enzyme i.e., at the rate of 1, 2 and 3 mL/kg. The dietary pellets were prepared and air dried and fed to the fish at the rate of three percent of wet body weight twice daily. Prior to the start of study fish were acclimatized for a period of two weeks on experimental diets. Weights of the fish were recorded at the start and end of trial fortnightly in between. At the end result was deduced through the data of weight gain. The results revealed that Laccasse supplemented at a concentration of 2 mL/kg has higher growth, however it is insignificant (p>0.05) with a concentration of 3 mL/kg. So addition of laccasse in higher concentration or lower concentrations serve no purpose. We concluded that further detailed studies are added to evaluate the role of laccasse enzyme in feed utilization and growth enhancement of channel catfish juveniles. more...

The major conflict in the cotton-wheat-cropping system is the prolonged harvesting of cotton resulting in late planting of wheat causing decrease in yield for every day's delay in planting after 15 November. This clearly underlines the need for a solution of the above conflict. The now till technique is now being increasingly demonstrated as a way out. The major objective of the present study was to work out the profitability of planting wheat in standing cotton. The experiment was conducted at Adaptive Research Farm Rahim Yar Khan, during 2011- 12, to evaluate the technological feasibility and economic validity of relay cropping system by the different wheat seeding rates. The objective of this study was to check the different seed rates of wheat in standing cotton as relay crop. The experiment was laid out in Randomized Complete Block Design (RCBD) with three replications. Wheat variety Sehar-2006 was used with seed rates such as 125,150,175 and 200 kg/ha. The previous crop was cotton in this field, which was sown on 22 nd May 2011. Wheat was sown by surface seeding in standing cotton with different seeding rates. Seed rate of 200 kg ha -1 in relaying wheat by surface seeding produced higher grain yield than seeding rate of 150 kg/ha. Yield, yield components and quality traits of cotton were not affected significantly by any of the relay cropping systems. Substantially higher net field benefit was obtained from relay cropping system with seeding rate of 200 kg/ha as compared to wheat followed after cotton. more...

LAH 2 is a type of autosomal recessive hypotrichosis that affect hairs, eyebrows, scalp and eyelashes. Mutations in Lipase H gene result in LAH 2. Changes that result from mutation on physiochemical properties, post-translational modifications, functional sites, secondary structure and tertiary structure lipase H gene (LIPH) at molecular level were analyzed in the current study. Results indicate that the 3rd motif of LIPH deletes as a result of mutation. The number of alpha helices and beta sheets become varied in normal and abnormal protein. Tertiary structure of LIPH was predicted through homology modeling. Mutations were then inserted to reveal the difference between normal and abnormal structure. Ligands to target LIPH are also retrieved. ASP178, ASP207 and HIS248 constitute the active site of LIPH. Missense mutations in LIPH also brought drastic changes at molecular level that led to imbalanced function. All these changes can be studied through bioinformatics without going for expensive laborious and time consuming experimental techniques. Keywords : LAH2, LIPH, tertiary structure, secondary structure, physiochemical properties, ligands, active site African Journal of Biotechnology Vol. 12(16), pp. 2051-2057 more...

Bioremediation methods are a promising way of dealing with soil and subsoil contamination by organic substances. This biodegradation process is supported by micro-organisms which use the organic carbon from the pollutants as energy source and cells building blocks. There are several advantages of the implementation of such methods but mainly they have to do with the lack of interference with the ecology of the ecosystem. This study presents the use of technique in numerous ways such as olive oil industry and dairy industry. Although the use of bioremediation technique is not innovative in food industry and microbiology. The use of herbicides, pesticides and contaminated chemicals are producing pollutant compounds in ecosystem which is effecting the environment. Bioremediation method is very constructive method to converted contaminated compounds into non contaminated compounds. more...

Carbon dioxide (CO2) a major Green House Gas (GHG) in the atmosphere, is believed to be largely responsible for global climate change through industrial emissions. The level of CO2 concentration has exponentially increased from about 280 ppm at the start of the industrial revolution to about 380 ppm to date. Although Kyoto protocol has bound industrialized nations to reduce green house gas emissions by 5.2% below 1990 levels around year 2008-2012, but violation continues. The cement industry is one of the major emitter of green house gases, particularly CO2 due to its energy intensive production process. It is estimated that approximately 1 tone of CO2 is released during the manufacturing of each tone of Portland cement. Most of CO2 emissions originate from burning fossil fuels and de-carbonization of limestone in a cement plant. During past several decades, the use of by-product materials in concrete, either as components of blended cements or as admixtures, has increased significantly. In this study, another alternate Supplementary Cementing Material (SCM), Laterite has been used with the objectives: to evaluate the performance of cement containing different percentages of laterite (5, 10, 15, 20, 25, and 30 %); to identify the optimum replacement percentage; and to investigate the effects of different concentrations of laterite on various properties of cement. For that purpose, laterite was tested: before blending (for elemental and mineralogical composition by using XRF, SEM and XRD): after blending (Elemental analysis using XRF, fineness test by using Blaine's air permeability test and for particle size % on 45, 90 and 200 µ sieve, respectively); and after hydration (for mineralogical analysis using SEM). Furthermore, physical tests of manufactured cement, i.e., water consistency, setting time, Le-Chatlier-expansion and compressive strength were also evaluated and compared with limestone and fly-ash cement blends. The results show that with the replacement level of up to 15%, the quality of cement is not disturbed. In addition, the requirement of intake of energy has also decreased (~30%). Current findings indicate that by using Laterite, as SCM, cement production can be increased without consuming more energy and hence reduce GHG emissions. more...

Solanum nigrum is used in hepatic disorders in folk medicines. The present study was aimed to evaluate the efficacy of S. nigrum on the liver functions in CCl4 induced injuries. Enzymatic activities that are .AST, ALT and ALP, microscopic appearance of liver was used as parameter and hepatocurative studies were performed. In case of hepatocurative study that is post treatment of rats with aqueous extracts of plant (500mg/ orally, two doses with 24 h interval) prevented (p more...

Background: Hepatitis B virus causing acute and chronic hepatocellular carcinoma relics a serious health issue affecting more than 350 million people worldwide. Geographically, nine genotypes of HBV have been identified so far. Four open reading frames named (ORF P, S, F and X) renders it to specifically targets hepatocyte cells. Additionally, reverse transcription process present in the life cycle of HBV caused four order higher mutation rates as compared to adenovirus. The structural and functional differences between HBV genotypes are the mainstay to severity, complications, treatment and possibly vaccination against the virus. Hepatitis B genotyping is important for assessing its clinical implications and geographical distribution, but the sub-genotypes have been found useful for determination of specific genomic markers related to hepatocarcinogenesis and medical therapies. In Pakistan, there is no reported data available on molecular evolutionary analysis of HBV. A study was, therefore, much needed to evaluate the spectra of dominant strains prevalent here. Objectives: This study was aimed to figure out the prevalence of HBV genotypes among population in Pakistan. In this research, we focused to find out the new strains and sub genotypes of HBV. Pakistan is one of the HBV endemic countries but there is no data on subgenotypes and their recombination or the phylogenetic relatedness of the virus endemic in the country. The present study was carried out in this perspective. This study will help future researcher to study some other aspects of HBV related strains in Pakistan and also about its medical therapies. Place and duration of study: The present study was carried out at Polymerase Chain Reaction (PCR) lab, Nuclear Medicine, Oncology and Radiotherapy Institute [NORI], Islamabad, and the samples were collected between September 2012 to February 2014. Study design: A total of 450 Hepatitis B surface antigen HBsAg and HBV DNA positive samples were collected in the first step during the period of September 2012 to February 2014 and sent to Nuclear Medicine Oncology and Radiotherapy Institute [NORI], for further analysis. All the samples were genotyped by type specific nested PCR primer pair method for 8 HBV genotypes from A through H. The patients were randomly selected irrespective of their age and gender and a written consent (parental consent in case of less than 18 years of age) was obtained. The study was approved by ethical review committee. In our research, we have used the type specific primer technique to find out the dominant strain in Pakistani populations and furthermore its phylogenetic analysis with reference sequences retrieved from NCBI databases. Results: Our results showed a direct relationship between viral load and identified genotypes and pinpointed that genotype D is the most pre-dominant genotype and prevailing in high proportions among all genotypes in Pakistani population. Mix HBV genotype infections of genotype A with B & C, D with B and C constitute about 17 percent of all the samples. Subgenotypes of different HBV strains have been identified on the basis of differences in the complete nucleotide sequences. Positive PCR results were repeated twice for confirmation. Furthermore, phylogenetic analysis revealed a homology between our reported sequences and reference sequences. The phylogenetic method showed that genotypes/sub-genotypes varies in the geographical areas and correlate strongly with ethnicity. Conclusion: Genotype D was identified and come out to be the most dominant genotype in Pakistani community showing sub-genotypes of D1 & D3 in our study. Genotype A and D are present as co-infection with each other and contributed as the second prevailing genotypic group. Additionally, phylogenetic analysis revealed that genotypes varies in the geographical areas and correlate strongly with reference sequences from NCBI. more...

A genetic map of Spinach (Spinacia oleracea) was constructed in a classical back cross population using 101 AFLP and 9 microsatellite markers. The map was divided into seven linkage groups with a total length of 585 cM and an average distance between the markers of 5.18 cM. The linkage map was constructed with LOD 3.5, but was quite stable with seven linkage groups remaining until LOD 7.0. Gender segregated 1 male to 1 female in the mapping population and was mapped to a small area of one linkage group with a distance of 1.9 cM to a microsatellite marker termed SO4. This small chromosomal region co-segregating with sex determination in the species is in contrast to previous reports on a heterologous XY chromosome system in spinach. Microsatellite markers used as anchors in the map construction were isolated from sequences of known nuclear encoded genes in spinach. This enabled simultaneous positioning on the map of these genes: Rubisco activase (Rca), Photosytem 1 subunit V (PsaG), Protein Kinase (Pk), Nitrate reductase (Nir), ferrodoxin:thioredoxin reductase (Ftr), Ribosomal protein L1 (Rps22), Choline monooxygenase (Cmo), Pseudogene for BZIP protein (Bzip), Glycerol-3-phosphate acyltransferase (Act1) and stromal ascorbate peroxidase, thylakoid-bound ascorbate peroxidase (Apx2). Spinach has a small genome, which makes it suitable for basic genomic studies and many physiologically important genes have been cloned from the species. The present map anchored with user friendly microsatellite markers will be useful for future studies of physiology and genetics of the species as well as studies of the nature of gender determination. more...

The United Arab Emirates (UAE) has a unique experience in greening the desert. Huge efforts have been done to create green spaces across the country including afforestation and urban landscaping. Most of the landscaping designs were inspired from western landscapes comprises mostly of exotic species, which do not reconcile with the environmental conditions of the UAE. The intensive use of exotic species in artificial vegetation, high water requirements for the UAE greenery, coupled with water shortages and salinity, are causing major environmental and ecological challenges. Fortunately, the UAE hosts a unique flora and fauna that show remarkable adjustment to harsh weather conditions. Here we emphasize the use of native plants due to their potential to develop landscapes in saline and water shortage conditions, leading to reduced water usage for landscaping. The preservation of native biodiversity of the UAE will be an added benefit. In this article the main aspects of the UAE landscaping efforts, with the associated water resources using native plants in landscaping, problems in promoting native plants in landscaping and possible solutions are discussed. more...

The genome sequencing accomplishes complete genetic blue prints for hundreds of organisms, including humans. In the current era, we are trying to focus on analyzing, controlling and modifying functions of proteins encoded by these genomes. This task is attained by protein three dimensional structures. Three dimensional (3 D) structure is very useful for understanding biological functions. Gap junction beta 2 (GJB2), human gene encoding for gap junction beta 2 protein is involved in various hearing disorders in Pakistani families. After the first report of GJB2 involvement in Pakistani families, it was necessary to further study this protein. Therefore, a 3D structure of GJB2 was developed using comparative modeling approach. For modeling, a template was selected by blastp at NCBI and the best template selected was 2ZW3. By comparing the template-target sequence, a model was created using MODELLER, a program for homology modeling. The accuracy of the predicted structure was checked using Ramachandran plot which showed that the residue falling in the favored region was 92.4%. The predicted GJB2 model can be used to understand the defects that lead to deafness and eventually in drug designing. Domains and different properties of GJB2 were analyzed by applying online servers. Most frequent mutations of GJB2 were discussed by differentiating between damaging and benignity. Key words : GJB2, 3D structure, 2ZW3, DFNB1, MODELLER. more...

Background Head and neck cancer (HNC) belongs to a group of heterogeneous disease with distinct patterns of behavior and presentation. TNFRSF10B, a tumor suppressor gene mapped on chromosome 8. Mutation in candidate gene is responsible for the loss of chromosome p arm which is frequently observed in head and neck tumors. TNFRSF10B inhibits tumor formation through apoptosis but deregulation encourages metastasis, migration and invasion of tumor cell tissues. Results Structural modeling was performed by employing MODELLER (9v10). A suitable template [2ZB9] was retrieved from protein databank with query coverage and sequence identity of 84% and 30% respectively. Predicted Model evaluation form Rampage revealed 93.2% residues in favoured region, 5.7% in allowed region while only 1 residue is in outlier region. ERRAT and ProSA demonstrated 51.85% overall quality with a −1.08 Z-score of predicted model. Molecular Evolutionary Genetics Analysis (MEGA 5) tool was executed to infer an evolutionary history of TNFRSF10B candidate gene. Orthologs and paralogs [TNFRSF10A & TNFRSF10D] protein sequences of TNFRSF10B gene were retrieved for developed ancestral relationship. Topology of tree presenting TNFRSF10A gene considered as outgroup. Human and gorilla shared more than 90% similarities with conserved amino acid sequence. Virtual screening approach was appliedfor identification of novel inhibitors. Library (Mcule) was screened for novel inhibitors and utilized the scrutinized lead compounds for protein ligand docking. Screened lead compounds were further investigated for molecular docking studies. STRING server was employed to explore protein-protein interactions of TNFRSF10B target protein. TNFSF10 protein showed highest 0.999 confidence score and selected protein-protein docking by utilizing GRAMM-X server. In-silico docking results revealed I-58, S-90 and A-62 as most active interacting residues of TNFRSF10B receptor protein with R-130, S-156 and R-130 of TNFSF10B ligand protein. Conclusion Current research may provide a backbone for understanding structural and functional insights of TNFRSF10B protein. The designed novel inhibitors and predicted interactions might serve to inhibit the disease. Effective in-vitro potent ligands are required which will be helpful in future to design a drug to against Head and neck cancer disease. There is an urgent need for affective drug designing of head and neck cancer and computational tools for examining candidate genes more efficiently and accurately are required. more...