Evaluation of the Toxic Potential of Graphene Copper Nanocomposite (GCNC) in the Third Instar Larvae of Transgenic Drosophila melanogaster (hsp70-lacZ)Bg9

Graphene, a two-dimensional carbon sheet with single-atom thickness, have attracted the scientific world for its potential applications in various field including the biomedical areas. In the present study the graphene copper nanocomposite (GCNC) was synthesized, characterized and evaluated for its toxic potential on third instar larvae of transgenic Drosophila melanogaster (hsp70-lacZ)Bg⁹. The synthesized GCNC was analyzed by X-ray diffraction (XRD), scanning/transmission electron microscopy (SEM/TEM), atomic force microscopy (AFM), and fourier transform infrared spectroscopy (FTIR). The GCNC in 0.1% DMSO was sonicated for 10 min and the final concentration of 0.033, 0.099, 0.199 and 3.996 µg/µl of diet were established. The third instar larvae were allowed to feed on it separately for 24 and 48 hrs. The hsp70 expression was measured by O-nitrophenyl-β-D-galactopyranoside assay, tissue damage by trypan blue exclusion test and β-galactosidase activity was monitored by in situ histochemical β-galactosidase staining. Oxidative stress was monitored by performing lipid peroxidation assay and total protein estimation. Ethidium bromide/acridine orange staining was performed on midgut cells for apoptotic index and the comet assay was performed for the DNA damage. The results of the present study showed that the exposure of 0.199 and 3.996 µg/µl of GCNC were toxic for 24 hr of exposure and for 48 hr of exposure: 0.099, 0.199 and 3.996 µg/µl of GCNC was toxic. The dose of 0.033 µg/µl of GCNC showed no toxic effects on its exposure to the third instar larvae for 24 hr as well as 48 hrs. This dose can be considered as No Observed Adverse Effect Level (NOAEL).     

Solvent Effect on the Photolysis of Riboflavin

The kinetics of photolysis of riboflavin (RF) in water (pH 7.0) and in organic solvents (acetonitrile, methanol, ethanol, 1-propanol, 1-butanol, ethyl acetate) has been studied using a multicomponent spectrometric method for the assay of RF and its major photoproducts, formylmethylflavin and lumichrome. The apparent first-order rate constants (k_obs) for the reaction range from 3.19 (ethyl acetate) to 4.61 × 10⁻³ min⁻¹ (water). The values of k_obs have been found to be a linear function of solvent dielectric constant implying the participation of a dipolar intermediate along the reaction pathway. The degradation of this intermediate is promoted by the polarity of the medium. This indicates a greater stabilization of the excited-triplet states of RF with an increase in solvent polarity to facilitate its reduction. The rate constants for the reaction show a linear relation with the solvent acceptor number indicating the degree of solute–solvent interaction in different solvents. It would depend on the electron-donating capacity of RF molecule in organic solvents. The values of k_obs are inversely proportional to the viscosity of the medium as a result of diffusion-controlled processes.KEY WORDS: dielectric constant, kinetics, photolysis, riboflavin, solvent effect, viscosity     

Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis

Background

Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing.

Principal Findings

Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to cultivated safflower and formed a distinct cluster. The cluster analysis also distinguished diploid and tetraploid wild species of safflower.

Conclusion

Next generation sequencing of safflower genome generated a large set of microsatellite markers. The novel markers developed in this study will add to the existing repertoire of markers and can be used for diversity analysis, synteny studies, construction of linkage maps and marker-assisted selection.     

Warfarin pharmacogenetics: polymorphisms of the CYP2C9, CYP4F2, and VKORC1 loci in a genetically admixed Omani population

This is the first study to evaluate the spectrum and prevalence of dose-predictive genetic polymorphisms of the CYP2C9, CYP4F2 and VKORC1 loci together, in a geographically defined, ethnically admixed healthy adult Omani population sharing common lifestyle/environmental factors. Since the present-day Omani population is the result of an admixture of Caucasian, African and Asian ancestries, we compared the pharmacogenetic profile of these three loci in this population. Interestingly, the Omani pharmacogenetic profile, in terms of allele and genotype distribution, has values that are intermediate between Caucasians and African Americans, the African admixture further substantiated by the presence of the CYP2C9*8 allele. However, limitations and usefulness of such comparisons warrant caution, as the data from pharmacogenetic literature do not always represent bona fide population categories. Furthermore, definition of study population based on microgeographical scale would be more appropriate in pharmacogenetic research rather than the flawed racial, ethnic, or social categorizations since pharmacogenetic variation is clinal, and genetic influences will be further altered by lifestyle and environmental factors.     

Fungi as a source of marker compounds for the control of illicit use of drugs: mesterolone as a case study

Introduction

Anabolic steroids are frequently misused for performance enhancement during sports competitions. One of the major bottlenecks in the confident analysis of steroids and their metabolites is the non-availability/cost of standard reference compounds.

Objective

The study objective was to identify the common metabolites of prohibited anabolic steroids that are produced in both fungi and human and thus can be synthesized in bulk using fungal cultures. Mesterolone is used as a case study.

Methods

The study was conducted in three steps; we first studied the fungal transformation of mesterolone. In the second step, these metabolites were used as references to detect in human urine after the oral use of mesterolone using LC-ESI-QqQ-MS/MS. In the third step, 12 fungal cultures were screened to evaluate their potential to produce reference markers.

Results

This led to the detection of two metabolites, 6α-hydroxymesterolone (M1) and 7α-hydroxymesterolone (M2) that were found to be common in both, fungal cultures and human urine samples. Moreover, Rhizopus stolonifer and Beauveria bassiana can be considered as good candidates to produce M1 and M2 metabolites, respectively.

Conclusion

This approach can be employed for the synthesis of marker compounds of other prohibited anabolic steroids thus can be detected efficiently during national and international sports competitions.

     

Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data

MOTIVATION: Microarray data are used in a range of application areas in biology, although often it contains considerable numbers of missing values. These missing values can significantly affect subsequent statistical analysis and machine learning algorithms so there is a strong motivation to estimate these values as accurately as possible before using these algorithms. While many imputation algorithms have been proposed, more robust techniques need to be developed so that further analysis of biological data can be accurately undertaken. In this paper, an innovative missing value imputation algorithm called collateral missing value estimation (CMVE) is presented which uses multiple covariance-based imputation matrices for the final prediction of missing values. The matrices are computed and optimized using least square regression and linear programming methods. RESULTS: The new CMVE algorithm has been compared with existing estimation techniques including Bayesian principal component analysis imputation (BPCA), least square impute (LSImpute) and K-nearest neighbour (KNN). All these methods were rigorously tested to estimate missing values in three separate non-time series (ovarian cancer based) and one time series (yeast sporulation) dataset. Each method was quantitatively analyzed using the normalized root mean square (NRMS) error measure, covering a wide range of randomly introduced missing value probabilities from 0.01 to 0.2. Experiments were also undertaken on the yeast dataset, which comprised 1.7% actual missing values, to test the hypothesis that CMVE performed better not only for randomly occurring but also for a real distribution of missing values. The results confirmed that CMVE consistently demonstrated superior and robust estimation capability of missing values compared with other methods for both series types of data, for the same order of computational complexity. A concise theoretical framework has also been formulated to validate the improved performance of the CMVE algorithm. AVAILABILITY: The CMVE software is available upon request from the authors.     

Microarray: gateway to unravel the mystery of abiotic stresses in plants

Environmental factors, such as drought, salinity, extreme temperature, ozone poisoning, metal toxicity etc., significantly affect crops. To study these factors and to design a possible remedy, biological experimental data concerning these crops requires the quantification of gene expression and comparative analyses at high throughput level. Development of microarrays is the platform to study the differential expression profiling of the targeted genes. This technology can be applied to gene expression studies, ranging from individual genes to whole genome level. It is now possible to perform the quantification of the differential expression of genes on a glass slide in a single experiment. This review documents recently published reports on the use of microarrays for the identification of genes in different plant species playing their role in different cellular networks under abiotic stresses. The regulation pattern of differentially-expressed genes, individually or in group form, may help us to study different pathways and functions at the cellular and molecular level. These studies can provide us with a lot of useful information to unravel the mystery of abiotic stresses in important crop plants.     

Macrophomina phaseolina alters the biochemical pathway in Vigna radiata chastened by Zn2+ and FYM to improve plant growth

Mung bean [Vigna radiata (L.) Wilczek] is an important cash pulse crop extensively cultivated in the arid region of Pakistan, which encounters intimidating charcoal rot disease caused by Macrophomina phaseolina (Tassi) Goid. The current research was conducted to check the potential of Zn (1.25, 2.44 and 5?mg?kg^?1) and FYM [farmyard manure (1% and 2%)] in mono-, bi- and trilateral interaction in managing disease and improving yield. Suppression of plant immunity by M. phaseolina was indicated by the change in activities of antioxidant enzymes (CAT and SOD) and cell wall strengthening enzymes (POX and PAL) that revealed inability of the protein receptor to identify the pathogen elicitor. FYM improved soil physicochemical properties and beneficial microbes activity, which released antimicrobial protein- and plant defense-stimulating protein and in response to ROS (reactive oxygen species) signaling molecules plant susceptibility was reduced. However, Zn as a co-factor chastened the ROS in stressed cells by upregulation of antioxidant enzymes in favor of the plant. The complex interaction of FYM and Zn potentially hijacked the further multiplication of pathogen. Finally, soil amendment improved biological attributes and grain yield to profitable farming in terms of harvest index percentage and benefit–cost ratio.     

Influence of salinity and <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> as the stress factors on morpho-physiological and yield attributes in onion

Occurrence of salt stress with the soil borne fungus Fusarium oxysporum f. sp. cepa (FOC) are potential threat to the crop yield. This investigation reports effect of the concurrent stresses (salinity and FOC) on morpho-physiological and yield attributes in onion. In vitro growth tests revealed proliferation of FOC biomass at different levels of salinity (2–8 dS m^?1). A greenhouse pot experiment with the proposed levels of salinity (2.5, 3.5 and 4.5 dS m^?1) in combination with FOC inoculation showed more drastic effect of combined stress on disease severity, plant growth and bulb as compared to the individual stress. In general, osmotic potential, total chlorophyll content, membrane stability index and total protein content of the leaf were decreased, while total phenolics were increased due to the given stress/s. Total sugar content decreased due to effect of the  individual stress of FOC, while it increased under the individual stress of salinity and in combination with FOC. FOC infection did not change activity of polyphenol oxidase (PPO), while it improved peroxidase (POX) and phenylalanine ammonia lyase (PAL) and decreased catalase (CAT) activity. Activities of POX and PPO increased, however PAL and CAT declined under individual as well as simultaneous stress of salinity ?and ?FOC. The research work concluded that FOC will be a more severe disease threat for onion cultivation in saline soils.