Shahid Mahboob

Comparative Transcriptome Analysis Reveals the Genetic Basis of Skin Color Variation in Common Carp

Background The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied. Methodology/Principal Findings In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains. Conclusions In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Tissue Metal Distribution and Risk Assessment for Important Fish Species from Saudi Arabia

Abstract The concentrations of nine heavy metals (Cr, Cd, Pb, Ni, Cu, Zn, Mn, As and Fe) in the muscle tissue of four fish species (Oreochromis niloticus, Clarias gariepinus, Poecilia latipinna and Aphanius dispardispar) collected from Wadi Hanifah were detected in two different seasons. The concentrations of the studied heavy metals, except for Cd, Pb, Ni and Cu in A. d. dispar and P. latipinna, were found to be below the safe limits recommended by various authorities and thus provide an indication of the extent of pollution of these metals. The present study also demonstrates that Zn and Cr were the most and least accumulated metals, respectively, in the studied fish muscle tissues. From the standpoint of human health, this study suggests that there is a possible health risk to consumers due to the current consumption rate of A. d. dispar and P. latipinna in Saudi Arabia.

Electrochemical sensing platform based on molecularly imprinted polymer decorated N,S co-doped activated graphene for ultrasensitive and selective determination of cyclophosphamide

A novel electrochemical sensor has been facilely fabricated by applying composite elements consisting of nitrogen and sulfur co-doped activated graphene (N,S-AGR) and molecularly imprinted polymer (MIP). N,S-AGR was synthesized by one-pot pyrogenation of a mixture of thiourea, KOH and graphene oxide, which was introduced to improve electron transfer capability and surface area of the electrode, while the electro-polymerized MIP layer afforded simultaneous recognition and quantification of cyclophosphamide (CPA) by utilizing Fe(CN)63-/4- as probe to indicate electrical signals. Under the optimal conditions, a calibration curve of current shift versus concentration of CPA was got in the range of 8×10-12-8×10-7molL-1, and the developed sensor gave a remarkably low detection limit (LOD) of 3.4×10-12mol L-1 (S/N=3). Moreover, the as-prepared sensor illustrated other good merits like stability and selectivity, and played a role in real-time therapeutic drug monitoring after CPA administration in rabbit.

A novel sensitive and selective electrochemical sensor based on molecularly imprinted polymer on a nanoporous gold leaf modified electrode for warfarin sodium determination

Warfarin sodium (WFS) is a widely used oral anticoagulant drug but has a narrow therapeutic window. Since traditional detection methods applied for therapeutic drug monitoring suffer some shortcomings, including difficulty in obtaining timely reports, high costs and tedious operation, it is necessary to develop a detection system for the rapid monitoring of WFS in biological samples. Here we report a novel electrochemical sensor, which was facilely fabricated by coupling nanoporous gold leaf (NPGL) with molecularly imprinted polymer (MIP) to afford ultrasensitive and selective determination of WFS. The morphological characterization via scanning electron microscopy proved the successful modification of the sensor by NPGL followed with MIP layer modification. The influencing parameters including the type of monomer, pH and molar ratio of template to monomer were optimized during electro-polymerization. Using Fe(CN)63−/4− as a probe acting as an electrical indicator, a linear relationship of the current response versus the concentration of WFS was obtained in the range from 1.0 × 10−10 to 8.0 × 10−8 M under the optimal experimental conditions, with a detection limit of 4.1 × 10−11 M (S/N = 3). In addition, the as-prepared sensor exhibited specific detection of WFS over its structural analogues and interferents, and the established electrochemical approach was validated using the standard method – high performance liquid chromatography. Eventually, rapid and accurate determination of WFS in human blood was carried out after easy sample pretreatment.

Fish Cholinesterases as Biomarkers of Sublethal Effects of Organophosphorus and Carbamates in Tissues of Labeo Rohita

Organophosphates and carbamates are major agrochemicals that strongly affect different neuroenzymes and the growth of various fish species. Here, we study the effect of sublethal concentrations of profenofos and carbofuran on the activity of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) and the associated health risk in fish. Labeo rohita fingerlings were exposed to three sublethal concentrations of profenofos and carbofuran. The minimum cholinesterase activities in the brain, gills, muscle, kidney, liver, and blood were after exposure to profenofos (0.06 mg/L). The minimum AChE and BuChE activities in the brain, gills, muscle, kidney, liver, and blood were after exposure to carbofuran (0.28 and 0.198 mg/L). Exposure to both types of pesticides affected the functions of these organs, including metabolism and neurotransmission, to various extents at different exposure concentrations. These findings suggest that they are required to be properly monitored in the environment, to reduce their toxic effects on nontarget organisms

Monitoring of trace metals in tissues of Wallago attu (lanchi) from the Indus River as an indicator of environmental pollution

We aimed to assess the bioaccumulation of selected four trace metals (Cd, Ni, Zn and Co) in four tissues (muscles, skin, gills and liver) of a freshwater fish Wallago attu (lanchi) from three different sites (upstream, middle stream and downstream) of the Indus River in Mianwali district of Pakistan. Heavy metal contents in water samples and from different selected tissues of fish were examined by using flame atomic absorption spectrometry. The data were statistically compared to study the effects of the site and fish organs and their interaction on the bioaccumulation pattern of these metals at P < 0.05. In W. attu the level of cadmium ranged from 0.004 to 0.24; nickel 0.003–0.708; cobalt 0.002–0.768 and zinc 47.4–1147.5 μg/g wet weight. The magnitude of metal bioaccumulation in different organs of fish species had the following order gills > liver > skin > muscle. The order of bioaccumulation of these metals was Ni < Zn < Co < Cd. Heavy metal concentrations were increased during the dry season as compared to the wet season. The results of this study indicate that freshwater fish produced and marketed in Mianwali have concentrations below the standards of FEPA/WHO for these toxic metals.

Genome-wide identification, phylogeny, and expression of fibroblast growth genes in common carp

Fibroblast growth factors (FGFs) are a large family of polypeptide growth factors, which are found in organisms ranging from nematodes to humans. In vertebrates, a number of FGFs have been shown to play important roles in developing embryos and adult organisms. Among the vertebrate species, FGFs are highly conserved in both gene structure and amino-acid sequence. However, studies on teleost FGFs are mainly limited to model species, hence we investigated FGFs in the common carp genome. We identified 35 FGFs in the common carp genome. Phylogenetic analysis revealed that most of the FGFs are highly conserved, though recent gene duplication and gene losses do exist. By examining the copy number of FGFs in several vertebrate genomes, we found that eight FGFs in common carp have undergone gene duplications, including FGF6a, FGF6b, FGF7, FGF8b, FGF10a, FGF11b, FGF13a, and FGF18b. The expression patterns of all FGFs were examined in various tissues, including the blood, brain, gill, heart, intestine, muscle, skin, spleen and kidney, showing that most of the FGFs were ubiquitously expressed, indicating their critical role in common carp. To some extent, examination of gene families with detailed phylogenetic or orthology analysis verified the authenticity and accuracy of assembly and annotation of the recently published common carp whole genome sequences. Gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp FGF gene family provides an important genomic resource for future biochemical, physiological, and phylogenetic studies on FGFs in teleosts.

Variation in genotoxic susceptibility and biomarker responses in Cirrhinus mrigala and Catla catla from different ecological niches of the Chenab River

A large number of methods have been applied to evaluate genotoxic damage in different aquatic species. Comet assay, as a method for detecting DNA alterations, and micronucleus test, as an index of chromosomal damage are the most widely used and authentic methods in laboratory and field studies. The primary objective of the study was to evaluate the genotoxic effects of heavy metals generated by toxic industrial effluents and various kinds of pollutants from urban and agricultural areas and domestic waste on Catla catla and Cirrhinus mrigala due to water pollution in the Chenab River, Pakistan. The heavy metals Cd, Cu, Mn. Zn, Pb, Cr, Sn, and Hg were detected by atomic absorption spectrophotometry from water samples collected from predetermined sampling sites. All the physicochemical parameters and heavy metals were found to exceed the upper limits recommended by various agencies. Comet assays showed significant (p < 0.05) DNA damage in C. mrigala compared to C. catla for tail length and olive tail moment from three different sites. Significant (p < 0.05) differences were reported between fish collected from polluted sites and farmed fish, but only non-significant (p > 0.05) findings were observed between fish collected from farmed and non-polluted upstream waters. Micronucleus assays showed similar findings for single and double micronucleus induction in C. catla and C. mrigala. A significantly (p < 0.05) higher micronuclei induction and percent tail DNA was observed in C. mrigala specimen collected from the polluted site. These findings infer that DNA damage could be used as a biomarker of pollution load and its early monitoring by using simple and reliable techniques such as the comet and micronucleus assays, expedient methods for toxicity screening of aquatic environments. Regular monitoring is necessary to assess eco-health of the Chenab River by choosing perhaps C. mrigala, being a bottom feeder, as a bioindicator that could provide more reliable information to determine the status of the environmental quality of the river.

Effect of sodium cyanide on the activities of some oxidative enzymes and metabolites in Clarias gariepinus

-1 ) of sodium cyanide. Fish showed a gradual decrease in respiratory rate, increase in LDH and decrease in SDH levels, and lactic acid followed a similar trend with pyruvate in an eight-day trial. The changes in the levels of these enzyme activities may be as a result of impaired oxidative metabolism and cellular damage, which had effect on the release of these enzymes. Elevation in the level of lactic acid and decrease in pyruvic acid was due to shift from aerobic to anaerobic metabolism which resulted to a severe drop in the respiratory rate of the fish. It may be as a result of blockage of electron transfer from cytochrome-c oxidase to molecular oxygen which might lead to cellular hypoxia even in the presence of normal oxygenation of hemoglobin. Thus, inhibition of oxidative metabolism by sodium cyanide in C. garipenus was reconfirmed. Behavioral changes caused by sodium cyanide exposure in the fish were probably due to the combination of lactate acidosis with cytotoxic hypoxia, which might depress the central nervous system.

The genetic map of goldfish ( Carassius auratus ) provided insights to the divergent genome evolutions in the Cyprinidae family

A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.