12 research outputs found

    Immunoinformatics and Computer-Aided Drug Design as New Approaches against Emerging and Re-Emerging Infectious Diseases

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    Infectious diseases are initiated by small pathogenic living germs that are transferred from person to person by direct or indirect contact. Recently, different newly emerging and reemerging infectious viral diseases have become greater threats to human health and global stability. Investigators can anticipate epidemics through the advent of numerous mathematical tools that can predict specific pathogens and identify potential targets for vaccine and drug design and will help to fight against these challenges. Currently, computational approaches that include mathematical and essential tools have unfolded the way for a better understanding of newly originated emerging and re-emerging infectious disease, pathogenesis, diagnosis, and treatment option of specific diseases more easily, where immunoinformatics plays a crucial role in the discovery of novel peptides and vaccine candidates against the different viruses within a short time. Computational approaches include immunoinformatics, and computer-aided drug design (CADD)-based model trained biomolecules that offered reasonable and quick implementation approaches for the modern discovery of effective viral therapies. The essence of this review is to give insight into the multiple approaches not only for the detection of infectious diseases but also profound how people can pick appropriate models for the detection of viral therapeutics through computational approaches

    Compounds Identified from Marine Mangrove Plant (Avicennia alba) as Potential Antiviral Drug Candidates against WDSV, an In-Silico Approach

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    Walleye dermal sarcoma virus (WDSV) is a type of retrovirus, which affects most of the adult walleye fishes during the spawning time. The virus causes multiple epithelial tumors on the fish’s skin and fins that are liable for more than 50% of the mortality rate of fish around the world. Till now, no effective antiviral drug or vaccine candidates have been developed that can block the progression of the disease caused by the pathogen. It was found that the 582-amino-acid (aa) residues long internal structural gag polyprotein of the virus plays an important role in virus budding and virion maturation outside of the cell. Inhibition of the protein can block the budding and virion maturation process and can be developed as an antiviral drug candidate against the virus. Therefore, the study aimed to identify potential natural antiviral drug candidates from the tropical mangrove marine plant Avicennia alba, which will be able to block the budding and virion maturation process by inhibiting the activity of the gag protein of the virus. Initially, a homology modeling approach was applied to identify the 3D structure, followed by refinement and validation of the protein. The refined protein structures were then utilized for molecular docking simulation. Eleven phytochemical compounds have been isolated from the marine plant and docked against the virus gag polyprotein. Three compounds, namely Friedlein (CID244297), Phytosterols (CID12303662), and 1-Triacontanol (CID68972) have been selected based on their docking score −8.5 kcal/mol, −8.0 kcal/mol and −7.9 kcal/mol, respectively, and were evaluated through ADME (Absorption, Distribution, Metabolism and Excretion), and toxicity properties. Finally, molecular dynamics (MD) simulation was applied to confirm the binding stability of the protein-ligands complex structure. The ADME and toxicity analysis reveal the efficacy and non-toxic properties of the compounds, where MD simulation confirmed the binding stability of the selected three compounds with the targeted protein. This computational study revealed the virtuous value of the selected three compounds against the targeted gag polyprotein and will be effective and promising antiviral candidates against the pathogen in a significant and worthwhile manner. Although in vitro and in vivo study is required for further evaluation of the compounds against the targeted protein

    Heavy Metal Accumulation and Anti-Oxidative Feedback as a Biomarker in Seagrass Cymodocea serrulata

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    The pursuit of a good candidate to biomonitor environmental pollutants has been on the increase. In this study, the concentrations of Fe, Mn, Cu, Zn, Cd, Cr, Pb and Ni in sediment, seawater and seagrass Cymodocea serrulata compartments and antioxidant enzymes activities in C. serrulata were determined. Our results revealed that bioconcentration factors for all the metals were less than 1 (BCF < 1) and concentrations in seagrass compartments were in the order root > leaf > rhizome for Fe and Mn, leaf > root > rhizome for Cu, Zn, Pb and Ni, and root > rhizome > leaf for Cd and Cr. Effect range low concentrations (ER-L) revealed that Cu, Zn, Cd, Pb and Ni concentrations were above ER-L values and Cr concentration was below ER-L values while concentrations in seawater for all the heavy metals were above the estimate average element concentrations in seawater (ECS). Significant variation (p < 0.05) was recorded for heavy metals in sediment, seawater, seagrass compartments and heavy metal concentrations across stations. Influence of heavy metals on antioxidant enzymes activities; catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase (GST) and acetylcholinesterase (AChE) were recorded, and high activities of the antioxidants were recorded in station S8 corresponding to high concentrations of heavy metals in the same station. There is a need for the promotion of biomonitoring networks across the marine environment using C. serrulata and antioxidant enzymes as biomarkers of oxidative stress caused by environmental pollutants

    Monitoring Mangrove Forest Degradation and Regeneration: Landsat Time Series Analysis of Moisture and Vegetation Indices at Rabigh Lagoon, Red Sea

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    Rabigh Lagoon, located on the eastern coast of the Red Sea, is an ecologically rich zone in Saudi Arabia, providing habitat to Avicennia marina mangrove trees. The environmental quality of the lagoon has been decaying since the 1990s mainly from sedimentation, road construction, and camel grazing. However, because of remedial measures, the mangrove communities have shown some degree of restoration. This study aims to monitor mangrove health of Rabigh Lagoon during the time it was under stress from road construction and after the road was demolished. For this purpose, time series of EVI (Enhanced Vegetation Index), MSAVI (Modified, Soil-Adjusted Vegetation Index), NDVI (Normalized Difference Vegetation Index), and NDMI (Normalized Difference Moisture Index) have been used as a proxy to plant biomass and indicator of forest disturbance and recovery. Long-term trend patterns, through linear, least square regression, were estimated using 30 m annual Landsat surface-reflectance-derived indices from 1986 to 2019. The outcome of this study showed (1) a positive trend over most of the study region during the evaluation period; (2) most trend slopes were gradual and weakly positive, implying subtle changes as opposed to abrupt changes; (3) all four indices divided the times series into three phases: degraded mangroves, slow recovery, and regenerated mangroves; (4) MSAVI performed best in capturing various trend patterns related to the greenness of vegetation; and (5) NDMI better identified forest disturbance and recovery in terms of water stress. Validating observed patterns using only the regression slope proved to be a challenge. Therefore, water quality parameters such as salinity, pH/dissolved oxygen should also be investigated to explain the calculated trends

    Characterizing Global Patterns of Mangrove Canopy Height and Aboveground Biomass Derived from SRTM Data

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    Numerous studies have been done using remotely sensed data to produce global mangrove height and biomass maps; however, little is known about the worldwide pattern of mangroves in the Northern and Southern Hemispheres that corresponds to their height and biomass. The objective of this study was to investigate whether there is a specific pattern that can be seen between northern and southern mangroves according to height and biomass. Based on an empirical model, we processed Shuttle Radar Topographic Mission (SRTM) elevation data in combination with 450 field data points to produce a global mangrove height map and its corresponding aboveground biomass (AGB) per hectare at 30 m spatial resolution. We also refined the global mangrove area maps and provided a set of equations to determine the maximum mangrove height at any given latitude. Results showed that 10,639,916 ha of mangroves existed globally in the year 2000, with a total AGB of 1.696 Gt. Even though the areal coverage of mangroves was higher in the Northern Hemisphere, the total mangrove AGB was higher in the Southern Hemisphere. The majority of mangroves in both hemispheres were found to be between 6 and 8 m tall, although height distribution differed in each hemisphere. The global mangrove height equation for northern and southern mangroves produced from this study can be used by relevant stakeholders as an important reference for developing an appropriate management plan for the sustainability of the global mangrove ecosystem

    Elemental Composition of Above and Belowground Mangrove Tissue and Sediment in Managed and Unmanaged Compartments of the Matang Mangrove Forest Reserve

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    Mangrove productivity depends on the storage of nutrients and elements. Elemental concentrations were examined in leaves, roots, and sediments for three age stands (15, 25 years, and VJR) of Rhizophora apiculata in the Matang Mangrove Forest Reserve (MMFR). Six compartments with two compartments each for each age group were used to analyze sixteen elements. Four types of elemental patterns were examined with decreasing order during analysis: (1) Cd (S) (S) (S) (S) (S) (L) (L) (S) (R) (R) and P%(S) (S) (L) (R) collectively for all samples. Evidence that elements do not store primarily in above-ground biomass can be found in the observation that elements are stored more in sediment and roots. The outcome of the present study shows that the rate of increase of elements in trees (leaves and roots) was less as compared to sediments, where the elemental concentration increased considerably with time. Elemental concentration comparison within three age classes showed that C, N, and S were significantly different in all three types of samples. The δ15N ratios showed positive values in all six compartments which supported the concept that the δ15N ratio could not be observed in N concentration in this study. The δ13C values showed more negative values in all six compartments which represented less salinity and a freshwater intake. The S, P, and heavy metals concentrations were high. The concentrations of Cd, P, N, C, and S in the sediment influenced variations in four compartments in accordance with the three mangrove age groups. The results of this study can be utilized to create management plans for MMFR and conduct risk assessments of the elements’ concentration in sediment

    Rare Earth Elements and Bioavailability in Northern and Southern Central Red Sea Mangroves, Saudi Arabia

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    Different hypotheses have been tested about the fractionation and bioavailability of rare earth elements (REE) in mangrove ecosystems. Rare earth elements and bioavailability in the mangrove ecosystem have been of significant concern and are recognized globally as emerging pollutants. Bioavailability and fractionation of rare earth elements were assessed in Jazan and AlWajah mangrove ecosystems. Comparisons between rare earth elements, multi-elemental ratios, geo-accumulation index (Igeo), and bio-concentration factor (BCF) for the two mangroves and the influence of sediment grain size types on concentrations of rare earth elements were carried out. A substantial difference in mean concentrations (mg/kg) of REE (La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) was established, except for mean concentrations of Eu, Gd, Tb, Tm, and Lu. In addition, concentrations of REEs were higher in the Jazan mangrove ecosystem. However, REE composition in the two mangroves was dominated by the lighter REE (LREE and MREE), and formed the major contribution to the total sum of REE at 10.2–78.4%, which was greater than the HREE contribution of 11.3–12.9%. The Post Archean Australian Shale (PAAS) normalized values revealed that lighter REE (LREE and MREE) were steadily enriched above heavy REE. More so, low and negative values of R(H/M) were recorded in the Al Wajah mangrove, indicating higher HREE depletion there. The values of BCF for REEs were less than 1 for all the REEs determined; the recorded BCF for Lu (0.33) and Tm (0.32) were the highest, while the lowest BCF recorded was for Nd (0.09). There is a need for periodic monitoring of REE concentrations in the mangroves to keep track of the sources of this metal contamination and develop conservation and control strategies for these important ecosystems

    Marine-derived sea urchin compounds as potential anti-cancer drug candidate against colorectal cancer: In silico and in vitro studies

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    Sea urchin-derived compounds are potential candidates for the development of effective drugs for the treatment of cancer diseases. In this study, 19 compounds derived from sea urchin (Diadema savignyi) were used to treat colorectal cancer using the HCT116 cell line. However, molecular docking, ADME (absorption, distribution, metabolism, and excretion), toxicity, molecular dynamic (MD) simulation, and molecular mechanics generalized Born surface area (MM-GBSA) were used to confirm the ligand–protein interaction. Interactions of Importin-11 receptor with sea urchin compounds reveal that four compounds have higher binding affinities (ranging from -8.6 to -7.1 kcal/mol). In vitro testing revealed that the CID 6432458 compound was effective (docking score of −8.6 kcal/mol) against the HCT116 cell line. The cytotoxicity of HCT116 has been documented, with an IC50 value of 6.885 ± 4. MTT assay, apoptosis analysis, and cell cycle assay were utilized to examine cell death in colorectal cancer. In the MTT experiment, 15 µM and 20 µM dosages were associated with 77% cell death; however, flow cytometry analysis using the IC50 value revealed that the selected chemical induced greater apoptosis in the HCT116 cell line (58.5%). The gene expression data revealed that the apoptotic gene BAX is expressed at a higher level than the BCL-2 gene. The IPO11 gene was downregulated during treatment. In the experiment involving the cell cycle, the S phase for the 30  µM dose showed 75.1% apoptosis, which was greater than the other concentrations used alone. These in silico and in vitro analysis will not only provide new information about Importin-11 receptor and insight into colorectal cancer but will also facilitate the development of natural compounds in a significant and worthwhile manner

    Monitoring mangrove forest degradation and regeneration: landsat time series analysis of moisture and vegetation indices at Rabigh Lagoon, Red Sea

    No full text
    Rabigh Lagoon, located on the eastern coast of the Red Sea, is an ecologically rich zone in Saudi Arabia, providing habitat to Avicennia marina mangrove trees. The environmental quality of the lagoon has been decaying since the 1990s mainly from sedimentation, road construction, and camel grazing. However, because of remedial measures, the mangrove communities have shown some degree of restoration. This study aims to monitor mangrove health of Rabigh Lagoon during the time it was under stress from road construction and after the road was demolished. For this purpose, time series of EVI (Enhanced Vegetation Index), MSAVI (Modified, Soil-Adjusted Vegetation Index), NDVI (Normalized Difference Vegetation Index), and NDMI (Normalized Difference Moisture Index) have been used as a proxy to plant biomass and indicator of forest disturbance and recovery. Long-term trend patterns, through linear, least square regression, were estimated using 30 m annual Landsat surface-reflectance-derived indices from 1986 to 2019. The outcome of this study showed (1) a positive trend over most of the study region during the evaluation period; (2) most trend slopes were gradual and weakly positive, implying subtle changes as opposed to abrupt changes; (3) all four indices divided the times series into three phases: degraded mangroves, slow recovery, and regenerated mangroves; (4) MSAVI performed best in capturing various trend patterns related to the greenness of vegetation; and (5) NDMI better identified forest disturbance and recovery in terms of water stress. Validating observed patterns using only the regression slope proved to be a challenge. Therefore, water quality parameters such as salinity, pH/dissolved oxygen should also be investigated to explain the calculated trends

    Whole Genome Sequence of the Newly Prescribed Subspecies Oreochromis spilurus saudii: A Valuable Genetic Resource for Aquaculture in Saudi Arabia

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    Tilapia (Oreochromis spp.) have significant potential for aquaculture production around the world. There is an increasing demand among tilapia producers for strains with higher yields and for fish that can survive in highly saline water. Novel strains and consistent seedstock are critically important objectives for sustainable aquaculture, but for these required targets there is still not enough progress. Therefore, this study describes the genome sequence of Oreochromis spilurus to support the seawater culture of tilapia. The draft genome is 0.768 Gb (gigabases), with a scaffold N50 (the genome (50%) is in fragments of this length) of 0.22 Mb (megabases). The GC content is 40.4%, the heterozygosity rate is 0.35%, and the repeat content is 47.97%. The predicted protein-coding peptide encoded 51,642 and predicted 10,641 protein-coding genes in the O. spilurus genome. The predicted antimicrobial peptides were 262, bringing new hope for further research. This whole genome sequence provides new insights for biomedical and molecular research and will also improve the breeding of tilapia for high yields, resistance to disease, and adaptation to salt water
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