Molecular Characterization of Wild and Cultivated Strawberry (Fragaria × ananassa) through DNA Barcode Markers.

Background: DNA barcoding is a useful technique for the identification, conservation, and diversity estimation at the species level in plants. The current research work was carried out to characterize selected Fragaria species from northern Pakistan using DNA barcode markers. Methodology. Initially, the efficacy of eight DNA barcode markers was analyzed based on the amplification and sequencing of the genome of selected Fragaria species. The resultant sequences were analyzed using BLAST, MEGA 7.0, and Bio Edit software. The phylogenetic tree was constructed by using Fragaria current species sequences and reference sequences through the neighbor-joining method or maximum likelihood method. Results: Among eight DNA barcode markers, only two (ITS2 and rbclC) were amplified, and sequences were obtained. ITS2 sequence was BLAST in NCBI for related reference species which ranged from 89.79% to 90.05% along with Fragaria vesca (AF163517.1) which have 99.05% identity. Similarly, the rbclC sequence of Fragaria species was ranged from 96% to 99.58% along with Fragaria × ananassa (KY358226.1) which had 99.58% identity. Conclusion: It is recommended that DNA barcode markers are a useful tool to identify the genetic diversity of a species. Moreover, this study could be helpful for the identification of the Fragaria species cultivated in other regions of the world.

In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations.

The prolific spread of COVID-19 caused by a novel coronavirus (SARS-CoV-2) from its epicenter in Wuhan, China, to every nook and cranny of the world after December 2019, jeopardize the prevailing health system in the world and has raised serious concerns about human safety. Multi-directional efforts are made to design small molecule inhibitors, and vaccines and many other therapeutic options are practiced, but their final therapeutic potential is still to be tested. Using the old drug or vaccine or peptides could aid this process to avoid such long experimental procedures. Hence, here, we have repurposed a small peptide (ATLQAIAS) from the previous study, which reported the inhibitory effects of this peptide. We used in silico mutagenesis approach to design more peptides from the native wild peptide, which revealed that substitutions (T2W, T2Y, L3R, and A5W) could increase the binding affinity of the peptide towards the 3CLpro. Furthermore, using MD simulation and free energy calculation confirmed its dynamics stability and stronger binding affinities. Per-residue energy decomposition analysis revealed that the specified substitution significantly increased the binding affinity at the residue level. Our wide-ranging analyses of binding affinities disclosed that our designed peptide owns the potential to hinder the SARS-CoV-2 and will reduce the progression of SARS-CoV-2-borne pneumonia. Our research strongly suggests the experimental and clinical validation of these peptides to curtail the recent corona outbreak.

Impact of city effluents on water quality of Indus River: assessment of temporal and spatial variations in the southern region of Khyber Pakhtunkhwa, Pakistan.

The impact of city effluents on water quality of Indus River was assessed in the southern region of Khyber Pakhtunkhwa, Pakistan. Water samples were collected in dry (DS) and wet (WS) seasons from seven sampling zones along Indus River and the physical, bacteriological, and chemical parameters determining water quality were quantified. There were marked temporal and spatial variations in the water quality of Indus River. The magnitude of pollution was high in WS compared with DS. The quality of water varied across the sampling zones, and it greatly depended upon the nature of effluents entering the river. Water samples exceeded the WHO permissible limits for pH, EC, TDS, TS, TSS, TH, DO, BOD, COD, total coliforms, Escherichia coli, Ca2+, Mg2+, NO3-, and PO42-. Piper analysis indicated that water across the seven sampling zones along Indus River was alkaline in nature. Correlation analyses indicated that EC, TDS, TS, TH, DO, BOD, and COD may be considered as key physical parameters, while Na+, K+, Ca2+, Mg2+, Cl-, F-, NO3-, PO42-, and SO42- as key chemical parameters determining water quality, because they were strongly correlated (r > 0.70) with most of the parameters studied. Cluster analysis indicated that discharge point at Shami Road is the major source of pollution impairing water quality of Indus River. Wastewater treatment plants must be installed at all discharge points along Indus River for protecting the quality of water of this rich freshwater resource in Pakistan.

Assessing impact of effluent discharge on irrigation water quality in southern region of Khyber Pakhtunkhwa, Pakistan.

Chemical quality and extent of pollution in effluent-contaminated irrigation water collected from two sectors (X and Y) of peri-urban southern regions of Khyber Pakhtunkhwa, Pakistan, were investigated. Various physico-chemical parameters like pH, EC, TS, TSS, TDS, TH, cations (Na1+, K1+, Li1+, Ca2+, Mg2+), anions (Cl1-, F1-, HCO31-, NO31-, SO42-), and heavy metals (Cr, Fe, Cu, Zn, Pb, Cd) were determined. The data indicated wide ranges of variation in all the parameters. Concentration of physico-chemical properties such as EC, TS, TSS, TH, Li1+, Ca2+, Mg2+, and HCO31- and heavy metals (Cr, Fe, Cu, and Cd) exceeded WHO permissible limits. The distribution of heavy metals in two sampling areas followed the increasing order as Fe > Cr > Cd > Cu > Pb > Zn. The Piper diagram showed that water in the region was of alkaline type. Strong positive correlations were observed among most of the parameters; however, pH was negatively correlated with most of the parameters. According to principle component analysis, parameters causing variations in water quality were mainly EC, TDS, TS, TSS, TH, Na1+, K1+, Ca2+, Mg2+, F1-, NO31-, SO42-, Cr, Fe, Cu, and Zn. Linear regression analysis revealed that heavy metals like Cr, Fe, and Cu concentrations were strongly correlated having an R 2 value of 0.92 at P ≤ 0.001 with pH. Overall, the results suggested that irrigation water of the area was not fit for irrigation purposes and might cause serious threats for safe, healthy food and feed production. Proper monitoring of water of the said area should be carried out, and quality of irrigation water should be checked from time to time.

Computed tomography abnormalities and epidemiology of adult patients presenting with first seizure to the emergency department in Qatar.

OBJECTIVES: There is little information available from the Middle Eastern region on adult patients presenting with first seizure. The objectives of this study were to describe epidemiological characteristics of patients presenting to the emergency department (ED) in Doha, Qatar, with first seizure and to determine the incidence of computed tomographic (CT) scan abnormalities. METHODS: A retrospective cohort study was conducted on all adult patients with first seizure presenting to Hamad General Hospital ED over a 1-year period (June 2012 through May 2013). Electronic patient records were reviewed for demographics, neuroimaging, electroencephalography, laboratory test results, and medications administered. RESULTS: There were 439 patients who satisfied inclusion criteria. Patients were aged a mean of 35.3 years (95% confidence interval [CI] = 33.92 to 36.69 years) with a male-to-female ratio of five to one. CT abnormalities were detected in 154 patients (35.3%; 95% CI = 30.81% to 39.82%). Out of reported abnormal scans, 14.7% patients had significant abnormalities such as neurocysticercosis (9.2%); brain metastasis and neoplasm (3.4%); and subarachnoid and subdural hemorrhage, cavernous sinus thrombosis, acute stroke, and brain edema (2.0%). None of the patients had any electrolyte abnormalities, and three patients had hypoglycemia. Patients with initial abnormal CT brain results were more likely to have recurrent seizures (OR = 1.65; 95% CI = 1.11 to 2.45) within 6 months. CONCLUSIONS: Adults who presented with first seizure to the ED in Qatar had a young male predominance, and a high proportion of brain CT scans were reported as abnormal. It is recommended that all such patients in this population should undergo prompt CT scanning in the ED, but the utility of routine electrolyte tests requires further investigation.