The Computational Techniques Developed to Analyze DNA Gel Images

The analysis of gel electrophoresis images is very crucial for molecular biologists to comprehend and interpret their experimental results. Thus, enhancing current mathematical methods and developing new accurate ones is very important and challenging task for bioinformaticians. For example, enhancing the commonly used mathematical method in gel analysis known as "Fitting method estimation" and proposing a new efficient method entitled "Ruler estimation" for preprocessing a given image and detecting lanes and bands automatically. Both mathematical methods implemented in our newly developed software. Three mathematical models namely, linear, quadratic and cubic fitting are tested for the accuracy of detecting the bands and lanes in the gel image to determine the best fitting model. A friendly user interface is developed for this new program using MATLB GUI to extract useful bimolecular information accurately and automatically. The new software has the ability to manually add or delete any band(s) and estimate the size of any unknown band(s) on the gel. Moreover, the similarity and (dis)similarity between lanes "samples" are estimated based on comparing the numbers and sizes of bands to generate a phylogram tree

Treatment by agricultural by-products of Industrial effluents polluted with heavy metals

Due to the increasing concern about the environmental pollution problems, it is so important to perform a number of methods for removing hazardous heavy metals from industrial liquid wastes. Adsorption technique is the most effective and economical one. In the present study, two agricultural by-products namely; cottonseed and soybean hulls, resulting from the oil industry, have been used in the adsorption of thorium element from a wastewater effluent coming from different industries. The results obtained indicate that maximum removal of thorium from a prepared solution takes place at pH 5 where equilibrium was attained after 100 min; using an adsorbent dose of 3 and 3.5 g/L for cottonseed and soybean hulls, respectively. On the other hand, the obtained mathematical data together with the obtained adsorption kinetic parameters indicate that both of cottonseed and soybean hulls could be useful adsorbents for thorium removal from industrial liquid wastes, especially when the low cost, environmental issues and high availability of these materials are considered

Vancomycin MIC Distribution among Methicillin-Resistant Staphylococcus Aureus. Is Reduced Vancomycin Susceptibility Related To MIC Creep?

AIM: To determine the distribution of vancomycin MIC and the frequency of S. aureus strains with reduced vancomycin susceptibility among Methicillin-Resistant Staphylococcus aureus (MRSA) isolates. METHODS: MRSA isolates (n = 100) were tested for reduced susceptibility to vancomycin using  MIC broth microdilution method (BMD), vancomycin screening agar with different vancomycin concentrations with and without casein, and Vitek 2 system. RESULTS: BMD detected (22%) vancomycin-intermediate S. aureus (VISA) and (78%) vancomycin-susceptible S. aureus (VSSA) but couldn’t detect nine (Heterogeneous VISA) (hVISA)   isolates (9%) with MIC ≤ 2 µg/ml that grew on screening agar 4 µg/ml or 6 µg/ml. Adding casein to vancomycin screening agar increased detection rate of VISA by 4.5%.  Screening agar with 6 µg/ml vancomycin overall detection rate for VISA was 95.45%. Probable ‘pre-hVISA’isolates (17%) showed growth on vancomycin screening agar 2 µg/ml with casein. Vitek 2 system failed to detect any VISA isolates. CONCLUSION: Vancomycin screening agar; 2 µg/ml and (4 and 6 µg/ml) were able to detect; probable “pre hVISA and (hVISA and VISA) isolates respectively based on their BMD MIC values. Decreased vancomycin susceptibility in MRSA isolates might be related to MIC creep. Analysis of vancomycin MIC values over longer periods is recommended to further study this phenomenon and its impact on vancomycin treatment failure.   ABSTRACT Aims: Determine the distribution of vancomycin MIC and the frequency of S. aureus strains with reduced vancomycin susceptibility among MRSA isolates.  Methods:  MRSA isolates (n =100) were tested for reduced susceptibility to vancomycin using  MIC broth microdilution method(BMD), vancomycin screening agar with different vancomycin concentrations with and without casein, and Vitek 2 system.  Results: BMD detected (22%) vancomycin intermediate S. aureus(VISA) and (78%) vancomycin susceptible S. aureus(VSSA) but failed to detect nine (Heterogeneous VISA) (hVISA)  isolates (9%) with MIC ≤2ug/ml that grew on screening agar 4ug/ml or 6 ug/ml. Adding casein to vancomycin screening agar increased detection rate of VISA by 4.5%.  Screening agar with 6 ug/ml vancomycin over all detection rate for VISA was 95.45%. Probable ‘pre-hVISA’isolates (17%) showed growth on vancomycin screening agar 2µg/ml with casein. Vitek 2 system failed to detect any VISA isolates. Conclusion: vancomycin screening agar; 2 µg/ml and (4 and 6 µg/ml) were able to detect; probable “pre hVISA and (hVISA and VISA) isolates respectively based on their BMD MIC values. Decreased vancomycin susceptibility in MRSA isolates might be related to MIC creep. Analysis of vancomycin MIC values over longer periods of time is recommended to further study this phenomenon and its impact on vancomycin treatment failure.   &nbsp

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Anticoagulant effect of Feijoa sellowiana extracts generated by different biotechnological techniques

Blood clotting has become one of the most dangerous side effects associated with Corona virus, as well as the high level of cholesterol and triglycerides in the blood. Therefore, it has become necessary to use medicinal plants that are biologically safe and containing anti-clotting compound. Feijoa sellowiana represents a prolific source diverse compounds that may have thrombolytic activity. Therefore, the main research point is the production and scaling up of a target contents that have anticoagulants by using biotechnological techniques; calli production, and bioreactors and assessed their activity through in-vivo study. Murashige and Skoog (MS) medium enriched with varying concentrations of benzyl adenine (BA) and naphthalene acetic acid (NAA) was used to cultivate calli and cell suspension cultures from F. sellowiana seeds. Bioreactors were employed to boost active constituent's production. Moreover, the bioreactor physical factors such as effect of controlled or uncontrolled pH medium were investigated. The leaves of the main plant were extracted by ethanol 70% and polar and non-polar extracts were also prepared. The ethanol extract of calli and cells resulting from bioreactors were also prepared. All prepared extracts were subjected to chemical analysis by HPLC, in-vitro antioxidant assays, in-vivo anticoagulant activity and histopathological examination. Calli and cell suspension cultures were produced by using MS medium fortified with 1 mg/L BA+ 0.1 mg/L NAA. It was found that culturing of cell cultures in a bioreactor with uncontrolled pH and aeration at the value of 0.5 L/min gave the maximum and economical fresh and dry weights of the plants. After evaluation of all extracts; it was found that the calli ethanol extract for each plant was the highest value of total phenolic and total flavonoid contents either quantitatively or qualitatively. All extracts of Feijoa had antioxidant activity. The IC50 of the DPPH of Feijoa calli extract was 13.45 μg/mL, it was also confirmed by FRAP and ABTs values. Feijoa calli extract decreased platelet aggregation by suppression of thrombin, extended aPTT, PT, bleeding and clotting times. It was safer than warfarin medication. From these findings the authors can conclude that Feijoa had highly anticoagulant activity and the calli production achieved the goal of the enhancement of the phenolic constituent and thus their activity

Maternal vitamin D level and vitamin D receptor gene polymorphism as a risk factor for congenital heart diseases in offspring; An Egyptian case-control study

Vitamin D & vitamin D receptor (VDR) signaling play a very crucial role in early embryonic heart development. We construct this case-control study to investigate the association between maternal serum vitamin D level & VDR gene Fok1 polymorphism and risk of congenital heart defects (CHD) in offspring. Fifty mothers who had term neonates with CHD were considered as cases. Fifty age-comparable healthy mothers who had neonates without CHD were contemplated as controls. Maternal serum 25 hydroxyvitamin D [25(OH) D] level was tested using ELISA. Maternal VDR gene Fok1 polymorphism was analyzed using PCR-based RFLP-assay. There was a significant decrease in maternal vitamin D level (P = 0.002) and a significant increase in vitamin D deficient status (P = 0.007) among cases when compared to controls. VDR gene Fok1 genotypes distribution frequency were in accordance with Hardy Weinberg equilibrium (HW) among controls. A significant increase in VDR gene Fok1 F/f & f/f genotypes and f allele were observed in cases compared to controls with estimated odds ratio (95% confidence interval) & P-value of 3 (1–8) & P = 0.006, 11 (1–97) & P = 0.01 and 3 (2–6) & P = 0.001 respectively. There was a significant decrease in maternal vitamin D level in neonates with cyanotic CHD (P = 0.000) compared to those with a cyanotic CHD while there was no significant difference in VDR Fok1 genotype (P = 0.18) & allele (P = 0.05) distribution between two groups. We concluded that maternal vitamin D deficiency and VDR gene Fok1 F/f, f/f genotype and f allele were associated with increased risk of CHD in offspring. Keywords: Congenital heart disease, FoK1 polymorphism, Vitamin D, Vitamin D receptor gene, Maternal vitamin

Mathematical Modeling and Classification of Viruses from Herpesvirus Family

The process of modeling and classifications of viruses that belong to a specific family is an important for biologist and for many biological applications. There are many ways for Viruses families ' classification. The degree of similarity or diversity among the structure of the viruses capsid proteins is very useful in studying the Viruses families ' classification and their genetic evolution. It also important propose if we construct a mathematical model of the virus life cycle to be able to fully understand the life cycle of Viruses families ' activities. In this paper we introduce a proposed mathematical model for some Herpesvirus family viruses simple life cycle and comprehensive study for its classification using sequence alignment algorithms in order to demonstrate their genetic evolution according to the structure of their capsid protein. Herpesvirus family is considered one of the most important family in the families of the enveloped DNA viruses as it contain many dangerous viruses for human health. This family contain one of newly discovered viruses called Epstein–Barr virus (EBV), also called human herpesvirus 4 (HHV-4), which is one of the most common viruses in human. Infection with EBV occurs by the oral transfer of saliva [1] and genital secretions

Treatment by agricultural by-products of Industrial effluents polluted with heavy metals

270-278Due to the increasing concern about the environmental pollution problems, it is so important to perform a number of methods for removing hazardous heavy metals from industrial liquid wastes. Adsorption technique is the most effective and economical one. In the present study, two agricultural by-products namely; cottonseed and soybean hulls, resulting from the oil industry, have been used in the adsorption of thorium element from a wastewater effluent coming from different industries. The results obtained indicate that maximum removal of thorium from a prepared solution takes place at pH 5 where equilibrium was attained after 100 min; using an adsorbent dose of 3 and 3.5 g/L for cottonseed and soybean hulls, respectively. On the other hand, the obtained mathematical data together with the obtained adsorption kinetic parameters indicate that both of cottonseed and soybean hulls could be useful adsorbents for thorium removal from industrial liquid wastes, especially when the low cost, environmental issues and high availability of these materials are considered

Phenotypic and Genotypic Characterization of Methicillin Resistance in <i>Staphylococci</i> Isolated from an Egyptian University Hospital

Methicillin-resistant in Staphylococci is a serious public health issue. It is mostly encoded by the mecA gene. The mecC gene is a new mecA analog responsible for resistance to methicillin in some Staphylococcal clinical isolates. This mecC gene is still underestimated in Egypt. The aim of the current study was to detect mecA and mecC genes in clinical Staphylococci isolates from a tertiary care university hospital in Egypt compared to the different phenotypic methods. A total of 118 Staphylococcus aureus (S. aureus) and 43 coagulase-negative Staphylococci (CoNS) were identified from various hospital-acquired infections. Methicillin resistance was identified genotypically using the PCR technique and phenotypically using the cefoxitin disc diffusion test, oxacillin broth microdilution and the VITEK2 system in all Staphylococcal isolates. The mecA gene was detected in 82.2% of S. aureus and 95.3% of CoNS isolates, while all of the isolates tested negative for the mecC gene. Interestingly, 30.2% of CoNS isolates showed the unique character of inducible oxacillin resistance, being mecA-positive but oxacillin-susceptible (OS-CoNS). The dual use of genotypic and phenotypic methods is highly recommended to avoid missing any genetically divergent strains