Screening of Arabidopsis mutants for functional genomic studies

Eight photosynthetic Arabidopsis mutants were screened for co-segregation of a photosynthetic phenotype with the T-DNA insertion. These mutants were selected from 80 photosynthetic mutants with genetic background of Columbia-0. Two different screening approaches were used to study the T-DNA insertion in the genome of mutant Arabidopsis lines. The sulphonamide sulfadiazine was found to be an effective selective agent and a single copy of sulfonamide resistant gene was found to be completely resistant to the optimal concentration i.e., 5mg mL-1. The maximum number of Arabidopsis mutant plants had confirmed insertions. Some of the plants did not show any amplification with gene specific primer combination, and it was assumed that either they were wild type plants or they had random T-DNA insertion and the insertion was not found in the gene under study but it could be found in any where in the genome. Some mutant plants were morphologically different from the wild type plants e.g., ALP105. These plants grew as small in size and dark green in color. After PCR screening with gene specific and T-DNA border primers all such mutant plants were confirmed as heterozygous T-DNA insertion plants

Genetic diversity of rose germplasm in Pakistan characterized by random amplified polymorphic DNA (RAPD) markers

Random amplified polymorphic DNA (RAPD) markers have been found to be very useful in studying the genetic variability of different species, including Rosa. Present studies were undertaken for the identification and  analysis of genetic variation within a collection of 4 species and 30 accessions of rose using RAPD analysis  technique. The results showed the molecular distinctions among the genotypes when analysed using 25 RAPD primers. Total amplified bands were 146, out of which 110 were polymorphic, with an average of seven bands per primer. Maximum number of bands (10) was produced by primer GLD-20, while GLC-02 produced the  minimum number of bands (2). Maximum polymorphism in the present study was obtained by primer GLA-03, GLA-05, GLA-07, GLA-10, GLC-02, GLC-06, GLC-08, GLC-10, OPG-11 and OPE-19 which produced 100%  polymorphic bands, while primer GLB-11 produced only 42.85% polymorphic bands. This study demonstrated the potential of RAPD technique for the characterization of genetic variation within the rose germplasm.Key words: Random amplified polymorphic DNA, polymorphism, rose germplasm, primer

Exploring the Learning Styles of Postgraduates in a Public-Sector University at Karachi

Introduction: Learning styles is a term used to refer to the methods of gathering, processing, interpreting, organizing and thinking about information. Knowledge of the learning styles can be helpful in making teaching and learning process more efficient. Little is mentioned in medical education literature in Pakistan about the learning styles knowledge in deciphering the teaching and learning process. Objective: To identify the distribution of the learning styles among the postgraduate students and to find ways to improve the way the courses, the practical hours and training are performed. Methodology: The current study analyses the learning styles of post graduate students of Dow University of Health Sciences Karachi to guide facilitator as well as students in organizing their teaching sessions more efficiently and maximize the utility of educational resources with subsequent improvement in educational process. During Jan 2016 to Dec 2016, this cross-sectional study using Kolb’s learning inventory as the instrument to find out the learning styles was conducted among post-graduates’ students of a public-sector university by using English language versions of Learning Style Inventory (LSI)of 216 post-graduates ‘students. Results: According to observation and data analysis by Kolb’s learning Styles Inventory most of the postgraduates had their learning style reflector (Diverger). However, some were Theorist (Assimilators) and then very few were Activist (Accommodator) and Pragmatist (Converser) respectively. Conclusions: Differences in the learning styles and learning approaches have important implications in development of effective medical curricula in post graduate medical education.  Key words: Learning style, Postgraduate students, medical educatio

Mortality Trends In Pre COVID And Pandemic Era In A Tertiary Care Setting

Objective: The coronavirus pandemic has emphasized stay-at-home and social distancing policies. Since the beginning of the outbreak of COVID-19, there has been a declining trend of hospital mortality indicating that the pandemic might keep patients from seeking emergency care in a hospital setting. This study was carried out to determine the mortality trends pre-COVID and pandemic periods in a tertiary care hospital. Methods:  Study design: Retrospective observational study Place and Duration: 1st January 2019 to December 2021 at Federal Government Polyclinic (FGPC) Hospital Islamabad It was a retrospective review done on death data of pre-COVID (January-December 2019) and pandemic(January 2020-December 2021) period. Data on death was retrieved from medical male and female wards, medical ICU and isolation ward. The mortality rate was measured for both pre-COVID and pandemic periods along with co-morbid for the pandemic period. Descriptive statistics were measured with the SPSS software version. 23.  Association with age, gender and mortality was observed using a chi-square test taking p value ≤ 0.05 as significant. Result: In this study of the 366 deaths, the average age of patients in the pre-COVID and pandemic era was57.40±17.910 and 64.31±16.065 respectively. The males and females were 50.9% and 49.1% in the pre-COVID period while 61.5% and 38.5% in the pandemic period. The frequency of deaths was 46.7% in the pre COVID and 53.3% in the pandemic period with a p-value <0.05. Patients with co-morbid died more in the pandemic era. Conclusion: It was observed that hospital mortality trends were in decline during the COVID-19 pandemic in our setting which may be associated with lockdown, decreased access to the hospitals or fear of going to hospital

Perception and knowledge about dietary intake in patients with liver cirrhosis and its relationship with the level of education

Objective: To determine patients perception and knowledge regarding diet in cirrhosis and its relationship with the level of patients education. Study Design: Cross-sectional observational study. Place and Duration of Study: This study was conducted at Gastroenterology Outpatient Clinics at the Aga Khan University Hospital, Karachi, the Aga Khan Health Services, Malir, Karachi and Hamdard University, Karachi, from January to December 2010. Methodology: Consecutive adult patients with compensated cirrhosis were enrolled. Demographic data, level of education, type and reason of food restriction as well as the source of dietary information was asked. Baseline laboratory test were performed, and nutritional status was assessed by BMI normogram. Results: Ninety patients, 58% male were enrolled. Mean age of the patient was 49 11 years. Overall 73% of the patients were restricting fat, meat, fish and eggs in their diet; 53% were in uneducated group and 47% were in educated group (CI, 0.24-1.62, p-0.34). Twenty two patients (62.8%) in uneducated and 21 in educated group (68%) were restricting diet on the advice of their doctors, whereas 13 in uneducated group (37%) and 11 in educated group (32%) believed these dietary components to be harmful for the liver. Thirty two of uneducated patient (71.1%) and 28 of educated patients (62.2%) believed that vegetables, fruits and sugarcane had a beneficial effect on the liver. Main source of dietary information to the patients was the doctor. On sub-group analysis those who restricted diet irrespective of their educational level, had more patients with BMI less than 18.5 kg/m2, (CI 0.01-0.94, p-0.001), haemoglobin less than 12 g/dl (CI 0- 0.03, p-0.001) and serum albumin less than 3 g/dl (CI 0.1- 03, p-0.001). Conclusion: Both educated and uneducated classes of the patients have improper knowledge and perception of diet in cirrhosis. Patients with cirrhosis who restricted diet, had relatively low BMI, haemoglobin and albumin as compared to those who did not restrict. Main source of dietary information to cirrhotic patients were health care personnels

Nutritional status in patients with Hepatitis C

OBJECTIVE: To assess the nutritional status via the SGA (subjective global assessment) screening tool of patients at all stages of hepatitis C virus (HCV) liver disease. STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Out-patient Clinics of the Aga Khan University Hospital, Karachi, conducted from October 2009 to January 2011. METHODOLOGY: Patients with hepatitis C virus infection and their HCV-negative attendants were enrolled from the outpatient clinics, and categorized into 4 groups of 100 patients each: healthy controls (HC), those with chronic hepatitis C infection (CHC), compensated cirrhotics (CC) and decompensated cirrhotics (DC). The validated subjective global assessment (SGA) tool was used to assess nutritional status. RESULTS: A total of 400 patients were enrolled. Most of the patients in the HC group were class \u27A\u27 (best nutritional status). In contrast, the majority (64%) in the DC group were in the class \u27C\u27 (worst status). The compensated cirrhosis (CC) group showed that 90% of patients were malnourished, while 98% of all patients were malnourished in the DC group, predominantly class \u27C\u27. Most importantly, 14% of patients with chronic hepatitis C (CHC) also scored a \u27B\u27 on the SGA; which when compared to HC was statistically significant (p=0.005). As the groups progressed in their disease from CHC to DC, the transition in nutritional status from \u27A\u27 to \u27C\u27 between groups was statistically significant. CONCLUSION: Malnutrition occurs early in the course of HCV, and progresses relentlessly throughout the spectrum of HCVdisease

Anti-Helicobacter pylori activity and inhibition of Helicobacter pylori-induced release of IL-8 in AGS cells by plant extracts

Plants used in popular diet were studied for anti-Helicobacter pylori activity and their effect on the expression of interleukin-8 (IL-8) from H. pylori infected gastric epithelial cells. Extracts were prepared of Allium sativum (A. sativum), Cuminum cyminum (C. cyminum),Piper nigrum (P. nigrum) and their mix in two different dilutions. AGS cell line and H. pyloristrains were used for co-culture experiments. Extracts bactericidal activity was determined by a viable colony count. ELISA (Enzyme linked immunosorbent assay) was used to determine IL-8 expression. DNA extracted from bacterial cells was used for polymerase chain reaction (PCR) of cytotoxin-associated gene (cagA) and E (cagE). Results revealedH. pylori strains sensitivity to A. sativum (5.5 mg/ml) was 57% (39/69) (p=0.06), and to 11 mg/ml was 65% (45/69) (p=0.02) compared to amoxicillin, respectively. CagE positive H. pylori, 37% (11/30) (p=0.02) were sensitive to plant mixture (23.5 mg/ml), 60% (18/30) (pC. cyminum (PP. nigrum (P=0.0046) and A. sativum(P=0.0021), respectively compared to positive and negative controls. Thus, dietary plants demonstrated an anti-H. pylori effect. They reduced IL-8 expression from the H. pyloriinfected AGS cells. Key words: Helicobacter pylori; Allium sativum, Cuminum cyminum, Piper nigrum, gastric epithelial cells, interleukin-8, ELISA, cagA, cagE

Preparation, Characterization, and Pharmacological Investigation of Withaferin-A Loaded Nanosponges for Cancer Therapy; In Vitro, In Vivo and Molecular Docking Studies

From MDPI via Jisc Publications RouterHistory: accepted 2021-11-14, pub-electronic 2021-11-19Publication status: PublishedFunder: The Oman Research Council; Grant(s): BFP/RGP/HSS/19/198The rapidly growing global burden of cancer poses a major challenge to public health and demands a robust approach to access promising anticancer therapeutics. In parallel, nanotechnology approaches with various pharmacological properties offer efficacious clinical outcomes. The use of new artificial variants of nanosponges (NS) as a transporter of chemotherapeutic drugs to target cells has emerged as a very promising tool. Therefore, in this research, ethylcellulose (EC) NS were prepared using the ultrasonication assisted-emulsion solvent evaporation technique. Withaferin-A (WFA), an active ingredient in Withania somnifera, has been implanted into the nanospongic framework with enhanced anticancer properties. Inside the polymeric structure, WFA was efficiently entrapped (85 ± 11%). The drug (WFA) was found to be stable within polymeric nanosponges, as demonstrated by Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC) studies. The WFA-NS had a diameter of 117 ± 4 nm and zeta potential of −39.02 ± 5.71 mV with a polydispersity index (PDI) of 0.419 ± 0.073. In addition, scanning electron microscopy (SEM) revealed the porous surface texture of WFA-NS. In vitro anticancer activity (SRB assay) results showed that WFA–NS exhibited almost twice the anticancer efficacy against MCF-7 cells (IC50 = 1.57 ± 0.091 µM), as quantified by flow cytometry and comet tests. Moreover, fluorescence microscopy with DAPI staining and analysis of DNA fragmentation revealed apoptosis as a mechanism of cancer cell death. The anticancer activity of WFA-NS was further determined in vivo and results were compared to cisplatin. The anticancer activity of WFA-NS was further investigated in vivo, and the data were consistent to those obtained with cisplatin. At Day 10, WFA-NS (10 mg/kg) significantly reduced tumour volume to 72 ± 6%, which was comparable to cisplatin (10 mg/kg), which reduced tumour volume to 78 ± 8%. Finally, the outcomes of molecular modeling (in silico) also suggested that WFA established a stable connection with nanosponges, generating persistent hydrophobic contacts (polar and nonpolar) and helping with the attractive delayed-release features of the formulation. Collectively, all the findings support the use of WFA in nanosponges as a prototype for cancer treatment, and opened up new avenues for increasing the efficacy of natural product-derived medications

A Comparison of Re-Sampling Techniques for Detection of Multi-Step Attacks on Deep Learning Models

The increasing dependence on data analytics and artificial intelligence (AI) methodologies across various domains has prompted the emergence of apprehensions over data security and integrity. There exists a consensus among scholars and experts that the identification and mitigation of Multi-step attacks pose significant challenges due to the intricate nature of the diverse approaches utilized. This study aims to address the issue of imbalanced datasets within the domain of Multi-step attack detection. To achieve this objective, the research explores three distinct re-sampling strategies, namely over-sampling, under-sampling, and hybrid re-sampling techniques. The study offers a comprehensive assessment of several re-sampling techniques utilized in the detection of Multi-step attacks on deep learning (DL) models. The efficacy of the solution is evaluated using a Multi-step cyber attack dataset that emulates attacks across six attack classes. Furthermore, the performance of several re-sampling approaches with numerous traditional machine learning (ML) and deep learning (DL) models are compared, based on performance metrics such as accuracy, precision, recall, F-1 score, and G-mean. In contrast to preliminary studies, the research focuses on Multi-step attack detection. The results indicate that the combination of Convolutional Neural Networks (CNN) with Deep Belief Networks (DBN), Long Short-Term Memory (LSTM), and Recurrent Neural Networks (RNN) provides optimal results as compared to standalone ML/DL models. Moreover, the results also depict that SMOTEENN, a hybrid re-sampling technique, demonstrates superior effectiveness in enhancing detection performance across various models and evaluation metrics. The findings indicate the significance of appropriate re-sampling techniques to improve the efficacy of Multi-step attack detection on DL models