BCR-ABL1 Gene Mutation in Acute Lymphoblastic Leukemia

Objective:  Determination of frequency of BCR-ABL1 gene mutation in Acute Lymphoblastic Leukemia. Methodology: This cross sectional study was carried out at the Department of Molecular Haematology, Armed Forces Institute of Pathology between January 2018 to March 2021. All newly diagnosed patients of Acute Lymphoblastic Leukemia were included in the study while patients already on treatment and with secondary leukemia were excluded from the study. Blood counts were done and various parameters such as total leukocyte count, hemoglobin, and platelet count were calculated. Results: 623 patients were included in the study. BCR-ABL gene was positive in 105 (16.8%) patients. A total of 96 (92%) were positive for BCR ABL p190 rearrangement and 9 (8%) were positive for BCR ABL p210 rearrangement.  Mean age of patients was 21 years. The frequency of BCR ABL gene was positive in 72% males and 28% females. BCR-ABL positive ALL was associated with higher TLC count. CNS involvement was more common in Acute Lymphoblastic Leukemia with BCR-ABL. The likelihood of post-induction remission decreased with age. Conclusion: In our study population, a frequency of 16.8% patients were BCR ABL1 positive in acute lymphoblastic leukemia. BCR- ABL gene mutation in ALL is more prevalent in young adults. The frequency of p190 rearrangement is more common than p210 BCR-ABL rearrangement. BCR-ABL positive ALL is more prevalent in males than in females

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

Background: We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.Materials and methods: We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.Results: In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10-4. The most frequent mutations were 5\u27 UTR 241C \u3e T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site.Conclusions: The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic

Assessing the potential of different nano-composite (MgO, Al2O3-CaO and TiO2) for efficient conversion of Silybum eburneum seed oil to liquid biodiesel

This study investigated the potential of nano-composite MgO, Al2O3-CaO and TiO2 for efficient conversion of novel non edible seed oil of Silybum eburneum into liquid biodiesel. Silybum eburneum contains oil contents (37.7%) and low free fatty acid (FAA) value (0.16 mg KOH/g). The synthesized heterogeneous nano-catalysts were characterized using X-Ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FT-IR), Energy Dispersive X-Ray Spectroscopy (EDX) and Scanning Electron Microscopy (SEM) techniques. The highest conversion efficiency was achieved (91% biodiesel yield) using MgO catalyst followed by Al2O3-CaO and TiO2 at 0.1% catalysts loading. The optimized experimental variables comprised of molar ratio (1:3), temperature (70 degrees C), reaction time (3 h.) and stirring rate (600 rpm) using reflux transesterification route. The XRD analysis showed the sizes of the crystal lattices with a sequence of 13 nm for MgO, 29 nm for Al2O3-CaO and 37 nm for TiO2 which reveals that smaller the size of the crystal structure, higher will be the conversion efficiency. The SEM of MgO showed exclusively porous lamellar like smooth surface highly agglomerated with nano entities with a particle size of 50 +/- 10 nm length or width and about 20 nm thickness. SEM images of Al2O3-CaO nano-particles showed the size range from 27 nm to 75 nm having irregular morphology including spherical as well as rod shape with smooth surface and different size. The diameter of the microsphere calculated was about 26 mu m. SEM for TiO2 demonstrated that the average size was from 68.7 nm to 87.3 nm with interring particle dimension. The shape was proved to be sponge-like with spherical nano-holes. The FT-IR and EDX analysis of the catalyst also supported the study results. Gas Chromatography Mass Spectroscopy (GCMS), Nuclear Magnetic Resonance NMR and FT-IR results confirmed the conversion efficiency of applying nano-catalysts. The results observed a novel finding that the conversion efficiency may increase with reducing the size and increasing the surface area of the nano-heterogeneous catalysts. The prepared composites are cheaper and can be applied for industrial scale production of biomass energy making it more cost effective and economically feasible. (C) 2017 Elsevier B.V. All rights reserved

Upregulated type I interferon responses in asymptomatic COVID-19 infection are associated with improved clinical outcome

Understanding key host protective mechanisms against SARS-CoV-2 infection can help improve treatment modalities for COVID-19. We used a blood transcriptome approach to study biomarkers associated with differing severity of COVID-19, comparing severe and mild Symptomatic disease with Asymptomatic COVID-19 and uninfected Controls. There was suppression of antigen presentation but upregulation of inflammatory and viral mRNA translation associated pathways in Symptomatic as compared with Asymptomatic cases. In severe COVID-19, CD177 a neutrophil marker, was upregulated while interferon stimulated genes (ISGs) were downregulated. Asymptomatic COVID-19 cases displayed upregulation of ISGs and humoral response genes with downregulation of ICAM3 and TLR8. Compared across the COVID-19 disease spectrum, we found type I interferon (IFN) responses to be significantly upregulated (IFNAR2, IRF2BP1, IRF4, MAVS, SAMHD1, TRIM1), or downregulated (SOCS3, IRF2BP2, IRF2BPL) in Asymptomatic as compared with mild and severe COVID-19, with the dysregulation of an increasing number of ISGs associated with progressive disease. These data suggest that initial early responses against SARS-CoV-2 may be effectively controlled by ISGs. Therefore, we hypothesize that treatment with type I interferons in the early stage of COVID-19 may limit disease progression by limiting SARS-CoV-2 in the host

Investigating the impact of prior COVID-19 on IgG antibody and interferon γ responses after BBIBP-CorV vaccination in a disease endemic population: A prospective observational study

Background and aims: COVID-19 vaccinations have reduced morbidity and mortality from the disease. Antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) have been associated with immune protection. Seroprevalence studies revealed high immunoglobulin G (IgG) antibody levels to SARS-CoV-2 in the Pakistani population before vaccinations. We investigated the effect of BBIBP-CorV vaccination on circulating IgG antibodies and interferon (IFN)-γ from T cells measured in a cohort of healthy individuals, with respect to age, gender, and history of COVID-19. Methods: The study was conducted between April and October 2021. BBIBP-CorV vaccinated participants were followed up to 24 weeks. Antibodies to SARS-CoV-2 Spike protein and its receptor-binding domain (RBD) were measured. IFNγ secreted by whole blood stimulation of Spike protein and extended genome antigens was determined. Results: Study participants with a history of prior COVID-19 displayed a higher magnitude of IgG antibodies to Spike and RBD. IgG seropositivity was greater in those with prior COVID-19, aged 50 years or younger and in females. At 24 weeks after vaccination, 37.4% of participants showed IFN-γ responses to SARS-CoV-2 antigens. T cell IFN-γ release was higher in those with prior COVID-19 and those aged 50 years or less. Highest IFN-γ release was observed to extended genome antigens in individuals both with and without prior COVID-19. Conclusion: We found that IgG seropositivity to both Spike and RBD was affected by prior COVID-19, age and gender. Importantly, seropositive responses persisted up to 24 weeks after vaccination. Persistence of vaccine induced IgG antibodies may be linked to the high seroprevalence observed earlier in unvaccinated individuals. Increased T cell reactivity to Spike and extended genome antigens reflects cellular activation induced by BBIBP-CorV. COVID-19 vaccination may have longer lasting immune responses in populations with a higher seroprevalence. These data inform on vaccination booster policies for high-risk group

Humoral and T cell responses to SARS-CoV-2 reveal insights into immunity during the early pandemic period in Pakistan

Background: Protection against SARS-CoV-2 is mediated by humoral and T cell responses. Pakistan faced relatively low morbidity and mortality from COVID-19 through the pandemic. To examine the role of prior immunity in the population, we studied IgG antibody response levels, virus neutralizing activity and T cell reactivity to Spike protein in a healthy control group (HG) as compared with COVID-19 cases and individuals from the pre-pandemic period (PP).Methods: HG and COVID-19 participants were recruited between October 2020 and May 2021. Pre-pandemic sera was collected before 2018. IgG antibodies against Spike and its Receptor Binding Domain (RBD) were determined by ELISA. Virus neutralization activity was determined using a PCR-based micro-neutralization assay. T cell - IFN-γ activation was assessed by ELISpot.Results: Overall, the magnitude of anti-Spike IgG antibody levels as well as seropositivity was greatest in COVID-19 cases (90%) as compared with HG (39.8%) and PP (12.2%). During the study period, Pakistan experienced three COVID-19 waves. We observed that IgG seropositivity to Spike in HG increased from 10.3 to 83.5% during the study, whilst seropositivity to RBD increased from 7.5 to 33.3%. IgG antibodies to Spike and RBD were correlated positively in all three study groups. Virus neutralizing activity was identified in sera of COVID-19, HG and PP. Spike reactive T cells were present in COVID-19, HG and PP groups. Individuals with reactive T cells included those with and without IgG antibodies to Spike.Conclusions: Antibody and T cell responses to Spike protein in individuals from the pre-pandemic period suggest prior immunity against SARS-CoV-2, most likely from cross-reactive responses. The rising seroprevalence observed in healthy individuals through the pandemic without known COVID-19 may be due to the activation of adaptive immunity from cross-reactive memory B and T cells. This may explain the more favourable COVID-19 outcomes observed in this population