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The role of genomic islands in Escherichia coli K1 interactions with intestinal and kidney epithelial cells

Yousuf FA, Rafiq S, Siddiqui R, Khan NA

Microb Pathog, 2016 Apr;93:145-51.
PMID: 26867478 DOI: 10.1016/j.micpath.2016.02.002

The completion of Escherichia coli K1 genome has identified several genomic islands that are present in meningitis-causing E. coli RS218 but absent in the non-pathogenic E. coli MG1655. In this study, the role of various genomic islands in E. coli K1 interactions with intestinal epithelial cells (Caco-2) and kidney epithelial cells (MA104) was determined. Using association assays, invasion assays, and intracellular survival assays, the findings revealed that the genomic island deletion mutants of RS218 related to P fimbriae, S fimbriae, F17-like fimbriae, non-fimbrial adhesins, Hek and hemagglutinin, protein secretion system (T1SS for hemolysin; T2SS; T5SS for antigen 43), Iro system and hmu system), invasins (CNF1, IbeA), toxins (α-hemolysin), K1 capsule biosynthesis, metabolism (d-serine catabolism, dihydroxyacetone, glycerol, and glyoxylate metabolism), prophage genes, showed reduced interactions with both cell types. Next, we determined the role of various genomic islands in E. coli K1 resistance to serum. When exposed to the normal human serum, the viability of the genomic island deletion mutants related to adhesins such as S fimbriae, P fimbriae, F17-like fimbriae, non-fimbrial adhesins, Hek and hemagglutinin, antigen 43 and T5SS for antigen 43, T2SS, and T1SS for hemolysin, Iro system and hmu system, prophage genes, metabolism (sugar metabolism and d-serine catabolism), K1 capsule biosynthesis, and invasins such as CNF1 was affected, suggesting their role in bacteremia. The characterization of these genomic islands should reveal mechanisms of E. coli K1 pathogenicity that could be of value as therapeutic targets.
Multiplex real-time RT-PCR assay for transfusion transmitted viruses in sero-negative allogeneic blood donors: an experience from Southern Pakistan

Sultan S, Nasir MI, Rafiq S, Baig MA, Akbani S, Irfan SM

Malays J Pathol, 2017 Aug;39(2):149-154.
PMID: 28866696

BACKGROUND: Blood transfusion safety commences with healthy donor recruitment. The threat of transfusion transmitted infections is greatly minimized by serological tools but not entirely eliminated. Recently, nucleic-acid testing for blood donor screening has virtually eliminated this jeopardy.
METHODS: This prospective study was conducted from February 2015 to February 2016. Samples from seronegative donors were run on multiplex assay (Cobas, S-201 system platform, Roche) in a batch of six [MP-NAT]. In case of reactive pool, tests were run on every individual sample [IDNAT].
RESULTS: Of 16957 donors, 16836 (99.2%) were replacement donors and the remaining 121 (0.7%) were voluntary donors, with a mean age of 29.09 ± 7.04 years. After serologic screening of all 16957 donors, 955 (5.6%) were found to be reactive; 291(1.71%) were reactive for hepatitis-B surface antigen, 361 (2.12%) for antibody to hepatitis C virus (anti-HCV), 14 (0.08%) for antibody to human immunodeficiency virus, 287 (1.69%) for syphilis and 2 (0.01%) for malaria. 14 (0.08%) NAT reactive donors were identified after testing the 16002 seronegative donors, with an overall NAT yield of one reactivity out of 1143 blood donations; 10 donors for HBV-DNA (HBV NAT yield-1:1600) and remaining 4 for HCV-RNA (HCV-NAT yield-1:4000). None were HIV positive.
CONCLUSION: NAT has improved the safety attributes in blood products. Although the positivity rate for NAT testing is low but in view of the high prevalence of transfusion transmitted infections in our country, we recommend the parallel use of both serology and NAT screening of all donated blood.
Dissolution and delignification of bamboo biomass using amino acid-based ionic liquid

Muhammad N, Man Z, Bustam MA, Mutalib MI, Wilfred CD, Rafiq S

Appl Biochem Biotechnol, 2011 Oct;165(3-4):998-1009.
PMID: 21720837 DOI: 10.1007/s12010-011-9315-y

In the present work, the dissolution of bamboo biomass was tested using a number of ionic liquids synthesized in laboratory. It was observed that one of the synthesized amino acid-based ionic liquids, namely 1-ethyl-3-methylimidazolium glycinate, was capable of dissolving the biomass completely. The dissolved biomass was then regenerated using a reconstitute solvent (acetone/water) and was characterized using Fourier transform infrared spectroscopy, X-ray diffraction, and scanning electron microscopy. The results were compared to preconditioned bamboo biomass. The regenerated biomass was found to have a more homogenous macrostructure, which indicates that the crystalline form and structure of its cellulose has changed from type Ι to type ΙΙ during the dissolution and regeneration process.
Fulltext Serological response to influenza vaccination among children vaccinated for multiple influenza seasons

Rafiq S, Russell ML, Webby R, Fonseca K, Smieja M, Singh P, et al.

PLoS One, 2012;7(12):e51498.
PMID: 23240030 DOI: 10.1371/journal.pone.0051498

BACKGROUND: To evaluate if, among children aged 3 to 15 years, influenza vaccination for multiple seasons affects the proportion sero-protected.
METHODOLOGY/PRINCIPAL FINDINGS: Participants were 131 healthy children aged 3-15 years. Participants were vaccinated with trivalent inactivated seasonal influenza vaccine (TIV) over the 2005-06, 2006-07 and 2007-8 seasons. Number of seasons vaccinated were categorized as one (2007-08); two (2007-08 and 2006-07 or 2007-08 and 2005-06) or three (2005-06, 2006-07, and 2007-08). Pre- and post-vaccination sera were collected four weeks apart. Antibody titres were determined by hemagglutination inhibition (HAI) assay using antigens to A/Solomon Islands/03/06 (H1N1), A/Wisconsin/67/05 (H3N2) and B/Malaysia/2506/04. The proportions sero-protected were compared by number of seasons vaccinated using cut-points for seroprotection of 1:40 vs. 1:320. The proportions of children sero-protected against H1N1 and H3N2 was high (>85%) regardless of number of seasons vaccinated and regardless of cut-point for seroprotection. For B Malaysia there was no change in proportions sero-protected by number of seasons vaccinated; however the proportions protected were lower than for H1N1 and H3N2, and there was a lower proportion sero-protected when the higher, compared to lower, cut-point was used for sero-protection.
CONCLUSION/SIGNIFICANCE: The proportion of children sero-protected is not affected by number of seasons vaccinated.
Sustainable mixed matrix membranes containing porphyrin and polysulfone polymer for acid gas separations

Saqib S, Rafiq S, Muhammad N, Khan AL, Mukhtar A, Ullah S, et al.

J Hazard Mater, 2021 06 05;411:125155.
PMID: 33858108 DOI: 10.1016/j.jhazmat.2021.125155

The synergetic effect of nitrogen-rich and CO2-philic filler and polymer in mixed matrix-based membranes (MMMs) can separate CO2 competently. The introduction of well-defined nanostructured porous fillers of pores close to the kinetic diameter of the gas molecule and polymer matrix compatibility is a challenge in improving the gas transportation characteristics of MMMs. This study deals with the preparation of porphyrin filler and the polysulfone (PSf) polymer MMMs. The fillers demonstrated uniform distribution, uniformity, and successful bond formation. MMMs demonstrated high thermal stability with a glass transition temperature in the range of 480-610 °C. The porphyrin filler exhibited microporous nature with the presence of π-π bonds and Lewis's basic functionalities between filler-polymer resulted in a highly CO2-philic structure. The pure and mixed gas permeabilities and selectivity were successfully improved and surpass the Robeson's upper bound curve's tradeoff. Additionally, the temperature influence on CO2 permeability revealed lower activation energies at higher temperatures leading to the gas transport facilitation. This can be granted consistency and long-term durability in polymer chains. These results highlight the unique properties of porphyrin fillers in CO2 separation mixed matrix membranes and offer new knowledge to increase comprehension of PSf performance under various contents or environments.
Development of an extended model for the permeation of environmentally hazardous CO2 gas across asymmetric hollow fiber composite membranes

Jamil A, Ching OP, Iqbal T, Rafiq S, Zia-Ul-Haq M, Shahid MZ, et al.

J Hazard Mater, 2021 Sep 05;417:126000.
PMID: 33992016 DOI: 10.1016/j.jhazmat.2021.126000

This study presents an extended thermodynamic and phenomenological combined model to mitigate the environmental hazardous acid gas over composite membranes. The model has been applied to an acid gas such as carbon dioxide (CO2) for its permeation through polyetherimide incorporated montmorillonite (Mt) nanoparticles hollow fiber asymmetric composite membranes. The well-established non-equilibrium lattice fluid (NELF) model for penetrating low molecular weight penetrant in a glassy polyetherimide (PEI) was extended to incorporate the other important polymer/filler system features such as tortuosity in acid gas diffusion pathways resulted from layered filler aspect ratio and concentration. The model mentioned above predicts the behavior of acid gas in PEI-Mt composite membranes based on thermodynamic characteristics of CO2 and PEI and tortuosity due to Mt. The calculated results are compared to experimentally determined values of CO2 permeability through PEI-Mt composite asymmetric hollow fiber membranes at varying transmembrane pressures and Mt concentrations. A reasonable agreement was found between the model predicted behavior and experimentally determined data in terms of CO2 solubility, Mt concentration and aspect ratio were calculated based on average absolute relative error (%AARE). The proposed modified model efficiently predicts the CO2 permeance across MMMs up to 3 wt% Mt loadings and 6 bar pressure with ± 10%AARE.
Hazardous wastewater treatment by low-cost sorbent with in situ regeneration using hybrid solar energy-electrochemical system

Khan MM, Asghar HMA, Saulat H, Chawla M, Rafiq S, Khan MM, et al.

Water Environ Res, 2021 Sep;93(9):1554-1561.
PMID: 33583113 DOI: 10.1002/wer.1537

Hazardous industrial wastes negatively impact the environment by creating issues for aquatic as well as human's life. This study investigates the treatment of hazardous industrial wastewater using cost-effective graphite adsorbent along with electrochemical regeneration integrated with renewable solar energy. The synthetic industrial effluent containing crystal violet dye was treated using an adsorbent (Nyex™ 1000) having a surface area of 1.0 m2 g-1 . The efficiency of removing solute was found to be more than 90%. The adsorbent regeneration efficiency was achieved at 99.5% by passing a charge of 100 C g-1 at current density of 10 mA cm-2 for 1 h. Solar energy was integrated with electrochemical reactor for the regeneration of adsorbent to make the system cost-effective and self-sustainable. PRACTITIONER POINTS: Industrial hazardous wastewater treatment with a cost-effective graphite integrated adsorbent. Development of renewable solar energy-integrated with electrochemical system for regeneration. Regeneration efficiency of adsorbent Nyex™ 1000 was achieved around 99.5% with integrated system. Sustainable system was introduced to incorporate with renewable energy for waste water treatment.
Anaerobic membrane bioreactors for biohydrogen production: Recent developments, challenges and perspectives

Aslam M, Ahmad R, Yasin M, Khan AL, Shahid MK, Hossain S, et al.

Bioresour Technol, 2018 Dec;269:452-464.
PMID: 30145004 DOI: 10.1016/j.biortech.2018.08.050

Biohydrogen as one of the most appealing energy vector for the future represents attractive avenue in alternative energy research. Recently, variety of biohydrogen production pathways has been suggested to improve the key features of the process. Nevertheless, researches are still needed to overcome remaining barriers to practical applications such as low yields and production rates. Considering practicality aspects, this review emphasized on anaerobic membrane bioreactors (AnMBRs) for biological hydrogen production. Recent advances and emerging issues associated with biohydrogen generation in AnMBR technology are critically discussed. Several techniques are highlighted that are aimed at overcoming these barriers. Moreover, environmental and economical potentials along with future research perspectives are addressed to drive biohydrogen technology towards practicality and economical-feasibility.
Fabrication and performance evaluation of polymeric membrane using blood compatible hydroxyapatite for artificial kidney application

Zaman SU, Saif-Ur-Rehman, Zaman MKU, Rafiq S, Arshad A, Khurram MS, et al.

Artif Organs, 2021 Nov;45(11):1377-1390.
PMID: 34152645 DOI: 10.1111/aor.14020

In the current study, a phase inversion scheme was employed to fabricate hydroxyapatite (HA)/polysulfone (PSF)-based asymmetric membranes using a film applicator with water as a solvent and nonsolvent exchanging medium. Fourier Transform Infrared (FTIR) and X-ray diffraction (XRD) spectroscopic studies were conducted to confirm the bonding chemistry and purity of filler. The inherent thick nature of PSF generated sponge-like shape while the instantaneous demixing process produced finger-like pore networks in HA/PSF-based asymmetric membranes as exhibited by scanning electron microscope (SEM) micrographs. The FTIR spectra confirmed noncovalent weak attractions toward the polymer surface. The leaching ratio was evaluated to observe the dispersion behavior of HA filler in membrane composition. Hydrophilicity, pore profile, pure water permeation (PWP) flux, and molecular weight cutoff (MWCO) values of all formulated membranes were also calculated. Antifouling results revealed that HA modified PSF membranes exhibited 43% less adhesion of bovine serum albumin (BSA) together with >86% recovery of flux. Membrane composition showed 74% total resistance, out of which 60% was reversible resistance. Biocompatibility evaluation revealed that the modified membranes exhibited prothrombin time (PT), and thrombin time (TT) comparable with typical blood plasma, whereas proliferation of living cells over membrane surface proved its nontoxic behavior toward biomedical application. The urea and creatinine showed effective adsorption aptitude toward HA loaded PSF membranes.
Fulltext 2q36.3 is associated with prognosis for oestrogen receptor-negative breast cancer patients treated with chemotherapy

Li J, Lindström LS, Foo JN, Rafiq S, Schmidt MK, Pharoah PD, et al.

Nat Commun, 2014 Jun 17;5:4051.
PMID: 24937182 DOI: 10.1038/ncomms5051

Large population-based registry studies have shown that breast cancer prognosis is inherited. Here we analyse single-nucleotide polymorphisms (SNPs) of genes implicated in human immunology and inflammation as candidates for prognostic markers of breast cancer survival involving 1,804 oestrogen receptor (ER)-negative patients treated with chemotherapy (279 events) from 14 European studies in a prior large-scale genotyping experiment, which is part of the Collaborative Oncological Gene-environment Study (COGS) initiative. We carry out replication using Asian COGS samples (n=522, 53 events) and the Prospective Study of Outcomes in Sporadic versus Hereditary breast cancer (POSH) study (n=315, 108 events). Rs4458204_A near CCL20 (2q36.3) is found to be associated with breast cancer-specific death at a genome-wide significant level (n=2,641, 440 events, combined allelic hazard ratio (HR)=1.81 (1.49-2.19); P for trend=1.90 × 10(-9)). Such survival-associated variants can represent ideal targets for tailored therapeutics, and may also enhance our current prognostic prediction capabilities.