Department of Biology, Chemistry and Environmental Sciences

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Work by the faculty and students of the Department of Biology, Chemistry and Environmental Sciences


Recent Submissions

  • Publication
    Modifying cellulose fibres with carbon dots: a promising approach for the development of antimicrobial fibres
    (Royal Society, 2024-04-17) Radha, Remya; Makhlouf, Zinb; Diab, Rasha; Al-Sayah, Mohammad
    This study focuses on the development of antimicrobial fibres for use in medical and healthcare textile industries. Carbon dots (CDs) were designed with boronic acid groups for the attachment to cellulose fibres found in cotton textiles and to enhance their attachment to glycogens on bacterial surfaces. Boronic acid-based and curcumin-based CDs were prepared and characterized using various techniques, showing a nanoscale size and zeta potential values. The CDs inhibited the growth of both Staphylococcus epidermidis and Escherichia coli bacteria, with UV-activated CDs demonstrating improved antibacterial activity. The antimicrobial activity of the CDs was then tested, revealing strong adherence to cellulose paper fibres with no CD diffusion and potent inhibition of bacterial growth. Cytotoxicity assays on human cell lines showed no toxicity towards cells at concentrations of up to 100 µg ml−1 but exhibited increased toxicity at concentrations exceeding 1000 µg ml−1. However, CD-modified cellulose paper fibres showed no toxicity against human cell lines, highlighting the antimicrobial properties of the CD-modified cellulose fibres are safe for human use. These findings show promising potential for applications in both industrial and clinical settings.
  • Publication
    Environmental Management Systems in Public Sector
    (Edward Elgar, 2023) Waxin, Marie-France; Bartholomew, Aaron; Zhao, Fang; Knuteson, Sandra; Makda, Areej
    This chapter focuses on environmental management systems (EMS) in public sector organisations (PSOs). Our objectives are to 1) explain what is an EMS, describe the two main EMS standards (ISO 14001 and EMAS) and how to implement them in PSOs, 2) present the benefits of EMS adoption in PSOs, and 3) present the key factors of successful EMS implementation in PSOs. The major benefits of EMS implementation in PSOs are improved environmental management practices, environmental awareness and image, organizational cost-efficiency, and environmental performance. The major key success factors are management's support, employees' and managers' awareness, competence and involvement, adoption of a collaborative management approach, allocation of sufficient organizational resources, and stakeholder involvement. We conclude by identifying interesting avenues for future research. This chapter will assist EMS scholars and practitioners in better understanding the specific issues related to EMS implementation in PSOs.
  • Publication
    Enhancement of the corrosion resistance of mild steel with femtosecond laser- nanostructuring and CrCoNi medium entropy alloy coating
    (Elsevier, 2022) Ahmad, Shahbaz; Ahmad, Waqas; Abu Baker, Aya; Egilmez, Mehmet; Abuzaid, Wael; Orhan, Mehmet Fatih; Ibrahim, Taleb; Khamis, Mustafa; Alnaser, Ali
    In this work, the corrosion resistance of mild steel surface nanostructured with a femtosecond laser and coated with high corrosion resistant CrCoNi (CCN) medium entropy alloy through magnetron sputtering is studied. Substantial improvement in corrosion protection was achieved by applying a combination of high-power femtosecond laser surface nano-structuring at ambient conditions and thin-film coating with (CCN) medium entropy alloy. XRD analysis revealed that femtosecond laser structuring increases the susceptibility of the surfaces to Fe₂O₃ nucleation through oxidation. The surface wettability measurements and electrochemical polarization tests revealed that the combined approach of femtosecond laser structuring and magnetron sputter coating is the best for desired high corrosion resistance. Through this novel method, the resulting corrosion resistance of mild steel was improved by more than one-fold. The results are explained considering the detailed microstructural analysis. The presented findings open new possibilities for corrosion prevention using a combination of new powerful technologies that yield to unprecedented corrosion-inhibition efficacy.
  • Publication
    Drivers, Challenges and Outcomes of Environmental Management System Implementation in Public Sector Organizations: A Systematic Review of Empirical Evidence
    (MDPI, 2023-04-28) Waxin, Marie-France; Bartholomew, Aaron; Zhao, Fang; Siddiqi, Ayesha
    Our research objectives were to conduct a systematic literature review of the empirical articles on the drivers, challenges and outcomes of environmental management system (EMS) implementation in public sector organizations (PSOs) in the Scopus database, published in English. Following the PRISMA guidelines, we identified, reviewed and analyzed 11 selected articles. We used content analysis to identify important themes and concepts. First, we mapped the selected literature. We then identified four main categories of drivers (environmentally strategic, social/stakeholders, regulatory and organizational efficiency), five categories of challenges (budgetary, human resource, technical, managerial and regulatory) and five categories of outcomes (improvement in environmental management practices, environmental performance, awareness of environmental issues, image and organizational efficiency). Finally, we identified important avenues for future research that should be explored further. This article synthesizes the knowledge on EMS implementation in PSOs and offers new insights. It will help EMS scholars and practitioners develop a broader and more critical understanding of the issues specific to EMS implementation in PSOs.
  • Publication
    Insights into rechargeable Zn-air batteries for future advancements in energy storing technology
    (Elsevier, 2023-02-27) Iqbal, Anum; El-Kadri, Oussama; Hamdan, Nasser
    Owing to its high theoretical specific energy density, low cost, abundance and environmental friendliness, the rechargeable Zn-Air batteries (ZAB) are becoming the most prevalent candidate as energy storage devices for consumer electronics, and electric vehicles. Nevertheless, the interaction of O2 as a fuel with the components of ZAB is highly challenging for practical implementations of this technology. The underlying electrochemical reactions in ZAB involving multi-electron transfer, adsorption/evolution of O2, and dissolution of Zn metal in electrolyte, need robust-electrocatalyst and stable Zn/electrolyte interface. This prominently evokes the need for an in-depth study of electrocatalytic reactions occurring at the electrode/electrolyte interphases as well as the physiochemical features of membranes in ZAB. Therefore, this review provides significant insights into the fundamentals of Zn air battery system in terms of the underlying electrochemical mechanism, composition/structural performance relationship of different battery components. A detailed section has been devoted in summarizing the evaluating factors for battery performance including power density, polarization curves, columbic efficiency and correlation of catalyst's redox activity (Eonset, Ehalf-way, and Jd) with the device performance parameters (OCV, Ohmic losses, and Pmax). Moreover, representative studies of in-situ/operando characterizations have also been summarized to reveal the structural stability, reaction kinetics, formation of by-products, and morphological evolution. The intriguing advanced features of ZABs including flexibility, photo-recharge ability, economic feasibility, fast charging, high energy density, improved stability and hybrid Zn battery systems are particularly discussed. For the accomplishment of these functionalities, the chemical heterogeneity and structural modifications of materials (electrode, electrolyte and membranes) with improved electrical conductivity, reduced energy barrier, increased reactive surface area, and improved mass transport behavior at the nanoscale have been anticipated. This material survey could be highly beneficial for the development and modification of new catalysts in the field of electrocatalysis. Additionally, for the prospect of green energy technology, the economic viability and environmental sustainability of ZAB are also highlighted. Lastly, based on the discussion of recent achievements, some challenges and outlooks for maturing the rechargeable Zn air battery technology at the academic level and at the industrial scale are also set forth.
  • Publication
    The Role of AEBP1 in Sex-Specific Diet-Induced Obesity
    (Springer Nature, 2005) Zhang, Lei; Reidy, Shannon P.; Nicholson, Tara E.; Lee, Hyun-Jeong; Majdalawieh, Amin; Webber, Chris; Stewart, Bruce R.; Dolphin, Peter; Ro, Hyo-Sung
    Obesity is an important risk factor for heart disease, diabetes, and certain cancers, but the molecular basis for obesity is poorly understood. The transcriptional repressor AEBP₁, which functions as a negative regulator of PTEN through a protein-protein interaction, is highly expressed in the stromal compartment of adipose tissues, including proliferative preadipocytes, and its expression is abolished in terminally differentiated, nonproliferative adipocytes. Here we show that transgenic overexpression of AEBP₁ during adipogenesis coupled with a high-fat diet (HFD) resulted in massive obesity in female transgenic (AEBP₁ᵀᴳ) mice via adipocyte hyperplasia. AEBP₁ levels dynamically changed with aging, and HFD induced AEBP₁ expression in females. Thus, HFD-fed AEBP₁ᵀᴳ females display hyperinduction of AEBP₁ and a marked reduction of PTEN level with concomitant hyperactivation of the survival signal in white adipose tissue. Our results suggest that AEBP₁ plays a key functional role in in vivo modulation of adiposity via fat-cell proliferation and is involved in a sex-specific susceptibility to diet-induced obesity by the estrogen signaling pathway.
  • Publication
    Adipocyte Enhancer-binding Protein-1 Promotes Macrophage Inflammatory Responsiveness by Up-Regulating NF-κB via IκBα Negative Regulation
    (The American Society for Cell Biology, 2007) Majdalawieh, Amin; Zhang, Lei; Ro, Hyo-Sung
    Nuclear factor κB (NF-κB) subunits comprise a family of eukaryotic transcription factors that are critically involved in cell proliferation, inflammation, and apoptosis. Under basal conditions, NF-κB subunits are kept under inhibitory regulation by physical interaction with NF-κB inhibitors (IκB subunits) in the cytosol. Upon stimulation, IκB subunits become phosphorylated, ubiquitinated, and subsequently degraded, allowing NF-κB subunits to translocate to the nucleus and bind as dimers to κB responsive elements of target genes. Previously, we have shown that AEBP1 enhances macrophage inflammatory responsiveness by inducing the expression of various proinflammatory mediators. Herein, we provide evidence suggesting that AEBP1 manifests its proinflammatory function by up-regulating NF-κB activity via hampering IκBα, but not IκBβ, inhibitory function through protein–protein interaction mediated by the discoidin-like domain (DLD) of AEBP1. Such interaction renders IκBα susceptible to enhanced phosphorylation and degradation, subsequently leading to augmented NF-κB activity. Collectively, we propose a novel molecular mechanism whereby NF-κB activity is modulated by means of protein–protein interaction involving AEBP1 and IκBα. Moreover, our study provides a plausible mechanism explaining the differential regulatory functions exhibited by IκBα and IκBβ in various cell types. We speculate that AEBP1 may serve as a potential therapeutic target for the treatment of various chronic inflammatory diseases and cancer.
  • Publication
    The trans-10, cis-12 isomer of conjugated linoleic acid decreases adiponectin assembly by PPARγ-dependent and PPARγ-independent mechanisms
    (Elsevier, 2008) Miller, Jessica R.; Siripurkpong, Pilaiwan; Hawes, Jennifer; Majdalawieh, Amin; Ro, Hyo-Sung; McLeod, Roger S.
    The adipocyte-derived secretory protein adiponectin functions as an insulin-sensitizing agent. In plasma, adiponectin exists as low, medium, and high molecular weight oligomers. Treatment with trans-10, cis-12 conjugated linoleic acid (t-10, c-12 CLA) reduces levels of adiponectin as well as triglyceride (TG) in mice and adipocyte cell culture models. The aim of this study was to determine whether the effects of t-10, c-12 CLA on adiponectin and TG are mediated through modulation of the transcription factor peroxisome proliferator-activated receptor γ (PPARγ). 3T3-L1 cells were treated either during or after differentiation into adipocytes with 100 μM t-10, c-12 CLA with or without 10 μM troglitazone, a PPARγ agonist, or 1 μM GW9662, a PPARγ antagonist, and adiponectin and TG levels were analyzed. Treatment with t-10, c-12 CLA reduced TG as well as cellular and secreted adiponectin levels and impaired the assembly of adiponectin oligomers. These changes were accompanied by decreases in PPARγ mass. Troglitazone was able to reverse the t-10, c-12 CLA-mediated decrease in TG levels and restore the assembly of adiponectin oligomers but was unable to restore adiponectin synthesis. Conversely, treatment with GW9662 decreased TG mass and impaired adiponectin oligomer assembly but did not decrease total adiponectin mass. In a reporter assay, t-10, c-12 CLA appeared to be a partial PPARγ agonist and prevented the stimulation of reporter activity by troglitazone. Therefore, the t-10, c-12 CLA isomer appears to alter adipocyte adiponectin metabolism through PPARγ-dependent and PPARγ-independent mechanisms.
  • Publication
    PPARγ1 and LXRα face a new regulator of macrophage cholesterol homeostasis and inflammatory responsiveness, AEBP1
    (Sage, 2010) Majdalawieh, Amin; Ro, Hyo-Sung
    Peroxisome proliferator-activated receptor γ1 (PPARγ1) and liver X receptor α (LXRα) are nuclear receptors that play pivotal roles in macrophage cholesterol homeostasis and inflammation; key biological processes in atherogenesis. The activation of PPARγ1 and LXRα by natural or synthetic ligands results in the transactivation of ABCA1, ABCG1, and ApoE; integral players in cholesterol efflux and reverse cholesterol transport. In this review, we describe the structure, isoforms, expression pattern, and functional specificity of PPARs and LXRs. Control of PPARs and LXRs transcriptional activity by coactivators and corepressors is also highlighted. The specific roles that PPARγ1 and LXRα play in inducing macrophage cholesterol efflux mediators and antagonizing macrophage inflammatory responsiveness are summarized. Finally, this review focuses on the recently reported regulatory functions that adipocyte enhancer-binding protein 1 (AEBP1) exerts on PPARγ1 and LXRα transcriptional activity in the context of macrophage cholesterol homeostasis and inflammation.
  • Publication
    Regulation of I𝜅B𝛼 Function and NF-𝜅B Signaling: AEBP1 Is a Novel Proinflammatory Mediator in Macrophages
    (Hindawi, 2010) Majdalawieh, Amin; Ro, Hyo-Sung
    NF-𝜅B comprises a family of transcription factors that are critically involved in various inflammatory processes. In this paper, the role of NF-𝜅B in inflammation and atherosclerosis and the regulation of the NF-𝜅B signaling pathway are summarized. The structure, function, and regulation of the NF-𝜅B inhibitors, I𝜅Bα and I𝜅Bβ , are reviewed. The regulation of NF-𝜅B activity by glucocorticoid receptor (GR) signaling and I𝜅Bα sumoylation is also discussed. This paper focuses on the recently reported regulatory function that adipocyte enhancer-binding protein 1 (AEBP1) exerts on NF-𝜅B transcriptional activity in macrophages, in which AEBP1 manifests itself as a potent modulator of NF-𝜅B via physical interaction with I𝜅Bα and a critical mediator of inflammation. Finally, we summarize the regulatory roles that recently identified I𝜅Bα-interacting proteins play in NF-𝜅B signaling. Based on its proinflammatory roles in macrophages, AEBP1 is anticipated to serve as a therapeutic target towards the treatment of various inflammatory conditions and disorders.
  • Publication
    Adipocyte Enhancer-Binding Protein 1 (AEBP1) (a Novel Macrophage Proinflammatory Mediator) Overexpression Promotes and Ablation Attenuates Atherosclerosis in ApoE⁻′⁻ and LDLR⁻′⁻ Mice
    (Springer Nature, 2011) Bogachev, Oleg; Majdalawieh, Amin; Pan, Xuefang; Zhang, Lei; Ro, Hyo-Sung
    Atherogenesis is a long-term process that involves inflammatory response coupled with metabolic dysfunction. Foam cell formation and macrophage inflammatory response are two key events in atherogenesis. Adipocyte enhancer-binding protein 1 (AEBP1) has been shown to impede macrophage cholesterol efflux, promoting foam cell formation, via peroxisome proliferator-activated receptor (PPAR)-γl and liver X receptor α (LXRα) downregulation. Moreover, AEBP1 has been shown to promote macrophage inflammatory responsiveness by inducing nuclear factor (NF)-κB activity via IκBα downregulation. Lipopolysaccharide (LPS)-induced suppression of pivotal macrophage cholesterol efflux mediators, leading to foam cell formation, has been shown to be mediated by AEBP₁. Herein, we showed that AEBP₁-transgenic mice (AEBP1ᵀᴳ) with macrophage-specific AEBP1 overexpression exhibit hyperlipidemia and develop atherosclerotic lesions in their proximal aortas. Consistently, ablation of AEBP₁ results in significant attenuation of atherosclerosis (males: 3.2-fold, P = 0.001 (en face)), 2.7-fold, P = 0.0004 (aortic roots); females: 2.1-fold, P = 0.0026 (en face), 1.7-fold, P = 0.0126 (aortic roots)) in the AEBP₁⁻′⁻/low-density lipoprotein receptor (LDLR)⁻′⁻ double-knockout (KO) mice. Bone marrow (BM) transplantation experiments further revealed that LDLR⁻′⁻ mice reconstituted with AEBP₁⁻′⁻/LDLR⁻′⁻ BM cells (LDLR⁻′⁻/KO-BM chimera) display significant reduction of atherosclerosis lesions (en face: 2.0-fold, P = 0.0268; aortic roots: 1.7-fold, P = 0.05) compared with control mice reconstituted with AEBP₁⁺′⁺/LDLR⁻′⁻ BM cells (LDLR⁻′⁻/WT-BM chimera). Furthermore, transplantation of AEBP1TG BM cells with the normal apolipoprotein E (ApoE) gene into ApoE⁻′⁻ mice (ApoE⁻′⁻/TG-BM chimera) leads to significant development of atherosclerosis (males: 2.5-fold, P = 0.0001 (en face), 4.7-fold, P = 0.0001 [aortic roots]; females: 1.8-fold, P = 0.0001 (en face), 3.0-fold, P = 0.0001 [aortic roots]) despite the restoration of ApoE expression. Macrophages from ApoE⁻′⁻/TG-BM chimeric mice express reduced levels of PPARγ₁, LXRα, ATP-binding cassette A₁ (ABCA₁) and ATP-binding cassette G₁ (ABCG₁) and increased levels of the inflammatory mediators interleukin (IL)-6 and tumor necrosis factor (TNF)-α compared with macrophages of control chimeric mice (ApoE⁻′⁻/NT-BM) that received AEBP₁ nontransgenic (AEBP₁ᴺᵀ) BM cells. Our in vivo experimental data strongly suggest that macrophage AEBP₁ plays critical regulatory roles in atherogenesis, and it may serve as a potential therapeutic target for the prevention or treatment of atherosclerosis.
  • Publication
    Lactation Defect with Impaired Secretory Activation in AEBP1-Null Mice
    (Public Library of Science, 2011) Zhang, Lei; Reidy, Shannon P.; Bogachev, Oleg; Hall, Brian K.; Majdalawieh, Amin; Ro, Hyo-Sung
    Adipocyte enhancer binding protein 1 (AEBP1) is a multifunctional protein that negatively regulates the tumor suppressor PTEN and IκBα, the inhibitor of NF-κB, through protein-protein interaction, thereby promoting cell survival and inflammation. Mice homozygous for a disrupted AEBP1 gene developed to term but showed defects in growth after birth. AEBP1⁻′⁻ females display lactation defect, which results in the death of 100% of the litters nursed by AEBP1⁻′⁻dams. Mammary gland development during pregnancy appears normal in AEBP1⁻′⁻dams; however these mice exhibit expansion of the luminal space and the appearance of large cytoplasmic lipid droplets (CLDs) in the mammary epithelial cells at late pregnancy and parturition, which is a clear sign of failed secretory activation, and accumulation of milk proteins in the mammary gland, presumably reflecting milk stasis following failed secretory activation. Eventually, AEBP1⁻′⁻mammary gland rapidly undergoes involution at postpartum. Stromal restoration of AEBP1 expression by transplanting wild-type bone marrow (BM) cells is sufficient to rescue the mammary gland defect. Our studies suggest that AEBP1 is critical in the maintenance of normal tissue architecture and function of the mammary gland tissue and controls stromal-epithelial crosstalk in mammary gland development.
  • Publication
    A Density Functional Theory Study of the Cu⁺ · O₂ and Cu⁺ · N₂ Adducts
    (De Gruyter, 2011) Dawoud, Jamal N.; Fasfous, Ismail I.; Majdalawieh, Amin
    The geometries and harmonic vibration frequencies of the Cu⁺·O₂ and Cu⁺ ·N₂ are determined by various density functional theory (DFT) methods employing different basis sets. The potential energy surfaces (PES) are examined. The Cu⁺·O₂ adduct exhibits a bent structure with a binding energy of 12.4 kcal mol⁻­¹, whereas Cu⁺·N₂ exhibits a linear configuration with a binding energy of 23.5 kcal mol⁻¹. The binding energy values for the two adducts agree well with the available published experimental and theoretical data and hence are reliable.
  • Publication
    Stromal Adipocyte Enhancer-binding Protein (AEBP1) Promotes Mammary Epithelial Cell Hyperplasia via Proinflammatory and Hedgehog Signaling
    (Elsevier, 2012) Holloway, Ryan W.; Bogachev, Oleg; Bharadwaj, Alamelu G.; McCluske, Greg D.; Majdalawieh, Amin; Zhang, Lei; Ro, Hyo-Sung
    Disruption of mammary stromal-epithelial communication leads to aberrant mammary gland development and induces mammary tumorigenesis. Macrophages have been implicated in carcinogenesis primarily by creating an inflammatory microenvironment, which promotes growth of the adjacent epithelial cells. Adipocyte enhancer-binding protein 1 (AEBP1), a novel proinflammatory mediator, promotes macrophage inflammatory responsiveness by inducing NF-κB activity, which has been implicated in tumor cell growth and survival by aberrant sonic hedgehog (Shh) expression. Here, we show that stromal macrophage AEBP1 overexpression results in precocious alveologenesis in the virgin AEBP1 transgenic (AEBP1ᵀᴳ) mice, and the onset of ductal hyperplasia was accelerated in AEBP1ᵀᴳ mice fed a high fat diet, which induces endogenous AEBP1 expression. Transplantation of AEBP1ᵀᴳ bone marrow cells into non-transgenic (AEBP1ᴺᵀ) mice resulted in alveolar hyperplasia with up-regulation of NF-κB activity and TNFα expression as displayed in the AEBP1ᵀᴳ mammary macrophages and epithelium. Shh expression was induced in AEBP1ᵀᴳ macrophages and RAW264.7 macrophages overexpressing AEBP1. The Shh target genes Gli1 and Bmi1 expression was induced in the AEBP1ᵀᴳ mammary epithelium and HC11 mammary epithelial cells co-cultured with AEBP1ᵀᴳ peritoneal macrophages. The conditioned AEBP1ᵀᴳ macrophage culture media promoted NF-κB activity and survival signal, Akt activation, in HC11 cells, whereas such effects were abolished by TNFα neutralizing antibody treatment. Furthermore, HC11 cells displayed enhanced proliferation in response to AEBP1ᵀᴳ macrophages and their conditioned media. Our findings highlight the role of AEBP1 in the signaling pathways regulating the cross-talk between mammary epithelium and stroma that could predispose the mammary tissue to tumorigenesis.
  • Publication
    Evaluation of the interaction potential of synthetic ethylene glycol compounds with nuclear Factor κB
    (PKP, 2013) Narasimhan, Srinivasan; Majdalawieh, Amin; Abu-Yousef, Imad; Shanmugarajan, Dhivya; Ramasubramanian, Vishvanathan
    In the last three decades, nuclear factor κB (NF-κB) has been the focus of many researchers who are interested in understanding the various molecular mechanisms involved in inflammatory diseases and cancer. Interference with NF-κB activity can cause many cellular abnormalities including tumorigenesis. In this study, we focus on examining the potential of ten synthetic ethylene glycol based compounds to interact with the binding site of NF-κB. Computational analysis reveals that the ethylene glycol compounds examined in this study display differential ability to interact with NF-κB. Parameters such as ALOGP, dock score, and internal energy were determined for each of the studied compounds. Seven compounds were found to interact with specific amino acid residues within the binding site of NF-κB. The specific amino acids involved in the interaction were mapped and the nature of interaction was identified. Since NF-κB is implicated in the development of many inflammatory and immune-related conditions including cancer, we predict that the ethylene glycol compounds examined in this study can be targeted for the development of therapeutic agents that can be employed in the prevention and/or treatment of various diseases including cancer.
  • Publication
    Novel algorithms for accurate DNA base-calling
    (Scientific Research Publishing, 2013) Mohammed, Omniyah Gul; Assaleh, Khaled; Husseini, Ghaleb; Majdalawieh, Amin
    The ability to decipher the genetic code of different species would lead to significant future scientific achievements in important areas, including medicine and agriculture. The importance of DNA sequencing necessitated a need for efficient automation of identification of base sequences from traces generated by existing sequencing machines, a process referred to as DNA base-calling. In this paper, a pattern recognition technique was adopted to minimize the inaccuracy in DNA base-calling. Two new frameworks using Artificial Neural Networks and Polynomial Classifiers are proposed to model electropherogram traces belonging to Homo sapiens, Saccharomyces mikatae and Drosophila melanogaster. De-correlation, de-convolution and normalization were implemented as part of the pre-processing stage employed to minimize data imperfections attributed to the nature of the chemical reactions involved in DNA sequencing. Discriminative features that characterize each chromatogram trace were subsequently extracted and subjected to the chosen classifiers to categorize the events to their respective base classes. The models are trained such that they are not restricted to a specific species or to a specific chemical procedure of sequencing. The base- calling accuracy achieved is compared with the existing standards, PHRED (Phil’s Read Editor) and ABI (Applied Biosystems, version2.1.1) KB base-callers in terms of deletion, insertion and substitution errors. Experimental evidence indicates that the proposed models achieve a higher base-calling accuracy when compared to PHRED and a comparable performance when compared to ABI. The results obtained demonstrate the potential of the proposed models for efficient and accurate DNA base-calling.
  • Publication
    Preparation and characterization of gatifloxacin-loaded sodium alginate hydrogel membranes supplemented with hydroxypropyl methylcellulose and hydroxypropyl cellulose polymers for wound dressing
    (PKP, 2016) Prabu, Durai; Majdalawieh, Amin; Abu-Yousef, Imad; Inbasekaran, Kadambari; Balasubramaniam, Tharani; Nallaperumal, Narayanan; Gunasekar, Conjeevaram J.
    Introduction: The aim of this study is to evaluate gatifloxacin-loaded sodium alginate hydrogel membranes, supplemented with glycerol (a plasticizer), glutaraldehyde (a cross-linking agent), and hydroxypropyl methylcellulose (HPMC) or hydroxypropyl cellulose (HPC) polymers, as potential wound dressing materials based on their physicochemical properties and the sustain-release phenomenon. Materials and Methods: The physicochemical properties of the prepared hydrogel membranes were evaluated by several methods including Fourier transform infrared and differential scanning calorimetry. Different techniques were used to assess the swelling behavior, tensile strength and elongation, % moisture absorption, % moisture loss, water vapor transmission rate (WVTR), and microbial penetration for the hydrogel membranes. In vitro gatifloxacin release from the hydrogel membranes was examined using the United States Pharmacopeia XXIII dissolution apparatus. Four kinetics models (zero-order, first-order, Higuchi equation, and Korsmeyer- Peppas equation) were applied to study drug release kinetics. Results: The addition of glycerol, glutaraldehyde, HPMC, and HPC polymers resulted in a considerable increase in the tensile strength and flexibility/elasticity of the hydrogel membranes. WVTR results suggest that hydrated hydrogel membranes can facilitate water vapor transfer. None of the hydrogel membranes supported microbial growth. HPMC-treated and HPC-treated hydrogel membranes allow slow, but sustained, release of gatifloxacin for 48 h. Drug release kinetics revealed that both diffusion and dissolution play an important role in gatifloxacin release. Conclusions: Given their physicochemical properties and gatifloxacin release pattern, HPMC-treated and HPC-treated hydrogel membranes exhibit effective and sustained drug release. Furthermore, HPMC-treated and HPC-treated hydrogel membranes possess physiochemical properties that make them effective and safe wound dressing materials.
  • Publication
    Efficient and simple protocol employing borohydride systems to design a selective osthol-zirconium (OST-Zr) library from potential natural products
    (PKP, 2016) Viswanathan, Radhakrishnan; Abu-Yousef, Imad; Majdalawieh, Amin; Das, Prince Edwin; Narasimhan, Srinivasan
    “Drug likeness” of a molecule is the prime criterion for a molecule to exhibit the desired pharmaceutical activity. A pharmacophore, which describes molecular features that are necessary for molecular recognition of a ligand by a biological macromolecule, is well altered by the Structure Activity Relationship (SAR) guidelines through Hydrophobic Lipophilic Balance (HLB) demonstrated by the system. The tailoring is best accomplished by organic functional group interconversion on a potent natural product via a variety of synthetic methodologies available to date. Metal borohydrides (MBH₄) in particular are promising compounds as they can potentially serve varying HLB systems. The reagent acts on the substrate to cause reduction, hydroboration, or a combination of both outcomes for the purpose of rearrangement and fragmentation. Indeed, Zr(BH₄)₄ is expected to be more active and selective as a reducing agent compared to NaBH₄ . This study aims at evaluating zirconium borohydride (Zr(BH₄)₄ ) in tetrahydrofuran (THF) as a reducing system to realize a more selective, meaningful and combinatorial osthol (OST) library from potential natural products and attempt to alternate preparation of the same in THF from known metal borohydrides, limiting reduction of the metal center versus metathesis.
  • Publication
    Recent advances on the anti-cancer properties of Nigella sativa, a widely used food additive
    (Elsevier, 2016) Majdalawieh, Amin; Fayyad, Muneera W.
    The use of naturally-occurring agents to regulate tumorigenesis is on the rise. Several herbal extracts, pure plant-derived active constituents, and food additives have been reported to possess potent anti-cancer properties and cancer-ameliorating effects. The wide-range anti-cancer effects of Nigella sativa, also known as black seed or black cumin, have been extensively studied using different in vitro and in vivo models. Here, we provide a comprehensive, analytical review of the reported anti-cancer properties of N. sativa seed extracts. This review focuses on analyzing experimental findings related to the ability of N. sativa to exert anti-proliferative, pro-apoptotic, anti-oxidant, cytotoxic, anti-mutagenic, anti-metastatic, and NK cytotoxic activity enhancing effects against various primary cancer cells and cancer cell lines. Moreover, we underline the molecular mechanisms of action and the signal transduction pathways implicated in the suppression of tumorigenesis by N. sativa. The major signaling pathway utilized by N. sativa to manifest its anti-cancer activity is the iNOS signaling pathway. This review underscores the recent developments that highlight an effective therapeutic potential of N. sativa to suppress tumor development, reduce tumor incidence, and ameliorate carcinogenesis. In sum, experimental findings reported in the last two decades strongly suggest that N. sativa fractions could serve, alone or in combination with known chemotherapeutic drugs, as effective agents to control tumor initiation, growth, and metastasis, and hence, treatment of a wide range of cancers.
  • Publication
    Anti-Bacterial and Anti-Fungal Activity of Xanthones Obtained via Semi-Synthetic Modification of α-Mangostin from Garcinia mangostana
    (MDPI, 2017) Narasimhan, Srinivasan; Maheshwaran, Shanmugam; Abu-Yousef, Imad; Majdalawieh, Amin; Rethavathi, Janarthanam; Das, Prince Edwin; Poltronieri, Palmiro
    The microbial contamination in food packaging has been a major concern that has paved the way to search for novel, natural anti-microbial agents, such as modified α-mangostin. In the present study, twelve synthetic analogs were obtained through semi-synthetic modification of α-mangostin by Ritter reaction, reduction by palladium-carbon (Pd-C), alkylation, and acetylation. The evaluation of the anti-microbial potential of the synthetic analogs showed higher bactericidal activity than the parent molecule. The anti-microbial studies proved that I E showed high anti-bacterial activity whereas I I showed the highest anti-fungal activity. Due to their microbicidal potential, modified α-mangostin derivatives could be utilized as active anti-microbial agents in materials for the biomedical and food industry.