RSS 1.0Analytical Chemistry Core Lab
Recent Submissions
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Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens(Nature Communications, Springer Science and Business Media LLC, 2023-03-16) [Article]Antimicrobial peptides (AMPs) are promising next-generation antibiotics that can be used to combat drug-resistant pathogens. However, the high cost involved in AMP synthesis and their short plasma half-life render their clinical translation a challenge. To address these shortcomings, we report efficient production of bioactive amidated AMPs by transient expression of glycine-extended AMPs in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase (PAM). Cationic AMPs accumulate to substantial levels in PAM transgenic plants compare to nontransgenic N. benthamiana. Moreover, AMPs purified from plants exhibit robust killing activity against six highly virulent and antibiotic resistant ESKAPE pathogens, prevent their biofilm formation, analogous to their synthetic counterparts and synergize with antibiotics. We also perform a base case techno-economic analysis of our platform, demonstrating the potential economic advantages and scalability for industrial use. Taken together, our experimental data and techno-economic analysis demonstrate the potential use of plant chassis for large-scale production of clinical-grade AMPs.
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Metabolic biomarkers in cancer(Elsevier, 2023-01-27) [Book Chapter]Over the course of years healthcare systems have utilized various “-omics” approaches to prognose, diagnose, and evaluate the treatment efficacy of cancer diseases. Metabolomics is one of the latest prominent additions to the -omics approaches, characterized by its versatile methodology. Owing to constant improvements in the field, metabolomics aims to provide a faster and a more accurate diagnosis, as well as personalized and optimal strategies of treatment. In recent years, a growing number of studies have utilized metabolomics approach to find new disease-related biomarkers of cancer diseases. Here we present the summary of recent advances in biomarker discovery for various types of cancers such as leukemia, ovarian, lung, breast, and liver cancers as well as cancer-related cachexia.
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Chapter 1. Theory and Applications of NMR Spectroscopy in Biomolecular Structures and Dynamics of Proteins(Royal Society of Chemistry, 2022-08-17) [Book Chapter]Structural biology has come a long way since the first inception of multidimensional NMR. The dipole–dipole interaction between two spatially closed spins provides a powerful tool to probe macromolecules’ three-dimensional (3D) structure, such as proteins. However, the main challenge for macromolecules is to assign the NMR chemical shifts of all signals of the investigated protein. This chapter presents different 3D triple-resonance NMR experiments dedicated to assignments of NMR signals of protein backbone structure. In addition, the through-space correlation experiments, namely NOESY, ROESY, and HOESY, are presented with detailed information about the advantages and limitations of each. The main strength of NMR lies in obtaining molecular structures under natural conditions and detailed information on the molecular dynamics at different timescales. The detailed characterization of sub-nanosecond segmental motions in proteins was characterized long before the advent of the first solution structure by NMR. Herein, the basic concept behind structure determination and elucidating protein dynamics on different timescales is presented. This chapter also highlights the NMR methodologies regarding characterizing sparsely populated protein conformations and transient states, vital for macromolecular functions.
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Highly efficient size-sieving-based removal of arsenic(III) via defect-free interfacially-polymerized polyamide thin-film composite membranes(Journal of Membrane Science, Elsevier BV, 2022-03-30) [Article]Serious health problems have been linked to the consumption and exposure of arsenic-contaminated groundwater. In comparison to As(V), As(III) is smaller and predominantly present in its neutral form in groundwater, which hinders its efficient removal by conventional nanofiltration and reverse osmosis membranes. In this study, the removal of As(III) was investigated at different pH conditions using three defect-free interfacially polymerized thin-film composite (TFC) membranes made by an optimized in-house developed interfacial polymerization process (KRO). The membranes were fabricated from aromatic para-phenylenediamine (PPD) or meta-phenylenediamine (MPD) and cycloaliphatic piperazine (PIP) by reaction with trimesoyl chloride (TMC). The PPD-KRO, MPD-KRO, and PIP-KRO polyamide membranes were tested with a feed containing 5 ± 1 mg L−1 (ppm) As(III). Two commercial TFC membranes, a seawater (Sepro RO4) and a nanofiltration (DOW NF270) membrane, were also evaluated for comparison. At natural conditions (pH 6–8), the defect-free fully aromatic TFC membranes demonstrated unprecedented size-sieving performance for As(III) removal with a rejection of ∼99.5 and > 99.8% for PPD-KRO and MPD-KRO, respectively, in comparison to ∼95% for the commercial Sepro RO4 seawater membrane tested under the same conditions. In contrast, As(III) rejection of semi-aromatic piperazine-based TFCs, PIP-KRO and NF270, showed a strong dependence on the charge-exclusion mechanism with maximum As(III) rejections of 69.5 and 46.3% at pH 10, respectively. Most notably, we demonstrated that the MPD-KRO membrane achieved an As(III) concentration ∼5 μg L−1 in the permeate (less than the WHO permissible arsenic standard level of 10 μg L−1), whereas PPD-KRO achieved a slightly higher value of ∼14 μg L−1. Our results are very promising considering the arsenic standard level in highly As(III) contaminated groundwater in Bangladesh and India is set at 50 μg L−1.
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Metal contamination and food web changes alter exposure to upper trophic levels in upper Blackfoot River basin streams, Montana(Hydrobiologia, Springer Nature, 2018-12-19) [Article]Reduced invertebrate abundance and diversity are common responses to metals contamination in mining-impacted streams. The resulting changes in community composition may have implications for metals accumulation and transfer through the food web. We investigated how changes in invertebrate community composition (abundance, species richness, and food web complexity) influence metals bioaccumulation and exposure risk to upper trophic levels along a contamination gradient in the upper Blackfoot River Basin, Montana. Invertebrate species richness exhibited the strongest decline with increasing sediment metals concentrations, driven by the loss of metals-sensitive taxa. These changes in invertebrate community composition resulted in a decline in the proportion of invertebrates in the scraper functional feeding group, likely influencing dietary metals exposure to the invertebrate community. Additionally, invertebrates with a strong propensity-to-drift increased with sediment contamination, potentially facilitating metals transfer to fish and higher trophic levels through predation. Using invertebrate exposure values (invertebrate abundance × metals concentrations), we found that moderately contaminated sites in our study area produced both the highest invertebrate exposure values and the highest fish tissue metals concentrations. Considering both changes in invertebrate community composition and metal concentrations is an important step towards understanding and evaluating potential toxic effects to upper trophic levels in mining-impacted streams.
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Composite epigenetic biomarkers for accurate screening, diagnosis and prognosis of colorectal cancer(2018-11-22) [Patent]The present disclosure concerns particular biomarkers for screening, diagnosing and/or prognosticating colorectal cancer, in particular in an accurate manner. The methods and compositions concern analysis of methylation patterns of one or more of 176 methylatable genomic DNA regions identified as described herein. In particular embodiments there are methods of detecting methylatable regions in genomic sequences.
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Identification of a 3-Alkylpyridinium Compound from the Red Sea Sponge Amphimedon chloros with In Vitro Inhibitory Activity against the West Nile Virus NS3 Protease(Molecules, MDPI AG, 2018-06-18) [Article]Viruses are underrepresented as targets in pharmacological screening efforts, given the difficulties of devising suitable cell-based and biochemical assays. In this study we found that a pre-fractionated organic extract of the Red Sea sponge Amphimedon chloros was able to inhibit the West Nile Virus NS3 protease (WNV NS3). Using liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy, the identity of the bioactive compound was determined as a 3-alkylpyridinium with m/z = 190.16. Diffusion Ordered Spectroscopy (DOSY) NMR and NMR relaxation rate analysis suggest that the bioactive compound forms oligomers of up to 35 kDa. We observed that at 9.4 μg/mL there was up to 40-70% inhibitory activity on WNV NS3 protease in orthogonal biochemical assays for solid phase extracts (SPE) of A. chloros. However, the LC-MS purified fragment was effective at inhibiting the protease up to 95% at an approximate amount of 2 μg/mL with negligible cytotoxicity to HeLa cells based on a High-Content Screening (HCS) cytological profiling strategy. To date, 3-alkylpyridinium type natural products have not been reported to show antiviral activity since the first characterization of halitoxin, or 3-alkylpyridinium, in 1978. This study provides the first account of a 3-alkylpyridinium complex that exhibits a proposed antiviral activity by inhibiting the NS3 protease. We suggest that the here-described compound can be further modified to increase its stability and tested in a cell-based assay to explore its full potential as a potential novel antiviral capable of inhibiting WNV replication.
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Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia(BioMed Research International, Hindawi Limited, 2018-05-24) [Article]Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.
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Delivery of Brain-Derived Neurotrophic Factor by 3D Biocompatible Polymeric Scaffolds for Neural Tissue Engineering and Neuronal Regeneration(Molecular Neurobiology, Springer Nature, 2018-03-29) [Article]Biopolymers are increasingly employed for neuroscience applications as scaffolds to drive and promote neural regrowth, thanks to their ability to mediate the upload and subsequent release of active molecules and drugs. Synthetic degradable polymers are characterized by different responses ranging from tunable distension or shrinkage to total dissolution, depending on the function they are designed for. In this paper we present a biocompatible microfabricated poly-ε-caprolactone (PCL) scaffold for primary neuron growth and maturation that has been optimized for the in vitro controlled release of brain-derived neurotrophic factor (BDNF). We demonstrate that the designed morphology confers to these devices an enhanced drug delivery capability with respect to monolithic unstructured supports. After incubation with BDNF, micropillared PCL devices progressively release the neurotrophin over 21 days in vitro. Moreover, the bioactivity of released BDNF is confirmed using primary neuronal cultures, where it mediates a consistent activation of BDNF signaling cascades, increased synaptic density, and neuronal survival. These results provide the proof-of-principle on the fabrication process of micropatterned PCL devices, which represent a promising therapeutic option to enhance neuronal regeneration after lesion and for neural tissue engineering and prosthetics.
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Methods of analyzing carbon nanostructures, methods of preparation of analytes from carbon nanostructures, and systems for analyzing carbon nanostructures(2018-01-10) [Patent]Provided herein is a method determining the concentration of impurities in a carbon material, comprising: mixing a flux and a carbon material to form a mixture, wherein the carbon material is selected from the group consisting of graphene, carbon nanotubes, fullerene, carbon onions, graphite, carbon fibers, and a combination thereof; heating the mixture using microwave energy to form fused materials; dissolution of the fused materials in an acid mixture; and measuring the concentration of one or more impurities.
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Polyoxadiazole hollow fibers for produced water treatment by direct contact membrane distillation(Desalination, Elsevier BV, 2018-01-08) [Article]Treatment of produced water in the petroleum industry has been a challenge worldwide. In this study, we evaluated the use of direct contact membrane distillation (DCMD) for this purpose, removing oil and dissolved elements and supplying clean water from waste. We synthesized fluorinated polyoxadiazole, a highly hydrophobic polymer, to fabricate hollow fiber membranes, which were optimized and tested for simulated produced water and real produced water treatment. The process performance was investigated under different operating parameters, such as feed temperature, feed flow velocity and length of the membrane module for 4 days. The results indicate that by increasing feed temperature and feed flow rate the vapor flux increases. The flux decreased with increasing the length of the module due to the decrease of the driving force along the module. The fouling behavior, which corresponds to flux decline and cleaning efficiency of the membrane, was studied. The performance of the fabricated hollow fiber membranes was demonstrated for the treatment of produced water, complying with the industrial reuse and discharge limits.
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Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds(Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2017-11-28) [Article]Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.
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n-Heptane cool flame chemistry: Unraveling intermediate species measured in a stirred reactor and motored engine(Combustion and Flame, Elsevier BV, 2017-10-03) [Article]This work identifies classes of cool flame intermediates from n-heptane low-temperature oxidation in a jet-stirred reactor (JSR) and a motored cooperative fuel research (CFR) engine. The sampled species from the JSR oxidation of a mixture of n-heptane/O2/Ar (0.01/0.11/0.88) were analyzed using a synchrotron vacuum ultraviolet radiation photoionization (SVUV-PI) time-of-flight molecular-beam mass spectrometer (MBMS) and an atmospheric pressure chemical ionization (APCI) Orbitrap mass spectrometer (OTMS). The OTMS was also used to analyze the sampled species from a CFR engine exhaust. Approximately 70 intermediates were detected by the SVUV-PI-MBMS, and their assigned molecular formulae are in good agreement with those detected by the APCI-OTMS, which has ultra-high mass resolving power and provides an accurate elemental C/H/O composition of the intermediate species. Furthermore, the results show that the species formed during the partial oxidation of n-heptane in the CFR engine are very similar to those produced in an ideal reactor, i.e., a JSR.The products can be classified by species with molecular formulae of C7H14Ox (x = 0–5), C7H12Ox (x = 0–4), C7H10Ox (x = 0–4), CnH2n (n = 2–6), CnH2n−2 (n = 4–6), CnH2n+2O (n = 1–4), CnH2nO (n = 1–6), CnH2n−2O (n = 2–6), CnH2n−4O (n = 4–6), CnH2n+2O2 (n = 0–4, 7), CnH2nO2 (n = 1–6), CnH2n−2O2 (n = 2–6), CnH2n−4O2 (n = 4–6), and CnH2nO3 (n = 3–6). The identified intermediate species include alkenes, dienes, aldehyde/keto compounds, olefinic aldehyde/keto compounds, diones, cyclic ethers, peroxides, acids, and alcohols/ethers. Reaction pathways forming these intermediates are proposed and discussed herein. These experimental results are important in the development of more accurate kinetic models for n-heptane and longer-chain alkanes.
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One-Pot Synthesis of Size- and Composition-Controlled Ni-Rich NiPt Alloy Nanoparticles in a Reverse Microemulsion System and Their Application(ACS Applied Materials & Interfaces, American Chemical Society (ACS), 2017-08-29) [Article]Bimetallic nanoparticles have been the subject of numerous research studies in the nanotechnology field, in particular for catalytic applications. Control of the size, morphology, and composition has become a key challenge due to the relationship between these parameters and the catalytic behavior of the particles in terms of activity, selectivity, and stability. Here, we present a one-pot air synthesis of 2 nm NiPt nanoparticles with a narrow size distribution. Control of the size and composition of the alloy particles is achieved at ambient temperature, in the aqueous phase, by the simultaneous reduction of nickel and platinum precursors with hydrazine, using a reverse microemulsion system. After deposition on an alumina support, this Ni-rich nanoalloy exhibits unprecedented stability under the harsh conditions of methane dry reforming.
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Monitoring the on-surface synthesis of graphene nanoribbons by mass spectrometry(Analytical Chemistry, American Chemical Society (ACS), 2017-06-28) [Article]We present a mass spectrometric approach to monitor and characterize the intermediates of graphene nanoribbon (GNR) formation by chemical vapor deposition (CVD) on top of Au(111) surfaces. Information regarding the repeating units, lengths, and termini can be obtained directly from the surface sample by a modified matrix assisted laser desorption/ionization (MALDI) method. The mass spectrometric results reveal ample oxidative side reactions under CVD conditions which can, however, be diminished drastically by introduction of protective H2 gas at ambient pressure. Simultaneously, addition of hydrogen extends the lengths of the oligophenylenes and thus the final GNRs. Moreover, the prematurely formed cyclodehydrogenation products during the oligomer growth can be assigned by the mass spectrometric method. The obtained mechanistic insights provide valuable information for optimizing and upscaling the bottom-up fabrication of GNRs. Given the important role of GNRs as semiconductors, the mass spectrometric characterization provides a readily available tool to improve and characterize their structural perfection.
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Ultralow Self-Doping in 2D Hybrid Perovskite Single Crystals(Nano Letters, American Chemical Society (ACS), 2017-06-28) [Article]Unintentional self-doping in semiconductors through shallow defects is detrimental to optoelectronic device performance. It adversely affects junction properties and it introduces electronic noise. This is especially acute for solution-processed semiconductors, including hybrid perovskites, which are usually high in defects due to rapid crystallization. Here, we uncover extremely low self-doping concentrations in single crystals of (C6H5C2H4NH3)2PbI4･(CH3NH3PbI3)n-1 (n=1, 2, and 3)—over three orders of magnitude lower than those of typical three-dimensional hybrid perovskites—by analyzing their conductivity behavior. We propose that crystallization of hybrid perovskites containing large organic cations suppresses defect formation and thus favors a low self-doping level. To exemplify the benefits of this effect, we demonstrate extraordinarily high light-detectivity (1013 Jones) in (C6H5C2H4NH3)2PbI4･(CH3NH3PbI3)n-1 photoconductors due to the reduced electronic noise, which makes them particularly attractive for the detection of weak light signals. Furthermore, the low self-doping concentration reduces the equilibrium charge carrier concentration in (C6H5C2H4NH3)2PbI4･(CH3NH3PbI3)n-1, advantageous in the design of p-i-n heterojunction solar cells by optimizing band alignment and promoting carrier depletion in the intrinsic perovskite layer, thereby enhancing charge extraction.
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Novel Anoxybacillus flavithermus AK1: A Thermophile Isolated from a Hot Spring in Saudi Arabia(Arabian Journal for Science and Engineering, Springer Nature, 2017-06-14) [Article]Anoxybacillus flavithermus AK1 is a thermophilic bacterium that is able to survive at temperatures ranging from 55 to 60∘C. The AK1 strain was isolated from the hot spring “Al-Ain Alhara” located at a distance of 50 km southeast of the city of Gazan, Saudi Arabia. This study presents the morphological characterization of A. flavithermus AK1, including a detailed description of its complete genome sequence. A total of 50 contigs were used to produce a genome sequence of 2,630,664 bp that includes 2724 protein-coding genes and 75 RNA genes, 18 of which are rRNA genes. A comparison of this genome sequence with those of Anoxybacillus flavithermus strains that were previously submitted to NCBI revealed that the AK1 strain has the smallest genome size with the highest GC content. The strain can therefore be exploited for several biotechnological applications based on its high thermophilic potential.
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Anti-cancer agents in Saudi Arabian herbals revealed by automated high-content imaging(PLOS ONE, Public Library of Science (PLoS), 2017-06-13) [Article]Natural products have been used for medical applications since ancient times. Commonly, natural products are structurally complex chemical compounds that efficiently interact with their biological targets, making them useful drug candidates in cancer therapy. Here, we used cell-based phenotypic profiling and image-based high-content screening to study the mode of action and potential cellular targets of plants historically used in Saudi Arabia's traditional medicine. We compared the cytological profiles of fractions taken from Juniperus phoenicea (Arar), Anastatica hierochuntica (Kaff Maryam), and Citrullus colocynthis (Hanzal) with a set of reference compounds with established modes of action. Cluster analyses of the cytological profiles of the tested compounds suggested that these plants contain possible topoisomerase inhibitors that could be effective in cancer treatment. Using histone H2AX phosphorylation as a marker for DNA damage, we discovered that some of the compounds induced double-strand DNA breaks. Furthermore, chemical analysis of the active fraction isolated from Juniperus phoenicea revealed possible anti-cancer compounds. Our results demonstrate the usefulness of cell-based phenotypic screening of natural products to reveal their biological activities.
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The brassinosteroid receptor BRI1 can generate cGMP enabling cGMP-dependent downstream signaling(The Plant Journal, Wiley, 2017-06-12) [Article]The brassinosteroid receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1) is a member of the leucine rich repeat receptor like kinase family. The intracellular kinase domain of BRI1 is an active kinase and also encapsulates a guanylate cyclase catalytic centre. Using liquid chromatography tandem mass spectrometry, we confirmed that the recombinant cytoplasmic domain of BRI1 generates pmol amounts of cGMP per μg protein with a preference for magnesium over manganese as a co-factor. Importantly, a functional BRI1 kinase is essential for optimal cGMP generation. Therefore, the guanylate cyclase activity of BRI1 is modulated by the kinase while cGMP, the product of the guanylate cyclase, in turn inhibits BRI1 kinase activity. Furthermore, we show using Arabidopsis root cell cultures that cGMP rapidly potentiates phosphorylation of the downstream substrate BRASSINOSTEROID SIGNALING KINASE 1 (BSK1). Taken together, our results suggest that cGMP acts as a modulator that enhances downstream signaling while dampening signal generation from the receptor. This article is protected by copyright. All rights reserved.
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In Vitro Assessment of Guanylyl Cyclase Activity of Plant Receptor Kinases(Methods in Molecular Biology, Springer Nature, 2017-06-01) [Book Chapter]Cyclic nucleotides such as 3′,5′-cyclic adenosine monophosphate (cAMP) and 3′,5′-cyclic guanosine monophosphate (cGMP) are increasingly recognized as key signaling molecules in plants, and a growing number of plant mononucleotide cyclases, both adenylate cyclases (ACs) and guanylate cyclases (GCs), have been reported. Catalytically active cytosolic GC domains have been shown to be part of many plant receptor kinases and hence directly linked to plant signaling and downstream cellular responses. Here we detail, firstly, methods to identify and express essential functional GC domains of receptor kinases, and secondly, we describe mass spectrometric methods to quantify cGMP generated by recombinant GCs from receptor kinases in vitro.
