Recent Submissions

  • Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing.

    Bi, Chongwei; Ramos Mandujano, Gerardo; Tian, Yeteng; Hala, Sharif; Xu, Jinna; Mfarrej, Sara; Esteban, Concepcion Rodriguez; Delicado, Estrella Nuñez; Alofi, Fadwa S; Khogeer, Asim; Hashem, Anwar M; Almontashiri, Naif A M; Pain, Arnab; Izpisua Belmonte, Juan Carlos; Li, Mo (Med (New York, N.Y.), Elsevier BV, 2021-04-06) [Article]
    BackgroundStrategies for monitoring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are crucial for combating the pandemic. Detection and mutation surveillance of SARS-CoV-2 and other respiratory viruses require separate and complex workflows that rely on highly-specialized facilities, personnel, and reagents. To date, no method can rapidly diagnose multiple viral infections and determine variants in a high-throughput manner.MethodsWe describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes, termed NIRVANA. It can simultaneously detect SARS-CoV-2, influenza A, human adenovirus, and human coronavirus, and monitor mutations for up to 96 samples in real-time.FindingsNIRVANA showed high sensitivity and specificity for SARS-CoV-2 in 70 clinical samples with a detection limit of 20 viral RNA copies per μl of extracted nucleic acid. It also detected the influenza A co-infection in two samples. The variant analysis results of SARS-CoV-2 positive samples mirror the epidemiology of COVID-19. Additionally, NIRVANA could simultaneously detect SARS-CoV-2 and PMMoV (an omnipresent virus and water quality indicator) in municipal wastewater samples.ConclusionsNIRVANA provides high-confidence detection of both SARS-CoV-2 and other respiratory viruses and mutation surveillance of SARS-CoV-2 on the fly. We expect it to offer a promising solution for rapid field-deployable detection and mutational surveillance of pandemic viruses.FundingM.L. is supported by KAUST Office of Sponsored Research (BAS/1/1080-01). This work is supported by KAUST Competitive Research Grant (URF/1/3412-01-01, M.L. and J.C.I.B.) and Universidad Catolica San Antonio de Murcia (J.C.I.B.). A.M.H. is supported by Saudi Ministry of Education (project 436).
  • Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing.

    Bi, Chongwei; Ramos Mandujano, Gerardo; Tian, Yeteng; Hala, Sharif; Xu, Jinna; Mfarrej, Sara; Esteban, Concepcion Rodriguez; Delicado, Estrella Nuñez; Alofi, Fadwa S; Khogeer, Asim; Hashem, Anwar M; Almontashiri, Naif A M; Pain, Arnab; Izpisua Belmonte, Juan Carlos; Li, Mo (Med (New York, N.Y.), Elsevier BV, 2021-04-06) [Article]
    BackgroundStrategies for monitoring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are crucial for combating the pandemic. Detection and mutation surveillance of SARS-CoV-2 and other respiratory viruses require separate and complex workflows that rely on highly-specialized facilities, personnel, and reagents. To date, no method can rapidly diagnose multiple viral infections and determine variants in a high-throughput manner.MethodsWe describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes, termed NIRVANA. It can simultaneously detect SARS-CoV-2, influenza A, human adenovirus, and human coronavirus, and monitor mutations for up to 96 samples in real-time.FindingsNIRVANA showed high sensitivity and specificity for SARS-CoV-2 in 70 clinical samples with a detection limit of 20 viral RNA copies per μl of extracted nucleic acid. It also detected the influenza A co-infection in two samples. The variant analysis results of SARS-CoV-2 positive samples mirror the epidemiology of COVID-19. Additionally, NIRVANA could simultaneously detect SARS-CoV-2 and PMMoV (an omnipresent virus and water quality indicator) in municipal wastewater samples.ConclusionsNIRVANA provides high-confidence detection of both SARS-CoV-2 and other respiratory viruses and mutation surveillance of SARS-CoV-2 on the fly. We expect it to offer a promising solution for rapid field-deployable detection and mutational surveillance of pandemic viruses.FundingM.L. is supported by KAUST Office of Sponsored Research (BAS/1/1080-01). This work is supported by KAUST Competitive Research Grant (URF/1/3412-01-01, M.L. and J.C.I.B.) and Universidad Catolica San Antonio de Murcia (J.C.I.B.). A.M.H. is supported by Saudi Ministry of Education (project 436).
  • Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors.

    Naveed, Hammad; Reglin, Corinna; Schubert, Thomas; Gao, Xin; Arold, Stefan T.; Maitland, Michael L (Genomics, proteomics & bioinformatics, Elsevier BV, 2021-04-01) [Article]
    Current FDA-approved kinase inhibitors cause diverse adverse effects, some of which are due to the mechanism-independent effects of these drugs. Identifying these mechanism-independent interactions could improve drug safety and support drug repurposing. We have developed iDTPnd (integrated Drug Target Predictor with negative dataset), a computational approach for large-scale discovery of novel targets for known drugs. For a given drug, we construct a positive and a negative structural signature that captures the weakly conserved structural features of drug binding sites. To facilitate assessment of unintended targets, iDTPnd also provides a docking-based interaction score and its statistical significance. We were able to confirm the interaction of sorafenib, imatinib, dasatinib, sunitinib, and pazopanib with their known targets at a sensitivity and specificity of 52% and 55%, respectively. We have validated 10 predicted novel targets by using in vitro experiments. Our results suggest that proteins other than kinases, such as nuclear receptors, cytochrome P450, or MHC Class I molecules can also be physiologically relevant targets of kinase inhibitors. Our method is general and broadly applicable for the identification of protein-small molecule interactions, when sufficient drug-target 3D data are available. The code for constructing the structural signature is available at https://sfb.kaust.edu.sa/Documents/iDTP.zip.
  • Synergy and allostery in ligand binding by HIV-1 Nef

    Aldehaiman, Abdullah M; Momin, Afaque Ahmad Imtiyaz; Restouin, Audrey; Wang, Luyao; Shi, Xiaoli; Aljedani, Safia Salim Eid; Opi, Sandrine; Lugari, Adrien; Shahul Hameed, Umar F; Ponchon, Luc; Morelli, Xavier; Huang, Mingdong; Dumas, Christian; Collette, Yves; Arold, Stefan T. (Biochemical Journal, Portland Press Ltd., 2021-03-31) [Article]
    The Nef protein of human and simian immunodeficiency viruses boosts viral pathogenicity through its interactions with host cell proteins. By combining the polyvalency of its large unstructured regions with the binding selectivity and strength of its folded core domain, Nef can associate with many different host cell proteins, thereby disrupting their functions. For example, the combination of a linear proline-rich motif and hydrophobic core domain surface allows Nef to bind tightly and specifically to SH3 domains of Src family kinases. We investigated whether the interplay between Nef’s flexible regions and its core domain could allosterically influence ligand selection. We found that the flexible regions can associate with the core domain in different ways, producing distinct conformational states that alter the way in which Nef selects for SH3 domains and exposes some of its binding motifs. The ensuing crosstalk between ligands might promote functionally coherent Nef-bound protein ensembles by synergizing certain subsets of ligands while excluding others. We also combined proteomic and bioinformatics analyses to identify human proteins that select SH3 domains in the same way as Nef. We found that only 3% of clones from a whole-human fetal library displayed Nef-like SH3 selectivity. However, in most cases, this selectivity appears to be achieved by a canonical linear interaction rather than by a Nef-like “tertiary” interaction. Our analysis supports the contention that Nef’s mode of hijacking SH3 domains is a virus-specific adaptation with no or very few cellular counterparts. Thus, the Nef tertiary binding surface is a promising virus-specific drug target.
  • Microfluidic Integrated Organic Electrochemical Transistor with a Nanoporous Membrane for Amyloid-β Detection

    Koklu, Anil; Wustoni, Shofarul; Musteata, Valentina-Elena; Ohayon, David; Moser, Maximilian; McCulloch, Iain; Nunes, Suzana Pereira; Inal, Sahika (ACS Nano, American Chemical Society (ACS), 2021-03-30) [Article]
    Alzheimer’s disease (AD) is a neurodegenerative disorder associated with a severe loss in thinking, learning, and memory functions of the brain. To date, no specific treatment has been proven to cure AD, with the early diagnosis being vital for mitigating symptoms. A common pathological change found in AD-affected brains is the accumulation of a protein named amyloid-β (Aβ) into plaques. In this work, we developed a micron-scale organic electrochemical transistor (OECT) integrated with a microfluidic platform for the label-free detection of Aβ aggregates in human serum. The OECT channel–electrolyte interface was covered with a nanoporous membrane functionalized with Congo red (CR) molecules showing a strong affinity for Aβ aggregates. Each aggregate binding to the CR-membrane modulated the vertical ion flow toward the channel, changing the transistor characteristics. Thus, the device performance was not limited by the solution ionic strength nor did it rely on Faradaic reactions or conformational changes of bioreceptors. The high transconductance of the OECT, the precise porosity of the membrane, and the compactness endowed by the microfluidic enabled the Aβ aggregate detection over eight orders of magnitude wide concentration range (femtomolar–nanomolar) in 1 μL of human serum samples. We expanded the operation modes of our transistors using different channel materials and found that the accumulation-mode OECTs displayed the lowest power consumption and highest sensitivities. Ultimately, these robust, low-power, sensitive, and miniaturized microfluidic sensors helped to develop point-of-care tools for the early diagnosis of AD.
  • Organic J-Aggregate Nanodots with Enhanced Light Absorption and Near-Unity Fluorescence Quantum Yield

    Piwonski, Hubert Marek; Nozue, Shuho; Fujita, Hiroyuki; Michinobu, Tsuyoshi; Habuchi, Satoshi (Nano Letters, American Chemical Society (ACS), 2021-03-30) [Article]
    Development of biocompatible fluorophores with small size, bright fluorescence, and narrow spectrum translate directly into major advances in fluorescence imaging and related techniques. Here, we discover that a small donor–acceptor–donor-type organic molecule consisting of a carbazole (Cz) donor and benzothiazole (BT) acceptor (CzBTCz) assembles into quasi-crystalline J-aggregates upon a formation of ultrasmall nanoparticles. The 3.5 nm CzBTCz Jdots show a narrow absorption spectrum (fwhm = 27 nm), near-unity fluorescence quantum yield (ϕfl = 0.95), and enhanced peak molar extinction coefficient. The superior spectroscopic characteristics of the CzBTCz Jdots result in two orders of magnitude brighter photoluminescence of the Jdots compared with semiconductor quantum dots, which enables continuous single-Jdots imaging over a 1 h period. Comparison with structurally similar CzBT nanoparticles demonstrates a critical role played by the shape of CzBTCz on the formation of the Jdots. Our findings open an avenue for the development of a new class of fluorescent nanoparticles based on J-aggregate.
  • Alteration of Anticancer and Protein-Binding Properties of Gold(I) Alkynyl by Phenolic Schiff Bases Moieties

    Babgi, Bandar A.; Alsayari, Jalal; Alenezi, Hana M.; Abdellatif, Magda H.; Eltayeb, Naser E.; Emwas, Abdul-Hamid M.; Jaremko, Mariusz; Hussien, Mostafa A. (Pharmaceutics, MDPI AG, 2021-03-29) [Article]
    A set of five gold complexes with the general formula Au(PR3)(C≡C-C6H4-4-R′) (R = PPh3, R′ = –CHO (1), R = PCy3, R′ = –CHO (2), R = PPh3, R′ = –N=CH-C6H4-2-OH (3), R = PPh3, R′ = –N=CH-C6H4-4-OH (4), R = PCy3, R′ = –N=CH-C6H4-2-OH (5)) were synthesized and characterized by elemental analysis, 1H-NMR spectroscopy, 31P-NMR spectroscopy, and mass spectrometry. The structures of complexes 2 and 5 were determined by X-ray crystallography. The effects of the structural modifications on the protein binding affinities and anticancer activities of the five gold complexes were assessed. Fluorescence quenching experiments to assess binding to human serum albumin (HSA) revealed that the Schiff base complexes (3, 4, and 5) had binding constants that were superior to their parent aldehyde complexes and highlighted the position of the hydroxy group because complex 4 (4-hydroxy) had a binding constant 6400 times higher than complex 3 (2-hydroxy). The anticancer activities of the complexes against the OVCAR-3 (ovarian carcinoma) and HOP-62 (non-small-cell lung) cancer cell lines showed that the Schiff bases (3–5) were more cytotoxic than the aldehyde-containing complexes (1 and 2). Notably, compound 4 had cytotoxic activity comparable to that of cisplatin against OVCAR-3, demonstrating the significance of the para position for the hydroxy group. Molecular docking studies against the enzyme thioredoxin reductase (TrxR) and human serum albumin were conducted, with docking scores in good agreement with the experimental data. The current study highlights how small structural modifications can alter physiochemical and anticancer properties. Moreover, this simple design strategy using the aldehyde group can generate extensive opportunities to explore new gold(I)-based anticancer drugs via condensation, cyclization, or nucleophilic addition reactions of the aldehyde.
  • Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.

    Sanderson, Leslie E; Lanko, Kristina; Alsagob, Maysoon; AlMass, Rawan; Al-Ahmadi, Nada; Najafi, Maryam; Al-Muhaizea, Mohammad A; Alzaidan, Hamad; AlDhalaan, Hesham; Perenthaler, Elena; van der Linde, Herma C; Nikoncuk, Anita; Kühn, Nikolas A; Antony, Dinu; Owaidah, Tarek Mustafa; Raskin, Salmo; Vieira, Luana Gabriela Dalla Rosa; Mombach, Romulo; Ahangari, Najmeh; Silveira, Tainá Regina Damaceno; Ameziane, Najim; Rolfs, Arndt; Alharbi, Aljohara; Sabbagh, Raghda M; AlAhmadi, Khalid; Alawam, Bashayer; Ghebeh, Hazem; AlHargan, Aljouhra; Albader, Anoud A; Binhumaid, Faisal S; Goljan, Ewa; Monies, Dorota; Mustafa, Osama M; Aldosary, Mazhor; AlBakheet, Albandary; Alyounes, Banan; Almutairi, Faten; Al-Odaib, Ali; Aksoy, Durdane Bekar; Basak, A Nazli; Palvadeau, Robin; Trabzuni, Daniah; Rosenfeld, Jill A; Karimiani, Ehsan Ghayoor; Meyer, Brian F; Karakas, Bedri; Al-Mohanna, Futwan; Arold, Stefan T.; Colak, Dilek; Maroofian, Reza; Houlden, Henry; Bertoli-Avella, Aida M; Schmidts, Miriam; Barakat, Tahsin Stefan; van Ham, Tjakko J; Kaya, Namik (Brain : a journal of neurology, Oxford University Press (OUP), 2021-03-25) [Article]
    Membrane trafficking is a complex, essential process in eukaryotic cells responsible for protein transport and processing. Deficiencies in vacuolar protein sorting (VPS) proteins, key regulators of trafficking, cause abnormal intracellular segregation of macromolecules and organelles and are linked to human disease. VPS proteins function as part of complexes such as the homotypic fusion and vacuole protein sorting (HOPS) tethering complex, composed of VPS11, VPS16, VPS18, VPS33A, VPS39 and VPS41. The HOPS-specific subunit VPS41 has been reported to promote viability of dopaminergic neurons in Parkinson's disease but to date has not been linked to human disease. Here, we describe five unrelated families with nine affected individuals, all carrying homozygous variants in VPS41 that we show impact protein function. All affected individuals presented with a progressive neurodevelopmental disorder consisting of cognitive impairment, cerebellar atrophy/hypoplasia, motor dysfunction with ataxia and dystonia, and nystagmus. Zebrafish disease modelling supports the involvement of VPS41 dysfunction in the disorder, indicating lysosomal dysregulation throughout the brain and providing support for cerebellar and microglial abnormalities when vps41 was mutated. This provides the first example of human disease linked to the HOPS-specific subunit VPS41 and suggests the importance of HOPS complex activity for cerebellar function.
  • Moonlighting adenylyl cyclases in plants: an Arabidopsis thaliana 9-cis-epoxycarotenoid dioxygenase as point in case

    Al-Younis, Inas; Wong, Aloysius Tze; Moosa, Basem; Kwiatkowski, Mateusz; Jaworski, Krzysztof; Gehring, Christoph A (Cold Spring Harbor Laboratory, 2021-03-23) [Preprint]
    Adenylyl cyclases (ACs) and their catalytic product cAMP are regulatory components of plant responses. AC domains are intrinsic components of complex molecules with multiple functions, some of which are co-regulated by cAMP. Here we used an amino acid search motif based on annotated ACs in organisms across species to identify 12 unique Arabidopsis thaliana candidate ACs, four of which have a role in the biosynthesis of the stress hormone abscisic acid (ABA). One of these, the 9-cis-epoxycarotenoid dioxygenase (NCED3, At3g14440), was identified by sequence and structural analysis as a putative AC and then tested experimentally for activity. We show that an NCED3 AC fragment can complement an AC deficient E. coli mutant and this rescue is nullified when key amino acids in the AC motif are mutated. AC activity was also confirmed by tandem liquid chromatography mass spectrometry (LC-MS/MS). Our results are consistent with a moonlighting role for mononucleotide cyclases in multi-domain proteins that have at least one other distinct molecular function such as catalysis or ion channel activation and promise to yield new insights into tuning mechanisms of ABA dependent plant responses. Finally, our search method can also be applied to discover ACs in other species including Homo sapiens.
  • MYH1 is a candidate gene for recurrent rhabdomyolysis in humans

    Alsaif, Hessa S.; Alshehri, Ali; Sulaiman, Raashda A.; Al-Hindi, Hindi; Guzmán-Vega, Francisco J.; Arold, Stefan T.; Alkuraya, Fowzan S. (American Journal of Medical Genetics Part A, Wiley, 2021-03-23) [Article]
    Rhabdomyolysis is a serious medical condition characterized by muscle injury, and there are recognized genetic causes especially in recurrent forms. The majority of these cases, however, remain unexplained. Here, we describe a patient with recurrent rhabdomyolysis in whom extensive clinical testing failed to identify a likely etiology. Whole-exome sequencing revealed a novel missense variant in MYH1, which encodes a major adult muscle fiber protein. Structural biology analysis revealed that the mutated residue is extremely well conserved and is located in the actin binding cleft. Furthermore, immediately adjacent mutations in that cleft in other myosins are pathogenic in humans. Our results are consistent with the finding that MYH1 is mutated in rhabdomyolysis in horses and suggest that this gene should be investigated in cases with recurrent rhabdomyolysis.
  • Biomedical computing in the Arab world

    Eldawlatly, Seif; Abouelhoda, Mohamed; Al-Kadi, Omar S.; Gojobori, Takashi; Jankovic, Boris R.; Khalil, Mohamad; Khandoker, Ahsan H.; Morsy, Ahmed (Communications of the ACM, Association for Computing Machinery (ACM), 2021-03-22) [Article]
    HEALTH CHALLENGES REPRESENT one of the longstanding issues in the Arab region that hinder its ability to develop. Prevalence of diseases such as cardiovascular diseases, liver cirrhosis and cancer among many others has contributed to the deteriorated health status across the region leading to lower life expectancy compared to other regions. For instance, the average life expectancy in the Arab world is approximately 70 years, which is at least 10 years lower than most high-income countries.
  • Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

    Rayapuram, Naganand; Jarad, Mai; Alhoraibi, Hanna; Bigeard, Jean; Abulfaraj, Aala A.; Volz, Ronny; Mariappan, Kiruthiga; Almeida-Trapp, Marilia; Schlöffel, Maria; Lastrucci, Emmanuelle; Bonhomme, Ludovic; Gust, Andrea A.; Mithöfer, Axel; Arold, Stefan T.; Pflieger, Delphine; Hirt, Heribert (NCBI, 2021-03-22) [Bioproject, Dataset]
    We report the transcriptome composition of ahl13-1 compared to WT (col-0) plant without treatment and after Pst hrcC-application Overall design: Illumina high-sequencing plateform was used to analyse the transcriptome composition of col0 and ahl13-1 under treated and untreated conditions. col0 samples are in GEO Series GSE118854.
  • STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline.

    Planell, Nuria; Lagani, Vincenzo; Sebastian-Leon, Patricia; van der Kloet, Frans; Ewing, Ewoud; Karathanasis, Nestoras; Urdangarin, Arantxa; Arozarena, Imanol; Jagodic, Maja; Tsamardinos, Ioannis; Tarazona, Sonia; Conesa, Ana; Tegner, Jesper; Gomez-Cabrero, David (Frontiers in genetics, Frontiers Media SA, 2021-03-22) [Article]
    Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of deciphering different regulatory layers. Yet, while there is a myriad of bioinformatics tools, each multi-omics analysis appears to start from scratch with an arbitrary decision over which tools to use and how to combine them. Therefore, it is an unmet need to conceptualize how to integrate such data and implement and validate pipelines in different cases. We have designed a conceptual framework (STATegra), aiming it to be as generic as possible for multi-omics analysis, combining available multi-omic anlaysis tools (machine learning component analysis, non-parametric data combination, and a multi-omics exploratory analysis) in a step-wise manner. While in several studies, we have previously combined those integrative tools, here, we provide a systematic description of the STATegra framework and its validation using two The Cancer Genome Atlas (TCGA) case studies. For both, the Glioblastoma and the Skin Cutaneous Melanoma (SKCM) cases, we demonstrate an enhanced capacity of the framework (and beyond the individual tools) to identify features and pathways compared to single-omics analysis. Such an integrative multi-omics analysis framework for identifying features and components facilitates the discovery of new biology. Finally, we provide several options for applying the STATegra framework when parametric assumptions are fulfilled and for the case when not all the samples are profiled for all omics. The STATegra framework is built using several tools, which are being integrated step-by-step as OpenSource in the STATegRa Bioconductor package.
  • Mixed Conduction in an N-Type Organic Semiconductor in the Absence of Hydrophilic Side-Chains

    Surgailis, Jokubas; Savva, Achilleas; Druet, Victor; Paulsen, Bryan D.; Wu, Ruiheng; Hamidi-Sakr, Amer; Ohayon, David; Nikiforidis, Georgios; Chen, Xingxing; McCulloch, Iain; Rivnay, Jonathan; Inal, Sahika (Advanced Functional Materials, Wiley, 2021-03-18) [Article]
    Organic electrochemical transistors (OECTs) are the building blocks of biosensors, neuromorphic devices, and complementary circuits. One rule in the materials design for OECTs is the inclusion of a hydrophilic component in the chemical structure to enable ion transport in the film. Here, it is shown that the ladder-type, side-chain free polymer poly(benzimidazobenzophenanthroline) (BBL) performs significantly better in OECTs than the donor–acceptor type copolymer bearing hydrophilic ethylene glycol side chains (P-90). A combination of electrochemical techniques reveals that BBL exhibits a more efficient ion-to-electron coupling and higher OECT mobility than P-90. In situ atomic force microscopy scans evidence that BBL, which swells negligibly in electrolytes, undergoes a drastic and permanent change in morphology upon electrochemical doping. In contrast, P-90 substantially swells when immersed in electrolytes and shows moderate morphology changes induced by dopant ions. Ex situ grazing incidence wide-angle X-ray scattering suggests that the particular packing of BBL crystallites is minimally affected after doping, in contrast to P-90. BBL's ability to show exceptional mixed transport is due to the crystallites’ connectivity, which resists water uptake. This side chain-free route for the design of mixed conductors could bring the n-type OECT performance closer to the bar set by their p-type counterparts.
  • Microbial communities of wheat plants inoculated with endophytic bacterium Enterobacter sp. SA187

    Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (NCBI, 2021-03-16) [Bioproject, Dataset]
    Global warming has become a critical challenge to food safety, causing severe yield losses of major crops worldwide. Here, we report that the endophytic bacterium Enterobacter sp. SA187 induces thermotolerance of crops in a sustainable manner. Microbiome diversity of wheat plants is positively influenced by SA187 in open field agriculture, indicating that beneficial microbes can be a powerful tool to enhance agriculture in open field agriculture. Overall design: We examined the effect the SA187 inoculation on the root endosphere microbiome of wheat plant growing under desert farming condition.
  • Molecular mechanisms of Enterobacter sp. SA187 induced thermotolerance in Arabidopsis thaliana

    Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (NCBI, 2021-03-16) [Bioproject, Dataset]
    Global warming and heat stress belong to the most critical environmental challenges to agriculture worldwide, causing severe losses of major crop yields. In present study we report that the endophytic bacterium Enterobacter sp. SA187 protects Arabidopsis thaliana to heat stress. To understand the mechanisms at molecular level we performed RNA-seq Overall design: mRNA seq to elucidate the SA187 mediated thermotolerance in Arabidopsis thaliana inoculated with entrobacter sp SA187
  • Quick and Easy Assembly of a One-Step qRT-PCR Kit for COVID-19 Diagnostics Using In-House Enzymes

    Takahashi, Masateru; Tehseen, Muhammad; Salunke, Rahul Pandurang; Takahashi, Etsuko; Mfarrej, Sara; Sobhy, Mohamed Abdelmaboud; Alhamlan, Fatimah S.; Hala, Sharif; Ramos Mandujano, Gerardo; Al-Qahtani, Ahmed A.; Alofi, Fadwa S.; Alsomali, Afrah; Hashem, Anwar M.; Khogeer, Asim; Almontashiri, Naif A. M.; Lee, Jae Man; Mon, Hiroaki; Sakashita, Kosuke; Li, Mo; Kusakabe, Takahiro; Pain, Arnab; Hamdan, Samir (ACS Omega, American Chemical Society (ACS), 2021-03-15) [Article]
    One-step reverse-transcription quantitative polymerase chain reaction (qRT-PCR) is the most widely applied method for COVID-19 diagnostics. Notwithstanding the facts that one-step qRT-PCR is well suited for the diagnosis of COVID-19 and that there are many commercially available one-step qRT-PCR kits in the market, their high cost and unavailability due to airport closures and shipment restriction became a major bottleneck that had driven the desire to produce the key components of such kits locally. Here, we provide a simple, economical, and powerful one-step qRT-PCR kit based on patent-free, specifically tailored versions of Moloney murine leukemia virus reverse transcriptase and Thermus aquaticus DNA polymerase and termed R3T (Rapid Research Response Team) one-step qRT-PCR. We also demonstrate the robustness of our enzyme production strategies and provide the optimal reaction conditions for their efficient augmentation in a one-step approach. Our kit was routinely able to reliably detect as low as 10 copies of the synthetic RNAs of SARS-CoV-2. More importantly, our kit successfully detected COVID-19 in clinical samples of broad viral titers with similar reliability and selectivity to that of the Invitrogen SuperScript III Platinum One-step qRT-PCR and TaqPath one-step RT-qPCR kits. Overall, our kit has shown robust performance in both laboratory settings and the Saudi Ministry of Health-approved testing facility.
  • LAMP-Coupled CRISPR–Cas12a Module for Rapid and Sensitive Detection of Plant DNA Viruses

    Mahas, Ahmed; Hassan, Norhan; Aman, Rashid; Maršić, Tin; Wang, Qiaochu; Ali, Zahir; Mahfouz, Magdy M. (Viruses, MDPI AG, 2021-03-12) [Article]
    One important factor for successful disease management is the ability to rapidly and accurately identify the causal agent. Plant viruses cause severe economic losses and pose a serious threat to sustainable agriculture. Therefore, optimization of the speed, sensitivity, feasibility, portability, and accuracy of virus detection is urgently needed. Here, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid diagnostic method utilizing the CRISPR–Cas12a system for detecting two geminiviruses, tomato yellow leaf curl virus (TYLCV) and tomato leaf curl New Delhi virus (ToLCNDV), which have single-stranded DNA genomes. Our assay detected TYLCV and ToLCNDV in infected plants with high sensitivity and specificity. Our newly developed assay can be performed in ~1 h and provides easy-to-interpret visual readouts using a simple, low-cost fluorescence visualizer, making it suitable for point-of-use applications.
  • Pheromone receptor of the globally invasive quarantine pest of the palm tree, the red palm weevil ( Rhynchophorus ferrugineus )

    Antony, Binu; Johny, Jibin; Montagne, Nicolas; Jacquin-Joly, Emmanuelle; Capoduro, Rémi; Cali, Khasim; Persaud, Krishna; Al-Saleh, Mohammed Ali; Pain, Arnab (Molecular Ecology, Wiley, 2021-03-09) [Article]
    Palm trees are of immense economic, sociocultural, touristic, and patrimonial significance all over the world, and date palm-related knowledge, traditions, and practices are now included in UNESCOs list of the Intangible Cultural Heritage of Humanity. Of all the pests that infest these trees, the red palm weevil (RPW), Rhynchophorus ferrugineus (Olivier), is its primary enemy. The RPW is a category-1 quarantine insect pest that causes enormous economic losses in palm tree cultivation worldwide. The RPW synchronizes mass gathering on the palm tree for feeding and mating, regulated by a male-produced pheromone composed of two methyl-branched compounds, (4RS, 5RS)-4-methylnonan-5-ol (ferrugineol) and 4(RS)-methylnonan-5-one (ferrugineone). Despite the importance of odorant detection in long-range orientation towards palm trees, palm colonization, and mating, the pheromone receptor has not been identified in this species. In this study, we report the identification and characterization of the first RPW pheromone receptor, RferOR1. Using gene silencing and functional expression in Drosophila olfactory receptor neurons, we demonstrate that RferOR1 is tuned to ferrugineol and ferrugineone and binds five other structurally related molecules. We reveal the lifetime expression of RferOR1, which correlates with adult mating success irrespective of age, a factor that could explain the wide distribution and spread of this pest. As palm weevils are challenging to control based on conventional methods, elucidation of the mechanisms of pheromone detection opens new routes for mating disruption and the early detection of this pest via the development of pheromone receptor-based biosensors.
  • Complete Genome Sequence of Cellulomonas sp. JZ18, a Root Endophytic Bacterium Isolated from the Perennial Desert Tussock-Grass Panicum turgidum

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Hirt, Heribert; Saad, Maged (Current Microbiology, Springer Science and Business Media LLC, 2021-03-08) [Article]
    Cellulomonas sp. JZ18 is a gram-positive, rod shaped bacterium that was previously isolated from the root endosphere of the perennial desert tussock-grass Panicum turgidum. Genome coverage of PacBio sequencing was approximately 199X. Genome assembly generated a single chromosome of 7,421,843 base pairs with a guanine-cytosine (GC) content of 75.60% with 3240 protein coding sequences, 361 pseudo genes, three ribosomal RNA operons, three non-coding RNAs and 45 transfer RNAs. Comparison of JZ18′s genome with type strains from the same genus, using digital DNA–DNA hybridization and average nucleotide identity calculations, revealed that JZ18 might potentially belong to a new species. Functional analysis revealed the presence of genes that may complement previously observed biochemical and plant phenotypes. Furthermore, the presence of a number of enzymes could be of potential use in industrial processes as biocatalysts. Genome sequencing and analysis, coupled with comparative genomics, of endophytic bacteria for their potential plant growth promoting activities under different soil conditions will accelerate the knowledge and applications of biostimulants in sustainable agriculture.

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