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Recent Submissions

  • An Organic Electrochemical Transistor Integrated Photodetector for High Quality Photoplethysmogram Signal Acquisition

    Zhong, Yizhou; Koklu, Anil; Rosas Villalva, Diego; Zhang, Yongcao; Hernandez, Luis Huerta; Moser, Maximilian; Hallani, Rawad; McCulloch, Iain; Baran, Derya; Inal, Sahika (Advanced Functional Materials, Wiley, 2022-11-27) [Article]
    The organic photodiode (OPD) is a promising building block for solution-processable, flexible, lightweight, and miniaturized photodetectors, ideal for wearable applications. Despite the advances in materials used in OPDs, their photocurrent and light responsivity are limited, and alternative methods are required to boost the signal response. Herein, a miniaturized organic electrochemical transistor (OECT) is integrated with an OPD module to unlock the potential of OPDs to acquire physiological signals. In this integrated photodetector (IPD) system, the light intensity regulates the OPD voltage output that modulates the OECT channel current. The high transconductance of the OECT provides efficient voltage-to-current conversion, enhancing the signal-to-noise ratio on the sensing site. A microscale, p-type enhancement-mode OECT with high gm and fast switching speed performs better in this application than depletion-mode OECT of the same geometry. The IPD achieves a photocurrent and responsivity 318 and 140 times higher than the standalone OPD, respectively. It is shown that with the IPD, the amplitude of the photoplethysmogram signals detected by the OPD is enhanced by a factor of 2.9 × 103, highlighting its potential as a wearable biosensor and to detect weak, often uncaptured, light-based signals from living systems.
  • A 5D Magnetic Tracking System for Placement Verification of Umbilical Catheters and Endotracheal Tubes in Neonates

    Swanepoel, Liam (2022-11-25) [Dissertation]
    Advisor: Kosel, Jürgen
    Committee members: Salama, Khaled N.; Inal, Sahika; Carrara, Sandro
    The use of subcutaneous medical devices has advanced the field of clinical medicine and surgery. However, localizing devices internally requires imaging techniques such as x-ray or ultrasound. A novel 5D magnetic tracking system for subcutaneous medical catheters is presented, providing the capability for precise device localization in an extremely compact and portable pocket-size format. It is entirely benign, avoids x-rays, and can be used to immediately confirm the proper instrument placement. The magnetic tracking system has been implemented on umbilical catheters and endotracheal tubes and is characterized by bench-test, cadaveric and in-vivo studies. The systems consist of a magnetic tip fixed to the distal end of the subcutaneous device, as well as a Magnetic Sensing Device that utilizes magnetic field sensors to localize the magnetic tip. Various Magnetic Sensing Devices have been developed, each with a specific use case in mind within the clinical environment. The magnetic tip is made from a soft, flexible, and lightweight magnetic composite material that is capable of sustaining a high magnetic remanence field whilst also being non-cytotoxic. The bench tests show high localization accuracy for a distance up to 4 cm. The accuracy is slightly reduced during cadaveric and in-vivo tests, due to external factors impacting the application, such as the dermal surface topography and the method of establishing the reference frame before radiographic imaging. A bias circuit has been developed and implemented to increase the operational depth of the magnetic tracking system and prevents sensor saturation at close distances. The magnetic tracking system has shown to be robust in performance and functionality in real-world clinical applications, and with its intuitive approach and portability, it has the potential to make real-time subcutaneous device tracking widely accessible.
  • Side chain engineering enhances the high-temperature resilience and ambient stability of organic synaptic transistors for neuromorphic applications

    Zhao, Yanfei; Haseena, Sheik; Ravva, Mahesh Kumar; Zhang, Shengjie; Li, Xiang; Jiang, Jiandong; Fu, Yujun; Inal, Sahika; Wang, Qi; Wang, Yazhou; Yue, Wan; McCullocn, Iain; He, Deyan (Nano Energy, Elsevier BV, 2022-11-12) [Article]
    Organic synaptic transistors are considered to be one of the most promising device concepts for neuromorphic systems. However, repressively low memory retention and high-temperature instability greatly preclude the development and real-world application of organic synaptic transistors. Herein, we reported three conjugated polymers based on a bithiophene-thienothiophene backbone and the traditional ethylene glycol (EG) chains substituted by more hydrophobic propylene glycol (PG) and butylene glycol (BG) counterparts for three-terminal organic neuromorphic memory devices (TONMD). The resulting TONMD exhibits superior viability in ambient and high-temperature environments. BG chain-based p(b2T-TT) show ultra-long memory retention of over 103 s and large analog switching range (>10 ×) at 180 °C, which represents the record-high high-temperature resilience for reported TONMD to date. They also demonstrated excellent endurance of over 105 write-read operations and ultra-high ambient stability with 96 % of its original conductance after 3 months. Data of molecular dynamic simulations and microstructure show that the superior high-temperature resilience and ambient stability originate from more rigid conformation and stable morphology with the increased hydrophobicity of the PG and BG functionalities. Overall, rational design of oligoether side-chains will boost the device's dual high-temperature and ambient stability without compromising synaptic function and provide promising strategies for high-temperature neuromorphic applications.
  • A personal, reference quality, fully annotated genome from a Saudi individual

    Kulmanov, Maxat; Tawfiq, Rund; Al Ali, Hatoon; Abdelhakim, Marwa; Alarawi, Mohammed; Aldakhil, Hind; Alhattab, Dana Majed; Alsolme, Ebtehal; Althagafi, Azza Th.; Angelov, Angel; Bougouffa, Salim; Driguez, Patrick; Liu, Yang; Park, Changsook; Putra, Alexander; Reyes-Ramos, Ana M; Hauser, Charlotte; Cheung, Ming Sin; Abedalthagafi, Malak S; Hoehndorf, Robert (Cold Spring Harbor Laboratory, 2022-11-08) [Preprint]
    We have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly. As a consequence, we provide a continguous assembly of the complete genome of an individual from Saudi Arabia for all chromosomes except chromosome Y, and label this assembly KSA001. We transferred genome annotations from reference genomes and predicted genome features using methods from Artificial Intelligence to fully annotate KSA001, and we make all primary sequencing data, the assembly, and the genome annotations freely available in public databases using the FAIR data principles.
  • Fabrication of lumen-forming colorectal cancer organoids using a newly designed laminin-derived bioink

    Perez Pedroza, Rosario; Al-Jalih, Fatimah; Xu, Jiayi; Moretti, Manola; Briola, Giuseppina R.; Hauser, Charlotte (INTERNATIONAL JOURNAL OF BIOPRINTING, Whioce Publishing Pte Ltd, 2022-11-04) [Article]
    Three-dimensional (3D) bioprinting systems, which are the prominent tools for biofabrication, should evolve around the cutting-edge technologies of tissue engineering. This is the case with organoid technology, which requires a plethora of new materials to evolve, including extracellular matrices with specific mechanical and biochemical properties. For a bioprinting system to facilitate organoid growth, it must be able to recreate an organ-like environment within the 3D construct. In this study, a well-established, self-assembling peptide system was employed to generate a laminin-like bioink to provide signals of cell adhesion and lumen formation in cancer stem cells. One bioink formulation led to the formation of lumen with outperforming characteristics, which showed good stability of the printed construct.
  • High-efficiency retron-mediated single-stranded DNA production in plants

    Jiang, Wenjun; Sivakrishna Rao, Gundra; Aman, Rashid; Butt, Haroon; Kamel, Radwa; Sedeek, Khalid Elwy Mohamed; Mahfouz, Magdy M. (Synthetic Biology, Oxford University Press (OUP), 2022-11-01) [Article]
    Retrons are a class of retroelements that produce multicopy single-stranded DNA and participate in anti-phage defenses in bacteria. Retrons have been harnessed for the over-production of single-stranded DNA (ssDNA), genome engineering, and directed evolution in bacteria, yeast, and mammalian cells. Retron-mediated ssDNA production in plants could unlock their potential applications in plant biotechnology. For example, ssDNA can be used as a template for homology-directed repair in several organisms. However, current gene editing technologies rely on the physical delivery of synthetic ssDNA, which limits their applications. Here, we demonstrated retron-mediated over-production of ssDNA in Nicotiana benthamiana. Additionally, we tested different retron architectures for improved ssDNA production and identified a new retron architecture that resulted in greater ssDNA abundance. Furthermore, co-expression of the gene encoding the ssDNA-protecting protein VirE2 from Agrobacterium tumefaciens with the retron systems resulted in a 10.7-fold increase in ssDNA production in vivo. We also demonstrated CRISPR-retron-coupled ssDNA over-production and targeted homology-directed repair in N. benthamiana. Overall, we present an efficient approach for in vivo ssDNA production in plants, which can be harnessed for biotechnological applications.
  • The Influence of Prenatal Exposure to Quetiapine Fumarate on the Development of Dopaminergic Neurons in the Ventral Midbrain of Mouse Embryos

    Alsanie, Walaa F.; Abdelrahman, Sherin; Alhomrani, Majid; Gaber, Ahmed; Alosimi, Ebtisam Abdulah; Habeeballah, Hamza; Alkhatabi, Heba A.; Felimban, Raed I.; Hauser, Charlotte; Tayeb, Hossam H.; Alamri, Abdulhakeem S.; Alamri, Abdulwahab; Raafat, Bassem M.; Alswat, Khaled A.; Althobaiti, Yusuf S.; Asiri, Yousif A. (International Journal of Molecular Sciences, MDPI AG, 2022-10-15) [Article]
    The effects of second-generation antipsychotics on prenatal neurodevelopment, apoptotic neurodegeneration, and postnatal developmental delays have been poorly investigated. Even at standard doses, the use of quetiapine fumarate (QEPF) in pregnant women might be detrimental to fetal development. We used primary mouse embryonic neurons to evaluate the disruption of morphogenesis and differentiation of ventral midbrain (VM) neurons after exposure to QEPF. The dopaminergic VM neurons were deliberately targeted due to their roles in cognition, motor activity, and behavior. The results revealed that exposure to QEPF during early brain development decreased the effects of the dopaminergic lineage-related genes Tyrosine hydroxylase(Th), Dopamine receptor D1 (Drd1), Dopamine transporter (Dat), LIM homeobox transcription factor 1 alfa (Lmx1a), and Cell adhesion molecule L1 (Chl1), and the senescent dopaminergic gene Pituitary homeobox 3 (Pitx3). In contrast, Brain derived neurotrophic factor (Bdnf) and Nuclear receptor-related 1 (Nurr1) expressions were significantly upregulated. Interestingly, QEPF had variable effects on the development of non-dopaminergic neurons in VM. An optimal dose of QEPF (10 µM) was found to insignificantly affect the viability of neurons isolated from the VM. It also instigated a non-significant reduction in adenosine triphosphate formation in these neuronal populations. Exposure to QEPF during the early stages of brain development could also hinder the formation of VM and their structural phenotypes. These findings could aid therapeutic decision-making when prescribing 2nd generation antipsychotics in pregnant populations.
  • A Novel Homozygous Founder Variant of RTN4IP1 in Two Consanguineous Saudi Families

    Aldosary, Mazhor; Alsagob, Maysoon; AlQudairy, Hanan; González-Álvarez, Ana C.; Arold, Stefan T.; Dababo, Mohammad Anas; Alharbi, Omar A.; AlMass, Rawan; AlBakheet, Albandary; AlSarar, Dalia; Qari, Alya; Al-Ansari, Mysoon M.; Oláhová, Monika; Al-Shahrani, Saif A.; AlSayed, Moeenaldeen; Colak, Dilek; Taylor, Robert W.; AlOwain, Mohammed; Kaya, Namik (Cells, MDPI AG, 2022-10-07) [Article]
    The genetic architecture of mitochondrial disease continues to expand and currently exceeds more than 350 disease-causing genes. Bi-allelic variants in RTN4IP1, also known as Optic Atrophy-10 (OPA10), lead to early-onset recessive optic neuropathy, atrophy, and encephalopathy in the afflicted patients. The gene is known to encode a mitochondrial ubiquinol oxidoreductase that interacts with reticulon 4 and is thought to be a mitochondrial antioxidant NADPH oxidoreductase. Here, we describe two unrelated consanguineous families from the northern region of Saudi Arabia harboring a missense variant (RTN4IP1:NM_032730.5; c.475G<T, p.Val159Phe) in the gene. Clinically affected individuals presented with intellectual disability, encephalopathy, ataxia, optic atrophy, and seizures. Based on whole exome sequencing and confirmatory Sanger sequencing, the variant was fully segregated with the phenotype in the families, absent among large ethnically matching controls as well as numerous in-house exomes, and predicted to be pathogenic by different in silico classifiers. Structural modeling and immunoblot analyses strongly indicated this variant to be pathogenic. Since the families belong to one of the tribal inhabitants of Saudi Arabia, we postulate that the variant is likely to be a founder. We provide the estimated age of the variant and present data confirming the disease-causality of this founder variant.
  • Biomass generation and heterologous isoprenoid milking from engineered microalgae grown in anaerobic membrane bioreactor effluent

    de Freitas, Barbara Caterina Bastos; Overmans, Sebastian; Medina, Julie Sanchez; Hong, Pei-Ying; Lauersen, Kyle J. (Cold Spring Harbor Laboratory, 2022-09-30) [Preprint]
    Wastewater (WW) treatment in anaerobic membrane bioreactors (AnMBR) is considered more sustainable than in their aerobic counterparts. However, outputs from AnMBR are mixed methane and carbon dioxide gas streams as well as ammonium- (N) and phosphate- (P) containing waters. Using AnMBR outputs as inputs for photoautotrophic algal cultivation can strip the CO2 and remove N and P from effluent which feed algal biomass generation. Recent advances in algal engineering have generated strains for concomitant high-value side product generation in addition to biomass, although only shown in heavily domesticated, lab-adapted strains. Here, investigated whether such a strain of Chlamydomonas reinhardtii could be grown directly in AnMBR effluent with CO2 at concentrations found in its off-gas. The domesticated strain was found to proliferate over bacteria in the non-sterile effluent, consume N and P to levels that meet general discharge or reuse limits, and tolerate cultivation in modelled (extreme) outdoor environmental conditions prevalent along the central Red Sea coast. High-value co-product milking was then demonstrated, up to 837 micro g / L culture in 96 h, in addition to algal biomass production, ~2.4 g CDW / L in 96 h, directly in effluents. This is the first demonstration of a combined bio-process that employs a heavily engineered algal strain to enhance the product generation potentials from AnMBR effluent treatment. This study shows it is possible to convert waste into value through use of engineered algae while also improve wastewater treatment economics through co-product generation.
  • Advanced software development of 2D and 3D model visualization for TwinPrint, a dual-arm 3D bioprinting system for multi-material printing

    AlZaid, Shaddin; Hammad, Noofa S; Albalawi, Hamed I.; Khan, Zainab N.; Othman, Eter; Hauser, Charlotte (Materials Science in Additive Manufacturing, Whioce Publishing Pte Ltd, 2022-09-28) [Article]
    This research highlights the development of a two-dimensional (2D) and three-dimensional (3D) preview software for additive manufacturing (AM). The presented software can produce a virtual representation of an actuator’s path movements by reading and parsing the orders of the desired geometric code (G-code) file. It then simulates the coded sections into separate 2D layers and colored 3D objects in a graphical model. This allows users to validate the shapes before the 3D printing process. G-code is an operation language which is based on command lines of code written in an alphanumeric format. Each line of these commands controls one machining operation; this instructs the machine’s motion to move in an arc, a circle, or a straight line to perform a specific shape after compiling all code lines. AM technology is widely used in most manufacturing fields (e.g., medical, chemical, and research laboratories) as a prototyping technology due to its ability to produce rapid prototyping models. 3D printing creates physical 3D models by extruding material layer by layer as 2D layers. At present, the most critical challenges in AM technology are drastically reducing prototyping materials’ consumption and time spent. To address these challenges, the proposed software allows for visualization of G-code files and predicting the overall layers’ shapes, allowing both structure prediction and subsequent printing error reduction.
  • Synthetic evolution of herbicide resistance using a T7 RNAP–based random DNA base editor

    Butt, Haroon; Moreno-Ramírez, Jose Luis; Mahfouz, Magdy M. (Life Science Alliance, Life Science Alliance, LLC, 2022-09-28) [Article]
    Synthetic directed evolution via localized sequence diversification and the simultaneous application of selection pressure is a promising method for producing new, beneficial alleles that affect traits of interest in diverse species; however, this technique has rarely been applied in plants. Here, we designed, built, and tested a chimeric fusion of T7 RNA Polymerase (RNAP) and deaminase to enable the localized sequence diversification of a target sequence of interest. We tested our T7 RNAP–DNA base editor in Nicotiana benthamiana transient assays to target a transgene expressing GFP under the control of the T7 promoter and observed C-to-T conversions. We then targeted the T7 promoter-driven acetolactate synthase sequence that had been stably integrated in the rice genome and generated C-to-T and G-to-A transitions. We used herbicide treatment as selection pressure for the evolution of the acetolactate synthase sequence, resulting in the enrichment of herbicide-responsive residues. We then validated these herbicide-responsive regions in the transgenic rice plants. Thus, our system could be used for the continuous synthetic evolution of gene functions to produce variants with improved herbicide resistance.
  • Enhancing the Backbone Coplanarity of n-Type Copolymers for Higher Electron Mobility and Stability in Organic Electrochemical Transistors

    Maria, Iuliana P.; Griggs, Sophie; Rashid, Reem B.; Paulsen, Bryan D.; Surgailis, Jokubas; Thorley, Karl; Le, Vianna N.; Harrison, George T.; Combe, Craig; Hallani, Rawad; Giovannitti, Alexander; Paterson, Alexandra F.; Inal, Sahika; Rivnay, Jonathan; McCulloch, Iain (Chemistry of Materials, American Chemical Society (ACS), 2022-09-27) [Article]
    Electron-transporting (n-type) conjugated polymers have recently been applied in numerous electrochemical applications, where both ion and electron transport are required. Despite continuous efforts to improve their performance and stability, n-type conjugated polymers with mixed conduction still lag behind their hole-transporting (p-type) counterparts, limiting the functions of electrochemical devices. In this work, we investigate the effect of enhanced backbone coplanarity on the electrochemical activity and mixed ionic-electronic conduction properties of n-type polymers during operation in aqueous media. Through substitution of the widely employed electron-deficient naphthalene diimide (NDI) unit for the core-extended naphthodithiophene diimide (NDTI) units, the resulting polymer shows a more planar backbone with closer packing, leading to an increase in the electron mobility in organic electrochemical transistors (OECTs) by more than two orders of magnitude. The NDTI-based polymer shows a deep-lying lowest unoccupied molecular orbital level, enabling operation of the OECT closer to 0 V vs Ag/AgCl, where fewer parasitic reactions with molecular oxygen occur. Enhancing the backbone coplanarity also leads to a lower affinity toward water uptake during cycling, resulting in improved stability during continuous electrochemical charging and ON–OFF switching relative to the NDI derivative. Furthermore, the NDTI-based polymer also demonstrates near-perfect shelf-life stability over a month-long test, exhibiting a negligible decrease in both the maximum on-current and transconductance. Our results highlight the importance of polymer backbone design for developing stable, high-performing n-type materials with mixed ionic-electronic conduction in aqueous media.
  • Teaching an old ‘doc’ new tricks for algal biotechnology: Strategic filter use enables multi-scale fluorescent protein signal detection

    Gutiérrez, Sergio; Wellman, Gordon B.; Lauersen, Kyle J. (Frontiers in Bioengineering and Biotechnology, Frontiers Media SA, 2022-09-23) [Article]
    Fluorescent proteins (FPs) are powerful reporters with a broad range of applications in gene expression and subcellular localization. High-throughput screening is often required to identify individual transformed cell lines in organisms that favor non-homologous-end-joining integration of transgenes into genomes, like in the model green microalga Chlamydomonas reinhardtii. Strategic transgene design, including genetic fusion of transgenes to FPs, and strain domestication have aided engineering efforts in this host but have not removed the need for screening large numbers of transformants to identify those with robust transgene expression levels. FPs facilitate transformant screening by providing a visual signal indicating transgene expression. However, limited combinations of FPs have been described in alga and inherent background fluorescence from cell pigments can hinder FP detection efforts depending on available infrastructure. Here, an updated set of algal nuclear genome-domesticated plasmid parts for seven FPs and six epitope tags were generated and tested in C. reinhardtii. Strategic filter selection was found to enable detection of up to five independent FPs signals from cyan to far-red separately from inherent chlorophyll fluorescence in live algae at the agar plate-level and also in protein electrophoresis gels. This work presents technical advances for algal engineering that can assist reporter detection efforts in other photosynthetic host cells or organisms with inherent background fluorescence.
  • A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics

    Sánchez, Edith; Ali, Zahir; Islam, Tofazzal; Mahfouz, Magdy M. (Plant Biotechnology Journal, Wiley, 2022-09-07) [Article]
    Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive, and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes, and phytopathogens in less than 1 hour, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome, and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering, and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility, and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.
  • Chlamydomonas reinhardtii Alternates Peroxisomal Contents in Response to Trophic Conditions

    Kato, Naohiro; McCuiston, Clayton; Szuska, Kimberly A.; Lauersen, Kyle J.; Nelson, Gabela; Strain, Alexis (Cells, MDPI AG, 2022-09-01) [Article]
    Chlamydomonas reinhardtii is a model green microalga capable of heterotrophic growth on acetic acid but not fatty acids, despite containing a full complement of genes for β-oxidation. Recent reports indicate that the alga preferentially sequesters, rather than breaks down, lipid acyl chains as a means to rebuild its membranes rapidly. Here, we assemble a list of potential Chlamydomonas peroxins (PEXs) required for peroxisomal biogenesis to suggest that C. reinhardtii has a complete set of peroxisome biogenesis factors. To determine involvements of the peroxisomes in the metabolism of exogenously added fatty acids, we examined transgenic C. reinhardtii expressing fluorescent proteins fused to N- or C-terminal peptide of peroxisomal proteins, concomitantly with fluorescently labeled palmitic acid under different trophic conditions. We used confocal microscopy to track the populations of the peroxisomes in illuminated and dark conditions, with and without acetic acid as a carbon source. In the cells, four major populations of compartments were identified, containing: (1) a glyoxylate cycle enzyme marker and a protein containing peroxisomal targeting signal 1 (PTS1) tripeptide but lacking the fatty acid marker, (2) the fatty acid marker alone, (3) the glyoxylate cycle enzyme marker alone, and (4) the PTS1 marker alone. Less than 5% of the compartments contained both fatty acid and peroxisomal markers. Statistical analysis on optically sectioned images found that C. reinhardtii simultaneously carries diverse populations of the peroxisomes in the cell and modulates peroxisomal contents based on light conditions. On the other hand, the ratio of the compartment containing both fatty acid and peroxisomal markers did not change significantly regardless of the culture conditions. The result indicates that β-oxidation may be only a minor occurrence in the peroxisomal population in C. reinhardtii, which supports the idea that lipid biosynthesis and not β-oxidation is the primary metabolic preference of fatty acids in the alga.
  • The exceptionally efficient quorum quenching enzyme LrsL suppresses Pseudomonas aeruginosa biofilm production

    Rehman, Zahid Ur; Momin, Afaque Ahmad Imtiyaz; Aldehaiman, Abdullah; Irum, Tayyaba; Grunberg, Raik; Arold, Stefan T. (Frontiers in Microbiology, Frontiers Media SA, 2022-08-22) [Article]
    Quorum quenching (QQ) is the enzymatic degradation of molecules used by bacteria for synchronizing their behavior within communities. QQ has attracted wide attention due to its potential to inhibit biofilm formation and suppress the production of virulence factors. Through its capacity to limit biofouling and infections, QQ has applications in water treatment, aquaculture, and healthcare. Several different QQ enzymes have been described; however, they often lack the high stability and catalytic efficiency required for industrial applications. Previously, we identified genes from genome sequences of Red Sea sediment bacteria encoding potential QQ enzymes. In this study, we report that one of them, named LrsL, is a metallo-β-lactamase superfamily QQ enzyme with outstanding catalytic features. X-ray crystallography shows that LrsL is a zinc-binding dimer. LrsL has an unusually hydrophobic substrate binding pocket that can accommodate a broad range of acyl-homoserine lactones (AHLs) with exceptionally high affinity. In vitro, LrsL achieves the highest catalytic efficiency reported thus far for any QQ enzyme with a Kcat/KM of 3 × 107. LrsL effectively inhibited Pseudomonas aeruginosa biofilm formation without affecting bacterial growth. Furthermore, LrsL suppressed the production of exopolysaccharides required for biofilm production. These features, and its capacity to regain its function after prolonged heat denaturation, identify LrsL as a robust and unusually efficient QQ enzyme for clinical and industrial applications.
  • Streamlined detection of SARS-CoV-2 via Cas13

    Ghouneimy, Ahmed; Mahfouz, Magdy M. (Nature biomedical engineering, Springer Science and Business Media LLC, 2022-08-19) [Article]
    Assays leveraging the CRISPR-associated enzyme Cas13 and isothermal RNA amplification for the detection of viral RNA are being simplified for point-of-care use.
  • PYK2 senses calcium through a disordered dimerization and calmodulin-binding element

    Momin, Afaque Ahmad Imtiyaz; Mendes, Tiago; Barthe, Philippe; Faure, Camille; Hong, Seungbeom; Yu, Piao; Kadaré, Gress; Jaremko, Mariusz; Girault, Jean Antoine; Jaremko, Lukasz; Arold, Stefan T. (Communications Biology, Springer Science and Business Media LLC, 2022-08-09) [Article]
    Multidomain kinases use many ways to integrate and process diverse stimuli. Here, we investigated the mechanism by which the protein tyrosine kinase 2-beta (PYK2) functions as a sensor and effector of cellular calcium influx. We show that the linker between the PYK2 kinase and FAT domains (KFL) encompasses an unusual calmodulin (CaM) binding element. PYK2 KFL is disordered and engages CaM through an ensemble of transient binding events. Calcium increases the association by promoting structural changes in CaM that expose auxiliary interaction opportunities. KFL also forms fuzzy dimers, and dimerization is enhanced by CaM binding. As a monomer, however, KFL associates with the PYK2 FERM-kinase fragment. Thus, we identify a mechanism whereby calcium influx can promote PYK2 self-association, and hence kinase-activating trans-autophosphorylation. Collectively, our findings describe a flexible protein module that expands the paradigms for CaM binding and self-association, and their use for controlling kinase activity.
  • Investigation of Antibiotic Resistome in Hospital Wastewater during the COVID-19 Pandemic: Is the Initial Phase of the Pandemic Contributing to Antimicrobial Resistance?

    Wang, Changzhi; Mantilla Calderon, David; Xiong, Yanghui; Alkahtani, Mohsen; Bashawri, Yasir M.; Al Qarni, Hamed; Hong, Pei-Ying (Environmental Science & Technology, American Chemical Society (ACS), 2022-08-02) [Article]
    Since the COVID-19 pandemic started, there has been much speculation about how COVID-19 and antimicrobial resistance may be interconnected. In this study, untreated wastewater was sampled from Hospital A designated to treat COVID-19 patients during the first wave of the COVID-19 pandemic alongside Hospital B that did not receive any COVID-19 patients. Metagenomics was used to determine the relative abundance and mobile potential of antibiotic resistant genes (ARGs), prior to determining the correlation of ARGs with time/incidence of COVID-19. Our findings showed that ARGs resistant to macrolides, sulfonamides, and tetracyclines were positively correlated with time in Hospital A but not in Hospital B. Likewise, minor extended spectrum beta-lactamases (ESBLs) and carbapenemases of classes B and D were positively correlated with time, suggesting the selection of rare and/or carbapenem-resistant genes in Hospital A. Non-carbapenemase blaVEB also positively correlated with both time and intI1 and was copresent with other ARGs including carbapenem-resistant genes in 6 metagenome-assembled genomes (MAGs). This study highlighted concerns related to the dissemination of antimicrobial resistance (AMR) during the COVID-19 pandemic that may arise from antibiotic use and untreated hospital wastewater.
  • Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways

    Santos Correa, Sulamita; Schultz, Junia; Lauersen, Kyle J.; Soares Rosado, Alexandre (Journal of advanced research, Elsevier BV, 2022-07-30) [Article]
    Background: Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin–Benson–Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms. Aim of Review: In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field. Key Scientific Concepts of Review: Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging “omics” data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.

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