Recent Submissions

  • Generation of iPSC lines (KAUSTi011-A, KAUSTi011-B) from a Saudi patient with epileptic encephalopathy carrying homozygous mutation in the GLP1R gene.

    Alowaysi, Maryam; Astro, Veronica; Fiacco, Elisabetta; AlZahrani, Fatema; Alkuraya, Fowzan S; Adamo, Antonio (Stem cell research, Elsevier BV, 2021-01-09) [Article]
    Glucagon-like peptide-1 receptor (GLP1R) is a seven-transmembrane-spanning helices membrane protein expressed in multiple human tissues including pancreatic islets, lung, brain, heart and central nervous system (CNS). GLP1R agonists are commonly used as antidiabetic drugs, but a neuroprotective function in neurodegenerative disorders is emerging. Here, we established two iPSC lines from a patient harboring a rare homozygous splice site variant in GLP1R (NM_002062.3; c.402 + 3delG). This patient displays severe developmental delay and epileptic encephalopathy. Therefore, the derivation of these iPSC lines constitutes a primary model to study the molecular pathology of GLP1R dysfunction and develop novel therapeutic targets.
  • 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 (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-01-08) [Article]
    In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
  • Elucidating the Role of Virulence Traits in the Survival of Pathogenic E. coli PI-7 Following Disinfection

    Sivakumar, Krishnakumar; Lehmann, Robert; Rachmadi, Andri Taruna; Augsburger, Nicolas; Zaouri, Noor A.; Tegner, Jesper; Hong, Pei-Ying (Frontiers in bioengineering and biotechnology, Frontiers Media SA, 2021-01-08) [Article]
    Reuse and discharge of treated wastewater can result in dissemination of microorganisms into the environment. Deployment of disinfection strategies is typically proposed as a last stage remediation effort to further inactivate viable microorganisms. In this study, we hypothesize that virulence traits, including biofilm formation, motility, siderophore, and curli production along with the capability to internalize into mammalian cells play a role in survival against disinfectants. Pathogenic E. coli PI-7 strain was used as a model bacterium that was exposed to diverse disinfection strategies such as chlorination, UV and solar irradiation. To this end, we used a random transposon mutagenesis library screening approach to generate 14 mutants that exhibited varying levels of virulence traits. In these 14 isolated mutants, we observed that an increase in virulence traits such as biofilm formation, motility, curli production, and internalization capability, increased the inactivation half-lives of mutants compared to wild-type E. coli PI-7. In addition, oxidative stress response and EPS production contributed to lengthening the lag phase duration (defined as the time required for exposure to disinfectant prior to decay). However, traits related to siderophore production did not help with survival against the tested disinfection strategies. Taken together, the findings suggested that selected virulence traits facilitate survival of pathogenic E. coli PI-7, which in turn could account for the selective enrichment of pathogens over the nonpathogenic ones after wastewater treatment. Further, the study also reflected on the effectiveness of UV as a more viable disinfection strategy for inactivation of pathogens.
  • Molecular basis for the adaptive evolution of environment sensing by H-NS proteins

    Zhao, Xiaochuan; Shahul Hameed, Umar Farook; Kharchenko, Vladlena; Liao, Chenyi; Huser, Franceline; Remington, Jacob M; Radhakrishnan, Anand K; Jaremko, Mariusz; Jaremko, Lukasz; Arold, Stefan T.; Li, Jianing (eLife, eLife Sciences Publications, Ltd, 2021-01-07) [Article]
    The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less NMR spectroscopy and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS–mediated environmental sensing and suggests that this sensing mechanism resulted from the exaptation of an ancestral protein feature.
  • Assembly of Two CCDD Rice Genomes, Oryza grandiglumis and Oryza latifolia, and the Study of Their Evolutionary Changes

    Alsantely, Aseel O. (2021-01) [Thesis]
    Advisor: Wing, Rod Anthony
    Committee members: Gojobori, Takashi; Zuccolo, Andrea
    Every day more than half of the world consumes rice as a primary dietary resource. Thus, rice is one of the most important food crops in the world. Rice and its wild relatives are part of the genus Oryza. Studying the genome structure, function, and evolution of Oryza species in a comparative genomics framework is a useful approach to provide a wealth of knowledge that can significantly improve valuable agronomic traits. The Oryza genus includes 27 species, with 11 different genome types as identified by genetic and cytogenetic analyses. Six genome types, including that of domesticated rice - O. sativa and O. glaberrima, are diploid, and the remaining 5 are tetraploids. Three of the tetraploid species contain the CCDD genome types (O. grandiglumis, O. latifolia, and O. alta), which arose less than 2 million years ago. Polyploidization is one of the major contributors to evolutionary divergence and can thereby lead to adaptation to new environmental niches. An important first step in the characterization of the polyploid Oryza species is the generation of a high-quality reference genome sequence. Unfortunately, up until recently, the generation of such an important and fundamental resource from polyploid species has been challenging, primarily due to their genome complexity and repetitive sequence content. In this project, I assembled two high-quality genomes assemblies for O. grandiglumis and O. latifolia using PacBio long-read sequencing technology and an assembly pipeline that employed 3 genome assemblers (i.e., Canu/2.0, Mecat2, and Flye/2.5) and multiple rounds of sequence polishing with 5 both Arrow and Pilon/1.23. After the primary assembly, sequence contigs were arranged into pseudomolecules, and homeologous chromosomes were assigned to their respective genome types (i.e., CC or DD). Finally, the assemblies were extensively edited manually to close as many gaps as possible. Both assemblies were then analyzed for transposable element and structural variant content between species and homoeologous chromosomes. This enabled us to study the evolutionary divergence of those two genomes, and to explore the possibility of neo-domesticating either species in future research for my PhD dissertation.
  • Engineered Microgels—Their Manufacturing and Biomedical Applications

    Alzanbaki, Hamzah; Moretti, Manola; Hauser, Charlotte (Micromachines, MDPI AG, 2021-01-01) [Article]
    Microgels are hydrogel particles with diameters in the micrometer scale that can be fabricated in different shapes and sizes. Microgels are increasingly used for biomedical applications and for biofabrication due to their interesting features, such as injectability, modularity, porosity and tunability in respect to size, shape and mechanical properties. Fabrication methods of microgels are divided into two categories, following a top-down or bottom-up approach. Each approach has its own advantages and disadvantages and requires certain sets of materials and equipments. In this review, we discuss fabrication methods of both top-down and bottom-up approaches and point to their advantages as well as their limitations, with more focus on the bottom-up approaches. In addition, the use of microgels for a variety of biomedical applications will be discussed, including microgels for the delivery of therapeutic agents and microgels as cell carriers for the fabrication of 3D bioprinted cell-laden constructs. Microgels made from well-defined synthetic materials with a focus on rationally designed ultrashort peptides are also discussed, because they have been demonstrated to serve as an attractive alternative to much less defined naturally derived materials. Here, we will emphasize the potential and properties of ultrashort self-assembling peptides related to microgels.
  • Arabidopsis Plant Natriuretic Peptide Is a Novel Interactor of Rubisco Activase

    Turek, Ilona; Gehring, Christoph A; Irving, H R (Life, MDPI AG, 2020-12-31) [Article]
    Plant natriuretic peptides (PNPs) are a group of systemically acting peptidic hormones affecting solute and solvent homeostasis and responses to biotrophic pathogens. Although an increasing body of evidence suggests PNPs modulate plant responses to biotic and abiotic stress, which could lead to their potential biotechnological application by conferring increased stress tolerance to plants, the exact mode of PNPs action is still elusive. In order to gain insight into PNP-dependent signalling, we set out to identify interactors of PNP present in the model plant Arabidopsis thaliana, termed AtPNP-A. Here, we report identification of rubisco activase (RCA), a central regulator of photosynthesis converting Rubisco catalytic sites from a closed to an open conformation, as an interactor of AtPNP-A through affinity isolation followed by mass spectrometric identification. Surface plasmon resonance (SPR) analyses reveals that the full-length recombinant AtPNP-A and the biologically active fragment of AtPNP-A bind specifically to RCA, whereas a biologically inactive scrambled peptide fails to bind. These results are considered in the light of known functions of PNPs, PNP-like proteins, and RCA in biotic and abiotic stress responses.
  • Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes

    Bi, Chongwei; Wang, Lin; Fan, Yong; Ramos Mandujano, Gerardo; Yuan, Baolei; Zhou, Xuan; Wang, Jincheng; Shao, Yanjiao; Zhang, Pu-Yao; Huang, Yanyi; Yu, Yang; Izpisua Belmonte, Juan Carlos; Li, Mo (Cold Spring Harbor Laboratory, 2020-12-29) [Preprint]
    The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods. We developed individual Mitochondrial Genome sequencing (iMiGseq) of full-length mtDNA for ultra-sensitive variant detection, complete haplotyping, and unbiased evaluation of heteroplasmy levels, all at the individual mtDNA molecule level. iMiGseq uncovers unappreciated levels of heteroplasmic variants in single healthy human oocytes well below the current 1% detection limit, of which numerous variants are detrimental and could contribute to late-onset mitochondrial disease and cancer. Extreme mtDNA heterogeneity among oocytes of the same mouse female, and a strong selection against deleterious mutations in human oocytes are observed. iMiGseq could comprehensively characterize and haplotype single-nucleotide and structural variants of mtDNA and their genetic linkage in NARP/Leigh syndrome patient-derived cells. Therefore, iMiGseq could not only elucidate the mitochondrial etiology of diseases, but also help diagnose and prevent mitochondrial diseases with unprecedented precision.
  • Performance of Commercially Available Rapid Serological Assays for the Detection of SARS-CoV-2 Antibodies.

    Hashem, Anwar M; Alhabbab, Rowa Y; Algaissi, Abdullah; Alfaleh, Mohamed A; Hala, Sharif; Abujamel, Turki S; ElAssouli, M-Zaki; AL-Somali, Afrah A; Alofi, Fadwa S; Khogeer, Asim A; Alkayyal, Almohanad A; Mahmoud, Ahmad Bakur; Almontashiri, Naif A M; Pain, Arnab (Pathogens (Basel, Switzerland), MDPI AG, 2020-12-23) [Article]
    The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread globally. Although several rapid commercial serological assays have been developed, little is known about their performance and accuracy in detecting SARS-CoV-2-specific antibodies in COVID-19 patient samples. Here, we have evaluated the performance of seven commercially available rapid lateral flow immunoassays (LFIA) obtained from different manufacturers, and compared them to in-house developed and validated ELISA assays for the detection of SARS-CoV-2-specific IgM and IgG antibodies in RT-PCR-confirmed COVID-19 patients. While all evaluated LFIA assays showed high specificity, our data showed a significant variation in sensitivity of these assays, which ranged from 0% to 54% for samples collected early during infection (3-7 days post symptoms onset) and from 54% to 88% for samples collected at later time points during infection (8-27 days post symptoms onset). Therefore, we recommend prior evaluation and validation of these assays before being routinely used to detect IgM and IgG in COVID-19 patients. Moreover, our findings suggest the use of LFIA assays in combination with other standard methods, and not as an alternative.
  • The pangenome analysis of the soil-borne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource: RsolaniDB

    Kaushik, Abhinav; Roberts, Daniel P; Ramaprasad, Abhinay; Mfarrej, Sara; Nair, Mridul B; Lakshman, Dilip; Pain, Arnab (Cold Spring Harbor Laboratory, 2020-12-22) [Preprint]
    Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungus that damages economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host range. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and selected subgroups (AG1-IA, AG1-IB, AG1-IC, AG2-2IIIB, AG3-PT (isolates Rhs 1AP and the hypovirulent Rhs1A1), AG3-TB, AG4-HG-I (isolates Rs23 and R118-11), AG5, AG6, and AG8), in which six genomes are reported for the first time, wherein we discovered unique and shared secretomes, CAZymes, and effectors across the AGs. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other basidiomycetes, we also elucidated the molecular factors potentially involved in determining the AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms, to assist mycologists in formulating new hypotheses.
  • assayM: a web application to monitor mutations in COVID-19 diagnostic assays.

    Naeem, Raeece; Pain, Arnab (Cold Spring Harbor Laboratory, 2020-12-22) [Preprint]
    Reverse Transcriptase - Polymerase Chain Reaction (RT-PCR) is the gold standard as diagnostic assays for the detection of COVID-19 and the specificity and sensitivity of these assays depend on the complementarity of the RT-PCR primers to the genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the virus mutates over time during replication cycles, there is an urgent need to continuously monitor the virus genome for appearances of mutations and mismatches in the PCR primers used in these assays. Here we present assayM, a web application to explore and monitor mutations introduced in the primer and probe sequences published by the World Health Organisation (WHO) or in any custom-designed assay primers for SARS-CoV-2 detection assays in globally available SARS-CoV-2 genome datasets.
  • KAUST Metagenomic Analysis Platform (KMAP), Enabling Access to Massive Analytics of Re-Annotated Metagenomic Data.

    Alam, Intikhab; Kamau, Allan; Gugi, David; Gojobori, Takashi; Duarte, Carlos M.; Bajic, Vladimir B. (Research Square, 2020-12-14) [Preprint]
    Abstract Exponential rise of metagenomics sequencing is delivering massive functional environmental genomics data. However, this also generates a procedural bottleneck for on-going re-analysis as reference databases grow and methods improve, and analyses need be updated for consistency, which require acceess to increasingly demanding bioinformatic and computational resources. Here, we present the KAUST Metagenomic Analysis Platform (KMAP), a new integrated open web-based tool for the comprehensive exploration of shotgun metagenomic data. We illustrate the capacities KMAP provides through the re-assembly of ~27,000 public metagenomic samples captured in ~450 studies sampled across ~77 diverse habitats, resulting in 36 new habitat-specific gene catalogs, all based on full-length (complete) genes. Extensive taxonomic and gene annotations are stored in Gene Information Tables (GITs), a simple tractable data integration format useful for analysis through command line or for database management. KMAP facilitates the exploration and comparison of microbial GITs across different habitats with over 275 million genes.
  • Unforgettable: Optogenetic Stimulation of Prelimbic Pyramidal Neurons Maintains Fear Memories by Modulating Amygdala Pyramidal Neuron Transcriptome

    Laricchiuta, Daniela; Sciamanna, Giuseppe; Gimenez, Juliette; Termine, Andrea; Fabrizio, Carlo; Caioli, Silvia; Balsamo, Francesca; Panuccio, Anna; De Bardi, Marco; Saba, Luana; Passarello, Noemi; Cutuli, Debora; Mattioni, Anna; Zona, Cristina; Orlando, Valerio; Petrosini, Laura (MDPI AG, 2020-12-11) [Preprint]
    Fear extinction requires coordinated neural activity within the amygdala and medial prefrontal cortex (mPFC). Any behavior has a transcriptomic signature that is modified by environmental experiences, and specific genes are involved in functional plasticity and synaptic wiring during fear extinction. Here, we investigated the effects of optogenetic manipulations of prelimbic (PrL) pyramidal neurons on amygdala gene expression to analyze the specific transcriptional pathways involved in adaptive and maladaptive fear extinction. To this aim, transgenic mice were (or not) fear-conditioned and during the extinction phase they received optogenetic (or sham) stimulations over PrL pyramidal neurons. At the end of behavioral testing, electrophysiological (neural cellular excitability and Excitatory Post-Synaptic Currents) and morphological (spinogenesis) correlates were evaluated in the PrL pyramidal neurons. Furthermore, transcriptomic cell-specific RNA-analyses (differential gene expression profiling and functional enrichment analyses) were performed in amygdala pyramidal neurons. Our results show that the optogenetic activation of PrL pyramidal neurons in fear-conditioned mice induces fear extinction deficits, reflected in an increase of cellular excitability, excitatory neurotransmission, and spinogenesis of PrL pyramidal neurons, and in strong modifications of the transcriptome of amygdala pyramidal neurons. Understanding the electrophysiological, morphological and transcriptomic architecture of fear extinction may facilitate the comprehension of fear-related disorders.
  • Engineering rules that minimize germline silencing of transgenes in simple extrachromosomal arrays in C. elegans

    Al Johani, Mohammed; El Mouridi, Sonia; Priyadarshini, Monika; Vargas-Velazquez, Amhed M.; Frøkjær-Jensen, Christian (Nature Communications, Springer Science and Business Media LLC, 2020-12-09) [Article]
    AbstractTransgenes are prone to progressive silencing due to their structure, copy number, and genomic location. In C. elegans, repressive mechanisms are particularly strong in the germline with almost fully penetrant transgene silencing in simple extrachromosomal arrays and frequent silencing of single-copy transgene insertions. A class of non-coding DNA, Periodic An/Tn Clusters (PATCs) can prevent transgene-silencing in repressive chromatin or from small interfering RNAs (piRNAs). Here, we describe design rules (codon-optimization, intron and PATC inclusion, elevated temperature (25 °C), and vector backbone removal) for efficient germline expression from arrays in wildtype animals. We generate web-based tools to analyze PATCs and reagents for the convenient assembly of PATC-rich transgenes. An extensive collection of silencing resistant fluorescent proteins (e.g., gfp, mCherry, and tagBFP) can be used for dissecting germline regulatory elements and a set of enhanced enzymes (Mos1 transposase, Cas9, Cre, and Flp recombinases) enable efficient genetic engineering in C. elegans.
  • Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients.

    Hashem, Anwar M; Algaissi, Abdullah; Almahboub, Sarah A; Alfaleh, Mohamed A; Abujamel, Turki S; Alamri, Sawsan S; Alluhaybi, Khalid A; Hobani, Haya I; AlHarbi, Rahaf H; Alsulaiman, Reem M; ElAssouli, M-Zaki; Hala, Sharif; Alharbi, Naif K; Alhabbab, Rowa Y; AlSaieedi, Ahdab A; Abdulaal, Wesam H; Bukhari, Abdullah; AL-Somali, Afrah A; Alofi, Fadwa S; Khogeer, Asim A; Pain, Arnab; Alkayyal, Almohanad A; Almontashiri, Naif A M; Ahmad, Bakur Mahmoud; Li, Xuguang (Viruses, MDPI AG, 2020-12-09) [Article]
    The Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2, continues to spread globally with significantly high morbidity and mortality rates. Antigen-specific responses are of unquestionable value for clinical management of COVID-19 patients. Here, we investigated the kinetics of IgM, IgG against the spike (S) and nucleoproteins (N) proteins and their neutralizing capabilities in hospitalized COVID-19 patients with different disease presentations (i.e., mild, moderate or severe), need for intensive care units (ICU) admission or outcomes (i.e., survival vs death). We show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Interestingly, significantly higher levels of nAbs as well as anti-S1 and -N IgG and IgM antibodies were found in patients with more severe symptoms, patients requiring admission to ICU or those with fatal outcomes. More importantly, early after symptoms onset, we found that the levels of anti-N antibodies correlated strongly with disease severity. Collectively, these findings provide new insights into the kinetics of antibody responses in COVID-19 patients with different disease severity.
  • MRE11 Is Crucial for Malaria Parasite Transmission and Its Absence Affects Expression of Interconnected Networks of Key Genes Essential for Life.

    Guttery, David; Ramaprasad, Abhinay; Ferguson, David J P; Zeeshan, Mohammad; Pandey, Rajan; Brady, Declan; Holder, Anthony A; Pain, Arnab; Tewari, Rita (Cells, MDPI AG, 2020-12-08) [Article]
    The meiotic recombination 11 protein (MRE11) plays a key role in DNA damage response and maintenance of genome stability. However, little is known about its function during development of the malaria parasite $\textit{Plasmodium}$. Here, we present a functional, ultrastructural and transcriptomic analysis of $\textit{Plasmodium}$ parasites lacking MRE11 during its life cycle in both mammalian and mosquito vector hosts. Genetic disruption of $\textit{Plasmodium berghei mre11}$ (PbMRE11) results in significant retardation of oocyst development in the mosquito midgut associated with cytoplasmic and nuclear degeneration, along with concomitant ablation of sporogony and subsequent parasite transmission. Further, absence of PbMRE11 results in significant transcriptional downregulation of genes involved in key interconnected biological processes that are fundamental to all eukaryotic life including ribonucleoprotein biogenesis, spliceosome function and iron-sulfur cluster assembly. Overall, our study provides a comprehensive functional analysis of MRE11's role in $\textit{Plasmodium}$ development during the mosquito stages and offers a potential target for therapeutic intervention during malaria parasite transmission.
  • MXene improves the stability and electrochemical performance of electropolymerized PEDOT films

    Wustoni, Shofarul; Saleh, Abdulelah; El Demellawi, Jehad K.; Koklu, Anil; Hama, Adel; Druet, Victor; Wehbe, Nimer; Zhang, Yi Zhou; Inal, Sahika (APL Materials, AIP Publishing, 2020-12-01) [Article]
    Poly(3,4-ethylenedioxythiophene) (PEDOT) doped with poly(styrene sulfonate) (PSS) is the most commonly used conducting polymer in organic bioelectronics. However, electrochemical capacitances exceeding the current state-of-the-art are required for enhanced transduction and stimulation of biological signals. The long-term stability of conducting polymer films during device operation and storage in aqueous environments remains a challenge for routine applications. In this work, we electrochemically synthesize a PEDOT composite comprising the water dispersible two-dimensional conducting material Ti3C2 MXene. We find that incorporating MXene as a co-dopant along with PSS leads to PEDOT:PSS:MXene films with remarkably high volumetric capacitance (607.0 ± 85.3 F cm−3) and stability (capacity retention = 78.44% ± 1.75% over 500 cycles), outperforming single dopant-comprising PEDOT films, i.e., PEDOT:PSS and PEDOT:MXene electropolymerized under the same conditions on identical surfaces. The stability of microfabricated PEDOT:PSS:MXene electrodes is evaluated under different conditions, i.e., when the films are exposed to sonication (∼100% retention over 6 min), upon immersion in cell culture media for 14 days (∆|Z| = 2.13%), as well as after continuous electrical stimulation. Furthermore, we demonstrate the use of a PEDOT:PSS:MXene electrode as an electrochemical sensor for sensitive detection of dopamine (DA). The sensor exhibited an enhanced electrocatalytic activity toward DA in a linear range from 1 μM to 100 μM validated in mixtures containing common interferents such as ascorbic acid and uric acid. PEDOT:PSS:MXene composite is easily formed on conductive substrates with various geometries and can serve as a high performance conducting interface for chronic biochemical sensing or stimulation applications.
  • Microfluidics integrated n-type organic electrochemical transistor for metabolite sensing

    Koklu, Anil; Ohayon, David; Wustoni, Shofarul; Hama, Adel; Chen, Xingxing; McCulloch, Iain; Inal, Sahika (Sensors and Actuators, B: Chemical, Elsevier BV, 2020-12-01) [Article]
    The organic electrochemical transistor (OECT) can translate biochemical binding events between a recognition unit and its analyte into an electrical signal. We present an OECT comprising an n-type (electron transporting) conjugated polymer-based channel and lateral gate electrode functionalized with the enzyme, glucose oxidase. The device is integrated with a microfluidic system for real-time glucose monitoring in a flow-through manner. The n-type polymer has direct electrical communication with glucose oxidase, allowing glucose detection while surpassing hydrogen peroxide production. The microfluidic-integrated OECT shows superior features compared to its microfluidic-free counterpart, including higher current and transconductance values as well as improved signal-to-noise (SNR) ratios, which enhances the sensor sensitivity and its detection limit. Thanks to the low noise endowed by the integrated microfluidics, the gate current changes upon metabolite recognition could be resolved, revealing that while the relative changes in gate and drain currents are similar, the drain current output has a higher SNR. This is the first demonstration of the integration of a microfluidic system with an n-type accumulation mode OECT for real-time enzymatic metabolite detection. The microfluidic-integrated design provides new insights into the mechanisms leading to high sensor sensitivities, crucial for the development of portable and autonomous lab-on-a-chip technologies.
  • Polaron Delocalization in Donor-Acceptor Polymers and its Impact on Organic Electrochemical Transistor Performance

    Moser, Maximilian; Savva, Achilleas; Thorley, Karl; Paulsen, Bryan D.; Hidalgo, Tania Cecilia; ohayon, David; Chen, Hu; Giovannitti , Alexander; Marks, Adam; Gasparini, Nicola; Wadsworth, Andrew; Rivnay, Jonathan; Inal, Sahika; McCulloch, Iain (Angewandte Chemie, Wiley, 2020-12) [Article]
    Donor-acceptor (D-A) polymers are promising materials for organic electrochemical transistors (OECTs), as they minimize detrimental faradaic side-reactions during OECT operation, yet their steady-state OECT performance still lags far behind their all-donor counterparts. Here, we report three D-A polymers based on the diketopyrrolopyrrole unit that afford OECT performances similar to those of all-donor polymers, hence representing a significant improvement to the previously developed D-A copolymers. In addition to improved OECT performance, DFT simulations of the polymers and their respective hole polarons also revealed a positive correlation between hole polaron delocalization and steady-state OECT performance, providing new insights into the design of OECT materials. More importantly, we demonstrate how polaron delocalization can be tuned directly at the molecular level by selection of the building blocks comprising the polymers’ conjugated backbone, thus paving the way for the development of even higher performing OECT polymers.
  • Generation of an iPSC cohort of isogenic iPSC lines (46-XY and 47-XXY) from a non-mosaic Klinefelter Syndrome Patient (47-XXY) (KAUSTi008-A, KAUSTi008-B, KAUSTi008-C, KAUSTi008-D, KAUSTi008-E, KAUSTi008-F, KAUSTi008-G)

    Fiacco, Elisabetta; Alowaysi, Maryam; Astro, Veronica; Adamo, Antonio (Stem Cell Research, Elsevier BV, 2020-12) [Article]
    Klinefelter Syndrome (KS) is the most common X chromosome aneuploidy in males characterized by highly heterogeneous clinical manifestations including a subtle cognitive impairment and multisystemic disorders such as infertility, metabolic syndrome, gynecomastia and cardiovascular diseases. To date dosage-dependent correlation studies of X-linked genes and low- and high-grade KS clinical phenotypes have not been performed. Here we generated multiple isogenic 47-XXY and 46-XY iPSC lines from one 47-XXY patient. Leveraging on a fully matched genetic background, our cohort represents a highly informative tool to study the impact of X chromosome dosage on KS pathophysiology.

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