Recent Submissions

  • 3D -printed high-NA catadioptric thin lens for suppression of XPM background in Stimulated Raman Scattering microscopy

    Bertoncini, Andrea; Laptenok, Siarhei; Genchi, Luca; Rajamanickam, Vijayakumar Palanisamy; Liberale, Carlo (Journal of Biophotonics, Wiley, 2020-07-13) [Article]
    Stimulated Raman Scattering (SRS) is a fast chemical imaging technique with remarkable bio-science applications. Cross Phase Modulation (XPM) is a ubiquitous non-linear phenomenon that can create spurious background signals that render difficult a high-contrast imaging in SRS measurements. The XPM-induced signal is usually suppressed using high Numerical Aperture (NA) microscope objectives or condensers to collect the transmitted excitation beam. However, these high-NA optics feature short working distances, hence they are not compatible with stage-top incubators, that are necessary to perform live-cell time-lapse experiments in controlled environments. Here,we showa 3D printed high-NAcompact catadioptric lens that fits inside stage-top incubators and allows the collection of XPM-free SRS signals. The lens delivers SRS images and spectra with a quality comparable to a signal collection with a high-NA microscope objective. We also demonstrate the compatibility of the 3D printed lens with other non-linear microscopies usually associated with SRS in multimodal microscopes.
  • Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management

    Aylagas, Eva; Aylagas, Eva; Pochon, Xavier; Zaiko, Anastasija; Keeley, Nigel; Bruce, Kat; Hong, Pei-Ying; Ruiz, Gregory M.; Stein, Eric D.; Theroux, Susanna; Geraldi, Nathan; Ortega, Alejandra; Gajdzik, Laura; Coker, Darren James; Katan, Yasser; Hikmawan, Tyas; Saleem, Ammar; Alamer, Sultan; Jones, Burton; Duarte, Carlos M.; Pearman, John; Carvalho, Susana (Science of The Total Environment, Elsevier BV, 2020-07-12) [Article]
    Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology – the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is the key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.
  • Simplified detection of polyhistidine-tagged proteins in gels and membranes using a UV-excitable dye and a multiple chelator head pair

    Raducanu, Vlad-Stefan; Isaioglou, Ioannis; Raducanu, Daniela-Violeta; Merzaban, Jasmeen; Hamdan, Samir (Journal of Biological Chemistry, American Society for Biochemistry & Molecular Biology (ASBMB), 2020-07-09) [Article]
    <jats:p>The polyhistidine tag (His-tag) is one of the most popular protein tags used in the life sciences. Traditionally, the detection of His-tagged proteins relies on immunoblotting with anti-His antibodies. This approach is laborious for certain applications such as protein purification, where time and simplicity are critical. The His-tag can also be directly detected by metal ion–loaded N-nitrilotriacetic acid–based chelator heads conjugated to fluorophores, which is a convenient alternative method to immunoblotting. Typically, such chelator heads are conjugated to either green or red fluorophores, the detection of which requires specialized excitation sources and detection systems. Here, we demonstrate that post-run staining is ideal for His-tag detection by metal ion–loaded and fluorescently labeled chelator heads in PAGE and blot membranes. Additionally, by comparing the performances of different chelator heads, we show how differences in microscopic affinity constants translate to macroscopic differences in the detection limits in environments with limited diffusion, such as PAGE. On the basis of these results, we devise a simple approach, called UVHis-PAGE, that uses metal ion–loaded and fluorescently labeled chelator heads to detect His-tagged proteins in PAGE and blot membranes. Our method uses a UV transilluminator as an excitation source, and the results can be visually inspected by the naked eye.</jats:p>
  • NIR multiphoton ablation of cancer cells, fluorescence quenching and cellular uptake of dansyl-glutathione-coated gold nanoparticles

    Buonerba, Antonio; Lapenta, Rosita; Donniacuo, Anna; Licasale, Magda; Vezzoli, Elena; Milione, Stefano; Capacchione, Carmine; Tecce, Mario Felice; Falqui, Andrea; Piacentini, Roberto; Grassi, Claudio; Grassi, Alfonso (Scientific Reports, Springer Science and Business Media LLC, 2020-07-09) [Article]
    Theranostics based on two-photon excitation of therapeutics in the NIR region is an emerging and powerful tool in cancer therapy since this radiation deeply penetrates healthy biological tissues and produces selective cell death. Aggregates of gold nanoparticles coated with glutathione corona functionalized with the dansyl chromophore (a-DG-AuNPs) were synthesized and found efficient nanodevice for applications in photothermal therapy (PTT). Actually the nanoparticle aggregation enhances the quenching of radiative excitation and the consequent conversion into heat. The a-DG-AuNPs are readily internalized in Hep G2 where the chromophore acts as both antenna and transducer of the NIR radiation under two-photons excitation, determining efficient cell ablation via photothermal effect.
  • SARS-CoV-2 infections and COVID-19 mortalities strongly correlate with ACE1 I/D genotype.

    Yamamoto, Naoki; Ariumi, Yasuo; Nishida, Nao; Yamamoto, Rain; Bauer, Georg; Gojobori, Takashi; Shimotohno, Kunitada; Mizokami, Masashi (Gene, Elsevier BV, 2020-07-07) [Article]
    Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). The relentless spread and pathogenicity of the virus have become a global public health emergency. One of the striking features of this pandemic is the pronounced impact on specific regions and ethnic groups. In particular, compared with East Asia, where the virus first emerged, SARS-CoV-2 has caused high rates of morbidity and mortality in Europe. This has not been experienced in past global viral infections, such as influenza, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and is unique to SARS-CoV-2. For this reason, we investigated the involvement of genetic factors associated with SARS-CoV-2 infection with a focus on angiotensin-converting enzyme (ACE)-related genes, because ACE2 is a receptor for SARS-CoV-2. We found that the ACE1 II genotype frequency in a population was significantly negatively correlated with the number of SARS-CoV-2 cases. Similarly, the ACE1 II genotype was negatively correlated with the number of deaths due to SARS-CoV-2 infection. These data suggest that the ACE1 II genotype may influence the prevalence and clinical outcome of COVID-19 and serve as a predictive marker for COVID-19 risk and severity.
  • Deracemization and Stereoinversion of Alcohols Using Two Mutants of Secondary Alcohol Dehydrogenase from Thermoanaerobacter pseudoethanolicus

    Nafiu, Sodiq A.; Takahashi, Masateru; Takahashi, Etsuko; Hamdan, Samir; Musa, Musa M. (European Journal of Organic Chemistry, Wiley, 2020-07-03) [Article]
    We developed a one-pot two-step deracemization approach for alcohols using two mutants of Thermoanaerobacter pseudoethanolicus secondary alcohol dehydrogenase ( Te SADH). This approach relies on consecutive non-stereospecific oxidation of alcohols and stereoselective reduction of their prochiral ketones using two mutants of Te SADH with poor and good stereoselectivities, respectively. More specifically, W110G Te SADH enables a non-stereospecific oxidation of alcohol racemates to their corresponding prochiral ketones, followed by W110V Te SADH-catalyzed stereoselective reduction of the resultant ketone intermediates to enantiopure ( S )-configured alcohols in up to >99% enantiomeric excess. A heat treatment after the oxidation step was required to avoid the interference of the marginally stereoselective W110G Te SADH in the reduction step; this heat treatment was eliminated by using sol-gel encapsulated W110G Te SADH in the oxidation step. Moreover, this bi-enzymatic approach was implemented in the stereoinversion of ( R )-configured alcohols, and ( S )-configured alcohols with up to >99% enantiomeric excess were obtained by this Mitsunobu-like stereoinversion reaction.
  • Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1.

    Tauber, Maria; Kreuz, Sarah; Lemak, Alexander; Mandal, Papita; Yerkesh, Zhadyra; Veluchamy, Alaguraj; Al-Gashgari, Bothayna; Aljahani, Abrar; Cortés-Medina, Lorena V; Azhibek, Dulat; Fan, Lixin; Ong, Michelle S; Duan, Shili; Houliston, Scott; Arrowsmith, Cheryl H; Fischle, Wolfgang (Nucleic acids research, Oxford University Press (OUP), 2020-07-02) [Article]
    UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.
  • DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques.

    Thafar, Maha A.; Olayan, Rawan S.; Ashoor, Haitham; Albaradei, Somayah; Bajic, Vladimir B.; Gao, Xin; Gojobori, Takashi; Essack, Magbubah (Journal of Cheminformatics, Springer Science and Business Media LLC, 2020-07-02) [Article]
    In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. However, developing such computational methods is not an easy task, but is much needed, as current methods that predict potential drug–target interactions suffer from high false-positive rates. Here we introduce DTiGEMS+, a computational method that predicts Drug–Target interactions using Graph Embedding, graph Mining, and Similarity-based techniques. DTiGEMS+ combines similarity-based as well as feature-based approaches, and models the identification of novel drug–target interactions as a link prediction problem in a heterogeneous network. DTiGEMS+ constructs the heterogeneous network by augmenting the known drug–target interactions graph with two other complementary graphs namely: drug–drug similarity, target–target similarity. DTiGEMS+ combines different computational techniques to provide the final drug target prediction, these techniques include graph embeddings, graph mining, and machine learning. DTiGEMS+ integrates multiple drug–drug similarities and target–target similarities into the final heterogeneous graph construction after applying a similarity selection procedure as well as a similarity fusion algorithm. Using four benchmark datasets, we show DTiGEMS+ substantially improves prediction performance compared to other state-of-the-art in silico methods developed to predict of drug-target interactions by achieving the highest average AUPR across all datasets (0.92), which reduces the error rate by 33.3% relative to the second-best performing model in the state-of-the-art methods comparison.
  • A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples

    Ramos Mandujano, Gerardo; Salunke, Rahul; Mfarrej, Sara; Rachmadi, Andri Taruna; Hala, Sharif; Xu, Jinna; Alofi, Fadwa S; Khogeer, Asim; Hashem, Anwar M; Almontashiri, Naif AM; Alsomali, Afrah; Hamdan, Samir; Hong, Pei-Ying; Pain, Arnab; Li, Mo (Cold Spring Harbor Laboratory, 2020-06-29) [Preprint]
    <jats:p>Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method called Magnetic- nanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. MAVRICS is scalable and thus could become an enabling technology for widespread community testing and wastewater monitoring in the current and future pandemics.</jats:p>
  • Attempting to synthesize lasso peptides using high pressure

    Waliczek, Mateusz; Wierzbicka, Magdalena; Arkuszewski, Maciej; Kijewska, Monika; Jaremko, Lukasz; Rajagopal, Priyadharshni; Szczepski, Kacper; Sroczyńska, Amanda; Jaremko, Mariusz; Stefanowicz, Piotr (PLOS ONE, Public Library of Science (PLoS), 2020-06-24) [Article]
    Lasso peptides are unique in that the tail of the lasso peptide threads through its macrolactam ring. The unusual structure and biological activity of lasso peptides have generated increased interest from the scientific community in recent years. Because of this, many new types of lasso peptides have been discovered. These peptides can be synthesized by microorganisms efficiently, and yet, their chemical assembly is challenging. Herein, we investigated the possibility of high pressure inducing the cyclization of linear precursors of lasso peptides. Unlike other molecules like rotaxanes which mechanically interlock at high pressure, the threaded lasso peptides did not form, even at pressures the high pressure up to 14000 kbar.
  • Intramolecularly stapled amphiphatic peptides via boron-sugar interaction

    Kijewska, Monika; Czerwinska, Angelika; Al-Harthi, Samah; Wołczański, Grzegorz; Waliczek, Mateusz; Emwas, Abdul-Hamid M.; Jaremko, Mariusz; Jaremko, Lukasz; Stefanowicz, Piotr; Szewczuk, Zbigniew (Chemical Communications, Royal Society of Chemistry (RSC), 2020-06-23) [Article]
    Amadori products (deoxyfructosyllysine derivatives) that can selectively interact with phenylboronic acids and borate ions were synthesized. The intramolecular interactions between the fructosyl moiety and phenylboronic acid incorporated in various positions of peptide chain was investigated using high-resolution mass spectrometry (HR-MS), circular dichroism (CD), and nuclear magnetic resonance (NMR).
  • A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of a malaria parasite during gametogony and transmission.

    Balestra, Aurélia C; Zeeshan, Mohammad; Rea, Edward; Pasquarello, Carla; Brusini, Lorenzo; Mourier, Tobias; Subudhi, Amit; Klages, Natacha; Arboit, Patrizia; Pandey, Rajan; Brady, Declan; Vaughan, Sue; Holder, Anthony A.; Pain, Arnab; Ferguson, David J P; Hainard, Alexandre; Tewari, Rita; Brochet, Mathieu (eLife, eLife Sciences Publications, Ltd, 2020-06-23) [Article]
    Cell cycle transitions are generally triggered by variation in the activity of cyclin-dependent kinases (CDKs) bound to cyclins. Malaria-causing parasites have a life cycle with unique cell-division cycles, and a repertoire of divergent CDKs and cyclins of poorly understood function and interdependency. We show that Plasmodium berghei CDK-related kinase 5 (CRK5), is a critical regulator of atypical mitosis in the gametogony and is required for mosquito transmission. It phosphorylates canonical CDK motifs of components in the pre-replicative complex and is essential for DNA replication. During a replicative cycle, CRK5 stably interacts with a single Plasmodium-specific cyclin (SOC2), although we obtained no evidence of SOC2 cycling by transcription, translation or degradation. Our results provide evidence that during Plasmodium male gametogony, this divergent cyclin/CDK pair fills the functional space of other eukaryotic cell-cycle kinases controlling DNA replication.
  • Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens.

    Vu, Trieu-Duc; Iwasaki, Yuki; Shigenobu, Shuji; Maruko, Akiko; Oshima, Kenshiro; Iioka, Erica; Huang, Chao-Li; Abe, Takashi; Tamaki, Satoshi; Lin, Yi-Wen; Chen, Chih-Kuan; Lu, Mei-Yeh; Hojo, Masaru; Wang, Hao-Ven; Tzeng, Shun-Fen; Huang, Hao-Jen; Kanai, Akio; Gojobori, Takashi; Chiang, Tzen-Yuh; Sun, H Sunny; Li, Wen-Hsiung; Okada, Norihiro (PLoS genetics, Public Library of Science (PLoS), 2020-06-20) [Article]
    Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and brain-transcriptomic changes during the fight between the two opponents. At the behavioral level, surface-breathing, and biting/striking occurred only during intervals between mouth-locking. Eventually, the behaviors of the two opponents became synchronized, with each pair showing a unique behavioral pattern. At the physiological level, we examined the expression patterns of 23,306 brain transcripts using RNA-sequencing data from brains of fighting pairs after a 20-min (D20) and a 60-min (D60) fight. The two opponents in each D60 fighting pair showed a strong gene expression correlation, whereas those in D20 fighting pairs showed a weak correlation. Moreover, each fighting pair in the D60 group showed pair-specific gene expression patterns in a grade of membership analysis (GoM) and were grouped as a pair in the heatmap clustering. The observed pair-specific individualization in brain-transcriptomic synchronization (PIBS) suggested that this synchronization provides a physiological basis for the behavioral synchronization. An analysis using the synchronized genes in fighting pairs of the D60 group found genes enriched for ion transport, synaptic function, and learning and memory. Brain-transcriptomic synchronization could be a general phenomenon and may provide a new cornerstone with which to investigate coordinating and sustaining social interactions between two interacting partners of vertebrates.
  • Cytosine deamination in SARS-CoV-2 leads to progressive CpG depletion.

    Sadykov, Mukhtar; Mourier, Tobias; Guan, Qingtian; Pain, Arnab (Cold Spring Harbor Laboratory, 2020-06-20) [Preprint]
    <jats:p>RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanism is still largely unknown. To address this, we used rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. SARS-CoV-2 genomes show a progressive increase of C-to-U substitutions resulting in CpG loss over just a few months. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in viral genome for two known host molecular defense mechanisms, the APOBEC and ZAP proteins.</jats:p>
  • Influx of diverse, drug resistant and transmissible Plasmodium falciparum into a malaria-free setting in Qatar.

    Al-Rumhi, Abir; Al-Hashami, Zainab; Al-Hamidhi, Salama; Gadalla, Amal; Naeem, Raeece; Ranford-Cartwright, Lisa; Pain, Arnab; Sultan, Ali A; Babiker, Hamza A (BMC infectious diseases, 2020-06-17) [Article]
    BACKGROUND:Successful control programs have impeded local malaria transmission in almost all Gulf Cooperation Council (GCC) countries: Qatar, Bahrain, Kuwait, Oman, the United Arab Emirates (UAE) and Saudi Arabia. Nevertheless, a prodigious influx of imported malaria via migrant workers sustains the threat of local transmission. Here we examine the origin of imported malaria in Qatar, assess genetic diversity and the prevalence of drug resistance genes in imported Plasmodium falciparum, and finally, address the potential for the reintroduction of local transmission. METHODS:This study examined imported malaria cases reported in Qatar, between 2013 and 2016. We focused on P. falciparum infections and estimated both total parasite and gametocyte density, using qPCR and qRT-PCR, respectively. We also examined ten neutral microsatellites and four genes associated with drug resistance, Pfmrp1, Pfcrt, Pfmdr1, and Pfkelch13, to assess the genetic diversity of imported P. falciparum strains, and the potential for propagating drug resistance genotypes respectively. RESULTS:The majority of imported malaria cases were P. vivax, while P. falciparum and mixed species infections (P. falciparum / P. vivax) were less frequent. The primary origin of P. vivax infection was the Indian subcontinent, while P. falciparum was mostly presented by African expatriates. Imported P. falciparum strains were highly diverse, carrying multiple genotypes, and infections also presented with early- and late-stage gametocytes. We observed a high prevalence of mutations implicated in drug resistance among these strains, including novel SNPs in Pfkelch13. CONCLUSIONS:The influx of genetically diverse P. falciparum, with multiple drug resistance markers and a high capacity for gametocyte production, represents a threat for the reestablishment of drug-resistant malaria into GCC countries. This scenario highlights the impact of mass international migration on the reintroduction of malaria to areas with absent or limited local transmission.
  • Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing

    Perdigão, João; Silva, Carla; Maltez, Fernando; Machado, Diana; Miranda, Anabela; Couto, Isabel; Rabna, Paulo; Florez de Sessions, Paola; Phelan, Jody; Pain, Arnab; McNerney, Ruth; Hibberd, Martin L.; Mokrousov, Igor; Clark, Taane G.; Viveiros, Miguel; Portugal, Isabel (Emerging Microbes & Infections, Informa UK Limited, 2020-06-15) [Article]
    The Beijing genotype comprises a highly disseminated strain type that is frequently associated with multidrug resistant (MDR) tuberculosis (TB) and increased transmissibility but, countries such as Portugal and Guinea-Bissau fall outside the regions phylogeographically associated with this specific genotype. Nevertheless, recent data shows that this genotype might be gradually emerging in these two countries as an underlying cause of primary MDR-TB. Here, we describe the emergence of Mycobacterium tuberculosis Beijing strains associated with MDR-TB in Portugal and Guinea-Bissau demonstrating the presence of the well described superclusters 100-32 and 94-32 in Portugal and Guinea-Bissau, respectively. Genome-wide analysis and comparison with a global genomic dataset of M. tuberculosis Beijing strains, revealed the presence of two genomic clusters encompassing isolates from Portugal and Guinea-Bissau, GC1 (n = 121) and GC2 (n = 39), both of which bore SNP signatures compatible with the 100-32/B0/W148 and 94-32/Central Asia Outbreak clades, respectively. Moreover, GC2 encompasses a cross-border cluster between Portugal, Guinea-Bissau and Brazil thus supporting migration-associated introduction of MDR-TB and subsequent clonal expansion at the community-level. The comparison with global Beijing datasets demonstrates the global reach of the disease and its complex dissemination across multiple countries while in parallel there are clear microevolutionary trajectories towards extensively drug resistant TB.
  • Fully Inkjet-Printed, Ultrathin and Conformable Organic Photovoltaics as Power Source Based on Cross-Linked PEDOT:PSS Electrodes

    Bihar, Eloise; Corzo Diaz, Daniel Alejandro; Hidalgo, Tania C.; Rosas-Villalva, Diego; Salama, Khaled N.; Inal, Sahika; Baran, Derya (Advanced Materials Technologies, Wiley, 2020-06-15) [Article]
    Ultra-lightweight solar cells have attracted enormous attention due to their ultra-conformability, flexibility, and compatibility with applications including electronic skin or miniaturized electronics for biological applications. With the latest advancements in printing technologies, printing ultrathin electronics is becoming now a reality. This work offers an easy path to fabricate indium tin oxide (ITO)-free ultra-lightweight organic solar cells through inkjet-printing while preserving high efficiencies. A method consisting of the modification of a poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) ink with a methoxysilane-based cross-linker (3-glycidyloxypropyl)trimethoxysilane (GOPS)) is presented to chemically modify the structure of the electrode layer. Combined with plasma and solvent post-treatments, this approach prevents shunts and ensures precise patterning of solar cells. By using poly(3-hexylthiophene) along rhodanine-benzothiadiazole-coupled indacenodithiophene (P3HT:O-IDTBR), the power conversion efficiency (PCE) of the fully printed solar cells is boosted up to 4.73% and fill factors approaching 65%. All inkjet-printed ultrathin solar cells on a 1.7 µm thick biocompatible parylene substrate are fabricated with PCE reaching up to 3.6% and high power-per-weight values of 6.3 W g−1. After encapsulation, the cells retain their performance after being exposed for 6 h to aqueous environments such as water, seawater, or phosphate buffered saline, paving the way for their integration in more complex circuits for biological systems.
  • Multiplex Isothermal Amplification Coupled with Nanopore Sequencing for Rapid Detection and Mutation Surveillance of SARS-CoV-2

    Bi, Chongwei; Ramos Mandujano, Gerardo; Hala, Sharif; Xu, Jinna; Mfarrej, Sara; Alofi, Fadwa S; Khogeer, Asim; Hashem, Anwar M; Almontashiri, Naif A.M.; Pain, Arnab; Li, Mo (Cold Spring Harbor Laboratory, 2020-06-14) [Preprint]
    <jats:p>Molecular testing and surveillance of the spread and mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical public health measures to combat the pandemic. There is an urgent need for methods that can rapidly detect and sequence SARS-CoV-2 simultaneously. Here we describe a method for multiplex isothermal amplification of the SARS-CoV-2 genome in 20 minutes. Based on this, we developed NIRVANA (Nanopore sequencing of Isothermal Rapid Viral Amplification for Near real-time Analysis) to detect viral sequences and monitor mutations in multiple regions of SARS-CoV-2 genome for up to 96 patients at a time. NIRVANA uses a newly developed algorithm for on-the-fly data analysis during Nanopore sequencing. The whole workflow can be completed in as short as 3.5 hours, and all reactions can be done in a simple heating block. NIRVANA provides a rapid field-deployable solution of SARS-CoV-2 detection and surveillance of pandemic strains.</jats:p>
  • Water stable molecular n-doping produces organic electrochemical transistors with high transconductance and record stability

    Paterson, Alexandra; Savva, Achilleas; Wustoni, Shofarul; Tsetseris, Leonidas; Paulsen, Bryan D.; Faber, Hendrik; Emwas, Abdul-Hamid M.; Chen, Xingxing; Nikiforidis, Georgios; Hidalgo, Tania C.; Moser, Maximillian; Maria, Iuliana Petruta; Rivnay, Jonathan; McCulloch, Iain; Anthopoulos, Thomas D.; Inal, Sahika (Nature Communications, Springer Science and Business Media LLC, 2020-06-12) [Article]
    From established to emergent technologies, doping plays a crucial role in all semiconducting devices. Doping could, theoretically, be an excellent technique for improving repressively low transconductances in n-type organic electrochemical transistors – critical for advancing logic circuits for bioelectronic and neuromorphic technologies. However, the technical challenge is extreme: n-doped polymers are unstable in electrochemical transistor operating environments, air and water (electrolyte). Here, the first demonstration of doping in electron transporting organic electrochemical transistors is reported. The ammonium salt tetra-nbutylammonium fluoride is simply admixed with the conjugated polymer poly(N,N’-bis(7-glycol)-naphthalene-1,4,5,8 bis(dicarboximide)-co-2,2’-bithiophene-co-N,N’-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide), and found to act as a simultaneous molecular dopant and morphology-additive. The combined effects enhance the n-type transconductance with improved channel capacitance and mobility. Furthermore, operational and shelflife stability measurements showcase the first example of water-stable n-doping in a polymer. Overall, the results set a precedent for doping/additives to impact organic electrochemical transistors as powerfully as they have in other semiconducting devices.
  • Monitoring supported lipid bilayers with n-type organic electrochemical transistors

    Kawan, Malak; Hidalgo, Tania C.; du, weiyuan; Pappa, Anna-Maria; Owens, R. M.; Wadsworth, Andrew; Inal, Sahika (Materials Horizons, Royal Society of Chemistry (RSC), 2020-06-11) [Article]
    <p>An n-type, accumulation mode, microscale organic electrochemical transistor monitors the activity of a pore-forming protein integrated into a lipid bilayer.</p>

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