Recent Submissions

  • LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes

    Della Valle, Francesco; Reddy, Pradeep; Yamamoto, Mako; Liu, Peng; Saera-Vila, Alfonso; Bensaddek, Dalila; Zhang, Huoming; Prieto Martinez, Javier; Abassi, Leila; Celii, Mirko; Ocampo, Alejandro; Nuñez Delicado, Estrella; Mangiavacchi, Arianna; Aiese Cigliano, Riccardo; Rodriguez Esteban, Concepcion; Horvath, Steve; Belmonte, Juan Carlos Izpisua; Orlando, Valerio (Science Translational Medicine, American Association for the Advancement of Science (AAAS), 2022-08-10) [Article]
    Constitutive heterochromatin is responsible for genome repression of DNA enriched in repetitive sequences, telomeres, and centromeres. During physiological and pathological premature aging, heterochromatin homeostasis is profoundly compromised. Here, we showed that LINE-1 (Long Interspersed Nuclear Element-1; L1) RNA accumulation was an early event in both typical and atypical human progeroid syndromes. L1 RNA negatively regulated the enzymatic activity of the histone-lysine N-methyltransferase SUV39H1 (suppression of variegation 3-9 homolog 1), resulting in heterochromatin loss and onset of senescent phenotypes in vitro. Depletion of L1 RNA in dermal fibroblast cells from patients with different progeroid syndromes using specific antisense oligonucleotides (ASOs) restored heterochromatin histone 3 lysine 9 and histone 3 lysine 27 trimethylation marks, reversed DNA methylation age, and counteracted the expression of senescence-associated secretory phenotype genes such as p16, p21, activating transcription factor 3 (ATF3), matrix metallopeptidase 13 (MMP13), interleukin 1a (IL1a), BTG anti-proliferation factor 2 (BTG2), and growth arrest and DNA damage inducible beta (GADD45b). Moreover, systemic delivery of ASOs rescued the histophysiology of tissues and increased the life span of a Hutchinson-Gilford progeria syndrome mouse model. Transcriptional profiling of human and mouse samples after L1 RNA depletion demonstrated that pathways associated with nuclear chromatin organization, cell proliferation, and transcription regulation were enriched. Similarly, pathways associated with aging, inflammatory response, innate immune response, and DNA damage were down-regulated. Our results highlight the role of L1 RNA in heterochromatin homeostasis in progeroid syndromes and identify a possible therapeutic approach to treat premature aging and related syndromes.
  • 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.
  • Differential role of neuronal glucose and PFKFB3 in memory formation during development

    Cruz, Emmanuel; Bessières, Benjamin; Magistretti, Pierre J.; Alberini, Cristina M (Glia, 2022-08-02) [Article]
    The consumption of glucose in the brain peaks during late childhood; yet, whether and how glucose metabolism is differentially regulated in the brain during childhood compared to adulthood remains to be understood. In particular, it remains to be determined how glucose metabolism is involved in behavioral activations such as learning. Here we show that, compared to adult, the juvenile rat hippocampus has significantly higher mRNA levels of several glucose metabolism enzymes belonging to all glucose metabolism pathways, as well as higher levels of the monocarboxylate transporters MCT1 and MCT4 and the glucose transporters endothelial-GLUT1 and GLUT3 proteins. Furthermore, relative to adults, long-term episodic memory formation in juvenile animals requires significantly higher rates of aerobic glycolysis and astrocytic-neuronal lactate coupling in the hippocampus. Only juvenile but not adult long-term memory formation recruits GLUT3, neuronal 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) and more efficiently engages glucose in the hippocampus. Hence, compared to adult, the juvenile hippocampus distinctively regulates glucose metabolism pathways, and formation of long-term memory in juveniles involves differential neuronal glucose metabolism mechanisms.
  • 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.
  • Peptide nanogels as a scaffold for fabricating dermal grafts and 3D vascularized skin models

    Arab, Wafaa; Susapto, Hepi Hari; Alhattab, Dana Majed; Hauser, Charlotte (Journal of Tissue Engineering, SAGE Publications, 2022-07-29) [Article]
    Millions of people worldwide suffer from skin injuries, which create significant problems in their lives and are costly to cure. Tissue engineering is a promising approach that aims to fabricate functional organs using biocompatible scaffolds. We designed ultrashort tetrameric peptides with promising properties required for skin tissue engineering. Our work aimed to test the efficacy of these scaffolds for the fabrication of dermal grafts and 3D vascularized skin tissue models. We found that the direct contact of keratinocytes and fibroblasts enhanced the proliferation of the keratinocytes. Moreover, the expression levels of TGF-β1, b-FGF, IL-6, and IL-1α is correlated with the growth of the fibroblasts and keratinocytes in the co-culture. Furthermore, we successfully produced a 3D vascularized skin co-culture model using these peptide scaffolds. We believe that the described results represent an advancement in the fabrication of skin tissue equivalent, thereby providing the opportunity to rebuild missing, failing, or damaged parts.
  • Modular safe-harbor transgene insertion (MosTI) for targeted single-copy and extrachromosomal array integration in C. elegans

    El Mouridi, Sonia; Alkhaldi, Faisal; Frøkjær-Jensen, Christian (G3 Genes|Genomes|Genetics, Oxford University Press (OUP), 2022-07-28) [Article]
    Efficient and reproducible transgenesis facilitates and accelerates research using genetic model organisms. Here we describe a modular safe harbor transgene insertion (MosTI) for use in C. elegans which improves targeted insertion of single-copy transgenes by homology directed repair and targeted integration of extrachromosomal arrays by non-homologous end-joining. MosTI allows easy conversion between selection markers at insertion site and a collection of universal targeting vectors with commonly used promoters and fluorophores. Insertions are targeted at three permissive safe-harbor intergenic locations and transgenes are reproducibly expressed in somatic and germ cells. Chromosomal integration is mediated by CRISPR/Cas9, and positive selection is based on a set of split markers (unc-119, hygroR, and gfp) where only animals with chromosomal insertions are rescued, resistant to antibiotics, or fluorescent, respectively. Single-copy insertion is efficient using either constitutive or heat-shock inducible Cas9 expression (25 - 75%) and insertions can be generated from a multiplexed injection mix. Extrachromosomal array integration is also efficient (7 - 44%) at MosTI landing sites or at the endogenous unc-119 locus. We use short-read sequencing to estimate the plasmid copy numbers for eight integrated arrays (6 to 37 copies) and long-read Nanopore sequencing to determine the structure and size (5.4 Mb) of one array. Using universal targeting vectors, standardized insertion strains, and optimized protocols, it is possible to construct complex transgenic strains which should facilitate the study of increasingly complex biological problems in C. elegans.
  • Establishment of 3D culture protocols for the maintenance and expansion of human pluripotent stem cell aggregates in a low scale platform and in the DASbox® Mini-Bioreactor System

    Hernandez-Bautista, Carlos Alberto (2022-07-27) [Thesis]
    Advisor: Adamo, Antonio
    Committee members: Merzaban, Jasmeen; Ibrahim, Leena Ali
    The human Embryonic Stem Cells (hESCs) and human induced Pluripotent Stem Cells (hiPSCs) have offered numerous advantages including but not limited to model diseases, high-throughput drug screening, and regenerative purposes. However, the employment of monolayer cultures has not been sufficient to mimic the in vivo stem cells niche. Thus, three-dimensional suspension cultures have helped us to advance our knowledge and ease the development of the human organs’ counterparts, commonly referred as organoids. Currently, the challenge is the generation of homogenous and reproducible human Pluripotent Stem Cell (hPSC) aggregates, the basic cellular unit to derive organoids. To date, the Ultra-Low Attachment (ULA) 6-well plates have been routinary used for the hPSC aggregates formation, which mainly relies on the inhibition of the Rho-associated kinase (ROCK) pathway resulting in the enhancement of cell survival coming from cryopreserved stocks or when passaging. However, little is known in this regard when analyzing the aggregate formation of hPSCs with two widely used compounds: RevitaCellTM Supplement and Y27632. Importantly, due to the high demand required from the regenerative medicine, I aimed to upscale the hPSC aggregates production in the DASbox® Mini-Bioreactor System. In this thesis, I established protocols for the hPSC aggregates formation by using two different types of media in two platforms being the ULA 6-well plates and the DASbox® Mini-Bioreactor System. In addition, I demonstrated that monolayer confluence cultures before single cell inoculations are paramount for the formation of bona fide hPSC aggregates in healthy and X aneuploid hiPSCs, precisely two hESCs and five hiPSCs.
  • Theileria annulata histone deacetylase 1 (TaHDAC1) initiates schizont to merozoite stage conversion

    Tajeri, Shahin; Momeux, Laurence; Saintpierre, Benjamin; Mfarrej, Sara; Chapple, Alexander; Mourier, Tobias; Shiels, Brian; Ariey, Frédéric; Pain, Arnab; Langsley, Gordon (Scientific Reports, Springer Science and Business Media LLC, 2022-07-26) [Article]
    A fungal metabolite, FR235222, specifically inhibits a histone deacetylase of the apicomplexan parasite Toxoplasma gondii and TgHDAC3 has emerged as a key factor regulating developmental stage transition in this species. Here, we exploited FR235222 to ask if changes in histone acetylation regulate developmental stage transition of Theileria annulata, another apicomplexan species. We found that FR235222 treatment of T. annulata-infected transformed leukocytes induced a proliferation arrest. The blockade in proliferation was due to drug-induced conversion of intracellular schizonts to merozoites that lack the ability to maintain host leukocyte cell division. Induction of merogony by FR235222 leads to an increase in expression of merozoite-marker (rhoptry) proteins. RNA-seq of FR235222-treated T. annulata-infected B cells identified deregulated expression of 468 parasite genes including a number encoding parasite ApiAP2 transcription factors. Thus, similar to T. gondii, FR235222 inhibits T. annulata HDAC (TaHDAC1) activity and places parasite histone acetylation as a major regulatory event of the transition from schizonts to merozoites.
  • DES-Amyloidoses “Amyloidoses through the looking-glass”: A knowledgebase developed for exploring and linking information related to human amyloid-related diseases

    Bajic, Vladan P.; Salhi, Adil; Lakota, Katja; Radovanovic, Aleksandar; Razali, Rozaimi; Zivkovic, Lada; Spremo-Potparevic, Biljana; Uludag, Mahmut; Tifratene, Faroug; Motwalli, Olaa; Marchand, Benoit; Bajic, Vladimir B.; Gojobori, Takashi; Isenovic, Esma R.; Essack, Magbubah (PLOS ONE, Public Library of Science (PLoS), 2022-07-25) [Article]
    More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer’s disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities’ influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore "amyloid network systems" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and relevant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data mining of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this information through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome-amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid-related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses.
  • Simultaneous Performance and Stability Improvement of a p-Type Organic Electrochemical Transistor through Additives

    Hidalgo, Tania C.; Moser, Maximilian; Cendra, Camila; Nayak, Prem Depan; Salleo, Alberto; McCulloch, Iain; Inal, Sahika (Chemistry of Materials, American Chemical Society (ACS), 2022-07-25) [Article]
    Advancements in organic electrochemical transistor (OECT) applications have been largely driven by the development of organic electronic materials that allow for simultaneous ionic and electronic transport in the bulk of their films. These studies focus on achieving high steady-state OECT performance, governed by the electronic charge mobility and the capacitance of the polymer film in the channel, and an often underlooked property is the long-term operational stability. In this work, we present a strategy to improve the performance of p-type OECTs along with operational stability via two additives, i.e., a high-boiling-point solvent (chlorobenzene) and a Lewis acid (tris(pentafluoro phenyl)borane). Addition of a small amount of a cosolvent additive changes the arrangement of glycolated thiophene-based copolymer chains on the substrate toward a direction that allows for more efficient hole transport. The Lewis acid, on the other hand, boosts the OECT stability, mainly by preventing oxidative degradation. Using both additives in the solution grants OECTs with high operational stability and performance through changes in the film microstructure and the polymer’s sensitivity to oxygen. This study highlights the use of additives as a means to enhance the OECT figure of merits without the need for new polymer synthesis.
  • Zaxinone Synthase controls arbuscular mycorrhizal colonization level in rice

    Votta, Cristina; Fiorilli, Valentina; Haider, Imran; Wang, Jian You; Balestrini, Raffaella; Petřík, Ivan; Tarkowská, Danuše; Novak, Ondrej; Serikbayeva, Akmaral; Bonfante, Paola; Al-Babili, Salim; Lanfranco, Luisa (The Plant Journal, Wiley, 2022-07-25) [Article]
    The rice carotenoid cleavage dioxygenase OsZAS was described to produce zaxinone, a novel plant-growth promoting apocarotenoid. A zas mutant line showed a reduced arbuscular mycorrhizal (AM) colonization but the mechanisms underlying this behavior are unknown. Here, we investigated how OsZAS and exogenous zaxinone treatment regulate mycorrhization. Micromolar exogenous supply of zaxinone rescued the root growth but not the mycorrhizal defects of the zas mutant and even reduced mycorrhization in wild type and zas genotypes. The zas line did not display an increase in strigolactones (SLs) level as observed in wild type plants at 7 day post inoculation with the AM fungus. Moreover, an exogenous treatment with the synthetic SLs analog, GR24, rescued the zas mutant mycorrhizal phenotype, indicating that the lower AM colonization rate of zas is due to a SLs deficiency at the early stages of the interaction and pointing out that, during this phase, OsZAS activity is required to induce SLs production, possibly mediated by the Dwarf14-Like (D14L) signaling pathway. OsZAS is expressed in arbuscule-containing cells and OsPT11prom
  • Target-dependent suppression of siRNA production modulates the levels of endogenous siRNAs in C. elegans germline

    Gajic, Zoran; Kaur, Diljeet; Ni, Julie; Zhu, Zhaorong; Zhebrun, Anna; Gajic, Maria; Kim, Matthew; Hong, Julia; Priyadarshini, Monika; Frøkjær-Jensen, Christian; Gu, Sam (Development, The Company of Biologists, 2022-07-25) [Article]
    Despite the prominent role of endo-siRNAs in transposon silencing, their expression is not limited to these “nonself” DNA elements. Transcripts of protein-coding genes (“self” DNA) in some cases also produce endo-siRNAs in yeast, plants, and animals (Piatek and Werner 2014). How cells distinguish these two populations of siRNAs to prevent unwanted silencing of active genes in animals is not well understood. To address this question, we inserted various self-gene or gfp fragments into an LTR retrotransposon that produces abundant siRNAs and examined the propensity of these gene fragments to produce ectopic siRNAs in C. elegans germline. We found that fragments of germline genes are generally protected from production of ectopic siRNAs. This phenomenon, which we termed “target-directed suppression of siRNA production” (or siRNA suppression), is dependent on the germline expression of target mRNA and requires germline P-granule components. We found that siRNA suppression can also occur to naturally produced endo-siRNAs. We suggest that siRNA suppression plays an important role in regulating siRNA expression and preventing self-genes from aberrant epigenetic silencing.
  • ZAXINONE SYNTHASE 2 regulates growth and arbuscular mycorrhizal symbiosis in rice

    Ablazov, Abdugaffor; Votta, Cristina; Fiorilli, Valentina; Wang, Jian You; Aljedaani, Fatimah R.; Jamil, Muhammad; Balakrishna, Aparna; Balestrini, Raffaella; Liew, Kit Xi; Rajan, Chakravarthy; Berqdar, Lamis; Blilou, Ikram; Lanfranco, Luisa; Al-Babili, Salim (Cold Spring Harbor Laboratory, 2022-07-23) [Preprint]
    Carotenoid cleavage, catalyzed by CAROTENOID CLEAVAGE DIOXYGENASES (CCDs), provides signaling molecules and precursors of plant hormones. Recently, we showed that zaxinone, a novel apocarotenoid metabolite formed by the CCD Zaxinone Synthase (ZAS), is a growth regulator required for normal rice growth and development. The rice genome encodes three OsZAS homologs, called here OsZAS1b, OsZAS1c, and OsZAS2, with unknown functions. Here, we investigated the enzymatic activity, expression pattern, and subcellular localization of OsZAS2, and generated and characterized loss-of-function CRISPR/Cas9-Oszas2 mutants. We show that OsZAS2 formed zaxinone in vitro. OsZAS2 is a plastid-localized enzyme mainly expressed in the root cortex under phosphate starvation. Moreover, OsZAS2 expression increased during mycorrhization, specifically in arbuscule-containing cells. Oszas2 mutants contained lower zaxinone content in roots and exhibited reduced root and shoot biomass, less productive tiller, and higher strigolactone (SL) levels. Exogenous zaxinone application repressed SL biosynthesis and partially rescued the growth retardation of Oszas2 mutant. Consistent with the OsZAS2 expression pattern, Oszas2 mutants displayed a lower frequency of AM colonization. In conclusion, OsZAS2 encodes a further zaxinone-forming enzyme that determines rice growth and architecture and strigolactone content and is required for optimal mycorrhization.
  • Pseudomonas fluorescens Complex and Its Intrinsic, Adaptive, and Acquired Antimicrobial Resistance Mechanisms in Pristine and Human-Impacted Sites

    Silverio, Myllena Pereira; Kraychete, Gabriela Bergiante; Rosado, Alexandre S.; Bonelli, Raquel Regina (MDPI AG, 2022-07-22) [Article]
    Pseudomonas spp. are ubiquitous microorganisms that exhibit intrinsic and acquired resistance to many antimicrobial agents. Pseudomonas aeruginosa is the most studied species of this genus due to its clinical importance. In contrast, the Pseudomonas fluorescens complex consists of environmental and, in some cases, pathogenic opportunistic microorganisms. The records of antimicrobial-resistant P. fluorescens are quite scattered, which hinders the recognition of patterns. This review compiles published data on antimicrobial resistance in species belonging to the P. fluorescens complex, which were identified through phylogenomic analyses. Additionally, we explored the occurrence of clinically relevant antimicrobial resistance genes in the genomes of the respective species available in the NCBI database. Isolates were organized into two categories: strains isolated from pristine sites and strains isolated from human-impacted or metal-polluted sites. Our review revealed that many reported resistant phenotypes in this complex might be related to intrinsic features, whereas some of them might be ascribed to adaptive mechanisms such as colistin resistance. Moreover, a few studies reported antimicrobial resistance genes (ARGs), mainly β-lactamases. In-silico analysis corroborated the low occurrence of transferable resistance mechanisms in this Pseudomonas complex. Both phenotypic and genotypic assays are necessary to gain insights into the evolutionary aspects of antimicrobial resistance in the P. fluorescens complex and the possible role of these ubiquitous species as reservoirs of clinically important and transmissible ARGs.
  • MetastaSite: Predicting metastasis to different sites using deep learning with gene expression data

    Albaradei, Somayah; Albaradei, Abdurhman; Alsaedi, Asim; Uludag, Mahmut; Thafar, Maha A.; Gojobori, Takashi; Essack, Magbubah; Gao, Xin (Frontiers in Molecular Biosciences, Frontiers Media SA, 2022-07-22) [Article]
    Deep learning has massive potential in predicting phenotype from different omics profiles. However, deep neural networks are viewed as black boxes, providing predictions without explanation. Therefore, the requirements for these models to become interpretable are increasing, especially in the medical field. Here we propose a computational framework that takes the gene expression profile of any primary cancer sample and predicts whether patients’ samples are primary (localized) or metastasized to the brain, bone, lung, or liver based on deep learning architecture. Specifically, we first constructed an AutoEncoder framework to learn the non-linear relationship between genes, and then DeepLIFT was applied to calculate genes’ importance scores. Next, to mine the top essential genes that can distinguish the primary and metastasized tumors, we iteratively added ten top-ranked genes based upon their importance score to train a DNN model. Then we trained a final multi-class DNN that uses the output from the previous part as an input and predicts whether samples are primary or metastasized to the brain, bone, lung, or liver. The prediction performances ranged from AUC of 0.93–0.82. We further designed the model’s workflow to provide a second functionality beyond metastasis site prediction, i.e., to identify the biological functions that the DL model uses to perform the prediction. To our knowledge, this is the first multi-class DNN model developed for the generic prediction of metastasis to various sites.
  • Prenatal Exposure to Gabapentin Alters the Development of Ventral Midbrain Dopaminergic Neurons

    Alsanie, Walaa F; Abdelrahman, Sherin; Alhomrani, Majid; Gaber, Ahmed; Habeeballah, Hamza; Alkhatabi, Heba A; Felimban, Raed I; Hauser, Charlotte; Tayeb, Hossam H; Alamri, Abdulhakeem S; Raafat, Bassem M; Anwar, Sirajudheen; Alswat, Khaled A; Althobaiti, Yusuf S; Asiri, Yousif A (Frontiers in pharmacology, Frontiers Media SA, 2022-07-22) [Article]
    Background: Gabapentin is widely prescribed as an off-label drug for the treatment of various diseases, including drug and alcohol addiction. Approximately 83–95% of the usage of gabapentin is off-label, accounting for more than 90% of its sales in the market, which indicates an alarming situation of drug abuse. Such misuse of gabapentin has serious negative consequences. The safety of the use of gabapentin in pregnant women has always been a serious issue, as gabapentin can cross placental barriers. The impact of gabapentin on brain development in the fetus is not sufficiently investigated, which poses difficulties in clinical decisions regarding prescriptions. Methods: The consequences effect of prenatal gabapentin exposure on the development of ventral midbrain dopaminergic neurons were investigated using three-dimensional neuronal cell cultures. Time-mated Swiss mice were used to isolate embryos. The ventral third of the midbrain was removed and used to enrich the dopaminergic population in 3D cell cultures that were subsequently exposed to gabapentin. The effects of gabapentin on the viability, ATP release, morphogenesis and genes expression of ventral midbrain dopaminergic neurons were investigated. Results: Gabapentin treatment at the therapeutic level interfered with the neurogenesis and morphogenesis of vmDA neurons in the fetal brain by causing changes in morphology and alterations in the expression of key developmental genes, such as Nurr1, Chl1, En1, Bdnf, Drd2, and Pitx3. The TH + total neurite length and dominant neurite length were significantly altered. We also found that gabapentin could halt the metabolic state of these neuronal cells by blocking the generation of ATP. Conclusion: Our findings clearly indicate that gabapentin hampers the morphogenesis and development of dopaminergic neurons. This implies that the use of gabapentin could lead to serious complications in child-bearing women. Therefore, caution must be exercised in clinical decisions regarding the prescription of gabapentin in pregnant women.
  • Harnessing the microbiome to prevent global biodiversity loss

    Peixoto, Raquel S; Voolstra, Christian R.; Sweet, Michael; Duarte, Carlos M.; Carvalho, Susana; Villela, Helena D. M.; Lunshof, Jeantine E.; Gram, Lone; Woodhams, Douglas C.; Walter, Jens; Roik, Anna Krystyna; Hentschel, Ute; Thurber, Rebecca Vega; Daisley, Brendan; Ushijima, Blake; Daffonchio, Daniele; Costa, Rodrigo; Keller-Costa, Tina; Bowman, Jeff S.; Rosado, Alexandre S.; Reid, Gregor; Mason, Christopher E.; Walke, Jenifer B.; Thomas, Torsten; Berg, Gabriele (Nature Microbiology, Springer Science and Business Media LLC, 2022-07-21) [Article]
    Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
  • Sars-Cov-2 Intra-Host Evolution in Immunocompromised Patients for the Emergence of Variants of Concerns, Including Omicron.

    Bantan, Azari I. (2022-07-21) [Thesis]
    Advisor: Gojobori, Takashi
    Committee members: Mineta, Katsuhiko; Pain, Arnab
    Unexpected high mutations detected in new emerging variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially in the case of omicron, raises concerns and efforts to understand their evolutionary trajectory. Several hypotheses have been discussed in literature to conceptualize the source of their emergence, including intra-host viral evolution in immunocompromised patients. These patients grant opportunities for the emergence of new variants through a persisting virus winning against host immunity, and selection for viral mutations driven by treatment interventions. VOCs have in common high mutation rate exceeding the average rate of 1-2 mutations per month. Not many studies have investigated the evolutionary rate of SARS-CoV-2 in immunocompromised candidates. Therefore, the purpose of this study is to reveal potential mechanisms underlying the emergence of VOCs by exploring substitution rate of SARS-CoV-2 genomes from surveyed COVID-19 immunocompromised patient’s studies. First, SARS-CoV-2 genome sequences were collected at sequential time series throughout host infection, which were reported in the previous studies. Filtration criteria was applied to reanalyze patients with prolonged infection documented for ≥ 2 months, and comprehensive sequenced samples for ≥ 6 time points. Then, phylogenetic analysis was conducted using Nextclade (, followed by mutation rate analysis using two substantial similar approaches to calculate the rate in i) substitutions per month and ii) substitutions per site (per year). The mutation tendency of SARS-CoV-2 in immunocompromised hosts was compared to reported VOCs, particularly to omicron. The highest observed mutation rate accounted for approximately 2.2 mutations per month, which is higher than the average rate. High mutation rate was due to prolonged infection and selection pressure by treatment interventions (i.e., convalescent plasma and antibodies). Here, higher rate of intra-host viral evolution in immunocompromised patients is detected, potentially leading to the emergence of VOC. Hence, this research highlights the need for sequencing efforts in high-risk individuals, updating treatment strategies along with further analysis on adaptive mutants pronounced due to intra-host evolution. Together, such findings provide an ultimate synergy for future public health guidelines and infection control measures.
  • Donor Engineering Tuning the Analog Switching Range and Operational Stability of Organic Synaptic Transistors for Neuromorphic Systems

    Zhao, Yanfei; Su, Chaohui; Shen, Guangyue; Xie, Zhichao; Xiao, Wei; Fu, Yujun; Inal, Sahika; Wang, Qi; Wang, Yazhou; Yue, Wan; McCulloch, Iain; He, Deyan (Advanced Functional Materials, Wiley, 2022-07-20) [Article]
    Organic artificial synapses are becoming the most desirable format for neuromorphic computing due to their highly tunable resistive states. However, repressively low analog switching range, inferior memory retention, and operational instability greatly hinder the further development of organic synapses. Herein, two donor-acceptor copolymers consisting of electron-deficient isoindigo coupled with variable donating moieties for three-terminal organic synaptic transistors (TOSTs) are reported. It is found that the synaptic function and device stability of TOSTs are significantly improved by enhancing the electron-donating strength of donor units. Polymer alkylated isoindigo-bis-ethylenedioxythiophene exhibits high analog switching range of 170 ×, two orders of magnitude higher than that of normal organic neuromorphic devices. They also demonstrate excellent memory retention of over 5 × 103 s, low switching energy of 13 fJ, and ultrahigh operational stability with 99% of its original current after 100 000 write-read events in air. Furthermore, the high viability of strong donor strategy is showcased by demonstrating flexible TOSTs with stable synaptic function after repeated mechanical bending as well as organic synapses capable of simulating image information processing. Overall, this work highlights the advantages of the strong donor functionalization strategy to boost the synaptic performance and device stability of TOSTs.
  • De novo genome-scale prediction of protein-protein interaction networks using ontology-based background knowledge

    Niu, Kexin (2022-07-18) [Thesis]
    Advisor: Hoehndorf, Robert
    Committee members: Inal, Sahika; Moshkov, Mikhail
    Proteins and their function play one of the most essential roles in various biological processes. The study of PPI is of considerable importance. PPI network data are of great scientific value, however, they are incomplete and experimental identification is time and money consuming. Available computational methods perform well on model organisms’ PPI prediction but perform poorly for a novel organism. Due to the incompleteness of interaction data, it is challenging to train a model for a novel organism. Also, millions to billions of interactions need to be verified which is extremely compute-intensive. We aim to improve the performance of predicting whether a pair of proteins will interact, with only two sequences as input. And also efficiently predict a PPI network with a proteome of sequences as input. We hypothesize that information about cellular locations where proteins are active and proteins' 3D structures can help us to significantly improve predict performance. To overcome the lack of experimental data, we use predicted structures by AlphaFold2 and cellular locations by DeepGoPlus. We believe that proteins belonging to disjoint biological components have very little chance to interact. We manually choose several disjoint pairs and further confirmed it by experimental PPI. We generate new no-interaction pairs with disjoint classes to update the D-SCRIPT dataset. As result, the AUPR has improved by 10% compared to the D-SCRIPT dataset. Besides, we pre-filter the negatives instead of enumerating all the potential PPI for de-novo PPI network prediction. For E.coli, we can pass around a million negative interactions. To combine the structure and sequence information, we generate a graph for each protein. A graph convolution network using Self-Attention Graph Pooling in Siamese architecture is used to learn these graphs for PPI prediction. In this way, we can improve around 20% in AUPR compared to our baseline model D-SCRIPT.

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