bluuebunny/crossref_metadata_2025 huggingface dataset:
Cellular and molecular signatures of in vivo GABAergic neurotransmission in the human brain
Authors: Lukow PB , Martins D , Veronese M , Vernon AC , McGuire P , Turkheimer FE , Modinos G
Published: June 2021

Diverse GABAergic interneuron microcircuits orchestrate information processing in the brain. Understanding the cellular and molecular composition of these microcircuits, and whether these can be imaged by available non-invasive in vivo methods is crucial for the study of GABAergic neurotransmission in health and disease. Here, we use human gene expression data and state-of-the-art imaging transcriptomics to uncover co-expression patterns between GABAA receptor subunits and interneuron subtype-specific markers, and to decode the cellular and molecular signatures of gold-standard GABA PET radiotracers, [11C]Ro15-4513 and [11C]flumazenil. We find that the interneuron marker somatostatin is co-expressed with GABAA receptor-subunit genes GABRA5 and GABRA2, and their distribution maps onto [11C]Ro15-4513 binding in vivo. In contrast, the interneuron marker parvalbumin co-expressed with more predominant GABAA receptor subunits (GABRA1, GABRB2 and GABRG2), and their distribution tracks [11C]flumazenil binding in vivo. These results have important implications for the non-invasive study of GABAergic microcircuit dysfunction in psychiatric conditions.
Multi-omics network-based functional annotation of unknown Arabidopsis genes
Authors: Depuydt Thomas , Vandepoele Klaas
Published: June 2021

Unraveling gene functions is pivotal to understand the signaling cascades controlling plant development and stress responses. Given that experimental profiling is costly and labor intensive, the need for high-confidence computational annotations is evident. In contrast to detailed gene-specific functional information, transcriptomics data is widely available in both model and crop species. Here, we developed a novel automated function prediction (AFP) algorithm, leveraging complementary information present in multiple expression datasets through the analysis of study-specific gene co-expression networks. Benchmarking the prediction performance on recently characterizedArabidopsis thalianagenes, we showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n=15,790) and unknown (n=11,865) genes inA. thalianaand validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 thousand interactions in total), obtaining a set of high-confidence functional annotations. 5,054 (42.6%) unknown genes were assigned at least one validated annotation, and 3,408 (53.0%) genes with only computational annotations gained at least one novel validated function. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help alleviate the knowledge gap of biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our AFP approach can be applied in future studies to facilitate gene discovery for crop improvement.

Significance statement

For the majority of plant genes, it is unknown in which processes they are involved. Using a multi-omics approach, leveraging transcriptome, protein-DNA and protein-protein interaction data, we functionally annotated 42.6% of unknownArabidopsis thalianagenes, providing insight into a variety of developmental processes and molecular responses, as well as a resource of annotations which can be explored by the community to facilitate future research.
Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella
Authors: Rempfer Christine , Wiedemann Gertrud , Schween Gabriele , Kerres Klaus L. , Lucht Jan M. , Horres Ralf , Decker Eva L. , Reski Ralf
Published: June 2021

Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome, might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant bryophytes. Whereas angiosperms repair DNA double strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in bryophytes homologous recombination (HR) is the main DNA-DSB repair pathway facilitating the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in the moss Physcomitrella using haploid plants and autodiploid plants, generated via an artificial duplication of the whole genome. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the whole genome duplication event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p<0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.
Strategic decision support for long-term conservation management planning
Authors: Abelson Eric S. , Reynolds Keith M. , Manley Patricia , Paplanus Steven
Published: June 2021

Forward thinking conservation-planning can benefit from modeling future landscapes that result from multiple alternative management scenarios. However, long-term landscape modeling and downstream analyses of modeling results can lead to massive amounts of data that are difficult to assemble, analyze, and to report findings in a way that is easily accessible to decision makers. In this study, we developed a decision support process to evaluate modeled forest conditions resulting from five management scenarios, modeled across 100 years in California’s Lake Tahoe basin; to this end we drew upon a large and complex hierarchical dataset intended to evaluate landscape resilience. Trajectories of landscape characteristics used to inform an analysis of landscape resilience in the Lake Tahoe basin were modeled with the spatially explicit LANDIS-II vegetation simulator. Downstream modeling outputs of additional landscape characteristics were derived from the LANDIS-II outputs (e.g., wildlife conditions, water quality, effects of fire). The later modeling processes resulted in the generation of massive data sets with high dimensionality of landscape characteristics at both high spatial and temporal resolution. Ultimately, our analysis distilled hundreds of data inputs into trajectories of the performance of the five management scenarios over the 100-year time horizon of the modeling. We then evaluated each management scenario based on inter-year variability, and absolute and relative performance. We found that the management scenario that relied on prescribed fire, outperformed the other four management approaches. Both these results, and the process that led to them, provided decision makers with easy-to-understand results based on a rational, transparent, and repeatable decision support process.

One sentence description

We present a novel approach to employ decision support tools for conservation over long time horizons.
Oligomeric α-Synuclein induces skin degeneration in a reconstructed human epidermis model
Authors: Oliveira Júlia T. , De Vecchi Rodrigo , Dakic Vanja , Vitória Gabriela , Pedrosa Carolina , Mendes Mayara , Aragão Luiz Guilherme H.S. , Cardim-Pires Thyago R. , Furtado Daniel Rodrigues , Pinheiro Roberta O. , Foguel Débora , Breton Lionel , Bouez Charbel , Guimarães Marilia Zaluar P. , Rehen Stevens
Published: June 2021

Cell senescence may promote epidermal inflammation and degeneration, termed as inflammaging, which is accompanied by keratinocyte loss, resulting in fine lines of wrinkles. Recent findings showed that healthy elderly skin expresses age- and neuron-related amyloidogenic proteins, such as tau, β-Amyloid34, and α-synuclein (α-Syn), typically found in patients with neurodegenerative diseases. These proteins form toxic aggregates that trigger inflammatory signals. Herein, we investigated the impact of oligomeric α-Syn (Oα-Syn) on the neurosphere (NP) and the reconstructed human epidermis (RHE) 3D models. First, we found the expression of α-Syn, β-Amyloid, and amyloid precursor protein (APP) in the RHE. Second, we challenged the RHE and NP with Oα-Syn, which decreased RHE regeneration, measured by the percentage of cell proliferation and thickness of the stratum basale, but did not affect NP neurite outgrowth. Oα-Syn did not decrease the number of human neonatal epidermal keratinocytes (HEKn) but, as seen for the RHE, it also decreased the proliferation of HEKn. We confirmed that the oligomeric, and not the monomeric α-Syn species, accounted for the proliferation-decreasing effect. Oα-Syn also increased the NF-kB nuclear translocation in HEKn analyzed by nucleus/cytoplasm NF-κB fluorescence intensity. In addition, Oα-Syn triggered inflammation in the RHE, by increasing the mRNA levels of IL-1β and tumor necrosis factor-alpha (TNF-α), and the release of TNF-α in a time-dependent manner. These findings show that Oα-Syn does not affect neurite outgrowth but induces a decrease in keratinocyte proliferation along with epidermal inflammation. With our tridimensional models, we demonstrated that the neurodegenerative protein Oα-Syn also degenerates the epidermis, drawing attention to the need of target-based screening to prevent and treat the effects of skin aging.
Visual and Quantitative Analyses of Virus Genomic Sequences using a Metric-based Algorithm
Authors: Belinsky Alexandra , Kouzaev Guennadi A.
Published: June 2021

This work aims to study the virus RNAs using a novel algorithm for accelerated exploring any-length genomic fragments in sequences using Hamming distance between the binary-expressed characters of an RNA and query patterns. The found repetitive genomic sub-sequences of different lengths were placed on one plot as genomic trajectories (walks) to increase the effectiveness of geometrical multi-scale genomic studies. Primary attention was paid to the building and analysis of theatg-triplet walks composing the schemes or skeletons of the viral RNAs. The 1-D distributions of these codon-startingatg-triplets were built with the single-symbol walks for full-scale analyses. The visual examination was followed by calculating statistical parameters of genomic sequences, including the estimation of geometry deviation and fractal properties of inter-atgdistances. This approach was applied to the SARS CoV-2, MERS CoV, Dengue and Ebola viruses, whose complete genomic sequences are taken from GenBank and GISAID databases. The relative stability of these distributions for SARS CoV-2 and MERS CoV viruses was found, unlike the Dengue and Ebola distributions that showed an increased deviation of their geometrical and fractal characteristics ofatg-distributions. The results of this work can found in classification of the virus families and in the study of their mutation.
Progesterone receptor-A isoform interaction with RUNX transcription factors controls chromatin remodelling at promoters during ovulation
Authors: Dinh DT , Breen J , Nicol B , Smith KM , Nicholls M , Emery A , Wong YY , Barry SC , Yao HHC , Robker RL , Russell DL
Published: June 2021

Progesterone receptor (PGR) plays diverse roles in reproductive tissues and thus coordinates mammalian fertility. In the ovary, acutely induced PGR is the key determinant of ovulation through transcriptional control of a unique set of genes that culminates in follicle rupture. However, the molecular mechanisms for PGR’s specialised function in ovulation is poorly understood. To address this, we assembled a detailed genomic profile of PGR action through combined ATAC-seq, RNA-seq and ChIP-seq analysis in wildtype and isoform-specific PGR null mice. We demonstrated the unique action of PGR-A isoform in the ovary through a transcriptional complex involving physical interaction with RUNX and JUN/FOS transcription factors. The assembly of this unique complex directs targeting of PGR binding to proximal promoter regions and enables chromatin accessibility, leading to ovulatory gene induction. This PGR signalling mechanism is specific to ovulation and provides potential targets for infertility treatments as well as new contraceptives that block ovulation.
Rotavirus NSP1 contributes to intestinal viral replication, pathogenesis, and transmission
Authors: Hou Gaopeng , Zeng Qiru , Matthijnssens Jelle , Greenberg Harry B. , Ding Siyuan
Published: June 2021

Rotavirus (RV)-encoded non-structural protein 1 (NSP1), the product of gene segment 5, effectively antagonizes host interferon (IFN) signaling via multiple mechanisms. Recent studies with the newly established RV reverse genetics system indicate that NSP1 is not essential for the replication of simian RV SA11 strain in cell culture. However, the role of NSP1 in RV infection in vivo remains poorly characterized due to the limited replication of heterologous simian RVs in the suckling mouse model. Here, we used an optimized reverse genetics system and successfully recovered recombinant murine RVs with or without NSP1 expression. While the NSP1-null virus replicated comparably with the parental murine RV in IFN-deficient and IFN-competent cell lines in vitro, it was highly attenuated in 5-day-old wild-type suckling pups. In the absence of NSP1 expression, murine RV had significantly reduced replication in the ileum, systemic spread to mesenteric lymph nodes, fecal shedding, diarrhea occurrence, and transmission to uninoculated littermates. Of interest, the replication and pathogenesis defects of NSP1-null RV were only minimally rescued in Stat1 knockout pups, suggesting that NSP1 facilitates RV replication in an IFN-independent manner. Our findings highlight a pivotal function of NSP1 during homologous RV infections in vivo and identify NSP1 as an ideal viral protein for targeted attenuation for future vaccine development.

IMPORTANCE

Rotavirus remains one of the most important causes of severe diarrhea and dehydration in young children worldwide. Although NSP1 is dispensable for rotavirus replication in cell culture, its exact role in virus infection in vivo remains unclear. In this study, we demonstrate that in the context of a fully replication-competent, pathogenic, and transmissible murine rotavirus, loss of NSP1 expression substantially attenuated virus replication in the gastrointestinal tract, diarrheal disease, and virus transmission in suckling mice. Notably, the NSP1-deficient murine rotavirus also replicated poorly in mice lacking host interferon signaling. Our data provide the first piece of evidence that NSP1 is essential for murine rotavirus replication in vivo, making it an attractable target for developing improved next-generation rotavirus vaccines better suited for socioeconomically disadvantaged and immunocompromised individuals.
Characterization of a flexible AAV-DTR/DT mouse model of acute epithelial lung injury
Authors: Griesser Eva , Schönberger Tanja , Stierstorfer Birgit , Wyatt Hannah , Rist Wolfgang , Lamla Thorsten , Thomas Matthew James , Lamb David , Geillinger-Kästle Kerstin
Published: June 2021

Background & aim

Recurring epithelial injury and aberrant repair are considered as a major driver of idiopathic pulmonary fibrosis (IPF) leading to chronic inflammation, fibroblast activation and ultimately to scarring and stiffening of the lung. As decline of lung function is the first reported symptom by IPF patients and occurs once fibrosis is firmly established, animal models are required to study early disease-driving mechanisms.

Methods

We developed a novel and flexible mouse model of acute epithelial injury based on adeno-associated virus (AAV) variant 6.2 mediated expression of the human diphtheria toxin receptor (DTR). Following intratracheal administration of diphtheria toxin (DT), a cell-specific death of bronchial epithelial and alveolar epithelial type II cells can be observed.

Results

Detailed characterization of the AAV-DTR/DT mouse model revealed increasing cell numbers in bronchoalveolar lavage (BAL; macrophages, neutrophils, and atypical cells) and elevation of apoptotic cells and infiltrated leukocytes in lung tissue, which were dependent of viral genome load and DT dose. Cytokine levels in BAL fluid showed different patterns dependent of viral genome load with IFNγ, TNFα, and IP-10 increasing and IL-5 and IL-6 decreasing, while lung function was not affected. Additionally, laser-capture microdissection-based proteomics of bronchial and alveolar epithelium showed upregulated immune and inflammatory response in all epithelial cell regions and extracellular matrix deposition in infiltrated alveoli, while proteins involved in pulmonary surfactant synthesis, alveolar fluid clearance and alveolar-capillary barrier were downregulated in the parenchyma.

Conclusion

Our novel AAV-DTR/DT model resembles specific aspects of pulmonary diseases like IPF and acute respiratory distress syndrome.

Short summary for social media

A novel and flexible mouse model of acute epithelial lung injury based on AAV-mediated expression of the human diphtheria toxin receptor followed by intratracheal instillation of diphtheria toxin resembles specific aspects of pulmonary diseases like IPF.
Human bone marrow milieu identifies a clinically actionable driver of niche-mediated treatment resistance in leukaemia
Authors: Pal Deepali , Blair Helen , Boyd Sophie , Sharon Angel Hanmy , Nizami Salem , Isa Asmida , Beckett Melanie , Nelson Ryan , Wilson Aaron , Singh Mankaran , Sankar Shalini , Tirtakusuma Ricky , Sirintra Nakjang , Knill Carly , Fuller Andrew , McNeill Hesta , Russell Lisa , Schwab Claire , Zhous Peixun , Sinclair Paul , Coxhead Jonathan , Filby Andrew , Halsey Christina , Allan James M. , Harrison J. Christine , Moorman Anthony , Olaf Heidenreich , Vormoor Josef
Published: June 2021

Leukaemia cells re-program their microenvironment to provide proliferation support and protection from standard chemotherapy, molecularly targeted therapies, and immunotherapy. Although much is becoming known about molecules that drive niche-dependent treatment resistance; means of targeting these in the clinics has remained a key obstacle. To address this challenge, we have developed human induced pluripotent stem cell engineered nichesex vivoto reveal insights into druggable cancer-niche dependencies. We show that mesenchymal (iMSC) and vascular niche-like (iANG) cells supportex vivoproliferation of patient-derived leukaemia cells, impact dormancy and mediate therapy resistance. iMSC protected both non-cycling and cycling blasts against dexamethasone treatment while iANG protected only dormant blasts. Leukaemia proliferation and protection from dexamethasone induced-apoptosis was dependent on direct cell-cell contact and mediated by CDH2. To explore the therapeutic potential of disrupting this cell-cell interaction, we tested the CDH2 antagonist ADH-1 (previously in phase I / II for solid tumours) in a very aggressive patient-derived xenograft leukaemia mouse model. ADH-1 showed highin vivoefficacy. ADH-1/ dexamethasone combination therapy was superior to dexamethasone alone with no ADH1 conferred additional toxicity. These findings provide a proof-of-concept starting point to develop novel, potentially safer therapeutics that target niche-mediated cancer cell dependencies in haematological malignancies.

CDH2 mediated niche-dependent cancer proliferation and treatment resistance is clinically targetable via ADH-1, a low toxic agent that could be potentially repurposed for future clinical trials in acute leukaemia.
Zebrafish Cre/loxregulated UFlip alleles generated by CRISPR/Cas targeted integration provide cell-type specific conditional gene inactivation
Authors: Almeida Maira P. , Kambakam Sekhar , Liu Fang , Ming Zhitao , Welker Jordan M. , Wierson Wesley A. , Schultz-Rogers Laura E. , Ekker Stephen C. , Clark Karl J. , Essner Jeffrey J. , McGrail Maura
Published: June 2021

The ability to regulate gene activity spatially and temporally is essential to investigate cell type specific gene function during development and in postembryonic processes and disease models. The Cre/loxsystem has been widely used for performing cell and tissue-specific conditional analysis of gene function in zebrafish, but simple and efficient methods for isolation of stable, Cre/loxregulated alleles are lacking. Here we applied our GeneWeld CRISPR/Cas9 short homology-directed targeted integration strategy to generate floxed conditional alleles that provide robust gene knockdown and strong loss of function phenotypes. A universal targeting vector, UFlip, with sites for cloning short 24-48 bp homology arms flanking a floxed mRFP gene trap plus secondary reporter cassette, was integrated into an intron inhdac1, rbbp4, andrb1. Active, gene off orientationhdac1-UFlip-Offandrb1-UFlip-Offintegration alleles result in >99% reduction of gene expression in homozygotes and recapitulate known indel loss of function phenotypes. Passive, gene on orientationrbbp4-UFlip-Onandrb1-UFlip-Onintegration alleles do not cause phenotypes in trans-heterozygous combination with an indel mutation. Cre recombinase injection leads to recombination at alternating pairs ofloxPandlox2272sites, inverting and locking the cassette into the active, gene off orientation, and the expected mutant phenotypes. In combination with our endogenous neural progenitor Cre drivers we demonstraterbbp4-UFlip-Onandrb1-UFlip-Ongene inactivation phenotypes can be restricted to specific neural cell populations. Replacement of the UFlip mRFP primary reporter gene trap with a 2A-RFP inrbbp4-UFlip-Off, or 2A-KalTA4 inrb1-UFlip-Off, shows strong RFP expression in wild type or UAS:RFP injected embryos, respectively. Together these results validate a simplified approach for efficient isolation of highly mutagenic Cre/loxresponsive conditional gene alleles to advance zebrafish Cre recombinase genetics.
Imaging transcriptomics: Convergent cellular, transcriptomic, and molecular neuroimaging signatures in the healthy adult human brain
Authors: Martins Daniel , Giacomel Alessio , Williams Steven CR , Turkheimer Federico , Dipasquale Ottavia , Veronese Mattia ,   PET templates working group
Published: June 2021

The expansion of neuroimaging techniques over the last decades has opened a wide range of new possibilities to characterize brain dysfunction in several neurological and psychiatric disorders. However, the lack of specificity of most of these techniques, such as magnetic resonance imaging (MRI)-derived measures, to the underlying molecular and cellular properties of the brain tissue poses limitations to the amount of information one can extract to inform precise models of brain disease. The integration of transcriptomic and neuroimaging data, known as ‘imaging transcriptomics’, has recently emerged as an indirect way forward to test and/or generate hypotheses about potential cellular and transcriptomic pathways that might underly specific changes in neuroimaging MRI biomarkers. However, the validity of this approach is yet to be examined in-depth. Here, we sought to bridge this gap by performing imaging transcriptomic analyses of the regional distribution of well-known molecular markers, assessed by positron emission tomography (PET), in the healthy human brain. We focused on tracers spanning different elements of the biology of the brain, including neuroreceptors, synaptic proteins, metabolism, and glia. Using transcriptome-wide data from the Allen Brain Atlas, we applied partial least square regression to rank genes according to their level of spatial alignment with the regional distribution of these neuroimaging markers in the brain. Then, we performed gene set enrichment analyses to explore the enrichment for specific biological and cell-type pathways among the genes most strongly associated with each neuroimaging marker. Overall, our findings show that imaging transcriptomics can recover plausible transcriptomic and cellular correlates of the regional distribution of benchmark molecular imaging markers, independently of the type of parcellation used to map gene expression and neuroimaging data. Our data support the plausibility and robustness of imaging transcriptomics as an indirect approach for bridging gene expression, cells and macroscopical neuroimaging and improving our understanding of the biological pathways underlying regional variability in neuroimaging features.
Estimates of persistent inward currents are reduced in upper limb motor units of older adults
Authors: Hassan Altamash S , Fajardo Melissa E , Cummings Mark , McPherson Laura Miller , Negro Francesco , Dewald Julius P A , Heckman C J , Pearcey Gregory E P
Published: June 2021

Aging is a natural process that causes alterations in the neuromuscular system, which contribute to weakness and reduced quality of life. Reduced firing rates of individual motor units (MUs) likely contribute to weakness, but the mechanisms underlying reduced firing rates are not clear. Persistent inward currents (PICs) are crucial for the initiation, gain control, and maintenance of motoneuron firing, and are directly proportional to the level of monoaminergic input. Since the concentration of monoamines (i.e. serotonin and norepinephrine) are reduced with age, we sought to determine if estimates of PICs are reduced in older (>60 years old) compared to younger adults (<35 years old). We decomposed MU spike trains from high-density surface electromyography over the biceps brachii and triceps brachii during isometric ramp contractions to 20% of maximum. Estimates of PICs (i.e. ΔF) were computed using the paired MU analysis technique. Regardless of the muscle, peak firing rates of older adults were reduced by ~1.6 pulses per second (pps) (P = 0.0292), and ΔF was reduced by ~1.9 pps (P < 0.0001), compared to younger adults. We further found that age predicted ΔF in older adults (P = 0.0261), resulting in a reduction of ~1pps per decade, but there was no relationship in younger adults (P = 0.9637). These findings suggest that PICs are reduced in older adults, and, further, age is a significant predictor of estimates of PICs in older adults. Reduced PIC magnitude represents one plausible mechanism for reduced firing rates and weakness in older individuals.

KEY POINTS

Persistent inward currents play an important role in the neural control of human movement and are influenced by neuromodulation via monoamines originating in the brainstem.

During aging, motor unit firing rates are reduced, and there is deterioration of brainstem nuclei, which may reduce persistent inward currents in alpha motoneurons.

Here we show that estimates of persistent inward currents (ΔF) of both elbow flexor and extensor motor units are reduced in older adults.

Estimates of persistent inward currents have a negative relationship with age in the older adults, but not young.

This novel mechanism may play a role in alteration motor firing rates that occurs with aging, which may have consequences for motor control.
Nanoscale surface topography reduces focal adhesions and cell stiffness by enhancing integrin endocytosis
Authors: Li Xiao , Klausen Lasse H. , Zhang Wei , Jahed Zeinab , Tsai Ching-Ting , Li Thomas L. , Cui Bianxiao
Published: June 2021

Both substrate stiffness and surface topography regulate cell behavior through mechanotransduction signaling pathways. Such intertwined effects suggest that engineered surface topographies might substitute or cancel the effects of substrate stiffness in biomedical applications. However, the mechanisms by which cells recognize topographical features are not fully understood. Here we demonstrate that the presence of nanotopography drastically alters cell behavior such that neurons and stem cells cultured on rigid glass substrates behave as if they were on soft hydrogels. We further show that rigid nanotopography resembles the effect of soft hydrogels in reducing cell stiffness and membrane tension as measured by atomic force microscopy. Finally, we demonstrate that nanotopography reduces focal adhesions and cell stiffness by enhancing the endocytosis and the subsequent removal of integrin receptors. This mechanistic understanding will support the rational design of nanotopography that directs cells on rigid materials to behave as if they were on soft ones.

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Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics
Authors: Crowe-McAuliffe Caillan , Murina Victoriia , Kasari Marje , Takada Hiraku , Turnbull Kathryn Jane , Polikanov Yury S. , Sundsfjord Arnfinn , Hegstad Kristin , Atkinson Gemma C. , Wilson Daniel N. , Hauryliuk Vasili
Published: June 2021

PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF) that confer resistance to oxazolidinone, such as linezolid, and phenicol antibiotics, such as chloramphenicol. PoxtA/OptrA are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria. These target protection proteins are thought to confer resistance by binding to the ribosome and dislodging the antibiotics from their binding sites. However, a structural basis for their mechanism of action has been lacking. Here we present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome at 2.9–3.1 Å, as well as the complete E. faecalis 70S ribosome at 2.2–2.5 Å. The structures reveal that PoxtA binds within the ribosomal E-site with its antibiotic resistance domain (ARD) extending towards the peptidyltransferase center (PTC) on the large ribosomal subunit. At its closest point, the ARD of PoxtA is still located >15 Å from the linezolid and chloramphenicol binding sites, suggesting that drug release is elicited indirectly. Instead, we observe that the ARD of PoxtA perturbs the CCA-end of the P-site tRNA causing it to shift by ∼4 Å out of the PTC, which correlates with a register shift of one amino acid for the attached nascent polypeptide chain. Given that linezolid and chloramphenicol are context-specific translation elongation inhibitors, we postulate that PoxtA/OptrA confer resistance to oxazolidinones and phenicols indirectly by perturbing the P-site tRNA and thereby altering the conformation of the attached nascent chain to disrupt the drug binding site.
External fertilization is orchestrated by a pH-regulated soluble adenylyl cyclase controlling sperm motility and chemotaxis
Authors: Körschen H.G. , Hamzeh H. , Pascal R. , Alvarez L. , Bönigk W. , Kaur N. , Levin L.R. , Buck J. , Kambach C. , Michino M. , Jennings A. , Sato A. , Seifert R. , Strünker T. , Steegborn C. , Kaupp U.B.
Published: June 2021

The reaction of CO2with H2O to form HCO3-and H+is one of the most important chemical equilibria in cells. In mammalian sperm, a soluble adenylyl cyclase (sAC) serves as cellular HCO3-sensor that conveys the equilibrium state via cAMP synthesis to cAMP-signaling molecules. The function of sAC and cAMP in non-mammalian sperm is largely unknown. Here, we identify sAC orthologs in sea urchin and salmon sperm that, surprisingly, are activated by alkaline pH rather than HCO3-. Two amino-acid residues required for HCO3-binding of mammalian sAC are lacking in pH-regulated sAC. Orthologs identified in ten other phyla are also lacking either one of these key residues, suggesting that pH control is widespread among non-mammalian metazoan. The pH-sensitive sAC controls several functions of sperm from external fertilizers. Upon spawning, alkalization triggers cAMP synthesis and, thereby, activates motility of quiescent sperm. Egg-derived chemoattractants also alkalize sperm and elevate cAMP, which then-modulates pacemaker HCN channels to trigger a chemotactic Ca2+response. Finally, the sAC and the voltage- and cAMP-activated Na+/H+exchanger sNHE mutually control each other. A picture of evolutionary significance is emerging: motility and sensory signaling of sperm from both internal and external fertilizers rely on cAMP, yet, their sAC is regulated by HCO3-or pHi, respectively. Acidification of aquatic habitats due to climate change may adversely affect pH-sensing by sAC and thereby sexual reproduction in the sea.

Statement of significance

Adenylyl cyclases synthesize cAMP, a prominent cellular messenger. A bicarbonate-sensitive AC family member, soluble AC (sAC), is tied to the chemical equilibrium: H2O + CO2↔ HCO3-(bicarbonate) + H+. The sAC is required for fertilization: Mammals lacking sAC are infertile and sperm immotile. We now identify a new sAC form in sperm of non-mammalian animals that reproduce in the sea. This novel sAC is activated at alkaline pH rather than bicarbonate. It controls sperm motility and chemotaxis. The switch from HCO3-to pH rests on substitution of two amino-acids, which represents an adaptation to aquatic environments low in bicarbonate. Acidification of aquatic habitats due to climate change may adversely affect sAC activity and, thereby, fertilization.
Concealed identity information detection with pupillometry in rapid serial visual presentation
Authors: Chen Ivory Y. , Karabay Aytaç , Mathot Sebastiaan , Bowman Howard , Akyürek Elkan G.
Published: June 2021

The concealed information test (CIT) relies on bodily reactions to stimuli that are hidden in mind. However, people can use countermeasures, such as purposely focusing on irrelevant things, to confound the CIT. A new method designed to prevent countermeasures uses rapid serial visual presentation (RSVP) to present stimuli on the fringe of awareness. Previous studies that used RSVP in combination with electroencephalography (EEG) showed that participants exhibit a clear reaction to their real first name, even when they try to prevent such a reaction (i.e., when their name is concealed information). Since EEG is not easily applicable outside the laboratory, we investigated here whether pupil size, which is easier to measure, can also be used to detect concealed identity information. In our first study, participants adopted a fake name, and searched for this name in an RSVP task, while their pupil sizes were recorded. Apart from this fake name, their real name and a control name also appeared in the task. We found pupil dilation in response to the task-irrelevant real name, as compared to control names. However, while most participants showed this effect qualitatively, it was not statistically significant for most participants individually. In a second study, we preregistered the proof-of-concept methodology and replicated the original findings. Taken together, our results show that the current RSVP task with pupillometry can detect concealed identity information at a group level. Further development of the method is needed to create a valid and reliable concealed identity information detector at the individual level.
Notch1mutation drives clonal expansion in normal esophageal epithelium but impairs tumor growth
Authors: Abby Emilie , Dentro Stefan C , Hall Michael W J , Fowler Joanna C , Ong Swee Hoe , Sood Roshan , Siebel Christian W , Gerstung Moritz , Hall Benjamin A , Jones Philip H
Published: June 2021

NOTCH1mutant clones occupy the majority of normal human esophagus by middle age, but are comparatively rare in esophageal cancers, suggestingNOTCH1mutations may promote clonal expansion but impede carcinogenesis1–3. Here we test this hypothesis. Visualizing and sequencingNOTCH1mutant clones in aging normal human esophagus reveals frequent biallelic mutations that block NOTCH1 signaling. In mouse esophagus, heterozygousNotch1mutation confers a competitive advantage over wild type cells, an effect enhanced by loss of the second allele.Notch1loss alters transcription but has minimal effects on epithelial structure and cell dynamics. In a carcinogenesis model,Notch1mutations were less prevalent in tumors than normal epithelium. Deletion ofNotch1reduced tumor growth, an effect recapitulated by anti-NOTCH1 antibody treatment. We conclude thatNotch1mutations in normal epithelium are beneficial as wild typeNotch1promotes tumor expansion. NOTCH1 blockade may have therapeutic potential in preventing esophageal squamous cancer.
Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity
Authors: Zhao Victor Y. , Rodrigues Joao V. , Lozovsky Elena R. , Hartl Daniel L. , Shakhnovich Eugene I.
Published: June 2021

To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study sub-domain modularity by creating 20 chimeras of an enzyme, E. coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. We performed molecular dynamics simulations using replica exchange with solute-tempering. Chimeras with low catalytic activity exhibit non-helical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.

Statement of Significance

α-helices are ubiquitous components of protein structure that exhibit a degree of independent folding behavior, making them plausible structural modules within proteins. Here, we assess the effects of switching the sequence of an α-helix in an essential enzyme for α-helical sequences from evolutionarily unrelated proteins. The resultant chimeric proteins can still fold but enzymatic activity, stability, and cellular growth rates are negatively affected. Computational investigations reveal how residues in an α-helix have been shaped by selection pressure to maintain catalytic activity and a specific, helical conformation of the protein. More broadly, we illustrate how molecular and fitness effects of switching protein segments depend on the protein and cellular context.
The functional specialization of visual cortex emerges from training parallel pathways with self-supervised predictive learning
Authors: Bakhtiari Shahab , Mineault Patrick , Lillicrap Tim , Pack Christopher C. , Richards Blake A.
Published: June 2021

The visual system of mammals is comprised of parallel, hierarchical specialized pathways. Different pathways are specialized in so far as they use representations that are more suitable for supporting specific downstream behaviours. In particular, the clearest example is the specialization of the ventral (“what”) and dorsal (“where”) pathways of the visual cortex. These two pathways support behaviours related to visual recognition and movement, respectively. To-date, deep neural networks have mostly been used as models of the ventral, recognition pathway. However, it is unknown whether both pathways can be modelled with a single deep ANN. Here, we ask whether a single model with a single loss function can capture the properties of both the ventral and the dorsal pathways. We explore this question using data from mice, who like other mammals, have specialized pathways that appear to support recognition and movement behaviours. We show that when we train a deep neural network architecture with two parallel pathways using a self-supervised predictive loss function, we can outperform other models in fitting mouse visual cortex. Moreover, we can model both the dorsal and ventral pathways. These results demonstrate that a self-supervised predictive learning approach applied to parallel pathway architectures can account for some of the functional specialization seen in mammalian visual systems.
Investigation of crevice corrosion of metallic fastened joints in carbon fiber reinforced polymer (CFRP) exposed to coastal seawater
Authors: Abdulsalam Mohammed I. , Presuel-Moreno Francisco
Published: June 2021

Purpose

The purpose of this paper is to study the susceptibility of these three commonly used corrosion resistance fasteners in seawater. For a more practical scenario, a local Atlantic coastal seawater as received was used.

Design/methodology/approach

Carbon fiber reinforced polymer (CFRP) was fabricated with T700 carbon fiber (Toray Inc.) and VE8084 vinyl ester resin (Ashland) to make a unidirectional composite panel of thickness 1.8 mm. A conductive paint was applied to one of the sample edges that was perpendicular to the fiber direction, providing an electrical contact with carbon fibers to connect a copper wire. This external electric connection was used for potential measurements of both the open circuit potential (OCP) of the CFRP sample, and the mixed potential of the fastened set: consisting of the CFRP and the metallic fastener fastened to it. Three common fastener alloys were selected: 316SS, Monel and Titanium. For this purpose, a high impedance voltmeter was used in conjunction with a saturated calomel reference electrode. Measurements were taken daily. For longer time measurements, a four-channel high impedance analog data logger was used with 30 min sampling rate.

Findings

For both 316SS and Monel fastened sets, crevice corrosion occurred inside the occluded regions of the set, when immersed in coastal seawater. The attack was more severe for 316 stainless steel set. An isolated island attack of faceted surfaces morphology was seen for 316SS set. While, a circular ring of preferential grain boundary attack appeared for Monel set, indicating an IR (voltage) drop mechanism is more likely operating. Titanium-fastened sets showed high resistance to crevice corrosion when simmered in seawater. However, for long-time exposure, the sets became more susceptible to crevice corrosion attack supported by CFRP attachment (oxygen reduction reaction taking place at the carbon fibers).

Originality/value

Evidently, titanium, stainless steels and Monel are good candidates for galvanic corrosion resistance. However, their susceptibility to crevice corrosion when coupled with CFRP is a new challenging topic that needs further investigation. This is very important today because the vast application witnessed for CFRP material. This work involves developing an original methodology for this kind of investigation and was done at advanced laboratories of SeaTech at Florida Atlantic University by the Atlantic coastline.
The interplay between the Internet of things and supply chain management: challenges and opportunities based on a systematic literature review
Authors: Rebelo Rômulo Marcos Lardosa , Pereira Susana Carla Farias , Queiroz Maciel M.
Published: June 2021

Purpose

This study aims to identify and analyze how Internet of things (IoT) technology affects supply chain management (SCM) performance.

Design/methodology/approach

A systematic literature review was conducted (using Scopus, JSTOR, Emerald, ProQuest, Science Direct and Web of Science) covering a 20-year timeframe (2000–2020). Out of 2,572 papers identified, 171 peer-reviewed papers from the most important journals were selected. Content analysis was used following the Global Supply Chain Forum (GSCF) SCM framework.

Findings

Regarding the GSCF SCM framework processes, most IoT-based studies have addressed improving order fulfilment, manufacturing flow management and demand management processes. However, no studies addressing the Supplier relationship management process were identified, suggesting that IoT-based applications are perceived to add more value in downstream than upstream SCM processes. The importance of using enabling technologies to realize the potential of value generation of IoT was also revealed. Findings suggest new research avenues related to product development and commercialization process, the supplier relationship management process, the returns management process, servitization strategies, new SCM models and new business models.

Research limitations/implications

The review encompasses only academic papers from journals considered the most relevant (retrieved from specific databases), using the impact factor as the quality criterion.

Practical implications

The findings can help business managers better understand the potential of IoT technology, such as the main applications identified in the literature and their impacts on SCM processes. Their importance in enabling technologies to leverage SCM performance is identified and the emerging SCM models/business models that IoT deployment can enable are highlighted.

Originality/value

This study contributes to filling a gap in the literature using a systematic literature review of how IoT technology affects SCM performance through content analysis, using an SCM framework to clarify which SCM processes are affected. Academic articles from the most important journals from 2000 to 2020 are identified.
Traditional marketing analytics, big data analytics and big data system quality and the success of new product development
Authors: Aljumah Ahmad Ibrahim , Nuseir Mohammed T. , Alam Md. Mahmudul
Published: June 2021

Purpose

This study investigates the impact of traditional marketing analytics and big data analytics on the success of a new product. Moreover, it assesses the mediating effects of the quality of big data system.

Design/methodology/approach

This study is based on primary data that were collected through an online questionnaire survey from large manufacturing firms operating in UAE. Out of total distributed 421 samples, 327 samples were used for final data analysis. The survey was conducted from March–April 2020, and data analysis was done via Structural Equation Modelling (SEM-PLS).

Findings

It emerges that big data analysis (BDA), traditional marketing analysis (TMA) and big data system quality (BDSQ) are significant determinants of new product development (NPD) success. Meanwhile, the BDA and TMA significantly affect the BDSQ. Results of the mediating role of BDSQ in the relationship between the BDA and NPD, as well as TMA and NPD, are significant.

Practical implications

There are significant policy implications for practitioners and researchers concerning the role of analytics, particularly big data analytics and big data system quality, when attempting to achieve success in developing new products.

Originality/value

This is an original study based on primary data from UAE.