bluuebunny/crossref_metadata_2025 huggingface dataset:
Compared with SARS-CoV2 wild type’s spike protein, the SARS-CoV2 omicron’s receptor binding motif has adopted a more SARS-CoV1 and/or bat/civet-like structure
Authors: Glocker Michael O. , Opuni Kwabena F.M. , Thiesen Hans-Juergen
Published: December 2021

Our study focuses on free energy calculations of SARS-CoV2 spike protein receptor binding motives (RBMs) from wild type and variants-of-concern with particular emphasis on currently emerging SARS- CoV2 omicron variants of concern (VOC). Our computational free energy analysis underlines the occurrence of positive selection processes that specify omicron host adaption and bring changes on the molecular level into context with clinically relevant observations. Our free energy calculations studies regarding the interaction of omicron’s RBM with human ACE2 shows weaker binding to ACE2 than alpha’s, delta’s, or wild type’s RBM. Thus, less virus is predicted to be generated in time per infected cell. Our mutant analyses predict with focus on omicron variants a reduced spike-protein binding to ACE2-receptor protein possibly enhancing viral fitness / transmissibility and resulting in a delayed induction of danger signals as trade-off. Finally, more virus is produced but less per cell accompanied with delayed Covid-19 immunogenicity and pathogenicity. Regarding the latter, more virus is assumed to be required to initiate inflammatory immune responses.
From Diversity to Complexity: Microbial Networks in Soils
Authors: Guseva Ksenia , Darcy Sean , Simon Eva , Alteio Lauren V. , Montesinos-Navarro Alicia , Kaiser Christina
Published: December 2021

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.
Single-cell resolution unravels spatial alterations in metabolism, transcriptome and epigenome of ageing liver
Authors: Nikopoulou Chrysa , Kleinenkuhnen Niklas , Parekh Swati , Sandoval Tonantzi , Schneider Farina , Giavalisco Patrick , Bozukova Mihaela , Vesting Anna Juliane , Altmüller Janine , Wunderlich Thomas , Kondylis Vangelis , Tresch Achim , Tessarz Peter
Published: December 2021

Epigenetic ageing clocks have revealed that tissues within an organism can age with different velocity. However, it has not been explored whether cells of one type experience different ageing trajectories within a tissue depending on their location. Here, we employed lipidomics, spatial transcriptomics and single-cell ATAC-seq in conjunction with available single-cell RNA-seq data to address how cells in the murine liver are affected by age-related changes of the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. Particularly periportal hepatocytes were characterized by decreased mitochondrial function and strong alterations in the epigenetic landscape, while pericentral hepatocytes – despite accumulation of large lipid droplets – did not show apparent functional differences. In general, chromatin alterations did not correlate well with transcriptional changes, hinting at post-transcriptional processes that shape gene expression during ageing. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.
NAD+capping of RNA in Archaea and Mycobacteria
Authors: Ruiz-Larrabeiti Olatz , Benoni Roberto , Zemlianski Viacheslav , Hanišáková Nikola , Schwarz Marek , Brezovská Barbora , Benoni Barbora , Hnilicová Jarmila , Kaberdin Vladimir R. , Cahová Hana , Vítězová Monika , Převorovský Martin , Krásný Libor
Published: December 2021

Chemical modifications of RNA affect essential properties of transcripts, such as their translation, localization and stability. 5’-end RNA capping with the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD+) has been discovered in organisms ranging from bacteria to mammals. However, the hypothesis that NAD+capping might be universal in all domains of life has not been proven yet, as information on this RNA modification is missing for Archaea. Likewise, this RNA modification has not been studied in the clinically importantMycobacteriumgenus. Here, we demonstrate that NAD+capping occurs in the archaeal and mycobacterial model organismsMethanosarcina barkeriandMycobacterium smegmatis.Moreover, we identify the NAD+-capped transcripts inM. smegmatis,showing that this modification is more prevalent in stationary phase, and revealing that mycobacterial NAD+-capped transcripts include non-coding small RNAs, such as Ms1. Furthermore, we show that mycobacterial RNA polymerase incorporates NAD+into RNA, and that the genes of NAD+-capped transcripts are preceded by promoter elements compatible with σA/σFdependent expression. Taken together, our findings demonstrate that NAD+capping exists in the archaeal domain of life, suggesting that it is universal to all living organisms, and define the NAD+-capped RNA landscape in mycobacteria, providing a basis for its future exploration.
Cell polarity determinant Dlg1 facilitates epithelial invagination by promoting tissue-scale mechanical coordination
Authors: Fuentes Melisa A. , He Bing
Published: December 2021

Epithelial folding mediated by apical constriction serves as a fundamental mechanism to convert flat epithelial sheets into multilayered structures. It remains elusive whether additional mechanical inputs are required for folding mediated by apical constriction. Using Drosophila mesoderm invagination as a model, we identified an important role for the non-constricting, lateral mesodermal cells adjacent to the constriction domain (“flanking cells”) in facilitating epithelial folding. We found that depletion of the basolateral determinant, Dlg1, disrupts the transition between apical constriction and invagination without affecting the rate of apical constriction. Strikingly, the observed delay in invagination is associated with ineffective apical myosin contractions in the flanking cells that lead to overstretching of their apical domain. The defects in the flanking cells impede ventral-directed movement of the lateral ectoderm, suggesting reduced mechanical coupling between tissues. Specifically disrupting the flanking cells in wildtype embryos by laser ablation or optogenetic depletion of cortical actin is sufficient to delay the apical constriction-to-invagination transition. Our findings indicate that effective mesoderm invagination requires intact flanking cells and suggest a role for tissue-scale mechanical coupling during epithelial folding.
Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae
Authors: Mahrou Bahareh , Pirhanov Azady , Alijanvand Moluk Hadi , Cho Yong Ku , Shin Yong-Jun
Published: December 2021

Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable the control of physiological outcomes in biotechnology applications. Timed periodic changes in protein levels play a critical role in the cell division cycle, cellular stress response, and development. Here we report the generation of robust protein level oscillations by controlling the protein degradation rate in the yeast Saccharomyces cerevisiae. Using a photo-sensitive degron and red fluorescent proteins as reporters, we show that under constitutive transcriptional induction, repeated triangular protein level oscillations as fast as 5-10 minute-scale can be generated by modulating the protein degradation rate. Consistent with oscillations generated though transcriptional control, we observed a continuous decrease in the magnitude of oscillations as the input modulation frequency increased, indicating low-pass filtering of input perturbation. By using two red fluorescent proteins with distinct maturation times, we show that the oscillations in protein level is largely unaffected by delays originating from functional protein formation. Our study demonstrates the potential for repeated control of protein levels by controlling the protein degradation rate without altering the transcription rate.
Revisiting the Role of Notch in Nephron Segmentation: Notch is Required for Proximal, Not Distal Fate Selection During Mouse and Human Nephrogenesis
Authors: Duvall Kathryn , Bice Lauren , Perl Alison J. , Shakked Naomi Pode , Chaturvedi Praneet , Kopan Raphael
Published: December 2021

Notch signaling promotes maturation of nephron epithelia, but its proposed contribution to nephron segmentation into proximal and distal domains has been called into doubt. We leveraged single cell and bulk RNA-seq, quantitative immunofluorescent lineage/fate tracing, and genetically modified human iPSC to revisit this question in developing mouse kidneys and human kidney organoids. We confirmed that Notch signaling is needed for maturation of all nephron lineages, and thus mature lineage markers fail to detect a fate bias. By contrast, early markers identified a distal fate bias in cells lacking Notch2, and a concomitant increase in early proximal and podocyte fates in cells expressing hyperactive Notch1 was observed. Orthogonal support for a conserved role for Notch signaling in the distal/proximal axis segmentation is provided by the ability of Nicastrin-deficient hiPSCs-derived organoids to differentiate into TFA2B+ distal tubule and CDH1 connecting segment progenitors, but not into HNF4A+ or LTL+ proximal progenitors.

Notch signaling acts in nephron segmentation to select early proximal, but not distal tubule fate downstream of a global role promoting epithelial growth and maturation in mouse and human.
Physiochemically distinct SU-8 surfaces tailor Xylella fastidiosa cell-surface holdfast and colonization
Authors: Anbumani Silambarasan , da Silva Aldeliane M. , Alaferdov Andrei , Puydinger dos Santos Marcos V. , Carvalho Isis G. B. , de Souza e Silva Mariana , Moshkalev Stanislav , Carvalho Hernandes F. , de Souza Alessandra A. , Cotta Monica A.
Published: December 2021

SU-8 polymer is an excellent platform for diverse applications due to its high aspect ratio of micro/nanostructures fabrication and exceptional optical, chemical, and biocompatible properties. Although SU-8 has been often investigated for a variety of biological applications, how its surface properties influence both the interaction of bacterial cells with the substrate and its colonization is poorly understood. In this work, we tailor SU-8 nanoscale surface properties to investigate single cell motility, adhesion and successive colonization of a phytopathogenic bacteria, Xylella fastidiosa. Different surface properties of SU-8 thin films have been prepared using photolithography processing and oxygen plasma treatment. We found a significant difference in bacterial cell behavior and subsequent colonization on SU-8 as surface property changes. A larger density of carboxyl groups in hydrophilic plasma-treated SU-8 surfaces promotes faster cell motility in the earlier stage of the growth. The hydrophobic nature of pristine SU-8 surfaces has no trackable bacterial motility with 5 to 10 times more single cells adhered to surface than its plasma-treated counterpart. In fact, plasma-treated SU-8 samples suppressed bacterial adhesion, with surfaces showing less than 5% coverage. These results not only showcase that SU-8 surface properties can impact the bacterial behavior in a spatiotemporal manner, but also provide insights on the prominent ability of pathogens to evolve and adapt to different surface properties.
The intrarenal renin-angiotensin system in hypertension: Insights from mathematical modelling
Authors: Smith Delaney , Layton Anita
Published: December 2021

The renin-angiotensin system (RAS) plays a pivotal role in the maintenance of volume homeostasis and blood pressure. In addition to the well-studied systemic RAS, local RAS have been documented in various tissues, including the kidney. Given the role of the intrarenal RAS in the pathogenesis of hypertension, a role established via various pharmacologic and genetic studies, substantial efforts have been made to unravel the processes that govern intrarenal RAS activity. In particular, several mechanisms have been proposed to explain the rise in intrarenal angiotensin II (Ang II) that accompanies Ang II infusion, including increased angiotensin type 1 receptor (AT1R)-mediated uptake of Ang II and enhanced intrarenal Ang II production. However, experimentally isolating their contribution to the intrarenal accumulation of Ang II in Ang II–induced hypertension is challenging, given that they are fundamentally connected. Computational modelling is advantageous because the feedback underlying each mechanism can removed and the effect on intrarenal Ang II can be studied. In this work, the mechanisms governing the intrarenal accumulation of Ang II during Ang II infusion experiments are delineated and the role of the intrarenal RAS in Ang II-induced hypertension is studied. To accomplish this, a compartmental ODE model of the systemic and intrarenal RAS is developed and Ang II infusion experiments are simulated. Simulations indicate that AT1Rmediated uptake of Ang II is the primary mechanism by which Ang II accumulates in the kidney during Ang II infusion. Enhanced local Ang II production is unnecessary. The results demonstrate the role of the intrarenal RAS in the pathogenesis of Ang II-induced hypertension and consequently, clinical hypertension associated with an overactive RAS.
Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration
Authors: Amamoto Ryoji , Wallick Grace K. , Cepko Constance L.
Published: December 2021

Retinitis Pigmentosa (RP) is a wide array of progressive, debilitating visual disorders caused by mutations in a diverse set of genes. In both human patients and mouse models of RP, rod photoreceptor dysfunction leads to loss of night vision, and is followed by secondary cone photoreceptor dysfunction and degeneration, leading to loss of daylight color vision. A strategy to prevent secondary cone death could provide a generalized RP therapy to preserve daylight color vision regardless of the underlying mutation. In mouse models of RP, cones in the far peripheral retina survive long-term, despite complete rod loss. The mechanism for such peripheral cone survival had not been explored. Here, we found that active retinoic acid (RA) signaling in peripheral Muller glia is both sufficient and necessary for the extended cone survival. RA depletion by conditional knockout of RA synthesis enzymes, or overexpression of an RA degradation enzyme, abrogated peripheral cone survival. Conversely, constitutive activation of RA signaling in the central retina promoted long-term cone survival. These results indicate that RA signaling mediates the prolonged peripheral cone survival in the rd1 mouse model of retinal degeneration, and provide a basis for a generic strategy for cone survival in the many diseases that lead to loss of cone-mediated vision.
Development and Characterization of Recombinant Vesicular Stomatitis Virus (rVSV)-based Bivalent Vaccine Against COVID-19 Delta Variant and Influenza Virus
Authors: Ao Zhujun , Jing Ouyang Maggie , Olukitibi Titus Abiola , Warner Bryce , Vendramelli Robert , Truong Thang , Zhang Manli , Kung Sam , Fowke Keith R , Kobasa Darwyn , Yao Xiaojian
Published: December 2021

COVID-19 and influenza are both highly contagious respiratory diseases with a wide range of severe symptoms and cause great disease burdens globally. It has become very urgent and important to develop a bivalent vaccine that is able to target these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant VSV (rVSV) vaccine candidates. These rVSV-based vaccines co-express SARS-CoV-2 Delta variant spike protein (SP) or the receptor binding domain (RBD) and four copies of the highly conserved M2 ectodomain (M2e) of influenza A fused with the Ebola glycoprotein DC-targeting/activation domain. Animal studies have shown that immunization with these bivalent rVSV vaccines induced efficient but variable levels of humoral and cell-mediated immune responses against both SARS-CoV-2 and influenza M2e protein. Significantly, our vaccine candidates induced production of high levels of neutralizing antibodies that protected cells against SARS-CoV-2 Delta and other SP-pseudovirus infections in culture. Furthermore, vaccination with the bivalent VSV vaccine via either intramuscular or intranasal route efficiently protected mice from the lethal challenge of H1N1 and H3N2 influenza viruses and significantly reduced viral load in the lungs. These studies provide convincing evidence for the high efficacy of this bivalent vaccine to prevent influenza replication and initiate robust immune responses against SARS-CoV-2 Delta variants. Further investigation of its efficacy to protect against SARS-CoV-2 Delta variants will provide substantial evidence for new avenues to control two contagious respiratory infections, COVID-19 and influenza.
SARS-CoV-2 Spike protein activates TMEM16F-mediated platelet pro-coagulant activity
Authors: Cappelletto Ambra , Allan Harriet E. , Crescente Marilena , Schneider Edoardo , Bussani Rossana , Ali Hashim , Secco Ilaria , Vodret Simone , Simeone Roberto , Mascaretti Luca , Zacchigna Serena , Warner Timothy D. , Giacca Mauro
Published: December 2021

Background

Thrombosis of the lung micro-vasculature is a characteristic of COVID-19 disease, which is observed in large excess compared to other forms of acute respiratory distress syndrome and thus suggests a trigger for thrombosis endogenous to the lung. Our recent work has shown that the SARS-CoV-2 Spike protein activates the cellular TMEM16F chloride channel and scramblase. Through a screening on >3,000 FDA/EMA approved drugs, we identified Niclosamide and Clofazimine as the most effective molecules at inhibiting this activity. As TMEM16F plays an important role in the stimulation of the pro-coagulant activity of platelets, and considering that platelet abnormalities are common in COVID-19 patients, we investigated whether Spike directly affects platelet activation and pro-thrombotic function and tested the effect of Niclosamide and Clofazimine on these processes.

Methods

We produced SARS-CoV-2 Spike or VSV-G protein-pseudotyped virions, or generated cells expressing Spike on their plasma membrane, and tested their effects on platelet adhesion (fluorescence), aggregation (absorbance), exposure of phosphatidylserine (flow cytometry for annexin V binding), calcium flux (flow cytometry for fluo-4 AM), and clot formation and retraction. These experiments were also conducted in the presence of the TMEM16F activity inhibitors Niclosamide and Clofazimine.

Results

Here we show that exposure to SARS-CoV-2 Spike promotes platelet activation, adhesion and spreading, both when present on the envelope of virions or upon expression on the plasma membrane of cells. Spike was effective both as a sole agonist or by enhancing the effect of known platelet activators, such as collagen and collagen-related peptide. In particular, Spike exerted a noticeable effect on the procoagulant phenotype of platelets, by enhancing calcium flux, phosphatidylserine externalisation, and thrombin generation. Eventually, this resulted in a striking increase in thrombin-induced clot formation and retraction. Both Niclosamide and Clofazimine almost abolished this Spike-induced pro-coagulant response.

Conclusions

Together, these findings provide a pathogenic mechanism to explain thrombosis associated to COVID-19 lung disease, by which Spike present in SARS-CoV-2 virions or exposed on the surface of infected cells, leads to local platelet stimulation and subsequent activation of the coagulation cascade. As platelet TMEM16F is central in this process, these findings reinforce the rationale of repurposing drugs targeting this protein, such as Niclosamide, for COVID-19 therapy.
Qualifying a human Liver-Chip for predictive toxicology: Performance assessment and economic implications
Authors: Ewart Lorna , Apostolou Athanasia , Briggs Skyler A. , Carman Christopher V. , Chaff Jake T. , Heng Anthony R. , Jadalannagari Sushma , Janardhanan Jeshina , Jang Kyung-Jin , Joshipura Sannidhi R. , Kadam Mahika M. , Kanellias Marianne , Kujala Ville J. , Kulkarni Gauri , Le Christopher Y. , Lucchesi Carolina , Manatakis Dimitris V. , Maniar Kairav K. , Quinn Meaghan E. , Ravan Joseph S. , Rizos Ann Catherine , Sauld John F.K. , Sliz Josiah D. , Tien-Street William , Trinidad Dennis Ramos , Velez James , Wendell Max , Irrechukwu Onyi , Mahalingaiah Prathap Kumar , Ingber Donald E. , Scannell Jack W. , Levner Daniel
Published: December 2021

Human organ-on-a-chip (Organ-Chip) technology has the potential to disrupt preclinical drug discovery and improve success in drug development pipelines as it can recapitulate organ-level pathophysiology and clinical responses. The Innovation and Quality (IQ) consortium formed by multiple pharmaceutical and biotechnology companies to confront this challenge has published guidelines that define criteria for qualifying preclinical models, however, systematic and quantitative evaluation of the predictive value of Organ-Chips has not yet been reported. Here, 870 Liver-Chips were analyzed to determine their ability to predict drug-induced liver injury (DILI) caused by small molecules identified as benchmarks by the IQ consortium. The Liver-Chip met the qualification guidelines across a blinded set of 27 known hepatotoxic and non-toxic drugs with a sensitivity of 87% and a specificity of 100%. A computational economic value analysis suggests that with this performance the Liver-Chip could generate $3 billion annually for the pharmaceutical industry due to increased R&D productivity.
Alternation emerges as a multi-modal strategy for turbulent odor navigation
Authors: Rigolli Nicola , Reddy Gautam , Seminara Agnese , Vergassola Massimo
Published: December 2021

Foraging mammals exhibit a familiar yet poorly characterized phenomenon, “alternation”, a momentary pause to sniff in the air often preceded by the animal rearing on its hind legs or raising its head. Intriguingly, rodents executing an olfactory search task spontaneously exhibit alternation in the presence of airflow, suggesting that alternation may serve an important role during turbulent plume-tracking. To test this hypothesis, we combine fully-resolved numerical simulations of turbulent odor transport and Bellman optimization methods for decision-making under partial observability. We show that an agent trained to minimize search time in a realistic odor plume exhibits extensive alternation together with the characteristic cast-and-surge behavior commonly observed in flying insects. Alternation is tightly linked with casting and occurs more frequently when the agent is far downwind of the source, where the likelihood of detecting airborne cues is higher relative to cues close to the ground. Casting and alternation emerge as complementary tools for effective exploration when cues are sparse. We develop a model based on marginal value theory to capture the interplay between casting, surging and alternation. More generally, we show how multiple sensorimotor modalities can be fruitfully integrated during complex goal-directed behavior.
Using Deep Clustering to Improve fMRI Dynamic Functional Connectivity Analysis
Authors: Spencer Arthur P C , Goodfellow Marc
Published: December 2021

Dynamic functional connectivity (dFC) analysis of resting-state fMRI data is commonly performed by calculating sliding-window correlations (SWC), followed by k-means clustering in order to assign each window to a given state. Studies using synthetic data have shown that k-means performance is highly dependent on sliding window parameters and signal-to-noise ratio. Additionally, sources of heterogeneity between subjects may affect the accuracy of group-level clustering, thus affecting measurements of dFC state temporal properties such as dwell time and fractional occupancy. This may result in spurious conclusions regarding differences between groups (e.g. when comparing a clinical population to healthy controls). Therefore, is it important to quantify the ability of k-means to estimate dFC state temporal properties when applied to cohorts of multiple subjects, and to explore ways in which clustering performance can be maximised.

Here, we explore the use of dimensionality reduction methods prior to clustering in order to map high-dimensional data to a lower dimensional space, providing salient features to the subsequent clustering step. We assess the use of deep autoencoders for feature selection prior to applying k-means clustering to the encoded data. We compare this deep clustering method to feature selection using principle component analysis (PCA), uniform manifold approximation and projection (UMAP), as well as applying k-means to the original feature space using either L1 or L2 distance. We provide extensive quantitative evaluation of clustering performance using synthetic datasets, representing data from multiple heterogeneous subjects. In synthetic data we find that deep clustering gives the best performance, while other approaches are often insufficient to capture temporal properties of dFC states. We then demonstrate the application of each method to real-world data from human subjects and show that the choice of feature selection method has a significant effect on group-level measurements of state temporal properties. We therefore advocate for the use of deep clustering as a precursor to clustering in dFC.
Mice identify subgoal locations through an action-driven mapping process
Authors: Shamash Philip , Branco Tiago
Published: December 2021

Mammals instinctively explore and form mental maps of their spatial environments. Models of cognitive mapping in neuroscience mostly depict map-learning as a process of random or biased diffusion. In practice, however, animals explore spaces using structured, purposeful, sensory-guided actions. Here we test the hypothesis that executing specific exploratory actions is a key strategy for building a cognitive map. Previous work has shown that in arenas with obstacles and a shelter, mice spontaneously learn efficient multi-step escape routes by memorizing allocentric subgoal locations. We thus used threat-evoked escape to probe the relationship between ethological exploratory behavior and allocentric spatial memory. Using closed-loop neural manipulations to interrupt running movements during exploration, we found that blocking runs targeting an obstacle edge abolished subgoal learning. In contrast, blocking other movements while sparing edge-directed runs had no effect on memorizing subgoals. Finally, spatial analyses suggest that the decision to use a subgoal during escape takes into account the mouse’s starting position relative to the layout of the environment. We conclude that mice use an action-driven learning process to identify subgoals and that these subgoals are then integrated into a map-based planning process. We suggest a conceptual framework for spatial learning that is compatible with the successor representation from reinforcement learning and sensorimotor enactivism from cognitive science.
One of these morphs is not like the others: orange morphs exhibit different escape behavior than other morphs in a color polymorphic lizard
Authors: Brock Kinsey M. , Madden Indiana E.
Published: December 2021

Variation in color morph behavior is an important factor in the maintenance of color polymorphism. Alternative anti-predator behaviors are often associated with morphological traits such as coloration, possibly because predator-mediated viability selection favors certain combinations of anti-predator behavior and color. The Aegean wall lizard,Podarcis erhardii, is color polymorphic and populations can have up to three monochromatic morphs: orange, yellow, and white. We investigated whether escape behaviors differ among coexisting color morphs, and if morph behaviors are repeatable across different populations with the same predator species. Specifically, we assessed color morph flight initiation distance (FID), distance to the nearest refuge (DNR), and distance to chosen refuge (DR) in two populations of Aegean wall lizards from Naxos island. We also analyzed the type of refugia color morphs selected and their re-emergence behavior following a standardized intrusion event. We found that orange morphs have different escape behaviors from white and yellow morphs, and these differences are consistent in both of the populations we sampled. Orange morphs have shorter FIDs, DNRs, and DRs, select different refuge types, and re-emerge less often after an intruder event compared to white and yellow morphs. Observed differences in color morph escape behaviors support the idea that morphs have evolved alternative behavioral strategies that may play a role in population-level morph maintenance and loss.
Neural mechanism of experience-dependent sensory gain control in C. elegans
Authors: Ikejiri Yosuke , Tanimoto Yuki , Fujita Kosuke , Hiramatsu Fumie , Yamazaki Shuhei J. , Endo Yuto , Iwatani Yasushi , Fujimoto Koichi , Kimura Koutarou D.
Published: December 2021

Animals’ sensory systems adjust their responsiveness to environmental stimuli that vary greatly in their intensity. Here we report the neural mechanism of experience-dependent sensory adjustment, especially gain control, in the ASH nociceptive neurons in Caenorhabditis elegans. Using calcium imaging under gradual changes in stimulus intensity, we find that the ASH neurons of naive animals respond to concentration increases in a repulsive odor 2-nonanone regardless of the magnitude of the concentration increase. However, after preexposure to the odor, the ASH neurons exhibit significantly weak responses to a small gradual increase in odor concentration while their responses to a large gradual increase remain strong. Thus, preexposure changes the slope of stimulus–response relationships (i.e., gain control). Behavioral analysis suggests that this gain control contributes to the preexposure-dependent enhancement of odor avoidance behavior. Mathematical analysis reveals that the ASH response consists of fast and slow components, and that the fast component is specifically suppressed by preexposure. In addition, genetic analysis suggests that G protein signaling is required for the fast component. Thus, our integrative study demonstrates how prior experience dynamically modulates stimulus–response relationships in sensory neurons, eventually leading to adaptive modulation of behavior.
Potential and action mechanism of favipiravir as an antiviral against Junin virus
Authors: Zadeh Vahid Rajabali , Urata Shuzo , Afowowe Tosin Oladipo , Yasuda Jiro
Published: December 2021

Favipiravir is a nucleoside analogue that inhibits the replication and transcription of a broad spectrum of RNA viruses, including pathogenic arenaviruses. In this study, we isolated a favipiravir-resistant mutant of Junin virus (JUNV), which is the causative agent of Argentine hemorrhagic fever, and analyzed the antiviral mechanism of favipiravir against JUNV. Two amino acid substitutions, N462D in the RNA-dependent RNA polymerase (RdRp) and A168T in the glycoprotein precursor GPC, were identified in the mutant. GPC-A168T substitution enhanced the efficiency of JUNV internalization, which explains the robust replication kinetics of the mutant in the virus growth analysis. Although RdRp-N462D substitution did not affect polymerase activity levels in a minigenome system, comparisons of RdRp error frequencies showed that the virus with RdRp-D462 possessed a significantly higher fidelity. We also provided experimental evidence for the first time that favipiravir inhibited JUNV through the accumulation of transition mutations, confirming its role as a purine analogue against arenaviruses. Moreover, we showed that treatment with a combination of favipiravir and either ribavirin or remdesivir inhibited JUNV replication in a synergistic manner, blocking the generation of the drug-resistant mutant. Our findings provide new insights for the clinical management and treatment of Argentine hemorrhagic fever.
The homolog of human ecto-nucleoside triphosphate diphosphohydrolase MIG-23 is involved in sperm migration by modulating extracellular ATP levels in Ascaris suum
Authors: Wang Qiushi , He Ruijun , Chen Lianwan , Zhang Qi , Shan Jin , Zhao Yanmei , Wang Xia
Published: December 2021

In nematodes, spermiogenesis, which is also called sperm activation, is a process in which nonmotile spermatids are transformed into crawling spermatozoa, which is accompanied by a series of morphological, physiological and biochemical changes. Sperm motility acquisition during this process is essential for successful fertilization. However, the mechanisms of sperm motility regulation in nematodes remain to be clarified. Herein, we found that extracellular adenosine-5’-triphosphate (ATP) level mediation by MIG-23, which is a homolog of human ecto-nucleoside triphosphate diphosphohydrolase (E-NTPDase), was required for major sperm protein (MSP) filament dynamics and sperm motility in the nematode Ascaris suum. MIG-23 was localized on the sperm plasma membrane. During sperm activation, mitochondrial activity was increased dramatically, and a large amount of ATP was produced and stored in refringent granules (RGs). In addition, a portion of the produced ATP was released to the extracellular space through ATP channels, which were composed of innexins and localized on the sperm plasma membrane. Spermatozoa, instead of spermatids, hydrolyzed exogenous ATP and processed ecto-ATPase activity. MIG-23 contributed to the ecto-ATPase activity of spermatozoa. Once MIG-23 activity was interrupted, spermatozoa also decreased their ATP hydrolysis activity. Blocking MIG-23 activity resulted in an increase in the depolymerization rate of MSP filaments in pseudopodia, which eventually affected nematode sperm migration. Overall, our data imply that MIG-23, which contributes to the ecto-ATPase activity of spermatozoa, regulates sperm migration by modulating extracellular ATP levels.

Highlights

ATP is released to extracellular space through innexin channels which are identified in worm sperm.

Worm spematozoa show ecto-ATPase activity.

MIG-23 contributes to the ecto-ATPase activity of spermatozoa and regulates extracellular ATP level.

MIG-23 is required for MSP-based filament dynamics and sperm migration.
Artificial intelligence to solve the X-ray crystallography phase problem: a case study report
Authors: Barbarin-Bocahu Irène , Graille Marc
Published: December 2021

The determination of three dimensional structures of macromolecules is one of the actual challenge in biology with the ultimate objective of understanding their function. So far, X-ray crystallography is the most popular method to solve structure, but this technique relies on the generation of diffracting crystals. Once a correct data set has been obtained, the calculation of electron density maps requires to solve the so-called «phase problem » using different approaches. The most frequently used technique is molecular replacement, which relies on the availability of the structure of a protein sharing strong structural similarity with the studied protein. Its success rate is directly correlated with the quality of the models used for the molecular replacement trials. The availability of models as accurate as possible is then definitely critical.

Very recently, a breakthrough step has been made in the field of protein structure prediction thanks to the use of machine learning approaches as implemented in the AlphaFold or RoseTTAFold structure prediction programs. Here, we describe how these recent improvements helped us to solve the crystal structure of a protein involved in the nonsense-mediated mRNA decay pathway (NMD), an mRNA quality control pathway dedicated to the elimination of eukaryotic mRNAs harboring premature stop codons.
Arl15 upregulates the TGFβ family signaling by promoting the assembly of the Smad-complex
Authors: Shi Meng , Tie Hieng Chiong , Mahajan Divyanshu , Sun Xiuping , Zhou Yan , Boh Boon Kim , Vardy Leah A. , Lu Lei
Published: December 2021

The hallmark event of the canonical transforming growth factor β (TGFβ) family signaling is the assembly of the Smad-complex, consisting of the common Smad, Smad4, and phosphorylated receptor-regulated Smads. How the Smad-complex is assembled and regulated is still unclear. Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome. The binding relieves the autoinhibition of Smad4, which is imposed by the intramolecular interaction between its MH1 and MH2 domains. Activated Smad4 subsequently interacts with phosphorylated receptor-regulated Smads, forming the Smad-complex. Our observations suggest that Smad4 functions as an effector and a GTPase activating protein (GAP) of Arl15. Assembly of the Smad-complex enhances the GAP activity of Smad4 toward Arl15, therefore dissociating Arl15 before the nuclear translocation of the Smad-complex. Our data further demonstrate that Arl15 positively regulates the TGFβ family signaling.
Manganese modulates metabolic activity and redox homeostasis in translationally-blockedLactococcus cremoris, impacting metabolic persistence, cell-culturability, and flavor formation
Authors: Nugroho Avis Dwi Wahyu , van Olst Berdien , Bachtiar Stephanie Agnes , Boeren Sjef , Kleerebezem Michiel , Bachmann Herwig
Published: December 2021

Manganese (Mn) is an essential trace element that is supplemented in microbial media with varying benefits across species and growth conditions. We found that growth ofLactococcus cremoriswas unaffected by manganese omission from the growth medium. The main proteome adaptation to manganese omission involved increased manganese transporter production (up to 2000-fold), while the remaining 10 significant proteome changes were between 1.4 and 4 fold. Further investigation in translationally-blocked (TB), non-growing cells showed that Mn supplementation (20 μM) led to approximately 1.5X faster acidification compared to Mn-free conditions. However, this faster acidification stagnated within 24 hours, likely due to draining of intracellular NADH that coincides with substantial loss of culturability. Conversely, without manganese, non-growing cells persisted to acidify for weeks, albeit at a reduced rate, but maintaining redox balance and culturability. Strikingly, despite being unculturable, α-keto acid-derived aldehydes continued to accumulate in cells incubated in the presence of manganese, whereas without manganese cells predominantly formed the corresponding alcohols. This is most likely reflecting NADH availability for the alcohol dehydrogenase-catalyzed conversion. Overall, manganese influences the lactococcal acidification rate, and flavor formation capacity in a redox dependent manner. These are important industrial traits especially during cheese ripening, where cells are in a non-growing, often unculturable state.
The effect of anti-SARS-CoV-2 monoclonal antibody, bamlanivimab, on endogenous immune response to COVID-19 vaccination
Authors: Benschop Robert J. , Tuttle Jay L. , Zhang Lin , Poorbaugh Josh , Kallewaard Nicole L. , Vaillancourt Peter , Crisp Melissa , Vy Trinh Thi Ngoc , Freitas Joshua J. , Beasley Stephanie , Daniels Montanea , Haustrup Natalie , Higgs Richard E. , Nirula Ajay , Cohen Myron S. , Marovich Mary
Published: December 2021

As the COVID-19 pandemic evolves, and vaccine rollout progresses, the availability and demand for monoclonal antibodies for the prevention and treatment of SARS-CoV-2 infection are also accelerating. This longitudinal serological study evaluated the magnitude and potency of the endogenous antibody response to COVID-19 vaccination in participants who first received a COVID-19 monoclonal antibody in a prevention study. Over the course of six months, serum samples were collected from the prevention population (nursing home residents and staff) enrolled in the BLAZE-2 clinical trial who had received either bamlanivimab (4200 mg) or placebo. In an unplanned component of this trial, a subset of these participants was subsequently fully vaccinated with two doses of either SpikeVax (Moderna) or Comirnaty (BioNTech/Pfizer) COVID-19 mRNA vaccines, as part of the US vaccination program. This post-hoc analysis assessed the immune response to vaccination for the subset of participants (N=135) without prior SARS-CoV-2 infection. Antibody titers and potency were assessed using three assays against SARS-CoV-2 proteins that bamlanivimab does not significantly bind to, thereby reflecting the endogenous antibody response. All bamlanivimab and placebo participants mounted a robust immune response to full COVID-19 vaccination, irrespective of age, risk-category and vaccine type, with any observed differences unlikely to be clinically meaningful. These findings are pertinent for informing public health policy with results that suggest a complementary role for COVID-19 monoclonal antibodies (mAbs) with COVID-19 vaccines and that the benefit of receiving COVID-19 vaccination at the earliest opportunity outweighs the minimal effect on the endogenous immune response due to prior prophylactic COVID-19 mAb infusion.

One Sentence Summary

Individuals infused with an anti-SARS-CoV-2 antibody demonstrated a robust immune response to subsequent full COVID-19 vaccination.
Heterogenous Cellular and Humoral Immune Trajectories after SARS-CoV-2 Infection: Compensatory Responses in a Population-Based Cohort
Authors: Menges Dominik , Zens Kyra D. , Ballouz Tala , Caduff Nicole , Llanas-Cornejo Daniel , Aschmann Hélène E. , Domenghino Anja , Pellaton Céline , Perreau Matthieu , Fenwick Craig , Pantaleo Giuseppe , Kahlert Christian R. , Münz Christian , Puhan Milo A. , Fehr Jan S.
Published: December 2021

To better understand the development of immunity against SARS-CoV-2 over time, we evaluated humoral and cellular responses a population-based cohort of SARS-CoV-2-infected individuals covering the full spectrum of COVID-19 up to 217 days after diagnosis. We characterized anti-Spike (S)-IgA and -IgG antibody responses in 431 individuals and found that about 85% develop and maintain anti-S-IgG responses over time. In a subsample of 64 participants selected for a detailed characterization of immune responses, we additionally evaluated anti-Nucleocapsid (N)-IgG antibodies and T cell responses specific to viral Membrane (M), N, and S proteins. Most participants had detectable T cell responses to at least one of the four peptide pools analyzed, which were more frequent than antibody seropositivity. We found a moderate correlation between antibody and T cell responses, which declined over time and suggests important variability in response patterns between individuals. The heterogeneity of immune trajectories was further analyzed using cluster analyses taking into account joint antibody and T cell responses over time. We identified five distinct immune trajectory patterns, which were characterized by specific antibody, T cell and T cell subset patterns along with disease severity and demographic factors. Higher age, male sex, higher disease severity and being a non-smoker was significantly associated with stronger immune responses. Overall, the results highlight that there is a consistent and maintained antibody response among most SARS-CoV-2-infected individuals, while T cell responses appear to be more heterogenous but potentially compensatory among those with low antibody responses.

One Sentence Summary

Presence of heterogenous immune response trajectories after SARS-CoV-2 infection with potential compensatory role of T cells among individuals with low antibody responses.
Antibody-mediated Immunogenicity against SARS-CoV-2 following priming, boosting and hybrid immunity: insights from 11 months of follow-up of a healthcare worker cohort in Israel, December 2020-October 2021
Authors: Edelstein Michael , Beiruti Karine Wiegler , Ben-Amram Hila , Bar-Zeev Naor , Sussan Christian , Asulin Hani , Strauss David , Bathish Younes , Zarka Salman , Jabal Kamal Abu
Published: December 2021

Background

We determined circulating anti-S SARS-CoV-2 IgG antibody titres in a vaccinated healthcare workers (HCWs) cohort from Northern Israel in the 11 months following primary vaccination according to age, ethnicity, boosting timing and previous infection status.

Methods

All consenting HCWs were invited to have their circulating IgG levels measured before vaccination and at 6 subsequent timepoints. All HCWs with suspected COVID-19 were PCR tested. We described trends in circulating IgG geometric mean concentration by age, ethnicity, timing of boosting and previous infection status and compared strata using Kruskall-Wallis tests.

Results

Among 985 vaccinated HCWs. IgG titres gradually decreased in all groups over the study duration. Younger or previously infected individuals had higher initial IgG levels (p<0.001 in both cases); differences substantially decreased or disappeared at 7-9 months, before boosting. Pre-infection IgG levels in infected participants were similar to levels measured at the same timepoint in HCWs who remained uninfected (p>0.3). IgG GMC in those boosted 6-7 months after dose 2 was lower compared with those boosted 8-9 months after (1999-vs 2736, p=0.02).

Conclusions

Immunity waned 6 months post-priming in all age groups and in previously infected individuals, reversed by boosting. IgG titres decrease among previously infected individuals and the proportion of reinfected individuals in this group, comparable to the proportion of breakthrough infection in previously uninfected individuals suggests individuals with hybrid immunity (infection+vaccination) may also require further doses. Our study also highlights the difficulty in determining protective IgG levels and the need to clarify the optimal timing in 3 dose regimens