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At least 235 records · Page 13

Culturing astrocytes on substrates that mimic brain tumors promotes enhanced mechanical forces

Highlights: • Human astrocytes increase traction forces of cells applied to the ECM in response to increased substrate stiffness. • Astrocytes apply intercellular stresses with noticeable increase in higher substrate stiffness. • Cell velocity decreases in human astrocytes in brain tumor like environment compared to normal brain environment. • Astrocytes mechanical strength and function could be potentially enhanced by increased stiffness of the microenvironment. Astrocytes are essential to brain homeostasis and their dysfunction can have devastating consequences on human quality of life. Such deleterious effects are generally due in part to changes that occur at the cellular level, which may be biochemical or biomechanical in nature. One biomechanical change that can occur is a change in tissue stiffness. Brain tumors are generally associated with increased brain tissue stiffness, but the impact increased tissue stiffness has on astrocyte biomechanical behavior is poorly understood. Therefore, in this study we cultured human astrocytes on flexible substrates with stiffness that mimicked the healthy human brain (1 kPa), meningioma (4 kPa), and glioma (11 kPa) and investigated astrocyte biomechanical behavior by measuring cell-substrate tractions, strain energies, cell-cell intercellular stresses, and cellular velocities. In general, tractions, intercellular stresses, and strain energy was observed to increase as a function of increased substrate stiffness, while cell velocities were observed to decrease with increased substrate stiffness. We believe this study will be of great importance to the fields of brain pathology and brain physiology.

60 APPLIED LIFE SCIENCES↗

A Pentavalent HIV-1 Subtype C Vaccine Containing Computationally Selected gp120 Strains Improves the Breadth of V1V2 Region Responses

Background: HIV-1 envelope (Env) variable loops 1 and 2 (V1V2) directed non-neutralizing antibodies were a correlate of decreased transmission risk in the RV144 vaccine trial. Thus, the elicitation and breadth of antibody responses against the V1V2 of HIV-1 Env are important considerations for HIV-1 vaccine candidates. The V1V2 region’s highly variable nature and the extensive diversity of subtype C HIV-1 Envelopes (Envs) make the V1V2 response breadth a high priority for HIV-1 vaccine regimens aiming for V1V2-mediated protection in Southern Africa. Here, we determined whether the breadth of the anti-V1V2 vaccine response can be broadened by including HIV-1 Env strains computationally designed to enhance the coverage of subtype C V1V2 sequence diversity. Methods: Three subtype C Env strains were selected to maximize antibody binding coverage while complementing subtype C vaccine gp120s that were given in human clinical trials in South Africa, as well as to improve epitope accessibility. Humoral immunogenicity of a novel trivalent gp120 vaccine immunogen, a bivalent gp120 boost already in clinical trials (1086C and TV1), and a pentavalent (all five gp120s combined) were evaluated in a preclinical immunization study in guinea pigs. The pentavalent combination was further evaluated with alum versus glucopyranosyl lipid adjuvants formulated in squalene-in-water emulsion (GLA-SE) adjuvants in non-human primates. The breadth of the anti-V1V2 response was assessed using an array of cross-subtype variable loops 1&2 (V1V2) scaffold proteins and linear V2 peptides. Results: The breadth of the IgG response against V1V2 antigens of the trivalent and pentavalent groups was comparable, and both were greater than the breadth of the bivalent group. Linear epitope mapping showed that two linear epitopes in V2 were targeted by the vaccinated animals: the V2 hotspot focused at 169K that potentially correlated with decreased HIV-1 risk in RV144 and the V2.2 site (179LDV/I181) that is part of the integrin α4β7 binding site. The bivalent vaccine elicited a significantly higher magnitude of binding to the V2 hotspot compared to the trivalent vaccine whereas the trivalent vaccine elicited significantly higher binding to the V2.2 epitope compared to the bivalent vaccine, while the pentavalent recognized both regions. Conclusions: These results demonstrate that the three new computationally selected subtype C Envs successfully complemented 1086C and TV1 for broader V1V2 antibody responses, and, in concert with adjuvants that stimulate V1V2 responses, can be considered as part of a rationale immunogen design to improve V1V2 IgG coverage in future vaccine trials in South Africa.

Immunology↗

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.

Trifan, Anda↗

Structural and functional analysis of the human cone‐rod homeobox transcription factor

Abstract The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.

59 BASIC BIOLOGICAL SCIENCES↗

The HHV-6B U20 glycoprotein binds ULBP1, masking it from recognition by NKG2D and interfering with natural killer cell activation

Human Herpesvirus 6B (HHV-6B) impedes host immune responses by downregulating class I MHC molecules (MHC-I), hindering antigen presentation to CD8+ T cells. Downregulation of MHC-I disengages inhibitory receptors on natural killer (NK) cells, resulting in activation and killing of the target cell if NK cell activating receptors such as NKG2D have engaged stress ligands upregulated on the target cells. Previous work has shown that HHV-6B downregulates three MHC-like stress ligands MICB, ULBP1, and ULBP3, which are recognized by NKG2D. The U20 glycoprotein of the related virus HHV-6A has been implicated in the downregulation of ULBP1, but the precise mechanism remains undetermined. We set out to investigate the role of HHV-6B U20 in modulating NK cell activity. We used HHV-6B U20 expressed as a recombinant protein or transduced into target cells, as well as HHV-6B infection, to investigate binding interactions with NK cell ligands and receptors and to assess effects on NK cell activation. Small-angle X-ray scattering was used to align molecular models derived from machine-learning approaches. We demonstrate that U20 binds directly to ULBP1 with sub-micromolar affinity. Transduction of U20 decreases NKG2D binding to ULBP1 at the cell surface but does not decrease ULBP1 protein levels, either at the cell surface or in toto. HHV-6B infection and soluble U20 have the same effect. Transduction of U20 blocks NK cell activation in response to cell-surface ULBP1. Structural modeling of the U20 – ULBP1 complex indicates some similarities to the m152-RAE1γ complex.

60 APPLIED LIFE SCIENCES↗

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Additionally, based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 -3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.

59 BASIC BIOLOGICAL SCIENCES↗

Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens

Chimeric antigen receptor (CAR) T cells have emerged as a promising class of therapeutic agents, generating remarkable responses in the clinic for a subset of human cancers. One major challenge precluding the wider implementation of CAR therapy is the paucity of tumor-specific antigens. Here, we describe the development of a CAR targeting the tumor-specific isocitrate dehydrogenase 2 (IDH2) with R140Q mutation presented on the cell surface in complex with a common human leukocyte antigen allele, HLA-B*07:02. Engineering of the hinge domain of the CAR, as well as crystal structure-guided optimization of the IDH2 R140Q- HLA-B*07:02-targeting moiety, enhances the sensitivity and specificity of CARs to enable targeting of this HLA-restricted neoantigen. This approach thus holds promise for the development and optimization of immunotherapies specific to other cancer driver mutations that are difficult to target by conventional means.

99 GENERAL AND MISCELLANEOUS↗

Treatment of antibiotic-manufacturing wastewater enriches for Aeromonas veronii, a zoonotic antibiotic-resistant emerging pathogen

Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, quantitative polymerase chain reaction, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment units in a full-scale antibiotic-manufacturing wastewater treatment plant processing wastewater from a β-lactam manufacturing facility. Both bacterial communities and antibiotic resistance gene compositions varied across the treatment units, but were associated. Certain antibiotic resistance gene persisted through treatment, either carried by identical bacterial species, or linked to mobile genetic elements in different species. Despite the satisfactory performance in chemical removal, this plant continuously enriched zoonotic antibiotic-resistant Aeromonas veronii (an emerging pathogen responsible for substantial economic losses in aquaculture and human health) from influent to effluent, probably due to prolonged β-lactam selection pressure and aquatic nature of A. veronii. This enrichment resulted in a significantly higher abundance of A. veronii than other aquatic samples worldwide. Furthermore, the closest evolutionary relative to the retrieved A. veronii was an isolate obtained from the stool of a local diarrhea patient. These findings highlighted a substantial public health risk posed by antibiotic-manufacturing wastewater treatment, underlining its potential role in enriching and disseminating zoonotic antibiotic-resistant pathogens. Beyond chemical monitoring, enhanced surveillance of antibiotic-resistant pathogens and antibiotic resistance genes is needed in effluent discharge standard for antibiotic-manufacturing wastewater treatment plants.

Wang, Xingshuo↗

Assessment of Electric Grid Transmission System Simulator for Human Factors Research

Over the past decades, various technologies have been developed for electric grid operations to support clean energy, meet rising electricity demands, and address infrastructure concerns. However, the human factors aspect is often overlooked during rapid integration. Questions persist about how these technologies impact human performance. Simulators play a critical role in supporting investigation of human factors design concepts and conducting comprehensive usability testing to evaluate human performance and assess human reliability. This paper aims to address human factors research simulator requirements and conduct a comparative study of six different simulators. A detailed evaluation reveals that the evaluated simulators lack the ability to customize user interfaces. Additionally, their user interface designs do not fulfill the basic human factors design principles, potentially leading to increased response variability and reduced statistical power when conducting controlled experimental research. In the future, it is essential to develop scripting tools to integrate customizable user interfaces and simulation models, ensuring meeting research requirements.

Li, Ruixuan↗

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes

Characterizing the gut microbiota in terms of their capacity to interfere with drug metabolism is necessary to achieve drug efficacy and safety. Although examples of drug-microbiome interactions are well-documented, little has been reported about a computational pipeline for systematically identifying and characterizing bacterial enzymes that process particular classes of drugs. The goal of our study is to develop a computational approach that compiles drugs whose metabolism may be influenced by a particular class of microbial enzymes and that quantifies the variability in the collective level of those enzymes among individuals. The present paper describes this approach, with microbial β-glucuronidases as an example, which break down drug-glucuronide conjugates and reactivate the drugs or their metabolites. We identified 100 medications that may be metabolized by β-glucuronidases from the gut microbiome. These medications included morphine, estrogen, ibuprofen, midazolam, and their structural analogues. The analysis of metagenomic data available through the Sequence Read Archive (SRA) showed that the level of β-glucuronidase in the gut metagenomes was higher in males than in females, which provides a potential explanation for the sex-based differences in efficacy and toxicity for several drugs, reported in previous studies. Our analysis also showed that infant gut metagenomes at birth and 12 months of age have higher levels of β-glucuronidase than the metagenomes of their mothers and the implication of this observed variability was discussed in the context of breastfeeding as well as infant hyperbilirubinemia. Overall, despite important limitations discussed in this paper, our analysis provided useful insights on the role of the human gut metagenome in the variability in drug response among individuals. Importantly, this approach exploits drug and metagenome data available in public databases as well as open-source cheminformatics and bioinformatics tools to predict drug-metagenome interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury

Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe atypical pneumonia in infected individuals, but the underlying mechanisms of pathogenesis remain unknown. While much has been learned from the few reported autopsy cases, an in-depth understanding of the cells targeted by MERS-CoV in the human lung and their relative contribution to disease outcomes is needed.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluating Automated Face Identity-Masking Methods with Human Perception and a Deep Convolutional Neural Network

Face de-identification (or “masking”) algorithms have been developed in response to the prevalent use of video recordings in public places. Here, we evaluated the success of face identity masking for human perceivers and a deep convolutional neural network (DCNN). Eight de-identification algorithms were applied to videos of drivers’ faces, while they actively operated a motor vehicle. These masks were pre-selected to be applicable to low-quality video and to maintain coarse information about facial actions. Humans studied high-resolution images to learn driver identities and were tested on their recognition of active drivers in low-resolution videos. Faces in the videos were either unmasked or were masked by one of the eight algorithms. When participants were tested immediately after learning (Experiment 1), all masks reduced identification, with six of eight masks reducing identification to extremely poor performance. In a second experiment, two of the most effective masks were tested after a delay of 7 or 28 days. The delay did not further reduce identification of the masked faces. In all masked conditions, participants maintained stringent decision criteria, with low confidence in recognition, further indicating the effectiveness of the masks. Next, the DCNN performed an identity-matching task between high-resolution images and masked videos—a task analogous to that done by humans. The pattern of accuracy for the DCNN mirrored some, but not all, aspects of human performance, highlighting the need to test the effectiveness of identity masking for both humans and machines. The DCNN was also tested on its ability to match identity between masked and unmasked versions of the same video, based only on the face. DCNN performance for the eight masks offers insight into the nature of the information in faces that is coded in these networks.

97 MATHEMATICS AND COMPUTING↗

Polymersomes Decorated with the SARS-CoV-2 Spike Protein Receptor-Binding Domain Elicit Robust Humoral and Cellular Immunity

The COVID-19 pandemic underscores the need for rapid, safe, and effective vaccines. In contrast to some traditional vaccines, nanoparticle-based subunit vaccines are particularly efficient in trafficking antigens to lymph nodes, where they induce potent immune cell activation. Here, we developed a strategy to decorate the surface of oxidation-sensitive polymersomes with multiple copies of the SARS-CoV-2 spike protein receptor-binding domain (RBD) to mimic the physical form of a virus particle. We evaluated the vaccination efficacy of these surface-decorated polymersomes (RBD surf ) in mice compared to RBD-encapsulated polymersomes (RBD encap ) and unformulated RBD (RBD free ), using monophosphoryl-lipid-A-encapsulated polymersomes (MPLA PS) as an adjuvant. While all three groups produced high titers of RBD-specific IgG, only RBD surf elicited a neutralizing antibody response to SARS-CoV-2 comparable to that of human convalescent plasma. Moreover, RBD surf was the only group to significantly increase the proportion of RBD-specific germinal center B cells in the vaccination-site draining lymph nodes. Both RBD surf and RBD encap drove similarly robust CD4 + and CD8 + T cell responses that produced multiple Th1-type cytokines. We conclude that a multivalent surface display of spike RBD on polymersomes promotes a potent neutralizing antibody response to SARS-CoV-2, while both antigen formulations promote robust T cell immunity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity via activation of the aryl hydrocarbon receptor (AHR) pathway. While the interaction between PAHs and the AHR is well-established, understanding which AHR-regulated transcriptional effects directly result in observable phenotypes and which are adaptive or benign is important to better understand PAH toxicity. Retene is a frequently detected PAH in environmental sampling and has been associated with AHR2-dependent developmental toxicity in zebrafish, though its mechanism of toxicity has not been fully elucidated. To interrogate transcriptional changes causally associated with retene toxicity, we conducted whole-animal RNA sequencing at 48 hours post-fertilization after exposure to eight retene concentrations. The concentrations were selected to produce effects ranging from no phenotype to mortality and malformations in 100% of animals at 5 days post-fertilization. We identified a concentration-response relationship between retene teratogenicity and differential gene expression in both number of DEGs and magnitude of expression change. Elevated expression of cyp1a at retene concentrations below the threshold for teratogenicity suggested that while cyp1a expression is a sensitive biomarker of AHR activation, it may be too sensitive to serve as a biomarker of AHR-dependent teratogenicity. Genes differentially expressed at only non-teratogenic concentrations were enriched for transforming growth factor-ß (TGF-ß) signaling pathway disruption while DEGs identified at only teratogenic concentrations were significantly enriched for response to xenobiotic stimulus and reduction-oxidation reaction activity. DEGs which spanned both non-teratogenic and teratogenic concentrations showed similar disrupted biological processes to those unique to teratogenic concentrations, indicating these processes were disrupted at low exposure concentrations. Gene co-expression network analysis identified several gene modules, including those associated with PAHs and AHR2 activation. One, Module 7, was strongly enriched for AHR2-associated genes and contained the strongest responses to retene. Benchmark concentration (BMC) of Module 7 genes identified a median BMC of 7.5 µM, nearly the highest retene concentration with no associated teratogenicity, supporting the hypothesis that Module 7 genes are largely responsible for retene toxicity.

Toxin, Zebrafish, Retene, Transcriptomics, network↗

Mathematical model of a personalized neoantigen cancer vaccine and the human immune system

Cancer vaccines are an important component of the cancer immunotherapy toolkit enhancing immune response to malignant cells by activating CD4 + and CD8 + T cells. Multiple successful clinical applications of cancer vaccines have shown good safety and efficacy. Despite the notable progress, significant challenges remain in obtaining consistent immune responses across heterogeneous patient populations, as well as various cancers. We present a mechanistic mathematical model describing key interactions of a personalized neoantigen cancer vaccine with an individual patient’s immune system. Specifically, the model considers the vaccine concentration of tumor-specific antigen peptides and adjuvant, the patient’s major histocompatibility complexes I and II copy numbers, tumor size, T cells, and antigen presenting cells. We parametrized the model using patient-specific data from a clinical study in which individualized cancer vaccines were used to treat six melanoma patients. Model simulations predicted both immune responses, represented by T cell counts, to the vaccine as well as clinical outcome (determined as change of tumor size). This model, although complex, can be used to describe, simulate, and predict the behavior of the human immune system to a personalized cancer vaccine.

60 APPLIED LIFE SCIENCES↗

Revealing functional insights into ER proteostasis through proteomics and interactomics

The endoplasmic reticulum (ER), responsible for processing approximately one-third of the human proteome including most secreted and membrane proteins, plays a pivotal role in protein homeostasis (proteostasis). Dysregulation of ER proteostasis has been implicated in a number of disease states. As such, continued efforts are directed at elucidating mechanisms of ER protein quality control which are mediated by transient and dynamic protein-protein interactions with molecular chaperones, co-chaperones, protein folding and trafficking factors that take place in and around the ER. Technological advances in mass spectrometry have played a pivotal role in characterizing and understanding these protein-protein interactions that dictate protein quality control mechanisms. Here, we highlight the recent progress from mass spectrometry-based investigation of ER protein quality control in revealing the topological arrangement of the proteostasis network, stress response mechanisms that adjust the ER proteostasis capacity, and disease specific changes in proteostasis network engagement. We close by providing a brief outlook on underexplored areas of ER proteostasis where mass spectrometry is a tool uniquely primed to further expand our understanding of the regulation and coordination of protein quality control processes in diverse diseases.

60 APPLIED LIFE SCIENCES↗

Fast Climate Responses to Aerosol Emission Reductions During the COVID-19 Pandemic

The reduced human activities and associated decreases in aerosol emissions during the COVID-19 pandemic are expected to affect climate. Assuming emission changes during lockdown, back-to-work and post-lockdown stages of COVID-19, climate model simulations show a surface warming over continental regions of the Northern Hemisphere. In January–March, there was an anomalous warming of 0.05–0.15 K in eastern China, and the surface temperature increase was 0.04–0.07 K in Europe, eastern United States, and South Asia in March–May. The longer the emission reductions undergo, the warmer the climate would become. The emission reductions explain the observed temperature increases of 10–40% over eastern China relative to 2019. A southward shift of the ITCZ is also seen in the simulations. This study provides an insight into the impact of COVID-19 pandemic on global and regional climate and implications for immediate actions to mitigate fast global warming.

54 ENVIRONMENTAL SCIENCES↗

Omics-Lethal Human Viruses, West Nile Experiment WLN003

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt) virus infection. Sample data was obtained from mouse popliteal draining lymph nodes for proteomics, metabolomics, and lipidomics expression analysis. See Experiment WLN002 for corresponding transcriptome analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics, metabolomics, and lipidomics dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗