Biology subjects

Hao, L.

Publications and source records attributed to Hao, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Proteasome regulation of petite-negativity in fission yeast

Mitochondria carry out essential functions in eukaryotic cells. The mitochondrial genome encodes factors critical to support oxidative phosphorylation and mitochondrial protein import necessary for these functions. However, organisms like budding yeast can readily lose their mitochondrial genome, yielding respiration-deficient petite mutants. The fission yeast Schizosaccharomyces pombe is petite-negative, but some nuclear mutations enable the loss of its mitochondrial genome. Here, we characterize the classical petite-positive mutation ptp1-1 as a loss of function allele of the proteasome 19S regulatory subunit component mts4/rpn1, involved in the Ubiquitin-dependent degradation pathway. The mutation results in an altered oxidative stress response, with increased levels of oxidized glutathione, and increased levels of mitochondrial and cytoplasmic chaperones. We propose that Ubiquitin-proteasome regulation of chaperones involved in the Unfolded Protein Response and mitochondrial protein import underlies petite-negativity in fission yeast.

genetics↗

bioRxiv2024

Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis

Mass spectrometry (MS) analysis is often challenged by contaminations from detergents, salts, and polymers that compromise the data quality and can damage the chromatography and mass spectrometry instruments. However, researchers may not discover contamination issues until after data acquisition. There is no existing contaminant assay that is sensitive enough to detect trace amounts of contaminants from a few microliters of samples prior to MS analysis. To address this crucial need in the field, we developed a sensitive, rapid, and low-cost contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in MS sample preparation workflow. Only one microliter of sample was used prior to MS injection to quantify contaminants by ContamSPOT colorimetric or fluorometric assay on a thin layer chromatography (TLC) plate. We also optimized contaminant removal methods to salvage samples with minimal loss when ContamSPOT showed a positive result. ContamSPOT was then successfully applied to evaluate commonly used bottom- up proteomic methods, regarding the effectiveness of removing detergents, peptide recovery, and reproducibility. We expect ContamSPOT to be widely adopted by MS laboratories as a last-step quality checkpoint prior to MS injection. ContamSPOT can also provide a unique readout of sample cleanness for developing and evaluating MS-based sample preparation methods. We provided a practical decision tree and a step-by-step protocol with a troubleshooting guide to facilitate the use of ContamSPOT by other researchers. Table of Contents (TOC) graphic(All images used in the TOC graphic are original, in compliance with copyright guidelines.) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/574392v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@7b6f0aorg.highwire.dtl.DTLVardef@1b6fcd9org.highwire.dtl.DTLVardef@9213a5org.highwire.dtl.DTLVardef@47b7fb_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

Orphan nuclear receptor NR2E3 and its small-molecule agonist induce cancer cell apoptosis through regulating p53, IFNα and MYC pathways

Orphan nuclear receptor NR2E3 activates p53 and induces cancer cell apoptosis. Further studies on p53-dependent and -independent functions of wild-type and mutated NR2E3 are needed. Herein, we showed that NR2E3 enhanced p53-DNA interactions in diverse cancer cells and up-regulated p53 and IFN pathways while down-regulating MYC pathway in cervical cancer cells. Studies of "All of Us" and TCGA databases showed NR2E3 nonsynonymous mutations associating with four cancers. We stratified NR2E3 SNVs for their cancer implications with the p53 reporter. A cancer-associated NR2E3R97Hmutation not only lost the wild-types tumor-suppressing functions but also prohibited the wild-type from enhancing p53 acetylation. These observations implicated the potential for pharmaceutically activating NR2E3 to suppress cancer. Indeed, NR2E3s small-molecule agonist 11a repressed 2-D and 3-D cultures of primary cells and cell lines of cervical cancer, in which screening FDA-approved anti-cancer drugs identified HDAC-1/2 inhibitor Romidepsin operating synergistically with 11a. The underlying molecular mechanisms included 11as down-regulating the transcription of Multidrug Resistance Protein ABCB1 that Romidepsin up-regulated. Transcriptomics studies revealed three synergy modes: (1) "sum-up" mode that the p53 pathway activated individually by 11a and Romidepsin got stronger by the combo; (2) "antagonism" mode that Romidepsin counteracted the activation of the Kras pathway by 11a; and (3) "de novo" mode that the combo instead of each individual drug repressed the MYC pathway. Conclusively, our experiments provide new data supporting tumor-suppressor like functions for wild-type NR2E3, reveal roles of mutated NR2E3 in cancer, and address values of NR2E3s agonist 11a in cancer therapy alone and combined.

cancer biology↗

bioRxiv2023

SntB triggers the antioxidant pathways to regulate development and aflatoxin biosynthesis in Aspergillus flavus

The epigenetic reader SntB was identified as an important transcriptional regulator of growth, development, and secondary metabolite synthesis in Aspergillus flavus. However, the underlying molecular mechanism is still unclear. In this study, sntB gene deletion ({Delta}sntB), complementary (Com-sntB), and HA tag fused to sntB (sntB-HA) strains were constructed by using the homologous recombination method, respectively. Our results revealed that deletion of sntB inhibited the processes of mycelia growth, conidial production, sclerotia formation, aflatoxin synthesis, and ability to colonize host, and the defective phenotype of knockout strain {Delta}sntB could be restored in its complementary strain Com-sntB. Chromatin immunoprecipitation sequencing (ChIP-seq) of sntB-HA and WT, and RNA sequencing (RNA-seq) of {Delta}sntB and WT strains revealed that SntB played key roles in oxidative stress response of A. flavus. The function of catC gene (encode a catalase) was further analyzed based on the integration results of ChIP-seq and RNA-seq. In {Delta}sntB strain, the relative expression level of catC was significantly higher than in WT strain, while a secretory lipase encoding gene (G4B84_008359) was down-regulated. Under the stress of oxidant menadione sodium bisulfite (MSB), the deletion of sntB obvious down-regulated the expression level of catC. After deletion of catC gene, the mycelia growth, conidial production, and sclerotia formation were inhibited, while ROS level and aflatoxin production were increased compared to the WT strain. Results also showed that the inhibition rate of MSB to {Delta}catC strain was significantly lower than that of WT group and AFB1 yield of the {Delta}catC strain was significantly decreased than that of WT strain under the stress of MSB. Our study revealed the potential machinery that SntB regulated fungal morphogenesis, mycotoxin anabolism, and fungal virulence through the axle of from SntB to fungal virulence and mycotoxin bio-synthesis, i.e. H3K36me3 modification-SntB-Peroxisomes-Lipid hydrolysis-fungal virulence and mycotoxin bio-synthesis. The results of this study shed light into the SntB mediated transcript regulation pathways of fungal mycotoxin anabolism and virulence, which provided potential strategy for control the contamination of A. flavus and its aflatoxins.

pharmacology and toxicology↗

bioRxiv2023

Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato

Lyme disease (LD), caused by spirochete bacteria of the genus Borrelia burgdorferi sensu lato, remains the most common vector-borne disease in the northern hemisphere. Borrelia outer surface protein A (OspA) is an integral surface protein expressed during the tick cycle, and a validated vaccine target. There are at least 20 recognized Borrelia genospecies, that vary in OspA serotype. Traditional serotyping of Borrelia isolates using OspA-specific monoclonal antibodies is technically challenging and reagent-constrained. This study presents a new in silico sequence-based method for OspA typing using next-generation sequence data. Using a compiled database of over 400 Borrelia genomes encompassing all major genospecies, we characterized OspA diversity in a manner that can accommodate existing and new OspA types and then defined boundaries for classification and assignment of OspA types based on the sequence similarity. To accommodate potential novel OspA types, we have developed a new nomenclature: OspA in silico type (IST). Beyond the ISTs which corresponded to existing OspA serotypes (ST1-8), we identified nine additional ISTs which cover new OspA variants in B. bavariensis (IST9-10), B. garinii (IST11-12), and other Borrelia genospecies (IST13-17). Compared to traditional OspA serotyping methods, this new computational pipeline provides a more comprehensive and broadly applicable approach for characterization of OspA type and Borrelia genospecies to support vaccine development. Impact StatementAs the incidence of LD continues to rise, so does the need to maintain genomic surveillance of disease-causing Borrelia spp. and support clinical development of new vaccines. Towards this goal, introducing the OspA in silico type (IST) nomenclature scheme, as well as the open-source release of this OspA analysis pipeline, will enable characterization of novel Borrelia OspA types using NGS data without the need for traditional, antibody-based serotyping systems.

genomics↗

bioRxiv2023

E. coli RecBCD Nuclease Domain Regulates Helicase Activity but not Single Stranded DNA Translocase Activity

Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as a consequence of mechanically pulling the DNA duplex across a wedge domain in the helicase by the single stranded (ss)DNA translocase activity of the ATPase motors, biochemical data indicate that processive DNA unwinding by the E. coli RecBCD helicase can occur in the absence of ssDNA translocation of the canonical RecB and RecD motors. Here, we present evidence that dsDNA unwinding is not a simple consequence of ssDNA translocation by the RecBCD motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecB{Delta}NucCD) unwinds dsDNA at significantly slower rates than RecBCD, while the rate of ssDNA translocation is unaffected. This effect is primarily due to the absence of the nuclease domain and not the absence of the nuclease activity, since a nuclease-dead mutant (RecBD1080ACD), which retains the nuclease domain, showed no significant change in rates of ssDNA translocation or dsDNA unwinding relative to RecBCD on short DNA substrates ([≤] 60 base pairs). This indicates that ssDNA translocation is not rate-limiting for DNA unwinding. RecB{Delta}NucCD also initiates unwinding much slower than RecBCD from a blunt-ended DNA, although it binds with higher affinity than RecBCD. RecB{Delta}NucCD also unwinds DNA [~]two-fold slower than RecBCD on long DNA ([~]20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecBD1080ACD unwinding are intermediate between RecBCD and RecB{Delta}NucCD. Surprisingly, significant pauses occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, rather than DNA translocation, possibly allosterically. Since the rate of DNA unwinding by RecBCD also slows after it recognizes a chi sequence, RecB{Delta}NucCD may mimic a post-chi state of RecBCD.

biophysics↗

bioRxiv2023

Inhalable point-of-care urinary diagnostic platform

The late-stage detection of lung cancer leads to a high global mortality rate. Although low-dose computed tomography screening improves lung cancer survival in at-risk groups, this test still suffers from high rates of false positive results. In addition, inequality remains in the diagnosis of lung cancer as access to medical imaging infrastructure is limited. Here, we designed a needleless and imaging-free platform, termed PATROL (point-of-care aerosolizable nanosensors with tumor-responsive oligonucleotide barcodes), to increase detection accuracy, to reduce resource disparities for early detection of lung cancer, and to enable timely interception. PATROL formulates a set of DNA-barcoded, activity-based nanosensors (ABNs) into inhalable formats that can be delivered using clinical nebulizers or inhalers. Lung cancer-associated proteases in the tumor microenvironment selectively cleave the ABNs, releasing synthetic DNA reporters that are eventually excreted via the urine. The barcoded nanosensor signatures present in urine samples are quantified within 20 minutes using a multiplexable paper-based lateral flow assay at room temperature. PATROL detects early-stage tumors in an autochthonous lung adenocarcinoma mouse model with high sensitivity and specificity. Tailoring the library of ABNs may enable the modular PATROL platform to not only lower the resource thresholds required for early detection of lung cancer, but also enable rapid detection of chronic pulmonary disorders and infections.

bioengineering↗

bioRxiv2023

Tumor microenvironment exploration and therapeutic target identification in bladder cancer based on Cuproptosis signature and chemotherapy-resistant model: results from bioinformatics and experimental validation

BackgroundThe discovery of cuproptosis provides a new way to make full use of the pathophysiological effects of copper for anticancer therapy and could help identify a therapeutic target in bladder cancer. MethodsIn this study, 411 BLCA tumor samples from the Cancer Genome Atlas (TCGA) cohort were obtained. Differentially expressed genes (DEGs) between chemotherapy-sensitive and chemotherapy-resistant mouse bladder cancers were also obtained. Sixteen genes were defined as cuproptosis-related genes (CRGs), and the cutoff score was calculated based on LASSO Cox regression. CCK-8 and Transwell assays were used to detect the migration and proliferation of 5637 and T24 cells, respectively. Liarozole dihydrochloride (L-D), a mild P450, inhibits the expression of CYP26B1. Multiple immunohistochemistry analyses were used to explore the association between the immune microenvironment and CRGs. ResultsA higher Cuproptosis score was significantly associated with worse overall survival in BLCA (p<0.0001, HR=2.32). Single-cell transcriptional data were used to assess the function of CYP26B1 and CYP26B1 may be negatively associated with DNA damage and repair. In vitro experiments indicated that overexpression of CYP26B1 enhanced the migration and proliferation of BLCA cells, while L-D inhibited the migration and proliferation of BLCA cells. A higher expression level of Dihydrolipoamide S-Succinyltransferase (DLST) serves could as a risk factor in patients treated with atezolizumab and higher expression of DLST suggest an immunosuppressive microenvironment. ConclusionsCYP26B1 may be a therapeutic target for bladder cancer, and the higher expression of DLST may suggest an immunosuppressive microenvironment in BLCA. Key MessagesCuproptosis may be associated with the chemotherapy-resistance of bladder cancer and our findings may provide new ideas for the treatment of bladder cancer.

genomics↗

bioRxiv2023

FLONE: fully Lorentz network embedding for inferring novel drug targets

MotivationTo predict novel drug targets, graph-based machine learning methods have been widely used to capture the relationships between drug, target, and disease entities in heterogeneous biological networks. However, most of the existing methods cannot explicitly consider disease types when predicting targets. More importantly, drug-disease-target (DDT) networks could exhibit multi-relational hierarchical sub-structures with the information of biological interactive functions, but these methods, especially those based on Euclidean space embedding cannot fully utilize such topology information, which might lead to sub-optimal prediction results. We hypothesized that, by properly importing hyperbolic space embedding specifically for modeling hierarchical DDT networks, graph-based machine learning algorithms could better capture the relationships between aforementioned entities, which ultimately improves the target prediction performance. ResultsTo test our hypothesis, we formulated the drug target prediction problem as a knowledge graph triple completion task explicitly considering disease types. To solve this problem, we proposed FLONE, a novel hyperbolic Lorentz space embedding-based method to capture the hierarchical structural information in the DDT network when inferring drug targets. We evaluated it on two different DDT networks, our experimental results showed that by introducing Lorentz space, one of the isomorphic models of hyperbolic space, FLONE generates more accurate candidate target predictions given the drug and disease than the Euclidean translation-based counterparts, which supports our hypothesis. Beyond these experiments, we also devised the hyperbolic encoders to fuse drug and target similarity information into FLONE, to make it capable to handle triples corresponding to previously unseen drugs and targets for more challenging prediction scenarios. Availability and implementationSource code and dataset information are at: https://github.com/arantir123/DDT_triple_prediction. Contacts.he@cs.bham.ac.uk

bioinformatics↗

bioRxiv2023

Multi-modal Proteomic Characterization of Lysosomal Function and Proteostasis in Progranulin-Deficient Neurons

Progranulin (PGRN) is a lysosomal protein implicated in various neurodegenerative diseases. Over 70 mutations discovered in the GRN gene all result in reduced expression of PGRN protein. However, the detailed molecular function of PGRN within lysosomes and the impact of PGRN deficiency on lysosomal biology remain unclear. Here we leveraged multifaceted proteomic techniques to comprehensively characterize how PGRN deficiency changes the molecular and functional landscape of neuronal lysosomes. Using lysosome proximity labeling and immuno-purification of intact lysosomes, we characterized lysosome compositions and interactomes in both human induced pluripotent stem cell (iPSC)-derived glutamatergic neurons (i3Neurons) and mouse brains. Using dynamic stable isotope labeling by amino acids in cell culture (dSILAC) proteomics, we measured global protein half-lives in i3Neurons for the first time and characterized the impact of progranulin deficiency on neuronal proteostasis. Together, this study indicated that PGRN loss impairs the lysosomes degradative capacity with increased levels of v-ATPase subunits on the lysosome membrane, increased catabolic enzymes within the lysosome, elevated lysosomal pH, and pronounced alterations in neuron protein turnover. Collectively, these results suggested PGRN as a critical regulator of lysosomal pH and degradative capacity, which in turn influences global proteostasis in neurons. The multi-modal techniques developed here also provided useful data resources and tools to study the highly dynamic lysosome biology in neurons.

neuroscience↗

bioRxiv2022

PfaSTer: A ML-powered serotype caller for Streptococcus pneumoniae genomes

Streptococcus pneumoniae (pneumococcus) is a leading cause of morbidity and mortality worldwide. Although multi-valent pneumococcal vaccines have curbed the incidence of disease, their introduction has resulted in shifted serotype distributions that must be monitored. Whole genome sequence (WGS) data provides a powerful surveillance tool for tracking isolate serotypes, which can be determined from nucleotide sequence of the capsular polysaccharide biosynthetic operon (cps). Although software exists to predict serotypes from WGS data, their use is constrained by the requirement of high-coverage Next Generation Sequencing (NGS) reads. This can present a challenge in so far as accessibility and data sharing. Here we present PfaSTer, a method to identify 65 prevalent serotypes from individual S. pneumoniae genome sequences rather than primary NGS data. PfaSTer combines dimensionality reduction from k-mer analysis with machine learning, allowing for rapid serotype prediction without the need for coverage-based assessments. We then demonstrate the robustness of this method, returning >97% concordance when compared to biochemical results and other in-silico serotypers. PfaSTer is open source and available at: https://github.com/pfizer-opensource/pfaster.

bioinformatics↗

bioRxiv2022

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

Current methods for evaluating the accuracy of germline variant calls are restricted to easy-to-detect high-confidence regions, thus ignoring a substantial portion of difficult variants beyond the benchmark regions. We established four DNA reference materials from immortalized cell lines derived from a Chinese Quartet including parents and monozygotic twins. We integrated benchmark calls of 4.2 million small variants and 15,000 structural variants from multiple platforms and bioinformatic pipelines for evaluating the reliability of germline variant calls inside the benchmark regions. The genetic built-in-truth of the Quartet family design not only improved sensitivity of benchmark calls by removing additional false positive variants with apparently high quality, but also enabled estimation of the precision of variants calls outside the benchmark regions. Batch effects of variant calling in large-scale DNA sequencing efforts can be effectively identified with the concurrent use of the Quartet DNA reference materials along with study samples, and can be alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Matched RNA and protein reference materials were also established in the Quartet project, thereby enabling benchmark calls constructed from DNA reference materials for evaluation of variants calling performance on RNA and protein data. The Quartet DNA reference materials from this study are a resource for objective and comprehensive assessment of the accuracy of germline variant calls throughout the whole-genome regions.

bioinformatics↗

bioRxiv2022

Growth mindset promotes children's working memory performance through cortico-striatal interaction and fronto-parietal activation

Growth mindset--the belief that abilities are malleable through effort--drives motivation, action and achievement. Yet, the underlying mechanisms remain elusive, necessitating a unified framework that integrates cognitive, neural, and developmental processes. Leveraging longitudinal neuroimaging and computational modeling to reveal moment-to-moment decision responses and brain state dynamics during working memory (WM), we show that growth mindset enhances WM development from middle childhood to adolescence via nuanced cortico-striatal network dynamics that balance between brain state flexibility and stability. Behaviorally, children with higher growth mindset exhibited better WM performance both cross-sectionally and longitudinally, attributed to faster evidence accumulation during moment-to-moment information updating, especially under high task demands. Neurally, a higher growth mindset was associated with greater activation of the dorsal striatum, cingulo-opercular (action-mode), and fronto-parietal networks during WM, which further accounted for longitudinal WM improvement and latent evidence accumulation. Such cortico-striatal activation covaried with neurochemical mediators critical for motivation and executive functioning. Analyzing non-stationary network dynamics revealed that growth mindset optimized dynamical organization of cortico-striatal networks, with an activated state highly flexible to support moment-to-moment information updating and a deactivated state remaining stable across blocks to suppress irrelevant information. This suggests a balanced allocation of resources for accumulating evidence while suppressing noise during WM. Together, our findings support a neurocognitive framework in which growth mindset enhances WM development via nuanced orchestration of cortico-striatal networks to enable efficient dynamic computations and foster far-reaching cognitive development.

neuroscience↗

bioRxiv2022

Efficacy of Parainfluenza Virus 5 (PIV5)-vectored Intranasal COVID-19 Vaccine as a Single Dose Vaccine and as a Booster against SARS-CoV-2 Variants

Immunization with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines has greatly reduced coronavirus disease 2019 (COVID-19)-related deaths and hospitalizations, but waning immunity and the emergence of variants capable of immune escape indicate the need for novel SARS-CoV-2 vaccines. An intranasal parainfluenza virus 5 (PIV5)-vectored COVID-19 vaccine CVXGA1 has been proven efficacious in animal models and blocks contact transmission of SARS-CoV-2 in ferrets. CVXGA1 vaccine is currently in human clinical trials in the United States. This work investigates the immunogenicity and efficacy of CVXGA1 and other PIV5-vectored vaccines expressing additional antigen SARS-CoV-2 nucleoprotein (N) or SARS-CoV-2 variant spike (S) proteins of beta, delta, gamma, and omicron variants against homologous and heterologous challenges in hamsters. A single intranasal dose of CVXGA1 induces neutralizing antibodies against SARS-CoV-2 WA1 (ancestral), delta variant, and omicron variant and protects against both homologous and heterologous virus challenges. Compared to mRNA COVID-19 vaccine, neutralizing antibody titers induced by CVXGA1 were well-maintained over time. When administered as a boost following two doses of a mRNA COVID-19 vaccine, PIV5-vectored vaccines expressing the S protein from WA1 (CVXGA1), delta, or omicron variants generate higher levels of cross-reactive neutralizing antibodies compared to three doses of a mRNA vaccine. In addition to the S protein, the N protein provides added protection as assessed by the highest body weight gain post-challenge infection. Our data indicates that PIV5-vectored COVID-19 vaccines, such as CVXGA1, can serve as booster vaccines against emerging variants. ImportanceWith emerging new variants of concern (VOC), SARS-CoV 2 continues to be a major threat to human health. Approved COVID-19 vaccines have been less effective against these emerging VOCs. This work demonstrates the protective efficacy, and strong boosting effect, of a new intranasal viral-vectored vaccine against SARS-CoV-2 variants in hamsters.

microbiology↗

bioRxiv2022

How do Protein Contaminants Influence DDA and DIA Proteomics

Mass spectrometry-based proteomics is constantly challenged by the presence of contaminant background signals. In particular, protein contaminants from reagents and sample handling are often abundant and almost impossible to avoid. For data-dependent acquisition (DDA) proteomics, exclusion list can be used to reduce the influence of protein contaminants. However, protein contamination has not been evaluated and is rarely addressed in data-independent acquisition (DIA). How protein contaminants influence proteomics data is also unclear. In this study, we established protein contaminant FASTA and spectral libraries that are applicable to all proteomic workflows and evaluated the impact of protein contaminants on both DDA and DIA proteomics. We demonstrated that including our contaminant libraries can reduce false discoveries and increase protein identifications, without influencing the quantification accuracy in various proteomic software platforms. With the pressing need to standardize proteomic workflow in the research community, we highly recommend including our contaminant FASTA and spectral libraries in all bottom-up proteomics workflow. Our contaminant libraries and a step-by-step tutorial to incorporate these libraries in different DDA and DIA data analysis platforms can be valuable resources for proteomics researchers, which are freely accessible at https://github.com/HaoGroup-ProtContLib.

systems biology↗

bioRxiv2022

Medial prefrontal-hippocampal concordance in child-parent dyads underlies children's psychological wellbeing

Family emotional climate is fundamental to childs emotional wellbeing and mental health. Negative family emotional climate may lead to heightened psychopathological symptoms via dysfunctional child-parent interactions. Single-brain paradigms have uncovered changes in brain systems and networks related to negative family environments, but how neurobiological reciprocity between child and parent brains is associated with childrens psychopathological symptoms remains unknown. In study1, we investigated the relationship between family emotional climate and childrens psychopathological symptoms in 395 child-parent dyads. In study2, using a naturalistic movie-watching functional magnetic imaging technique in a subsample of 100 children and parents, we investigate the neurobiological underpinnings of how family emotional climate is associated with childrens psychopathological symptoms through child-parent neural synchrony. Children from negative family emotional climate experienced more severe psychopathological symptoms. We revealed significantly higher inter-subject correlations in the dorsal and ventral portions of the medial prefrontal cortex (mPFC), and greater concordance of activity with widespread brain regions critical for socioemotional skills in child-parent than child-stranger dyads. Critically, negative family emotional climate was associated with decreased inter-subject functional correlation between the ventral mPFC and the hippocampus in child-parent dyads, which further accounted for higher childrens internalizing symptoms especially for anxious and depressed aspects. Family emotional climate might transmit into the brain of parent-child dyads, which may associate with child development outcomes. The present study identified that child-parent vmPFC-hippocampal circuitry is linked to childrens psychopathological symptoms. Our findings suggest a neurobiological mechanism of how negative family emotional climate affects childrens psychopathological symptoms through altered child-parent neural synchrony.

neuroscience↗

bioRxiv2022

Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid

SARS-CoV-2 continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (Mpro). Nirmatrelvir is a potent Mpro inhibitor and the antiviral component of Paxlovid. The significant viral sequencing effort during the ongoing COVID-19 pandemic represented a unique opportunity to assess potential nirmatrelvir escape mutations from emerging variants of SARS-CoV-2. To establish the baseline mutational landscape of Mpro prior to the introduction of Mpro inhibitors, Mpro sequences and its cleavage junction regions were retrieved from [~]4,892,000 high-quality SARS-CoV-2 genomes in GISAID. Any mutations identified from comparison to the reference sequence (Wuhan-hu-1) were cataloged and analyzed. Mutations at sites key to nirmatrelvir binding and protease functionality (e.g., dimerization sites) were still rare. Structural comparison of Mpro also showed conservation of key nirmatrelvir contact residues across the extended Coronaviridae family (alpha-, beta-, and gamma-coronaviruses). Additionally, we showed that over time the SARS-CoV-2 Mpro enzyme remained under purifying selection and was highly conserved relative to the spike protein. Now, with the EUA approval of Paxlovid and its expected widespread use across the globe, it is essential to continue large-scale genomic surveillance of SARS-CoV-2 Mpro evolution. This study establishes a robust analysis framework for monitoring emergent mutations in millions of virus isolates, with the goal of identifying potential resistance to present and future SARS-CoV-2 antivirals. ImportanceThe recent authorization of oral SARS-CoV-2 antivirals, such as Paxlovid, has ushered in a new era of the COVID-19 pandemic. Emergence of new variants, as well as selective pressure imposed by antiviral drugs themselves, raise concern for potential escape mutations in key drug binding motifs. To determine the potential emergence of antiviral resistance in globally circulating isolates and its implications for the clinical response to the COVID-19 pandemic, sequencing of SARS-CoV-2 viral isolates before, during, and after the introduction of new antiviral treatments is critical. The infrastructure built herein for active genetic surveillance of Mpro evolution and emergent mutations will play an important role in assessing potential antiviral resistance as the pandemic progresses and Mpro inhibitors are introduced. We anticipate our framework to be the starting point in a larger effort for global monitoring of the SARS-CoV-2 Mpro mutational landscape.

genomics↗

bioRxiv2022

Replicating RNA platform enables rapid response to the SARS-CoV-2 Omicron variant and elicits enhanced protection in naïve hamsters compared to ancestral vaccine

In late 2021, the SARS-CoV-2 Omicron (B.1.1.529) variant of concern (VoC) was reported with many mutations in the viral spike protein that were predicted to enhance transmissibility and allow viral escape of neutralizing antibodies. Within weeks of the first report of B.1.1.529, this VoC has rapidly spread throughout the world, replacing previously circulating strains of SARS-CoV-2 and leading to a resurgence in COVID-19 cases even in populations with high levels of vaccine- and infection-induced immunity. Initial studies have shown that B.1.1.529 is less sensitive to protective antibody conferred by previous infections and vaccines developed against earlier lineages of SARS-CoV-2. The ability of B.1.1.529 to spread even among vaccinated populations has led to a global public health demand for updated vaccines that can confer protection against B.1.1.529. We report here the rapid development of a replicating RNA vaccine expressing the B.1.1.529 spike and show that this B.1.1.529-targeted vaccine is immunogenic in mice and hamsters. Interestingly, we found that mice previously immunized with A.1-specific vaccines failed to elevate neutralizing antibody titers against B.1.1.529 following B.1.1.529-targeted boosting, suggesting pre-existing immunity may impact the efficacy of B.1.1.529-targeted boosters. Furthermore, we found that our B.1.1.529-targeted vaccine provides superior protection compared to the ancestral A.1-targeted vaccine in hamsters challenged with the B.1.1.529 VoC after a single dose of each vaccine. One Sentence SummaryRapidly developed RNA vaccine protects against SARS-CoV-2 Omicron variant

microbiology↗