Biology subjects

Zhong, G.

Publications and source records attributed to Zhong, G..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Chlamydia plasmid-encoded protein Pgp2 is a replication initiator with a unique beta-hairpin necessary for iteron-binding and plasmid replication

The virulence plasmid of the obligate intracellular bacterium Chlamydia encodes eight proteins. Among these, Pgp3 is crucial for pathogenicity, and Pgp4 functions as a transcriptional regulator of both plasmid and chromosomal genes. The remaining proteins, Pgp1, Pgp5, Pgp6, Pgp7, and Pgp8, are predicted to play various roles in plasmid replication or maintenance based on their amino acid sequences. However, the function of Pgp2 remains unknown, even though it is required for transformation. In this study, we utilized AlphaFold to predict the 3-dimensional (3-D) structure of C. trachomatis Pgp2. Despite a lack of apparent sequence homology, the AlphaFold structure exhibited high similarity to experimentally determined structures of several plasmid replication initiators. Notably, Pgp2 features a unique {beta}-hairpin motif near the DNA-binding domain, absent in other plasmid replication initiators with overall 3-D structures similar to Pgp2. This {beta}-hairpin motif was also present in AlphaFold models of Pgp2s across all 13 Chlamydia species. To assess its significance, we engineered a plasmid lacking the 11 amino acids constituting the {beta}-hairpin motif in C. trachomatis Pgp2. Although this deletion did not alter the overall structure of Pgp2, the mutated plasmid failed to transform plasmid-free C. trachomatis. These findings reveal that Pgp2 is a plasmid replication initiator, with the {beta}-hairpin motif playing a critical role in binding to its cognate iteron sequences in the replication origin of the chlamydial plasmid.

microbiology↗

bioRxiv2024

FtsK Initiates the Assembly of a Unique Divisome Complex in the FtsZ-less Chlamydia trachomatis

Chlamydia trachomatis serovar L2 (Ct), an obligate intracellular bacterium that does not encode FtsZ, divides by a polarized budding process. In the absence of FtsZ, we show that FtsK, a chromosomal translocase, is critical for divisome assembly in Ct. Chlamydial FtsK forms discrete foci at the septum and at the base of the progenitor mother cell, and our data indicate that FtsK foci at the base of the mother cell mark the location of nascent divisome complexes that form at the site where a daughter cell will emerge in the next round of division. The divisome in Ct has a hybrid composition, containing elements of the divisome and elongasome from other bacteria, and FtsK is recruited to nascent divisomes prior to the other chlamydial divisome proteins assayed, including the PBP2 and PBP3 transpeptidases, and MreB and MreC. Knocking down FtsK prevents divisome assembly in Ct and inhibits cell division and septal peptidoglycan synthesis. We further show that MreB does not function like FtsZ and serve as a scaffold for the assembly of the Ct divisome. Rather, MreB is one of the last proteins recruited to the chlamydial divisome, and it is necessary for the formation of septal peptidoglycan rings. Our studies illustrate the critical role of chlamydial FtsK in coordinating divisome assembly and peptidoglycan synthesis in this obligate intracellular bacterial pathogen.

microbiology↗

bioRxiv2024

A wheat tandem kinase sensor activates an NLR helper to trigger immunity

Most plant resistance genes encode membrane-anchored receptor-like proteins or intracellular nucleotide-binding and leucine-rich repeat (NLR) receptors. In wheat and barley, tandem kinases (TKs) have emerged as a new class of resistance determinants. To understand the modus operandi of the wheat stem rust resistance protein Sr62TK, we identified two genetic interactors-- a host gene required for Sr62TK function and the corresponding fungal AvrSr62 effector. We discovered that the SR62 locus consists of a digenic module encoding Sr62TK and an NLR (Sr62NLR). AvrSr62 binds to the N-terminal kinase of Sr62TK. This triggers displacement of the C-terminal kinase allowing it to recruit Sr62NLR for activation of immune responses. Understanding the mechanism of this two-component resistance complex will help engineering and breeding for durable resistance.

plant biology↗

bioRxiv2024

Analyzing RNA-Seq Data from Chlamydia with Super Broad Transcriptomic Activation: Challenges, Solutions, and Implications for Other Systems

MotivationRNA sequencing (RNA-Seq) offers profound insights into the complex transcriptomes of diverse biological systems. However, standard differential expression analysis pipelines based on DESeq2 and edgeR encounter challenges when applied to the immediate early transcriptomes of Chlamydia spp., obligate intracellular bacteria. These challenges arise from their reliance on assumptions that do not hold in scenarios characterized by extensive transcriptomic activation and limited repression. Standard analyses using unique chlamydial RNA-Seq reads alone identify nearly 300 upregulated and about 300 downregulated genes, significantly deviating from actual RNA-Seq read trends. ResultsBy incorporating both chlamydial and host reads or adjusting for total sequencing depth, the revised normalization methods each detected over 700 upregulated genes and 30 or fewer downregulated genes, closely aligned with observed RNA-Seq data. Further validation through qRT-PCR analysis confirmed the effectiveness of these adjusted approaches in capturing the true extent of transcriptomic activation during the immediate early phase of chlamydial infection. While the strategies employed are developed in the context of Chlamydia, the principles of flexible and context-aware normalization may inform adjustments in other systems with unbalanced gene expression dynamics, such as bacterial spore germination. Availability and implementationThe code for reproducing the presented bioinformatic analysis is available at https://zenodo.org/records/11201379.

bioinformatics↗

bioRxiv2024

Hepatitis E virus infection upregulates ING5 expression in vitro and vivo

Hepatitis E virus (HEV) is the major pathogen of viral hepatitis. Immunocompromised individual infected by HEV is prone to chronic hepatitis and increases the risk of hepato-cellular carcinoma (HCC). Inhibitor of growth family member 5 (ING5) is a tumor suppressor gene, is low expressed in cancer tumor or cells. However, the underlying relationship between ING5 and HEV infection is unclear. In the present study acute and chronic HEV animal models were employed to explore the interaction between ING5 and HEV. Notably, the expression of ING5 was significantly increased both in the liver of acute HEV infected BALB/c mice and chronic HEV infected rhesus macaques. In addition, the relationship between HEV infection and ING5 expression was further identified in human hepatoma (HepG-2) cells. In conclusion, HEV infection strongly upregulated ING5 expression in vivo and in vitro, bearing significant implications in further understanding the pathogenic mechanism of HEV infection.

microbiology↗

bioRxiv2024

Stimulation Effects Mapping for Standardizing Coil Placement in Transcranial Magnetic Stimulation

BackgroundThe position and orientation of transcranial magnetic stimulation (TMS) coil, which we collectively refer to as coil placement, significantly affect both the assessment and modulation of cortical excitability. TMS electric field (E-field) simulation can be used to identify optimal coil placement. However, the present E-field simulation required a laborious segmentation and meshing procedure to determine optimal coil placement. ObjectiveWe intended to create a framework that would enable us to offer optimal coil placement without requiring the segmentation and meshing procedure. MethodsWe constructed the stimulation effects map (SEM) framework using the CASIA dataset for optimal coil placement. We used leave-one-subject-out cross-validation to evaluate the consistency of the optimal coil placement and the target regions determined by SEM for the 74 target ROIs in MRI data from the CASIA, HCP15 and HCP100 datasets. Additionally, we contrasted the E-norms determined by optimal coil placements using SEM and auxiliary dipole method (ADM) based on the DP and CASIA II datasets. ResultsWe provided optimal coil placement in head-anatomy-based (HAC) polar coordinates and MNI coordinates for the target region. The results also demonstrated the consistency of the SEM framework for the 74 target ROIs. The normal E-field determined by SEM was more significant than the value received by ADM. ConclusionWe created the SEM framework using the CASIA database to determine optimal coil placement without segmentation or meshing. We provided optimal coil placement in HAC and MNI coordinates for the target region. The validation of several target ROIs from various datasets demonstrated the consistency of the SEM approach. By streamlining the process of finding optimal coil placement, we intended to make TMS assessment and therapy more convenient.

bioengineering↗

bioRxiv2024

PreMode predicts mode of action of missense variants by deep graph representation learning of protein sequence and structural context

Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenicity classification, but the functional impact of missense variants is multi-dimensional. Pathogenic missense variants in the same gene may act through different modes of action (i.e., gain/loss-of-function) by affecting different aspects of protein function. They may result in distinct clinical conditions that require different treatments. We developed a new method, PreMode, to perform gene-specific mode-of-action predictions. PreMode models effects of coding sequence variants using SE(3)-equivariant graph neural networks on protein sequences and structures. Using the largest-to-date set of missense variants with known modes of action, we showed that PreMode reached state-of-the-art performance in multiple types of mode-of-action predictions by efficient transfer-learning. Additionally, PreModes prediction of G/LoF variants in a kinase is consistent with inactive-active conformation transition energy changes. Finally, we show that PreMode enables efficient study design of deep mutational scans and optimization in protein engineering.

bioinformatics↗

bioRxiv2024

Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48

N6-methyladenosine (m6A), the most abundant internal modification on eukaryotic mRNA, and N6, 2'-O-dimethyladenosine (m6Am), are epitranscriptomic marks that function in multiple aspects of posttranscriptional regulation. Fat mass and obesity-associated protein (FTO) can remove both m6A and m6Am; however, little is known about how FTO achieves its substrate selectivity. Here, we demonstrate that ZBTB48, a C2H2-zinc finger protein that functions in telomere maintenance, associates with FTO and binds both mRNA and the telomere-associated regulatory RNA TERRA to regulate the functional interactions of FTO with target transcripts. Specifically, depletion of ZBTB48 affects targeting of FTO to sites of m6A/m6Am modification, changes cellular m6A/m6Am levels and, consequently, alters decay rates of target RNAs. ZBTB48 ablation also accelerates growth of HCT-116 colorectal cancer cells and modulates FTO- dependent regulation of Metastasis-associated protein 1 (MTA1) transcripts by controlling the binding to MTA1 mRNA of the m6A reader IGF2BP2. Our findings thus uncover a previously unknown mechanism of posttranscriptional regulation in which ZBTB48 co-ordinates RNA- binding of the m6A/m6Am demethylase FTO to control expression of its target RNAs.

molecular biology↗

bioRxiv2023

IL-23 receptor signaling licenses group 3-like innate lymphoid cells to restrict a live-attenuated oral Chlamydia vaccine in the gut

An IFN{gamma}-susceptible mutant of Chlamydia muridarum is attenuated in pathogenicity in the genital tract and recently licensed as an intracellular Oral vaccine vector or intrOv. Oral delivery of intrOv induces transmucosal protection in the genital tract but intrOv itself is cleared from the gut (without shedding any infectious particles externally) by IFN{gamma} from group 3-like innate lymphoid cells (ILC3s). We further characterized the intrOv interactions with ILC3s in the current study since the interactions may impact both the safety and efficacy of intrOv as an oral Chlamydia vaccine. Intracolonic inoculation with intrOv induced IFN{gamma} that in return inhibited intrOv. The intrOv-IFN{gamma} interactions were dependent on ROR{gamma}t, a signature transcriptional factor of ILC3s. Consistently, transfer of oral intrOv-induced ILC3s from ROR{gamma}t-GFP reporter mice to IFN{gamma}-deficient mice rescued the inhibition of intrOv. Thus, IFN{gamma} produced by intrOv-induced ILC3s is likely responsible for inhibiting intrOv, which is further supported by the observation that oral intrOv did induce significant levels of IFN{gamma}-producing LC3s (IFN{gamma}+ILC3s). Interestingly, IL-23 receptor knockout (IL-23R-/-) mice no longer inhibited intrOv, which was accompanied with reduced colonic IFN{gamma}. Transfer of oral intrOv-induced ILC3s rescued the IL-23R-/- mice to inhibit intrOv, validating the dependence of ILC3s on IL-23R signaling for inhibiting intrOv. Clearly, intrOv induces intestinal IFN{gamma}+ILC3s for its own inhibition in the gut, which is facilitated by IL-23R signaling. These findings have provided a mechanism for ensuring the safety of intrOv as an oral Chlamydia vaccine and a platform for investigating how oral intrOv induces transmucosal protection in the genital tract. SignificanceDespite the extensive efforts, no subunit vaccine is available for protecting humans against C. trachomatis infection and pathogenicity. Recent studies have led to a licensed live-attenuated oral vaccine (intrOv) that is both effective in inducing transmucosal protection in the genital tract and safe due to its susceptibility to IFN{gamma} delivered by ILC3s. Characterization of the intrOv interactions with IFN{gamma}-producing ILC3s in the current study has revealed a critical role of IL-23 receptor signaling in facilitating ILC3s to clear intrOv from the gut, which has provided a mechanism for ensuring the safety of intrOv and laid a foundation for further revealing the mechanisms by which oral intrOv induces transmucosal immunity in the genital tract since ILC3s can also function as antigen presenting cells.

immunology↗

bioRxiv2023

Preclinical screen for protection efficacy of chlamydial antigens that are immunogenic in humans

To search for subunit vaccine candidates, immunogenic chlamydial antigens identified in humans were evaluated for protection against both infection and pathology in a mouse genital tract infection model under three different immunization regimens. The intramuscular immunization regimen was first used to evaluate 106 chlamydial antigens, which revealed that two antigens significantly reduced while 11 increased genital chlamydial burden. The two infection-reducing antigens failed to prevent pathology and 23 additional antigens even exacerbated pathology. Thus, intranasal mucosal immunization was tested next since intranasal inoculation with live C. muridarum prevented both genital infection and pathology. Two of 29 chlamydial antigens evaluated were found to prevent genital infection but not pathology and three exacerbate pathology. To further improve protection efficacy, a combinational regimen (intranasal priming + intramuscular boosting + a 3rd intraperitoneal/subcutaneous boost) was tested. This regimen identified 4 infection-reducing antigens but only one of them prevented pathology. Unfortunately, this protective antigen was not advanced further due to its amino acid sequence homology with several human molecules. Two pathology-exacerbating antigens were also found. Nevertheless, intranasal mucosal priming with viable C. muridarum in control groups consistently prevented both genital infection and pathology regardless of the subsequent boosters. Thus, screening 140 different chlamydial antigens with 21 repeated multiple times in 17 independent experiments failed to identify a subunit vaccine candidate but the efforts have revealed pathogenic antigens and demonstrated the superiority of viable chlamydial organisms in inducing immunity against both genital infection and pathology, laying the foundation for developing an attenuated live Chlamydia vaccine. ImportanceThis manuscript describes a systematical effort in searching for a chlamydial subunit vaccine by taking advantage of both the immunogenic chlamydial antigens identified in humans and a robust mouse genital tract infection model for simultaneously evaluating protection against both genital infection and pathology. Screening 140 different chlamydial antigens (21 repeated multiple times) using three different immunization regimens in 17 independent experiments identified no subunit vaccine candidate. Nevertheless, the efforts revealed multiple pathogenic chlamydial antigens and demonstrated the superiority of mucosal inoculation with viable chlamydial organisms for inducing immunity against both genital infection and pathology, suggesting that a live attenuated Chlamydia vaccine strategy should be considered.

microbiology↗

bioRxiv2023

An intact amber-free HIV-1 system for in-virus protein bioorthogonal click labeling that delineates envelope conformational dynamics

The HIV-1 envelope (Env) glycoprotein is conformationally dynamic and mediates membrane fusion required for cell entry. Single-molecule fluorescence resonance energy transfer (smFRET) of Env using peptide tags has provided mechanistic insights into the dynamics of Env conformations. Nevertheless, using peptide tags risks potential effects on structural integrity. Here, we aim to establish minimally invasive smFRET systems of Env on the virus by combining genetic code expansion and bioorthogonal click chemistry. Amber stop-codon suppression allows site-specifically incorporating noncanonical/unnatural amino acids (ncAAs) at introduced amber sites into proteins. However, ncAA incorporation into Env (or other HIV-1 proteins) in the virus context has been challenging due to low copies of Env on virions and incomplete amber suppression in mammalian cells. Here, we developed an intact amber-free virus system that overcomes impediments from preexisting ambers in HIV-1. Using this system, we successfully incorporated dual ncAAs at amber-introduced sites into Env on intact virions. Dual-ncAA incorporated Env retained similar neutralization sensitivities to neutralizing antibodies as wildtype. smFRET of click-labeled Env on intact amber-free virions recapitulated conformational profiles of Env. The amber-free HIV-1 infectious system also permits in-virus protein bioorthogonal labeling, compatible with various advanced microscopic studies of virus entry, trafficking, and egress in living cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/530526v1_ufig1.gif" ALT="Figure 1000"> View larger version (30K): org.highwire.dtl.DTLVardef@10e7728org.highwire.dtl.DTLVardef@b1078aorg.highwire.dtl.DTLVardef@65f874org.highwire.dtl.DTLVardef@9ab0e8_HPS_FORMAT_FIGEXP M_FIG C_FIG Amber-free HIV-1 infectious systems actualized minimal invasive Env tagging for smFRET, versatile for in-virus bioorthogonal click labeling in advanced microscopic studies of virus-host interactions.

microbiology↗

bioRxiv2023

Broadly effective ACE2 decoy proteins protect mice from lethal SARS-CoV-2 infection

As SARS-CoV-2 variants have been causing increasingly serious drug resistance problem, development of broadly effective and hard-to-escape anti-SARS-CoV-2 agents is in urgent need. Here we describe further development and characterization of two SARS-CoV-2 receptor decoy proteins, ACE2-Ig-95 and ACE2-Ig-105/106. We found that both proteins had potent and robust in vitro neutralization activities against diverse SARS-CoV-2 variants including Omicron, with an average IC50 of up to 37 pM. In a stringent lethal SARS-CoV-2 infection mouse model, both proteins lowered lung viral load by up to [~]1000 fold, prevented the emergence of clinical signs in >75% animals, and increased animal survival rate from 0% (untreated) to >87.5% (treated). These results demonstrate that both proteins are good drug candidates for protecting animals from severe COVID-19. In a head-to-head comparison of these two proteins with five previously-described ACE2-Ig constructs, we found that two of these constructs, each carrying five surface mutations in the ACE2 region, had partial loss of neutralization potency against three SARS-CoV-2 variants. These data suggest that extensively mutating ACE2 residues near the RBD-binding interface should be avoided or performed with extra caution. Further, we found that both ACE2-Ig-95 and ACE2-Ig-105/106 could be produced to gram/liter level, demonstrating the developability of them as biologic drug candidates. Stress-condition stability test of them further suggests that more studies are required in the future to improve the stability of these proteins. These studies provide useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. Abstract ImportanceEngineering soluble ACE2 proteins that function as a receptor decoy to block SARS-CoV-2 infection is a very attractive approach to broadly effective and hard-to-escape anti-SARS-CoV-2 agents. This study here describes development of two antibody-like soluble ACE2 proteins that broadly block diverse SARS-CoV-2 variants including Omicron. In a stringent COVID-19 mouse model, both proteins successfully protected >87.5% animals from lethal SARS-CoV-2 infection. In addition, a head-to-head comparison of the two constructs developed in this study with five previously-described ACE2 decoy constructs were performed here. Two previously-described constructs with relatively more ACE2-surface mutations were found with less robust neutralization activities against diverse SARS-CoV-2 variants. Further, the developability of the two proteins as biologic drug candidates was also assessed here. This study provides two broadly anti-SARS-CoV-2 drug candidates and useful insight into critical factors for engineering and preclinical development of ACE2 decoy as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. TweetTwo antibody-like ACE2 decoy proteins could block diverse SARS-CoV-2 variants and prevent animals from severe COVID-19.

microbiology↗

bioRxiv2023

Induction of transmucosal protection by oral vaccination with an attenuated Chlamydia

Chlamydia muridarum has been used to study chlamydial pathogenesis since it induces mice to develop hydrosalpinx, a pathology observed in C. trachomatis-infected women. We identified a C. muridarum mutant that is no longer able to induce hydrosalpinx. In the current study, we evaluated the mutant as an attenuated vaccine. Following an intravaginal immunization with the mutant, mice were protected from hydrosalpinx induced by wild type C. muridarum. However, the mutant itself productively colonized the mouse genital tract and produced infectious organisms in vaginal swabs. Nevertheless, the mutant failed to produce infectious shedding in the rectal swabs following an oral inoculation. Importantly, mice orally inoculated with the mutant mounted transmucosal immunity against challenge infection of wild type C. muridarum in the genital tract. The protection was detected as early as day 3 following the challenge infection and the immunized mice were protected from any significant pathology in the upper genital tract. However, the same orally immunized mice failed to prevent the colonization of wild type C. muridarum in the gastrointestinal tract. The transmucosal immunity induced by the oral mutant was further validated in the airway. The orally vaccinated mice were protected from both lung infection and systemic toxicity caused by intranasally inoculated wild type C. muridarum although the same mice still permitted the gastrointestinal colonization by the wild type C. muridarum. These observations suggest that the mutant C. muridarum may be developed into an intracellular oral vaccine vector (or IntrOv) for selectively inducing transmucosal immunity in extra-gut tissues.

immunology↗

bioRxiv2022

A Unified Modular Framework to Incorporate Structural Dependency in Spatial Omics Data

Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates positional information into non-spatial models via modular priors and losses. In simulated and real datasets, Smoother enables accurate data imputation, cell-type deconvolution, and dimensionality reduction with remarkable efficiency. In colorectal cancer, Smoother-guided deconvolution revealed plasma cell and fibroblast subtype localizations linked to tumor microenvironment restructuring. Additionally, joint modeling of spatial and single-cell human prostate data with Smoother allowed for spatial mapping of reference populations with significantly reduced ambiguity.

bioinformatics↗

bioRxiv2022

Thermotaxis in an apolar, non-neuronal animal

Neuronal circuits are hallmarks of complex decision making processes in the animal world. How animals without neurons process information and respond to environmental cues promises a new window into studying precursors of neuronal control and origin of the nervous system as we know it today. Robust decision making in animals, such as in chemotaxis or thermotaxis, often requires internal symmetry breaking (such as A-P axis) provided naturally by a given body plan of an animal. Here we report the discovery of robust thermotaxis behavior in Trichoplax adhaerens, an early-divergent, enigmatic animal with no anterior-posterior symmetry breaking (apolar), and no known neurons or muscles. We present the first quantitative and robust behavioral response assay in placozoan, which present an apolar flat geometry. By exposing T. adhaerens to a thermal gradient under a long-term imaging setup, we observe robust thermotaxis that occurs over timescale of hours, independent of any circadian rhythms. We quantify that T. adhaerens can detect thermal gradients of at least 0.1 {degrees}C/cm. Positive thermotaxis is observed for a range of baseline temperatures from 17-22.5 {degrees}C with motility trajectories to be well-described by a Levy distribution. Interestingly, the organism does not maintain a fixed orientation while performing thermotaxis. Utilizing natural diversity in size of adult organisms (100um to a few mm), we also demonstrate a critical animal size above which thermotaxis behavior is hindered. Several TRP family homologs have been previously reported to be conserved in metazoans, including in T. adhaerens. We discover naringenin, a known TRPM3 antagonist, inhibits thermotaxis in T. adhaerens. The discovery of robust thermotaxis in T. adhaerens provides a tractable handle to interrogate information processing in a brainless animal. Understanding how divergent marine animals process thermal cues is also critical due to rapid temperature rise in our oceans.

animal behavior and cognition↗

bioRxiv2022

Single-cell RNA sequencing identifies regulators of differentiation and nutritional cues in Drosophila female germ cells

Drosophila ovarian germline stem cells (GSCs) are powerful model for stem cell research. However, due to the scarcity of GSCs in ovarian tissue, it is difficult to obtain the transcriptional profile of GSCs and identify novel GSC markers. In this study, we took advantage of single cell RNA sequencing (scRNA-seq) to profile the germline cells and somatic cells in wild type Drosophila ovary. We then performed an in vivo RNAi screen and network analysis to identify genes that are involved in the early stages of germ cell differentiation. We identified 33 genes with limited expression during early germ cell development and identified 19 genes that potentially regulate germ cell differentiation. Among these, an uncharacterized gene, which we named eggplant (eggpl), is highly expressed in GSC and downregulated in early daughter cells. Upon RNAi knockdown of eggpl, we observed an increase in germ cell proliferation, an accumulation of cysts in the early mitotic (2- and 4-cell) stages and an increase in overall ovary size compared to control when flies were maintained on a standard diet. In flies fed a rich yeast diet, the expression of eggpl was significantly lower and the effects of eggpl RNAi were suppressed, suggesting that downregulation of eggpl may link nutritional status to germ cell proliferation and differentiation. We also found that the matrix metalloproteases, Mmp1 and Mmp2 as well as the tissue inhibitor of metalloproteases (Timp) are additional regulators of eggpl. Collectively, this study provides new insight into the signaling networks that regulate early germ cell development and identifies eggpl as a key player in this process.

genetics↗

bioRxiv2022

Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLpro

The SARS-CoV-2 virus is the causal agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19). There is an urgent need for potent, specific antiviral compounds against SARS-CoV-2. The 3C-like protease (3CLpro) is an essential enzyme for the replication of SARS-CoV-2 and other coronaviruses, and thus is a target for coronavirus drug discovery. Nearly all inhibitors of coronavirus 3CLpro reported so far are covalent inhibitors. Here, we report the development of specific, non-covalent inhibitors of 3CLpro. The most potent one, WU-04, effectively blocks SARS-CoV-2 replications in human cells with EC50 values in the 10-nM range. WU-04 also inhibits the 3CLpro of SARS-CoV and MERS-CoV with high potency, indicating that it is a pan-inhibitor of coronavirus 3CLpro. WU-04 showed anti-SARS-CoV-2 activity similar to that of PF-07321332 (Nirmatrelvir) in K18-hACE2 mice when the same dose was administered orally. Thus, WU-04 is a promising drug candidate for coronavirus treatment. One-Sentence SummaryA oral non-covalent inhibitor of 3C-like protease effectively inhibits SARS-CoV-2 replication.

microbiology↗

bioRxiv2022

Integration of gene expression data in Bayesian association analysis of rare variants

We present VBASS, a Bayesian method that integrates single-cell expression and de novo variant (DNV) data to improve power of disease risk gene discovery. VBASS models disease risk prior as a function of expression profiles, approximated by deep neural networks. It learns the weights of neural networks and parameters of Poisson likelihood models of DNV counts jointly from expression and genetics data. On simulated data, VBASS shows proper error rate control and better power than state-of-the-art methods. We applied VBASS to published datasets and identified more candidate risk genes with supports from literature or data from independent cohorts.

bioinformatics↗