Hundreds of target specific peptides are routinely discovered by peptide display platforms. However, due to the high cost of peptide synthesis only a limited number of peptides are chemically made for further analysis. Here we describe an accurate and cost effective method to bin peptides on-phage based on binding region(s), without any requirement for peptide or protein synthesis. This approach, which integrates phage and yeast display platforms, requires display of target and its alanine variants on yeast. Flow cytometry was used to detect binding of peptides on-phage to the target on yeast. Once hits were identified, they were synthesized to confirm their binding region(s) by HDX (Hydrogen deuterium exchange) and crystallography. Moreover, we have successfully shown that this approach can be implemented as part of a panning process to deplete non-functional peptides. This technique can be applied to any target that can be successfully displayed on yeast; it narrows down the number of peptides requiring synthesis; and its utilization during selection results in enrichment of peptide population against defined binding regions on the target.

Laryngeal squamous cell carcinoma (LSCC) is a common aggressive head and neck cancer. Circular RNAs (circRNAs) are implicated in numerous physiological and pathological processes, including tumorigenesis. The present study aimed to investigate the expression profile and biological role of circMYLK in LSCC. We found that circMYLK was highly expressed in LSCC tissues and cell lines. circMYLK overexpression promoted LSCC cell proliferation and G1/S cell cycle transition; whereas circMYLK knockdown had the contrary effects. Mechanistically, circMYLK can serve as a competing endogenous RNA for miR-195 to increase cyclin D1 expression in LSCC, and rescue experiments further showed that restoration of miR-195 could block the oncogenic role of circMYLK in LSCC. In conclusion, our findings indicate that the circMYLK/miR-195/cyclin D1 regulatory axis could affect the proliferation and cell cycle progression of LSCC cells, and may provide a novel therapeutic target for the treatment of LSCC.

Recent completion of the global proteomic characterization of The Cancer Genome Atlas (TCGA) colorectal cancer (CRC) cohort resulted in the first tumor dataset with complete molecular measurements at DNA, RNA and protein levels. Using CRC as a paradigm, we describe the application of the NetGestalt framework to provide easy access and interpretation of multi-omics data.

Myelin sheaths are essential in maintaining the integrity of axons. Development of the platform for in vitro myelination would be especially useful for demyelinating disease modeling and drug screening. In this study, a fiber scaffold with a core-shell structure was prepared in one step by the coaxial electrospinning method. A high-molecular-weight polymer poly-L-lactic acid (PLLA) was used as the core, while the shell was a natural polymer material such as hyaluronic acid (HA), sodium alginate (SA), or chitosan (CS). The morphology, differential scanning calorimetry (DSC), Fourier transform infrared spectra (FTIR), contact angle, viability assay, and in vitro myelination by oligodendrocytes were characterized. The results showed that such fibers are bead-free and continuous, with an average size from 294 ± 53 to 390 ± 54 nm. The DSC and FTIR curves indicated no changes in the phase state of coaxial brackets. Hyaluronic acid/PLLA coaxial fibers had the minimum contact angle (53.1° ± 0.24°). Myelin sheaths were wrapped around a coaxial electrospun scaffold modified with water-soluble materials after a 14-day incubation. All results suggest that such a scaffold prepared by coaxial electrospinning potentially provides a novel platform for oligodendrocyte myelination.

Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates. To address this, we analyzed seropositivity in US adults who have not previously been diagnosed with COVID-19. Individuals with characteristics that reflect the US population (n = 11,382) and who had not previously been diagnosed with COVID-19 were selected by quota sampling from 241,424 volunteers (ClinicalTrials.gov NCT04334954 ). Enrolled participants provided medical, geographic, demographic, and socioeconomic information and 9,028 blood samples. The majority (88.7%) of samples were collected between May 10th and July 31st, 2020. Samples were analyzed via ELISA for anti-Spike and anti-RBD antibodies. Estimation of seroprevalence was performed by using a weighted analysis to reflect the US population. We detected an undiagnosed seropositivity rate of 4.6% (95% CI: 2.6 - 6.5%). There was distinct regional variability, with heightened seropositivity in locations of early outbreaks. Subgroup analysis demonstrated that the highest estimated undiagnosed seropositivity within groups was detected in younger participants (ages 18-45, 5.9%), females (5.5%), Black/African American (14.2%), Hispanic (6.1%), and Urban residents (5.3%), and lower undiagnosed seropositivity in those with chronic diseases. During the first wave of infection over the spring/summer of 2020 an estimate of 4.6% of adults had a prior undiagnosed SARS-CoV-2 infection. These data indicate that there were 4.8 (95% CI: 2.8-6.8) undiagnosed cases for every diagnosed case of COVID-19 during this same time period in the United States, and an estimated 16.8 million undiagnosed cases by mid-July 2020.

Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates in the United States and elsewhere. To address this, we analyzed seropositivity in 9089 adults in the United States who had not been diagnosed previously with COVID-19. Individuals with characteristics that reflected the U.S. population (n = 27,716) were selected by quota sampling from 462,949 volunteers. Enrolled participants (n = 11,382) provided medical, geographic, demographic, and socioeconomic information and dried blood samples. Survey questions coincident with the Behavioral Risk Factor Surveillance System survey, a large probability-based national survey, were used to adjust for selection bias. Most blood samples (88.7%) were collected between 10 May and 31 July 2020 and were processed using ELISA to measure seropositivity (IgG and IgM antibodies against SARS-CoV-2 spike protein and the spike protein receptor binding domain). The overall weighted undiagnosed seropositivity estimate was 4.6% (95% CI, 2.6 to 6.5%), with race, age, sex, ethnicity, and urban/rural subgroup estimates ranging from 1.1% to 14.2%. The highest seropositivity estimates were in African American participants; younger, female, and Hispanic participants; and residents of urban centers. These data indicate that there were 4.8 undiagnosed SARS-CoV-2 infections for every diagnosed case of COVID-19, and an estimated 16.8 million infections were undiagnosed by mid-July 2020 in the United States.

Long-term use of antipsychotics is a common cause of myocardial injury and even sudden cardiac deaths that often lead to drug withdrawn or discontinuation. Mechanisms underlying antipsychotics cardiotoxicity remain largely unknown. Herein we performed RNA sequencing and found that NLRP3 inflammasome-mediated pyroptosis contributed predominantly to multiple antipsychotics cardiotoxicity. Pyroptosis-based small-molecule compound screen identified cannabinoid receptor 1 (CB1R) as an upstream regulator of the NLRP3 inflammasome. Mechanistically, antipsychotics competitively bond to the CB1R and led to CB1R translocation to the cytoplasm, where CB1R directly interacted with NLRP3 inflammasome via amino acid residues 177-209, rendering stabilization of the inflammasome. Knockout of Cb1r significantly alleviated antipsychotic-induced cardiomyocyte pyroptosis and cardiotoxicity. Multi-organ-based investigation revealed no additional toxicity of newer CB1R antagonists. In authentic human cases, the expression of CB1R and NLRP3 inflammasome positively correlated with antipsychotics-induced cardiotoxicity. These results suggest that CB1R is a potent regulator of the NLRP3 inflammsome-mediated pyroptosis and small-molecule inhibitors targeting the CB1R/NLRP3 signaling represent attractive approaches to rescue cardiac side effects of antipsychotics.

Cancer recurrence post surgical resection is of considerable challenge especially in glioblastoma (GBM) therapy. Herein, we demonstrate that interferon-alpha (IFN) fused to a body temperature-sensitive elastin-like polypeptide (IFN-ELP(V)) formed a depot in situ when injected into GBM resection cavity in a mouse brain orthotopic model of GBM. Notably, IFN-ELP(V) in the depot showed a zero-order release kinetics, resulting in dramatically improved pharmacokinetics and biodistribution, and thus inhibited GBM recurrence by stimulating antitumor immunoresponse as compared to IFN. More importantly, when combined with subsequent intraperitoneal injection of temozolomide (TMZ), IFN-ELP(V) could much more effectively suppress post-surgical GBM recurrence than IFN, leading to a remarkably enhanced GBM-free survival rate (60%) over IFN (12.5%). Our findings implicate that the spatiotemporally-programmed combination of IFN-ELP(V) and TMZ leads to the synergy of post-surgical GBM immunochemotherapy, thereby providing a new and effective strategy for cancer therapy.

Combination therapy has shown an obvious efficacy on complex diseases and can greatly reduce the development of drug resistance. However, even with high-throughput screens, experimental methods are insufficient to explore novel drug combinations. In order to reduce the search space of drug combinations, there is an urgent need to develop more efficient computational methods to predict novel drug combinations. In recent decades, more and more machine learning (ML) algorithms have been applied to improve the predictive performance. The object of this study is to introduce and discuss the recent applications of ML methods and the widely used databases in drug combination prediction. In this study, we first describe the concept and controversy of synergism between drug combinations. Then, we investigate various publicly available data resources and tools for prediction tasks. Next, ML methods including classic ML and deep learning methods applied in drug combination prediction are introduced. Finally, we summarize the challenges to ML methods in prediction tasks and provide a discussion on future work.

Aflatoxin, a carcinogenic secondary metabolite produced by Aspergillus flavus, is a significant threat to human health and agricultural production. Histone 2-hydroxyisobutyrylation is a novel post-translational modification that regulates various biological processes, including secondary metabolism. In this study, we identified the novel histone 2-hydroxyisobutyryltransferase Afngg1 in A. flavus, and explored its role in cell growth, development and aflatoxin biosynthesis. Afngg1 gene deletion markedly decreased lysine 2-hydroxyisobutyrylation modification of histones H4K5 and H4K8 compared with the control strain. Additionally, Afngg1 deletion inhibited mycelial growth of A. flavus, and the number of conidia and hydrophobicity were significantly decreased. Notably, aflatoxin B1 biosynthesis and sclerotia production were completely inhibited in the ΔAfngg1 strain. Furthermore, the pathogenicity of the ΔAfngg1 strain infecting peanut and corn grains was also diminished, including reduced spore production and aflatoxin biosynthesis compared with A. flavus control and Afngg1 complementation strains. Transcriptome analysis showed that, compared with control strains, differentially expressed genes in ΔAfngg1 were mainly involved in chromatin remodelling, cell development, secondary metabolism and oxidative stress. These results suggest that Afngg1 is involved in histone 2-hydroxyisobutyrylation and chromatin modification, and thus affects cell development and aflatoxin biosynthesis in A. flavus. Our results lay a foundation for in-depth research on the 2-hydroxyisobutyrylation modification in A. flavus, and may provide a novel target for aflatoxin contamination prevention.

There exists an urgent medical demand at present to develop therapeutic strategies which can improve the treatment outcome of hepatocellular carcinoma (HCC). Here, we explore the biological functions and clinical significance of PBOV1 in HCC in order to push forward the diagnosis and treatment of HCC. Using theranostical nanomedicines, PBOV1 is verified to be a key oncogene which greatly promotes HCC proliferation, epithelial-to-mesenchymal transition, and stemness by activating the Wnt/β-catenin signaling pathway. Therefore, single-chain antibody for epidermal growth factor receptor (scAb-EGFR)-targeted nanomedicine effectively silencing the PBOV1 gene exhibits potent anticancer effects. In vivo HCC-targeting siRNA delivery mediated by the theranostical nanomedicine remarkably inhibits the tumor growth and metastasis. In addition, the superparamagnetic iron oxide nanocrystals (SPION)-encapsulated nanomedicines possess high MRI detection sensitivity, which endows them with the potential for MRI diagnosis of HCC. This study shows that PBOV1 represents a prognostic biomarker and therapeutic target for HCC.

Due to a combination of asymptomatic or undiagnosed infections, the proportion of the United States population infected with SARS-CoV-2 was unclear from the beginning of the pandemic. We previously established a platform to screen for SARS-CoV-2 positivity across a representative proportion of the US population, from which we reported that almost 17 million Americans were estimated to have had undocumented infections in the Spring of 2020. Since then, vaccine rollout and prevalence of different SARS-CoV-2 variants have further altered seropositivity trends within the United States population. To explore the longitudinal impacts of the pandemic and vaccine responses on seropositivity, we re-enrolled participants from our baseline study in a 6- and 12- month follow-up study to develop a longitudinal antibody profile capable of representing seropositivity within the United States during a critical period just prior to and during the initiation of vaccine rollout. Initial measurements showed that, since July 2020, seropositivity elevated within this population from 4.8% at baseline to 36.2% and 89.3% at 6 and 12 months, respectively. We also evaluated nucleocapsid seropositivity and compared to spike seropositivity to identify trends in infection versus vaccination relative to baseline. These data serve as a window into a critical timeframe within the COVID-19 pandemic response and serve as a resource that could be used in subsequent respiratory illness outbreaks.

Heat shock transcription factors (HSFs) play important roles in plant growth, development, and stress responses. However, the function of these transcription factors in abiotic stress responses in maize (Zea mays) remains largely unknown. In this study, we characterized a novel HSF transcription factor gene, ZmHsf08, from maize. ZmHsf08 was highly homologous to SbHsfB1, BdHsfB1, and OsHsfB1, and has no transcriptional activation activity. The expression profiles demonstrated that ZmHsf08 was differentially expressed in various organs of maize and was induced by salt, drought, and abscisic acid (ABA) treatment. Moreover, the overexpression of ZmHsf08 in maize resulted in enhanced sensitivity to salt and drought stresses, displaying lower survival rates, higher reactive oxygen species (ROS) levels, and increased malondialdehyde (MDA) contents compared with wild-type (WT) plants. Furthermore, RT-qPCR analyses revealed that ZmHsf08 negatively regulates a number of stress/ABA-responsive genes under salt and drought stress conditions. Collectively, these results indicate that ZmHsf08 plays a negative role in response to salt and drought stresses in maize.

Nucleobase:cation symporter 2 (NCS2) proteins are important for the transport of free nucleobases, participating in diverse plant growth and developmental processes, as well as response to abiotic stress. To date, a comprehensive analysis of the NCS2 gene family has not been performed in maize. In this study, we conducted a comparative genomics analysis of NCS2 genes in 28 plant species, ranging from aquatic algae to land plants, concentrating mainly on maize. Gene duplication events contributed to the expansion of NCS2 genes from lower aquatic plants to higher angiosperms, and whole-genome/segmental and single-gene duplication events were responsible for the expansion of the maize NCS2 gene family. Phylogenetic construction showed three NCS2 subfamilies, I, II, and III. According to homology-based relationships, members of subfamily I are NCS2/AzgA-like genes, whereas those in subfamilies II and III are NCS2/NATs. Moreover, subfamily I exhibited ancient origins. A motif compositional analysis showed that one symbolic motif (motif 4) of the NCS2/NAT genes was absent in subfamily I. In maize, three NCS2/AzgA-like and 21 NCS2/NAT genes were identified, and purifying selection influenced the duplication of maize NCS2 genes. Additionally, a population genetic analysis of NCS2 genes revealed that ZmNCS2-21 showed the greatest diversity between the 78 inbred and 22 wild surveyed maize populations. An expression profile analysis using transcriptome data and quantitative real-time PCR revealed that NCS2 genes in maize are involved in diverse developmental processes and responses to abiotic stresses, including abscisic acid, salt (NaCl), polyethylene glycol, and low (4°C) and high (42°C) temperatures. ZmNCS2 genes with relatively close relationships had similar expression patterns, strongly indicating functional redundancy. Finally, ZmNCS2-16 and ZmNCS2-23 localize in the plasma membrane, which confirmed their predicted membrane structures. These results provide a foundation for future studies regarding the functions of ZmNCS2 proteins, particularly those with potentially important roles in plant responses to abiotic stresses.

Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) is a critical inhibitory checkpoint molecule, and monoclonal antibodies (mAbs) targeting CTLA-4 that restore anti-tumor T cell immunity have achieved clinical success. Here, we report a humanized IgG1 mAb, namely JS007, with high binding affinity to CTLA-4. JS007 shows superior binding affinity and T-cell activating efficiency over ipilimumab. Moreover, it demonstrates substantial in vivo tumor suppression efficacy at low doses. The crystal structure of JS007/CTLA-4 complex (PDB: 8HIT) shows JS007 adopts a heavy-chain-dominant binding mode, and mainly contacts the BC loop, DE loop and FG loop of CTLA-4. Notably, two Tyr residues (VH-Y100 and VL-Y32) from the complementarity-determining region loops insert into the two cavities formed by the residues from the loops of CTLA-4, which may contribute to the stabilization of the binding. Comparative analysis with other anti-CTLA-4 mAbs indicates that the double "wedge-into-hole" binding mode is unique for JS007 and may be responsible for the high-affinity binding to CTLA-4. These findings have provided an important molecular understanding of the high-affinity CTLA-4 blockade mAbs and shed light on future development of agents targeting CTLA-4.

In clinical practice at Tibetan area of China, Traditional Tibetan Medicine formula Wuwei-Ganlu-Yaoyu-Keli (WGYK) is commonly added in warm water of bath therapy to treat rheumatoid arthritis (RA). However, its mechanism of action is not well interpreted yet. In this paper, we first verify WGYK's anti-RA effect by an animal experiment. Then, based on gene expression data from microarray experiments, we apply approaches of network pharmacology to further reveal the mechanism of action for WGYK to treat RA by analyzing protein-protein interactions and pathways. This study may facilitate our understanding of anti-RA effect of WGYK from perspective of network pharmacology.

The glycoside hydrolase family 18 chitinases degrade or alter chitin. Multiple catalytic domains in a glycoside hydrolase family 18 chitinase function synergistically during chitin degradation. Here, an insect group III chitinase from the agricultural pest Ostrinia furnacalis (OfChtIII) is revealed to be an arthropod-conserved chitinase that contains two nonsynergistic GH18 domains according to its catalytic properties. Both GH18 domains are active towards single-chained chitin substrates, but are inactive towards insoluble chitin substrates. The crystal structures of each unbound GH18 domain, as well as of GH18 domains complexed with hexa-N-acetyl-chitohexaose or penta-N-acetyl-chitopentaose, suggest that the two GH18 domains possess endo-specific activities. Physiological data indicated that the developmental stage-dependent gene-expression pattern of OfChtIII was the same as that of the chitin synthase OfChsA but significantly different from that of the chitinase OfChtI, which is indispensable for cuticular chitin degradation. Additionally, immunological staining indicated that OfChtIII was co-localized with OfChsA. Thus, OfChtIII is most likely to be involved in the chitin-synthesis pathway.

The latent HIV-1 reservoir is a major barrier to viral eradication. However, our understanding of how HIV-1 establishes latency is incomplete. Here, by performing a genome-wide CRISPR-Cas9 knockout library screen, we identify phosphatidylethanolamine-binding protein 1 (PEBP1), also known as Raf kinase inhibitor protein (RKIP), as a novel gene inducing HIV latency. Depletion of PEBP1 leads to the reactivation of HIV-1 in multiple models of latency. Mechanistically, PEBP1 de-phosphorylates Raf1/ERK/IκB and IKK/IκB signaling pathways to sequestrate NF-κB in the cytoplasm, which transcriptionally inactivates HIV-1 to induce latency. Importantly, the induction of PEBP1 expression by the green tea compound epigallocatechin-3-gallate (EGCG) prevents latency reversal by inhibiting nuclear translocation of NF-κB, thereby suppressing HIV-1 transcription in primary CD4+ T cells isolated from patients receiving antiretroviral therapy (ART). These results suggest a critical role for PEBP1 in the regulation of upstream NF-κB signaling pathways governing HIV transcription. Targeting of this pathway could be an option to control HIV reservoirs in patients in the future.

Ochratoxin A (OTA) is a well-known, natural contaminant in foods and feeds because of its toxic effects, such as nephrotoxicity in various animals. Recent studies have revealed that Alcaligenes faecalis could generate enzymes to efficiently degrade OTA to ochratoxin α (OTα) in vitro. In an effort to obtain the OTA degrading mechanism, we purified and identified a novel degrading enzyme, N-acyl-L-amino acid amidohydrolase (AfOTase), from A. faecalis DSM 16503 via mass spectrometry. The same gene of the enzyme was also encountered in other A. faecalis strains. AfOTase belongs to peptidase family M20 and contains metal ions at the active site. In this study, recombination AfOTase was expressed and characterized in Escherichia coli. The molecular mass of recombinant rAfOTase was approximately 47.0 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The enzyme exhibited a wide temperature range (30-70 °C) and pH adaptation (4.5-9.0) and the optimal temperature and pH were 50 °C and 6.5, respectively.

The interaction between Ca2+ and alkaline protease has been studied. Enzyme activity measurements demonstrated that Ca2+ with a suitable concentration could increase the activity of alkaline protease. Particle size and zeta potential measurements showed that Ca2+ bound to alkaline protease by electrostatic interaction. The combination of Ca2+ and alkaline protease promoted the structure of alkaline protease to become more stable, which was favorable for the increase of enzyme activity. Fluorescence spectra showed that alkaline protease had two Ca2+ binding sites and potent binding force to Ca2+. Thermodynamic parameters ΔH, ΔS and ΔG obtained by fluorescence spectra confirmed that the interaction between Ca2+ and alkaline protease was also electrostatic interaction and the binding process could proceed spontaneously. The results of molecular docking were also consistent with the conclusions obtained from the zeta potential and fluorescence spectrum measurements. In addition, the washing performance test showed that the detergent added with Ca2+ and alkaline protease had the best washing performance on protein-contaminated swatches JB02 and blood swatches.