Search Results (218)

Nilaparvata lugens is a migratory pest with high fecundity and outstanding drug resistance, which poses a devastating danger to rice production. This study investigated the reproductive regulation mechanism of N. lugens, specifically silencing the trehalose-6-phosphate synthase gene (TPS) via RNAi to elucidate how TPS governs the trehalose metabolic network through modulation of trehalose biosynthesis. Insect fecundity hinges on the synchronized progression of oogenesis and the tightly controlled expression of vitellogenin (Vg). In N. lugens, this coordination is orchestrated by an integrated molecular network that converges juvenile hormone signaling (JH), 20-hydroxyecdysone pathways (20E), insulin/IGF signaling (IIS), and the target of rapamycin cascade (TOR), collectively dictating the reproductive output of the species. Using TPS knockdown as the entry point, this study dissects the lipid-metabolic circuitry of N. lugens and uncovers how hormonal signaling cascades orchestrate reproduction by precisely modulating vitellogenin (Vg) and its cognate receptor VgR. Synthesized double-stranded terpene synthase genes (dsTPSs) can degrade mRNA, inhibit protein translation, and ultimately lead to the silencing of TPS genes, simultaneously crippling energy provision and hormonal signaling to orchestrate a multi-pronged suppression of reproduction. This dual-action intervention offers a promising molecular target for environmentally friendly management of N. lugens. Full article

Ovarian cancer (OC) is usually diagnosed at an advanced stage, contributing to its high mortality rate. The presence of concurrent bacterial infections in these patients is a common clinical observation, and the mechanisms by which this coinfection influences tumor progression are still not fully understood. This study investigates the role of polydisperse extracellular vesicles (PEVs) secreted by OC cells in response to bacterial components, aiming to elucidate a potential communication pathway between OC and the bacterial microenvironment. We stimulated a human OC cell line in vitro with a fraction of E. coli. Our results show that this bacterial stimulation significantly increases the secretion of PEVs by cancer cells. A subsequent proteomic analysis of these PEVs revealed an enrichment of proteins, including filamin A, filamin B, alpha-enolase, and heat shock cognate 71 kDa protein. In addition, the PEVs displayed protease activity (on fibronectin and gelatin) and phosphatase activity against para-nitrophenyl phosphate, indicating their capacity to alter cellular signaling. This represents a novel mechanism through which bacterial coinfection may influence the biological behavior of OC if bacteria interact with tumor cells, potentially contributing to their aggressiveness and the challenges associated with their treatment. Our work highlights the importance of studying the interplay between the tumor and its associated microbiota to better understand ovarian cancer progression and identify new therapeutic targets. Full article

During diabetic retinopathy (DR), cell death has been characterized in all of the major retinal cell types, but was observed initially in the microvasculature, particularly the mural cells: pericytes and vascular smooth muscle cells (VSMCs). Indeed, our ability to identify the mural cell corpses called “ghost cells” within the vascular basement membranes (BMs) in eyes of diabetic patients and animal models is indicative that removal of dead cells, or efferocytosis (EF), is dysfunctional during this disease. EF is the process whereby apoptotic cells are eliminated through phagocytic engulfment and digestion and is essential to maintain tissue integrity and immune homeostasis. The process occurs in three distinct phases: finding and recognition, engulfment, and digestion, under the direction of “find me” and “eat me” signals and a large array of their cognate receptors and bridging molecules. Efferocytosis can be performed by many cell types, but most efficiently by professional phagocytes, and with such rapidity that the process is extremely difficult to detect in healthy tissues. As delayed EF is a recognized cause of autoimmune and inflammatory disease, mural cell death in DR may create inflammatory foci in the neurovascular unit (NVU). Here we discuss the basic mechanisms of EF in the context of DR and the impact of diabetic metainflammation on EF effector cell dysfunction. Full article

Two-component systems (TCSs) are ubiquitous in bacteria and are central to their ability to sense and respond to diverse environmental and intracellular cues. Classically composed of a sensor histidine kinase and a cognate response regulator, TCSs control processes ranging from metabolism and development to virulence and antibiotic resistance. In addition to their biological roles, TCSs are garnering attention in synthetic biology and antimicrobial drug development. While canonical architectures have been extensively studied, increasing evidence highlights the remarkable diversity in their organization and regulation. Despite substantial progress, key questions remain regarding the prevalence and physiological relevance of non-canonical TCSs, the mechanisms ensuring signal fidelity, and the potential for engineering these systems. This review explores non-typical TCSs, focusing on their varied transcriptional regulation, alternative response regulator activities, varied control by phosphorylation, and negative control mechanisms. We discuss how bacteria manage signaling specificity among numerous TCSs through cross-talk, hierarchical interactions, and phosphorelay systems and how these features shape adaptive responses. By synthesizing current understanding and highlighting still existing knowledge gaps, this review offers a novel perspective on TCS diversity, indicating directions for future research and potential translational applications in biotechnology and medicine. Full article

The role of G-quadruplexes (G4s) in gene regulation has been widely documented, especially in gene promoters. However, the transcriptional mechanisms involving G4s in other regulatory regions remain largely unexplored. In this study, we integrated the G4-DNA data derived from 22 breast cancer patient-derived tumor xenograft (PDTX) models and MCF7 cell line as potential breast cancer-associated G4s (BC-G4s). Genome-wide analysis showed that BC-G4s are more prevalent in gene promoters and the first introns. The genes accommodating promoter or intronic BC-G4s show significantly higher transcriptional output than their non-G4 counterparts. The biased distribution of BC-G4s in close proximity to the transcription start site (TSS) is associated with an enrichment of transcription factor (TF) interactions. A significant negative correlation was detected between the G4–TF interactions within the first introns and their cognate promoters. These different interactions are complementary rather than redundant. Furthermore, the differentially expressed genes (DEGs) harboring promoter and first intron BC-G4s are significantly enriched in the cell cycle pathway. Notably, promoter BC-G4s of DEGs could be a central hub for TF–TF co-occurrence. Our analysis also revealed that G4-related single nucleotide variants (SNVs) affect the stability of G4 structures and the transcription of disease-related genes. Collectively, our results shed light on how BC-G4s within promoters and first introns regulate gene expression and reinforce the critical role of G4s and G4-related genes in breast cancer-associated processes. Full article

T-cell receptors (TCRs) exhibit degeneracy, enabling individual TCRs to recognize multiple altered peptide ligands (APLs) derived from a single cognate antigen. This characteristic has been involved in the pathogenesis of autoimmune diseases through cross-reactivity between microbial and self-antigens. Cytotoxic T lymphocytes (CTLs), which recognize peptide–MHC class I complexes via TCRs, play a critical role in the immune response against viral infections. However, the extent to which TCR degeneracy within a population of virus-specific CTLs contributes to effective viral control remains poorly understood. In this study, we investigated the magnitude and functional relevance of TCR degeneracy in CTLs targeting an immunodominant epitope of human T-cell leukemia virus type 1 (HTLV-1) in patients with HTLV-1-associated myelopathy (HAM). Using peripheral blood mononuclear cells (PBMCs) from these patients, we quantified TCR degeneracy at the population level by comparing CTL responses to a panel of APLs with responses to the cognate epitope. Our findings demonstrated that increased TCR degeneracy, particularly at the primary TCR contact residue at position 5 of the antigen, was inversely correlated with HTLV-1 proviral load (p = 0.038, R = −0.40), despite similar functional avidity across patient-derived CTLs. Viral sequencing further revealed that CTLs with high TCR degeneracy exerted stronger selective pressure on the virus, as indicated by a higher frequency of nonsynonymous substitutions within the epitope-encoding region in patients with highly degenerate TCR repertoires. Moreover, TCR degeneracy was positively correlated with the recognition rate of epitope variants (p = 0.018, R = 0.76), suggesting that CTLs with high TCR degeneracy exhibited enhanced recognition of naturally occurring epitope variants compared to those with low TCR degeneracy. Taken together, these results suggest that virus-specific CTLs with high TCR degeneracy possess superior antiviral capacity, characterized by broadened epitope recognition and more effective suppression of HTLV-1 infection. To our knowledge, this is the first study to systematically quantify TCR degeneracy in HTLV-1-specific CTLs and evaluate its contribution to viral control in HAM patients. These findings establish TCR degeneracy as a critical determinant of antiviral efficacy and provide a novel immunological insight into the mechanisms of viral suppression in chronic HTLV-1 infection. Full article

The co-evolution between plants and herbivorous insects has led to a continuous arms race on defense and anti-defense mechanisms. In this process, insect-derived effectors are crucial for suppressing plant defense. Despite considerable progress in plant–insect interaction studies, the functional role of heat shock cognate protein 70 (HSC70) as an effector in herbivorous insects remains poorly characterized. This study provides evidence that HSC70-3 functions as an effector in interactions between the cruciferous specialist diamondback moth (Plutella xylostella) and its host plant radish (Raphanus sativus ‘Nanpan Prefecture’). Using immunofluorescence labeling and in situ Western blot (WB), we demonstrated that HSC70-3 is secreted into plant wound sites through larval gut regurgitant during feeding. Short-term host transfer experiments revealed tissue-specific hsc70-3 expression changes, indicating a dynamic response to plant-derived challenges. These findings suggest hsc70-3 is differentially regulated at transcriptional and translational levels to facilitate insect adaptation to host plant shifts. Knockout of hsc70-3 using CRISPR/Cas9 technology significantly impaired larval growth, prolonged development duration, and reduced pupal weight on host plants, indicating its involvement in host adaptation. However, knockout mutants exhibited no significant developmental defects when reared on an artificial diet, suggesting that hsc70-3 primarily functions in modulating plant-induced defense responses rather than directly affecting insect physiology. Collectively, these findings provide evidence for the functional roles of HSC70-3 in P. xylostella and plant interactions, laying a foundation for further investigations into insect effectors and their mechanisms in modulating plant defense responses. Full article

In previous studies, we isolated a series of novel gentisides with nerve growth factor (NGF)-mimic activities from Gentiana rigescens Franch and conducted continuous structure–activity relationship (SAR) studies. Recently, a lead compound named TBG096 was discovered with significant NGF-mimic activity, low toxicity, and ability to pass through the blood–brain barrier (BBB). At the cell level, TBG096 exerts NGF-mimic activity by regulation of heat-shock cognate protein 70 (Hsc70) and downstream proteins. Subsequently, high-fat diet (HFD)-induced Alzheimer disease (AD) mouse models were used to evaluate the anti-AD efficacy of the compound. TBG096 significantly improved the memory dysfunction of AD mice at doses of 0.1, 5, and 20 mg/kg, respectively. In order to elucidate the mechanism of action of the compound against AD, the RNA-sequence analysis of transcriptomics, quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence staining, and Western blot analysis were performed using animal samples. TBG096 significantly increased the expression of the Wnt gene family (Wnt10b, Wnt5a, and Wnt1) and the number of mature neurons and newborn neurons in the hippocampus and cerebral cortex of AD mice, respectively. At the same time, it reduced the activity of microglia, astrocyte cells, and expression of inducible nitric oxide synthase (INOS) in the brain. Moreover, this compound significantly increased phosphorylated-adenosine 5′-monophosphate-activated protein kinase (AMPK), Hsc70, and lysosomal-associated membrane protein 2a (LAMP2A) and decreased the expression of hexokinase 2 (HK2), pyruvate kinase M2 (PKM2), amyloid precursor protein (APP), microtubule-associated protein tau (Tau), phosphoryl-Tau, and β-amyloid (Aβ) at the protein level. These results suggest that TBG096 produced the NGF-mimic activity and the anti-AD effect via promoting neurogenesis and modification of the Hsc70/HK2/PKM2/LAMP2A signaling pathway, proposing a potential novel approach to counteracting cognitive decline by developing small molecules that promote neurogenesis and the Hsc70 signaling pathway. Full article

Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural and binding mechanisms underlying the interaction of colicin-D, -E3 and -E8 to their respective immunity proteins (ImD, Im3 and Im8) using structure prediction, molecular dynamics (MD) simulations and MM-PBSA approach of free energy calculations. High-confidence colicin-immunity (Col-Im) complex structures predicted using AlphaFold2 were subjected to MD simulations of 150 ns with GROMACS and were analyzed for the binding free energy calculation using gmx_MMPBSA. Results showed that the complex of Col_E3-Im3 exhibited the most favorable binding free energy, driven by strong van der Waals and electrostatic interactions. Col_D-ImD and Col_E8-Im8 also showed the favorable binding. Electrostatics and hydrogen bonding emerged as a key factor driving binding and stability, while polar solvation acted as a destabilizing factor across all systems. These outcomes provide an understanding of the molecular mechanisms of Col-Im systems, with potential applications for developing natural antimicrobials for food safety. Full article

Antibodies are critical to the host’s immune defense against bacterial pathogens. Understanding the mechanisms of antibody–antigen interactions is essential for developing new targeted immunotherapies. Building computational workflows that can identify where an antibody binds its cognate antigen and deconvoluting the interaction interface in a high-throughput manner are critical for advancing this field. Cross-linking mass spectrometry (XL-MS) integrated with structural modeling offers a flexible and high-resolution strategy to map protein–protein interactions from low sample amounts. However, cross-linking and in silico modeling have limitations that require robust analytical workflows to make accurate inferences. In this study, we introduce Sidewinder, a modular high-throughput pipeline combining state-of-the-art computational structural prediction and molecular docking with rapid XL-MS analysis, enabling comprehensive interrogation of antibody–antigen systems. We validated this pipeline on antibodies targeting two Streptococcus pyogenes virulence factors. Using recently published data, we identified a well-defined monoclonal antibody epitope on Streptolysin O by generating and querying a large ensemble of interaction models probabilistically. We also showcased the utility of the Sidewinder pipeline by analyzing a more complex system, involving monoclonal antibodies that target the cell wall-anchored M1 protein. The flexibility and robustness of the Sidewinder pipeline provide a powerful framework for future studies of complex antibody–antigen systems, potentially leading to new therapeutic strategies. Full article

The serine protease prostasin on the surface of the exosomes released from epithelial cells can interact with ectopically over-expressed cell-surface serine protease matriptase in cancerous B cells to initiate the prostasin–matriptase proteolytic activation cascade. Matriptase activation and the ensuing self-activation result in its removal from cancer cells, reducing cell proliferation and migration. In this study, we tested the hypothesis that the matriptase in the lymphoid cells could be removed by the prostasin-initiated activation and self-activation using genetically engineered autologous cells carrying prostasin. In co-cultures with the prostasin-positive cells, the matriptase on the prostasin-negative vector-control cells was removed in a dose-dependent manner, as determined by flow cytometry. This paracrine phenotype requires the active sites of both proteases. In silico analysis of the RNA-seq profiles indicated an imbalanced expression of high matriptase and low prostasin, and their cognate protease inhibitors in B-cell lymphoma patient specimens. The impact of exosomal prostasin on the cluster of differentiation molecules in activated human peripheral blood mononuclear cells was investigated by flow cytometry, revealing candidate mechanisms for prostasin’s role in regulating cellular adaptive immunity. This autologous paracrine prostasin–matriptase interaction could be exploited as a method for targeting over-expressed matriptase in diseases such as B-cell lymphoma. Full article

Background: Rift Valley fever virus (RVFV) is a zoonotic virus that poses a significant threat to both livestock and human health and has caused outbreaks in endemic regions. In humans, most patients experience a febrile illness; however, in some patients, RVF disease may result in hemorrhagic fever, retinitis, or encephalitis. While several veterinary vaccines are being utilized in endemic countries, currently, there are no licensed RVF vaccines or therapeutics for human use. Neutralizing antibodies specifically targeting vulnerable pathogen epitopes are promising candidates for prophylactic and therapeutic interventions. In the case of RVFV, the surface glycoproteins Gc and Gn, which harbor neutralizing epitopes, represent the primary targets for vaccine and neutralizing antibody development. Methods: We report the implementation of advanced 10x Genomics technology, enabling high-throughput single-cell analysis for the identification of rare and potent antibodies against RVFV. Following the immunization of mice with live attenuated rMP-12-GFP virus and successive Gc/Gn boosts, memory B cell populations (both general and antigen-specific) were sorted from splenocytes by flow cytometry. Deep sequencing of the antibody repertoire at a single-cell resolution, together with bioinformatic analyses, was applied for BCR pair selection based on their abundance and specificity. Results: Twenty-three recombinant monoclonal antibodies (mAbs) were selected and expressed, and their antigen-binding capacities were characterized. About half of them demonstrated specific binding to their cognate antigen with relatively high binding affinities. Conclusions: These antibodies could be used for the future development of efficacious therapeutics, as well as for studying virus-neutralizing mechanisms. The current study, in which the single-cell sequencing approach was implemented for the development of antibodies targeting the RVFV surface proteins Gc and Gn, demonstrates the effective applicability of this technique for antibody discovery purposes. Full article

The human nuclear receptor (NR) superfamily consists of 48 genes that are ligand-activated transcription factors that play a key role in maintaining cellular homeostasis and in pathophysiology. NRs are important drug targets for both cancer and non-cancer endpoints as ligands for these receptors can act as agonists, antagonists or inverse agonists to modulate gene expression. With two exceptions, the classical mechanism of action of NRs involves their interactions as monomers, dimers or heterodimers with their cognate response elements (cis-elements) in target gene promoters. Several studies showed that a number of NR-regulated genes did not directly bind their corresponding cis-elements and promoter analysis identified that NR-responsive gene promoters contained GC-rich sequences that bind specificity protein 1 (Sp1), Sp3 and Sp4 transcription factors (TFs). This review is focused on identifying an important sub-set of Sp-regulated genes that are indirectly coregulated through interactions with NRs. Subsequent studies showed that many NRs directly bind Sp1 (or Sp3 and Sp4), the NR/Sp complexes bind GC-rich sites to regulate gene expression and the NR acts as a ligand-modulated nuclear cofactor. In addition, several reports show that NR-responsive genes contain cis-elements that bind both Sp TFs and NRs, and mutation of either cis-element results in loss of NR-responsive (inducible and/or basal). Regulation of these genes involves interactions between DNA-bound Sp TFs with proximal or distal DNA-bound NRs, and, in some cases, other nuclear cofactors are required for gene expression. Thus, many NR-responsive genes are regulated by NR/Sp complexes, and these genes can be targeted by ligands that target NRs and also by drugs that induce degradation of Sp1, Sp3 and Sp4. Full article

In the field of mechanical engineering, understanding mechanisms is essential for designing and developing devices and systems. Mechanisms, composed of interconnected elements, transform the energy applied to the input link into motion or force in the output link. Mechanisms are found in a wide variety of machines, from industrial machines to household machines. In this paper, a mechanism synthesis method is developed that can model four-bar linkages and build their cognate mechanisms to be able to select the mechanism that best suits the required work. Studying four-bar mechanisms offers a strong foundation for grasping more complex mechanical systems. The concepts and principles learned from four-bar mechanisms are widely applicable to advanced mechanical systems, making them a crucial starting point in mechanical engineering education and research. The mechanism synthesis method proposed in this article is organized into three main sections. The first section provides a comprehensive overview of the theoretical and mathematical foundations required for modeling mechanisms, laying the groundwork for understanding the subsequent calculations. The second section delves into the process of obtaining and analyzing the initial mechanism and constructing cognate mechanisms, detailing the procedures and algorithms used for modeling and calculating the coupling curve. Finally, the third section discusses the practical implementation of the method, including the graphical representation of mechanisms and a comparative analysis of the solutions obtained, assessing dimensional differences, design and manufacturing efficiency, and their suitability for various practical applications. The proposed four-bar mechanism synthesis method serves as a valuable tool for mechanism design, offering versatile and adaptable solutions that can optimize both technical performance and economic viability across a wide range of engineering applications. Full article

Fibroblast Growth Factors (FGFs) and their cognate receptors, FGFRs, play pivotal roles in a plethora of biological processes, including cell proliferation, differentiation, tissue repair, and metabolic homeostasis. This review provides a comprehensive overview of FGF-FGFR signaling pathways while highlighting their complex regulatory mechanisms and interconnections with other signaling networks. Further, we briefly discuss the FGFs involvement in developmental, metabolic, and housekeeping functions. By complementing current knowledge and emerging research, this review aims to enhance the understanding of FGF-FGFR-mediated signaling and its implications for health and disease, which will be crucial for therapeutic development against FGF-related pathological conditions. Full article