Specific Signaling Research Articles

TetR and OmpR family regulators in natural product biosynthesis and resistance.

This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.

CRISPR/dCas9-Mediated Specific Molecular Assembly Facilitates Genotyping of Mutant Circulating Tumor DNA.

Breakthroughs in circulating tumor DNA (ctDNA) analysis are critical in tumor liquid biopsies but remain a technical challenge due to the double-stranded structure, extremely low abundance, and short half-life of ctDNA. Here, we report an electrochemical CRISPR/dCas9 sensor (E-dCas9) for sensitive and specific detection of ctDNA at a single-nucleotide resolution. The E-dCas9 design harnesses the specific capture and unzipping of target ctDNA by dCas9 to introduce a complementary reporter probe for specific molecular assembly and signal amplification. By efficient homogeneous assembly and interfacial click reaction, the assay demonstrates superior sensitivity (up to 2.86 fM) in detecting single-base mutant ctDNA and a broad dynamic range spanning 6 orders of magnitude. The sensor is also capable of measuring 10 fg/μL of a mutated target in excess of wild-type ones (1 ng/μL), equivalent to probing 0.001% of the mutation relative to the wild type. In addition, our sensor can monitor the dynamic expression of cellular genomic DNA and allows accurate analysis of blood samples from patients with nonsmall cell lung cancer, suggesting the potential of E-dCas9 as a promising tool in ctDNA-based cancer diagnosis.

Dosimetry of [18F]TRACK, the first PET tracer for imaging of TrkB/C receptors in humans

BackgroundReduced expression or impaired signalling of tropomyosin receptor kinases (Trk receptors) are found in a vast spectrum of CNS disorders. [18F]TRACK is the first PET radioligand for TrkB/C with proven in vivo brain penetration and on-target specific signal. Here we report dosimetry data for [18F]TRACK in healthy humans. 6 healthy participants (age 22–61 y, 3 female) were scanned on a General Electric Discovery PET/CT 690 scanner. [18F]TRACK was synthesized with high molar activities (Am = 250 ± 75 GBq/µmol), and a dynamic series of 12 whole-body scans were acquired after injection of 129 to 147 MBq of the tracer. Images were reconstructed with standard corrections using the manufacturer’s OSEM algorithm. Tracer concentration time-activity curves (TACs) were obtained using CT-derived volumes-of-interest. Organ-specific doses and the total effective dose were estimated using the Committee on Medical Internal Radiation Dose equation for adults and tabulated Source tissue values (S values).ResultsAverage organ absorbed dose was highest for liver and gall bladder with 6.1E−2 (± 1.06E−2) mGy/MBq and 4.6 (± 1.18E−2) mGy/MBq, respectively. Total detriment weighted effective dose EDW was 1.63E−2 ± 1.68E−3 mSv/MBq. Organ-specific TACs indicated predominantly hepatic tracer elimination.ConclusionTotal and organ-specific effective doses for [18F]TRACK are low and the dosimetry profile is similar to other 18F-labelled radio tracers currently used in clinical settings.

Current Advances in Stimuli-Responsive Hydrogels as Smart Drug Delivery Carriers.

In recent years, significant advancements in the field of advanced materials and hydrogel engineering have enabled the design and fabrication of smart hydrogels and nanogels that exhibit sensitivity to specific signals or pathological conditions, leading to a wide range of applications in drug delivery and disease treatment. This comprehensive review aims to provide an in-depth analysis of the stimuli-responsive principles exhibited by smart hydrogels in response to various triggers, such as pH levels, temperature fluctuations, light exposure, redox conditions, or the presence of specific biomolecules. The functionality and performance characteristics of these hydrogels are highly influenced by both their constituent components and fabrication processes. Key design principles, their applications in disease treatments, challenges, and future prospects were also discussed. Overall, this review aims to contribute to the current understanding of gel-based drug delivery systems and stimulate further research in this rapidly evolving field.

Functional evidence that FGFR regulates MAPK signaling in organizer specification in the gastropod mollusk Lottia peitaihoensis.

The online version contains supplementary material available at 10.1007/s42995-023-00194-x.

Design and implementation of a virtual nuclear pulse signal generator

This paper presents a virtual nuclear pulse signal generator. The pulse generator can be used in specific scenarios such as calibration and maintenance of nuclear detection systems, validation of nuclear signal processing algorithms, and nuclear physics teaching experiments, as a substitute for real radioactive sources and detectors to generate nuclear pulse signals. This helps to avoid exposing experimental personnel to radiation hazards. The pulse generator is capable of generating specific nuclear pulse signals according to experimental requirements, and these signals has the same physical characteristics as real nuclear pulse signals, including amplitude distribution, time and amplitude randomness. In the pulse generator, we conducted theoretical analysis of the radioactive source and detector, and established a model library for both, to obtain crucial parameters of the nuclear pulse signals. The pulse generator is built on a hardware framework with field-programmable gate array (FPGA) as the core, utilizing these key parameters to generate signals with realistic physical characteristics of nuclear pulse signals, including amplitude and time characteristics. The counting rate of the output nuclear pulse signals can be adjusted by configuring the hardware parameters of the pulse generator.

Anti-cancer targets and molecular mechanisms of formononetin in treating osteosarcoma based on network pharmacology.

Osteosarcoma (OS) is a multifactorial bone malignancy that accounts for most cancers in children and adolescents. Formononetin has been proven to exhibit various pharmacological effects including anti-tumor, anti-obesity, anti-inflammation, and neuroprotective effects. Few studies have examined the pharmacological activities of formononetin in OS treatment, but the mechanism has not yet been completely elucidated. Network pharmacology is a new method based on the theory of system biology for analyzing the network of biological systems and selecting specific signal nodes for multi-target drug molecular design. Here, we used network pharmacology to explore the possible mechanism of formononetin in OS treatment. Human OS cell line MG63 was processed with four concentrations (0, 2, 5, 8 μg/mL) of formononetin. Subsequently, an MTT assay was performed to test cell proliferation and a scratch test was used to evaluate the migration ability of cancer cells. Caspase-3, p53, p21, and bcl-2 expression levels incubated with different concentrations of formononetin in MG63 cells were determined using Western blotting. After treated with formononetin for 48 h, MG63 cells exhibited marked apoptosis. The results revealed that certain concentrations of formononetin significantly exerted inhibitory effects on MG63 cell proliferation. Furthermore, formononetin decreased the bcl-2 level in MG63 cells but increased caspase-3, p21, and p53 levels in a concentration-dependent manner. Additionally, formononetin suppressed the expression of SATB2. Therefore, formononetin could dose-dependently inhibit MG63 cell proliferation and induce apparent cell apoptosis, providing a candidate treatment for OS, whereas SATB2 could be a potential prognostic biomarker for screening OS and therapeutic target of formononetin.

Immune cell abundance and T cell receptor landscapes suggest new patient stratification strategies in head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is a molecularly and spatially heterogeneous disease frequently characterized by impairment of immunosurveillance mechanisms. Despite recent success with immunotherapy treatment, disease progression still occurs quickly after treatment in the majority of cases, suggesting the need to improve patient selection strategies. In the quest for biomarkers that may help inform response to checkpoint blockade, we characterized the tumour microenvironment (TME) of 162 HNSCC primary tumours of diverse aetiological and spatial origin, through gene expression and immunohistochemistry (IHC) profiling of relevant immune proteins, T cell receptor (TCR) repertoire analysis and whole-exome sequencing. We identified five HNSCC TME categories based on immune/stromal composition: (1) cytotoxic, (2) plasma cell rich, (3) dendritic cell rich, (4) macrophage rich and (5) immune-excluded. Remarkably, the cytotoxic and plasma cell rich subgroups exhibited a phenotype similar to tertiary lymphoid structures (TLS), which have been previously linked to immunotherapy response. We also found an increased richness of the TCR repertoire in these two subgroups and in never smokers. Mutational patterns evidencing APOBEC activity were enriched in the plasma cell high subgroup. Furthermore, specific signal propagation patterns within the Ras/ERK and PI3K/AKT pathways associated with distinct immune phenotypes. While traditionally CD8/CD3 T cell infiltration and immune checkpoint expression (e.g. PD-L1) have been used in the patient selection process for checkpoint blockade treatment, we suggest that additional biomarkers, such as TCR productive clonality, smoking history and TLS index, may have the ability to pull out potential responders to benefit from immunotherapeutic agents.

Oxidative stress and the role of redox signalling in chronic kidney disease.

Chronic kidney disease (CKD) is a major public health concern, underscoring a need to identify pathogenic mechanisms and potential therapeutic targets. Reactive oxygen species (ROS) are derivatives of oxygen molecules that are generated during aerobic metabolism and are involved in a variety of cellular functions that are governed by redox conditions. Low levels of ROS are required for diverse processes, including intracellular signal transduction, metabolism, immune and hypoxic responses, and transcriptional regulation. However, excess ROS can be pathological, and contribute to the development and progression of chronic diseases. Despite evidence linking elevated levels of ROS to CKD development and progression, the use of low-molecular-weight antioxidants to remove ROS has not been successful in preventing or slowing disease progression. More recent advances have enabled evaluation of the molecular interactions between specific ROS and their targets in redox signalling pathways. Such studies may pave the way for the development of sophisticated treatments that allow the selective control of specific ROS-mediated signalling pathways.

Systems and synthetic biology-driven engineering of live bacterial therapeutics.

The past decade has seen growing interest in bacterial engineering for therapeutically relevant applications. While early efforts focused on repurposing genetically tractable model strains, such as Escherichia coli, engineering gut commensals is gaining traction owing to their innate capacity to survive and stably propagate in the intestine for an extended duration. Although limited genetic tractability has been a major roadblock, recent advances in systems and synthetic biology have unlocked our ability to effectively harness native gut commensals for therapeutic and diagnostic purposes, ranging from the rational design of synthetic microbial consortia to the construction of synthetic cells that execute "sense-and-respond" logic operations that allow real-time detection and therapeutic payload delivery in response to specific signals in the intestine. In this review, we outline the current progress and latest updates on microbial therapeutics, with particular emphasis on gut commensal engineering driven by synthetic biology and systems understanding of their molecular phenotypes. Finally, the challenges and prospects of engineering gut commensals for therapeutic applications are discussed.

CellCommuNet: an atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states.

Cell-cell communication, as a basic feature of multicellular organisms, is crucial for maintaining the biological functions and microenvironmental homeostasis of cells, organs, and whole organisms. Alterations in cell-cell communication contribute to many diseases, including cancers. Single-cell RNA sequencing (scRNA-seq) provides a powerful method for studying cell-cell communication by enabling the analysis of ligand-receptor interactions. Here, we introduce CellCommuNet (http://www.inbirg.com/cellcommunet/), a comprehensive data resource for exploring cell-cell communication networks in scRNA-seq data from human and mouse tissues in normal and disease states. CellCommuNet currently includes 376 single datasets from multiple sources, and 118 comparison datasets between disease and normal samples originating from the same study. CellCommuNet provides information on the strength of communication between cells and related signalling pathways and facilitates the exploration of differences in cell-cell communication between healthy and disease states. Users can also search for specific signalling pathways, ligand-receptor pairs, and cell types of interest. CellCommuNet provides interactive graphics illustrating cell-cell communication in different states, enabling differential analysis of communication strength between disease and control samples. This comprehensive database aims to be a valuable resource for biologists studying cell-cell communication networks.

Biocontrol mechanisms of Bacillus: Improving the efficiency of green agriculture.

Species of the genus Bacillus have been widely used for the biocontrol of plant diseases in the demand for sustainable agricultural development. New mechanisms underlying Bacillus biocontrol activity have been revealed with the development of microbiome and microbe-plant interaction research. In this review, we first briefly introduce the typical Bacillus biocontrol mechanisms, such as the production of antimicrobial compounds, competition for niches/nutrients, and induction of systemic resistance. Then, we discussed in detail the new mechanisms of pathogen quorum sensing interference and reshaping of the soil microbiota. The "cry for help" mechanism was also introduced, in which plants can release specific signals under pathogen attack to recruit biocontrol Bacillus for root colonization against invasion. Finally, two emerging strategies for enhancing the biocontrol efficacy of Bacillus agents, including the construction of synthetic microbial consortia and the application of rhizosphere-derived prebiotics, were proposed.

Modified prairie dog optimization algorithm for global optimization and constrained engineering problems.

The prairie dog optimization (PDO) algorithm is a metaheuristic optimization algorithm that simulates the daily behavior of prairie dogs. The prairie dog groups have a unique mode of information exchange. They divide into several small groups to search for food based on special signals and build caves around the food sources. When encountering natural enemies, they emit different sound signals to remind their companions of the dangers. According to this unique information exchange mode, we propose a randomized audio signal factor to simulate the specific sounds of prairie dogs when encountering different foods or natural enemies. This strategy restores the prairie dog habitat and improves the algorithm's merit-seeking ability. In the initial stage of the algorithm, chaotic tent mapping is also added to initialize the population of prairie dogs and increase population diversity, even use lens opposition-based learning strategy to enhance the algorithm's global exploration ability. To verify the optimization performance of the modified prairie dog optimization algorithm, we applied it to 23 benchmark test functions, IEEE CEC2014 test functions, and six engineering design problems for testing. The experimental results illustrated that the modified prairie dog optimization algorithm has good optimization performance.

Single-nuclei characterization of pervasive transcriptional signatures across organs in response to COVID-19.

Infection by coronavirus SARS-CoV2 is a severe and often deadly disease that has implications for the respiratory system and multiple organs across the human body. While the effects in the lung have been extensively studied, less is known about the impact COVID-19 has across other organs. Here, we contribute a single-nuclei RNA-sequencing atlas comprising six human organs across 20 autopsies where we analyzed the transcriptional changes due to COVID-19 in multiple cell types. The integration of data from multiple organs enabled the identification of systemic transcriptional changes. Computational cross-organ analysis for endothelial cells and macrophages identified systemic transcriptional changes in these cell types in COVID-19 samples. In addition, analysis of gene modules showed enrichment of specific signaling pathways across multiple organs in COVID-19 autopsies. Altogether, the COVID Tissue Atlas enables the investigation of both cell type-specific and cross-organ transcriptional responses to COVID-19, providing insights into the molecular networks affected by the disease and highlighting novel potential targets for therapies and drug development. The Chan-Zuckerberg Initiative, The Chan-Zuckerberg Biohub.

Armillaria ostoyae extracts inhibit EMT of cancer cell lines via TGF-β and Wnt/β-catenin signaling components

Armillaria ostoyae is an edible mushroom, appreciated in human nutrition, with several medicinal properties already proven. However, its phenolic composition and effects on cancer have never been investigated so far, especially regarding specific signaling pathways included in first steps of cancer metastatic process, epithelial-mesenchymal transition (EMT) and migration. We report phenolic profile of two Armillaria ostoyae extracts, ethanol and diethyl ether (E and DE) and their effects on colorectal carcinoma (HCT-116) and cervical adenocarcinoma (HeLa) cells. Phenolics were detected using HPLC, while effects on cancer cells were investigated using MTT test; expression of markers related to EMT on gene and protein level by flow cytometry, immunofluorescence and qRT-PCR method. Antimigratory potential was assessed on collective and individual type of migration by Wound healing assay and RTCA technique. Sinapic acid was detected as the main phenolic component in E, while rutin and naringin were dominant in DE type of extract. Extracts notably suppressed pro-EMT markers: vimentin, N-cadherin, β-catenin, Snail, Smad2 and MMP-9, and elevated anti-EMT marker E-cadherin. Consequently, collective and single cell migration were significantly inhibited via regulation of TGF-β and Wnt/β-catenin signaling components. DE extract was more efficient in suppression of EMT and migration of colorectal and cervical cancer cells.

Insights from the protein interaction Universe of the multifunctional "Goldilocks" kinase DYRK1A.

Human Dual specificity tyrosine (Y)-Regulated Kinase 1A (DYRK1A) is encoded by a dosage-dependent gene located in the Down syndrome critical region of human chromosome 21. The known substrates of DYRK1A include proteins involved in transcription, cell cycle control, DNA repair and other processes. However, the function and regulation of this kinase is not fully understood, and the current knowledge does not fully explain the dosage-dependent function of this kinase. Several recent proteomic studies identified DYRK1A interacting proteins in several human cell lines. Interestingly, several of known protein substrates of DYRK1A were undetectable in these studies, likely due to a transient nature of the kinase-substrate interaction. It is possible that the stronger-binding DYRK1A interacting proteins, many of which are poorly characterized, are involved in regulatory functions by recruiting DYRK1A to the specific subcellular compartments or distinct signaling pathways. Better understanding of these DYRK1A-interacting proteins could help to decode the cellular processes regulated by this important protein kinase during embryonic development and in the adult organism. Here, we review the current knowledge of the biochemical and functional characterization of the DYRK1A protein-protein interaction network and discuss its involvement in human disease.

Physiological characteristics of IRR 400 series rubber clones (Hevea brasiliensis Muell. Arg.) under drought stress

Background: Drought stress is one of the main causes of plant death. Strategies for plants survival are morphological adaptations, specific signaling pathways, and tolerance mechanisms. Rubber plantations have many uses, such as foreign exchange sources, job sources, forest revitalization, and a source of alternative wood for building materials and furniture. The rubber plant’s response to drought stress is a complex biological process. A tolerant rubber clone in a dry area is the right approach. The present study aimed to determine the mechanism of drought-tolerant clones, based on physiological characteristics, to obtain character selection and drought-tolerant clones early. Methods: The first factor examined for this work was clones (IRR 425, IRR 428, IRR 429, IRR 434, IRR 440, RRIC 100, and BPM 24) and the second factor was water content (30%, 60%, and 90%). The study was arranged on a factorial randomized block design and repeated three times. Characteristics observed were total sugar (µM), proline (mg/L), chlorophyll a, b, total (µg/mL), hydrogen peroxidase (µmol/g), ascorbate peroxidase (unit/mg), superoxide dismutase (unit/mg), and peroxide dismutase (unit/mg). Results: The tolerance ability of the IRR 400 series rubber clones to drought stress was determined by observing the characteristics of sugar total and proline. The concentration of total sugar and proline were higher when the plant was treated with a lower water content. The selected clones tolerant to drought stress are RR 425 and IR 434 with high total sugar content and proline. Other characteristics, namely chlorophyll a, b, and total, as well as hydrogen peroxidase, ascorbate peroxidase, super oxide dismutase, peroxide dismutase, cannot be used as selection characteristics for this study. Conclusions: This drought study of IRR 400 clones with varying water content percentages illustrated that the total sugar and proline characteristics could be used to distinguish tolerance levels from other observed characteristics.

Utilizing Ground-Penetrating Radar for Water Leak Detection and Pipe Material Characterization in Environmental Studies: A Case Study

Detecting and mapping subsurface utilities in urban areas is crucial for identifying defects or damages in drinking and sewage pipes that can cause leaks. These leaks make it difficult to accurately characterize the pipes due to changes in their reflective properties. This study focused on detecting leaks originating from underground pipes and distinguishing between these various types of pipes. It also aimed to create a visual fingerprint model that displays the reflection characteristics of these pipes during different leak conditions, enabling efficient maintenance and handling procedures on the pipes. To achieve this, a finite-difference time-domain (FDTD) method was used to simulate two types of pipe materials with and without leak areas to construct different scenarios. Additionally, a ground-penetrating radar (GPR) field survey was conducted using a 600 MHz antenna in a part of the El Hammam area on Egypt’s northwest coast. The simulated images produced with numerical modeling were compared with the radar profiles obtained using GPR at particular locations. The numerical simulations and radar profiles demonstrated the noticeable influence of water leaks from the different pipes, wherein the reflection of saturated soil waves was interrupted due to the presence of saturated soil. Envelope and migration techniques were employed in a new application to accurately distinguish between different pipe types, specifically focusing on leak areas. The strong correlation between the real radar profile and the specific signal of a water pipe leak in the simulated models suggests that GPR is a reliable non-destructive geophysical method for detecting water pipe leaks and distinguishing between the different pipe materials in various field conditions. The simulated models, which serve as image-matching fingerprints to identify and map water pipe leaks, help us to comprehend reality better.

MiRNA Expression Signatures Induced by Chicken Astrovirus Infection in Chickens.

miRNAs represent ubiquitous regulators of gene expression and play an important and pivotal regulatory role in viral disease pathogenesis and virus-host interactions. Although previous studies have provided basic data for understanding the role of miRNAs in the molecular mechanisms of viral infection in birds, the role of miRNAs in the regulation of host responses to chicken astrovirus (CAstV) infection in chickens is not yet understood. In our study, we applied next-generation sequencing to profile miRNA expression in CAstV-infected chickens and to decipher miRNA-targeted specific signaling pathways engaged in potentially vital virus-infection biological processes. Among the 1354 detected miRNAs, we identified 58 mature miRNAs that were significantly differentially expressed in infected birds. Target prediction resulted in 4741 target genes. GO and KEGG pathway enrichment analyses showed that the target genes were mainly involved in the regulation of cellular processes and immune responses.

Sucrose function on the bulbil formation of Lilium lancifolium

Lilium lancifolium is an important ornamental, edible and medicinal plant in China.Bulbil is the main propagation organ of L.lancifolium. Studies have shown that high concentration of sucrose can significantly promote the formation of bulbil in vitro, but the detail function mechanism of sucrose on the process of bulbil formation in lily has not been reported. In this study, we investigated the osmotic regulation, carbon source and signal molecular functions of sucrose during bulbil formation using L.lancifolium as material. Results indicated that the optimal concentration of sucrose inducing bulbil formatin was 262.93 mM. The results of osmotic potential and soluble sugars experiments indicated that the effect of sucrose on bulbil formation of L.lancifolium was not connected to its osmotic potential, nor entirely explained by it's function as carbon source and energy. We used non-metabolic sugar analogues to study the effect of sucrose specific signaling on bulbil formation. Results indicated that exogenous 3-OMG could not induce bulbil formation. Whereas palatinose could induce bulbil formation, although the induction time was delayed compared with control, further indicating the specific signalling of sucrose. The results of sugar absorption inhibitor experiments showed that sucrose induced the bulbil formation by itself and by its decomposed hexose. In addition, gene expression analysis was performed in leaf axils. The results showed that high sucrose concentration may promote the formation of bulbil by inducing the expression of SUS2, SUT2 and WOX11 genes. Overall, the effect of sucrose on inducing bulbil formation could be explained by it's function of carbon source and signaling molecule.