MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.

The precise prediction of Major Histocompatibility Complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning it with a specialized dataset consisting of exclusively high-resolution Class I MHC-peptide crystal structures. This tailored approach aimed to address the generalist nature of AlphaFold's original training, which, while broad-ranging, lacked the granularity necessary for the high-precision demands of Class I MHC-peptide interaction prediction. A comparative analysis was conducted against the homology-modeling-based method Pandora, as well as the AlphaFold multimer model. Our results demonstrate that our fine-tuned model outperforms others in terms of RMSD (median value for C-alpha atoms for peptides is 0.66 Å) and also provides enhanced predicted lDDT scores, offering a more reliable assessment of the predicted structures. These advances have substantial implications for computational immunology, potentially accelerating the development of novel therapeutics and vaccines by providing a more precise computational lens through which to view MHC-peptide interactions.

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

Generative ß-hairpin design using a residue-based physicochemical property landscape.

De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the ß-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of ß hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial ß-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.

CD4 dim CD8 bright T cells are inversely associated with neuro-inflammatory markers among people with HIV.

OBJECTIVE: HIV-associated neuroinflammation persists in the brain despite suppressive combination antiretroviral therapy (cART). We evaluated associations between a subset of CD8 + T cells, termed CD4 dim CD8 bright T cells, and soluble markers of immune activation and/or neuroinflammation in the cerebrospinal fluid (CSF) and plasma of people with HIV (PWH). DESIGN: Fifteen cART-naive PWH were enrolled and underwent blood draw, lumbar puncture for CSF collection, and neuropsychological tests at week 0 (pre-cART) and 24 weeks after cART initiation. METHODS: CSF and peripheral blood T cells were evaluated with flow cytometry and soluble markers of immune activation were measured by multiplex and singleplex assays. Spearman bootstrap correlation coefficients with 10 000 resamples were computed and reported with corresponding 95% confidence intervals (CIs) for each marker of interest and T-cell type. RESULTS: The frequency of CSF CD4 dim CD8 bright T cells at week 0 was inversely related with CSF neopterin. In contrast, at week 24, CSF CD4 - CD8 + T cells were positively correlated with CSF s100ß, a marker of brain injury. In the blood, at week 0, CD4 dim CD8 bright T cells were inversely correlated with MCP-1, IP-10, IL-8, IL-6, G-CSF, and APRIL and positively correlated with plasma RANTES and MMP1. At week 0, the frequency of blood CD4 - CD8 + were positively correlated with CRP and BAFF. CONCLUSION: CD4 dim CD8 bright T cells are associated with some anti-inflammatory properties, whereas CD4 - CD8 + T cells may contribute to inflammation and injury. Assessing the contrast between these two cell populations in neuroHIV may inform targeted therapeutic intervention to reduce neuroinflammation and associated neurocognitive impairment.

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.

The precise prediction of Major Histocompatibility Complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning it with a specialized dataset comprised by exclusively high-resolution MHC-peptide crystal structures. This tailored approach aimed to address the generalist nature of AlphaFold's original training, which, while broad-ranging, lacked the granularity necessary for the high-precision demands of MHC-peptide interaction prediction. A comparative analysis was conducted against the homology-modeling-based method Pandora [13], as well as the AlphaFold multimer model [8]. Our results demonstrate that our fine-tuned model outperforms both in terms of RMSD (median value is 0.65 Å) but also provides enhanced predicted lDDT scores, offering a more reliable assessment of the predicted structures. These advances have substantial implications for computational immunology, potentially accelerating the development of novel therapeutics and vaccines by providing a more precise computational lens through which to view MHC-peptide interactions.

An active HIV reservoir during ART is associated with maintenance of HIV-specific CD8+ T cell magnitude and short-lived differentiation status.

Before initiation of antiretroviral therapy (ART), HIV-specific CD8+ T cells are dysfunctional and short lived. To better understand the relationship between the HIV reservoir in CD4+ T cells and the magnitude and differentiation status of HIV-specific CD8+ T cells, we investigated these cells from acute and chronic HIV-infected individuals after 2 years of ART. Although both the HIV reservoir and the CD8+ T cell responses declined significantly after 2 years of ART, sustained HIV-specific CD8+ T cell responses correlated with a greater reduction of integrated HIV provirus. However, the magnitude of CD8+ T cells specific for HIV Gag, Pol, Nef, and Vif proteins positively associated with the active reservoir size during ART, measured as cell-associated RNA. Importantly, high HIV DNA levels strongly associate with maintenance of short-lived HIV-specific CD8+ T cells, regardless of ART initiation time. Our data suggest that the active reservoir maintains HIV-specific CD8+ T cell magnitude but prevents their differentiation into functional cells.

Initial productive and latent HIV infections originate in vivo by infection of resting T cells.

Productively infected cells are generally thought to arise from HIV infection of activated CD4+ T cells, and these infected activated cells are thought to be a recurring source of latently infected cells when a portion of the population transitions to a resting state. We discovered and report here that productively and latently infected cells can instead originate from direct infection of resting CD4+ T cell populations in lymphoid tissues in Fiebig I, the earliest stage of detectable HIV infection. We found that direct infection of resting CD4+ T cells was correlated with the availability of susceptible target cells in lymphoid tissues largely restricted to resting CD4+ T cells in which expression of pTEFb enabled productive infection, and we documented persistence of HIV-producing resting T cells during antiretroviral therapy (ART). Thus, we provide evidence of a mechanism by which direct infection of resting T cells in lymphoid tissues to generate productively and latently infected cells creates a mechanism by which the productively infected cells can replenish both populations and maintain two sources of virus from which HIV infection can rebound, even if ART is instituted at the earliest stage of detectable infection.

Feasibility of a text-mediated recall system to increase cardiovascular disease risk assessment in general practice: Mixed-methods pilot evaluation.

BACKGROUND AND OBJECTIVES: The uptake of formal cardiovascular disease risk assessment in the primary prevention setting is low. We tested the feasibility of an SMS recall system to invite eligible patients for a Heart Health Check in Australian general practice. METHOD: Of 332 general practices that expressed interest in the study, 231 were randomised to either an intervention or wait list control group. Intervention general practices sent SMS invitations linked to digital information to eligible patients via general practice software. Deidentified baseline and two-month data were extracted via clinical audit software. A survey was administered to 35 intervention general practices. RESULTS: General practice visits were similar between the control and intervention groups, but Heart Health Check billing increased 14-fold in the intervention group. DISCUSSION: This study showed that an SMS recall system for Heart Health Checks can be effective and acceptable in general practice. The findings will inform a broader implementation trial over 2022-23.

Study design and baseline profile for adults with type 2 diabetes in the once-weekly subcutaneous SEmaglutide randomized PRAgmatic (SEPRA) trial.

INTRODUCTION: Once-weekly subcutaneous semaglutide, a glucagon-like peptide-1 analog, is approved in the USA as an adjunct to diet and exercise for adults with inadequately controlled type 2 diabetes (T2D) to improve glycemic control and reduce the risk of major adverse cardiovascular events in people with T2D and established cardiovascular disease. The Semaglutide Unabated Sustainability in Treatment of Type 2 Diabetes (SUSTAIN) phase III clinical trial program demonstrated the efficacy and safety of once-weekly subcutaneous semaglutide; however, determining its effectiveness in a real-world setting could support decision-making by clinicians, payers and policy makers in routine clinical practice. RESEARCH DESIGN AND METHODS: SEmaglutide PRAgmatic (SEPRA) is an ongoing open-label, randomized, pragmatic clinical trial designed to compare the effects of once-weekly subcutaneous semaglutide versus standard of care in US health-insured adults with T2D and physician-determined inadequate glycemic control. The primary end point is the proportion of participants achieving glycated hemoglobin (HbA1c) <7.0% at year 1; other key outcomes include glycemic control, weight loss, healthcare utilization, and patient-reported outcomes. Individual-level data will be collected from routine clinical practice and health insurance claims. The last patient last visit is expected by June 2023. RESULTS: Between July 2018 and March 2021, 1278 participants were enrolled from 138 study sites across the USA. At baseline, 54% were male with mean±SD age 57.4±11.1 years and body mass index 35.7±8.0 kg/m2. Mean diabetes duration was 7.4±6.0 years and mean HbA1c was 8.5±1.6%. At baseline, concomitant antidiabetes medications included metformin, sulfonylureas, sodium-glucose co-transporter-2 inhibitors, and dipeptidyl peptidase-4 inhibitors. The majority of participants had hypertension and dyslipidemia. The trial design was self-assessed using the PRagmatic Explanatory Continuum Indicator Summary-2 tool by the study steering group and was scored 4-5 in all domains suggesting a highly pragmatic study. CONCLUSIONS: SEPRA, a highly pragmatic ongoing study, will provide data on the effects of once-weekly subcutaneous semaglutide in a real-world setting when used during routine management of T2D. TRIAL REGISTRATION NUMBER: NCT03596450.

HIV rapidly targets a diverse pool of CD4+ T cells to establish productive and latent infections.

Upon infection, HIV disseminates throughout the human body within 1-2 weeks. However, its early cellular targets remain poorly characterized. We used a single-cell approach to retrieve the phenotype and TCR sequence of infected cells in blood and lymphoid tissue from individuals at the earliest stages of HIV infection. HIV initially targeted a few proliferating memory CD4+ T cells displaying high surface expression of CCR5. The phenotype of productively infected cells differed by Fiebig stage and between blood and lymph nodes. The TCR repertoire of productively infected cells was heavily biased, with preferential infection of previously expanded and disseminated clones, but composed almost exclusively of unique clonotypes, indicating that they were the product of independent infection events. Latent genetically intact proviruses were already archived early in infection. Hence, productive infection is initially established in a pool of phenotypically and clonotypically distinct T cells, and latently infected cells are generated simultaneously.

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO226-234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

Long-term antiretroviral therapy initiated in acute HIV infection prevents residual dysfunction of HIV-specific CD8+ T cells.

BACKGROUND: Harnessing CD8+ T cell responses is being explored to achieve HIV remission. Although HIV-specific CD8+ T cells become dysfunctional without treatment, antiretroviral therapy (ART) partially restores their function. However, the extent of this recovery under long-term ART is less understood. METHODS: We analyzed the differentiation status and function of HIV-specific CD8+ T cells after long-term ART initiated in acute or chronic HIV infection ex vivo and upon in vitro recall. FINDINGS: ART initiation in any stage of acute HIV infection promoted the persistence of long-lived HIV-specific CD8+ T cells with high expansion (P<0·0008) and cytotoxic capacity (P=0·02) after in vitro recall, albeit at low cell number (P=0·003). This superior expansion capacity correlated with stemness (r=0·90, P=0·006), measured by TCF-1 expression, similar to functional HIV-specific CD8+ T cells found in spontaneous controllers. Importanly, TCF-1 expression in these cells was associated with longer time to viral rebound ranging from 13 to 48 days after ART interruption (r =0·71, P=0·03). In contrast, ART initiation in chronic HIV infection led to more differentiated HIV-specific CD8+ T cells lacking stemness properties and exhibiting residual dysfunction upon recall, with reduced proliferation and cytolytic activity. INTERPRETATION: ART initiation in acute HIV infection preserves functional HIV-specific CD8+ T cells, albeit at numbers too low to control viral rebound post-ART. HIV remission strategies may need to boost HIV-specific CD8+ T cell numbers and induce stem cell-like properties to reverse the residual dysfunction persisting on ART in people treated after acute infection prior to ART release. FUNDING: U.S. National Institutes of Health and U.S. Department of Defense.

Providing guideline-recommended preventive cardiovascular care to Aboriginal and Torres Strait Islander women: exploring gender differences with a medical record review in primary health care.

BACKGROUND: For Aboriginal and Torres Strait Islander women, the premature burden of cardiovascular disease is affecting their capacity to fulfil roles in society, and promote the health and wellbeing of future generations. In Australia, there is limited understanding of the difference in primary preventive cardiovascular care experienced by women, despite knowledge of sex and gender differentials in health profile and receipt of guideline-based acute care. This paper sought to explore the health profile and receipt of assessment and management of cardiovascular risk for Aboriginal and Torres Strait Islander women accessing preventive primary health care, and investigate gender differentials. METHOD: Records of 1200 current clients, 50% women, aged 18-74years from three Aboriginal Health Services in central and South Australia for the period 7/2018-6/2020 were reviewed. RESULTS: Twelve percent had documented cardiovascular disease. Compared with men, women with no recorded cardiovascular disease had a greater likelihood of being overweight or obese, a waist circumference indicative of risk, diabetes, and depression. Women were less likely to report being physically active. CONCLUSIONS: The research concluded that gaps exist in the provision and recording of guideline-recommended primary preventive care regardless of sex. These are stark, given the evident burden.

Development and Use of a Cardiac Clinical Guideline Mobile App in Australia: Acceptability and Multi-Methods Study.

BACKGROUND: Implementation of clinical guidelines into routine practice remains highly variable. Strategies to increase guideline uptake include developing digital tools and mobile apps for use in clinical practice. The National Heart Foundation of Australia in collaboration with the Cardiac Society of Australia and New Zealand published 3 key cardiac clinical guidelines, including the Australian clinical guidelines for the (1) prevention and detection of atrial fibrillation, (2) detection and management of heart failure, and (3) management of acute coronary syndromes. To improve access and uptake for health care providers, we developed the Smart Heart Guideline App. OBJECTIVE: This study aims to evaluate the acceptability, implementation, and usability of an Australian-specific cardiac guidelines mobile app. METHODS: We used an iterative multiple methods development and implementation approach. First, we conducted a cross-sectional web-based survey with end users (n=504 health professionals) in 2017 to determine the acceptability of an Australian-specific cardiac clinical guidelines mobile app. Second, the Smart Heart Guidelines app was created using a design, user testing, and revision process. The app includes interactive algorithms and flowcharts to inform diagnosis and management at the point of care. The freely available app was launched in October 2019 on iOS and Android operating systems and promoted and implemented using multiple methods. Third, data from 2 annual national cross-sectional general practitioner (GP) surveys in 2019 and 2020 were evaluated to understand the awareness and use of the clinical guidelines and the app. Fourth, data from the app stores were analyzed between October 1, 2019, and June 30, 2021, to evaluate usage. RESULTS: Most health professionals surveyed (447/504, 89%) reported accessing resources electronically, and most (318/504, 63%) reported that they would use an Australian-specific cardiac guidelines app. GPs surveyed in 2019 were aware of the heart failure (159/312, 51%) and atrial fibrillation (140/312, 45%) guidelines, and in 2020, a total of 34 of 189 (18%) reported that they were aware of the app. The app was downloaded 11,313 times (7483, 66% from the Apple App Store; 3830, 34% from Google Play) during the first 20-month period. Most downloads (6300/7483, 84%) were a result of searching for the app in the stores. Monthly download rates varied. App Store data showed that people used the app twice (on average 2.06 times) during the 20 months. Many (3256/3830, 85%) Android users deleted the app. CONCLUSIONS: Health professionals supported the development of the Smart Heart Guidelines app. Although initial downloads were promising, the frequency of using the app was low and deletion rates were high. Further evaluation of users' experience of the most and least useful components of the app is needed.

Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho.

Fibroblast growth factor 23 (FGF23) is a therapeutic target for treating hereditary and acquired hypophosphatemic disorders, such as X-linked hypophosphatemic (XLH) rickets and tumor-induced osteomalacia (TIO), respectively. FGF23-induced hypophosphatemia is mediated by signaling through a ternary complex formed by FGF23, the FGF receptor (FGFR), and α-Klotho. Currently, disorders of excess FGF23 are treated with an FGF23-blocking antibody, burosumab. Small-molecule drugs that disrupt protein/protein interactions necessary for the ternary complex formation offer an alternative to disrupting FGF23 signaling. In this study, the FGF23:α-Klotho interface was targeted to identify small-molecule protein/protein interaction inhibitors since it was computationally predicted to have a large fraction of hot spots and two druggable residues on α-Klotho. We further identified Tyr433 on the KL1 domain of α-Klotho as a promising hot spot and α-Klotho as an appropriate drug-binding target at this interface. Subsequently, we performed in silico docking of ∼5.5 million compounds from the ZINC database to the interface region of α-Klotho from the ternary crystal structure. Following docking, 24 and 20 compounds were in the final list based on the lowest binding free energies to α-Klotho and the largest number of contacts with Tyr433, respectively. Five compounds were assessed experimentally by their FGF23-mediated extracellular signal-regulated kinase (ERK) activities in vitro, and two of these reduced activities significantly. Both these compounds were predicted to have favorable binding affinities to α-Klotho but not have a large number of contacts with the hot spot Tyr433. ZINC12409120 was found experimentally to disrupt FGF23:α-Klotho interaction to reduce FGF23-mediated ERK activities by 70% and have a half maximal inhibitory concentration (IC50) of 5.0 ± 0.23 µM. Molecular dynamics (MD) simulations of the ZINC12409120:α-Klotho complex starting from in silico docking poses reveal that the ligand exhibits contacts with residues on the KL1 domain, the KL1-KL2 linker, and the KL2 domain of α-Klotho simultaneously, thereby possibly disrupting the regular function of α-Klotho and impeding FGF23:α-Klotho interaction. ZINC12409120 is a candidate for lead optimization.

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances.

SUMMARY: Easy-to-use, open-source, general-purpose programs for modeling a protein structure from inter-atomic distances are needed for modeling from experimental data and refinement of predicted protein structures. OpenMDlr is an open-source Python package for modeling protein structures from pairwise distances between any atoms, and optionally, dihedral angles. We provide a user-friendly input format for harnessing modern biomolecular force fields in an easy-to-install package that can efficiently make use of multiple compute cores. AVAILABILITY AND IMPLEMENTATION: OpenMDlr is available at https://github.com/BSDExabio/OpenMDlr-amber. The package is written in Python (versions 3.x). All dependencies are open-source and can be installed with the Conda package management system. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A systematic review on assessment and management of preventive cardiovascular care in primary health for Aboriginal and Torres Strait Islander women and men.

In promoting positive cardiovascular health for Aboriginal and Torres Strait Islander peoples, there is a need to ensure provision of high-quality risk assessment and management in primary healthcare settings. There is some evidence of gender gaps for Australian women in the provision of cardiovascular risk assessment and management; however, there is little understanding of whether these gaps are also present for Aboriginal and Torres Strait Islander women. A mixed-method systematic review was utilised to synthesise existing evidence on the provision of assessment and management against guideline-recommended care for Aboriginal and Torres Strait Islander women, and determine whether gender disparities in provision of care exist for this population. Sixteen studies that report gender-specific data indicate there are significant gaps in the provision of assessment and management for Aboriginal and Torres Strait Islander women and men alike. There is no evidence of incorporation of social and emotional wellbeing into cardiovascular care and limited studies outlining the assessment and management of behaviours and factors that may be protective of cardiovascular health. Furthermore, little is known about the provision of care in mainstream primary health services for Aboriginal and Torres Strait Islander peoples.

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis.

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.

Biological and Molecular Components for Genetically Engineering Biosensors in Plants.

Plants adapt to their changing environments by sensing and responding to physical, biological, and chemical stimuli. Due to their sessile lifestyles, plants experience a vast array of external stimuli and selectively perceive and respond to specific signals. By repurposing the logic circuitry and biological and molecular components used by plants in nature, genetically encoded plant-based biosensors (GEPBs) have been developed by directing signal recognition mechanisms into carefully assembled outcomes that are easily detected. GEPBs allow for in vivo monitoring of biological processes in plants to facilitate basic studies of plant growth and development. GEPBs are also useful for environmental monitoring, plant abiotic and biotic stress management, and accelerating design-build-test-learn cycles of plant bioengineering. With the advent of synthetic biology, biological and molecular components derived from alternate natural organisms (e.g., microbes) and/or de novo parts have been used to build GEPBs. In this review, we summarize the framework for engineering different types of GEPBs. We then highlight representative validated biological components for building plant-based biosensors, along with various applications of plant-based biosensors in basic and applied plant science research. Finally, we discuss challenges and strategies for the identification and design of biological components for plant-based biosensors.