Biology Approach Research Articles

MSC-derived exosome ameliorates pulmonary fibrosis by modulating NOD 1/NLRP3-mediated epithelial-mesenchymal transition and inflammation.

Pulmonary fibrosis (PF) is an irreversible and usually fatal lung disease. In recent years, the therapeutic role of exosomes derived from mesenchymal stem cells (MSC-exos) in anti-fibrotic treatment has received much attention. In this study, we aimed to determine the anti-fibrotic properties and related molecular mechanisms of MSC-exos in Bleomycin(BLM)-induced PF. We used BLM-induced mice model of PF and in vitro model. MSC-exos were isolated from BMSCs cells using Exo Quick-TC kit and identified using conventional methods. Using cell counting kit-8 (CCK-8) to detect cell viability. Classic molecular biology approaches such as RT-qPCR, Western blot, immunofluorescence, and ELISA were used to examine molecular pathways. Histopathological examination was performed using HE and Masson staining. MSC-exos alleviated inflammation, inhibited epithelial-mesenchymal transition (EMT), and ameliorated PF. Further studies showed that MSC-exos regulated NOD1/NF-kB signaling pathway to suppress the activation of NLRP3 inflammasomes both in vivo and in vitro. Additionally, overexpression of NLRP3 significantly reversed the anti-fibrotic effects of MSC-exos in BLM-induced lung epithelial cells. MSC-derived exosome ameliorates pulmonary fibrosis by modulating NOD 1/NLRP3-mediated epithelial-mesenchymal transition and inflammation.

Current insights into molecular mechanisms of environmental stress tolerance in Cyanobacteria.

The photoautotrophic nature of cyanobacteria, coupled with their fast growth and relative ease of genetic manipulation, makes these microorganisms very promising factories for the sustainable production of bio-products from atmospheric carbon dioxide. However, both in nature and in cultivation, cyanobacteria go through different abiotic stresses such as high light (HL) stress, heavy metal stress, nutrient limitation, heat stress, salt stress, oxidative stress, and alcohol stress. In recent years, significant improvement has been made in identifying the stress-responsive genes and the linked pathways in cyanobacteria and developing genome editing tools for their manipulation. Metabolic pathways play an important role in stress tolerance; their modification is also a very promising approach to adapting to stress conditions. Several synthetic as well as systems biology approaches have been developed to identify and manipulate genes regulating cellular responses under different stresses. In this review, we summarize the impact of different stresses on metabolic processes, the small RNAs, genes and heat shock proteins (HSPs) involved, changes in the metabolome and their adaptive mechanisms. The developing knowledge of the adaptive behaviour of cyanobacteria may also be utilised to develop better stress-responsive strains for various applications.

Editorial: Systems biology approaches to psychiatric and psychological disorders: unraveling the complexities

Editorial: Systems biology approaches to psychiatric and psychological disorders: unraveling the complexities

Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer

Cancer-associated fibroblasts (CAFs) play a key role in metabolic reprogramming and are well-established contributors to drug resistance in colorectal cancer (CRC). To exploit this metabolic crosstalk, we integrated a systems biology approach that identified key metabolic targets in a data-driven method and validated them experimentally. This process involved a novel machine learning-based method to computationally screen, in a high-throughput manner, the effects of enzyme perturbations predicted by a computational model of CRC metabolism. This approach reveals the network-wide effects of metabolic perturbations. Our results highlighted hexokinase (HK) as a crucial target, which subsequently became our focus for experimental validation using patient-derived tumor organoids (PDTOs). Through metabolic imaging and viability assays, we found that PDTOs cultured in CAF-conditioned media exhibited increased sensitivity to HK inhibition, confirming the model predictions. Our approach emphasizes the critical role of integrating computational and experimental techniques in exploring and exploiting CRC–CAF crosstalk.

A comprehensive review of biological and genetic control approaches for leishmaniasis vector sand flies; emphasis towards promoting tools for integrated vector management.

Leishmaniasis is a health problem in many regions with poor health and poor life resources. According to the World Health Organization (WHO), an estimated 700,000-1 million new cases arise annually. Effective control of sand fly vector populations is crucial for reducing the transmission of this disease. Therefore, this review aims to comprehensively examine and evaluate the current methods for controlling sand fly populations, focusing on biological and gene drive techniques. A detailed, comprehensive literature search was carried out using databases including Google Scholar, PubMed, ScienceDirect, and the National Library of Medicine (NIH). These searches were done using specific keywords related to the field of study. This current review identified several promising methods, including genetically modified sand flies, using transgenic approaches by taking advanced gene editing tools like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) and genetic modification of symbiotic microorganisms for controlling sand fly populations, which appeared to be proven under laboratory and field settings. Genetic control approaches have many benefits over chemical control, including long-lasting effects on targets, high specificity, and less environmental impact. Advances in genetic engineering technologies, particularly CRISPR/Cas9, sterile insect techniques, and gene drive insect modification, offer new avenues for precise and efficient sand fly management. Future research should prioritize optimizing rearing and sterilization techniques, conducting controlled field trials, and fostering collaboration across disciplines to realize the potential of genetic control strategies in combating leishmaniasis.

Isolation, characterization, and mycostimulation of fungi for the degradation of polycyclic aromatic hydrocarbons at a superfund site

Mycoremediation is a biological treatment approach that relies on fungi to transform environmental pollutants into intermediates with lower environmental burden. Basidiomycetes have commonly been used as the target fungal phylum for bioaugmentation in mycoremediation, however this phylum has been found to be unreliable when used at scale in the field. In this study, we isolated, characterized, and identified potential polycyclic aromatic hydrocarbon (PAH) degrading fungal isolates from creosote-contaminated sediment in the Elizabeth River, Virginia. Our goal was to identify non-basidiomycete PAH degrading fungi. A total of 132 isolates were isolated, of which the overwhelming majority belonged to the phylum Ascomycota. Isolates were screened for their ability to produce known PAH degrading enzymes, particularly laccase and manganese-dependent peroxidases, and to transform model PAH compounds [fluoranthene, phenanthrene, pyrene and benzo(a)pyrene]. Fungal isolates were subsequently biostimulated using complex amendments including chicken feathers, wheat seeds, grasshoppers, and maple saw dust. Following biostimulation, laccase expression and PAH transformation were assessed. The grasshopper amendment was found to yield the highest laccase upregulation improvement with a maximum increase of 18.9% for the Paraphaeosphaeria isolate. The Septoriella and Trichoderma isolates exposed to the chitin-based grasshopper amendment demonstrated an increase in PAH removal. Septoriella sp. increased its transformation of fluoranthene (44%), pyrene (54.2%, and benzo(a)pyrene (48.7%), while there was a 58.3% increase in the removal of benzo(a)pyrene by Trichoderma sp. While the results from this study demonstrate the potential of indigenous fungi to be biostimulated for the removal of PAHs, additional investigation is needed to determine if the response to the chitin-based grasshopper mycostimulation can be translated from the bench to the field.

Assessment of Evaluation of Tomato Seed Health and Sustainable Management Practices Using Biological and Chemical Approaches

An experiment was conducted to evaluate the seed health status of tomato and their affectivity against fungal pathogens. The eight tomato varieties viz. Binatomato-6 (V1), Binatomato-7 (V2), Binatomato-10 (V3), Binatomato-11 (V4), Binatomato-12 (V5), Binatomato-13 (V6), Ratan (V7) and Roma VF (V8) and sixteen bio–agents and fungicide treatments viz. control (T0), Garlic (w/v) @ 1:1 (T1), 1:2 (T2), 1:3 (T3), Neem (w/v) @ 1:1 (T4), 1:2 (T5), 1:3 (T6), Allamonda (w/v) @ 1:1 (T7), 1:2 (T8), 1:3 (T9), Trichoderma sp. (w/v) @ 1:1 (T10), 1:2 (T11), 1:3 (T12), Sinkar (w/v) @ 1:1 (T13), 1:2 (T14) and 1:3 (T15) were used for the study. Results revealed that the apparently healthy seed was significantly highest (84.42%) in Binatomato-13 which showed the lowest discolored (3.32%) and deformed (3.02%) seed included the highest seed germination (93.0%), longest shoot (6.5 cm) and highest vigor index (1239.31). Six seed–borne fungi namely A. flavus, A. niger, F. oxysporum, C. lunata, Rhizopus sp and Penicillium sp. were identified where Ratan had highly susceptible (20.0%) and Binatomato-12 was the highly effective against the fungal incidence (7.64%) with highest mean incidence of A. flavus (3.18%) and lowest with Penicillium sp. (0.10%), incases of plant extracts, neem @ 1:1 w/v showed the highest vigor index (1433.20) which showed highest significant influenced on normal seedling (79.67%) and lowest abnormal seedling (9.67%) with reduced rate of dead (4.33) and hard (2.33%) seed. Application of neem @ 1:1 w/v also effective for the highest reduction of A. flavus (1.67%), F. oxysporum (0.60%), C. lunata (1.33%), R. stolonifer (1.0%) and Penicillium sp. (0.10%) while T3 (Garlic @ 1:3) was for A. niger (1.06). So, Binatomato-13 was the best qualitative variety while Neem @ (1:1) w/v was the proposing plant extract which have higher capability to reduce the seed borne infection. SAARC J. Agric., 22(2): 139-151 (2024)

Optimal network sizes for most robust Turing patterns

Many cellular patterns exhibit a reaction-diffusion component, suggesting that Turing instability may contribute to pattern formation. However, biological gene-regulatory pathways are more complex than simple Turing activator-inhibitor models and generally do not require fine-tuning of parameters as dictated by the Turing conditions. To address these issues, we employ random matrix theory to analyze the Jacobian matrices of larger networks with robust statistical properties. Our analysis reveals that Turing patterns are more likely to occur by chance than previously thought and that the most robust Turing networks have an optimal size, consisting of only a handful of molecular species, thus significantly increasing their identifiability in biological systems. Broadly speaking, this optimal size emerges from a trade-off between the highest stability in small networks and the greatest instability with diffusion in large networks. Furthermore, we find that with multiple immobile nodes, differential diffusion ceases to be important for Turing patterns. Our findings may inform future synthetic biology approaches and provide insights into bridging the gap to complex developmental pathways.

Synthetic biology approaches to negative emissions technologies: a technological and ethical appraisal

This article explores the impact that synthetic biology approaches may have on Negative Emissions Technologies (NETs). Synthetic biology has both altered and created biological pathways inspired by nature to develop new NETs that sequester greenhouse gases into industrially useful chemicals, such as biomass and calcium carbonate. However, synthetic biology continues to encounter difficulties when implementing and scaling up production due to a combination of hard limits (within biology) and ‘soft’ limits (of social and economic costs). Additionally, NETs, along with Ecosystem Technologies in general, operate as climate technofixes, wherein insufficient thought is given to the ethical quandaries arising from releasing designed organisms into the environment, even under controlled conditions. In this paper, we provide a technological and ethical appraisal of synthetic biology approaches to NETs, in the context of climate change mitigation through Ecosystem Technology.

The unique structure of the highly conserved PPLP region in HIV-1 Vif is critical for the formation of APOBEC3 recognition interfaces.

The human cellular cytidine deaminases APOBEC3s (A3s) inhibit virion infectivity factor (Vif)-deficient HIV-1 replication. However, virus-encoded Vifs abolish this defense system by specifically recruiting A3s to an E3 ubiquitin ligase complex to induce their degradation. The highly conserved Vif PPLP motif is critical for the Vif-mediated antagonism of A3s and is believed to be important for Vif multimerization. However, how the PPLP motif dictates the functions of Vif remains unclear. Here, we aimed to elucidate this mechanism using biochemical and structural biology approaches. First, we found that no stable Vif multimer complexes formed in our tandem coimmunoprecipitation assays. Next, a series of Vif truncation mutants were constructed, and the short α-helix α6 just downstream of PPLP was found to be the smallest fragment essential for efficient A3G degradation in cells. In silico structural analysis suggested that PPLP-α6 adopts a stable L-shaped conformation when complexed in Vif/CBF-β and contributes to the structural integrity of Vif. In vitro ubiquitination assays with recombinant proteins confirmed that PPLP-α6 is necessary to form the functional complex of the E3 ligase adaptor of Vif/CBF-β/elongin B/elongin C. Additionally, mutations of the highly conserved PPLP-α6 hydrophobic residues severely disrupted Vif function. In the Vif structure, PPLP-α6 is positioned behind α1-α2 that constitutes the A3-binding Vif interfaces. Therefore, both the PPLP motif and α6 play critical allosteric roles in maintaining the integrity of the A3 interaction interfaces. Our findings will also provide important data for the design of novel anti-HIV-1 compounds that disrupt the A3-binding Vif interfaces.IMPORTANCEThe APOBEC3 (A3) family enzymes potently block the replication of retroviruses, such as HIV-1. However, HIV-1 expresses Vif, a small multifaceted protein that binds and specifically eliminates A3s in infected cells via ubiquitination-proteasome degradation. Thus, A3-Vif interactions are attractive targets for anti-HIV-1 drug development. The Vif PPLP motif that is distal from these interfaces is necessary for A3 degradation; however, the mechanism by which PPLP participates in A3 degradation is unknown. In this study, we performed biochemical and structural biology analyses to elucidate the underlying mechanisms involved. We found that the PPLP motif, in addition to the short downstream fragment α6, forms a stable L-shaped conformation and acts as a scaffold for the A3 recognition interfaces. Importantly, mutations in α6 abolished Vif function to antagonize multiple A3 family enzymes. These findings provide important data for the development of novel HIV-1 inhibitors that utilize A3s as cellular defense enzymes.

A synthetic biology approach for identifying de-SUMOylation enzymes of substrates.

A synthetic biology approach using a robust reconstitution system in Escherichia coli enables the identification of plant ubiquitin-like proteases responsible for removing the small ubiquitin-like modifier (SUMO) post-translational modifications from specific protein substrates.

The relevance of endoplasmic reticulum lumen and Anoctamin-8 for major depression: Results from a systems biology study.

Major depressive disorder (MDD) is a highly prevalent and debilitating disorder, yet its pathophysiology has not been fully elucidated. The aim of this study is to identify novel potential proteins and biological processes associated with MDD through a systems biology approach. Original articles involving the measurement of proteins in the blood of patients diagnosed with MDD were selected. Data on the differentially expressed proteins (DEPs) in each article were extracted and imported into R, and the pathfindR package was used to identify the main gene ontology terms involved. Data from the STRING database were combined with the DEPs identified in the original studies to create expanded networks of protein-protein interactions (PPIs). An R script was developed to obtain the five most reliable connections from each DEP and to create the networks, which were visualized through Cytoscape software. Out of 510 articles found, eight that contained all the values necessary for the analysis were selected, including 1112 adult patients with MDD and 864 controls. A total of 240 DEPs were identified, with the most significant gene ontology term being "endoplasmic reticulum lumen" (46 DEPs, p-value=5.5x10-13). An extended PPI network was obtained, where Anoctamin-8 was the most central protein. Using systems biology contributed to the interpretation of data obtained in proteomic studies on MDD and expanded the findings of these studies. The combined use of these methodologies can provide new insights into the pathophysiology of psychiatric disorders, identifying novel biomarkers to improve diagnostic, prognostic, and treatment strategies in MDD.

Transforming Agricultural Food Waste Into Bioplastics: Methods, Potential, and Technological Advances

AbstractThe improper disposal of agricultural food waste (AFW) and its associated plastic packaging significantly exacerbates environmental degradation, including pollution, greenhouse gas emissions, and loss of valuable resources, while imposing substantial economic burdens. These pressing challenges have spurred advancements in bioplastics as sustainable and eco‐friendly alternatives to conventional plastics. Here, the potential of AFW, rich in biopolymers such as starch and cellulose, as a renewable feedstock is examined for bioplastics such as polylactic acid, polybutylene succinate, and polyhydroxyalkanoates. It explores the characteristics of these bioplastics, focusing on production techniques such as extraction‐based processes, microbial fermentation, fermentation combined with polymerization, and synthesis from volatile fatty acids. Additionally, the role of AFW pretreatment methods, including physical, chemical, biological, and enzymatic approaches, in enhancing conversion efficiency is analyzed. Here, it is highlighted that recent advancements in bioplastic production have improved efficiency, biodegradability, and scalability, offering a viable substitute for traditional plastics. These findings demonstrate that valorizing AFW not only addresses plastic and food waste challenges but also promotes sustainability and circular economy principles, paving the way for greener industries and reduced ecological impact.

Potential role of formononetin as a novel natural agent in Alzheimer's disease and osteoporosis comorbidity.

The growing aging population has led to an increase in the prevalence of Alzheimer's disease (AD) and osteoporosis (OP), both of which significantly impair quality of life. The comorbid nature of these conditions suggests a shared genetic etiology, the understanding of which is crucial for developing targeted therapies. This study aims to explore the shared genetic etiology underlying AD and OP, using a system biology approach to identify potential therapeutic targets and natural compounds for treatment. We employed Weighted Gene Co-Expression Network Analysis (WGCNA) with molecular docking strategies to uncover the genetic links between AD and OP. MT2A and CACNA1C were identified as key pleiotropic hub genes potentially linking AD and OP. Molecular docking was utilized to screen for compounds with therapeutic potential, leading to the identification of formononetin as a compound with significant binding affinity to these hub genes. Quantitative real-time PCR (qRT-PCR) validation was conducted to confirm the gene expression changes in disease models. Our study indicate that formononetin exhibits strong binding affinity to the identified hub genes, MT2A and CACNA1C. qRT-PCR validation confirmed the upregulation of these genes in disease models, which was mitigated upon treatment with formononetin, suggesting a reversal of disease markers. This study advances our understanding of the genetic intersections between AD and OP and positions formononetin as a promising natural agent for further translational research. Formononetin's multi-target potential makes it a valuable candidate for managing these comorbid conditions, meriting further investigation and development as a therapeutic strategy.

Challenges of Dermanyssus gallinae in Poultry: Biological Insights, Economic Impact and Management Strategies.

Bird mites are parasites that feed on both wild and domesticated bird species, causing severe degradation in avian welfare. The chicken mite, Dermanyssus gallinae in particular, is a widespread ectoparasite in poultry, responsible for several challenges faced by the poultry industry, including poor animal health, which causes significant economic losses. This review, based on our current knowledge, aims to provide a comprehensive insight into the biology and distribution of these mites, as well as their impact on poultry health and production. It explores the most prevalent mites in avian species, with a focus on D. gallinae, and examines the different psychological and physiological alterations observed in infected stocks, such as decreased egg production, weight loss, and an increased susceptibility to diseases. This review will also cover existing control strategies, including chemical, biological, and environmental approaches, with attention to the growing concern around pesticide resistance. Additionally, it delves into genetic research conducted on these mites, primarily focusing on phylogenetic studies, which have provided insights into their evolutionary relationships and potential vulnerabilities. By compiling existing studies, this article underscores the urgent need for effective and sustainable countermeasures, as well as further genetic research to mitigate the substantial impact of D. gallinae on the poultry sector.

Comprehensive Review on Bio-Based Treatments for Polyvinyl Chloride Plastic.

Polyvinyl chloride (PVC) plastics are widespread around the globe, and each year, thousands of tons of PVC end up in the environment in the form of micro-/nanoplastics. Literature has reported extensively on the biodegradation of its PVC additives/plasticizers; however, bio-based treatment approaches for its polymers have been scanty. The current review has discussed elaborately all possible PVC degradation processes and the toxicity challenges faced during its mitigation. This review has also delineated and assessed all physical, chemical, and biological approaches reported for PVC treatments. All the biodeterioration, biocatalysis, and biodegradation mechanisms reported for PVC have been comprehensively discussed. Recent advances have also been highlighted like the direct application of invertebrate species and selective enzymes like peroxidases, alkane monooxygenase, and laccase during PVC treatment. Insights of functional genomes/genes and OMICS have been recommended, which might help predict and address any future issues during the mitigation of PVC pollution in the environment.

Gene expression analysis reveals mir-29 as a linker regulatory molecule among rheumatoid arthritis, inflammatory bowel disease, and dementia: Insights from systems biology approach.

Rheumatoid arthritis (RA) is a degenerative autoimmune disease, often managed through symptomatic treatment. The co-occurrence of the reported extra-articular comorbidities such as inflammatory bowel disease (IBD), and dementia may complicate the pathology of the disease as well as the treatment strategies. Therefore, in our study, we aim to elucidate the key genes, and regulatory elements implicated in the progression and association of these diseases, thereby highlighting the linked potential therapeutic targets. Ten microarray datasets each for RA, and IBD, and nine datasets for dementia were obtained from Gene Expression Omnibus. We identified common differentially expressed genes (DEGs) and constructed a gene-gene interaction network. Subsequently, topology analysis for hub gene identification, cluster and functional enrichment, and regulatory network analysis were performed. The hub genes were then validated using independent microarray datasets from Gene Expression Omnibus. A total of 198 common DEGs were identified from which CD44, FN1, IGF1, COL1A2, and POSTN were identified as the hub genes in our study. These hub genes were mostly enriched in significant processes and pathways like tissue development, collagen binding, cell adhesion, regulation of ERK1/2 cascade, PI3K-AKT signaling, and cell surface receptor signaling. Key transcription factors TWIST2, CEBPA, EP300, HDAC1, HDAC2, NFKB1, RELA, TWIST1, and YY1 along with the miRNA hsa-miR-29 were found to regulate the expression of the hub genes significantly. Among these regulatory molecules, miR-29 emerged as a significant linker molecule, bridging the molecular mechanisms of RA, IBD, and dementia. Validation of our hub genes demonstrated a similar expression trend in the independent datasets used for our study. Our study underscores the significant role of miR-29 in modulating the expression of hub genes and the associated transcription factors, which are crucial in the comorbidity status of RA, dementia, and IBD. This regulatory mechanism highlights miR-29 as a key player in the pathogenesis of these comorbid diseases.

Sustainable management of sheath blight in <i>Oryza sativa </i>L. by integrated biological approach

Rice sheath blight brought on by Rhizoctonia solani is one of the most significant diseases in the world, which results in significant yield losses. Application of chemical fungicides is the most preferred approach for the management of disease but extensive use of them results in environment pollution and resistance development to pathogen. Thus, there is a need to explore alternative strategies to overcome the problem of fungicide usage. The present study was done to develop sustainable strategy which is an environment friendly and alternative to chemical fungicides. Among various treatments, soil application of neem cake at 200 kg acre-1 + foliar spray of micronutrient mixture 5 g l-1 at 40 days after transplanting (DAT) + foliar spray of microbial consortia 5 g l-1 at 50 DAT was found very effective in reducing the disease severity (19.16%) and increasing growth promotion activity compared to control. Therefore, the findings of this investigation could be exploited under bio-intensive disease management programme for sustainable cultivation of rice.

Prenatal maternal stress in rats alters the epigenetic and transcriptomic landscape of the maternal-fetal interface across four generations

Prenatal maternal stress (PNMS) determines lifetime mental and physical health. Here, we show in rats that PNMS has consequences for placental function and fetal brain development across four generations (F0-F3). Using a systems biology approach, comprehensive DNA methylation (DNAm), miRNA, and mRNA profiling revealed a moderate impact of PNMS in the F1 generation, but drastic changes in F2 and F3 generations, suggesting compounding effects of PNMS with each successive generation. Both maternal and placental miRNA gene targets included de novo DNA methyltransferases, indicating robust PNMS-induced disruption in the complex epigenetic regulatory network between miRNAs and DNAm. Transgenerational programming mainly involved genes and biological pathways associated with neurological and psychiatric diseases which were linked to maternal-fetal crosstalk facilitated by the placenta. The highly correlated placenta-brain profiles support the use of placenta as a noninvasive biomarker resource to predict pathological changes in the neonatal brain. The transgenerational persistence of critical DNAm, miRNA and mRNA signatures may explain familial non-genetic disease risks.

The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.

The phosphoinositide family of membrane lipids play diverse and critical roles in eukaryotic molecular biology. Much of this biological activity derives from interactions of phosphoinositide lipids with integral and peripheral membrane proteins, leading to modulation of protein structure, function, and cellular distribution. Since the discovery of phosphoinositides in the 1940s, combined molecular biology, biophysical, and structural approaches have made enormous progress in untangling this vast and diverse cellular network of interactions. More recently, in silico approaches such as molecular dynamics simulations have proven to be an asset in prospectively identifying, characterising, explaining the structural basis of these interactions, and in the best cases providing atomic level testable hypotheses on how such interactions control the function of a given membrane protein. This review details a number of recent seminal discoveries in phosphoinositide biology, enabled by advanced biomolecular simulation, and its integration with molecular biology, biophysical, and structural biology approaches. The results of the simulation studies agree well with experimental work, and in a number of notable cases have arrived at the key conclusion several years in advance of the experimental structures. SUMMARY: Hedger and Yen review developments in simulations of phosphoinositides and membrane proteins.