Is the robotic revolution stunting surgical skills?

This perspective piece aims to examine the impact of the growing utilization of robotic platforms in general and minimally invasive surgery on surgical trainee experience, skill level, and comfort in performing general surgical and minimally invasive procedures following completion of training. We review current literature and explore the application of robotic surgery to surgical training, where minimum case thresholds and breadth distribution are well defined, and where development of surgical technique is historically gained through delicate tissue handling with haptic feedback rather than relying on visual feedback alone. We call for careful consideration as to how best to incorporate robotics in surgical training in order to embrace technological advances without endangering the surgical proficiency of the surgeons of tomorrow. Key message: The large-scale incorporation of robotics into general and minimally invasive surgical training is something that most, if not all, trainees must grapple with in today's world, and the proportion of robotics is increasing. This shift may significantly negatively affect trainees in terms of surgical skill upon completion of training and must be approached with an appropriate degree of concern and thoughtfulness so as to protect the surgeons of tomorrow.

Evaluating novel biodegradable polymer matrix fertilizers for nitrogen-efficient agriculture.

Enhanced efficiency fertilizers (EEFs) can reduce nitrogen (N) losses in temperate agriculture but are less effective in the tropics. We aimed to design a new EEF and evaluate their performance in simple-to-complex tests with tropical soils and crops. We melt-extruded urea at different loadings into biodegradable polymer matrix composites using biodegradable polyhydroxyalkanoate (PHA) or polybutylene adipate-co-terephthalate (PBAT) polymers with urea distributed throughout the pellet. These contrast with commercially coated EEF that have a polymer-coated urea core. We hypothesized that matrix fertilizers would have an intermediate N release rate compared to fast release from urea or slow release from coated EEF. Nitrogen release rates in water and sand-soil columns confirmed that the matrix fertilizer formulations had a more progressive N release than a coated EEF. A more complex picture emerged from testing sorghum [Sorghum bicolor (L.) Moench] grown to maturity in large soil pots, as the different formulations resulted in minor differences in plant N accumulation and grain production. This confirms the need to consider soil interactions, microbial processes, crop physiology, and phenology for evaluating fertilizer performance. Promisingly, crop δ15N signatures emerged as an integrated measure of efficacy, tracking likely N conversions and losses. The three complementary evaluations combine the advantages of standardized high-throughput screening and more resource-intensive and realistic testing in a plant-soil system. We conclude that melt-blended biodegradable polymer matrix fertilizers show promise as EEF because they can be designed toward more abiotically or more microbially driven N release by selecting biopolymer type and N loading rate.

Dead in the water - Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring.

DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.

Prevalence and odds of anxiety and depression in cutaneous malignant melanoma: a proportional meta-analysis and regression.

BACKGROUND: The psychological burden of cutaneous malignant melanoma (CM) is all-encompassing, affecting treatment adherence, recurrence and mortality. However, the prevalence and risk factors of anxiety and depression in CM remain unclear. OBJECTIVES: To establish a benchmark pooled prevalence of anxiety and depression in CM, to provide magnitudes of association for clinical, therapeutic and demographic correlates, and to elucidate temporal trends in anxiety and depression from the time of diagnosis. METHODS: This review followed the MOOSE guidelines. MEDLINE, Embase, PsychINFO, Web of Science and the Cochrane Library were queried from database inception to 24 August 2023. Study selection, data extraction and quality assessment were performed by two independent authors, utilizing both the Joanna Briggs Institute (JBI) and National Institutes of Health risk-of-bias tools for the latter. The GRADE approach was used to rate the certainty of evidence. Prevalence rates, 95% confidence intervals (CIs) and prediction intervals (PIs) were derived using a random-effects model and estimating between- and within-study variance. RESULTS: Nine longitudinal and 29 cross-sectional studies were included (7995 patients). Based on the JBI and NIH tools, respectively, quality assessment found 20 and 17 to be at low risk of bias, 12 and 15 to be at moderate risk and 6 and 5 to be at high risk of bias. The prevalence of anxiety [30.6% (95% CI 24.6-37.0; PI 18-47%)] and depression [18.4% (95% CI 13.4-23.9; PI 10-33%)] peaked during treatment, declining to pretreatment levels after 1 year [anxiety: 48% vs. 20% (P = 0.005); depression: 28% vs. 13% (P = 0.03)]. Female sex [odds ratio (OR) 1.8, 95% CI 1.4-2.3; P < 0.001], age < 60 years (OR 1.5, 95% CI 1.2-2.0; P = 0.002) and low educational level (OR 1.5, 95% CI 1.2-2.0; P < 0.001) were likely to result in a large increase in the odds of anxiety. Depression was 12.3% higher in those with stage IV vs. those with stage I CM (P = 0.05). Relative to immune checkpoint inhibition, the rates of depression were 22% (P = 0.002) and 34% (P < 0.001) higher among patients with advanced-stage CM receiving interferon-α and chemotherapy, respectively. A significant reduction in self-reported depression scores was demonstrated over time (P = 0.003). CONCLUSIONS: Notably, anxiety and depression in CM affect women, those younger than 60 years of age and the less educated, with up to 80% higher odds of anxiety in these groups. Anxiety and depression surge during chemotherapy and interferon treatment, especially in advanced CM. Our findings facilitate risk stratification and underscore the need for multidisciplinary vigilance.

Melanoma is a serious type of skin cancer that is becoming more prevalent, particularly in people with lighter skin. The UK-based ReconRegen research group conducted a study to understand the psychological impact of melanoma on people, focusing on anxiety and depression. To do this, a systematic review approach was used to analyse data from existing studies and gather a comprehensive perspective. The study discovered that 30% of people with melanoma are affected by anxiety and 18% by depression, significantly higher than the general population. Key risk factors for anxiety included being female, being younger than 60 years of age and having lower educational attainment. Women are 1.8 times more likely to experience anxiety than men, those under 60 years of age are 1.5 times more likely to experience it and individuals with lower educational levels are also 1.5 times more likely to experience anxiety. Findings showed that anxiety and depression levels peaked during treatment phases, especially in people undergoing chemotherapy and immunotherapy. This highlights the need for targeted mental health support during these treatment periods. The findings advocate for mental health considerations in melanoma care, suggesting regular mental health assessments, particularly for high-risk groups and during intense treatment phases. Highlighting the importance of a holistic treatment approach, the study suggests that future research should include long-term studies to understand the chronic impacts of anxiety and depression. Improved clarity and detail in research reporting are essential for developing effective mental health support for people with melanoma, enhancing overall patient care by addressing both physical and emotional health needs.

Estimating lighting direction in scenes with multiple objects.

To recover the reflectance and shape of an object in a scene, the human visual system must account for the properties of the light illuminating the object. Here, we examine the extent to which multiple objects within a scene are utilised to estimate the direction of lighting in a scene. In Experiment 1, we presented participants with rendered scenes that contained 1, 9, or 25 unfamiliar blob-like objects and measured their capacity to discriminate whether a directional light source was left or right of the participants' vantage point. Trends reported for ensemble perception suggest that the number of utilised objects-and, consequently, discrimination sensitivity-would increase with set size. However, we find little indication that increasing the number of objects in a scene increased discrimination sensitivity. In Experiment 2, an equivalent noise analysis was used to measure participants' internal noise and the number of objects used to judge the average light source direction in a scene, finding that participants relied on 1 or 2 objects to make their judgement regardless of whether 9 or 25 objects were present. In Experiment 3, participants completed a shape identification task that required an implicit judgement of light source direction, rather than an explicit judgement as in Experiments 1 and 2. We find that sensitivity for identifying surface shape was comparable for scenes containing 1, 9, and 25 objects. Our results suggest that the visual system relied on a small number of objects to estimate the direction of lighting in our rendered scenes.

Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells.

Background: Resolving causal genes for type 2 diabetes at loci implicated by genome-wide association studies (GWAS) requires integrating functional genomic data from relevant cell types. Chromatin features in endocrine cells of the pancreatic islet are particularly informative and recent studies leveraging chromosome conformation capture (3C) with Hi-C based methods have elucidated regulatory mechanisms in human islets. However, these genome-wide approaches are less sensitive and afford lower resolution than methods that target specific loci. Methods: To gauge the extent to which targeted 3C further resolves chromatin-mediated regulatory mechanisms at GWAS loci, we generated interaction profiles at 23 loci using next-generation (NG) capture-C in a human beta cell model (EndoC-ßH1) and contrasted these maps with Hi-C maps in EndoC-ßH1 cells and human islets and a promoter capture Hi-C map in human islets. Results: We found improvements in assay sensitivity of up to 33-fold and resolved ~3.6X more chromatin interactions. At a subset of 18 loci with 25 co-localised GWAS and eQTL signals, NG Capture-C interactions implicated effector transcripts at five additional genetic signals relative to promoter capture Hi-C through physical contact with gene promoters. Conclusions: High resolution chromatin interaction profiles at selectively targeted loci can complement genome- and promoter-wide maps.

Alterations in GLP-1 and PYY release with aging and body mass in the human gut.

The lining of our intestinal surface contains an array of hormone-producing cells that are collectively our bodies' largest endocrine cell reservoir. These "enteroendocrine" (EE) cells reside amongst the billions of absorptive epithelial and other cell types that line our gastrointestinal tract and can sense and respond to the ever-changing internal environment in our gut. EE cells release an array of important signalling molecules that can act as hormones, including glucagon-like peptide (GLP-1) and peptide YY (PYY) which are co-secreted from L cells. While much is known about the effects of these hormones on metabolism, insulin secretion and food intake, less is understood about their secretion from human intestinal tissue. In this study we assess whether GLP-1 and PYY release differs across human small and large intestinal tissue locations within the gastrointestinal tract, and/or by sex, body weight and the age of an individual. We identify that the release of both hormones is greater in more distal regions of the human colon, but is not different between sexes. We observe a negative correlation of GLP-1 and BMI in the small, but not large, intestine. Increased aging correlates with declining secretion of both GLP-1 and PYY in human large, but not small, intestine. When the data for large intestine is isolated by region, this relationship with age remains significant for GLP-1 in the ascending and descending colon and in the descending colon for PYY. This is the first demonstration that site-specific differences in GLP-1 and PYY release occur in human gut, as do site-specific relationships of L cell secretion with aging and body mass.

Aortic Arch Reconstruction Using Nonvalved Femoral Vein Homograft in High-Risk Neonates.

Aortic arch obstruction is often present with complex concomitant congenital heart defects (CHDs). The use of nonvalved femoral vein homograft (FVH) to reconstruct the aortic arch has distinct surgical advantages, including simplified reconstruction. We present an intraoperative video of a Yasui procedure utilizing FVH for aortic reconstruction in a 12-day-old (2.2 kg) neonate with right ventricular outflow tract obstruction, malalignment ventricular septal defect, aortic valve atresia, aortic arch hypoplasia, atrial septal defect, and ductal dependent systemic circulation. Further, we report outcomes for a series of three additional neonatal patients with complex CHD and aortic arch obstruction who underwent FVH arch reconstruction.

Development of an in vivo murine model of perineural invasion and spread of cutaneous squamous cell carcinoma of the head and neck.

Introduction: Cutaneous squamous cell carcinoma of the head and neck (cSCCHN) can metastasize by invading nerves and spread toward the central nervous system. This metastatic process is called perineural invasion (PNI) and spread (PNS). An in vivo sciatic nerve mouse model is used for cSCCHN PNI/PNS. Here we describe a complementary whisker pad model which allows for molecular studies investigating drivers of PNI/PNS in the head and neck environment. Methods: A431 cells were injected into the whisker pads of BALB/c Foxn1nu and NSG-A2 mice. Tumor progression was monitored by bioluminescence imaging and primary tumor resection was performed. PNI was detected by H&E and IHC. Tumor growth and PNI were assessed with inducible ablation of LOXL2. Results: The rate of PNI development in mice was 10%-28.6%. Tumors exhibited PNI/PNS reminiscent of the morphology seen in the human disease. Our model's utility was demonstrated with inducible ablation of LOXL2 reducing primary tumor growth and PNI. Discussion: This model consists in a feasible way to test molecular characteristics and potential therapies, offers to close a gap in the described in vivo methods for PNI/PNS of cSCCHN and has uses in concert with the established sciatic nerve model.

The Impact of Long-Term Macrolide Exposure on the Gut Microbiome and Its Implications for Metabolic Control.

Long-term low-dose macrolide therapy is now widely used in the treatment of chronic respiratory diseases for its immune-modulating effects, although the antimicrobial properties of macrolides can also have collateral impacts on the gut microbiome. We investigated whether such treatment altered intestinal commensal microbiology and whether any such changes affected systemic immune and metabolic regulation. In healthy adults exposed to 4 weeks of low-dose erythromycin or azithromycin, as used clinically, we observed consistent shifts in gut microbiome composition, with a reduction in microbial capacity related to carbohydrate metabolism and short-chain fatty acid biosynthesis. These changes were accompanied by alterations in systemic biomarkers relating to immune (interleukin 5 [IL-5], IL-10, monocyte chemoattractant protein 1 [MCP-1]) and metabolic (serotonin [5-HT], C-peptide) homeostasis. Transplantation of erythromycin-exposed murine microbiota into germ-free mice demonstrated that changes in metabolic homeostasis and gastrointestinal motility, but not systemic immune regulation, resulted from changes in intestinal microbiology caused by macrolide treatment. Our findings highlight the potential for long-term low-dose macrolide therapy to influence host physiology via alteration of the gut microbiome. IMPORTANCE Long-term macrolide therapy is widely used in chronic respiratory diseases although its antibacterial activity can also affect the gut microbiota, a key regulator of host physiology. Macrolide-associated studies on the gut microbiota have been limited to short antibiotic courses and have not examined its consequences for host immune and metabolic regulation. This study revealed that long-term macrolides depleted keystone bacteria and impacted host regulation, mediated directly by macrolide activity or indirectly by alterations to the gut microbiota. Understanding these macrolide-associated mechanisms will contribute to identifying the risk of long-term exposure and highlights the importance of targeted therapy for maintenance of the gut microbiota.

Impact of volatile solids destruction on the shear and solid-liquid separation behaviour of anaerobic digested sludge.

Systematic and comprehensive characterisation of shear and solid-liquid separation properties of sludge across a wide range of solids concentration and volatile solids destruction (VSD) is critical for design and optimization of the anaerobic digestion process. In addition, there is a need for studies at the psychrophilic temperature range as many unheated anaerobic digestion processes are operated under ambient conditions with minimal self-heating. In this study, two digesters were operated at different combinations of operating temperature (15-25 °C) and hydraulic retention time (16-32 d) to ensure a wide range of VSD in the range of 0.42-0.7 was obtained. For shear rheology, the viscosity increased 1.3 to 3.3 times with the increase of VSD from 43 % to 70 %, while other parameters (temperature, VS fraction) having a negligible impact. Analysis of a hypothetical digester indicated that there is an optimum VSD range 65-80 % where increase in viscosity due to the higher VSD is balanced by the decrease in solids concentration. For solid-liquid separation, a thickener model and a filtration model were used. No significant impact of VSD on the solids flux, underflow solids concentrations or specific solids throughput was observed in the thickener and filtration model. However, there was an increase in average cake solids concentration from 21 % to 31 % with increase of VSD from 55 % to 76 %, indicating better dewatering behaviour.

Lactic acid production from food waste at an anaerobic digestion biorefinery: effect of digestate recirculation and sucrose supplementation.

Low lactic acid (LA) yields from direct food waste (FW) fermentation restrict this production pathway. However, nitrogen and other nutrients within FW digestate, in combination with sucrose supplementation, may enhance LA production and improve feasibility of fermentation. Therefore, this work aimed to improve LA fermentation from FWs by supplementing nitrogen (0-400 mgN·L-1) as NH4Cl or digestate and dosing sucrose (0-150 g·L-1) as a low-cost carbohydrate. Overall, NH4Cl and digestate led to similar improvements in the rate of LA formation (0.03 ± 0.02 and 0.04 ± 0.02 h-1 for NH4Cl and digestate, respectively), but NH4Cl also improved the final concentration, though effects varied between treatments (5.2 ± 4.6 g·L-1). While digestate altered the community composition and increased diversity, sucrose minimised community diversion from LA, promoted Lactobacillus growth at all dosages, and enhanced the final LA concentration from 25 to 30 g·L-1 to 59-68 g·L-1, depending on nitrogen dosage and source. Overall, the results highlighted the value of digestate as a nutrient source and sucrose as both community controller and means to enhance the LA concentration in future LA biorefinery concepts.

Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level.

BACKGROUND: The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and the related sub-lineage BA.5. Following resolution of the global BA.5 wave, a diverse grouping of Omicron sub-lineages emerged derived from BA.2, BA.5 and recombinants thereof. Whilst emerging from distinct lineages, all shared similar changes in the Spike glycoprotein affording them an outgrowth advantage through evasion of neutralising antibodies. METHODS: Over the course of 2022, we monitored the potency and breadth of antibody neutralization responses to many emerging variants in the Australian community at three levels: (i) we tracked over 420,000 U.S. plasma donors over time through various vaccine booster roll outs and Omicron waves using sequentially collected IgG pools; (ii) we mapped the antibody response in individuals using blood from stringently curated vaccine and convalescent cohorts. (iii) finally we determine the in vitro efficacy of clinically approved therapies Evusheld and Sotrovimab. FINDINGS: In pooled IgG samples, we observed the maturation of neutralization breadth to Omicron variants over time through continuing vaccine and infection waves. Importantly, in many cases, we observed increased antibody breadth to variants that were yet to be in circulation. Determination of viral neutralization at the cohort level supported equivalent coverage across prior and emerging variants with isolates BQ.1.1, XBB.1, BR.2.1 and XBF the most evasive. Further, these emerging variants were resistant to Evusheld, whilst increasing neutralization resistance to Sotrovimab was restricted to BQ.1.1 and XBF. We conclude at this current point in time that dominant variants can evade antibodies at levels equivalent to their most evasive lineage counterparts but sustain an entry phenotype that continues to promote an additional outgrowth advantage. In Australia, BR.2.1 and XBF share this phenotype and, in contrast to global variants, are uniquely dominant in this region in the later months of 2022. INTERPRETATION: Whilst the appearance of a diverse range of omicron lineages has led to primary or partial resistance to clinically approved monoclonal antibodies, the maturation of the antibody response across both cohorts and a large donor pools importantly observes increasing breadth in the antibody neutralisation responses over time with a trajectory that covers both current and known emerging variants. FUNDING: This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (SGT, GM & WDR), Medical Research Future Fund Antiviral Development Call grant (WDR), the New South Wales Health COVID-19 Research Grants Round 2 (SGT & FB) and the NSW Vaccine Infection and Immunology Collaborative (VIIM) (ALC). Variant modeling was supported by funding from SciLifeLab's Pandemic Laboratory Preparedness program to B.M. (VC-2022-0028) and by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 101003653 (CoroNAb) to B.M.

First-in-human technique translation of oxygen-enhanced MRI to an MR Linac system in patients with head and neck cancer.

BACKGROUND AND PURPOSE: Tumour hypoxia is prognostic in head and neck cancer (HNC), associated with poor loco-regional control, poor survival and treatment resistance. The advent of hybrid MRI - radiotherapy linear accelerator or 'MR Linac' systems - could permit imaging for treatment adaptation based on hypoxic status. We sought to develop oxygen-enhanced MRI (OE-MRI) in HNC and translate the technique onto an MR Linac system. MATERIALS AND METHODS: MRI sequences were developed in phantoms and 15 healthy participants. Next, 14 HNC patients (with 21 primary or local nodal tumours) were evaluated. Baseline tissue longitudinal relaxation time (T1) was measured alongside the change in 1/T1 (termed ΔR1) between air and oxygen gas breathing phases. We compared results from 1.5 T diagnostic MR and MR Linac systems. RESULTS: Baseline T1 had excellent repeatability in phantoms, healthy participants and patients on both systems. Cohort nasal concha oxygen-induced ΔR1 significantly increased (p < 0.0001) in healthy participants demonstrating OE-MRI feasibility. ΔR1 repeatability coefficients (RC) were 0.023-0.040 s-1 across both MR systems. The tumour ΔR1 RC was 0.013 s-1 and the within-subject coefficient of variation (wCV) was 25% on the diagnostic MR. Tumour ΔR1 RC was 0.020 s-1 and wCV was 33% on the MR Linac. ΔR1 magnitude and time-course trends were similar on both systems. CONCLUSION: We demonstrate first-in-human translation of volumetric, dynamic OE-MRI onto an MR Linac system, yielding repeatable hypoxia biomarkers. Data were equivalent on the diagnostic MR and MR Linac systems. OE-MRI has potential to guide future clinical trials of biology guided adaptive radiotherapy.

Resource recovery using enriched purple phototrophic bacteria in an outdoor flat plate photobioreactor: Suspended vs. attached growth.

Purple phototrophic bacteria (PPB) can produce single-cell protein from wastewater at high yields. Growing in a biofilm vs suspended can improve product quality and consistency. This study compares suspended and attached growths of enriched PPB cultures in an outdoor flat plate photobioreactor treating poultry-processing wastewater. Attached growth had lower VFA removal efficiencies (95 ± 2.7 vs 84 ± 6.4 %) due to light limitations and low substrate diffusion rates. Nevertheless, similar overall treatment performances and productivities were achieved (16 ± 2.2 and 18 ± 2.4 gCOD·m-2·d-1 for attached and suspended) at loading rates of 1.2-1.5 gCOD·L-1·d-1. Biofilms had higher quality than suspended biomass, with lower ash contents (6.9(0.6)% vs 57(16)%) and higher PPB abundances (0.45-0.67 vs 0.30-0.45). The biofilm (20-50 % of the total biomass) might be used as feed and the suspended fraction as fertiliser, improving the economics of the process. Semi-continuous PPB growth outdoors as biofilm is technically feasible, obtaining a superior product without jeopardising performance.

Comparative Transcriptomics Profiling of Perennial Ryegrass Infected with Wild Type or a ΔvelA Epichloë festucae Mutant Reveals Host Processes Underlying Mutualistic versus Antagonistic Interactions.

Epichloë species form bioprotective endophytic symbioses with many cool-season grasses, including agriculturally important forage grasses. Despite its importance, relatively little is known about the molecular details of the interaction and the regulatory genes involved. VelA is a key global regulator in fungal secondary metabolism and development. In previous studies, we showed the requirement of velA for E. festucae to form a mutualistic interaction with Lolium perenne. We showed that VelA regulates the expression of genes encoding proteins involved in membrane transport, fungal cell wall biosynthesis, host cell wall degradation, and secondary metabolism, along with several small-secreted proteins in Epichloë festucae. Here, by a comparative transcriptomics analysis on perennial ryegrass seedlings and mature plants, which are endophyte free or infected with wild type (mutualistic interaction) or mutant ΔvelA E. festucae (antagonistic or incompatible interaction), regulatory effects of the endophytic interaction on perennial ryegrass development was studied. We show that ΔvelA mutant associations influence the expression of genes involved in primary metabolism, secondary metabolism, and response to biotic and abiotic stresses compared with wild type associations, providing an insight into processes defining mutualistic versus antagonistic interactions.