Genomics analysis of Drosophila sechellia response to Morinda citrifolia fruit diet.

Drosophila sechellia is an island endemic host specialist that has evolved to consume the toxic fruit of Morinda citrifolia, also known as noni fruit. Recent studies by our group and others have examined genome-wide gene expression responses of fruit flies to individual highly abundant compounds found in noni responsible for the fruit's unique chemistry and toxicity. In order to relate these reductionist experiments to the gene expression responses to feeding on noni fruit itself, we fed rotten noni fruit to adult female D. sechellia and performed RNA-sequencing. Combining the reductionist and more wholistic approaches, we have identified candidate genes that may contribute to each individual compound and those that play a more general role in response to the fruit as a whole. Using the compound specific and general responses, we used transcription factor prediction analyses to identify the regulatory networks and specific regulators involved in the responses to each compound and the fruit itself. The identified genes and regulators represent the possible genetic mechanisms and biochemical pathways that contribute to toxin resistance and noni specialization in D. sechellia.

Genomics analysis of hexanoic acid exposure in Drosophila species.

Drosophila sechellia is a dietary specialist endemic to the Seychelles islands that has evolved to consume the fruit of Morinda citrifolia. When ripe, the fruit of M. citrifolia contains octanoic acid and hexanoic acid, two medium-chain fatty acid volatiles that deter and are toxic to generalist insects. Drosophila sechellia has evolved resistance to these volatiles allowing it to feed almost exclusively on this host plant. The genetic basis of octanoic acid resistance has been the focus of multiple recent studies, but the mechanisms that govern hexanoic acid resistance in D. sechellia remain unknown. To understand how D. sechellia has evolved to specialize on M. citrifolia fruit and avoid the toxic effects of hexanoic acid, we exposed adult D. sechellia, D. melanogaster and D. simulans to hexanoic acid and performed RNA sequencing comparing their transcriptional responses to identify D. sechellia specific responses. Our analysis identified many more genes responding transcriptionally to hexanoic acid in the susceptible generalist species than in the specialist D. sechellia. Interrogation of the sets of differentially expressed genes showed that generalists regulated the expression of many genes involved in metabolism and detoxification whereas the specialist primarily downregulated genes involved in the innate immunity. Using these data, we have identified interesting candidate genes that may be critically important in aspects of adaptation to their food source that contains high concentrations of HA. Understanding how gene expression evolves during dietary specialization is crucial for our understanding of how ecological communities are built and how evolution shapes trophic interactions.

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease.

The intestinal microbiome is a key determinant of responses to biologic therapy in inflammatory bowel disease (IBD). However, diverse therapeutics and variable responses among IBD patients have posed challenges in predicting clinical therapeutic success. In this prospective study, we profiled baseline stool and blood in patients with moderate-to-severe Crohn's disease or ulcerative colitis initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy. Patients were assessed at 14 weeks for clinical remission and 52 weeks for clinical and endoscopic remission. Baseline microbial richness indicated preferential responses to anti-cytokine therapy and correlated with the abundance of microbial species capable of 7α/ß-dehydroxylation of primary to secondary bile acids. Serum signatures of immune proteins reflecting microbial diversity identified patients more likely to achieve remission with anti-cytokine therapy. Remission-associated multi-omic profiles were unique to each therapeutic class. These profiles may facilitate a priori determination of optimal therapeutics for patients and serve as targets for newer therapies.

Genomics Analysis of L-DOPA Exposure in Drosophila sechellia.

Drosophila sechellia is a dietary specialist fruit fly that evolved from a generalist ancestor to specialize on the toxic fruit of Morinda citrifolia This species pair has been the subject of numerous studies where the goal has largely been to determine the genetic basis of adaptations associated with host specialization. Because one of the most striking features of M. citrifolia fruit is the production of toxic volatile compounds that kill insects, most genomic studies in D. sechellia to date have focused on gene expression responses to the toxic compounds in its food. In this study, we aim to identify new genes important for host specialization by profiling gene expression response to 3,4-dihydroxyphenylalanine (L-DOPA). Recent work found it to be highly abundant in M. citrifolia, critical for reproductive success of D. sechellia, and supplementation of diet with the downstream pathway product dopamine can influence toxin resistance phenotypes in related species. Here we used a combination of functional genetics and genomics techniques to identify new genes that are important for D. sechellia ecological adaptation to this new niche. We show that L-DOPA exposure can affect toxin resistance phenotypes, identify genes with plastic responses to L-DOPA exposure, and functionally test an identified candidate gene. We found that knock-down of Esterase 6 (Est6) in a heterologous species alters toxin resistance suggesting Est6 may play an important role in D. sechellia host specialization.

An Interscholastic Network To Generate LexA Enhancer Trap Lines in Drosophila.

Binary expression systems like the LexA-LexAop system provide a powerful experimental tool kit to study gene and tissue function in developmental biology, neurobiology, and physiology. However, the number of well-defined LexA enhancer trap insertions remains limited. In this study, we present the molecular characterization and initial tissue expression analysis of nearly 100 novel StanEx LexA enhancer traps, derived from the StanEx1 index line. This includes 76 insertions into novel, distinct gene loci not previously associated with enhancer traps or targeted LexA constructs. Additionally, our studies revealed evidence for selective transposase-dependent replacement of a previously-undetected KP element on chromosome III within the StanEx1 genetic background during hybrid dysgenesis, suggesting a molecular basis for the over-representation of LexA insertions at the NK7.1 locus in our screen. Production and characterization of novel fly lines were performed by students and teachers in experiment-based genetics classes within a geographically diverse network of public and independent high schools. Thus, unique partnerships between secondary schools and university-based programs have produced and characterized novel genetic and molecular resources in Drosophila for open-source distribution, and provide paradigms for development of science education through experience-based pedagogy.

Transcriptomic Analysis of Octanoic Acid Response in Drosophila sechellia Using RNA-Sequencing.

The dietary specialist fruit fly Drosophila sechellia has evolved to specialize on the toxic fruit of its host plant Morinda citrifolia Toxicity of Morinda fruit is primarily due to high levels of octanoic acid (OA). Using RNA interference (RNAi), prior work found that knockdown of Osiris family genes Osiris 6 (Osi6), Osi7, and Osi8 led to increased susceptibility to OA in adult D. melanogaster flies, likely representing genes underlying a Quantitative Trait Locus (QTL) for OA resistance in D. sechellia While genes in this major effect locus are beginning to be revealed, prior work has shown at least five regions of the genome contribute to OA resistance. Here, we identify new candidate OA resistance genes by performing differential gene expression analysis using RNA-sequencing (RNA-seq) on control and OA-exposed D. sechellia flies. We found 104 significantly differentially expressed genes with annotated orthologs in D. melanogaster, including six Osiris gene family members, consistent with previous functional studies and gene expression analyses. Gene ontology (GO) term enrichment showed significant enrichment for cuticle development in upregulated genes and significant enrichment of immune and defense responses in downregulated genes, suggesting important aspects of the physiology of D. sechellia that may play a role in OA resistance. In addition, we identified five candidate OA resistance genes that potentially underlie QTL peaks outside of the major effect region, representing promising new candidate genes for future functional studies.

A randomized trial of coenzyme Q10 in patients with statin myopathy: rationale and study design.

BACKGROUND: Statins are the most commonly prescribed and effective medications for reducing low-density lipoprotein levels. Some patients experience myopathic symptoms during statin treatment. The etiology is not known, but depletion of mevalonate pathway metabolites, including coenzyme Q10 (CoQ10), has been suggested. Despite a lack of conclusive evidence supporting its utility, CoQ10 supplementation has been recommended to patients who experience myalgic symptoms. OBJECTIVE: The Co-Enzyme Q10 in Statin Myopathy study is designed to examine the effect of CoQ10 supplementation on the extent and intensity of muscle pain during treatment with simvastatin. METHODS: We will recruit patients with a documented history of myalgia during statin treatment. The presence of statin-related myalgia will be confirmed in a crossover run-in trial during which the presence and absence of symptoms will be documented during statin and placebo treatment, respectively. Individuals experience myalgic symptoms while taking statins but not placebo will be randomized to receive simvastatin 20 mg daily plus either 600 mg daily of CoQ10 or placebo. Muscle pain intensity will be documented during weekly phone calls via use of the Brief Pain Inventory, Short Form. Treatment will continue for 8 weeks or until muscle symptoms are reported continuously for 1 week or become intolerable, and then subjects will crossover to the alternative treatment (CoQ10 or placebo). RESULTS: This study is an ongoing clinical trial. CONCLUSIONS: This study will determine the utility of CoQ10 for reducing pain intensity in myalgic patients and will provide guidance for clinicians treating patients with hypercholesterolemia who are intolerant to statins.

Effects of a short-term carbohydrate-restricted diet on strength and power performance.

The purpose of the study was to examine the effects of switching from a habitual diet to a carbohydrate-restricted diet (CRD) on strength and power performance in trained men (n = 16) and women (n = 15). Subjects performed handgrip dynamometry, vertical jump, 1RM bench press and back squat, maximum-repetition bench press, and a 30-second Wingate anaerobic cycling test after consuming a habitual diet (40.7% carbohydrate, 22.2% protein, and 34.4% fat) for 7 days and again after following a CRD (5.4% carbohydrate, 35.1% protein, and 53.6% fat) for 7 days. Before both testing sessions, body weight and composition were examined using bioelectrical impedance analysis. Three 2 × 2 multiple analyses of variance were used to compare performance variables between the habitual diet and CRD. Subjects consumed significantly fewer (p < 0.05) total kilocalories during the CRD (2,156.55 ± 126.7) compared with the habitual diet (2,537.43 ± 99.5). Body mass decreased significantly (p < 0.05). Despite a reduction in body mass, strength and power outputs were maintained for men and women during the CRD. These findings may have implications for sports that use weight classes, and in which strength and power are determinants of success. A CRD may be an alternative method for short-term weight loss without compromising strength and power outputs. The use of a 7-day CRD could replace weight loss methods employing severe dehydration before competition.

Exercise-induced insulin-like growth factor I system concentrations after training in women.

INTRODUCTION: This study examined the effects of short-term physical training on the acute hormonal response (i.e., growth hormone, total and free insulin-like growth factor I [IGF-I], and IGF binding proteins [IGFBP]-1, IGFBP-2, and IGFBP-3) to resistance exercise (RE) in women. METHODS: Forty-six women (20.3 ± 0.3 yr, mass = 64.1 ± 7.3 kg, height = 165.7 ± 1.0 cm) were randomly assigned to an endurance training (E), resistance training (R), combined training (R + E), or control (C) group for 8wk. Subjects completed a standardized bout of RE (six sets of back squats at 10 repetition maximum) before and after training. Blood samples were obtained at rest (PRE), after the third set, immediately postexercise (POST), and at 15 min and 30 min after exercise. RESULTS: Acute RE significantly increased (P < 0.05) serum growth hormone (mean ± SD; change from PRE to POST = +10.9 ± 7.5 µg·L-1), total IGF-I (+66.1 ± 25.4 µg·L-1), IGFBP-1 (+2.5 ± 3.1 µg·L-1), IGFBP-2 (+86.0 ± 86.8 µg·L-1), and IGFBP-3 (+0.69 ± 0.25 mg·L-1) concentrations and decreased free IGF-I concentrations (-0.14 ± 0.21 µg·L-1). After 8 wk of training, total IGF-I concentrations were significantly increased (change in POST concentrations from week 0 to week 8 = +82.5 ± 120.8 µg·L-1), and IGFBP-1 concentrations were significantly decreased (-6.7 ± 13.6 µg·L-1) during exercise in groups that participated in resistance training (R and R + E); no significant changes were seen after E or C. CONCLUSIONS: Participation in resistance training increased total IGF-I and reduced IGFBP-1 concentrations during acute RE, indicating exercise mode-specific adaptations in the circulating IGF-I system.

Preservation of fat-free mass after two distinct weight loss diets with and without progressive resistance exercise.

BACKGROUND: Preserving fat-free mass (FFM) during weight loss is important in older adults. The purpose was to examine a low-fat diet (LFD) versus a carbohydrate-restricted diet (CRD) with and without progressive resistance exercise (PRE) on preservation of FFM in older men with metabolic syndrome. METHODS: A total of 42 men (59±7 years) were matched [body mass index (BMI)] and randomized to LFD, LFD&PRE, CRD, and CRD&PRE. PRE groups performed supervised strength training three times per week. Body weight, composition, metabolic syndrome criteria, and strength were measured at baseline and week 12. A 3-day diet record was kept at baseline and at weeks 1, 6, and 12. RESULTS: Attrition (24%) was similar between groups. Depicted as % carbohydrate:fat:protein, the intervention diet was: LFD=55:24:18, LFD&PRE=57:20:20, CRD=16:54:28, and CRD&PRE=12:56:31. Weight (lb) decreased similarly in all groups (LFD, -18.0±7.4; LFD&PRE, -19.8±12.8; CRD, -20.2±8.0; CRD&PRE, -22.7±6.0; P<0.001), and number of participants with metabolic syndrome decreased in all groups (-3, -6, -3, -4, respectively). Percent of weight loss from appendicular FFM was 27.5%, 15.9%, 15.7%, and 17.3% respectively. A trend was found when comparing LFD and LFD&PRE (P=0.068), and when comparing LFD&CRD (P=0.072). Triglycerides improved more for the LFD&PRE, CRD, and CRD&PRE groups compared to the LFD group (P<0.05). Improvements in high-density lipoprotein-cholesterol were better in the CRD&PRE group (4.1±5.1 mg/dL) versus the LFD group (-5.0±5.9 mg/dL; P<0.01). CONCLUSIONS: LFD&PRE, CRD, and CRD&PRE preserve FFM similarly. PRE is an important component of a LFD during weight loss in this population.

Physical activity, cognitive function, and brain health: what is the role of exercise training in the prevention of dementia?

Tor preventive measures are necessary to attenuate the increased economic and social burden of dementia. This review will focus on the potential for physical activity and exercise training to promote brain health and improve cognitive function via neurophysiological changes. We will review pertinent animal and human research examining the effects of physical activity on cognitive function and neurophysiology. We will discuss cross-sectional and longitudinal studies addressing the relationship between neurocognitive health and cardiorespiratory fitness or habitual activity level. We will then present and discuss longitudinal investigations examining the effects of exercise training on cognitive function and neurophysiology. We will conclude by summarizing our current understanding of the relationship between physical activity and brain health, and present areas for future research given the current gaps in our understanding of this issue.

Effects of dietary macronutrient distribution on vascular integrity in obesity and metabolic syndrome.

Metabolic syndrome is a condition characterized by a clustering of risk factors for cardiovascular disease. Emerging data suggest vascular integrity is disrupted in metabolic syndrome. Vascular integrity may be determined using several measurements, including pulse wave velocity, augmentation index, and flow-mediated dilation. Arterial stiffness has become an important clinical indicator of cardiovascular disease risk. Several circulating inflammatory peptides also impact vascular integrity. The present review examines the efficacy of nutritional interventions aimed at improving vascular integrity and reducing levels of associated inflammatory peptides in individuals with metabolic syndrome, with a specific focus on the effect of dietary macronutrient redistribution on these factors.

Lack of circulating bioactive and immunoreactive IGF-I changes despite improved fitness in chronic kidney disease patients following 48 weeks of physical training.

OBJECTIVE: As known abnormalities exist in the insulin-like growth factor (IGF) system in chronic kidney disease (CKD) patients, the measurement of bioactive IGF-I may provide further insight into the therapeutic potential of long-term exercise training. DESIGN: Patients (N=21) with stages 3 and 4 CKD were recruited from a local nephrology practice in Springfield, MA and randomized into matched treatment and control groups. The treatment group participated in 48 weeks of supervised, progressive exercise training and dietary counseling, while the control group received only usual care. Treadmill testing, anthropometric measurements, and blood samples for analysis of immunoreactive IGF-I, IGF-II, IGFBP-1 and -2, and bioactive IGF-I were taken at baseline, 24 weeks, and 48 weeks. RESULTS: There were no significant differences in any of the components of the IGF system (all p-values>0.05). Immunoreactive IGF-I levels correlated significantly with bioactive IGF-I at baseline (r=0.50, p=0.02) and at 48 weeks (r=0.64, p=0.01). There was a significant interaction between group and time for both VO(2peak) (p=0.03) and total treadmill time (TT) (p<0.01). CONCLUSIONS: Despite improvements in physical performance, a 48-week training program did not affect any of the circulating IGF system measurements. Disparities between these findings and those of other researchers reporting a biphasic response to long-term training may be explained by differences in study groups and exercise programs.