Oxford nanopore sequencing in clinical microbiology and infection diagnostics.

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.

Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing.

Nanopore sequencing device analysis systems simultaneously generate multiple picoamperage current signals representing the passage of DNA or RNA nucleotides ratcheted through a biomolecule nanopore array by motor proteins. Squiggles are a noisy and time-distorted representation of an underlying nucleotide sequence, "gold standard model", due to experimental and algorithmic artefacts. Other research fields use dynamic time warped-space averaging (DTWA) algorithms to produce a consensus signal from multiple time-warped sources while preserving key features distorted by standard, linear-averaging approaches. We compared the ability of DTW Barycentre averaging (DBA), minimize mean (MM) and stochastic sub-gradient descent (SSG) DTWA algorithms to generate a consensus signal from squiggle-space ensembles of RNA molecules Enolase, Sequin R1-71-1 and Sequin R2-55-3 without knowledge of their associated gold standard model. We propose techniques to identify the leader and distorted squiggle features prior to DTWA consensus generation. New visualization and warping-path metrics are introduced to compare consensus signals and the best estimate of the "true" consensus, the study's gold standard model. The DBA consensus was the best match to the gold standard for both Sequin studies but was outperformed in the Enolase study. Given an underlying common characteristic across a squiggle ensemble, we objectively evaluate a novel "voting scheme" that improves the local similarity between the consensus signal and a given fraction of the squiggle ensemble. While the gold standard is not used during voting, the increase in the match of the final voted-on consensus to the underlying Enolase and Sequin gold standard sequences provides an indirect success measure for the proposed voting procedure in two ways: First is the decreased least squares warped distance between the final consensus and the gold model, and second, the voting generates a final consensus length closer to the known underlying RNA biomolecule length. The results suggest considerable potential in marrying squiggle analysis and voted-on DTWA consensus signals to provide low-noise, low-distortion signals. This will lead to improved accuracy in detecting nucleotides and their deviation model due to chemical modifications (a.k.a. epigenetic information). The proposed combination of ensemble voting and DTWA has application in other research fields involving time-distorted, high entropy signals.

Grip Strength Is Associated with Longitudinal Health Maintenance and Improvement in Adolescents.

OBJECTIVE: To assess the effects of muscle strength, as determined by grip strength, on changes in health status in adolescents. STUDY DESIGN: Risk variables included excess body fat, elevated fasting glucose, high blood pressure, elevated serum triglycerides, and low high-density lipoprotein cholesterol. Multinomial logistic regression was used to quantify the odds of experiencing health maintenance (no risk factors identified at either time point) or health improvement (presence of ≥1 baseline risk factor and fewer or no risk factors at follow-up) over a 2-year period. The primary exposure variable was grip strength normalized by body mass (normalized grip strength [NGS]), and previous cut-offs were used to determine whether adolescents were weak or strong. RESULTS: Adolescents who had low NGSs had a significantly greater prevalence of health decline or poor health persistence as compared with those who were strong (boys: 60.2% vs 15.3%; girls: 51% vs 21.9%; all P < .001). Moreover, adolescents who were strong had an increased adjusted odds for health maintenance (OR 3.54; 95% CI 1.80-6.97) and health improvement (OR 1.30; 95% CI 1.05-1.60), even after we adjusted for baseline fat-free mass index, cardiorespiratory fitness, and objectively measured physical activity. CONCLUSIONS: Greater NGS is associated with longitudinal health maintenance and health improvements in adolescents. Low NGS could be used as a prognostic indicator of cardiometabolic risk and to identify adolescents who would benefit most from lifestyle interventions to improve muscular fitness.

The lifelong impact of fetal growth restriction on cardiac development.

BACKGROUND: Maternal nutrient restriction (MNR) is a widespread cause of fetal growth restriction (FGR), an independent predictor of heart disease and cardiovascular mortality. Our objective was to examine the developmental and long-term impact of MNR-induced FGR on cardiac structure in a model that closely mimics human development. METHODS: A reduction in total caloric intake spanning pregestation through to lactation in guinea pig sows was used to induce FGR. Proliferation, differentiation, and apoptosis of cardiomyocytes were assessed in late-gestation fetal, neonatal, and adult guinea pig hearts. Proteomic analysis and pathway enrichment were performed on fetal hearts. RESULTS: Cardiomyocyte proliferation and the number of mononucleated cells were enhanced in the MNR-FGR fetal and neonatal heart, suggesting a delay in cardiomyocyte differentiation. In fetal hearts of MNR-FGR animals, apoptosis was markedly elevated and the total number of cardiomyocytes reduced, the latter remaining so throughout neonatal and into adult life. A reduction in total cardiomyocyte number in adult MNR-FGR hearts was accompanied by exaggerated hypertrophy and a disorganized architecture. Pathway analysis identified genes related to cell proliferation, differentiation, and survival. CONCLUSIONS: FGR influences cardiomyocyte development during critical windows of development, leading to a permanent deficiency in cardiomyocyte number and compensatory hypertrophy in a rodent model that recapitulates human development.

Immune adaptation to chronic intense exercise training: new microarray evidence.

BACKGROUND: Endurance exercise training, especially the high-intensity training, exhibits a strong influence on the immune system. However, the mechanisms underpinning the immune-regulatory effect of exercise remain unclear. Consequently, we chose to investigate the alterations in the transcriptional profile of blood leukocytes in young endurance athletes as compared with healthy sedentary controls, using Affymetrix human gene 1.1 ST array. RESULTS: Group differences in the transcriptome were analyzed using Intensity-based Hierarchical Bayes method followed by a Logistic Regression-based gene set enrichment method. We identified 72 significant transcripts differentially expressed in the leukocyte transcriptome of young endurance athletes as compared with non-athlete controls with a false discovery rate (FDR) < 0.05, comprising mainly the genes encoding ribosomal proteins and the genes involved in mitochondrial oxidative phosphorylation. Gene set enrichment analysis identified three major gene set clusters: two were up-regulated in athletes including gene translation and ribosomal protein production, and mitochondria oxidative phosphorylation and biogenesis; one gene set cluster identified as transcriptionally downregulated in athletes was related to inflammation and immune activity. CONCLUSION: Our data indicates that in young healthy individuals, intense endurance exercise training (exemplifed by athletic training) can chronically induce transcriptional changes in the peripheral blood leukocytes, upregulating genes related to protein production and mitochondrial energetics, and downregulating genes involved in inflammatory response. The findings of the study also provide support for the notion that peripheral blood can be used as a surrogate tissue to study the systemic effect of exercise training.

The Relationship between Coronary Artery Disease Risk Factors and Carotid Intima-Media Thickness in Children.

OBJECTIVE: To determine the number of coronary artery disease risk factors and the individual coronary artery disease risk factors that have a negative influence on carotid intima-media thickness in children. STUDY DESIGN: One hundred and nineteen children (mean age 10.51 ± 0.52 years; 51% female) participated. Each subject was assessed for carotid intima-media thickness, total cholesterol, high-density lipoprotein cholesterol (HDL-C), glucose, body mass index (BMI), and resting blood pressure. Surveys assessed family history of cardiovascular disease, and physical activity. Ultrasound assessment was completed on the right and left common carotid arteries. Statistical analyses included the t test, χ2 test, one-way ANOVA, and stepwise regression. RESULTS: An increase in carotid intima-media thickness was observed with 2 vs 0 coronary artery disease risk factors for left carotid intima-media thickness (P < .001). With 3+ vs 0 coronary artery disease risk factors, increases in left (P < .001) and combined left and right carotid intima-media thickness (P < .05) were observed. BMI independently predicted carotid intima-media thickness (r = 0.410; P < .01), but HDL-C did not. However, HDL-C was significantly inversely related to BMI (r = -0.534; P < .01). Combining BMI and HDL-C provided the strongest prediction of carotid intima-media thickness (r = 0.451; adjusted R2 = 0.190). Compared with children with a healthy and overweight BMI, children in the obese category had greater right (P < .00), left (P < .001), and combined right and left carotid intima-media thickness (P < .001). CONCLUSIONS: Carotid intima-media thickness is negatively influenced by 2+ coronary artery disease risk factors. Weight status appears to have the greatest negative impact on carotid intima-media thickness in children. These findings support the need for strategies to lower BMI in children.

Acute and Long-Term Impact of High-Protein Diets on Endocrine and Metabolic Function, Body Composition, and Exercise-Induced Adaptations.

BACKGROUND: High-protein diets have been shown to improve body composition through alterations in satiety, muscle protein synthesis, and the thermic effect of food. AIM: Given these findings, the purpose of this review is to discuss the integration of the specific hormonal and metabolic effects of high-protein diets following both acute and long-term usage, especially with regard to body composition. METHODS: Full-text articles were obtained through PubMed by using the terms "high-protein diet and body composition," "high-protein diet and exercise," "high-protein diet risk," "high-protein diet side effects," "protein quality PDCAAS," "RDA for protein," and "daily protein recommendation." Articles were initially screened according to their title and abstract; careful evaluation of the full manuscripts was then used to identify relevant articles. RESULTS: The higher satiety exerted by high-protein diets is generated through increments in anorexigenic, as well as decrements in orexigenic hormones. Improvements in muscle mass are achieved by activation of muscle protein synthesis acting through the mTOR pathway. High thermic effect of food is caused due to necessary deamination, gluconeogenesis, and urea synthesis caused by high-protein diets. Interestingly, high-protein diets in both hypo- and normocaloric conditions have shown to improve body composition, whereas in combination with hypercaloric conditions does not seem to increase fat mass, when the excess energy comes from protein. CONCLUSIONS: High protein diets effectively improve body composition by acting through different pathways.

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.

BACKGROUND: Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them. RESULTS: SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data. CONCLUSIONS: SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.

Sleep duration predicts cardiometabolic risk in obese adolescents.

OBJECTIVE: To examine the independent contributions of objectively measured sleep duration and fragmentation on cardiometabolic risk accumulation in free-living obese adolescents. STUDY DESIGN: Characteristics of metabolic syndrome (waist circumference, mean arterial pressure, fasting high-density lipoprotein cholesterol, triglycerides, glucose) were measured in obese adolescents and standardized residuals (z-scores) were summed (inverse high-density lipoprotein cholesterol) to create a continuous cardiometabolic risk score (cMetScore), adjusted for age, sex, and race. Sleep and physical activity were objectively measured in habitual, free-living conditions for 7 days (SenseWear Pro3, BodyMedia, Pittsburgh, Pennsylvania; n = 37; 54% female, ages 11-17 years). Associations between sleep duration and cMetScore were assessed via multiple linear regression. RESULTS: Body mass index, total sleep time, and sleep session length were each correlated with cMetScore (P < .05 all). Total sleep time was inversely and independently associated with cMetScore (r = -0.535, P = .001) and was the best independent predictor of metabolic risk. CONCLUSIONS: Sleep duration inversely predicts cardiometabolic risk in obese adolescents, even when we controlled for various measures of physical activity, anthropometry, and adiposity. Further research should investigate the biological mechanism of this relationship and the potential treatment effect of sleep intervention in decreasing cardiometabolic risk in this population.

An expression-directed linear mixed model discovering low-effect genetic variants.

Detecting genetic variants with low-effect sizes using a moderate sample size is difficult, hindering downstream efforts to learn pathology and estimating heritability. In this work, by utilizing informative weights learned from training genetically predicted gene expression models, we formed an alternative approach to estimate the polygenic term in a linear mixed model. Our linear mixed model estimates the genetic background by incorporating their relevance to gene expression. Our protocol, expression-directed linear mixed model, enables the discovery of subtle signals of low-effect variants using moderate sample size. By applying expression-directed linear mixed model to cohorts of around 5,000 individuals with either binary (WTCCC) or quantitative (NFBC1966) traits, we demonstrated its power gain at the low-effect end of the genetic etiology spectrum. In aggregate, the additional low-effect variants detected by expression-directed linear mixed model substantially improved estimation of missing heritability. Expression-directed linear mixed model moves precision medicine forward by accurately detecting the contribution of low-effect genetic variants to human diseases.

Genomic compartmentalization of gene families encoding core components of metazoan signaling systems.

To investigate the role of gene localization and genome organization in cell-cell signalling and regulation, we mapped the distribution pattern of gene families that comprise core components of intercellular communication networks. Our study is centered on the distinct evolutionarily conserved metazoan signalling pathways that employ proteins in the receptor tyrosine kinase, WNT, hedgehog, NOTCH, Janus kinase/STAT, transforming growth factor beta, and nuclear hormone receptor protein families. Aberrant activity of these signalling pathways is closely associated with the promotion and maintenance of human cancers. The cataloguing and mapping of genes encoding these signalling proteins and comparisons across species has led us to propose that the genome can be subdivided into six genome-wide primary linkage groups (PLGs). PLGs are composed of assemblages of gene families that are often mutually exclusive, raising the possibility of unique functional identities for each group. Examination of the localization patterns of genes with distinct functions in signal transduction demonstrates dichotomous segregation patterns. For example, gene families of cell-surface receptors localize to genomic compartments that are distinct from the locations of their cognate ligand gene families. Additionally, genes encoding negative-acting components of signalling pathways (inhibitors and antagonists) are topologically separated from their positive regulators and other signal transducer genes. We, therefore, propose the existence of conserved genomic territories that encode key proteins required for the proper activity of metazoan signaling and regulatory systems. Disruption in this pattern of topologic genomic organization may contribute to aberrant regulation in hereditary or acquired diseases such as cancer. We further propose that long-range looping genomic regulatory interactions may provide a mechanism favouring the remarkable retention of these conserved gene clusters during chordate evolution.

Recumbent cross-training is a feasible and safe mode of physical activity for significantly motor-impaired adults with cerebral palsy.

OBJECTIVE: To examine the feasibility and potential benefits of using recumbent cross-training for nonambulatory adults with cerebral palsy (CP). DESIGN: Observational. SETTING: Clinical center for CP treatment and rehabilitation. PARTICIPANTS: Significantly motor-impaired adults with CP (N=11) with a mean age ± SD of 36.3±13.2 years and Gross Motor Function Classification System (GMFCS) levels III and IV. INTERVENTIONS: Participants completed a 40-minute session of aerobic exercise using the NuStep Recumbent Cross Trainer, in which resistance was progressively increased at 5-minute intervals. MAIN OUTCOME MEASURES: Every 5 minutes during the exercise session, heart rate, blood pressure, oxygen consumption (VO(2)), energy expenditure, and respiratory exchange ratios (RERs) were recorded along with rating of perceived exertion. Immediately after, and 24 hours postexercise, participants received a standard survey to assess levels of pain and discomfort. RESULTS: All participants were able to complete the 40-minute exercise protocol. Five of the 11 participants achieved a heart rate of at least 60% maximum throughout the duration, 10 participants had a significant elevation in VO(2) from baseline, and all participants had elevated RER values. Six participants reported pain during exercise, but only 2 reported pain after exercise was over. CONCLUSIONS: The NuStep Recumbent Cross Trainer is a feasible exercise modality for significantly motor-impaired adults with CP, GMFCS III and IV. Moreover, this mode was sufficient to stimulate a significant cardiorespiratory response in all participants, and thus it and similar devices may serve as a viable option for aerobic exercise interventions in this population, to prevent obesity and related cardiometabolic consequences.

Sequential multi-omics analysis identifies clinical phenotypes and predictive biomarkers for long COVID.

The post-acute sequelae of COVID-19 (PASC), also known as long COVID, is often associated with debilitating symptoms and adverse multisystem consequences. We obtain plasma samples from 117 individuals during and 6 months following their acute phase of infection to comprehensively profile and assess changes in cytokines, proteome, and metabolome. Network analysis reveals sustained inflammatory response, platelet degranulation, and cellular activation during convalescence accompanied by dysregulation in arginine biosynthesis, methionine metabolism, taurine metabolism, and tricarboxylic acid (TCA) cycle processes. Furthermore, we develop a prognostic model composed of 20 molecules involved in regulating T cell exhaustion and energy metabolism that can reliably predict adverse clinical outcomes following discharge from acute infection with 83% accuracy and an area under the curve (AUC) of 0.96. Our study reveals pertinent biological processes during convalescence that differ from acute infection, and it supports the development of specific therapies and biomarkers for patients suffering from long COVID.

Kupffer cell-like syncytia replenish resident macrophage function in the fibrotic liver.

Kupffer cells (KCs) are localized in liver sinusoids but extend pseudopods to parenchymal cells to maintain their identity and serve as the body's central bacterial filter. Liver cirrhosis drastically alters vascular architecture, but how KCs adapt is unclear. We used a mouse model of liver fibrosis and human tissue to examine immune adaptation. Fibrosis forced KCs to lose contact with parenchymal cells, down-regulating "KC identity," which rendered them incapable of clearing bacteria. Commensals stimulated the recruitment of monocytes through CD44 to a spatially distinct vascular compartment. There, recruited monocytes formed large aggregates of multinucleated cells (syncytia) that expressed phenotypical KC markers and displayed enhanced bacterial capture ability. Syncytia formed via CD36 and were observed in human cirrhosis as a possible antimicrobial defense that evolved with fibrosis.

Secondary muscle pathology and metabolic dysregulation in adults with cerebral palsy.

Cerebral palsy (CP) is caused by an insult to or malformation of the developing brain which affects motor control centers and causes alterations in growth, development, and overall health throughout the life span. In addition to the disruption in development caused by the primary neurological insult, CP is associated with exaggerated sedentary behaviors and a hallmark accelerated progression of muscle pathology compared with typically developing children and adults. Factors such as excess adipose tissue deposition and altered partitioning, insulin resistance, and chronic inflammation may increase the severity of muscle pathology throughout adulthood and lead to cardiometabolic disease risk and/or early mortality. We describe a model of exaggerated health risk represented in adults with CP and discuss the mechanisms and secondary consequences associated with chronic sedentary behavior, obesity, aging, and muscle spasticity. Moreover, we highlight novel evidence that implicates aberrant inflammation in CP as a potential mechanism linking both metabolic and cognitive dysregulation in a cyclical pattern.

Principal component analysis reveals gender-specific predictors of cardiometabolic risk in 6th graders.

BACKGROUND: The purpose of this study was to determine the sex-specific pattern of pediatric cardiometabolic risk with principal component analysis, using several biological, behavioral and parental variables in a large cohort (n = 2866) of 6th grade students. METHODS: Cardiometabolic risk components included waist circumference, fasting glucose, blood pressure, plasma triglycerides levels and HDL-cholesterol. Principal components analysis was used to determine the pattern of risk clustering and to derive a continuous aggregate score (MetScore). Stratified risk components and MetScore were analyzed for association with age, body mass index (BMI), cardiorespiratory fitness (CRF), physical activity (PA), and parental factors. RESULTS: In both boys and girls, BMI and CRF were associated with multiple risk components, and overall MetScore. Maternal smoking was associated with multiple risk components in girls and boys, as well as MetScore in boys, even after controlling for children's BMI. Paternal family history of early cardiovascular disease (CVD) and parental age were associated with increased blood pressure and MetScore for girls. Children's PA levels, maternal history of early CVD, and paternal BMI were also indicative for various risk components, but not MetScore. CONCLUSIONS: Several biological and behavioral factors were independently associated with children's cardiometabolic disease risk, and thus represent a unique gender-specific risk profile. These data serve to bolster the independent contribution of CRF, PA, and family-oriented healthy lifestyles for improving children's health.

Variants of the ankyrin repeat domain 6 gene (ANKRD6) and muscle and physical activity phenotypes among European-derived American adults.

Ankyrin repeat domain 6 (ANKRD6) is a ubiquitous protein that associates with early development in mammals and is highly expressed in the brain, spinal cord, and heart of humans. We examined the role of 8 ANKRD6 single-nucleotide polymorphisms (SNPs) on muscle performance and habitual physical activity (PA). Single-nucleotide polymorphisms were 545 T>A (rs9362667), 485 M>L (rs61736690), 233 T>M (rs2273238), 128 I>L (rs3748085), 631 P>L (rs61739327), 122 Q>E (rs16881983), 197805 G>A (rs9344950), and 710 L>X (NOVEL). This study consisted of 922 healthy, untrained, European-derived American men (n = 376, 23.6 ± 0.3 years, 25.0 ± 0.2 kg·m(-2)) and women (n = 546, 23.2 ± 0.2 years, 24.0 ± 0.2 kg·m(-2)). Muscle strength (maximum voluntary contraction [MVC] and 1 repetition maximum [1RM]) and size (cross-sectional area [CSA]) were assessed before and after 12 weeks of unilateral resistance training (RT). A subsample (n = 536, 23.4 ± 0.2 years, 24.6 ± 0.2 kg·m(-2)) completed the Paffenbarger Physical Activity Questionnaire. Associations among ANKRD6 genotypes and muscle phenotypes were tested with repeated measure analysis of covariance (ANCOVA) and PA phenotypes with multivariate ANCOVA, with age and body mass index as covariates. ANKRD6 122 Q>E was associated with increased baseline biceps CSA. ANKRD6 545 A>T and ANKRD6 710 L>X were associated with increased 1RM and MVC in response to RT, respectively. ANKRD6 631 P>L was associated with increased biceps CSA response to RT and time spent in moderate-intensity PA among the total sample and women. ANKRD6 genetic variants were associated with the muscle size and strength response to RT and habitual PA levels. Further research is needed to validate our results and explore mechanisms for the associations we observed.

Methylene blue in combination with sunlight as a low cost and effective disinfection method for coronavirus-contaminated PPE.

Using the Murine Hepatitis Virus (MHV) A59 coronavirus as a SARS-CoV-2 animal surrogate, we validated that methylene blue (MB) in combination with sunlight exposure is a robust, fast, and low-cost decontamination method for PPE that should be added to the toolbox of practical pandemic preparedness.

Impaired proteostasis in obese skeletal muscle relates to altered immunoproteasome activity.

Obesity-associated inflammation and/or oxidative stress can damage intramuscular proteins and jeopardize muscle integrity. The immunoproteasome (iProt) is vital to remove oxidatively modified proteins, but this function may be compromised with obesity. We sought to elucidate whether diet-induced obesity alters intramuscular iProt content and activity in mice to identify a possible mechanism for impaired muscle proteostasis in the obese state. Total proteasome content and activity and estimates of muscle oxidative damage, inflammation, muscle mass and strength were also assessed. Twenty-three male, 5-week-old C57BL/6J mice were fed a high-fat, high-sucrose (HFS; 45% kcal fat, 17% sucrose, n = 12) or low-fat, low-sucrose (LFS; 10% kcal fat, 0% sucrose, n = 11) diet for 12 weeks. Strength was assessed via a weightlifting test. Despite no change in pro-inflammatory cytokines (P > 0.05), oxidative protein damage was elevated within the gastrocnemius (P = 0.036) and tibialis anterior (P = 0.033) muscles of HFS-fed mice. Intramuscular protein damage coincided with reduced iProt and total proteasome activity (P < 0.05), and reductions in relative muscle mass (P < 0.001). Therefore, proteasome dysregulation occurs in obese muscle and may be a critical link in muscle oxidative stress. Novelty: Our results show for the first time that immunoproteasome and total proteasome function is significantly reduced within obese muscle. Visceral fat mass is a significant predictor of diminished proteasome activity in skeletal muscle. Proteasome function is inversely correlated with an intramuscular accumulation of oxidatively damaged proteins.

AKT1 polymorphisms are associated with risk for metabolic syndrome.

Converging lines of evidence suggest that AKT1 is a major mediator of the responses to insulin,insulin-like growth factor 1 (IGF1), and glucose. AKT1 also plays a key role in the regulation of both muscle cell hypertrophy and atrophy. We hypothesized that AKT1 variants may play a role in the endophenotypes that makeup metabolic syndrome. We studied a 12-kb region including the first exon of the AKT1 gene for association with metabolic syndrome-related phenotypes in four study populations [FAMUSS cohort (n = 574; age 23.7 ± 5.7 years), Strong Heart Study (SHS) (n = 2,134; age 55.5 ± 7.9 years), Dynamics of Health, Aging and Body Composition (Health ABC) (n = 3,075; age 73.6 ± 2.9 years), and Studies of a Targeted Risk Reduction Intervention through Defined Exercise (STRRIDE)(n = 175; age 40­65 years)]. We identified a three SNP haplotype that we call H1, which represents the ancestral alleles eles at the three loci and H2, which represents the derived alleles at the three loci. In young adult European Americans (FAMUSS), H1 was associated with higher fasting glucose levels in females. In middle age Native Americans (SHS), H1 carriers showed higher fasting insulin and HOMA in males, and higher BMI in females. Inolder African-American and European American subjects(Health ABC) H1 carriers showed a higher incidence of metabolic syndrome. Homozygotes for the H1 haplotype showed about twice the risk of metabolic syndrome in both males and females (p < 0.001). In middle-aged European Americans with insulin resistance (STRRIDE) studied by intravenous glucose tolerance test (IVGTT), H1 carriers showed increased insulin resistance due to the Sg component (p = 0.021). The 12-kb haplotype is a risk factor for metabolic syndrome and insulin resistance that needs to be explored in further populations.