The COG database: an updated version includes eukaryotes

Background

The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies.

Results

We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (~1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes.

Conclusion

The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.     

Post-translational regulation of human indoleamine 2,3-dioxygenase activity by nitric oxide

The heme protein indoleamine 2,3-dioxygenase (IDO) is induced by the proinflammatory cytokine interferon-gamma (IFNgamma) and plays an important role in the immune response by catalyzing the oxidative degradation of L-tryptophan (Trp) that contributes to immune suppression and tolerance. Here we examined the mechanism by which nitric oxide (NO) inhibits human IDO activity. Exposure of IFNgamma-stimulated human monocyte-derived macrophages (MDM) to NO donors had no material impact on IDO mRNA or protein expression, yet exposure of MDM or transfected COS-7 cells expressing active human IDO to NO donors resulted in reversible inhibition of IDO activity. NO also inhibited the activity of purified recombinant human IDO (rhIDO) in a reversible manner and this correlated with NO binding to the heme of rhIDO. Optical absorption and resonance Raman spectroscopy identified NO-inactivated rhIDO as a ferrous iron (Fe(II))-NO-Trp adduct. Stopped-flow kinetic studies revealed that NO reacted most rapidly with Fe(II) rhIDO in the presence of Trp. These findings demonstrate that NO inhibits rhIDO activity reversibly by binding to the active site heme to trap the enzyme as an inactive nitrosyl-Fe(II) enzyme adduct with Trp bound and O2 displaced. Reversible inhibition by NO may represent an important mechanism in controlling the immune regulatory actions of IDO.     

Decreasing the Burden of Type 2 Diabetes in South Africa: The Impact of Taxing Sugar-Sweetened Beverages

Introduction

Type 2 diabetes poses an increasing public health burden in South Africa (SA) with obesity as the main driver of the epidemic. Consumption of sugar sweetened beverages (SSBs) is linked to weight gain and reducing SSB consumption may significantly impact the prevalence of obesity and related diseases. We estimated the effect of a 20% SSB tax on the burden of diabetes in SA.

Methods and Findings

We constructed a life table-based model in Microsoft Excel (2010). Consumption data from the 2012 SA National Health and Nutrition Examination Survey, previously published own- and cross-price elasticities of SSBs and energy balance equations were used to estimate changes in daily energy intake and its projected impact on BMI arising from increased SSB prices. Diabetes relative risk and prevalent years lived with disability estimates from the Global Burden of Disease Study and modelled disease epidemiology estimates from a previous study were used to estimate the effect of the BMI changes on diabetes burden. Diabetes cost estimates were obtained from the South African Council for Medical Schemes. Over 20 years, a 20% SSB tax could reduce diabetes incident cases by 106 000 in women (95% uncertainty interval (UI) 70 000–142 000) and by 54 000 in men (95% UI: 33 000–80 000); and prevalence in all adults by 4.0% (95% UI: 2.7%-5.3%). Cumulatively over twenty years, approximately 21 000 (95% UI: 14 000–29 000) adult T2DM-related deaths, 374 000 DALYs attributed to T2DM (95% UI: 299 000–463 000) and over ZAR10 billion T2DM healthcare costs (95% UI: ZAR6.8–14.0 billion) equivalent to USD860 million (95% UI: USD570 million–USD1.2 billion) may be averted.

Conclusion

Fiscal policy on SSBs has the potential to mitigate the diabetes epidemic in South Africa and contribute to the National Department of Health goals stated in the National NCD strategic plan.     

Lifestyle Behaviors in Metabolically Healthy and Unhealthy Overweight and Obese Women: A Preliminary Study

Background

Few studies have examined dietary data or objective measures of physical activity (PA) and sedentary behavior among metabolically healthy overweight/obese (MHO) and metabolically unhealthy overweight/obese (MUO). Thus, the purpose is to determine whether PA, sedentary behavior and/or diet differ between MHO and MUO in a sample of young women.

Methods

Forty-six overweight/obese (BMI ≥25 kg/m²) African American and Caucasian women 19–35 years were classified by cardiometabolic risk factors, including elevated blood pressure, triglyceride, glucose and C-reactive protein, low high density lipoprotein, and insulin resistance (MUO ≥2; MHO, <2). Time (mins/day) in light, moderate, vigorous PA, and sedentary behavior were estimated using an accelerometer (≥3 days; ≥8 hrs wear time). Questionnaires were used to quantify sitting time, TV/computer use and usual daily activity. The Block Food Frequency Questionnaire assessed dietary food intake. Differences between MHO and MUO for lifestyle behaviors were tested with linear regression (continuous data) or logistic regression (categorical data) after adjusting for age, race, BMI, smoking and accelerometer wear and/or total kilocalories, as appropriate.

Results

Women were 26.7±4.7 years, with a mean BMI of 31.1±3.7 kg/m², and 61% were African American. Compared to MUO (n = 9), MHO (n = 37; 80%) spent less mins/day in sedentary behavior (difference: -58.1±25.5, p = 0.02), more mins/day in light PA (difference: 38.2±16.1, p = 0.02), and had higher daily METs (difference: 0.21±0.09, p = 0.03). MHO had higher fiber intakes (g/day of total fiber, soluble fiber, fruit/vegetable fiber, bean fiber) and daily servings of vegetables; but lower daily dairy servings, saturated fat, monounsaturated fat and trans fats (g/day) compared to MUO.

Conclusion

Compared to MUO, MHO young women demonstrate healthier lifestyle habits with less sedentary behavior, more time in light PA, and healthier dietary quality for fat type and fiber. Future studies are needed to replicate findings with larger samples that include men and women of diverse race/ethnic groups.     

Comparison of High-Calorie,Low-Nutrient-Dense Food Consumption among Obese and Non-Obese Adolescents

BANDINI, LINDA G. DUNG VU, AVIVA MUST, HELENE CYR, ALISON GOLDBERG, AND WILLIAM H. DIETZ. Comparison of high-calorie, low-nutrient-dense food consumption among obese and non-obese adolescents. ObesRes. Objective: The purpose of this study was to determine whether obese adolescents eat more high-calorie low-nutrient-dense foods than non-obese adolescents. Research Methods and Procedures: Using a cross-sectional design, 22 non-obese and 21 obese adolescents kept 14-day food records. Records provided estimates of total daily energy intake and caloric intake from five categories of high-calorie, low-nutrient-dense (HC) foods: candy, chips, soda, baked goods, and ice cream. Body composition was determined by ¹⁸O dilution and daily energy expenditure by doubly labeled water. Percentage of energy intake reported (%report) was calculated as the ratio of reported energy intake to measured energy expenditure (x 100%). Results: Both groups underreported energy intake, but the percentage reported was significantly greater in the non-obese group (78. ±20. 5% non-obese vs. 55. 5±21. 8% obese, p<0. 001). Consumption of calories from chips and soda was similar among non-obese and obese adolescents. However, total energy intake from all HC foods was higher in the non-obese group than among the obese (617±356 kcal/day vs. 362plusnum;223 kcallday; p<0. 01) and represented 27. 2±10. 5% and 19. 9±9. 6% of reported energy intake in the non-obese and obese groups, respectively. After adjustment for underreporting, the percentage of calories provided by each of the HC foods was similar in the obese and non-obese groups except for ice cream, which remained significantly greater in the non-obese group (p<0. 05). Discussion: Our findings suggest that both non-obese and obese adolescents consume a substantial portion of reported calories from HC foods and that obese adolescents do not consume more calories from these foods than non-obese adolescents. These data offer no evidence to support the widespread notion that obese adolescents eat more “junk food” than non-obese adolescents. Health professionals who treat obese adolescents must be aware that the excess calories in their diets may come from a variety of food sources and not solely from high-calorie snack foods.     

Immunological aspects of recombinant adeno-associated virus delivery to the mammalian brain

Recombinant adeno-associated viruses (rAAV) are highly efficient vectors for gene delivery into the central nervous system (CNS). However, host inflammatory and immune responses may play a critical role in limiting the use of rAAV vectors for gene therapy and functional genomic studies in vivo. Here, we evaluated the effect of repeated injections of five rAAV vectors expressing different genetic sequences (coding or noncoding) in a range of combinations into the rat brain. Specifically, we wished to determine whether a specific immune or inflammatory response appeared in response to the vector and/or the transgene protein after repeated injections under conditions of mannitol coinjection. We show that readministration of the same rAAV to the CNS is possible if the interval between the first and second injection is more than 4 weeks. Furthermore, our data demonstrate that rAAV vectors carrying different genetic sequences can be administered at intervals of 2 weeks. Our data therefore suggest that the AAV capsid structure is altered by the vector genetic sequence, such that secondary structures of the single-stranded genome have an impact on the antigenicity of the virus. This study provides guidelines for more rational design of gene transfer studies in the rodent brain and, in addition, suggests the use of repeated administration of rAAV as a viable form of therapy for the treatment of chronic diseases.     

Insights into the mechanism of enhanced mobilization of hematopoietic progenitor cells and release of CXCL12 by a combination of AMD3100 and aminoglycoside-polyarginine conjugates

Mobilization of hematopoietic stem and progenitor cells (HSPCs) from the bone marrow to the peripheral blood is utilized in clinical HSPC transplantation protocols. Retention of HSPCs in the bone marrow is determined by relationships between the chemokine chemokine (C-X-C motif) ligand 12 (CXCL12) and its major receptor C-X-C chemokine receptor type 4 (CXCR4), and disruption of this retention by CXCR4 antagonists such as AMD3100 induces rapid HSPC mobilization. Here, we report that aminoglycoside-polyarginine conjugates (APACs) and N-α-acetyl-nona-D-arginine (r9) induce mobilization of white blood cells and, preferentially, immature hematopoietic progenitor cells (HPCs) in mice, similarly to AMD3100. Remarkably, administration of AMD3100 with each one of the APACs or r9 caused additional HPC mobilization. The mobilizing activity of APACs and r9 was accompanied by a significant elevation in plasma CXCL12 levels. To further understand how APACs, r9 and their combinations with AMD3100 compete with CXCL12 binding to CXCR4, as well with antibody against CXCR4 for CXCR4 binding, we have undertaken an approach combining experimental validation and docking to determine plausible binding modes for these ligands. On the basis of our biological and docking findings, and recently published NMR data, we suggest that combination of pairs of compounds such as APACs (or r9) with AMD3100 induces more efficient disruption of the CXCL12-CXCR4 interaction than AMD3100 alone, resulting in enhanced HPC mobilization.