SIRT6 protects against pathological damage caused by diet‐induced obesity

The NAD+‐dependent SIRT6 deacetylase is a therapeutic candidate against the emerging metabolic syndrome epidemic. SIRT6, whose deficiency in mice results in premature aging phenotypes and metabolic defects, was implicated in a calorie restriction response that showed an opposite set of phenotypes from the metabolic syndrome. To explore the role of SIRT6 in metabolic stress, wild type and transgenic (TG) mice overexpressing SIRT6 were fed a high fat diet. In comparison to their wild‐type littermates, SIRT6 TG mice accumulated significantly less visceral fat, LDL‐cholesterol, and triglycerides. TG mice displayed enhanced glucose tolerance along with increased glucose‐stimulated insulin secretion. Gene expression analysis of adipose tissue revealed that the positive effect of SIRT6 overexpression is associated with down regulation of a selective set of peroxisome proliferator‐activated receptor‐responsive genes, and genes associated with lipid storage, such as angiopoietin‐like protein 4, adipocyte fatty acid‐binding protein, and diacylglycerol acyltransferase 1, which were suggested as potential targets for drugs to control metabolic syndrome. These results demonstrate a protective role for SIRT6 against the metabolic consequences of diet‐induced obesity and suggest a potentially beneficial effect of SIRT6 activation on age‐related metabolic diseases.     

Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast

Evolution maintains organismal fitness by preserving genomic information. This is widely assumed to involve conservation of specific genomic loci among species. Many genomic encodings are now recognized to integrate small contributions from multiple genomic positions into quantitative dispersed codes, but the evolutionary dynamics of such codes are still poorly understood. Here we show that in yeast, sequences that quantitatively affect nucleosome occupancy evolve under compensatory dynamics that maintain heterogeneous levels of A+T content through spatially coupled A/T-losing and A/T-gaining substitutions. Evolutionary modeling combined with data on yeast polymorphisms supports the idea that these substitution dynamics are a consequence of weak selection. This shows that compensatory evolution, so far believed to affect specific groups of epistatically linked loci like paired RNA bases, is a widespread phenomenon in the yeast genome, affecting the majority of intergenic sequences in it. The model thus derived suggests that compensation is inevitable when evolution conserves quantitative and dispersed genomic functions.     

The Involvement of IL-17A in the Murine Response to Sub-Lethal Inhalational Infection with Francisella tularensis

Background

Francisella tularensis is an intercellular bacterium often causing fatal disease when inhaled. Previous reports have underlined the role of cell-mediated immunity and IFNγ in the host response to Francisella tularensis infection.

Methodology/Principal Findings

Here we provide evidence for the involvement of IL-17A in host defense to inhalational tularemia, using a mouse model of intranasal infection with the Live Vaccine Strain (LVS). We demonstrate the kinetics of IL-17A production in lavage fluids of infected lungs and identify the IL-17A-producing lymphocytes as pulmonary γδ and Th17 cells. The peak of IL-17A production appears early during sub-lethal infection, it precedes the peak of immune activation and the nadir of the disease, and then subsides subsequently. Exogenous airway administration of IL-17A or of IL-23 had a limited yet consistent effect of delaying the onset of death from a lethal dose of LVS, implying that IL-17A may be involved in restraining the infection. The protective role for IL-17A was directly demonstrated by in vivo neutralization of IL-17A. Administration of anti IL-17A antibodies concomitantly to a sub-lethal airway infection with 0.1×LD₅₀ resulted in a fatal disease.

Conclusion

In summary, these data characterize the involvement and underline the protective key role of the IL-17A axis in the lungs from inhalational tularemia.     

Expansion and characterization of human melanoma tumor-infiltrating lymphocytes (TILs)

Background

Various immunotherapeutic strategies for cancer are aimed at augmenting the T cell response against tumor cells. Adoptive cell therapy (ACT), where T cells are manipulated ex vivo and subsequently re-infused in an autologous manner, has been performed using T cells from various sources. Some of the highest clinical response rates for metastatic melanoma have been reported in trials using tumor-infiltrating lymphocytes (TILs). These protocols still have room for improvement and furthermore are currently only performed at a limited number of institutions. The goal of this work was to develop TILs as a therapeutic product at our institution.

Principal Findings

TILs from 40 melanoma tissue specimens were expanded and characterized. Under optimized culture conditions, 72% of specimens yielded rapidly proliferating TILs as defined as at least one culture reaching ≥3×10⁷ TILs within 4 weeks. Flow cytometric analyses showed that cultures were predominantly CD3+ T cells, with highly variable CD4+:CD8+ T cell ratios. In total, 148 independent bulk TIL cultures were assayed for tumor reactivity. Thirty-four percent (50/148) exhibited tumor reactivity based on IFN-γ production and/or cytotoxic activity. Thirteen percent (19/148) showed specific cytotoxic activity but not IFN-γ production and only 1% (2/148) showed specific IFN-γ production but not cytotoxic activity. Further expansion of TILs using a 14-day “rapid expansion protocol” (REP) is required to induce a 500- to 2000-fold expansion of TILs in order to generate sufficient numbers of cells for current ACT protocols. Thirty-eight consecutive test REPs were performed with an average 1865-fold expansion (+/− 1034-fold) after 14 days.

Conclusions

TILs generally expanded efficiently and tumor reactivity could be detected in vitro. These preclinical data from melanoma TILs lay the groundwork for clinical trials of ACT.     

A comparison of phasing algorithms for trios and unrelated individuals

Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of statistical and computational methods that infer haplotype phase from genotype data. Although a substantial number of such methods have been developed, they have focused principally on inference from unrelated individuals, and comparisons between methods have been rather limited. Here, we describe the extension of five leading algorithms for phase inference for handling father-mother-child trios. We performed a comprehensive assessment of the methods applied to both trios and to unrelated individuals, with a focus on genomic-scale problems, using both simulated data and data from the HapMap project. The most accurate algorithm was PHASE (v2.1). For this method, the percentages of genotypes whose phase was incorrectly inferred were 0.12%, 0.05%, and 0.16% for trios from simulated data, HapMap Centre d'Etude du Polymorphisme Humain (CEPH) trios, and HapMap Yoruban trios, respectively, and 5.2% and 5.9% for unrelated individuals in simulated data and the HapMap CEPH data, respectively. The other methods considered in this work had comparable but slightly worse error rates. The error rates for trios are similar to the levels of genotyping error and missing data expected. We thus conclude that all the methods considered will provide highly accurate estimates of haplotypes when applied to trio data sets. Running times differ substantially between methods. Although it is one of the slowest methods, PHASE (v2.1) was used to infer haplotypes for the 1 million-SNP HapMap data set. Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8.     

Real-Time Sensing of Enteropathogenic E. coli-Induced Effects on Epithelial Host Cell Height,Cell-Substrate Interactions,and Endocytic Processes by Infrared Surface Plasmon Spectroscopy

Enteropathogenic Escherichia coli (EPEC) is an important, generally non-invasive, bacterial pathogen that causes diarrhea in humans. The microbe infects mainly the enterocytes of the small intestine. Here we have applied our newly developed infrared surface plasmon resonance (IR-SPR) spectroscopy approach to study how EPEC infection affects epithelial host cells. The IR-SPR experiments showed that EPEC infection results in a robust reduction in the refractive index of the infected cells. Assisted by confocal and total internal reflection microscopy, we discovered that the microbe dilates the intercellular gaps and induces the appearance of fluid-phase-filled pinocytic vesicles in the lower basolateral regions of the host epithelial cells. Partial cell detachment from the underlying substratum was also observed. Finally, the waveguide mode observed by our IR-SPR analyses showed that EPEC infection decreases the host cell''s height to some extent. Together, these observations reveal novel impacts of the pathogen on the host cell architecture and endocytic functions. We suggest that these changes may induce the infiltration of a watery environment into the host cell, and potentially lead to failure of the epithelium barrier functions. Our findings also indicate the great potential of the label-free IR-SPR approach to study the dynamics of host-pathogen interactions with high spatiotemporal sensitivity.     

Can hair steroids predict pregnancy longevity?

Maintaining pregnancy to term is important as preterm delivery is a risk factor for impaired infant development, which may have negative long-term consequences. Therefore, developing biomarkers that can predict pregnancy longevity during early gestation is essential for the prevention of preterm birth. Here we explored whether maternal hair testosterone and cortisol, representing the pre-conception and first trimester periods respectively, may be used to predict pregnancy longevity. We recruited 125 pregnant women that contributed hair samples and answered a personal information questionnaire that included pre-conception smoking. We quantified steroids using commercial enzyme-linked immunosorbent assay kits. Gestational age at delivery was obtained from medical records. We used General Linear Models to predict gestation length. The model that included first trimester cortisol, pre-conception smoking, pre-conception testosterone and the interaction between first trimester cortisol and pre-conception smoking predicted 13% of the variance in gestation length (R² = 0.130; n?=?105; p?=? 0.007). First trimester cortisol was the best predictor of gestational length. Women with high levels of cortisol in their first trimester had an increased probability of a full-term delivery. The effect of cortisol was especially pronounced in smokers (ß?=?1.69), compared to non-smokers (ß?=?0.45). Pre-conception testosterone also contributed to the model. Our study suggests that hair steroids may be used to predict pregnancy longevity, together with other contributing factors.     

Watershed Glacier Coverage Influences Dissolved Organic Matter Biogeochemistry in Coastal Watersheds of Southeast Alaska

The Coast Mountains of southeast Alaska are currently experiencing some of the highest rates of glacier volume loss on Earth, with unknown implications for proglacial stream biogeochemistry. We analyzed streamwater for δ¹⁸O and dissolved organic matter (DOM) biogeochemistry (concentration, δ¹³C-dissolved organic carbon (DOC), and fluorescence characterization) during the 2012 glacial runoff season from three coastal watersheds in southeast Alaska that ranged in glacier coverage from 0 to 49% and a glacier outflow stream. Our goal was to assess how DOM biogeochemistry may change as receding glaciers are replaced by forests and glaciers contribute less meltwater to streamflow. Discharge and streamwater δ¹⁸O varied seasonally reflecting varying contributions of rainfall and snow/icemelt to streamflow over the runoff season. Mean DOC concentrations were lowest in the glacial outflow and highest in the non-glacial stream reflecting an increasing contribution of vascular plant-derived carbon with decreasing watershed glaciation. Fluorescence and δ¹³C-DOC signatures indicated that DOM shifted from vascular plant-derived, humic-like material in the non-glacial stream toward more δ¹³C-DOC enriched, glacier-derived DOM in the glacial outflow. Streamwater δ¹⁸O was significantly correlated to DOC concentration, δ¹³C-DOC, and protein-like fluorescence of streamwater DOM (all P < 0.05), demonstrating that changes in the source of streamwater across the glacial watershed continuum have important implications for the amount and quality of stream DOM export. Overall, our findings show that continued glacial recession and subsequent changes in glacial runoff could substantially influence the biogeochemistry of coastal temperature watersheds by altering the timing, magnitude, and chemical signature of DOM delivered to streams.