Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila

Overexpression of sirtuins (NAD(+)-dependent protein deacetylases) has been reported to increase lifespan in budding yeast (Saccharomyces cerevisiae), Caenorhabditis elegans and Drosophila melanogaster. Studies of the effects of genes on ageing are vulnerable to confounding effects of genetic background. Here we re-examined the reported effects of sirtuin overexpression on ageing and found that standardization of genetic background and the use of appropriate controls abolished the apparent effects in both C. elegans and Drosophila. In C. elegans, outcrossing of a line with high-level sir-2.1 overexpression abrogated the longevity increase, but did not abrogate sir-2.1 overexpression. Instead, longevity co-segregated with a second-site mutation affecting sensory neurons. Outcrossing of a line with low-copy-number sir-2.1 overexpression also abrogated longevity. A Drosophila strain with ubiquitous overexpression of dSir2 using the UAS-GAL4 system was long-lived relative to wild-type controls, as previously reported, but was not long-lived relative to the appropriate transgenic controls, and nor was a new line with stronger overexpression of dSir2. These findings underscore the importance of controlling for genetic background and for the mutagenic effects of transgene insertions in studies of genetic effects on lifespan. The life-extending effect of dietary restriction on ageing in Drosophila has also been reported to be dSir2 dependent. We found that dietary restriction increased fly lifespan independently of dSir2. Our findings do not rule out a role for sirtuins in determination of metazoan lifespan, but they do cast doubt on the robustness of the previously reported effects of sirtuins on lifespan in C. elegans and Drosophila.     

Human-specific loss of regulatory DNA and the evolution of human-specific traits

Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.     

Attack and brood production by the Douglas-fir beetle (Coleoptera: Scolytidae) in Douglas-fir, Pseudotsuga menziesii var. glauca (Pinaceae), following a wildfire

In 1994 ground fire ignited in forests of Douglas-fir, Pseudotsuga menziesii var. glauca (Mirb.) Franco, on Beaver Mountain, Utah. The Douglas-fir beetle, Dendroctonus pseudotsugae Hopkins, attacked a range of moderately fire-injured host conifers in 1995. Logistic regression models run for 1995 data illustrated that 1 year after the fire event the Douglas-fir beetle selected and attacked large-diameter Douglas-fir with 60%-80% bole char, 60%-80% crown volume scorch, and 50%-70% probability of mortality due to fire. In 1996 beetle preference shifted to smallerdiameter trees with lighter fire injury, because most large, fire-damaged conifers were colonized by beetles in 1995. Although beetle populations did not reach outbreak proportions outside the fire boundary, host selection shifted to green trees in 1997 along the burn perimeter. Log linear analysis indicated that increased brood production was conditioned by increased diameter and moderate fire damage to the trees.     

Problems and promises: How to tell the story of a Genome Wide Association Study?

The promise of treatments for common complex diseases (CCDs) is understood as an important force driving large scale genetics research over the last few decades. This paper considers the phenomenon of the Genome Wide Association Study (GWAS) via one high profile example, the Wellcome Trust Case Control Consortium (WTCCC). The WTCCC despite not fulfilling promises of new health interventions is still understood as an important step towards tackling CCDs clinically. The ‘sociology of expectations’ has considered many examples of failure to fulfil promises and the subsequent negative consequences including disillusionment, disappointment and disinvestment. In order to explore why some domains remain resilient in the face of apparent failure, I employ the concept of the ‘problematic’ found in the work of Giles Deleuze. This alternative theoretical framework challenges the idea that the failure to reach promised goals results in largely negative outcomes for a given field. I will argue that collective scientific action is motivated not only by hopes for the future but also by the drive to create solutions to the actual setbacks and successes which scientists encounter in their day-to-day work. I draw on eighteen interviews.     

Body size, body composition, and behavior of juvenile Belding ground squirrels

Juvenile Belding ground squirrels were studied in the Sierra Nevada. Females were more trappable, had smaller home ranges, and tended to enter hibernation earlier than males. The primary sex ratio was 1:1. Individuals first emerged from the natal burrow at three to four weeks of age and a body weight of 35 g. Body weight and linear dimensions increased thereafter until hibernation began. Maximum prehibernatory weight of 200 to 260 g was attained at about 12 weeks of age. Prehibernatory fattening began at about six weeks of age. Maximum lipid stores attained weighed about 80 percent of the lean, dry body compartment. Seasonal changes occurred in weight of white and brown fat depots, adrenal glands, spleen, heart, kidneys, liver, and testes. Annual variations in snowpack and emergence schedule caused the reproductive period, and thus phenology of juveniles, to vary by as much as three weeks. The last animals to immerge were unusually small, being from late litters. Nonetheless, they may have had lipid stores sufficient for surviving hibernation.     

Microbial spatial heterogeneity in microbiotic crusts in Colorado National Monument. II Bacteria

Microbial spatial heterogeneity and bacterial composition of homogeneous surface soils showing evident microbiotic crust development located under Utah juniper canopies in Colorado National Monument were studied. Four distinct homogeneous sampling sites positioned along a 12-m transect were compared on the basis of bacterial density and taxa composition. Bacterial densities showed a range differing by several orders of magnitude. In comparisons of adjacent soil samples or samples taken from two different sampling sites within close proximity, adjacent samples showed no more similarity to each other on the basis of bacterial density or taxa composition than did more widely separated samples. The bacterial composition of these soils included members of the genera Bacillus , Micrococcus , and Arthrobacter . Actinomycetes were also prevalent.     

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

Pancreatic cancer is an aggressive malignancy with a five-year mortality of 97-98%, usually due to widespread metastatic disease. Previous studies indicate that this disease has a complex genomic landscape, with frequent copy number changes and point mutations, but genomic rearrangements have not been characterized in detail. Despite the clinical importance of metastasis, there remain fundamental questions about the clonal structures of metastatic tumours, including phylogenetic relationships among metastases, the scale of ongoing parallel evolution in metastatic and primary sites, and how the tumour disseminates. Here we harness advances in DNA sequencing to annotate genomic rearrangements in 13 patients with pancreatic cancer and explore clonal relationships among metastases. We find that pancreatic cancer acquires rearrangements indicative of telomere dysfunction and abnormal cell-cycle control, namely dysregulated G1-to-S-phase transition with intact G2-M checkpoint. These initiate amplification of cancer genes and occur predominantly in early cancer development rather than the later stages of the disease. Genomic instability frequently persists after cancer dissemination, resulting in ongoing, parallel and even convergent evolution among different metastases. We find evidence that there is genetic heterogeneity among metastasis-initiating cells, that seeding metastasis may require driver mutations beyond those required for primary tumours, and that phylogenetic trees across metastases show organ-specific branches. These data attest to the richness of genetic variation in cancer, brought about by the tandem forces of genomic instability and evolutionary selection.     

Diversity, stability and resilience of the human gut microbiota

Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.