Computational approaches to identify genetic interactions for cancer therapeutics

The development of improved cancer therapies is frequently cited as an urgent unmet medical need. Here we describe how genetic interactions are being therapeutically exploited to identify novel targeted treatments for cancer. We discuss the current methodologies that use ‘omics data to identify genetic interactions, in particular focusing on synthetic sickness lethality (SSL) and synthetic dosage lethality (SDL). We describe the experimen- tal and computational approaches undertaken both in humans and model organisms to identify these interac- tions. Finally we discuss some of the identified targets with licensed drugs, inhibitors in clinical trials or with compounds under development

A Deglacial and Holocene Record of Climate Variability in South-Central Alaska from Stable Oxygen Isotopes and Plant Macrofossils in Peat

We used stable oxygen isotopes derived from bulk peat (delta-O-18(sub TOM) in conjunction with plant macrofossils and previously published carbon accumulation records, in a approximately14,500 cal yr BP peat core (HT Fen) from the Kenai lowlands in south-central Alaska to reconstruct the climate history of the area. We find that patterns are broadly consistent with those from lacustrine records across the region, and agree with the interpretation that major shifts in delta-O-18(sub TOM) values indicate changes in strength and position of the Aleutian Low (AL), a semi-permanent low-pressure cell that delivers winter moisture to the region. We find decreased strength or a more westerly position of the AL (relatively higher delta-O-18(sub TOM) values) during the Bolling-Allerod, Holocene Thermal Maximum (HTM), and late Holocene, which also correspond to warmer climate regimes. These intervals coincide with greater peat preservation and enhanced carbon (C) accumulation rates at the HT Fen and with peatland expansion across Alaska. The HTM in particular may have experienced greater summer precipitation as a result of an enhanced Pacific subtropical high, a pattern consistent with modern delta-O-18 values for summer precipitation. The combined warm summer temperatures and greater summer precipitation helped promote the observed rapid peat accumulation. A strengthened AL (relatively lower delta-O-18(sub TOM) values) is most evident during the Younger Dryas, Neoglaciation, and the Little Ice Age, consistent with lower peat preservation and C accumulation at the HT Fen, suggesting less precipitation reaches the leeward side of the Kenai Mountains during periods of enhanced AL strength. The peatlands on the Kenai Peninsula thrive when the AL is weak and the contribution of summer precipitation is higher, highlighting the importance of precipitation seasonality in promoting peat accumulation. This study demonstrates that delta-O-18(sub TOM) values in peat can be applied toward understand large-scale shifts in atmospheric circulation over millennial timescales

'Big data' approaches for novel anti-cancer drug discovery

Introduction: The development of improved cancer therapies is frequently cited as an urgent unmet medical need. Here we review how recent advances in platform technologies and the increasing availability of biological ‘big data’ are providing an unparalleled opportunity to systematically identify the key genes and pathways involved in tumorigenesis. We then discuss how these discoveries may be amenable to therapeutic interventions. Areas covered: We discuss the current approaches that use ‘big data’ to identify cancer drivers. These approaches include genomic sequencing, pathway data, multi-platform data, identifying genetic interactions such as synthetic lethality and using cell line data. We review how big data is being used to assess the tractability of potential drug targets and how systems biology is being utilised to identify novel drug targets. We finish the review with an overview of available data repositories and tools being used at the forefront of cancer drug discovery. Expert opinion: Targeted therapies based on the genomic events driving the tumour will eventually inform treatment protocols. However, using a tailored approach to treat all tumour patients may require developing a large repertoire of targeted drugs

Isotopic and molecular distributions of biochemicals from fresh and buried Rhizophora mangle leaves†

Rhizophora mangle L. (red mangrove) is the dominant species of mangrove in the Americas. At Twin Cays, Belize (BZ) red mangroves are present in a variety of stand structures (tall >5 m in height, transition ~2–4 m and dwarf ~1–1.5 m). These height differences are coupled with very different stable carbon and nitrogen isotopic values[1] (mean tall δ(13)C = -28.3‰, δ(15)N = 0‰; mean tall δ(13)C = -25.3‰, δ(15)N = -10‰). To determine the utility of using these distinct isotopic compositions as 'biomarkers' for paleoenvironmental reconstruction of mangrove ecosystems and nutrient availability, we investigated the distribution and isotopic (δ(13)C and δ(15)N) composition of different biochemical fractions (water soluble compounds, free lipids, acid hydrolysable compounds, individual amino acids, and the residual un-extractable compounds) in fresh and preserved red mangrove leaves from dwarf and tall trees. The distribution of biochemicals are similar in dwarf and tall red mangrove leaves, suggesting that, regardless of stand structure, red mangroves use nutrients for biosynthesis and metabolism in a similar manner. However, the δ(13)C and δ(15)N of the bulk leaf, the biochemical fractions, and seven amino acids can be used to distinguish dwarf and tall trees at Twin Cays, BZ. The data support the theory that the fractionation of carbon and nitrogen occurs prior to or during uptake in dwarf and tall red mangrove trees. Stable carbon and nitrogen isotopes could, therefore, be powerful tools for predicting levels of nutrient limitation at Twin Cays. The δ(13)C and δ(15)N of biochemical fractions within preserved leaves, reflect sedimentary cycling and nitrogen immobilization. The δ(15)N of the immobilized fraction reveals the overlying stand structure at the time of leaf deposition. The isotopic composition of preserved mangrove leaves could yield significant information about changes in ecosystem dynamics, nutrient limitation and past stand structure in mangrove paleoecosystems

Radiocarbon age-offsets in an arctic lake reveal the long-term response of permafrost carbon to climate change

Author Posting. © American Geophysical Union, 2014. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Biogeosciences 119 (2014): 1630–1651, doi:10.1002/2014JG002688.Continued warming of the Arctic may cause permafrost to thaw and speed the decomposition of large stores of soil organic carbon (OC), thereby accentuating global warming. However, it is unclear if recent warming has raised the current rates of permafrost OC release to anomalous levels or to what extent soil carbon release is sensitive to climate forcing. Here we use a time series of radiocarbon age-offsets (14C) between the bulk lake sediment and plant macrofossils deposited in an arctic lake as an archive for soil and permafrost OC release over the last 14,500 years. The lake traps and archives OC imported from the watershed and allows us to test whether prior warming events stimulated old carbon release and heightened age-offsets. Today, the age-offset (2 ka; thousand of calibrated years before A.D. 1950) and the depositional rate of ancient OC from the watershed into the lake are relatively low and similar to those during the Younger Dryas cold interval (occurring 12.9–11.7 ka). In contrast, age-offsets were higher (3.0–5.0 ka) when summer air temperatures were warmer than present during the Holocene Thermal Maximum (11.7–9.0 ka) and Bølling-Allerød periods (14.5–12.9 ka). During these warm times, permafrost thaw contributed to ancient OC depositional rates that were ~10 times greater than today. Although permafrost OC was vulnerable to climate warming in the past, we suggest surface soil organic horizons and peat are presently limiting summer thaw and carbon release. As a result, the temperature threshold to trigger widespread permafrost OC release is higher than during previous warming events.National Science Foundation. Grant Number: ARC-09021692015-02-2

Repression of transcription at DNA breaks requires cohesin throughout interphase and prevents genome instability

Cohesin subunits are frequently mutated in cancer, but how they function as tumor suppressors is unknown. Cohesin mediates sister chromatid cohesion, but this is not always perturbed in cancer cells. Here, we identify a previously unknown role for cohesin. We find that cohesin is required to repress transcription at DNA double-strand breaks (DSBs). Notably, cohesin represses transcription at DSBs throughout interphase, indicating that this is distinct from its known role in mediating DNA repair through sister chromatid cohesion. We identified a cancer-associated SA2 mutation that supports sister chromatid cohesion but is unable to repress transcription at DSBs. We further show that failure to repress transcription at DSBs leads to large-scale genome rearrangements. Cancer samples lacking SA2 display mutational patterns consistent with loss of this pathway. These findings uncover a new function for cohesin that provides insights into its frequent loss in cancer

Designing physical activity environments to accrue physical and psychological effects

Understanding how best to accrue benefits from designing physical activity and exercise programmes is needed to tackle global health problems related to physical inactivity and poor mental health. Some studies have implicated an important role for green exercise and physical activity, but there is a lack of clarity in current research. Therefore, more work is needed to understand how to design green physical activity and exercise environments that afford (invite) physical and psychological benefits to individuals. We examined whether exercising while viewing a dynamic or static image of a scene from nature would offer different affordances (invitations for behaviours to emerge), compared to the common conditions of self-selected entertainment. For this purpose, 30 participants (18 males and 12 females; age 27.5 ± 9 yrs; mass 67.6 ± 11.1 kg; stature 173.7 ± 8.2 cm) exercised in three experimental conditions in a counterbalanced design while: (i) viewing a video of a green environment, (ii) viewing a single static image of the green environment; and (iii), when using typical self-selected entertainment without viewing images of nature. A twenty-minute treadmill run was undertaken at the participants’ own self-selected speed in a laboratory while energy expenditure and psychological states (using PANAS) were assessed. Results showed no differences in energy expenditure (p > .05) or negative affect (p > .05) between conditions. However, data revealed significant differences in positive affect when participants ran with a static image and their own entertainment compared to running with a dynamic image. Results revealed how differences in affordances designed into physical activity environments can shape psychological states that emerge during exercise. Further research is needed on affordance design in physical activity and exercise by engineers, designers, planners and psychologists to explore effects of a range of simulated environments, with different target groups, such as fit and unfit individuals, elderly and children

The stable isotope composition of organic and inorganic fossils in lake sediment records: current understanding, challenges, and future directions

This paper provides an overview of stable isotope analysis (H, C, N, O, Si) of the macro and microscopic remains from aquatic organisms found in lake sediment records and their application in (palaeo)environmental science. Aquatic organisms, including diatoms, macrophytes, invertebrates, and fish, can produce sufficiently robust remains that preserve well as fossils and can be identified in lake sediment records. Stable isotope analyses of these remains can then provide valuable insights into habitat-specific biogeochemistry, feeding ecology, but also on climatic and hydrological changes in and around lakes. Since these analyses focus on the remains of known and identified organisms, they can provide more specific and detailed information on past ecosystem, food web and environmental changes affecting different compartments of lake ecosystems than analyses on bulk sedimentary organic matter or carbonate samples. We review applications of these types of analyses in palaeoclimatology, palaeohydrology, and palaeoecology. Interpretation of the environmental ‘signal’ provided by taxon-specific stable isotope analysis requires a thorough understanding of the ecology and phenology of the organism groups involved. Growth, metabolism, diet, feeding strategy, migration, taphonomy and several other processes can lead to isotope fractionation or otherwise influence the stable isotope signatures of the remains from aquatic organisms. This paper includes a review of the (modern) calibration, culturing and modeling studies used to quantify the extent to which these factors influence stable isotope values and provides an outlook for future research and methodological developments for the different examined fossil groups

Gravitational sliding of the Mt. Etna massif along a sloping basement

Geological field evidence and laboratory modelling indicate that volcanoes constructed on slopes slide downhill. If this happens on an active volcano, then the movement will distort deformation data and thus potentially compromise interpretation. Our recent GPS measurements demonstrate that the entire edifice of Mt. Etna is sliding to the ESE, the overall direction of slope of its complex, rough sedimentary basement. We report methods of discriminating the sliding vector from other deformation processes and of measuring its velocity, which averaged 14 mm year−1 during four intervals between 2001 and 2012. Though sliding of one sector of a volcano due to flank instability is widespread and well-known, this is the first time basement sliding of an entire active volcano has been directly observed. This is important because the geological record shows that such sliding volcanoes are prone to devastating sector collapse on the downslope side, and whole volcano migration should be taken into account when assessing future collapse hazard. It is also important in eruption forecasting, as the sliding vector needs to be allowed for when interpreting deformation events that take place above the sliding basement within the superstructure of the active volcano, as might occur with dyke intrusion or inflation/deflation episodes