The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression

High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks, on the reproducibility of global proteome measurements in Shewanella oneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with data demonstrating that “aerobic” flask cultures were O₂ deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research.     

8,000 years of climate,vegetation, fire and land-use dynamics in the thermo-mediterranean vegetation belt of northern Sardinia (Italy)

Vegetation History and Archaeobotany - Knowledge about the vegetation history of Sardinia, the second largest island of the Mediterranean, is scanty. Here, we present a new sedimentary record...     

Cytotoxic effect of Erythroxylum daphnites extract is associated with G1 cell cycle arrest and apoptosis in oral squamous cell carcinoma

Plant-derived molecules showing antineoplastic effects have recently gained increased attention as potential adjuvants to traditional therapies for various cancers. Cerrado biome in Brazil contains high floral biodiversity, but knowledge about the potential therapeutic effects of compounds derived from that flora is still limited. The present study investigated the antineoplastic activity of Erythroxylum daphnites Mart., a Brazilian native plant from Cerrado biome, in the SCC-9 oral squamous cell carcinoma cell line. Cells were treated with various concentrations of hexane extract of Erythroxylum daphnites leaves (EDH) and assessed for cytotoxicity, proliferation, and apoptosis. Thin layer chromatography was conducted to characterize the substances present in EDH. Our results showed that EDH exerted anti-proliferative effects in SCC-9 cells by stabilizing the cell cycle at G₁ phase in association with reduced intracellular levels of cyclins D and E and increased level of p21. EDH also demonstrated pro-apoptotic properties, as shown by an increased expression of caspase-3. Triterpenes were the major constituents of EDH. Our findings demonstrated a cytotoxic effect of EDH against SCC-9 cells in vitro mediated by the restraint of cellular proliferation and induction of apoptosis. Taken together, these findings support EDH constituents as potential therapeutic adjuvants for oral cancer.     

Tundra and boreal forest of interior Alaska during terminal MIS 6 and MIS 5e

Two sites within the boreal forest of interior Alaska shed light on the climate and vegetation of terminal marine isotope stage (MIS) 6 (ca. 140–130 kyr ago) and MIS 5e (125–116 kyr ago). The Birch Creek and Koyukuk localities are river-cut exposures with sediments dating from the penultimate glaciation (at least) to the present. Plant macrofossils, pollen, and beetles were analyzed at these sites. Terminal MIS 6-aged samples indicate a cooler than modern climate and the presence of shrub tundra. During MIS 5e, boreal forest grew at the sites and temperatures were similar to modern times. However, the forest may also have been more mesic than today, as indicated by relatively abundant ferns. Winters may have been warmer than today, as suggested by beetle-based climatic reconstructions as well as the presence of two extralimital taxa that today live in regions where winter temperatures are up to 15 °C warmer than at the site localities.     

Using pedigree reconstruction to estimate population size: genotypes are more than individually unique marks

Estimates of population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Noninvasive genetic methods are increasingly used to estimate population size, particularly in elusive species such as large carnivores, which are difficult to count by most other methods. In most such studies, genotypes are treated simply as unique individual identifiers. Here, we develop a new estimator of population size based on pedigree reconstruction. The estimator accounts for individuals that were directly sampled, individuals that were not sampled but whose genotype could be inferred by pedigree reconstruction, and individuals that were not detected by either of these methods. Monte Carlo simulations show that the population estimate is unbiased and precise if sampling is of sufficient intensity and duration. Simulations also identified sampling conditions that can cause the method to overestimate or underestimate true population size; we present and discuss methods to correct these potential biases. The method detected 2–21% more individuals than were directly sampled across a broad range of simulated sampling schemes. Genotypes are more than unique identifiers, and the information about relationships in a set of genotypes can improve estimates of population size.     

Transparency improves concealment in cryptically coloured moths

Predation is a ubiquitous and strong selective pressure on living organisms. Transparency is a predation defence widespread in water but rare on land. Some Lepidoptera display transparent patches combined with already cryptic opaque patches. A recent study showed that transparency reduced detectability of aposematic prey with conspicuous patches. However, whether transparency has any effect at reducing detectability of already cryptic prey is still unknown. We conducted field predation experiments with free avian predators where we monitored and compared survival of a fully opaque grey artificial form (cryptic), a form including transparent windows and a wingless artificial butterfly body. Survival of the transparent forms was similar to that of wingless bodies and higher than that of fully opaque forms, suggesting a reduction of detectability conferred by transparency. This is the first evidence that transparency decreases detectability in cryptic terrestrial prey. Future studies should explore the organization of transparent and opaque patches in animals and their interplay on survival, as well as the costs and other potential benefits associated with transparency on land.