Comparative context analysis of codon pairs on an ORFeome scale

Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.     

Hydrologic regulation of gross methyl chloride and methyl bromide uptake from Alaskan Arctic tundra

The Arctic tundra has been shown to be a potentially significant regional sink for methyl chloride (CH₃Cl) and methyl bromide (CH₃Br), although prior field studies were spatially and temporally limited, and did not include gross flux measurements. Here we compare net and gross CH₃Cl and CH₃Br fluxes in the northern coastal plain and continental interior. As expected, both regions were net sinks for CH₃Cl and CH₃Br. Gross uptake rates (−793 nmol CH₃Cl m⁻² day⁻¹ and −20.3 nmol CH₃Br m⁻² day⁻¹) were 20–240% greater than net fluxes, suggesting that the Arctic is an even greater sink than previously believed. Hydrology was the principal regulator of methyl halide flux, with an overall trend towards increasing methyl halide uptake with decreasing soil moisture. Water table depth was one of the best predictors of net and gross uptake, with uptake increasing proportionately with water table depth. In drier areas, gross uptake was very high, averaging −1201 nmol CH₃Cl m⁻² day⁻¹ and −34.9 nmol CH₃Br m⁻² day⁻¹; in flooded areas, gross uptake was significantly lower, averaging −61 nmol CH₃Cl m⁻² day⁻¹ and −2.3 nmol CH₃Br m⁻² day⁻¹. Net and gross uptake was greater in the continental interior than in the northern coastal plain, presumably due to drier inland conditions. Within certain microtopographic features (low‐ and high‐centered polygons), uptake rates were positively correlated with soil temperature, indicating that temperature played a secondary role in methyl halide uptake. Incubations suggested that the inverse relationship between water content and methyl halide uptake was the result of mass transfer limitation in saturated soils, rather than because of reduced microbial activity under anaerobic conditions. These findings have potential regional significance, as the Arctic is expected to become warmer and drier due to anthropogenic climate forcing, potentially enhancing the Arctic sink for CH₃Cl and CH₃Br.     

Comparison of techniques for the measurement of skin temperature during exercise in a hot,humid environment

Exercising or working in a hot, humid environment can results in the onset of heat-related illness when an individual''s temperature is not carefully monitored. The purpose of the present study was to compare three techniques (data loggers, thermal imaging, and wired electrodes) for the measurement of peripheral (bicep) and central (abdominal) skin temperature. Young men and women (N = 30) were recruited to complete the present study. The three skin temperature measurements were made at 0 and every 10-min during 40-min (60% VO₂max) of cycling in a hot (39±2°C), humid (45±5% RH) environment. Data was statistically analyzed using the Bland-Altman method and correlation analysis. For abdominal skin temperature, the Bland-Altman limits of agreement indicated that data loggers (1.5) were a better index of wired than was thermal imaging (3.5), For the bicep skin temperature the limits of agreement was similar between data loggers (1.9) and thermal (1.9), suggesting the both were suitable measurements. We also found that when skin temperature exceeded 35°C, we observed progressively better prediction between data loggers, thermal imaging, and wired skin sensors. This report describes the potential for the use of data loggers and thermal imaging to be used as alternative measures of skin temperature in exercising, human subjects.     

Long-term effects of ungulates on phytophagous insects

Abstract.  1. Most plants interact with a diverse suite of herbivores, allowing the opportunity for the existence of positive and negative interactions between highly dissimilar organisms. However, most studies on herbivorous interactions have been performed under the assumption that they occur mainly between similar species. Consequently, ecologists are still far from a full understanding of the ecological factors that determine insect population dynamics.
2. In this study, a 7-year field experiment was conducted that manipulated the presence of ungulates to evaluate their effects on the abundance, attack rate, and survival of four guilds of co-occurring herbivorous insects living on the same host plant: seed predators, stem borers, gall makers and sap suckers. These four guilds differed in habits and behaviour, the first three being sessile and endophytic and the last being free-living.
3. This study shows that the abundance of all four guilds was negatively affected by ungulates. However, the effect on attack rate differed among guilds, as mammals do not affect the seed predator attack rate. Ungulates also differentially affected insect survival, ingesting only seed predators and gall makers.
4. In summary, this study suggests that diverse mechanisms may affect different insect guilds in different ways. Therefore, competition between disparate herbivores appears to be complex and can be provoked by multiple mechanisms.     

More than multiple introductions: Multiple taxa contribute to the genesis of the invasive California’s wild artichoke thistle

The history of some invasive species is so complex that their origins can be difficult to determine. One example of such invasive species is the California invasive known as “wild artichoke thistle” (Cynara cardunculus var. sylvestris), found in natural and disturbed ecosystems. Wild artichoke thistle is a Mediterranean native and the progenitor of two domesticated horticultural taxa, artichoke and cardoon. Different hypotheses regarding the origins of California plants have included introductions by 19th century Italian immigrants and the de-domestication (evolutionary reversion to wild-type morphology) of feral (escaped, free-living) cultivars. Using microsatellite markers, we compared the genetic constitutions of 12 artichoke thistle populations in California with possible progenitor populations: 17 Spanish and Italian wild populations and eight different artichoke and cardoon cultivars. Each California population was compared with its putative progenitors using STRUCTURE analysis. Our results suggest that California's artichoke thistle populations are polyphyletic. Surprisingly, two-thirds of California's populations closely matched populations from the Iberian Peninsula. Three populations matched domesticated artichoke. One population appears to have wild and cultivar hybrid ancestry. Alleles specific to Italian populations were found at low frequencies in some California plants, suggesting that Italian wild plants may have been in California, but have left a trivial genetic legacy. Given that the de-domesticated plants in this study appear to be as invasive as the wild taxon, we conclude with a discussion of the role that ferality and de-domestication may have in plant invasions.     

Effect of physical constraints on the mechanisms of membrane fusion: bolaform lipid vesicles as model systems.

Monolayers of an enantiomeric and a racemic triple-chain phosphatidylcholine (PC) at the air/water interface are studied by film balance measurements and x-ray diffraction. Although the area per three tails exceeds that per head, we observe tail ordering dependent on headgroup chirality and chain tilt. This indicates lateral headgroup interactions. The influence of the chiral carbon is suppressed at higher lateral pressures, and a centered-rectangular unit cell with tails tilted into the nearest neighbor (NN) direction is observed for both the enantiomer and the racemate. The distortion of the lattice changes at medium pressures from NN to NNN (next-nearest neighbor direction) with decreasing temperature. The phase behavior of the racemate at 15 degrees C is compared with that of a triple-chain PC with a branched chain of reduced length. Whereas the PC with the longer branched chain exhibits only a NN tilted phase at all pressures, the PC with the shorter branched chain has a rich polymorphism (NNN-NN-upright hexagonal packing) under increased lateral pressure.     

Different ataxin-3 amyloid aggregates induce intracellular Ca2 + deregulation by different mechanisms in cerebellar granule cells

This work aims at elucidating the relation between morphological and physicochemical properties of different ataxin-3 (ATX3) aggregates and their cytotoxicity. We investigated a non-pathological ATX3 form (ATX3Q24), a pathological expanded form (ATX3Q55), and an ATX3 variant truncated at residue 291 lacking the polyQ expansion (ATX3/291Δ). Solubility, morphology and hydrophobic exposure of oligomeric aggregates were characterized. Then we monitored the changes in the intracellular Ca^2 + levels and the abnormal Ca^2 + signaling resulting from aggregate interaction with cultured rat cerebellar granule cells. ATX3Q55, ATX3/291Δ and, to a lesser extent, ATX3Q24 oligomers displayed similar morphological and physicochemical features and induced qualitatively comparable time-dependent intracellular Ca^2 + responses. However, only the pre-fibrillar aggregates of expanded ATX3 (the only variant which forms bundles of mature fibrils) triggered a characteristic Ca^2 + response at a later stage that correlated with a larger hydrophobic exposure relative to the two other variants. Cell interaction with early oligomers involved glutamatergic receptors, voltage-gated channels and monosialotetrahexosylganglioside (GM1)-rich membrane domains, whereas cell interaction with more aged ATX3Q55 pre-fibrillar aggregates resulted in membrane disassembly by a mechanism involving only GM1-rich areas. Exposure to ATX3Q55 and ATX3/291Δ aggregates resulted in cell apoptosis, while ATX3Q24 was substantially innocuous. Our findings provide insight into the mechanisms of ATX3 aggregation, aggregate cytotoxicity and calcium level modifications in exposed cerebellar cells.     

A new Late Jurassic turtle from Spain: phylogenetic implications,taphonomy and palaeoecology

Abstract: The Jurassic was an important period in the evolution of Testudinata and encompasses the origin of many clades, and this is especially true of Jurassic turtles from Western Europe. A new genus and species of Late Jurassic turtle, Hispaniachelys prebetica gen. et sp. nov. from the upper Oxfordian of the Prebetic (Southern Spain), is described on the basis of postcranial material. The specimen is the only known tetrapod from the Mesozoic of the Prebetic and the oldest turtle from southern Europe. A mosaic of characters indicates this is a new genus: it displays basal features including dorsal epiplastral processes/reduced cleithra, no medial contact of the extragulars and a long first thoracic rib, alongside derived characters including an absence of mesoplastra and the vertebral 3/4 sulcus crossing neural 5. The phylogenetic position of the new taxon is hard to resolve, and it might be either a paracryptodire or a basal testudine, but it is distinct from Plesiochelys. A complex taphonomic history is shown by a range of overlying grazing traces and bioerosion on the carapace. The carapace was subsequently overturned and buried ventrally up, terminating grazing activity, and was then bored by sponges before final burial. Scanning electron microscopy reveals phosphatic microspheroids associated with bacterial decay in the vascular cavities of the cancellous bone, suggesting the carapace may have acted as a closed microenvironment in which decay‐derived authigenic minerals formed.     

Late Miocene marine ostracods from Santa Maria island,Azores (NE Atlantic): Systematics,palaeoecology and palaeobiogeography

The nine oceanic islands that comprise the Azores archipelago are located in the middle of the northern Atlantic Ocean. In this isolated archipelago, there is a rich fossil record in one of the islands, Santa Maria. In this island, samples were collected in the Upper Miocene composite section of Malbusca outcrop, located in the southern shore of the island, and the fossil marine Ostracoda were studied. This work represents the first report of fossil ostracods from the Azores archipelago. Thirteen species were found, representing seven families and 12 genera (Xestoleberis, Loxoconcha, Callistocythere, Leptocythere, Dameriacella, Aurila, Heliocythere, Pachycaudites, Neonesidea, Cyamocytheridea, ?Quadracythere and Paracypris). Among the identified species, one new species, Leptocythere azorica n. sp., is described. Loxoconcha (two species) was the most diversified genus. The collected species are mainly ornamented and typical of warm waters and epi-neritic habitats (～ 10–50 m of depth).