Molecular evolution of rodent insulins

Several trees of amino acid sequences of rodent insulins were derived with the maximum-parsimony procedure. Possible orthologous and paralogous relationships were investigated. Except for a recent gene duplication in the ancestor of rat and mouse, there are no strong arguments for other paralogous relationships. Therefore, a tree in agreement with other biological data is the most reasonable one. According to this tree, the capacity to form zinc-binding hexamers was lost once in the ancestor of the hystricomorph rodents, followed by moderately increased evolutionary rates in the lineages to African porcupine and chinchilla but highly increased rates in at least three independent lines to other taxa of this suborder: guinea pig, cuis, and Octodontoidea (coypu and casiragua).      

Genotypic differences in embryonic life history traits of Folsomia quadrioculata (Collembola: Isotomidae) across a wide geographical range

1. Life history traits play a central role in adaptation to specific environmental conditions. Egg development time, hatchling, and egg batch size in 10 populations of the soil‐dwelling collembolan species Folsomia quadrioculata (Tullberg, 1871) from diverse habitats across arctic and temperate regions, ranging in latitude from 43 to 81°N were studied. 2. For all traits, 15 °C was used as the reference temperature. Phenotypic plasticity was studied by changing temperature to 10 and 20 °C in hatchling size, and to 20 °C in egg development time. The effect of latitude, climatic zone, and summer temperature at their sites of sampling was tested to address the hypotheses that populations from cooler areas would have (i) a faster temperature‐dependent egg development, (ii) a larger hatchling size, (iii) smaller egg batches and (iv) higher phenotypic plasticity 3. The first and fourth hypothesis were not supported, whereas the second and third were partly supported when including the whole latitudinal gradient, but not within regions. Plasticity showed a complex pattern, including large differences between populations from similar macroclimates and considerable similarity between some populations from contrasting climates. Small effects of latitude and macroclimatic variables emphasised that local climate and microhabitat should be taken into account when evaluating thermal conditions as possible drivers of population‐specific differences in soil‐dwelling ectotherms. 4. There was a trade‐off between egg batch and hatchling sizes. A weak correlation between the population mean egg development time and the mean hatchling size suggested that the populations are, or have been, exposed to differential selection.     

Miocene methane‐derived carbonates from southwestern Washington,USA and a model for silicification at seeps

Kuechler, R.R., Birgel, D, Kiel, S, Freiwald, A, Goedert, J.L., Thiel, V & Peckmann, J. 2011: Miocene methane‐derived carbonates from southwestern Washington, USA and a model for silicification at seeps. Lethaia, Vol. 45, pp. 259–273. Exotic limestone masses with silicified fossils, enclosed within deep‐water marine siliciclastic sediments of the Early to Middle Miocene Astoria Formation, are exposed along the north shore of the Columbia River in southwestern Washington, USA. Samples from four localities were studied to clarify the origin and diagenesis of these limestone deposits. The bioturbated and reworked limestones contain a faunal assemblage resembling that of modern and Cenozoic deep‐water methane‐seeps. Five phases make up the paragenetic sequence: (1) micrite and microspar; (2) fibrous, banded and botryoidal aragonite cement, partially replaced by silica or recrystallized to calcite; (3) yellow calcite; (4) quartz replacing carbonate phases and quartz cement; and (5) equant calcite spar and pseudospar. Layers of pyrite frequently separate different carbonate phases and generations, indicating periods of corrosion. Negative δ¹³C_carbonate values as low as ?37.6‰ V‐PDB reveal an uptake of methane‐derived carbon. In other cases, δ¹³C_carbonate values as high as 7.1‰ point to a residual, ¹³C‐enriched carbon pool affected by methanogenesis. Lipid biomarkers include ¹³C‐depleted, archaeal 2,6,10,15,19‐pentamethylicosane (PMI; δ¹³C: ?128‰), crocetane and phytane, as well as various iso‐ and anteiso‐carbon chains, most likely derived from sulphate‐reducing bacteria. The biomarker inventory proves that the majority of the carbonates formed as a consequence of sulphate‐dependent anaerobic oxidation of methane. Silicification of fossils and early diagenetic carbonate cements as well as the precipitation of quartz cement – also observed in other methane‐seep limestones enclosed in sediments with abundant diatoms or radiolarians – is a consequence of a preceding increase of alkalinity due to anaerobic oxidation of methane, inducing the dissolution of silica skeletons. Once anaerobic oxidation of methane has ceased, the pH drops again and silica phases can precipitate. □Biomarkers, carbonates, isotopes, methane, Miocene, silicification, Washington.     

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Gene co‐expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co‐expression analysis asks the question ‘what are the genes that are co‐expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?’. Genes that are highly co‐expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co‐expression results, calculation of co‐expression scores and P values, and the influence of data sets used for co‐expression analysis. Finally, examples from the literature will be presented, wherein co‐expression has been used to corroborate and discover various aspects of plant biology.     

Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy

Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive graphical interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki ( http://www.codeplex.com/XeO ) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.     

Decadal vegetation changes in a northern peatland, greenhouse gas fluxes and net radiative forcing

Thawing permafrost in the sub‐Arctic has implications for the physical stability and biological dynamics of peatland ecosystems. This study provides an analysis of how permafrost thawing and subsequent vegetation changes in a sub‐Arctic Swedish mire have changed the net exchange of greenhouse gases, carbon dioxide (CO₂) and CH₄ over the past three decades. Images of the mire (ca. 17 ha) and surroundings taken with film sensitive in the visible and the near infrared portion of the spectrum, [i.e. colour infrared (CIR) aerial photographs from 1970 and 2000] were used. The results show that during this period the area covered by hummock vegetation decreased by more than 11% and became replaced by wet‐growing plant communities. The overall net uptake of C in the vegetation and the release of C by heterotrophic respiration might have increased resulting in increases in both the growing season atmospheric CO₂ sink function with about 16% and the CH₄ emissions with 22%. Calculating the flux as CO₂ equivalents show that the mire in 2000 has a 47% greater radiative forcing on the atmosphere using a 100‐year time horizon. Northern peatlands in areas with thawing sporadic or discontinuous permafrost are likely to act as larger greenhouse gas sources over the growing season today than a few decades ago because of increased CH₄ emissions.     

Translocation of 32P between interacting mycelia of a wood-decomposing fungus and ectomycorrhizal fungi in microcosm systems

Interactions between saprotrophic and ectomycorrhizal fungi have been largely ignored, although their mycelia often share the same microsites. The mycelial systems show general similarity to each other and, although the enzymatic potential of the saprotrophic fungi is generally considered to be higher, the importance of organic nutrient sources to ectomycorrhizal fungi is now widely accepted. In the experiments described here, nutritional interactions involving transfer of elements from one mycelium to the other have been monitored dynamically using radioactive tracers and a non-destructive electronic autoradiography system. Microcosms were used in which mycelial systems of the ectomycorrhizal fungi Suillus variegatus and Paxillus involutus , extending from Pinus sylvestris host plants, were confronted with mycelia of the saprotroph Hypholoma fasciculare extending from wood blocks. The fungi showed a clear morphological confrontation response. The mycorrhizal mycelium often formed dense patches over the Hypholoma mycelia. Up to 25% of the ³²P present in the Hypholoma mycelium was captured by the mycorrhizal fungi and translocated to the plant host within 30 d. The transfer of ³²P to the saprotroph from labelled mycorrhizal mycelium was one to two orders of magnitude lower. The significance of this transfer as a 'short cut' in nutrient cycling is discussed.     

Ceratophyllum demersum hampers phytoplankton development in some small Norwegian lakes over a wide range of phosphorus concentrations and geographical latitude

1. Data on submerged and floating-leafed macrophytes, phytoplankton, nutrients (N, P) and calcium were collected from twenty-four small lakes ( 1 km²) over a wide range of latitudes in Norway. The majority of the investigated lakes were mesotrophic or eutrophic, and most of the lakes were markedly affected by diffuse and point-source runoff from agriculture. According to their macrophyte species composition, the majority of the lakes can be classified as Potamogeton lakes or Chara lakes, or a combination of these.
2. This study is consistent with the 'two alternative stable states' hypothesis. We observed clearwater lakes with dense macrophyte cover over a wider range of total P concentration than has been reported previously: from 30 to more than 700 mg P m^–3. The clearwater state was only observed in lakes with mean depths of less than 1.9 m.
3. Most clear lakes with high cover of submerged vegetation showed indications of N limitation.
4. In this study nearly all the macrophyte-dominated lakes with P concentrations above 30 mg m^–3 had dense stands of Ceratophyllum demersum (L.). This indicates that Ceratophyllum may also play an important role in stabilizing and maintaining a clearwater state at high P concentrations.     

Demographic and genetic effects on reproduction as related to population size in a rare, perennial herb, Senecio integrifolius (Asteraceae)

Seed-set of the rare and threatened plant Senecio integrifolius increased significantly with population size. Experimental studies as well as field observations showed this to be due to density-dependent seed-set (Allee effect). Hand-pollination revealed lower seed-set, and a lower germination rate of inbred progeny than of outbred progeny, with great differences among populations. Contrary to general predictions in models of minimum viable population sizes, the present study indicates little negative effects of inbreeding in small populations. A genetic load model was invoked to explain the results, hypothesizing that purging of deleterious alleles in small populations has reduced inbreeding depression. However, no clear correlation between population size and genetic load was found. The results in this paper suggest that demographic and environmental factors are of greater immediate importance than population genetics in determining extinction probabilities of small plant populations.     

Seasonal Effects on Photosynthetic Electron Transport and Fluorescence Properties in Isolated Chloroplasts of Pinus silvestris

Chloroplasts were isolated from primary needles of 1-year-old seedlings and from secondary needles of a 20-year-old pine tree in a natural stand. In autumn the electron transport capacities of PSII, PSI and PS (II + I) decreased and the electron transport between PSII and PSI became inhibited in October in the 20-year-old tree. This inhibition lasted until May the following year. The partial reactions of PSI and PSII still showed low but fairly constant rates during the whole winter seedlings. Seasonal changes in the electron transport properties of 1-year-old showed the same general trends as observed in the 20-year-old tree, but the changes were less pronounced. However, in snow-covered seedlings the PSI-mediated electron transport and the electron transport from H₂O to NADP increased during the late winter when the seedlings were still covered by snow. The total chlorophyll content of the needles decreased in autumn and winter. Low temperature fluorescence ratios of F692/F680 and F726/F680 indicated more severe destruction of the chlorophyll a antennae closely associated with the two photosystems than of the light harvesting chlorophyll a/b complex. In this case, too, the changes were more pronounced in the 20-year-old tree than in the 1-year-old seedlings. The chlorophyll/P700 ratios indicated a more marked reduction in the reaction centre molecules during autumn than in the antennae chlorophyll molecules. The changes in electron transport and low temperature fluorescence properties which occurred during autumn and winter were mainly reversed during spring.