Prediction of partial membrane protein topologies using a consensus approach

We have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally characterized proteins, we find that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms. Whole-genome analysis reveals that a reliable partial consensus topology can be predicted for approximately 70% of all membrane proteins in a typical bacterial genome and for approximately 55% of all membrane proteins in a typical eukaryotic genome. The average fraction of sequence length covered by a partial consensus topology is 44% for the prokaryotic proteins and 17% for the eukaryotic proteins in our test set, and similar numbers are found when the algorithm is applied to whole genomes. Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology.     

Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331

Plasmid pTer331 from the bacterium Collimonas fungivorans Ter331 is a new member of the pIPO2/pSB102 family of environmental plasmids. The 40 457-bp sequence of pTer331 codes for 44 putative ORFs, most of which represent genes involved in replication, partitioning and transfer of the plasmid. We confirmed that pTer331 is stably maintained in its native host. Deletion analysis identified a mini-replicon capable of replicating autonomously in Escherichia coli and Pseudomonas putida. Furthermore, plasmid pTer331 was able to mobilize and retromobilize IncQ plasmid pSM1890 at typical rates of 10(-4) and 10(-8), respectively. Analysis of the 91% DNA sequence identity between pTer331 and pIPO2 revealed functional conservation of coding sequences, the deletion of DNA fragments flanked by short direct repeats (DR), and sequence preservation of long DRs. In addition, we experimentally established that pTer331 has no obvious contribution in several of the phenotypes that are characteristic of its host C. fungivorans Ter331, including the ability to efficiently colonize plant roots. Based on our findings, we hypothesize that cryptic plasmids such as pTer331 and pIPO2 might not confer an individual advantage to bacteria, but, due to their broad-host-range and ability to retromobilize, benefit bacterial populations by accelerating the intracommunal dissemination of the mobile gene pool.     

The genetics of rheumatoid arthritis and the need for animal models to find and understand the underlying genes

The causes of rheumatoid arthritis (RA) are largely unknown. However, RA is most probably a multifactorial disease with contributions from genetic and environmental factors. Searches for genes that influence RA have been conducted in both human and experimental model materials. Both types of study have confirmed the polygenic inheritance of the disease. It has become clear that the features of RA complicate the human genetic studies. Animal models are therefore valuable tools for identifying genes and determining their pathogenic role in the disease. This is probably the fastest route towards unravelling the pathogenesisis of RA and developing new therapies.     

Mobility of moose—comparing the effects of wolf predation risk,reproductive status,and seasonality

In a predator–prey system, prey species may adapt to the presence of predators with behavioral changes such as increased vigilance, shifting habitats, or changes in their mobility. In North America, moose (Alces alces) have shown behavioral adaptations to presence of predators, but such antipredator behavioral responses have not yet been found in Scandinavian moose in response to the recolonization of wolves (Canis lupus). We studied travel speed and direction of movement of GPS‐collared female moose (n = 26) in relation to spatiotemporal differences in wolf predation risk, reproductive status, and time of year. Travel speed was highest during the calving (May–July) and postcalving (August–October) seasons and was lower for females with calves than females without calves. Similarly, time of year and reproductive status affected the direction of movement, as more concentrated movement was observed for females with calves at heel, during the calving season. We did not find support for that wolf predation risk was an important factor affecting moose travel speed or direction of movement. Likely causal factors for the weak effect of wolf predation risk on mobility of moose include high moose‐to‐wolf ratio and intensive hunter harvest of the moose population during the past century.     

Climate warming and heat waves affect reproductive strategies and interactions between submerged macrophytes

Extreme climatic events, such as heat waves, are predicted to increase in frequency and intensity during the next hundred years, which may accelerate shifts in hydrological regimes and submerged macrophyte composition in freshwater ecosystems. Since macrophytes are profound components of aquatic systems, predicting their response to extreme climatic events is crucial for implementation of climate change adaptation strategies. We therefore performed an experiment in 24 outdoor enclosures (400 L) separating the impact of a 4 °C increase in mean temperature with the same increase, that is the same total amount of energy input, but resembling a climate scenario with extreme variability, oscillating between 0 °C and 8 °C above present conditions. We show that at the moderate nutrient conditions provided in our study, neither an increase in mean temperature nor heat waves lead to a shift from a plant‐dominated to an algal‐dominated system. Instead, we show that species‐specific responses to climate change among submerged macrophytes may critically influence species composition and thereby ecosystem functioning. Our results also imply that more fluctuating temperatures affect the number of flowers produced per plant leading to less sexual reproduction. Our findings therefore suggest that predicted alterations in climate regimes may influence both plant interactions and reproductive strategies, which have the potential to inflict changes in biodiversity, community structure and ecosystem functioning.     

Soil carbon stocks in stable tropical landforms are dominated by geochemical controls and not by land use

Soil organic carbon (SOC) dynamics depend on soil properties derived from the geoclimatic conditions under which soils develop and are in many cases modified by land conversion. However, SOC stabilization and the responses of SOC to land use change are not well constrained in deeply weathered tropical soils, which are dominated by less reactive minerals than those in temperate regions. Along a gradient of geochemically distinct soil parent materials, we investigated differences in SOC stocks and SOC (Δ¹⁴C) turnover time across soil profile depth between montane tropical forest and cropland situated on flat, non-erosive plateau landforms. We show that SOC stocks and soil Δ¹⁴C patterns do not differ significantly with land use, but that differences in SOC can be explained by the physicochemical properties of soils. More specifically, labile organo-mineral associations in combination with exchangeable base cations were identified as the dominating controls over soil C stocks and turnover. We argue that due to their long weathering history, the investigated tropical soils do not provide enough reactive minerals for the stabilization of C input in either high input (tropical forest) or low-input (cropland) systems. Since these soils exceeded their maximum potential for the mineral related stabilization of SOC, potential positive effects of reforestation on tropical SOC storage are most likely limited to minor differences in topsoil without major impacts on subsoil C stocks. Hence, in deeply weathered soils, increasing C inputs may lead to the accumulation of a larger readily available SOC pool, but does not contribute to long-term SOC stabilization.     

Implementing an energetic life cycle analysis to prove the benefits of lignocellulosic feedstocks with protein separation for the chemical industry from the existing bioethanol industry

The biofuel ethanol is currently being produced in large quantities from corn in the US and from wheat in the EU and further capacity expansion is expected. Relying on the so-called 1st generation technology, only the starch contained in the edible portion of the crops (ears/grains) is subjected to fermentation. Following life cycle calculations reveals minute levels of fossil fuel replacement placing doubt on its renewability and an imbalance on the domestic animal feed markets are immerging due to the by-product distiller grains. Additional utilization of the lignocellulosic and protein components of the by-product through new developments has the potential to alleviate both setbacks. A cradle-to-factory gate analysis was performed on a variety of bioethanol production layouts incorporating the newest technological developments to determine the maximum fossil fuel reduction potential. Expanding to include lignocellulose pretreatment for ethanol production with protein separation for amine-based chemical production can increase the fossil fuel mitigation potential by seven- to ninefold for US-corn and five- to eightfold for EU-wheat bioethanol facilities.     

Grouping by Proximity in Haptic Contour Detection

We investigated the applicability of the Gestalt principle of perceptual grouping by proximity in the haptic modality. To do so, we investigated the influence of element proximity on haptic contour detection. In the course of four sessions ten participants performed a haptic contour detection task in which they freely explored a haptic random dot display that contained a contour in 50% of the trials. A contour was defined by a higher density of elements (raised dots), relative to the background surface. Proximity of the contour elements as well as the average proximity of background elements was systematically varied. We hypothesized that if proximity of contour elements influences haptic contour detection, detection will be more likely when contour elements are in closer proximity. This should be irrespective of the ratio with the proximity of the background elements. Results showed indeed that the closer the contour elements were, the higher the detection rates. Moreover, this was the case independent of the contour/background ratio. We conclude that the Gestalt law of proximity applies to haptic contour detection.     

Diagnostic properties of metabolic perturbations in rheumatoid arthritis

Introduction  

The aim of this study was to assess the feasibility of diagnosing early rheumatoid arthritis (RA) by measuring selected metabolic biomarkers.