Abiotic formation of particles from extracellular organic carbon released by phytoplankton

¹⁴C-labeled extracellular organic carbon (EOC) released by the phytoplankton in a Danish Estuary was shown immediately to form particles (>0.2m) when the products were added to a natural water sample. About 14%–20% of the added activity could be recovered as particles. Any bacterial assimilation of the extracellular products was thus masked. The abiotic origin of the particulate EOC was verified, and it was shown that the particle formation was due to some factors present in the estuarine water with a nominal diameter >0.2m. Precaution must be taken to avoid misinterpretations in studies concerning carbon flow from algae to bacteria.     

DNA replication in Physarum polycephalum: electron microscopic and autoradiographic analysis of replicating DNA from defined stages of the S-period.

Electron microscopic and autoradiographic analysis of replicating DNA from Physarum showed that replication occurs at a rate of 0.4 micron/min/per replicon and that replicons of size 10--15 mu occur in temporal clusters with an average of about 4 replicons per cluster. These results are compared with previous hydrodynamic measurements and with those obtained in other organisms.     

Modelling the Human Immune System by Combining Bioinformatics and Systems Biology Approaches

Over the past decade a number of bioinformatics tools have been developed that use genomic sequences as input to predict to which parts of a microbe the immune system will react, the so-called epitopes. Many predicted epitopes have later been verified experimentally, demonstrating the usefulness of such predictions. At the same time, simulation models have been developed that describe the dynamics of different immune cell populations and their interactions with microbes. These models have been used to explain experimental findings where timing is of importance, such as the time between administration of a vaccine and infection with the microbe that the vaccine is intended to protect against. In this paper, we outline a framework for integration of these two approaches. As an example, we develop a model in which HIV dynamics are correlated with genomics data. For the first time, the fitness of wild type and mutated virus are assessed by means of a sequence-dependent scoring matrix, derived from a BLOSUM matrix, that links protein sequences to growth rates of the virus in the mathematical model. A combined bioinformatics and systems biology approach can lead to a better understanding of immune system-related diseases where both timing and genomic information are of importance.     

Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics

Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction. Specifically, we focus on the role of steered molecular dynamics (SMD) simulations in providing details at the atomic level on a group of protein domains, which play a fundamental role in signal exchange by responding properly to mechanical strain. We start by giving a brief introduction to the SMD technique and general properties of mechanically stable protein folds, followed by specific examples illustrating three general regimes of signal transfer utilizing mechanical energy: purely mechanical, mechanical to chemical, and chemical to mechanical. Whenever possible the physiological importance of the example at hand is stressed to highlight the diversity of the processes in which mechanical signaling plays a key role. We also provide an overview of future challenges and perspectives for this rapidly developing field.     

Chromophore distortions in the bacteriorhodopsin photocycle: evolution of the H-C14-C15-H dihedral angle measured by solid-state NMR.

In recent years, structural information about bacteriorhodopsin has grown substantially with the publication of several crystal structures. However, precise measurements of the chromophore conformation in the various photocycle states are still lacking. This information is critical because twists about the chromophore backbone chain can influence the Schiff base nitrogen position, orientation, and proton affinity. Here, we focus on the C14-C15 bond, using solid-state nuclear magnetic resonance spectroscopy to measure the H-C14-C15-H dihedral angle. In the resting state (bR(568)), we obtain an angle of 164 +/- 4 degrees, indicating a 16 degrees distortion from a planar all-trans chromophore. The dihedral angle is found to decrease to 147 +/- 10 degrees in the early M intermediate (M(o)) and to 150 +/- 4 degrees in the late M intermediate (M(n)). These results demonstrate changes in the chromophore conformation undetected by recent X-ray diffraction studies.     

Screening for antimicrobial resistance genes and virulence factors via genome sequencing

Second-generation genome sequencing and alignment of the resulting reads to in silico genomes containing antimicrobial resistance and virulence factor genes were used to screen for undesirable genes in 28 strains which could be used in human nutrition. No virulence factor genes were detected, while several isolates contained antimicrobial resistance genes.     

Accuracy and repeatability of moose (<Emphasis Type="Italic">Alces alces</Emphasis>) age as estimated from dental cement layers

Optimal research and management of species with age structure often depends on estimates of age-specific population parameters, which in turn depends on reliable methods for age determination. By counting annuli in the cementum of incisor root tips from 51 known-age moose (Alces alces) between 1 and 12 years old, we examined the variation in accuracy and repeatability of age estimates provided by three research technicians with different experiences of aging moose. The most experienced technician estimated the moose age correctly in up to 90% of the cases, while the technician with no prior experience estimated age correctly in up to 73% of the cases. The medium-experienced technician achieved a lower accuracy (up to 53%), indicating that experience alone is not sufficient if the basic training or lack of routine checks against other colleagues or a known-age material are not undertaken. The percentage moose aged within ±1 year from correct age was significantly higher in all technicians (94–98%). After the generally high accuracy, we also found high repeatability (0.980–0.994) within technicians. We conclude that this method of age-determination provides reliable estimates that can be used by management and research to gain information about age-specific patterns in moose populations. However, to obtain estimates of high accuracy the technicians should be well trained, have gained the necessary experience, and most preferably, have access to a sample of teeth from known-age moose.     

The vertical distribution of N and K uptake in relation to root distribution and root uptake capacity in mature Quercus robur, Fagus sylvatica and Picea abies stands

We have measured the uptake capacity of nitrogen (N) and potassium (K) from different soil depths by injecting ¹⁵N and caesium (Cs; as an analogue to K) at 5 and 50 cm soil depth and analysing the recovery of these markers in foliage and buds. The study was performed in monocultures of 40-year-old pedunculate oak (Quercus robur), European beech (Fagus sylvatica) and Norway spruce (Picea abies (L.) Karst.) located at an experimental site in Palsgård, Denmark. The markers were injected as a solution through plastic tubes around 20 trees of each species at either 5 or 50 cm soil depth in June 2003. After 65 days foliage and buds were harvested and the concentrations of ¹⁵N and Cs analysed. The recovery of ¹⁵N in the foliage and buds tended to be higher from 5 than 50 cm soil depth in oak whereas they where similar in spruce and beech after compensation for differences in immobilization of ¹⁵N in the soil. In oak more Cs was recovered from 5 than from 50 cm soil depth whereas in beech and spruce no difference could be detected. Out of the three investigated tree species, oak was found to have the lowest capacity to take up Cs at 50 cm soil depth compared to 5 cm soil depth also after compensating for differences in discrimination against Cs by the roots. The uptake capacity from 50 cm soil depth compared with 5 cm was higher than expected from the root distribution except for K in oak, which can probably be explained by a considerable overlap of the uptake zones around the roots and mycorrhizal hyphae in the topsoil. The study also shows that fine roots at different soil depths with different physiological properties can influence the nutrient uptake of trees. Estimates of fine root distribution alone may thus not reflect the nutrient uptake capacity of trees with sufficient accuracy. Our study shows that deep-rooted trees such as oak may have lower nutrient uptake capacity at deeper soil layers than more shallow-rooted trees such as spruce, as we found no evidence that deep-rooted trees obtained proportionally more nutrients from deeper soil layers. This has implications for models of nutrient cycling in forest ecosystems that use the distribution of roots as the sole criterion for predicting uptake of nutrients from different soil depths.