Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats

The distribution and abundance of Betaproteobacteria and three of its genera - Limnohabitans (R-BT065 lineage), Polynucleobacter (including subclusters Polynucleobacter necessarius and Polynucleobacter acidiphobus/Polynucleobacter difficilis), and Methylophilus - across the epilimnia of 72 limnologically diverse freshwater habitats were investigated using fluorescence in situ hybridization. Moreover, seasonal development of Betaproteobacteria subgroups along the longitudinal axis of a reservoir was followed. Betaproteobacteria comprised on average 29.1%, Polynucleobacter 11.6%, P.?necessarius 10.1%, P.?acidiphobus/difficilis 0.5%, Limnohabitans 8.9%, and Methylophilus 0.9% of total bacterioplankton cells in the investigated habitats. Polynucleobacter necessarius and Limnohabitans coexisted in the majority of habitats but showed contrasting abundance patterns along the pH gradient of habitats (pH, 3.8-8.5). The observed distribution patterns could theoretically be explained by different preferences for substrate sources, that is, substances of humic origin in acidic waters and algal-derived substances in alkaline waters. However, substrate utilization patterns observed in laboratory experiments indicate no coherent group-specific differences in substrate preferences. Interestingly, similar distribution patterns were revealed for Limnohabitans and P.?acidiphobus/difficilis, suggesting similar ecological adaptations of these distantly related taxa. Our findings further emphasize that at least two taxa of freshwater Betaproteobacteria represent ecologically diversified groups. Investigations at higher phylogenetic resolution are required for obtaining further insights into their ecology.     

The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living polynucleobacter population

Background

The bacterial taxon Polynucleobacter necessarius subspecies asymbioticus represents a group of planktonic freshwater bacteria with cosmopolitan and ubiquitous distribution in standing freshwater habitats. These bacteria comprise <1% to 70% (on average about 20%) of total bacterioplankton cells in various freshwater habitats. The ubiquity of this taxon was recently explained by intra-taxon ecological diversification, i.e. specialization of lineages to specific environmental conditions; however, details on specific adaptations are not known. Here we investigated by means of genomic and experimental analyses the ecological adaptation of a persistent population dwelling in a small acidic pond.

Findings

The investigated population (F10 lineage) contributed on average 11% to total bacterioplankton in the pond during the vegetation periods (ice-free period, usually May to November). Only a low degree of genetic diversification of the population could be revealed. These bacteria are characterized by a small genome size (2.1 Mb), a relatively small number of genes involved in transduction of environmental signals, and the lack of motility and quorum sensing. Experiments indicated that these bacteria live as chemoorganotrophs by mainly utilizing low-molecular-weight substrates derived from photooxidation of humic substances.

Conclusions

Evolutionary genome streamlining resulted in a highly passive lifestyle so far only known among free-living bacteria from pelagic marine taxa dwelling in environmentally stable nutrient-poor off-shore systems. Surprisingly, such a lifestyle is also successful in a highly dynamic and nutrient-richer environment such as the water column of the investigated pond, which was undergoing complete mixis and pronounced stratification in diurnal cycles. Obviously, metabolic and ecological versatility is not a prerequisite for long-lasting establishment of abundant bacterial populations under highly dynamic environmental conditions. Caution should be exercised when generalizing the obtained insights into the ecology and adaptation of the investigated lineage to other Polynucleobacter lineages.     

Benefits for dominant red deer hinds under a competitive feeding system: food access behavior, diet and nutrient selection

Social dominance is widely known to facilitate access to food resources in many animal species such as deer. However, research has paid little attention to dominance in ad libitum access to food because it was thought not to result in any benefit for dominant individuals. In this study we assessed if, even under ad libitum conditions, social rank may allow dominant hinds to consume the preferred components of food. Forty-four red deer hinds (Cervus elaphus) were allowed to consume ad libitum meal consisting of pellets of sunflower, lucerne and orange, and seeds of cereals, corn, cotton, and carob tree. The meal was placed only in one feeder, which reduced accessibility to a few individuals simultaneously. During seven days, feeding behavior (order of access, time to first feeding bout, total time spent feeding, and time per feeding bout) were assessed during the first hour. The relative abundance of each meal component was assessed at times 0, 1 and 5 h, as well as its nutritional composition. Social rank was positively related to the amount of time spent feeding during the 1(st) h (P = 0.048). Selection indices were positively correlated with energy (P = 0.018 during the 1(st) h and P = 0.047 from 1(st) to 5(th)) and fat (only during the 1(st) h; P = 0.036), but also negatively with certain minerals. Thus, dominant hinds could select high energy meal components for longer time under an ad libitum but restricted food access setting. Selection indices showed a higher selectivity when food availability was higher (1(st) hour respect to 1(st) to 5(th)). Finally, high and low ranking hinds had longer time per feeding bout than mid ones (P = 0.011), suggesting complex behavioral feeding tactics of low ranking social ungulates.     

Circular dichroism and guanine quadruplexes

Circular dichroism (CD) is remarkably sensitive to the conformational states of nucleic acids; therefore, CD spectroscopy has been used to study most features of DNA and RNA structures. Quadruplexes are among the significant noncanonical nucleic acids architectures that have received special attentions recently. This article presents examples on the contribution of CD spectroscopy to our knowledge of quadruplex structures and their polymorphism. The examples were selected to demonstrate the potential of this simple method in the quadruplex field. As CD spectroscopy detects only the global feature of a macromolecule, it should preferably be used in combination with other techniques. On the other hand, CD spectroscopy, often as a pioneering approach, can reveal the formation of particular structural arrangements, to search for the conditions stabilizing the structures, to follow the transitions between various structural states, to explore kinetics of their appearance, to determine thermodynamic parameters and also detect formation of higher order structures. This article aims to show that CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies.     

The influence of spin-labeled fluorene compounds on the assembly and toxicity of the aβ peptide

Background

The deposition and oligomerization of amyloid β (Aβ) peptide plays a key role in the pathogenesis of Alzheimer''s disease (AD). Aβ peptide arises from cleavage of the membrane-associated domain of the amyloid precursor protein (APP) by β and γ secretases. Several lines of evidence point to the soluble Aβ oligomer (AβO) as the primary neurotoxic species in the etiology of AD. Recently, we have demonstrated that a class of fluorene molecules specifically disrupts the AβO species.

Methodology/Principal Findings

To achieve a better understanding of the mechanism of action of this disruptive ability, we extend the application of electron paramagnetic resonance (EPR) spectroscopy of site-directed spin labels in the Aβ peptide to investigate the binding and influence of fluorene compounds on AβO structure and dynamics. In addition, we have synthesized a spin-labeled fluorene (SLF) containing a pyrroline nitroxide group that provides both increased cell protection against AβO toxicity and a route to directly observe the binding of the fluorene to the AβO assembly. We also evaluate the ability of fluorenes to target multiple pathological processes involved in the neurodegenerative cascade, such as their ability to block AβO toxicity, scavenge free radicals and diminish the formation of intracellular AβO species.

Conclusions

Fluorene modified with pyrroline nitroxide may be especially useful in counteracting Aβ peptide toxicity, because they posses both antioxidant properties and the ability to disrupt AβO species.     

Technical means for objectification of medical treatments in the area of the deep stabilisation spinal system

Information regarding two versions of an instrument called a muscle dynamometer, which enables detailed information about muscle activity in the deep stabilisation spinal system (DSSS), presented in this article. The MD01 (muscle dynamometer ver. 01) is a simple electromechanical instrument that allows measurement of muscle activity in two areas of the lumbar spine region. Measurements on patients have confirmed the usefulness of quantifying the initial state of a patient before rehabilitation as well as monitoring rehabilitation treatment; the MD01 is a suitable device for obtaining these measurements. However, a new and improved version of the MD01, the MD02, has been developed. The MD02 allows measurements in four different body regions and now has a PC interface, which allows achieving of patient information and data export for use with statistical software.     

Sucking and allosucking duration in farmed red deer (Cervus elaphus)

Sucking duration in ungulates does not only mean milk transfer, but is also associated with maternal care in general. It seems to be a reflection of offspring demand rather than solely milk transfer rate. Thus, the objective of this study was to discriminate between sucking and allosucking (i.e. sucking non-maternal hind) behaviour in red deer according to the sucking duration.We hypothesized that: (1) calves should suck longer from their mothers than allosuck from non-maternal hinds; (2) sucking duration of calves frequently nursed by a particular non-maternal hind should be longer than that of calves occasionally allonursed; (3) sucking duration should be longer for bouts including one calf than two or more calves sucking simultaneously; (4) male calves should suck and allosuck longer than female calves; and (5) primiparous hinds should nurse and allonurse longer than multiparous hinds. We observed sucking behaviour of 25 hinds and their 38 calves (from birth until the youngest calf reached one month of age) in two seasons. We recorded 1730 sucking bouts, of which 11.62% in the first season and 4.37% in the second season were non-filial. The duration of filial sucking was significantly longer than non-filial sucking. A large individual variance in the incidence of non-filial sucking in both the calves and hinds was found. Therefore, the non-filial hind–calf pairs were categorized in two clusters according to the frequency of nursing non-filial calves for one hind in relationship to all nursing events for this hind by a cluster analysis (PROC CLUSTER, SAS). We used a general linear mixed model, GLMM (PROC MIXED, SAS) to test the influence of hind relationship to the nursed calf (filial, frequently allosucking non-filial, or occasionally allosucking non-filial pair). Sucking duration of occasionally allosucking non-filial calves was only marginally different from that of filial calves. There was no difference between the two groups of non-filial calves. Multiple sucking bouts were shorter than those with one calf. Male calves sucked longer than female calves; however, the greatest difference was recorded between frequently allosucking non-filial pairs of both sexes. Frequently allosucking non-filial males sucked the longest and differently from occasionally allosucking non-filial males. Frequently allosucking non-filial females sucked the shortest and differently from filial calves of both sexes. It is more likely that allosucking seems to be more important for male rather than female calves.Therefore, it is concluded that allosucking calves differ in their sucking behaviour and two types of allosuckers (frequent and occasional) should be taken into account when analyzing allosuckling behaviour.     

VDAC2 and aldolase A identified as membrane proteins of K562 cells with increased expression under iron deprivation

We have shown previously that iron deprivation significantly stimulates the uptake of non-transferrin ferric iron from ferric citrate by erythroleukemia K562 cells and that this stimulation depends on protein synthesis. However, we have not detected increased expression of any known iron transport protein (Kovar J. et al. (2006) Blood Cells Mol Dis 37:95–99). Therefore, in order to identify membrane proteins of K562 cells with increased expression under iron deprivation, we employed the isolation of membrane proteins by two-phase partitioning system, protein separation by high-resolution 2D electrophoresis, computer differential analysis, and tandem mass spectrometry. Employing these techniques we identified two proteins with statistically significant upregulation, i.e., aldolase A (ALDA) and voltage-dependent anion channel 2 (VDAC2). The upregulation of aldolase A and VDAC2 in K562 cells under iron deprivation was also confirmed by western blot analysis. This is the first time when the control of aldolase A and VDAC2 levels by iron status of the cell is demonstrated.