Shaping the Growth Behaviour of Biofilms Initiated from Bacterial Aggregates.

Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious biofilms originate wholly or partially from pre-formed cell aggregates. Here, we use agent-based computer simulations to investigate the role of pre-formed aggregates in biofilm development. Focusing on the initial shape the aggregate forms on the surface, we find that the degree of spreading of an aggregate on a surface can play an important role in determining its eventual fate during biofilm development. Specifically, initially spread aggregates perform better when competition with surrounding unaggregated bacterial cells is low, while initially rounded aggregates perform better when competition with surrounding unaggregated cells is high. These contrasting outcomes are governed by a trade-off between aggregate surface area and height. Our results provide new insight into biofilm formation and development, and reveal new factors that may be at play in the social evolution of biofilm communities.

Similar Intracellular Location and Stimulus Reactivity, but Differential Mobility of Tailless (Vicia faba) and Tailed Forisomes (Phaseolus vulgaris) in Intact Sieve Tubes.

Sieve elements of legumes contain forisomes-fusiform protein bodies that are responsible for sieve-tube occlusion in response to damage or wound signals. Earlier work described the existence of tailless and tailed forisomes. This study intended to quantify and compare location and position of tailless (in Vicia faba) and tailed (in Phaseolus vulgaris) forisomes inside sieve elements and to assess their reactivity and potential mobility in response to a remote stimulus. Location (distribution within sieve elements) and position (forisome tip contacts) of more than altogether 2000 forisomes were screened in 500 intact plants by laser scanning confocal microscopy in the transmission mode. Furthermore, we studied the dispersion of forisomes at different locations in different positions and their positional behaviour in response to distant heat shocks. Forisome distribution turned out to be species-specific, whereas forisome positions at various locations were largely similar in bushbean (Phaseolus) and broadbean (Vicia). In general, the tailless forisomes had higher dispersion rates in response to heat shocks than the tailed forisomes and forisomes at the downstream (basal) end dispersed more frequently than those at the upstream end (apical). In contrast to the tailless forisomes that only oscillate in response to heat shocks, downstream-located tailed forisomes can cover considerable distances within sieve elements. This displacement was prevented by gentle rubbing of the leaf (priming) before the heat shock. Movement of these forisomes was also prohibited by Latrunculin A, an inhibitor of actin polymerization. The apparently active mobility of tailed forisomes gives credence to the idea that at least the latter forisomes are not free-floating, but connected to other sieve-element structures.

Factors Affecting Growth of Tengmalm's Owl (Aegolius funereus) Nestlings: Prey Abundance, Sex and Hatching Order.

In altricial birds, energy supply during growth is a major predictor of the physical condition and survival prospects of fledglings. A number of experimental studies have shown that nestling body mass and wing length can vary with particular extrinsic factors, but between-year observational data on this topic are scarce. Based on a seven-year observational study in a central European Tengmalm's owl population we examine the effect of year, brood size, hatching order, and sex on nestling body mass and wing length, as well as the effect of prey abundance on parameters of growth curve. We found that nestling body mass varied among years, and parameters of growth curve, i.e. growth rate and inflection point in particular, increased with increasing abundance of the owl's main prey (Apodemus mice, Microtus voles), and pooled prey abundance (Apodemus mice, Microtus voles, and Sorex shrews). Furthermore, nestling body mass varied with hatching order and between sexes being larger for females and for the first-hatched brood mates. Brood size had no effect on nestling body mass. Simultaneously, we found no effect of year, brood size, hatching order, or sex on the wing length of nestlings. Our findings suggest that in this temperate owl population, nestling body mass is more sensitive to prey abundance than is wing length. The latter is probably more limited by the physiology of the species.

Contrasting Strategies of Alfalfa Stem Elongation in Response to Fall Dormancy in Early Growth Stage: The Tradeoff between Internode Length and Internode Number.

Fall dormancy (FD) in alfalfa (Medicago sativa L.) can be described using 11 FD ratings, is widely used as an important indicator of stress resistance, productive performance and spring growth. However, the contrasting growth strategies in internode length and internode number in alfalfa cultivars with different FD rating are poorly understood. Here, a growth chamber study was conducted to investigate the effect of FD on plant height, aboveground biomass, internode length, and internode number in alfalfa individuals in the early growth stages. In order to simulate the alfalfa growth environment in the early stage, 11 alfalfa cultivars with FD ratings from one to 11 were chosen and seeded at the greenhouse, and then were transplanted into an artificial growth chamber. The experimental design was a randomized complete block in a split-plot arrangement with three replicates. Plant height, above-ground biomass, internode length, and internode number were measured in early growth stage in all individuals. Our findings showed that plant height and the aboveground biomass of alfalfa did not significantly differ among 11 different FD rated cultivars. Also, internode length and internode number positively affected plant height and the aboveground biomass of alfalfa individuals and the average internode length significantly increased with increasing FD rating. However, internode number tended to sharply decline when the FD rating increased. Moreover, there were no correlations, slightly negative correlations, and strongly negative correlations between internode length and internode number in alfalfa individuals among the three scales, including within-FD ratings, within-FD categories and inter-FD ratings, respectively. Therefore, our results highlighted that contrasting growth strategies in stem elongation were adopted by alfalfa with different FD ratings in the early growth stage. Alfalfa cultivars with a high FD rating have longer internodes, whereas more dormant alfalfa cultivars have a larger number of internodes. There were tradeoffs between internode length and internode number in response to FD in alfalfa, which reflected certain scale-dependence.

Opposite Distortions in Interval Timing Perception for Visual and Auditory Stimuli with Temporal Modulations.

When an object is presented visually and moves or flickers, the perception of its duration tends to be overestimated. Such an overestimation is called time dilation. Perceived time can also be distorted when a stimulus is presented aurally as an auditory flutter, but the mechanisms and their relationship to visual processing remains unclear. In the present study, we measured interval timing perception while modulating the temporal characteristics of visual and auditory stimuli, and investigated whether the interval times of visually and aurally presented objects shared a common mechanism. In these experiments, participants compared the durations of flickering or fluttering stimuli to standard stimuli, which were presented continuously. Perceived durations for auditory flutters were underestimated, while perceived durations of visual flickers were overestimated. When auditory flutters and visual flickers were presented simultaneously, these distortion effects were cancelled out. When auditory flutters were presented with a constantly presented visual stimulus, the interval timing perception of the visual stimulus was affected by the auditory flutters. These results indicate that interval timing perception is governed by independent mechanisms for visual and auditory processing, and that there are some interactions between the two processing systems.

Trophic ecology of Atlantic Bluefin Tuna (Thunnus thynnus) [corrected] larvae from the Gulf of Mexico and NW Mediterranean spawning grounds: A Comparative Stable Isotope Study.

The present study uses stable isotopes of nitrogen and carbon (δ15Nandδ13C) as trophic indicators for Atlantic bluefin tuna larvae (BFT) (6-10 mm standard length) in the highly contrasting environmental conditions of the Gulf of Mexico (GOM) and the Balearic Sea (MED). These regions are differentiated by their temperature regime and relative productivity, with the GOM being significantly warmer and more productive. MED BFT larvae showed the highest δ15N signatures, implying an elevated trophic position above the underlying microzooplankton baseline. Ontogenetic dietary shifts were observed in the BFT larvae from the GOM and MED which indicates early life trophodynamics differences between these spawning habitats. Significant trophic differences between the GOM and MED larvae were observed in relation to δ15N signatures in favour of the MED larvae, which may have important implications in their growth during their early life stages.These low δ15N levels in the zooplankton from the GOM may be an indication of a shifting isotopic baseline in pelagic food webs due to diatrophic inputs by cyanobacteria. Lack of enrichment for δ15N in BFT larvae compared to zooplankton implies an alternative grazing pathway from the traditional food chain of phytoplankton-zooplankton-larval fish. Results provide insight for a comparative characterization of the trophic pathways variability of the two main spawning grounds for BFT larvae.

Molecular Interactions of the Min Protein System Reproduce Spatiotemporal Patterning in Growing and Dividing Escherichia coli Cells.

Oscillations of the Min protein system are involved in the correct midcell placement of the divisome during Escherichia coli cell division. Based on molecular interactions of the Min system, we formulated a mathematical model that reproduces Min patterning during cell growth and division. Specifically, the increase in the residence time of MinD attached to the membrane as its own concentration increases, is accounted for by dimerisation of membrane-bound MinD and its interaction with MinE. Simulation of this system generates unparalleled correlation between the waveshape of experimental and theoretical MinD distributions, suggesting that the dominant interactions of the physical system have been successfully incorporated into the model. For cells where MinD is fully-labelled with GFP, the model reproduces the stationary localization of MinD-GFP for short cells, followed by oscillations from pole to pole in larger cells, and the transition to the symmetric distribution during cell filamentation. Cells containing a secondary, GFP-labelled MinD display a contrasting pattern. The model is able to account for these differences, including temporary midcell localization just prior to division, by increasing the rate constant controlling MinD ATPase and heterotetramer dissociation. For both experimental conditions, the model can explain how cell division results in an equal distribution of MinD and MinE in the two daughter cells, and accounts for the temperature dependence of the period of Min oscillations. Thus, we show that while other interactions may be present, they are not needed to reproduce the main characteristics of the Min system in vivo.

Effect of temperature on biochemical composition, growth and reproduction of the ornamental red cherry shrimp Neocaridina heteropoda heteropoda (Decapoda, Caridea).

The effect of water temperature on biochemical composition, growth and reproduction of the ornamental shrimp, Neocaridina heteropoda heteropoda, was investigated to determine the optimum temperature for its culture. The effect of embryo incubation temperature on the subsequent performance of juveniles was also evaluated. Ovigerous females and recently hatched juveniles (JI) were maintained during egg incubation and for a 90-day period, respectively, at three temperatures (24, 28 and 32 °C). Incubation period increased with decreasing water temperature, but the number and size of JI were similar among treatments. At day 30 of the 90-day period, body weight and growth increment (GI) at 24 °C were lower than those at 28 and 32 °C. On subsequent days, GI at 24 °C exceeded that at 28 and 32 °C, leading to a similar body weight among treatments. These results suggest growth was delayed at 24 °C, but only for 30 days after hatching. The lipid concentration tended to be lowest, intermediate and highest at 28, 32 and 24 °C, respectively, possibly as a consequence of the metabolic processes involved in growth and ovarian maturation. Protein and glycogen concentrations were similar among treatments. Both the growth trajectory and biochemical composition of shrimps were affected by the temperature experienced during the 90-day growth period independently of the embryo incubation temperature. During the growth period, shrimps reached sexual maturity and mated, with the highest proportion of ovigerous females occurring at 28 °C. All the females that matured and mated at 32 °C lost their eggs, indicating a potentially stressful effect of high temperature on ovarian maturation. Based on high survival and good growth performance of shrimps at the three temperatures tested over the 90-day period it is concluded that N. heteropoda heteropoda is tolerant to a wide range of water temperatures, with 28 °C being the optimum temperature for its culture.

Conspicuous female ornamentation and tests of male mate preference in threespine sticklebacks (Gasterosteus aculeatus).

Sexual selection drives the evolution of exaggerated male ornaments in many animal species. Female ornamentation is now acknowledged also to be common but is generally less well understood. One example is the recently documented red female throat coloration in some threespine stickleback (Gasterosteus aculeatus) populations. Although female sticklebacks often exhibit a preference for red male throat coloration, the possibility of sexual selection on female coloration has been little studied. Using sequential and simultaneous mate choice trials, we examined male mate preferences for female throat color, as well as pelvic spine color and standard length, using wild-captured threespine sticklebacks from the Little Campbell River, British Columbia. In a multivariate analysis, we found no evidence for a population-level mate preference in males, suggesting the absence of directional sexual selection on these traits arising from male mate choice. Significant variation was detected among males in their preference functions, but this appeared to arise from differences in their mean responsiveness across mating trials and not from variation in the strength (i.e., slope) of their preference, suggesting the absence of individual-level preferences as well. When presented with conspecific intruder males, male response decreased as intruder red throat coloration increased, suggesting that males can discriminate color and other aspects of phenotype in our experiment and that males may use these traits in intrasexual interactions. The results presented here are the first to explicitly address male preference for female throat color in threespine sticklebacks.

Papel de los micro-RNA en el cribado del cáncer colorrectal / Role of micro-RNA in colorectal cancer screening

Los micro-RNAs son responsables de la regulación de múltiples procesos biológicos de índole metabólica, de proliferación, de diferenciación, de apoptosis, del desarrollo y de la oncogénesis. En la carcinogénesis, los micro-RNA pueden ejercer su función a través de la alteración de los genes supresores de tumores o mediante la interacción con los oncogenes. Se ha determinado la presencia de diferentes micro-RNA en distintas enfermedades neoplásicas como cáncer de colon, próstata, mama, estómago, páncreas, pulmón, etc. Existen datos prometedores sobre la utilidad de cuantificar los micro-RNA en diferentes fluidos orgánicos y tejidos. Se ha realizado una revisión sobre las determinaciones de los micro-RNA en el diagnóstico del cáncer colorrectal

MicroRNAs are involved in carcinogenesis through postranscriptional gene regulatory activity. These molecules are involved in various physiological and pathological functions, such as apoptosis, cell proliferation and differentiation, which indicates their functionality in carcinogenesis as tumour suppressor genes or oncogenes. Several studies have determined the presence of microRNAs in different neoplastic diseases such as colon, prostate, breast, stomach, pancreas, and lung cancer. There are promising data on the usefulness of quantifying microRNAs in different organic fluids and tissues. We have conducted a review of the determinations of microRNAs in the diagnosis of colorectal cancer

On the role of the simplest S-nitrosothiol, HSNO, in atmospheric and biological processes.

Using state-of-the-art theoretical methods, we investigate the lowest electronic states of singlet and triplet spin multiplicities of HSNO. These computations are done using configuration interaction ab initio methods and the aug-cc-pV5Z basis set. One-dimensional cuts of the six-dimensional potential energy surfaces of these electronic states along the HS, SN stretches and HSN, SNO bending and torsion coordinates are calculated. Several avoided crossings and conical intersections are found. We computed also radiative lifetimes and spin-orbit couplings of these electronic states. Our work shows that the dynamics on these excited states is very complex, and suggest that multi-step mechanisms will populate the ground state via radiationless processes or lead to predissociation or intramolecular isomerization. For instance, these potentials are used to propose mechanisms for the IR, Vis, and UV light-induced cis-trans interconversions of HSNO and reactivity towards HS + NO and H + SNO products. Our findings are in good agreement with previous experimental studies on the photochemistry of HSNO. The atmospheric implication of HSNO is also discussed.

Competition for one nutrient with internal storage and toxin mortality.

This study presents a mathematical model of two species competing in a chemostat for one resource that is stored internally, and who also compete through allelopathy. Each species produces a toxin to that increases mortality rate of its competitor. The two species system and its single species subsystem follow mass conservation constraints characteristic of chemostat models. Persistence of a single species occurs if the nutrient supply of an empty habitat allows it to acquire a threshold of stored nutrient quota, sufficient to overcome loss to outflow after accounting for the cost of toxin production. For the two-species system, a semitrivial equilibrium with one species resident is unstable to invasion by the missing species according to a similar threshold condition. The invader increases if acquires a stored nutrient quota sufficient to overcome loss to outflow and toxin-induced mortality, after accounting for the cost of the invader's own toxin production. If both semitrivial equilibria for the two-species system are invasible then there is at least one coexistence equilibrium. Numerical analyses indicate another possibility: bistability in which both semitrivial equilibria are stable against invasion. In such a case there is competitive exclusion of one species, whose identity depends on initial conditions. When there is a tradeoff between abilities to compete for the nutrient and to compete through toxicity, the more toxic species can dominate only under nutrient-rich conditions. Bistability under such conditions could contribute to the unpredictability of toxic algal blooms.

Improved method for protein complex detection using bottleneck proteins.

BACKGROUND: Detecting protein complexes is one of essential and fundamental tasks in understanding various biological functions or processes. Therefore accurate identification of protein complexes is indispensable. METHODS: For more accurate detection of protein complexes, we propose an algorithm which detects dense protein sub-networks of which proteins share closely located bottleneck proteins. The proposed algorithm is capable of finding protein complexes which allow overlapping with each other. RESULTS: We applied our algorithm to several PPI (Protein-Protein Interaction) networks of Saccharomyces cerevisiae and Homo sapiens, and validated our results using public databases of protein complexes. The prediction accuracy was even more improved over our previous work which used also bottleneck information of the PPI network, but showed limitation when predicting small-sized protein complex detection. CONCLUSIONS: Our algorithm resulted in overlapping protein complexes with significantly improved F1 score over existing algorithms. This result comes from high recall due to effective network search, as well as high precision due to proper use of bottleneck information during the network search.

The biology of cultural conflict.

Although culture is usually thought of as the collection of knowledge and traditions that are transmitted outside of biology, evidence continues to accumulate showing how biology and culture are inseparably intertwined. Cultural conflict will occur only when the beliefs and traditions of one cultural group represent a challenge to individuals of another. Such a challenge will elicit brain processes involved in cognitive decision-making, emotional activation and physiological arousal associated with the outbreak, conduct and resolution of conflict. Key targets to understand bio-cultural differences include primitive drives-how the brain responds to likes and dislikes, how it discounts the future, and how this relates to reproductive behaviour-but also higher level functions, such as how the mind represents and values the surrounding physical and social environment. Future cultural wars, while they may bear familiar labels of religion and politics, will ultimately be fought over control of our biology and our environment.

Discovering networks of perturbed biological processes in hepatocyte cultures.

The liver plays a vital role in glucose homeostasis, the synthesis of bile acids and the detoxification of foreign substances. Liver culture systems are widely used to test adverse effects of drugs and environmental toxicants. The two most prevalent liver culture systems are hepatocyte monolayers (HMs) and collagen sandwiches (CS). Despite their wide use, comprehensive transcriptional programs and interaction networks in these culture systems have not been systematically investigated. We integrated an existing temporal transcriptional dataset for HM and CS cultures of rat hepatocytes with a functional interaction network of rat genes. We aimed to exploit the functional interactions to identify statistically significant linkages between perturbed biological processes. To this end, we developed a novel approach to compute Contextual Biological Process Linkage Networks (CBPLNs). CBPLNs revealed numerous meaningful connections between different biological processes and gene sets, which we were successful in interpreting within the context of liver metabolism. Multiple phenomena captured by CBPLNs at the process level such as regulation, downstream effects, and feedback loops have well described counterparts at the gene and protein level. CBPLNs reveal high-level linkages between pathways and processes, making the identification of important biological trends more tractable than through interactions between individual genes and molecules alone. Our approach may provide a new route to explore, analyze, and understand cellular responses to internal and external cues within the context of the intricate networks of molecular interactions that control cellular behavior.

Time-dependent corrections to effective rate and event statistics in Michaelis-Menten kinetics.

The authors generalise the concept of the geometric phase in stochastic kinetics to a non-cyclic evolution. Its application is demonstrated on kinetics of the Michaelis-Menten reaction. It is shown that the non-periodic geometric phase is responsible for the correction to the Michaelis-Menten law when parameters, such as a substrate concentration, are changing with time. The authors apply these ideas to a model of chemical reactions in a bacterial culture of a growing size, where the geometric correction qualitatively changes the outcome of the reaction kinetics.

Matrix factorization for recovery of biological processes from microarray data.

We explore a number of matrix factorization methods in terms of their ability to identify signatures of biological processes in a large gene expression study. We focus on the ability of these methods to find signatures in terms of gene ontology enhancement and on the interpretation of these signatures in the samples. Two Bayesian approaches, Bayesian Decomposition (BD) and Bayesian Factor Regression Modeling (BFRM), perform best. Differences in the strength of the signatures between the samples suggest that BD will be most useful for systems modeling and BFRM for biomarker discovery.

Computer-aided design of functional protein interactions.

Predictive methods for the computational design of proteins search for amino acid sequences adopting desired structures that perform specific functions. Typically, design of 'function' is formulated as engineering new and altered binding activities into proteins. Progress in the design of functional protein-protein interactions is directed toward engineering proteins to precisely control biological processes by specifically recognizing desired interaction partners while avoiding competitors. The field is aiming for strategies to harness recent advances in high-resolution computational modeling-particularly those exploiting protein conformational variability-to engineer new functions and incorporate many functional requirements simultaneously.