Changes in the macrobenthic community structure following the introduction of the invasive algae <Emphasis Type="Italic">Didymosphenia geminata</Emphasis> in the Matapedia River (Québec,Canada)

In July 2006, blooms of Didymosphenia geminata (didymo) were, for the first time, officially observed and identified in the Matapedia River, an Atlantic salmon river of the Gaspesie peninsula (Québec, Canada). This invasive diatom can form thick and extensive benthic layers in stable flow and oligotrophic rivers. This study aimed to evaluate the potential effect of didymo on the macrobenthic community structure of the Matapedia River. Macrobenthic samples were obtained in 2006, upstream of the blooms and, at the same sampling sites a year later, when they were affected by didymo. The Causapscal River remained free of didymo blooms for both years; therefore, this tributary is considered as a control site. Results show a significant difference (P < 0.001) in the community distribution before and after didymo presence in two of the three sites. Significant data show an increase Chironomidae proportions in all the sites (P = 0.011). Significantly higher benthic macroinvertebrate (BMI) densities were also observed in 2007 (P < 0.001). Simpson’s Evenness Index and total family richness was not significantly different when comparing pre- and post-incursion data (P = 0.90 and P = 0.83, respectively). Nevertheless, it is concluded that the presence of didymo has an effect on the base of the aquatic food web of the Matapedia River. This study is the first to assess the effect of this invasive alga on BMIs in Eastern Canada.     

The effects of membrane compartmentalization of csk on TCR signaling

The TCR signal transduction is initiated by the activation of Src-family kinases (SFK) which phosphorylate Immunoreceptor tyrosine-based activation motifs (ITAM) present in the intracellular parts of the T-cell receptor (TCR) signaling subunits. Numerous data suggest that after stimulation TCR interacts with membrane rafts and thus it gains access to SFK and other important molecules involved in signal transduction. However, the precise mechanism of this process is unclear. One of the key questions is how SFK access TCR and what is the importance of non-raft and membrane raft-associated SFK for the initiation and maintenance of the TCR signaling. To answer this question we targeted a negative regulator of SFK, C-terminal Src kinase (Csk) to membrane rafts, recently described “heavy rafts” or non-raft membrane. Our data show that only Csk targeted into “classical” raft but not to “heavy raft” or non-raft membrane effectively inhibits TCR signaling, demonstrating the critical role of membrane raft-associated SFK in this process.     

A review of evolutionary graph theory with applications to game theory

Evolutionary graph theory (EGT), studies the ability of a mutant gene to overtake a finite structured population. In this review, we describe the original framework for EGT and the major work that has followed it. This review looks at the calculation of the “fixation probability” - the probability of a mutant taking over a population and focuses on game-theoretic applications. We look at varying topics such as alternate evolutionary dynamics, time to fixation, special topological cases, and game theoretic results. Throughout the review, we examine several interesting open problems that warrant further research.     

How does the immune response get started?

An effective adaptive immune response requires the prior induction of the regulatory effector T-helper (eTh). There are two competing models of how this cell is induced to effectors. Under the Associative Recognition of Antigen (ARA) or “two signal” model, the T-helper requires eTh in order to be induced to eTh, an “autocatalytic” process. Under the “costimulation” model eTh are induced by an antigen-unspecific signal derived from an “activated” APC. Under the ARA model the problem of the origin of the primer eTh is posed. A nonself antigen-independent pathway to eTh is proposed as well as an experiment to reveal its existence. In the costimulation framework no primer eTh need be postulated but it lacks a mechanism that, in the absence of ARA, accounts for the self-nonself discrimination and the determination of effector class.     

Peach fruit ripening: A proteomic comparative analysis of the mesocarp of two cultivars with different flesh firmness at two ripening stages

A proteomic analysis was conducted on peach fruit mesocarp in order to better elucidate the biochemical and physiological events which characterize the transition of fruit from the “unripe” to the “ripe” phase.The first goal of the present work was to set-up a protocol suitable for improving protein extraction from peach mesocarp. The use of freeze-dried powdered tissue, together with the addition of phenol prior to the extraction with an aqueous buffer, significantly increased the protein yield and the quality of 2-DE gels. The proteomic profiles of the mesocarp from peach fruit of a non-melting flesh (NMF; ‘Oro A’) and a melting flesh (MF; ‘Bolero’) cultivar, at “unripe” and “ripe” stages as defined by some parameters typical of ripening, were then analyzed.The comparative analysis of the 2-DE gels showed that in NMF and MF peaches the relative volumes of 53 protein spots significantly changed in relation to both the ripening stage (“unripe” versus “ripe”) and/or the genetic background of the cultivar (‘Oro A’ versus ‘Bolero’).Thirty out of the 53 differently abundant spots were identified by LC-ESI-MS/MS. The analysis revealed enzymes involved in primary metabolism (e.g. C-compounds, carbohydrates, organic acids and amino acids) and in ethylene biosynthesis as well as proteins involved in secondary metabolism and responses to stress.Among these, 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) appeared to be one of the proteins with the largest change in relative abundance during the fruit transition from the pre-climacteric (“unripe”) to the climacteric (“ripe”) phase. Other proteins, such as S-adenosylmethionine synthetase and β-cyanoalanine synthase involved in ethylene metabolism, were also identified. Moreover, the changes in the relative abundances of a sucrose synthase and an α-amylase suggested differences between the two cultivars in the carbohydrate import activity of ripe fruit. The different accumulation of a few typical ROS-scavenger enzymes suggested that a higher oxidative stress occurred in MF with respect to NMF fruit. This result, together with data concerning the levels of total proteins and free amino acids and those regarding proteins involved in the maintenance of tissue integrity, was consistent with the hypothesis that the last phase of ripening in MF fruit is characterized by the appearance of a senescence status.The present study appears to define well some of the biochemical and physiological events that characterize the ripening of peach and, at the same time, provides interesting indications that could be employed in future marker assisted selection (MAS) programmes aimed to obtain MF fruits with higher ability to preserve tissue functionality maintaining for a longer time their organoleptic characteristics.     

Combining livestock and wildlife surveillance data to assess the likelihood of freedom from bovine tuberculosis in New Zealand

Bovine tuberculosis (Tb) has historically occurred in livestock throughout most of New Zealand, and also in wildlife over about 40% of the country. Using a test-and-cull strategy to eliminate Tb from livestock, intensive control of the major wildlife host (brushtail possums), and surveillance of key spillover hosts (wild ferrets, pigs and deer), the Animal Health Board has reduced the number of infected cattle herds by over 90% since 1994. Many formerly infected areas appear to now be free of the disease, so a key question is whether the disease control programme can be stopped in those places. We have developed a Bayesian framework for combining spatially explicit data derived from livestock testing and surveys of Tb prevalence in key wildlife hosts, and using those data to updating or refine an estimate of the probability of Tb freedom from wildlife provided by a priori prediction derived from a model of how Tb levels in possum are likely to have been affected by the duration and intensity of control. This paper outlines the conceptual framework, and some preliminary “case-study” steps toward implementation.     

Improvement of yield of Pleurotus eryngii var. eryngii by substrate supplementation and use of a casing overlay

Improved yield and biological efficiency (BE) of Pleurotus eryngii var. eryngii were achieved by supplementation of substrate with a commercial delayed-release nutrient and use of a casing overlay. Yield increases of 14% were achieved from cased substrates that were supplemented at time of casing with delayed-release nutrient (Remo’s). Use of a casing layer enhanced yield by 141% over non-cased substrates. When casing and substrate supplementation were combined, yield increased 179% over non-cased/non-supplemented substrates. Mushrooms harvested from cased substrates were darker in color and solids contents were lower compared to non-cased substrates. An additional break of mushrooms was harvested from non-cased “spent” substrate by fragmenting and re-supplementing the substrate prior to the application of a casing overlay. Three production methods were compared for their effect on mushroom yield: “standard”, “casing” and “casing after first break”. Casing of the substrate before first break (“casing” production method) resulted in the highest yield and biological efficiency.     

Developing population models for guiding reintroductions of extirpated bird species back to the New Zealand mainland

Population models are useful tools to guide management as they allow us to project growth and persistence of wildlife populations under different scenarios. Nevertheless, good data are needed to produce reliable models, and this requirement is problematic in some situations. North Island saddlebacks (Philesturnus rufusater) were reintroduced to Boundary Stream Mainland Island in September 2004, and this was the first time this species had occurred in an unfenced mainland area since their extirpation in the 19th century. This situation creates a challenging scenario for population modelling, as this species has never been studied in the presence of mainland predators, and management of these predators will be the key factor determining whether the population survives. In this paper we present an approach for developing a “prior model” before a reintroduction takes place. We use data from the reintroduced saddleback population on Mokoia Island to develop a model of how saddleback populations are regulated in the absence of mammalian predators. We use this model to project growth of a reintroduced population when vital rates are reduced by predation and also to project responses of source populations to harvesting of birds for translocation. We then incorporate data from the reintroduced North Island robin (Petroica longipes) population at Paengaroa Mainland Island to model the relationship between population parameters and predator tracking rates. The combined model can be used to predict the level of predator control needed to ensure growth of the saddleback population, but the prediction is contingent on guessing the relative vulnerability of robins and saddlebacks to predation. We envision using a Bayesian approach to update such prior models as site-specific data become available after reintroduction.     

Bayesian inference in ecology

Bayesian inference is an important statistical tool that is increasingly being used by ecologists. In a Bayesian analysis, information available before a study is conducted is summarized in a quantitative model or hypothesis: the prior probability distribution. Bayes’ Theorem uses the prior probability distribution and the likelihood of the data to generate a posterior probability distribution. Posterior probability distributions are an epistemological alternative to P‐values and provide a direct measure of the degree of belief that can be placed on models, hypotheses, or parameter estimates. Moreover, Bayesian information‐theoretic methods provide robust measures of the probability of alternative models, and multiple models can be averaged into a single model that reflects uncertainty in model construction and selection. These methods are demonstrated through a simple worked example. Ecologists are using Bayesian inference in studies that range from predicting single‐species population dynamics to understanding ecosystem processes. Not all ecologists, however, appreciate the philosophical underpinnings of Bayesian inference. In particular, Bayesians and frequentists differ in their definition of probability and in their treatment of model parameters as random variables or estimates of true values. These assumptions must be addressed explicitly before deciding whether or not to use Bayesian methods to analyse ecological data.     

The Effects of Phosphomimetic Lid Mutation on the Thermostability of the N-terminal Domain of MDM2

The multidomain E3 ubiquitin ligase MDM2 catalyzes p53 ubiquitination by a “dual-site” docking mechanism whereby MDM2 binding to at least two distinct peptide motifs on p53 promotes ubiquitination. One protein-protein interaction occurs between the N-terminal hydrophobic pocket of MDM2 and the transactivation motif of p53, and the second interaction occurs between the acidic domain of MDM2 and a motif in the DNA-binding domain of p53. A flexible N-terminal pseudo-substrate or “lid” adjacent to the N-terminal hydrophobic pocket of MDM2 has a phosphorylation site, and there are distinct models proposed on how the phosphorylated lid could affect MDM2 function. Biochemical studies have predicted that phosphomimetic mutation will stabilize the lid on the surface of MDM2 and will “open” the hydrophobic pocket and stabilize the MDM2-p53 complex, while NMR studies proposed that phosphomimetic mutation “closes” the lid over the MDM2 pocket and inhibits MDM2-p53 complex formation. To resolve these discrepancies, we utilized a quantitative fluorescence-based dye binding assay to measure the thermal unfolding of wild-type (wt), ΔLid, and S17D N-terminal domains of MDM2 as a function of increasing ligand concentration. Our data reveal that S17D lid mutation increases, rather than decreases, the thermostability of the N-terminal domain of MDM2 in the absence or in the presence of ligand. ΔLid mutation, by contrast, increases MDM2 thermoinstability. This is consistent with biochemical data, using full-length MDM2, showing that the S17D mutation stabilizes the MDM2-p53 complex and increases the specific activity of the E3 ubiquitin ligase function of MDM2. These data indicate that phosphomimetic lid mutation results in an “opening,” rather than a “closing,” of the pocket of MDM2 and highlight the ability of small intrinsically disordered or unstructured peptide motifs to regulate the specific activity of a protein.     

The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow

This paper is concerned with a model of “isolation with an initial period of migration”, where a panmictic ancestral population split into n descendant populations which exchanged migrants symmetrically at a constant rate for a period of time and subsequently became completely isolated. In the limit as the population split occurred an infinitely long time ago, the model becomes an “isolation after migration” model, describing completely isolated descendant populations which arose from a subdivided ancestral population. The probability density function of the coalescence time of a pair of genes and the probability distribution of the number of pairwise nucleotide differences are derived for both models. Whilst these are theoretical results of interest in their own right, they also give an exact analytical expression for the likelihood, for data consisting of the numbers of nucleotide differences between pairs of DNA sequences where each pair is at a different, independent locus. The behaviour of the distribution of the number of pairwise nucleotide differences under these models is illustrated and compared to the corresponding distributions under the “isolation with migration” and “complete isolation” models. It is shown that the distribution of the number of nucleotide differences between a pair of DNA sequences from different descendant populations in the model of “isolation with an initial period of migration” can be quite different from that under the “isolation with migration model”, even if the average migration rate over time (and hence the total number of migrants) is the same in both scenarios. It is also illustrated how the results can be extended to other demographic scenarios that can be described by a combination of isolated panmictic populations and “symmetric island” models.     

Configural processing of different topologically structured figures: an ERP Study

According to Chen’s theory, topological differences are perceived faster than feature differences in early visual perception. We hypothesized that topological perception is caused by the sensitivity in discriminating figures with and without “holes”. An ERP experiment was conducted utilizing a passive paradigm to investigate the differences in perceiving figures with “hole” and with “no-hole”. The results showed differences in N170 components between figures with “holes” and with “no-holes”. The inversion of the “hole” could influence the latency of N170, but the inversion of the “no-hole” could not, which indicated that global features are processed first in the “hole” perception whilst local features are given priority to the “no-hole” perception. This result was similar to studies concerning face and non-face objects, suggesting a configural processing of the “hole”.     

Amino-terminal domain interactions of lambda integrase on arm-type DNA

In contrast to the other tyrosine recombinase family members, integrase protein (Int) of bacteriophage λ has an additional amino-terminal domain that binds to “arm-type” DNA sequences distant from those involved in strand exchange. The homomeric interaction between neighboring amino-terminal domains of Int is contributed by R30-D71 salt-bridge in a non-equivalent manner on Holliday-junction intermediates. In this report, R30 and D71 residues were investigated in regard to Int’s cooperative binding to “arm-type” DNA and the attenuating function of “arm-type” DNA. The results suggest the electrostatic interaction between residues 30 and 71 is dependent on “arm-type” DNA and contributes the “selective” inhibition of catalytic activity of λ Int by “arm-type” DNA.     

The sense of water in the blowfly Protophormia terraenovae

The gustatory system of the blowfly, Protophormia terraenovae, is a relatively simple biological model for studies on chemosensory input and behavioral output. It appears to have renewed interest as a model for studies on the role of water channels, namely aquaporins or aquaglyceroporins, in water detection. To this end, we investigated the presence of water channels, their role in “water” and “salt” cell responsiveness and the transduction mechanism involved. For the first time our electrophysiological results point to the presence of an aquaglyceroporin in the chemoreceptor membrane of the “water” cell in the blowfly taste chemosensilla whose transduction mechanism ultimately involves an intracellular calcium increase and consequently cell depolarization. This hypothesis is also supported by calcium imaging data following proper stimulation. This mechanism is triggered by “water” cell stimulation with hypotonic solutions and/or solutes such as glycerol which crosses the membrane by way of aquaglyceroporins. Behavioral output indicates that the “sense” of water in blowflies is definitely not dependent on the “water” cell only, but also on the “salt” cell sensitivity. These findings also hypothesize a new role for aquaglyceroporin in spiking cell excitability.     

Survivor's dilemma: Defend the group or flee?

We consider a survival game of gregarious individuals, in which the aim of the players is survival to reproductive age under predator attacks. The survivor’s dilemma (shortly: SVD) game consists in the following: a group member either surely survives alone by fleeing, while its defensive mate may be killed; or tries to save its mate’s life, risking to get killed. The dilemma is that, in every single attack, fleeing ensures maximal survival probability, but if its mate survives by fighting both, and they remain together, its risk to be killed at the next attack will be lower. We show that, if defense is successful enough, then the one-attack game is a prisoner’s dilemma (PD), where fleeing is the strict ESS. We have additively decomposed the SVD game, according to the survival of the group mate of the focal prey, into two games: the aim of the “collective game” is survival of the group of prey. Counter-wise, the aim of the “hostile game” is survival alone (focal prey survives and its mate is killed by the predator). We obtain the following results: if the attack number is large enough, the multi-attack SVD game is dominated by the “collective game” in the sense that each individual can ensure its own maximal survival probability by maximizing the group survival probability in each attack. In the hostile game, the only strict ESS is the fleeing strategy. In the collective game there are two different cases: either defense is a unique strict ESS, or the collective game is bistable, i.e. fleeing and defense are local strict ESS’s. If defense is the only strict ESS in the collective game, and the attack number is large enough, defense replaces fleeing strategy in the multi-attack SVD game. However, in the bistable case, defense cannot invade into the fleeing population. It is shown that, if the interaction between relatives is frequent enough, than defense can replace fleeing strategy, in spite of the fact that in the well-mixed population the collective game is bistable.     

The hidden variables of leadership

The dynamics of a collective move can be untangled into three components: initiation, following and cancellation. Varying the response function parameters attached to one individual can switch the collective phenomenology from an absence of well identified leader (“distributed leadership”) to the emergence of a “despotic regime”, i.e. this individual leading more often the collective moves. I show that not all parameters have the same impact but rather that only a large increase of the initiation rate can empower an obvious leader, up to the “despotic” regime. Being more readily followed, or cancelling less often can enhance the leader's prominence only up to a limited level. To overtake this limit would then further require to affect also the parameters attached to the others (e.g. to lower their eagerness to initiate group motion as well as their probability to be followed when they do).     

Dynamic positional fate map of the primary heart-forming region

Here we show the temporal-spatial orchestration of early heart morphogenesis at cellular level resolution, in vivo, and reconcile conflicting positional fate mapping data regarding the primary heart-forming field(s). We determined the positional fates of precardiac cells using a precision electroporation approach in combination with wide-field time-lapse microscopy in the quail embryo, a warm-blooded vertebrate (HH Stages 4 through 10). Contrary to previous studies, the results demonstrate the existence of a “continuous” circle-shaped heart field that spans the midline, appearing at HH Stage 4, which then expands to form a wide arc of progenitors at HH Stages 5-7. Our time-resolved image data show that a subset of these cardiac progenitor cells do not overlap with the expression of common cardiogenic factors, Nkx-2.5 and Bmp-2, until HH Stage 10, when a tubular heart has formed, calling into question when cardiac fate is specified and by which key factors. Sub-groups and anatomical bands (cohorts) of heart precursor cells dramatically change their relative positions in a process largely driven by endodermal folding and other large-scale tissue deformations. Thus, our novel dynamic positional fate maps resolve the origin of cardiac progenitor cells in amniotes. The data also establish the concept that tissue motion contributes significantly to cellular position fate — i.e., much of the cellular displacement that occurs during assembly of a midline heart tube (HH Stage 9) is NOT due to “migration” (autonomous motility), a commonly held belief. Computational analysis of our time-resolved data lays the foundation for more precise analyses of how cardiac gene regulatory networks correlate with early heart tissue morphogenesis in birds and mammals.     

Inducing visibilities: an attempt at Santiago Ramón y Cajal's aesthetic epistemology

In this paper, I consider Santiago Ramón y Cajal’s strategy of histological observation and imaging in terms of what I call “induction of visibility” (Fiorentini, 2011). Cajal’s strategy of visibility induction drew upon both rational and aesthetic visual sensibility, and considered this interplay to be a constitutive element of knowledge production. I propose to describe Cajal’s fundamental attitude towards visually inferred knowledge in terms of an “aesthetic epistemology”.