Swarm Cognition: an interdisciplinary approach to?the?study of self-organising biological collectives

Basic elements of cognition have been identified in the behaviour displayed by animal collectives, ranging from honeybee swarms to human societies. For example, an insect swarm is often considered a ??super-organism?? that appears to exhibit cognitive behaviour as a result of the interactions among the individual insects and between the insects and the environment. Progress in disciplines such as neurosciences, cognitive psychology, social ethology and swarm intelligence has allowed researchers to recognise and model the distributed basis of cognition and to draw parallels between the behaviour of social insects and brain dynamics. In this paper, we discuss the theoretical premises and the biological basis of Swarm Cognition, a novel approach to the study of cognition as a distributed self-organising phenomenon, and we point to novel fascinating directions for future work.     

The exposure,sensitivity and vulnerability of natural vegetation in China to climate thermal variability (1901–2013): An indicator-based approach

Vulnerability assessments can be helpful in assessing the impact of climate change on natural ecosystems and are expected to support adaptation and/or mitigation strategies in the 21st century. A challenge when conducting such assessments is the integration of the multi-level properties and processes of ecosystems into an assessment framework. Focusing on the primary stresses of climate thermal variability (at both upper and lower extremes), this study proposes a quantitative indicator system—following the IPCC framework of vulnerability assessment—that assesses the impact of historical climate change, during 1901–2013, on the natural terrestrial vegetation types in China. The final output of the vulnerability assessment was expressed as a composite index, composed of ecosystem exposure, sensitivity and resilience to climate thermal change, and including biological, ecological and spatial traits of vegetation types in the assessment. The exposure to temperature variability was generally higher in January than in July, and higher in non-arborous vegetation types than forests. In contrast, sensitivity was higher for forests, wetlands and alpine tundra regions, especially for small areas and areas with scattered patterns. Original forests—especially those distributed in the north—had lower resilience than other vegetation types. The vulnerability of natural vegetation types in China to the temperature variability of the past century was very low to moderate, with a few exceptions, including tropical mangroves and the semi-arid to arid vegetation types in northwestern China, which had high vulnerability. Vulnerability was stronger in winter than in summer. Our results are generally in accord with the scenario-based projections on the geographical pattern of vegetation vulnerability to climate change, and revealed the difference caused by not considering moisture. The risks for these fragmented and narrow-range ecosystems are highlighted, and the importance of natural resilience is stressed for the assessment of vegetation vulnerability to climate change. Given the inadequate coverage of the natural reserve network in China (after the large investment in recent decades) found in the high-vulnerability vegetation types (with a few exceptions), the assessment of natural resilience of ecosystems could be critical for the optimal design of socio-economic strategies in response to the impacts of future climate change.     

The role of vegetation in methane flux to the atmosphere: should vegetation be included as a distinct category in the global methane budget?

Currently, the global annual flux of methane (CH₄) to the atmosphere is fairly well constrained at ca. 645 Tg CH₄ year^?1. However, the relative magnitudes of the fluxes generated from different natural (e.g. wetlands, deep seepage, hydrates, ocean sediments) and anthropogenic sources remain poorly resolved. Of the identified natural sources, the contribution of vegetation to the global methane budget is arguably the least well understood. Historically, reviews of the contribution of vegetation to the global methane flux have focused on the role of plants as conduits for soil-borne methane emissions from wetlands, or the aerobic production of methane within plant tissues. Many recent global budgets only include the latter pathway (aerobic methane production) in estimating the importance of terrestrial vegetation to atmospheric CH₄ flux. However, recent experimental evidence suggests several novel pathways through which vegetation can contribute to the flux of this globally important, trace greenhouse gas (GHG), such as plant cisterns that act as cryptic wetlands, heartwood rot in trees, the degradation of coarse woody debris and litter, or methane transport through herbaceous and woody plants. Herein, we synthesize the existing literature to provide a comprehensive estimate of the role of modern vegetation in the global methane budget. This first, albeit uncertain, estimate indicates that vegetation may represent up to 22 % of the annual flux of methane to the atmosphere, contributing ca. 32–143 Tg CH₄ year^?1 to the global flux of this important trace GHG. Overall, our findings emphasize the need to better resolve the role of vegetation in the biogeochemical cycling of methane as an important component of closing the gap in the global methane budget.     

Hydrodynamics of bolus flow—An analytical approach to blood flow in capillaries

A model which was used by Prothero and Burton to simulate a particular configuration in capillary blood vessels is investigated from a hydrodynamic point of view. In this model, the erythrocytes are approximated by rigid pistons, and plasma is assumed to be an incompressible Newtonian fluid. An order of magnitude analysis using the physiologically realistic values for various parameters reduces the exact equations of motion to an equation describing the creeping motion of the fluid. An analytical approach to the solution of the equation is proposed and some results are reported here. The solution of the flow field is given in terms of a stream function which is represented by two infinite series composed of known functions. Two coupled infinite systems of algebraic equations determining the coefficients of the two series have been derived. This method of solution is proposed as an alternative to the entirely numerical procedure of solving the similar problem proposed by Bugliarelloet al. A limiting case of large aspect ratio (the ratio of the axial spacing of the two successive erythrocytes to the capillary diameter) is studied and the solution, valid away from the erythrocyte surface, has been obtained in simple form. It resembles the classical Poisenille flow, but the pressure gradient is related to the erythrocyte speed.     

The role of outcrops in the diversity of Patagonian vegetation: Relicts of glacial palaeofloras?

Outcrops around the world enhance biodiversity as they provide heterogeneous environments and varied habitats for species with different requirements than those living in the surroundings, and in this way they increase alpha and beta diversity. We studied the floristic composition of the vegetation of rock outcrops in northwestern Patagonia, Argentina, and compared them to the surrounding matrix of shrubland and steppe. For this we sampled 50 outcrops and 50 matrix plots close to them, identified all the species present, and analyzed their floristic composition with Detrended Correspondence Analysis (DCA). We also analyzed the floras of the north and south faces of the outcrops. The resulting ordinations were related to geographic gradients of the region. The proportions of alien to native species, different life forms, and phylogenetic groups of the outcrop floras were compared to the matrix with G-tests. Our results showed similar dominant families, life form proportions and percentage of alien species in the outcrops and the surrounding matrix. However, species composition of the outcrops was markedly different. North Patagonian outcrops present several taxa not found in the matrix, especially in their southern, less insolated walls. The previously recorded distribution of most of these exclusive species is found in colder areas further south. Thus, we hypothesize that outcrops could be acting as relicts of cold-adapted glacial paleofloras that were probably more extended during glacial times and retreated south after the last glacial maximum.     

The ordered secretion of bioactive peptides: oldest or newest first?

The order of secretion of newly synthesized and older bioactive peptides was investigated using primary rat intermediate pituitary melanotropes, which synthesize, store, and secrete peptides derived from pro-ACTH/endorphin (PAE; also POMC). PAE-derived peptides produced by the cells were biosynthetically labeled by incubating the cells with radioactive amino acids at various times preceding the period during which secretion was examined; secreted and cellular peptides were characterized and quantitated by immunoprecipitation, using affinity-purified antibodies to selected regions of PAE, followed by polyacrylamide gel electrophoretic analysis. Release in the absence of secretagogues (basal or constitutive release) was compared to release in the presence of maximally effective levels of 8-bromo-cAMP and BaCl2 (stimulated or regulated release). Both cell types showed short-lived preferential basal release of newly synthesized and not fully mature peptides (less than 2-3 h old). Conversely, the cells showed preferential stimulated secretion of older peptides. A process of maturation occurred, taking 2-4 h, after which the secretion of newly synthesized and older peptides in response to secretagogues was nearly indistinguishable for the smallest product peptides. The data support a model of gradual processing of peptides from precursors into smaller products and maturation from molecules only available for basal release into peptides available for stimulated secretion as well as for basal release. Basal secretion was found to include mature peptides as well as intermediates and precursor molecules. The data do not support the existence of any preferential regulated secretion of newly synthesized peptides.     

The genomics of local adaptation in trees: are we out of the woods yet?

There is substantial interest in uncovering the genetic basis of the traits underlying adaptive responses in tree species, as this information will ultimately aid conservation and industrial endeavors across populations, generations, and environments. Fundamentally, the characterization of such genetic bases is within the context of a genetic architecture, which describes the mutlidimensional relationship between genotype and phenotype through the identification of causative variants, their relative location within a genome, expression, pleiotropic effect, environmental influence, and degree of dominance, epistasis, and additivity. Here, we review theory related to polygenic local adaptation and contextualize these expectations with methods often used to uncover the genetic basis of traits important to tree conservation and industry. A broad literature survey suggests that most tree traits generally exhibit considerable heritability, that underlying quantitative genetic variation (Q_ST) is structured more so across populations than neutral expectations (F_ST) in 69% of comparisons across the literature, and that single-locus associations often exhibit small estimated per-locus effects. Together, these results suggest differential selection across populations often acts on tree phenotypes underlain by polygenic architectures consisting of numerous small to moderate effect loci. Using this synthesis, we highlight the limits of using solely single-locus approaches to describe underlying genetic architectures and close by addressing hurdles and promising alternatives towards such goals, remark upon the current state of tree genomics, and identify future directions for this field. Importantly, we argue, the success of future endeavors should not be predicated on the shortcomings of past studies and will instead be dependent upon the application of theory to empiricism, standardized reporting, centralized open-access databases, and continual input and review of the community’s research.     

Application of laccase-natural mediator systems to sisal pulp: An effective approach to biobleaching or functionalizing pulp fibres?

The effects of laccase-natural mediator systems (LMS) on sisal pulp and their potential for either biobleaching or functionalizing (via radical-coupling) its fibres were investigated. The enzyme treatment (L stage) was followed by extraction with hydrogen peroxide in order to determine whether observable effects could be enhanced by removing LMS-modified lignin. Four different plant phenols [viz. the p-hydroxycinnamic compounds sinapic acid (SNC), ferulic acid (FRC), coniferyl aldehyde (CLD) and sinapyl aldehyde (SLD)] were used as laccase redox mediators and their effects on pulp and effluents compared with those of the synthetic compound 1-hydroxybenzotriazole (HBT). During the L stage performed with HBT, laccase underwent a loss of 99% and 78% of the initial activity, in the absence and presence of pulp, respectively. With natural mediators inactivation was markedly reduced, being the residual activity between 65% and 100% of the initial one, in the presence of pulp. The pulp was found to protect the enzyme against inactivation: the activity was only reduced by 45% in its presence. Under the operating conditions used the natural mediators proved less efficient than HBT in facilitating pulp bleaching; rather, they tended to bind to pulp fibres. This effect could be used to functionalize fibres in order to improve intrinsic properties of pulp or introducing novel ones (e.g. antimicrobial, antioxidant, optical properties, etc.). This paper shows for the first time the application of laccase-mediator systems to sisal pulp.     

Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis

A number of observations have led researchers to postulate that, despite being replication‐defective, human endogenous retroviruses (HERVs) may have retained the potential to cause or contribute to disease. However, mechanisms of HERV pathogenicity might differ substantially from those of modern infectious retroviruses or of the infectious precursors of HERVs. Therefore, novel pathways of HERV involvement in disease pathogenesis should be investigated. Recent technological advances in sequencing and bioinformatics are making this task increasingly feasible. The accumulating knowledge of HERV biology may also facilitate the definition and general acceptance of criteria that establish HERV pathogenicity. Here, we explore possible mechanisms whereby HERVs may cause disease and examine the evidence that either has been or should be obtained in order to decisively address the pathogenic potential of HERVs.