Improvement of growth conditions and gas exchange of<Emphasis Type="Italic"> Fagus sylvatica</Emphasis> L. seedlings planted below a recently thinned<Emphasis Type="Italic"> Pinus sylvestris</Emphasis> L. stand

Abstract Gas exchange and growth of beech seedlings planted in the understory of a recently thinned pinewood were recorded for 2 years. Relative irradiance was assessed by hemispherical photographs taken just after the thinning. Predawn water potential (_pd), daily gas exchange and chlorophyll fluorescence were measured several times during the two growing seasons. Maximum values of photosynthesis (A _max) and stomatal conductance to water vapour (g _wvmax) were established from daily data. Maximum quantum efficiency of PS II was recorded at dawn by taking the variable to maximum chlorophyll fluorescence ratio on dark adapted leaves (F _v/F _m). In the middle of each summer, leaf nitrogen content and leaf mass per area were evaluated, and height growth and basal area increment were recorded at the end of the season. The thinning treatment removed half the trees and generated around 10% more available relative irradiance (GLF). This was followed by an increase in net photosynthesis at saturating PPFD (A _sat) and in maximum stomatal conductance to water vapour (g _wvmax). Moreover, specific leaf mass (SLM) and mass based nitrogen content (N_m) showed higher values for seedlings in the thinned stand. In both years, a positive relationship was established between the area based nitrogen content (N_a) and maximum net photosynthesis (A _max). In 1998, a year with a dry summer, seedlings suffered a significant drop in daily A _max irrespective of the thinning regime. This was a response to an increase in stomatal limitation to net photosynthesis, g _wvmax reaching the lowest value on dates with the highest drought. A lack of decrease of Fv/Fm confirmed the absence of significant non-stomatal limitation to A as a consequence of photoinhibition after opening the pinewood. A higher maximum quantum efficiency of open PS II centres (Fv/Fm) was registered in seedlings in the thinned stand. The significance of the differences between the treatments was stronger in the second year after thinning. In 1999, a year with frequent summer storms, water availability increased for seedlings growing under the thinned pinewood. Overall, the reduced pine overstory had a positive effect on physiological responses of beech seedlings, which was translated into improved seedling growth.     

Individual Pause-and-Go Motion Is Instrumental to the Formation and Maintenance of Swarms of Marching Locust Nymphs

The principal interactions leading to the emergence of order in swarms of marching locust nymphs was studied both experimentally, using small groups of marching locusts in the lab, and using computer simulations. We utilized a custom tracking algorithm to reveal fundamental animal-animal interactions leading to collective motion. Uncovering this behavior introduced a new agent-based modeling approach in which pause-and-go motion is pivotal. The behavioral and modeling findings are largely based on motion-related visual sensory inputs obtained by the individual locust. Results suggest a generic principle, in which intermittent animal motion can be considered as a sequence of individual decisions as animals repeatedly reassess their situation and decide whether or not to swarm. This interpretation implies, among other things, some generic characteristics regarding the build-up and emergence of collective order in swarms: in particular, that order and disorder are generic meta-stable states of the system, suggesting that the emergence of order is kinetic and does not necessarily require external environmental changes. This work calls for further experimental as well as theoretical investigation of the neural mechanisms underlying locust coordinative behavior.     

The PHA Test as an Indicator of Phagocytic Activity in a Passerine Bird

Several techniques in ecological immunology have been used to assess bird immunocompetence thus providing useful information to understand the contribution of the immunological system in life-history decisions. The phytohaemagglutinin (PHA)-skin test has been the most widely employed technique being interpreted as the sole result of T lymphocytes proliferation and hence used to evaluate acquired immunological capacity. However, the presence of high numbers of phagocytic cells in the swelling point has cast some doubt about such an assumption. To address this issue, we collected blood from 14 days-old nestlings of spotless starling (Sturnus unicolor), administered subcutaneous PHA immediately after and then measured the swelling response 24 hours later. Differential counts of white blood cells suggested that an intense development of acquired immunological defences was taking place. The phagocytic activity of both heterophiles and monocytes was also very intense as it was the swelling response. Moreover, our results show, for the first time in birds, a positive relationship between the phagocytic activity of both kinds of cells and the swelling response. This broadens the significance of the PHA test from reflecting T lymphocytes proliferation -as previously proposed but still undetermined in vivo- to evaluate phagocytosis as well. In other words, our data suggest that the PHA swelling response may not be considered as the only consequence of processes of specific and induced immunity –T lymphocytes proliferation- but also of constitutive and nonspecific immunity –heterophiles and monocytes phagocytosis. We propose the extensive use of PHA-skin test as an optimal technique to assess immunocompetence.     

Productivity in Physical and Chemical Science Predicts the Future Economic Growth of Developing Countries Better than Other Popular Indices

Scientific productivity of middle income countries correlates stronger with present and future wealth than indices reflecting its financial, social, economic or technological sophistication. We identify the contribution of the relative productivity of different scientific disciplines in predicting the future economic growth of a nation. Results show that rich and poor countries differ in the relative proportion of their scientific output in the different disciplines: countries with higher relative productivity in basic sciences such as physics and chemistry had the highest economic growth in the following five years compared to countries with a higher relative productivity in applied sciences such as medicine and pharmacy. Results suggest that the economies of middle income countries that focus their academic efforts in selected areas of applied knowledge grow slower than countries which invest in general basic sciences.     

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to “reproducibility maps” that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one’s own laboratory.     

Bee Products Prevent Agrichemical-Induced Oxidative Damage in Fish

In southern South America and other parts of the world, aquaculture is an activity that complements agriculture. Small amounts of agrichemicals can reach aquaculture ponds, which results in numerous problems caused by oxidative stress in non-target organisms. Substances that can prevent or reverse agrichemical-induced oxidative damage may be used to combat these effects. This study includes four experiments. In each experiment, 96 mixed-sex, 6-month-old Rhamdia quelen (118±15 g) were distributed into eight experimental groups: a control group that was not exposed to contaminated water, three groups that were exposed to various concentrations of bee products, three groups that were exposed to various concentrations of bee products plus tebuconazole (TEB; Folicur 200 CE™) and a group that was exposed to 0.88 mg L⁻¹ of TEB alone (corresponding to 16.6% of the 96-h LC₅₀). We show that waterborne bee products, including royal jelly (RJ), honey (H), bee pollen (BP) and propolis (P), reversed the oxidative damage caused by exposure to TEB. These effects were likely caused by the high polyphenol contents of these bee-derived compounds. The most likely mechanism of action for the protective effects of bee products against tissue oxidation and the resultant damage is that the enzymatic activities of superoxide dismutase (SOD), catalase (CAT) and glutathione-S-transferase (GST) are increased.     

Recent advances in extraction and analysis procedures of natural chlorogenic acids

Phytochemistry Reviews - Chlorogenic acids (CQAs), the esters of caffeic and quinic acid, are biologically important phenolic compounds present in many plant species. Nowadays the knowledge about...     

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

Background  

The alignment of biological sequences is of chief importance to most evolutionary and comparative genomics studies, yet the two main approaches used to assess alignment accuracy have flaws: reference alignments are derived from the biased sample of proteins with known structure, and simulated data lack realism.     

The effects of pH on glucosinolate degradation by a thioglucoside glucohydrolase preparation

An active thioglucoside glucohydrolase extract was prepared from commercial mustard powder and its effect on the degradation of two pure glucosinolates was investigated. During reaction in a distilled water medium the pH of the solution decreased markedly and the ratio of products (isothiocyanate and nitrile) varied considerably. After 20–30 min, when the pH had fallen to ca 5.6, isothiocyanate production ceased whilst nitrile continued to be produced and in amounts which increased linearly with time for at least 40 min. This behaviour can be correlated with the changing pH of the medium. In controlled pH experiments it was confirmed that nitrile formation is favoured at lower pH levels and that the ratio of nitrile to isothiocyanate is directly related to the hydrogen ion concentration of the medium. No reason could therefore be found for the observed formation of nitrile in some natural systems at pHs greater than 7.     

Nitrate removal by immobilized cells of Phormidium uncinatum in batch culture and a continuous-flow photobioreactor

Cells of the non-N₂-fixing cyanobacterium Phormidium uncinatum were immobilized by adsorption into polyvinyl (PV-50) foam pieces. The effect of inoculum size as well as the initial inoculum/support ratio on the cell immobilization process was investigated. After 2 months of immobilization similar net O₂-exchange activity was measured in immobilized and free-living cells. Polyvinyl-adsorbed cells also showed similar nitrate uptake capacity to free-living cells. Nitrogen starvation promoted a remarkable increase in nitrate uptake rate of both free-living and immobilized cells. A lab-scale photobioreactor packed with polyvinyl foam pieces colonized in situ by cells was used for nitrate removal in a continuous mode. In the best working conditions found, nearly 90% of nitrate supplied in the influent (50 mg l^–1) was removed by cells having a residence time of 3–4 h. Correspondence to: J. L. Serra