How to increase juvenile shrimps in mangrove waters?

The distribution, density and species composition of juvenile shrimps were studied in three mangrove zones of Pichavaram, situated on the southeast coast of India. Nine species of shrimps dominated with Metapenaeus monoceros, M. brevicornis and Penaeus indicus were recorded. This shrimp resource was higher in mangrove-lined waters than that in neritic waters. This field observation was experimentally proved using litter bags. The average catch around the litter bags was 0.80 individuals day^–1 for Rhizophora leaves, 1.6 ind. day^–1 for Avicennia leaves and 0.16 ind. day^–1 in control. In general, abundance of juvenile shrimps was the highest around the leaves that were decomposed for 40 days and colonized with high counts of nitrogen-fixing azotobacters. Finally, a vegetation trap technique using mangrove leaves has been proposed for efficient schooling of juvenile shrimps. There was about 3-fold increase in number of shrimp juveniles around the trap than at control waters.     

How to ‘catch’ floating populations? Research and the fixing of migration in space and time

Abstract

The recent ‘mobilities turn’ in the social sciences suggests that research always fixes mobility somehow in time and space, in order to understand it. Migration, being a form of mobility, has to be fixed on certain times and spaces in order to make it possible to define and research it. Being a geographer, I build on this insight in the first part of the article to re-read the critiques on post-war methodological nationalism. Reflecting on my own past research practice, I argue in the second part that leaving behind the methodological nationalism paradigm does not mean leaving behind the necessity to fix migration in time and space, on either the ontological or the practical methodological level. New ways of fixing are chosen and, out of recurring ontological and methodological choices, new migration stereotypes are developing such as what might be called ‘methodological ruralism’ in the case of Romanian migration.     

How do weeds differ in their response to the timing of tillage? A study of 61 species across the northeastern United States

Previous research has demonstrated that the season in which soil is tilled (spring versus fall) can strongly influence weed community assembly and subsequent species composition and abundance in annual cropping systems. Despite this understanding, it is unknown whether finer‐scale, within‐season variation in the timing of tillage has similar impacts on weed community assembly. We conducted an experiment on four research farms across the northeastern USA to test the effects of tillage timing on weed emergence periodicity. Soil was tilled at 12 different times that were 2 weeks apart from 29 April to 30 September (the entire growing season) and the composition and abundance of the weed seedlings that emerged was measured 6 weeks later. Weed species clustered into three tillage timing groups at the two New York locations and clustered into five tillage timing groups at the New Hampshire and Maine locations. Individual species associated with each window of tillage time varied by location. No single trait or combination of traits were consistently associated with species‐by‐tillage time groupings across locations; however, within each location several traits were associated with particular groups of species, including: (a) seed length, (b) seed weight, (c) cotyledon type, (d) life span, (e) ploidy level and (f) photosynthetic pathway. These results suggest that fine‐scale variation in the timing of tillage can lead to predictable changes in the species composition and trait distribution of weed communities in annually tilled agroecosystems.     

The shape of things to come in the study of the origin of species?

Perhaps Darwin would agree that speciation is no longer the mystery of mysteries that it used to be. It is now generally accepted that evolution by natural selection can contribute to ecological adaptation, resulting in the evolution of reproductive barriers and, hence, to the evolution of new species (Schluter & Conte 2009 ; Meyer 2011 ; Nosil 2012 ). From genes that encode silencing proteins that cause infertility in hybrid mice (Mihola et al. 2009 ), to segregation distorters linked to speciation in fruit flies (Phadnis & Orr 2009 ), or pollinator‐mediated selection on flower colour alleles driving reinforcement in Texan wildflowers (Hopkins & Rausher 2012 ), characterization of the genes that drive speciation is providing clues to the origin of species (Nosil & Schluter 2011 ). It is becoming apparent that, while recent work continues to overturn historical ideas about sympatric speciation (e.g. Barluenga et al. 2006 ), ecological circumstances strongly influence patterns of genomic divergence, and ultimately the establishment of reproductive isolation when gene flow is present (Elmer & Meyer 2011 ). Less clear, however, are the genetic mechanisms that cause speciation, particularly when ongoing gene flow is occurring. Now, in this issue, Franchini et al. ( 2014 ) employ a classic genetic mapping approach augmented with new genomic tools to elucidate the genomic architecture of ecologically divergent body shapes in a pair of sympatric crater lake cichlid fishes. From over 450 segregating SNPs in an F2 cross, 72 SNPs were linked to 11 QTL associated with external morphology measured by means of traditional and geometric morphometrics. Annotation of two highly supported QTL further pointed to genes that might contribute to ecological divergence in body shape in Midas cichlids, overall supporting the hypothesis that genomic regions of large phenotypic effect may be contributing to early‐stage divergence in Midas cichlids.     

How to localize epigenetics in the landscape of biological research?

Today, epigenetics is a very fashionable field of research. Modification of DNA by methylation, and of chromatin by histone modification or substitution represents a major fraction of the studies; but this special issue shows that epigenetic studies are very diverse, and not limited to the study of chromatin. What is common behind these different uses of the word epigenetics? A brief historical survey shows that epigenetics was invented twice, with different meanings: in the 1940s, by Conrad Waddington, as the study of the relations between the genotype and the phenotype; in the 1960s, as the global mechanisms of gene regulation involved in differentiation and development; what is common is that an approach distinct from genetics was in both cases considered as necessary because genetic models were incapable to address these problems. A good way to appreciate the relations between genetics and epigenetics is to realize that the main aim of organisms is to reproduce, and to consider the way organisms perform this task. Genetics is the precise means organisms have invented to reproduce the structure of their macromolecular components; the genome is also used to control the level and place of this reproduction. All the other means organisms have used to reproduce were more or less the result of tinkering, and constitute the field of epigenetics, with its diversity and richness.     

How to contend with paraphyly in the taxonomy of the delphinine cetaceans?

Molecular phylogenetic analyses conducted over the past 15 yr have consistently had difficulties resolving relationships among the cetacean species in the subfamily Delphininae. In addition, paraphyly of the genera Tursiops and Stenella in these molecular phylogenies has been a recurrent problem since the first appearance of such a phylogeny in 1999, suggesting that these genera do not accurately reflect the evolutionary relationships of the species they contain. Morphological analyses have not resolved the issues. The genera in Delphininae originated in the 19th Century on questionable morphological grounds. The species were nearly all originally described in the genus Delphinus of Linnaeus. Recent molecular phylogenies based on various mitochondrial and nuclear DNA markers have suggested a wide range of possible relationships among these taxa, and several authors have suggested synonymizing all the taxa (Lagenodelphis, Stenella, Sousa, and Tursiops) under Delphinus. Until molecular and/or morphological analyses adequately sort out relationships in this very recently radiated group, one possible solution indeed would be to merge all the delphinine genera with Delphinus. Implications of such a move and alternatives are discussed.

Editor's Note: Papers from past Norris Award winners have primarily been a revised or reduced version of the actual presentation given as a plenary talk at the biennial conference. Dr. Perrin requested being allowed to take a topic from his presentation and expand on it to present a set of ideas in the form of an essay that could pass the rigors of the peer‐review process. As a result, this Norris Award paper has undergone peer‐review and has taken longer than usual for a Norris Award paper to appear in the journal following its presentation at the biennial conference. It also has co‐authors, with varying opinions on the issues discussed in the essay, to cover appropriately and more thoroughly those components of the paper that required additional expertise. I believe this approach has produced an excellent, thought‐provoking essay and is an approach that should be available to future Norris Award winners if they so choose to take it. Since this essay is meant to elicit dialogue, comments are welcome and will be considered for publication in Letters to the Editor.

     

How to prove the existence of metabolons?

Sequential enzymes in biosynthetic pathways are organized in metabolons. It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein–protein interactions. Many different methods are being applied, each with strengths and weaknesses. We will present and evaluate several techniques that have been applied in providing evidence for the orchestration of the biosynthetic pathways of cyanogenic glucosides and glucosinolates in metabolons. These evolutionarily related pathways have ER-localized cytochromes P450 that are proposed to function as anchoring site for assembly of the enzymes into metabolons. Additionally, we have included commonly used techniques, even though they have not been used (yet) on these two pathways. In the review, special attention will be given to less-exploited fluorescence-based methods such as FCS and FLIM. Ultimately, understanding the orchestration of biosynthetic pathways may contribute to successful engineering in heterologous hosts.     

How is the indentation modulus of bone tissue related to its macroscopic elastic response? A validation study

This work consists of the validation of a novel approach to estimate the local anisotropic elastic constants of the bone extracellular matrix using nanoindentation. For this purpose, nanoindentation on two planes of material symmetry were analyzed and the resulting longitudinal elastic moduli compared to the moduli measured with a macroscopic tensile test. A combined lathe and tensile system was designed that allows machining and testing of cylindrical microspecimens of approximately 4mm in length and 300 microm in diameter. Three bovine specimens were tested in tension and their outer geometry and porosity assessed by synchrotron radiation microtomography. Based on the results of the traction test and the precise outer geometry, an apparent longitudinal Young's modulus was calculated. Results between 20.3 and 27.6 GPa were found that match with previously reported values for bovine compact bone. The same specimens were then characterized by nanoindentation on a transverse and longitudinal plane. A longitudinal Young's modulus for the bone matrix was then derived using the numerical scheme proposed by Swadener and Pharr and the fabric-elasticity relationship by Zysset and Curnier. Based on the matrix modulus and a power law effective volume fraction, an apparent longitudinal Young's modulus was predicted for each microspecimen. This alternative approach provided values between 19.9 and 30.0 GPa, demonstrating differences between 2% and 13% to the values provided by the initial tensile test. This study therefore raises confidence in our nanoindentation protocol of the bone extracellular matrix and supports the underlying hypotheses used to extract the anisotropic elastic constants.     

How predictable are the responses of ant and dung beetle assemblages to patch and landscape attributes in fragmented tropical forest landscapes?

Landscape and Ecological Engineering - One of the most effective means of evaluating the effects of habitat loss and landscape configuration is to assess the response of bioindicators. The present...     

How to model the events in cutaneous fibrosis?

Skin fibrosis is classically seen as the consequence of chronic inflammation and altered healing response that is characterized by the differentiation of fibroblasts into secretory myofibroblasts and accumulation of connective tissue. Although fibrosis severely affects organ function and causes esthetic defects, no effective therapy is currently available to attenuate the fibrogenic process probably because the fibrogenic process is more complex than previously thought. Indeed, it might involve several interacting and mutually dependent cell types (fibroblasts, keratinocytes, endothelial cells, inflammatory cells), numerous paracrine factors, bio-active molecules and micro-environmental stimuli (growth factors, vasoactive peptides, balance between pro- and anti-inflammatory cytokines, coagulation system, reactive oxygen species, extracellular matrix...). In this perspective, the traditional approach that model individual cell response in simple cell culture system is probably inadequate and too simplistic. This article reviews the new models used to study skin fibrosis in vitro, in organotypic culture systems and in vivo and examines how these different models might be used to identify new molecular pathways involved in fibrogenesis. The monolayer cultures allow the study of fibrogenic signals induced by a single factor on a single cell type. Isolation of cells from fibrotic tissue allows to define the fibrogenic differentiation acquired in vivo. The organotypic models allow cell to cell and cell to matrix interaction and the experimental models in pigs and mice allowed studies in integrated physiological systems. These various and complementary models would also provide new tools to develop and test new drugs and treatments.     

How does GAP catalyze the GTPase reaction of Ras? A computer simulation study

The formation of a complex between p21(ras) and GAP accelerates the GTPase reaction of p21(ras) and terminates the signal for cell proliferation. The understanding of this rate acceleration is important for the elucidation of the role of Ras mutants in tumor formation. In principle there are two main options for the origin of the effect of GAP. One is a direct electrostatic interaction between the residues of GAP and the transition state of the Ras-GAP complex and the other is a GAP-induced shift of the structure of Ras to a configuration that increases the stabilization of the transition state. This work examines the relative importance of these options by computer simulations of the catalytic effect of Ras. The simulations use the empirical valence bond (EVB) method to study the GTPase reaction along the alternative associative and dissociative paths. This approach reproduces the trend in the overall experimentally observed catalytic effect of GAP: the calculated effect is 7 +/- 3 kcal/mol as compared to the observed effect of approximately 6.6 kcal/mol. Furthermore, the calculated effect of mutating Arg789 to a nonpolar residue is 3-4 kcal/mol as compared to the observed effect of 4.5 kcal/mol for the Arg789Ala mutation. It is concluded, in agreement with previous proposals, that the effect of Arg789 is associated with its direct interaction with the transition state charge distribution. However, calculations that use the coordinates of Ras from the Ras-GAP complex (referred to here as Ras') reproduce a significant catalytic effect relative to the Ras coordinates. This indicates that part of the effect of GAP involves a stabilization of a catalytic configuration of Ras. This configuration increases the positive electrostatic potential on the beta-phosphate (relative to the corresponding situation in the free Ras). In other words, GAP stabilizes the GDP bound configuration of Ras relative to that of the GTP-bound conformation. The elusive oncogenic effect of mutating Gln61 is also explored. The calculated effect of such mutations in the Ras-GAP complex are found to be small, while the observed effect is very large (8.7 kcal/mol). Since the Ras is locked in its Ras-GAP configuration in our simulations, we conclude that the oncogenic effect of mutation of Gln61 is indirect and is associated most probably with the structural changes of Ras upon forming the Ras-GAP complex. In view of these and the results for the Ras' we conclude that GAP activates Ras by both direct electrostatic stabilization of the transition state and an indirect allosteric effect that stabilizes the GDP-bound form. The present study also explored the feasibility of the associative and dissociative mechanism in the GTPase reaction of Ras. It is concluded that the reaction is most likely to involve an associative mechanism.     

How to determine the susceptibility of Meligethes aeneus to neonicotinoids?

Three different bioassays were used to determine the susceptibility to the neonicotinoid Biscaya^® of oilseed rape pollen beetles collected from fields in Bavaria. The one in which the test substance was applied to the inner wall of glass tubes is recommended for future studies on pollen beetles because it is not dependent on the availability of plant material and provides precise information on the amount of insecticide required per unit area.     

Applying GPS to the study of primate ecology: A useful tool?

Data on the spatiotemporal distribution of resources can be collected and plotted using GPS (global positioning system) and GIS (geographical information system) technologies. By combining such data with information on foraging and ranging behavior of nonhuman primates, one can analyze the influence of resource distribution on social organization and group cohesion. We investigated the abilities of a three-channel GPS receiver to collect location data under varying canopy densities in both temperate and tropical forests. Eighty randomly selected points were sampled in a beech–maple forest in northeast Ohio, USA; 65 points also were sampled at several tropical forests in Costa Rica and Trinidad. At each point we attempted to obtain a GPS position fix; we also determined the speed of satellite acquisition and measured canopy density using a spherical densiometer. The ability to obtain a reading differed greatly between the two forest types (χ² = 53.79, P < 0.001). Ninety-seven percent of all attempts were successful in the temperate forest, whereas only a 34% acquisition rate was obtained in the tropical forests. Logistic regression showed that the probability of obtaining a reading in Neotropical forests was 75% but only when canopy cover was less than 20%. Thus, these minimal-channel GPS units may be of limited utility for behavioral ecologists working in closed-canopy Neotropical forests. Am. J. Primatol. 46:167–172, 1998. © 1998 Wiley-Liss, Inc.