Perspectives from early career researchers on the publication process in ecology – a response to Statzner & Resh (2010)

1. Two senior ecologists summarised their experience of the scientific publication process ( Statzner & Resh, Freshwater Biology, 2010 ; 55 , 2639) to generate discussion, particularly among early career researchers (ECRs). As a group of eight ECRs, we comment on the six trends they described. 2. We generally agree with most of the trends identified by Statzner & Resh (2010) , but also highlight a number of divergent perspectives and provide recommendations for change. Trends of particular concern are the use of inappropriate metrics to evaluate research quality (e.g. impact factor) and the salami slicing of papers to increase paper count. We advocate a transparent and comprehensive system for evaluating the research. 3. We stress the importance of impartiality and independence in the peer review process. We therefore suggest implementation of double‐blind review and quality control measures for reviewers and possibly editors. Besides such structural changes, editors should be confident to overrule biased reviewer recommendations, while reviewers should provide helpful reviews but be explicit if a submission does not meet quality standards. Authors should always conduct a thorough literature search and acknowledge historical scientific ideas and methods. Additionally, authors should report low‐quality copy editing and reviews to the editors. 4. Both early and late career researchers should jointly implement these recommendations to reverse the negative trends identified by Statzner & Resh (2010) . However, more senior scientists will always have to take the lead with respect to structural changes in the publication system given that they occupy the majority of decision‐making positions.     

Interspecies variation in nitrogen uptake kinetic responses of temperate forest species to elevated CO2: potential causes and consequences

Despite the recognition that the capacity to acquire N is critical in plant response to CO₂ enrichment, there is little information on how elevated CO₂ affects root N uptake kinetics. The few available data indicate a highly variable pattern of response to elevated CO₂, but it is presently unclear if the observed inconsistencies are caused by differences in experimental protocols or by true species differences. Furthermore, if there are interspecific variations in N uptake responses to elevated CO₂, it is not clear whether these are associated with different functional groups. Accordingly, we examined intact root‐system NH₄⁺ and NO₃^– uptake kinetic responses to elevated CO₂ in seedlings of six temperate forest tree species, representing (i) fast‐ vs. slow‐growers and (ii) broad‐leaves vs. conifers, that were cultured and assayed in otherwise similar conditions. In general, the species tested had a higher uptake capacity (V_max) for NH₄⁺ than for NO₃^–. Species substantially differed in their NO₃^– and NH₄⁺ uptake capacities, but the interspecific differences were markedly greater for NO₃^– than NH₄⁺ uptake. Elevated CO₂ had a species‐dependent effect on root uptake capacity for NH₄⁺ ranging from an increase of 215% in Acer negundo L. to a decrease of about 40% in Quercus macrocarpa Michx. In contrast, NO₃^– uptake capacity responded little to CO₂ in all the species except A. negundo in which it was significantly down‐regulated at elevated CO₂. Across species, the capacity for NH₄⁺ uptake was positively correlated with the relative growth rate (RGR) of species; however, the CO₂ effect on NH₄⁺ uptake capacity could not be explained by changes in RGR. The observed variation in NH₄⁺ uptake response to elevated CO₂ was also inconsistent with life‐form differences. Other possible mechanisms that may explain why elevated CO₂ elicits a species‐specific response in root N uptake kinetics are discussed. Despite the fact that the exact mechanism(s) for such interspecific variation remains unresolved, these differences may have a significant implication for competitive interactions and community responses to elevated CO₂ environment. We suggest that differential species responses in nutrient uptake capacity could be one potential mechanism for the CO₂‐induced shifts in net primary productivity and species composition that have been observed in experimental communities exposed to elevated levels of CO₂.     

The ecology of the River Endrick: present status and changes since 1960

Long-term changes in water quality, sources of pollution, and the fish and benthic macroinvertebrate communities in the River Endrick catchment are described. The conservation status and management of the river are discussed and the need for research on nutrient loadings and the impact of recent fish introductions is emphasized.     

Sinistral snail shells in the sea: developmental causes and consequences

The paucity of sinistral (left-coiling) relative to dextral (right-coiling) species of gastropods in the marine realm is an enigma. In Conus , one of the most diverse marine animal genera, sinistral shell coiling has evolved as a species-wide character only once. Fossils of this species, Conus adversarius , are found in Upper Pliocene and lowermost Pleistocene deposits in the southeastern USA. Conus adversarius had nonplanktonic larval development; this may have been a critical factor for the early establishment of the species, as well as sinistral marine species in other clades. Notably, most specimens of aberrantly sinistral modern Conus are derived from typically dextral species that have nonplanktonic development. If C. adversarius was reproductively isolated from dextral conspecifics, then this species may provide an example of nearly instantaneous sympatric speciation in the fossil record. Furthermore, the common and widespread – while geologically short-lived – fossil shells of C. adversarius show large amounts of variability in form and this variation may be related, at least in part, to a pleiotropic effect associated with the reversed coiling direction of this species.     

Fraud and misconduct in science: the stem cell seduction

Scientific misconduct and fraud occur in science. The (anonymous) peer review process serves as goalkeeper of scientific quality rather than scientific integrity. In this brief paper we describe some limitations of the peer-review process. We describe the catastrophic facts of the ‘Woo-Suk Hwang fraud case’ and raise some ethical concerns about the issue. Finally, we pay attention to plagiarism, autoplagiarism and double publications. (Neth Heart J 2009;17:25-9.)     

The causes and consequences of variation in offspring size: a case study using Daphnia

Offspring size can have large and direct fitness implications, but we still do not have a complete understanding of what causes offspring size to vary. Daphnia (water fleas) generally produce fewer and larger offspring when food is limited. Here, we use a mathematical model to show that this could be explained by either: (1) an advantage of producing larger eggs when food is limited; or (2) a lower boundary on egg volume (below which eggs do not have sufficient resources to be viable), that is similar in volume to the evolutionarily stable egg volume predicted by standard clutch size models. We tested the first possibilities experimentally by placing offspring from mothers kept at two food treatments (high and low - leading to relatively small and large eggs respectively) into two food treatments (same as maternal treatments, in a fully factorial design) and measuring their fitness (reproduction, age at maturity, and size at maturity). We also tested survival under starvation conditions of offspring produced from mothers at low and high food treatments. We found that (larger) offspring produced by low-food mothers actually had lower fitness as they took longer to reproduce, regardless of their current food treatment. Additionally, we found no survival advantage to being born of a food-stressed mother. Consequently, our results do not support the hypothesis that there is an advantage to producing larger eggs when food is limited. In contrast, data from the literature support the importance of a lower boundary on egg size.     

Human amyloid-beta causes changes in the levels of endothelial protein kinase C and its alpha isoform in vitro

Amyloid-beta (A(beta)) deposits and neurofibrillary pathology are characteristic features of Alzheimer's disease (AD). The association of A(beta) with cerebral vessels is an intriguing feature of AD. While there is considerable evidence of altered activities of the major isoforms of protein kinase C (PKC) in the vasculature and neurons of AD brains, little is known about the relationship between the Abeta toxicity and the altered PKC levels in cerebral endothelial cells.In this study, cultured brain endothelial cells exposed to A(beta)1-40 revealed a translocation of PKC from the membrane fraction to the cytosol. The content of the isoform PKC(alpha), involved in the regulation of amyloid precursor protein (APP) secretion, was decreased in the membrane-bound fraction of rat endothelial cells and increased in the cytosol after A(beta)1-40 treatment. These data suggest that the accumulation of A(beta) peptide in the cerebral vasculature may play a significant role in the down-regulation of PKC seen in the AD cerebral vasculature.     

Energetics in Homo erectus and other early hominins: the consequences of increased lower-limb length

Previous studies of daily energy expenditure (DEE) in hominin fossils have estimated locomotor costs using a formula that was based on six species, all 18 kg or less in mass, including no primates, and that has a number of other problems when applied in an ecological context. It is well established that the energetic cost of human walking is lower than that of representative mammals, particularly for individuals with long lower limbs. The current study reevaluates the daily energy expenditures of a variety of hominin species using more appropriate approaches to estimating locomotor costs. To estimate DEE for primates, I relied on published data on body mass, day range, and the percentage of time spent in various activities. Based on those data, I calculated a value for nonlocomotor DEE. I then used a variant of a method that I have suggested elsewhere to calculate the daily cost due to locomotion (DEEL) and summed the two to calculate total DEE. The more up-to-date methods for calculating the cost of travel result in lower estimates of this aspect of the energy budget than seen in previous studies. Values obtained here for DEE in various representatives of Australopithecus are lower than reported previously by around 200 kcal/day. Taking into account the greater economy of human walking, particularly the effect of the longer lower limbs found in many later Homo species, also results in lowered estimates of DEE. Elongation of the lower limbs in H. erectus reduced relative travel costs nearly 50% in comparison to A.L. 288-1 (A. afarensis). The present method for calculating DEE indicates that female H. erectus DEE was 84% greater than that of female Australopithecus; this disparity is even larger than that suggested by previous workers.     

Harnessing the potential of the multi‐indicator palaeoecological approach: an assessment of the nature and causes of ecological change in a eutrophic shallow lake

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Historical and recent changes in the Spanish forests: A socio-economic process

The evolution of Spanish landscapes through history is mainly a story of deforestation. Through time, exploitation of natural resources increased to cope with the requirements of more and more complex civilizations. In this work, a review of how the Spanish forests were influenced by human activities and their changes is provided. Forests were cleared for mining, charcoal, shipbuilding and caulking. The most fertile lands were converted into cultivation and more productive cultivars were introduced. Mobile livestock, in particular sheep, became widespread, and with it the burning of wooded land to produce pastures. Woods were privatized through a series of disentailments. All these factors have occurred during the history of Spain, linked to profound changes in the landscape and vegetation. Not until the beginning of the 20th century were real efforts devoted to invert the trend to deforestation inherited from the negative woodland management of previous centuries.     

Automated image analysis with the potential for process quality control applications in stem cell maintenance and differentiation

The translation of laboratory processes into scaled production systems suitable for manufacture is a significant challenge for cell based therapies; in particular there is a lack of analytical methods that are informative and efficient for process control. Here the potential of image analysis as one part of the solution to this issue is explored, using pluripotent stem cell colonies as a valuable and challenging exemplar. The Cell‐IQ live cell imaging platform was used to build image libraries of morphological culture attributes such as colony “edge,” “core periphery” or “core” cells. Conventional biomarkers, such as Oct3/4, Nanog, and Sox‐2, were shown to correspond to specific morphologies using immunostaining and flow cytometry techniques. Quantitative monitoring of these morphological attributes in‐process using the reference image libraries showed rapid sensitivity to changes induced by different media exchange regimes or the addition of mesoderm lineage inducing cytokine BMP4. The imaging sample size to precision relationship was defined for each morphological attribute to show that this sensitivity could be achieved with a relatively low imaging sample. Further, the morphological state of single colonies could be correlated to individual colony outcomes; smaller colonies were identified as optimum for homogenous early mesoderm differentiation, while larger colonies maintained a morphologically pluripotent core. Finally, we show the potential of the same image libraries to assess cell number in culture with accuracy comparable to sacrificial digestion and counting. The data supports a potentially powerful role for quantitative image analysis in the setting of in‐process specifications, and also for screening the effects of process actions during development, which is highly complementary to current analysis in optimization and manufacture. © 2015 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers, 32:215–223, 2016     

Integrating individual behavior and population ecology: the potential for habitat-dependent population regulation in a reef fish

We used the predictions of the ideal free and ideal despoticdistributions (IFD and IDD, respectively) as a basis to evaluatethe link between spatial heterogeneity, behavior, and populationdynamics in a Caribbean coral reef fish. Juvenile three-spotdamselfish (Stegastes planifrons) were more closely aggregatedin patch reef habitat than on continuous back reef. Agonisticinteractions were more frequent but feeding rates were lowerin the patch versus the continuous reef habitat. Growth rateswere lower in patch reef habitat than on the continuous reef,but mortality rates did not differ. A separate experiment usingstandard habitat units demonstrated that the patterns observedin natural habitat were the result of the spatial distributionof the habitat patches rather than resource differences between habitats. Our results do not follow the predictions of simpleIFD or IDD models. This deviation from IFD and IDD predictionsmay be the result of a number of factors, including lack ofperfect information about habitat patches, high movement costs,and higher encounter rates of dispersed patches. Our resultsdemonstrate that behavioral interactions are an integral partof population dynamics and that it is necessary to considerthe spatial organization of the habitat in both behavioraland ecological investigations.     

Fungal parasitism in freshwater calanoid population: ecological consequences and possible mechanisms involved in the infection process

This paper reports the results of a study on a zoosporic fungus (Saprolegniaceae) parasitizing populations of Eudiaptomus intermedius (Copepoda, Calanoida) in mountain lakes located in the Northern Apennines, Italy. The dynamics of this infectious process was previously described in one of the lakes of the study area. The virulence is particularly high at the end of the calanoid reproductive phase, when the fungal hyphae penetrate the host eggs provoking their degeneration. Here new data are presented and the phenology of the host–parasite interaction is comparatively analyzed in different years and in different sites. The occurrence of the parasite was assessed at a regional scale. Possible mechanisms involved in the pathogen dispersal and in the host recognition are proposed, and the ecological impact of the fungal parasitism on the calanoid populations is discussed.     

Fermentanomics: Relating quality attributes of a monoclonal antibody to cell culture process variables and raw materials using multivariate data analysis

Fermentanomics is an emerging field of research and involves understanding the underlying controlled process variables and their effect on process yield and product quality. Although major advancements have occurred in process analytics over the past two decades, accurate real‐time measurement of significant quality attributes for a biotech product during production culture is still not feasible. Researchers have used an amalgam of process models and analytical measurements for monitoring and process control during production. This article focuses on using multivariate data analysis as a tool for monitoring the internal bioreactor dynamics, the metabolic state of the cell, and interactions among them during culture. Quality attributes of the monoclonal antibody product that were monitored include glycosylation profile of the final product along with process attributes, such as viable cell density and level of antibody expression. These were related to process variables, raw materials components of the chemically defined hybridoma media, concentration of metabolites formed during the course of the culture, aeration‐related parameters, and supplemented raw materials such as glucose, methionine, threonine, tryptophan, and tyrosine. This article demonstrates the utility of multivariate data analysis for correlating the product quality attributes (especially glycosylation) to process variables and raw materials (especially amino acid supplements in cell culture media). The proposed approach can be applied for process optimization to increase product expression, improve consistency of product quality, and target the desired quality attribute profile. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1586–1599, 2015     

Changing the phospholipid composition of Staphylococcus aureus causes distinct changes in membrane proteome and membrane‐sensory regulators

The dynamic lipid composition of bacterial cytoplasmic membranes has a profound impact on vital bacterial fitness and susceptibility to membrane‐damaging agents, temperature, or osmotic stress. However, it has remained largely unknown how changes in lipid patterns affect the abundance and expression of membrane proteins. Using recently developed gel‐free proteomics technology, we explored the membrane proteome of the important human pathogen Staphylococcus aureus in the presence or absence of the cationic phospholipid lysyl‐phosphatidylglycerol (Lys‐PG). We were able to detect almost half of all theoretical integral membrane proteins and could reliably quantify more than 35% of them. It is worth noting that the deletion of the Lys‐PG synthase MprF did not lead to a massive alteration but a very distinct up‐ or down‐regulation of only 1.5 or 3.5% of the quantified proteins. Lys‐PG deficiency had no major impact on the abundance of lipid‐biosynthetic enzymes but significantly affected the amounts of the cell envelope stress‐sensing regulatory proteins such as SaeS and MsrR, and of the SaeS‐regulated proteins Sbi, Efb, and SaeP. These data indicate very critical interactions of membrane‐sensory proteins with phospholipids and they demonstrate the power of membrane proteomics for the characterization of bacterial physiology and pathogenicity.     

Combining mechanistic and data‐driven approaches to gain process knowledge on the control of the metabolic shift to lactate uptake in a fed‐batch CHO process

A growing body of knowledge is available on the cellular regulation of overflow metabolism in mammalian hosts of recombinant protein production. However, to develop strategies to control the regulation of overflow metabolism in cell culture processes, the effect of process parameters on metabolism has to be well understood. In this study, we investigated the effect of pH and temperature shift timing on lactate metabolism in a fed‐batch Chinese hamster ovary (CHO) process by using a Design of Experiments (DoE) approach. The metabolic switch to lactate consumption was controlled in a broad range by the proper timing of pH and temperature shifts. To extract process knowledge from the large experimental dataset, we proposed a novel methodological concept and demonstrated its usefulness with the analysis of lactate metabolism. Time‐resolved metabolic flux analysis and PLS‐R VIP were combined to assess the correlation of lactate metabolism and the activity of the major intracellular pathways. Whereas the switch to lactate uptake was mainly triggered by the decrease in the glycolytic flux, lactate uptake was correlated to TCA activity in the last days of the cultivation. These metabolic interactions were visualized on simple mechanistic plots to facilitate the interpretation of the results. Taken together, the combination of knowledge‐based mechanistic modeling and data‐driven multivariate analysis delivered valuable insights into the metabolic control of lactate production and has proven to be a powerful tool for the analysis of large metabolic datasets. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1657–1668, 2015     

Variation in scorpion metabolic rate and rate-temperature relationships: implications for the fundamental equation of the metabolic theory of ecology

The fundamental equation of the metabolic theory of ecology (MTE) indicates that most of the variation in metabolic rate are a consequence of variation in organismal size and environmental temperature. Although evolution is thought to minimize energy costs of nutrient transport, its effects on metabolic rate via adaptation, acclimatization or acclimation are considered small, and restricted mostly to variation in the scaling constant, b(0). This contrasts strongly with many conclusions of evolutionary physiology and life-history theory, making closer examination of the fundamental equation an important task for evolutionary biologists. Here we do so using scorpions as model organisms. First, we investigate the implications for the fundamental equation of metabolic rate variation and its temperature dependence in the scorpion Uroplectes carinatus following laboratory acclimation. During 22 days of acclimation at 25 degrees C metabolic rates declined significantly (from 127.4 to 78.2 microW; P = 0.0001) whereas mean body mass remained constant (367.9-369.1 mg; P = 0.999). In field-fresh scorpions, metabolic rate-temperature (MRT) relationships varied substantially within and among individuals, and therefore had low repeatability values (tau = 0.02) and no significant among-individual variation (P = 0.181). However, acclimation resulted in a decline in within-individual variation of MRT slopes which subsequently revealed significant differences among individuals (P = 0.0031) and resulted in a fourfold increase in repeatability values (tau = 0.08). These results highlight the fact that MRT relationships can show substantial, directional variation within individuals over time. Using a randomization model we demonstrate that the reduction in metabolic rate with acclimation while body mass remains constant causes a decline both in the value of the mass-scaling exponent and the coefficient of determination. Furthermore, interspecific comparisons of activation energy, E, demonstrated significant variation in scorpions (0.09-1.14 eV), with a mean value of 0.77 eV, significantly higher than the 0.6-0.7 eV predicted by the fundamental equation. Our results add to a growing body of work questioning both the theoretical basis and empirical support for the MTE, and suggest that alternative models of metabolic rate variation incorporating explicit consideration of life history evolution deserve further scrutiny.