Are all economic facts greatly exaggerated? Theory competition and selectivity

There is growing concern and mounting evidence of selectivity in empirical economics. Most empirical economic literatures have a truncated distribution of results. The aim of this paper is to explore the link between publication selectivity and theory contests. This link is confirmed through the analysis of 87 distinct empirical economics literatures, involving more than three and a half thousand separate empirical studies, using objective measures of both selectivity and contests. Our meta–meta-analysis shows that publication selection is widespread, but not universal. It distorts scientific inference with potentially adverse effects on policy making, but competition and debate between rival theories reduces this selectivity and thereby improves economic inference.

Substrate Selectivity and Molecular Adaptation in the Outer Membrane Proteases of Yersinia pestis and Salmonella enterica

Proteolysis is important in bacterial pathogenesis and colonization of animal and plant hosts. In this work I have investigated the functions of the bacterial outer membrane proteases, omptins, of Yersinia pestis and Salmonella enterica. Y. pestis is a zoonotic pathogen that causes plague and has evolved from gastroenteritis-causing Yersinia pseudotuberculosis about 13 000 years ago. S. enterica causes gastroenteritis and typhoid fever in humans. Omptins are transmembrane β-barrels with ten antiparallel β-strands and five surface-exposed loops. The loops are important in substrate recognition, and variation in the loop sequences leads to different substrate selectivities between omptins, which makes omptins an ideal platform to investigate functional adaptation and to alter their polypeptide substrate preferences. The omptins Pla of Y. pestis and PgtE of S. enterica are 75% identical in their amino acid sequences. Pla is a multifunctional protein with proteolytic and non-proteolytic functions, and it increases bacterial penetration and proliferation in the host. Functions of PgtE increase migration of S. enterica in vivo and bacterial survival in mouse macrophages, thus enhancing bacterial spread within the host. Mammalian plasminogen/fibrinolytic system maintains the balance between coagulation and fibrinolysis and participates in several cellular processes, e.g., cell migration and degradation of extracellular matrix proteins. This system consists of activation cascades, which are strictly controlled by several regulators, such as plasminogen activator inhibitor 1 (PAI-1), α2-antiplasmin (α2AP), and thrombin-activatable fibrinolysis inhibitor (TAFI). This work reveals novel interactions of the omptins of Y. pestis and S. enterica with the regulators of the plasminogen/fibrinolytic system: Pla and PgtE inactivate PAI-1 by cleavage at the reactive site peptide bond, and degrade TAFI, preventing its activation to TAFIa. Structure-function relationship studies with Pla showed that threonine 259 of Pla is crucial in plasminogen activation, as it prevents degradation of the plasmin catalytic domain by the omptin and thus maintains plasmin stability. In this work I constructed chimeric proteins between Pla and Epo of Erwinia pyrifoliae that share 78% sequence identity to find out which amino acids and regions in Pla are important for its functions. Epo is neither a plasminogen activator nor an invasin, but it degrades α2AP and PAI-1. Cumulative substitutions towards Pla sequence turned Epo into a Pla-like protein. In addition to threonine 259, loops 3 and 5 are critical in plasminogen activation by Pla. Turning Epo into an invasin required substitution of 31 residues located at the extracellular side of the Epo protein above the lipid bilayer, and also of the β1-strand in the N-terminal transmembrane region of the protein. These studies give an example of how omptins adapt to novel functions that advantage their host bacteria in different ecological niches.

Impact of zooplankton food selectivity on plankton dynamics and nutrient cycling

Within models, zooplankton grazing is typically defined as being dependent on total prey concentration, with feeding selectivity expressed only as a function of prey size. This behavior ignores taxonomic preferences shown by the preda- tors and the capacity of some zooplankton to actively select or reject individual prey items from mixtures. We carried out two model experiments comparing impacts of zooplankton displaying passive and active selection, which resulted in contrasting dynamics for the pelagic system. Passive selection by the grazer resulted in a top down control on the prey with a fast turn-over of nutrients. Active selection, on the other hand led to a bottom-up control, with slower nutrient turnover constraining primary production by changing the system toward export of particulate matter. Our results suggest that selective feeding behavior is an important trait, and should be considered alongside size and taxonomy when studying the role of zooplankton impact in the ecosystem.

Feeding rates and prey selectivity of planktonic decapod larvae in the Western English Channel

Meroplankton are seasonally important contributors to the zooplankton, particularly at inshore sites, yet their feeding ecology is poorly known relative to holoplankton. While several studies have measured feeding in decapod larvae, few studies have examined the feeding rates of decapod larvae on natural prey assemblages throughout the reproductive season. We conducted 8 feeding experiments with Necora puber, Liocarcinus spp. and Upogebia spp. zoea larvae collected from the L4 monitoring site off Plymouth (50°15.00′N, 4°13.02′W) during spring–summer 2009 and 2010. This period spanned moderate-to-high food availability (0.5–1.6 µg chl-a L−1), but a great range in food composition with small cells <20 µm dominating in 2010. Daily rations averaged 17, 60 and 22 % of body C for the 3 respective decapod species. Clearance rates differed according to prey type, and all 3 decapod genera showed evidence of selection of dinoflagellates. Importantly, small cells including nano- and pico-plankton were ingested, this being demonstrated independently by flow cytometric analysis of the feeding experiments and molecular analysis. PCR-based analysis of the haptophyte portion of the diet revealed ingestion of Isochrysis galbana by decapod larvae in the bottle incubations and Isochrysis galbana and Phaeocystis globosa by decapod larvae collected directly from the field. This study has shown that pico- and nano-sized plankton form an important supplement to the diverse and variable diet of decapod larvae.

Feeding selectivity of bivalve larvae on natural plankton assemblages in the Western English Channel

Meroplankton, including bivalve larvae, are an important and yet understudied component of coastal marine food webs. Understanding the baseline of meroplankton ecology is imperative to establish and predict their sensitivity to local and global marine stressors. Over an annual cycle (October 2009–September 2010), bivalve larvae were collected from the Western Channel Observatory time series station L4 (50°15.00′N, 4°13.02′W). The morphologically similar larvae were identified by analysis of the 18S nuclear small subunit ribosomal RNA gene, and a series of incubation experiments were conducted to determine larval ingestion rates on natural plankton assemblages. Complementary gut content analysis was performed using a PCR-based method for detecting prey DNA both from field-collected larvae and those from the feeding experiments. Molecular identification of bivalve larvae showed the community composition to change over the course of the sampling period with domination by Phaxas in winter and higher diversity in autumn. The larvae selected for nanoeukaryotes (2–20 µm) including coccolithophores (<20 µm) which together comprised >75 % of the bivalve larvae diet. Additionally, a small percentage of carbon ingested originated from heterotrophic ciliates (<30 µm). The molecular analysis of bivalve larvae gut content provided increased resolution of identification of prey consumed and demonstrated that the composition of prey consumed established through bottle incubations conferred with that established from in situ larvae. Despite changes in bivalve larvae community structure, clearance rates of each prey type did not change significantly over the course of the experiment, suggesting different bivalve larvae species may consume similar prey.

Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity

Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.

Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity

Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.

PROLINE-BASED CHIRAL STATIONARY PHASES: INSIGHTS INTO THE MECHANISM OF CHIRAL SELECTIVITY

Proline (Pro) is a unique amino acid that has been examined previously as a potential chiral selector for high-performance liquid chromatography. In recent years, a new class of promising Pro based enantioselective stationary phases has been studied and the longer peptides were found to be competitive with commercial chiral stationary phases (CSPs). Here, we aim to perform a comprehensive examination of a t-butoxycarbonyl- (t-Boc-) terminated monoproline selector. This selector was grafted through an amide linkage to an aminopropyl siloxane-terminated Si (111) wafer and to a silicon atomic force microscopy tip. To ensure a flat, homogeneous overlayer of selectors suitable for force spectrometric measurements, the prepared surfaces were characterized using XPS, AFM and contact angle measurements. Chemical force spectrometry (CFS) has been used to examine the chiral discrimination in our monoproline CSP by measuring the interaction forces between two D- or L-monoproline monolayers in water and in the presence of a series of amino acids in solution to explore the degree to which binding of amino acids impacts self-selectivity. Chemical force titration (CFT) has been used to observe the influence of variations in pH on the binding interaction of proline modified chiral surfaces. Here we aim to explore the connection between side-chain hydrophobicity and differences in the nature of the binding between different ionic forms of amino acids and the t-Boc-Pro interface, and thereby to gain insight into the mechanism of chiral selectivity. The CFS results show several trends for different proline selector/amino acid combinations and indicate that the binding characteristics of amino acid to the proline surface is strongly dependent on the amino acid side chain where hydrophilic side chain amino acids exhibit a selectivity opposite to that seen for those with hydrophobic side chains. The CFT studies also provide valuable insights into interactions between the proline selector and the amino acids under a wide range of pH conditions, indicating that protonated amine groups of alanine and serine are closely involved in the binding mechanism to proline surfaces. On the other hand, the presence of the second carboxylic group in aspartic acid plays an important role while interacting with proline.

Choosing "interesting" research methods and facing the challenges for publication

This paper discusses the choice to use two less conventional or “interesting” research methods, Q Methodology and Experience Sampling Method, rather than “status quo” research methods so common in the marketing discipline. It is argued that such methods have value for marketing academics because they widen the potential for discovery. The paper outlines these two research methods, providing examples of how they have been used in an experiential consumption perspective. Additionally the paper identifies some of the challenges to be faced when trying to publish research that use such less conventional methods, as well as offering suggestions to address them.