Where's the ecology in molecular ecology?

Molecular techniques have had a profound impact in biology. Major disciplines, including evolutionary biology, now consistently utilize molecular tools. In contrast, molecular techniques have had a more limited impact in ecology. This discrepancy is surprising. Here, we describe the unexpected paucity of ecological research in the field colloquially referred to as 'molecular ecology.' Publications over the past 15 years from the journals Ecology , Evolution and Molecular Ecology reveal that much of the research published under the molecular ecology banner is in fact evolutionary in nature, and that comparatively little ecological research incorporates molecular tools. This failure to more broadly utilize molecular techniques in ecology is alarming because several promising lines of ecological inquiry could benefit from molecular approaches. Here we summarize the use of molecular tools in ecology and evolution, and suggest several ways to renew the ecological focus in 'molecular ecology'.     

Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes

Because current molecular haplotyping methods are expensive and not amenable to automation, many researchers rely on statistical methods to infer haplotype pairs from multilocus genotypes, and subsequently treat these inferred haplotype pairs as observations. These procedures are prone to haplotype misclassification. We examine the effect of these misclassification errors on the false-positive rate and power for two association tests. These tests include the standard likelihood ratio test (LRTstd) and a likelihood ratio test that employs a double-sampling approach to allow for the misclassification inherent in the haplotype inference procedure (LRTae). We aim to determine the cost-benefit relationship of increasing the proportion of individuals with molecular haplotype measurements in addition to genotypes to raise the power gain of the LRTae over the LRTstd. This analysis should provide a guideline for determining the minimum number of molecular haplotypes required for desired power. Our simulations under the null hypothesis of equal haplotype frequencies in cases and controls indicate that (1) for each statistic, permutation methods maintain the correct type I error; (2) specific multilocus genotypes that are misclassified as the incorrect haplotype pair are consistently misclassified throughout each entire dataset; and (3) our simulations under the alternative hypothesis showed a significant power gain for the LRTae over the LRTstd for a subset of the parameter settings. Permutation methods should be used exclusively to determine significance for each statistic. For fixed cost, the power gain of the LRTae over the LRTstd varied depending on the relative costs of genotyping, molecular haplotyping, and phenotyping. The LRTae showed the greatest benefit over the LRTstd when the cost of phenotyping was very high relative to the cost of genotyping. This situation is likely to occur in a replication study as opposed to a whole-genome association study.     

The molecular dissection of the chaperone–usher pathway

Secretion systems are specialized in transport of proteins, DNA or nutrients across the cell envelope of bacteria and enable them to communicate with their environment. The chaperone–usher (CU) pathway is used for assembly and secretion of a large family of long adhesive protein polymers, termed pili, and is widespread among Gram-negative pathogens [1]. Moreover, recent evidence has indicated that CU secretion systems are also involved in sporulation  and . In this review we focus on the structural biology of the paradigmatic type 1 and P pili CU systems encoded by uropathogenic Escherichia coli (UPEC), where recent progress has provided unprecedented insights into pilus assembly and secretion mechanism. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.     

Elucidating molecular mechanisms of septic cardiomyopathy — the cardiomyocyte model

In the multiple organ dysfunction syndrome of sepsis and septic shock the heart is one of the organs subject to failure. Many new insights into the mechanisms underlying septic cardiomyopathy were gained in the last years. Experimental work with neonatal and adult cardiomyocytes considerably contributed to this progress, facilitating the documentation of direct attenuation of the contractions of the heart muscle cell by toxins and mediators, as well as investigating the underlying cellular mechanisms. With this respect, contractile-depressant effects have been found in cardiomyocytes for many toxins and sepsis mediators, with endotoxin, Pseudomonas exotoxin A, tumor necrosis factor a, interleukin-1 and nitric oxide being the most relevant ones identified. These substances interfere at clinically relevant concentrations with several main inotropic axes, not only with the -adrenoceptor/adenylyl cyclase and with the NO-cGMP-system — on which most of the interest is focused at present — but also with the ₁-adrenoceptor/phosphoinositide pathway and the Ca²⁺ homeostasis of the cardiomyocyte, the latter representing the common final inotropic pathway. Not a single cardiodepressant factor, but more likely a total bunch of toxins and mediators with different attack mechanisms seem to contribute to the picture of septic cardiomyopathy.     

Phylogenetic patterns in the fleshy-fruited Myrtaceae – preliminary molecular evidence

A phylogenetic study of selected fleshy-fruited genera of the Myrtaceae was conducted using sequences from the ITS region of nuclear DNA and the psbA-trnH region of plastid DNA. Studies to date have suggested that the fleshy-fruited state has arisen on several occasions in the Myrtaceae. The previously accepted and predominantly Neotropical tribe Myrteae has traditionally been divided into three groups, the subtribes Myrtinae, Eugeniinae and Myrciinae. This subtribal arrangement is analysed in detail here for the first time. The monophyly of the tribe and subtribes are tested and relationships of the genera within them, in particular those of the Myrciinae and anomalous genera sometimes associated with it, are discussed. Combined analyses of these two DNA regions revealed 40 shortest trees, all of which resolve Myrteae (excluding the Acmena group) as monophyletic. Myrciinae appears to be monophyletic whereas Myrtinae and Eugeniinae appear polyphyletic. The phylogenetic positions and relationships of the anomalous genera Myrceugenia, Luma and Blepharocalyx are unclear, but Myrceugenia is never included within the Myrciinae s.str. A Myrciinae s.str. clade emerges within which Myrcia, Calyptranthes and Marlierea appear polyphyletic. Clades emerge, however, that may reflect some natural groupings within the subtribe.We thank David Simpson, Lazlo Csiba, Edith Kapinos and many others from Kew for invaluable advice and support. It would not have been possible to collect the Brazilian samples without the patience and careful guidance of Dr. Vinicius C. Souza, Fiorella F. Mazine (Universidade de São Paulo, ESALQ), Professor Gert Hatschbach, Joel M. de Silva (Museu Botânico Municipal, Curitiba) and many others from the ESA and MBM herbaria. Thanks also to Les Landrum, Andrew Salywon, Marcos Sobral and an anonymous reviewer for helpful comments at different stages of this work. British Airways are gratefully acknowledged for providing a flight to Brazil under their Community and Conservation programme.     

Biotechnology and molecular biology of the α-glucosidase inhibitor acarbose

The -glucosidase inhibitor acarbose, O-{4,6-dideoxy-4[1s-(1,4,6/5)-4,5,6-trihydroxy-3-hydroxymethyl-2-cyclohexen-1-yl]-amino--d-glucopyranosyl}-(14)-O--d-glucopyranosyl-(14)-d-glucopyranose, is produced in large-scale fermentation by the use of strains derived from Actinoplanes sp. SE50. It has been used since 1990 in many countries in the therapy of diabetes type II, in order to enable patients to better control blood sugar contents while living with starch-containing diets. Thus, it is one of the latest successful products of bacterial secondary metabolism to be introduced into the pharmaceutical world market. Cultures of Actinoplanes sp. also produce various other acarbose-like components, of which component C is hard to separate during downstream processing, which is one of the most modern work-up processes developed to date. The physiology, genetics and enzymology of acarbose biosynthesis and metabolism in the producer have been studied to some extent, leading to the proposal of a new pathway and metabolic cycle, the carbophore. These data could give clues for further biotechnological developments, such as the suppression of side-products, enzymological or biocombinatorial production of new metabolites and the engineering of production rates via genetic regulation in future.     

A molecular modelling study of the interaction between β-cyclodextrin and the organophosphorothioate pesticide parathion

The interaction between parathion and -cyclodextrin was investigated by Molecular Dynamics. Several in vacuo trajectories were calculated for the system imposing a 1:1 stoichiometry. The influence of the solvent and temperature was considered. The results account for the formation of adducts which are stable at room temperature and involve mainly the nitrophenoxy group of the guest molecules which interacts with the hydrophobic cavity of the host by van der Waals forces.     

Modeling the molecular basis for α4β1 integrin antagonism

We report a 3D QSAR study of almost 300 structurally diverse small molecule antagonists of the integrin α4β1 whose biological activity spans six orders of magnitude. The alignment of the molecules was based on the conformation of a structurally related ligand bound to the αIIBβ3 and αvβ3 integrins in X-ray crystallographic studies. The molecular field method, CoMSIA, was used to generate the 3D QSAR models. The resulting models showed that the lipophilic properties were the most important, with hydrogen bond donor and steric properties less relevant. The models were highly significant (r(2)=0.89, q2(LOO)=0.67, r(2) (test set)=0.76), and could make robust predictions of the data (SEE=0.46, SEP=0.78, SEP (test set)=0.66). We predicted the antagonist activities of a further ten compounds with useful accuracy. The model appears capable of predicting α4β1 integrin antagonist activity to within a factor of five for compounds within its domain of applicability. The implications for design of improved integrin antagonists will be discussed.     

Do stress and long-term potentiation share the same molecular mechanisms?

Stress is a biological, significant factor shown to influence hippocampal synaptic plasticity and cognitive functions. Although numerous studies have reported that stress produces a suppression in long-term potentiation (LTP; a putative synaptic mechanism underlying learning and memory), little is known about the mechanism by which this occurs. Because the effects of stress on LTP and its converse process, long-term depression (LTD), parallel the changes in synapticity that occur following the establishment of LTP with tetanic stimulation (i.e., occluding LTP and enhancing LTD induction), it has been proposed that stress affects subsequent hippocampal plasticity by sharing the same molecular machinery required to support LTP. This article summarizes recent findings from ours and other laboratories to assess this view and discusses relevant hypotheses in the study of stress-related modifications of synaptic plasticity.     

The molecular diversity of α-gliadin genes in the tribe Triticeae

Many of the unique properties of wheat flour are derived from seed storage proteins such as the α-gliadins. In this study these α-gliadin genes from diploid Triticeae species were systemically characterized, and divided into 3 classes according to the distinct organization of their protein domains. Our analyses indicated that these α-gliadins varied in the number of cysteine residues they contained. Most of the α-gliadin genes were grouped according to their genomic origins within the phylogenetic tree. As expected, sequence alignments suggested that the repetitive domain and the two polyglutamine regions were responsible for length variations of α-gliadins as were the insertion/deletion of structural domains within the three different classes (I, II, and III) of α-gliadins. A screening of celiac disease toxic epitopes indicated that the α-gliadins of the class II, derived from the Ns genome, contain no epitope, and that some other genomes contain much fewer epitopes than the A, S(B) and D genomes of wheat. Our results suggest that the observed genetic differences in α-gliadins of Triticeae might indicate their use as a fertile ground for the breeding of less CD-toxic wheat varieties.     

What is the essential proton-translocating molecular machinery in cytochrome oxidase?

Pulses of O2 added to anaerobic mitochondria in the presence of antimycin, but in the absence of exogenous reductants, led to H+ translocation until the amount of oxidizing equivalents exceeded the number of endogenous reducing equivalents capable of rapid reduction of cytochrome oxidase. This demonstrates that either the heme of cytochrome alpha or that CuA is the redox center, the function of which is coupled to proton translocation in cytochrome oxidase. Chemical labeling of subunit III of cytochrome oxidase by dicyclocarbodiimide (DCCD), or removal of this subunit by treatment of the enzyme at high pH, results in loss of proton translocation by the isolated and membrane-reconstituted enzyme. Possible roles of subunit III in proton translocation are discussed.     

Rho GTPases and exocytosis: what are the molecular links?

Delivery of proteins or lipids to the plasma membrane or into the extracellular space occurs through exocytosis, a process that requires tethering, docking, priming and fusion of vesicles, as well as F-actin rearrangements in response to specific extracellular cues. GTPases of the Rho family have been implicated as important regulators of exocytosis, but how Rho proteins control this process is an open question. In this review, we focus on molecular connections that drive Rho-dependent exocytosis in polarized and regulated exocytosis. Specifically, we present data showing that Rho proteins interaction with the exocyst complex and IQGAP mediates polarized exocytosis, whereas interaction with actin-binding proteins like N-WASP mediates regulated exocytosis.     

Are the molecular strategies that control apoptosis conserved in bacteria?

The Staphylococcus aureus cid and lrg operons have been shown to encode putative membrane proteins that are involved in the regulation of murein hydrolase activity and penicillin tolerance. Cid proteins enhance murein hydrolase activity and penicillin sensitivity, whereas Lrg proteins have an inhibitory effect on these processes. It has been proposed that the Cid and Lrg proteins function in a way analogous to bacteriophage-encoded holins and antiholins, respectively, which control the timing of bacteriophage-induced lysis. This article explores the possibility that the Cid-Lrg regulatory system controls bacterial programmed cell death using a molecular strategy that it is functionally analogous to that mediated by the eukaryotic Bcl-2 family of apoptosis regulatory proteins.