The yeast F(1)F(0)-ATP synthase: analysis of the molecular organization of subunit g and the importance of a conserved GXXXG motif

The F(1)F(0)-ATP synthase enzyme is located in the inner mitochondrial membrane, where it forms dimeric complexes. Dimerization of the ATP synthase involves the physical association of the neighboring membrane-embedded F(0)-sectors. In yeast, the F(0)-sector subunits g and e (Su g and Su e, respectively) play a key role in supporting the formation of ATP synthase dimers. In this study we have focused on Su g to gain a better understanding of the function and the molecular organization of this subunit within the ATP synthase complex. Su g proteins contain a GXXXG motif (G is glycine, and X is any amino acid) in their single transmembrane segment. GXXXG can be a dimerization motif that supports helix-helix interactions between neighboring transmembrane segments. We demonstrate here that the GXXXG motif is important for the function and in particular for the stability of Su g within the ATP synthase. Using site-directed mutagenesis and cross-linking approaches, we demonstrate that Su g and Su e interact, and our findings emphasize the importance of the membrane anchor regions of these proteins for their interaction. Su e also contains a conserved GXXXG motif in its membrane anchor. However, data presented here would suggest that an intact GXXXG motif in Su g is not essential for the Su g-Su e interaction. We suggest that the GXXXG motif may not be the sole basis for a Su g-Su e interaction, and possibly these dimerization motifs may enable both Su g and Su e to interact with another mitochondrial protein.     

Niche conservatism as an emerging principle in ecology and conservation biology

The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within‐species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?).     

A whole-genome association study for pig reproductive traits

A whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of informative QTL and the genes within the QTL for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. Many QTL identified in this study are new for pig reproductive traits. Around 48% of total genes located in the identified QTL regions were predicted to be involved in placental functions. The genomic regions containing genes important for foetal developmental (e.g. MEF2C) and uterine functions (e.g. PLSCR4) were associated with TNB and NBA in the first two parities. Similarly, QTL in other foetal developmental (e.g. HNRNPD and AHR) and placental (e.g. RELL1 and CD96) genes were associated with SB and MUM in different parities. The QTL with genes related to utero-placental blood flow (e.g. VEGFA) and hematopoiesis (e.g. MAFB) were associated with GL differences among sows in this population. Pathway analyses using genes within QTL identified some modest underlying biological pathways, which are interesting candidates (e.g. the nucleotide metabolism pathway for SB) for pig reproductive traits in different parities. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.     

Insights from intralocus tactical conflict: adaptive states,interactions with ecology and population divergence

Alternative reproductive tactics (ARTs) have improved our understanding of the evolution of adaptive variation; for instance, their study has led us to understand that the best phenotype (e.g. large and flashy) for a tactic that uses one mating behavior (e.g. court females) is often not the best phenotype (e.g. small and inconspicuous) for a tactic that uses a different mating behavior (e.g. chase and force‐copulate females). However, genetic correlations of shared traits across ARTs can constrain ARTs from reaching their optimal states, resulting in intralocus tactical conflict (IATC). While constraints on evolution in general have been well‐established and studied, there are some important implications of constraints due to intralocus tactical conflict on ARTs that have not been incorporated into the field of evolutionary ecology. Here we describe how an appreciation of IATC, including how to detect it and when to expect it, can change our perspectives in three areas: 1) adaptive states for traits associated with ARTs (e.g. growth rates, behavioural plasticity); 2) how selection due to ecological variation across populations can produce patterns of divergence between ARTS; 3) and the evolutionary stability of polymorphisms (e.g. how IATC can explain losses of one ART, and why this can lead to rapid speciation).     

Concentration–response relationships and temporal patterns in hepatic gene expression of Chinook salmon (Oncorhynchus tshawytscha) exposed to sewage

Changes in liver gene expression were examined in juvenile Chinook salmon (Oncorhynchus tshawytscha) exposed in vivo for 8 d to seawater (control) or one of 5 concentrations of sewage (environmentally-relevant dilutions of 0.05%, 0.1%, and 0.7%; 2%, 5% or 10%) and subsequently transferred to clean seawater for an 8-d recovery period. Livers were sampled on days 1, 4, 8 (sewage-exposed) and 16 (8 d of sewage exposure plus 8 d of recovery). A custom cDNA microarray using a universal DNA reference design was used to examine trends of altered gene expression across sewage concentrations, across timepoints, and at the end of the recovery period. Alterations in gene expression followed four distinct concentration-dependent patterns: (1) concentration response (e.g. estrogen receptor alpha), (2) inverse-concentration response (e.g. insulin receptor beta), U-shaped (e.g. mineralocorticoid receptor), (3) inverse U-shaped (e.g. benzodiazepine receptor), and (4) concentration-independent responses (e.g. ubiquitin). Temporal trends included: (1) peak gene expression at one of the sewage exposure timepoints with recovery to baseline levels after the depuration phase (e.g. vitelline envelope protein beta), (2) gene expression alterations that did not recover (e.g. glucose transporter 3), and (3) delayed gene expression alterations initiated only at the recovery timepoint (e.g. insulin-like growth factor 2). In summary, patterns in gene expression changes were found across sewage concentrations and exposure timepoints. This study is the first to show gene expression trends of this nature.     

Mechanisms for the selective action of Vitamin D analogs

The non-classical effects of 1,25(OH)(2)D(3) create possible therapeutic applications for immune modulation (e.g. auto-immune diseases and graft rejection), inhibition of cell proliferation (e.g. psoriasis, cancer) and induction of cell differentiation (e.g. cancer). The major drawback related to the use of 1,25(OH)(2)D(3) is its calcemic effect, which prevents the application of pharmacological concentrations. Several analogs are now available that show modest to good selectivity with regard to specific effects (e.g. anticancer or immune effects or bone anabolism versus hypercalcemia) when tested in appropriate in vivo models. The molecular basis for this selectivity is only partially understood and probably a variable mixture of mechanisms.     

Random-effects ordination: describing and predicting multivariate correlations and co-occurrences

Ecology is inherently multivariate, but high-dimensional data are difficult to understand. Dimension reduction with ordination analysis helps with both data exploration and clarification of the meaning of inferences (e.g., randomization tests, variation partitioning) about a statistical population. Most such inferences are asymmetric, in that variables are classified as either response or explanatory (e.g., factors, predictors). But this asymmetric approach has limitations (e.g., abiotic variables may not entirely explain correlations between interacting species). We study symmetric population-level inferences by modeling correlations and co-occurrences, using these models for out-of-sample prediction. Such modeling requires a novel treatment of ordination axes as random effects, because fixed effects only allow within-sample predictions. We advocate an iterative methodology for random-effects ordination: (1) fit a set of candidate models differing in complexity (e.g., number of axes); (2) use information criteria to choose among models; (3) compare model predictions with data; (4) explore dimension-reduced graphs (e.g., biplots); (5) repeat 1–4 if model performance is poor. We describe and illustrate random-effects ordination models (with software) for two types of data: multivariate-normal (e.g., log morphometric data) and presence–absence community data. A large simulation experiment with multivariate-normal data demonstrates good performance of (1) a small-sample-corrected information criterion and (2) factor analysis relative to principal component analysis. Predictive comparisons of multiple alternative models is a powerful form of scientific reasoning: we have shown that unconstrained ordination can be based on such reasoning.     

Active oxygen in neuromuscular disorders

Although muscle and nerve are reasonably well protected against active oxygen and related free radicals, environmental or inherited malfunctions can overpower their defences. Active oxygen is involved in many neuropathies and myopathies. In every case the damage is caused by agents which exert effects disproportionately greater than the quantites encountered, through a variety of amplification mechanisms. We can categorize these amplification mechanisms as follows: (a) non-replacement of targets (e.g. loss of genetic information, ataxia telangectasia being an hereditary ataxia in which an oxygen mediated chromosomal instability is apparent), (b) non-removal of unwanted materials (e.g. lipofuscin accumulation in brain and heart), (c) redox cycling, usually involving catalysis by trace-metal ions (e.g. some forms of Parkinsonism), (d) non-redox catalysis (e.g. toxicity in cardiac muscle or brain due to vanadium or aluminium respectively), (e) modification of ion transport (e.g. calcium ionophore or acrylamide induce histopathological changes in muscle, similar in some respects to those seen in Duchenne muscular dystrophy), (f) compromised defences (e.g. muscle and nerve become particularly susceptible to free radical damage after loss of the protective actions of vitamin E), and (g) amplification by inflammatory and immune responses (e.g. multiple sclerosis, reperfusion injury to brain and heart, and traumatic injury to nervous tissue). Unfortunately, a variety of therapeutic agents which might be expected to protect against almost every conceivable form of oxygen mediated damage have proved clinically ineffective in most of these disorders. The reasons for this will be explored with an emphasis on common features, differences, mechanisms, and potential therapeutic approaches.     

Nanostructured luminescently labeled nucleic acids

Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron); (ii) the labeling of bulk nucleic acids (e.g. single‐stranded DNA, double‐stranded DNA) with nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver nanoclusters). This review surveys recent advances in these three different approaches to the generation of nanostructured luminescently labeled nucleic acids, and includes both direct and indirect labeling methods.     

Ergot alkaloids: Quantitation and recognition challenges

Bread, flour, infant formula and baby food samples (n=109, from which n=54 made of or containing rye), collected in 2001, 2003, and 2005, were analysed for ergot alkaloids. Samples were extracted using acidic conditions and the extracts subjected to an automated solid-phase clean up using combined cation exchange/reversed-phase sorbent cartridges (Oasis-MCX). Subsequent chromatographic separation and analysis was performed by liquid chromatography (LC) with fluorescence detection (FLD) and by LC with mass spectrometric detection (MS/MS). The ergot alkaloid (EAs) content of a sample was defined as the sum of the 16 alkaloids ergometrin(in)e, ergosin(in)e, ergotamin(in)e, ergostin(in)e, ergocornin(in)e, α-ergocryptin(in)e, β-ergocryptin(in)e and ergocristin(in)e. Comparability of results obtained by LC-FLD and LC-MS/MS was satisfactory, but varied for different alkaloids. The use of dihydro-ergocristine as an internal standard considerably improved the reliability of analytical data from LC-MS/MS. Compared with earlier data (Baumannet al., 1985) for median levels of ergot alkaloids in rye flour (140 ng/g) and bread (21.3 ng/g) from Switzerland, the median values for ergot alkaloids in rye flour collected in 2001 (n=13) and in 2005 (n=2) were 172 ng/g and 160 ng/g, respectively. The median values for bread (fresh weight) collected in 2001 (n=14), 2003 (n=7), and 2005 (n=2) were 87 ng/g, 120 ng/g, and 156 ng/g, respectively. Low levels of ergot alkaloids were also found in wheat products and in some infant formulae and baby foods containing rye. By additional LC-MS/MS experiments, the possible natural occurrence of ergot congeners containing the 9,10-unsaturated ergoline cation (m/z=223) was investigated. In a few samples, ergovalin(in)e was tentatively identified by these means. Presented at the 29^th Mykotoxin-Workshop, Fellbach, Germany, May 14–16, 2007     

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing 'global views' of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein-protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein-protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V(-b), for attribute value V and constant exponent b), with a few folds having large values and most having small values.     

Prenatal diagnosis: a chance? risk? dilemma?

In research on congenital metabolic disorders, a biochemist can choose between the theoretical and the practical approach. The diagnosis of metabolic diseases relies on 1) the determination of the presence of metabolites under normal conditions that are direct substrates of the defective enzyme (e.g., the Gm2 ganglioside in the brain tissue of a patient with Tay-Sachs disease); 2) the determination of the lack or insufficiency of the direct product of the defective enzyme (e.g., aryl sulfatase A in the cells of patients with metachromatic leukodystrophy), hormone (hypothyroidism), or receptor (congenital hypercholesterolemia); 3) determination of substance whose reduction was established by experimentation, but the cause of the decrease is not known (ceruloplasmin in Wilson's disease); and 4) DNA analysis. Metabolic impairment of genetic origin is not treatable. The disease can be prevented by 1) removing the inappropriate metabolite (e.g., copper accumulation can be avoided by giving penicillamine or zinc salts); 2) limiting those substances in the critical phase of childhood that are components of the defective enzyme (e.g. gluten reduction in colic and protein in phenylketonuria); 3) supplementing the insufficient metabolite (e.g., phosphate in hypophosphatemia by sound for 12 hours a day); 4) protecting the patients (e.g. from light in porphyria); and 5) treatment by substances (giving coagulation factor VIII in hemophilia and thyroid hormones in hypothyroidism). There is a dilemma in subjecting patients to a diagnosis of progression to Huntington's chorea 20 years in advance or informing them about the high risk of hereditary disease for the next child (25% for the recessive and 50% for the dominant mode). Ethical committees have usually opted for a recommendation of selective abortion in clear-cut cases. Increasingly refined diagnostic methods have magnified the responsibility of the biochemist.     

Nouvelles formulations des regles ecologiques connues sous le nom de reegle de Bergmann et loi de Jordan: Amendments of the ecological rules known as Bergmann's and Jordan's rules

Measurements of populations of planktonic and micronektonicspecies from the Atlanto-mediterranean region (about 10,000specimens) have lead to improvements in Bergmann's rule relatingto the increase in size with latitude. There are three cases : Mediterranean specimens may be smaller(e.g. the mysid Eucopia hansent), equal to (e.g. the decapodcrustacean Gennadas elegans) or larger than Atlantic ones (e.g.the thecosomatous genus Cymbulia). All the species in the last group have their principal distributionin warm ocean waters. In the Atlantic, tropical species (e.g.the euphausiid Euphausia gibboides) decrease in size in thenorthern parts of their range while temperate species (e.g.the decapod crustacean Sergesles corniculum) decrease in sizetowards both the pole and the equator. The comparison with the number of vertebrae of fish, which increasesas does the size according to Jordan's rule, is interesting:though correct for cold water species (e.g. Merlucdus merluccius),this rule cannot be applied to warm water species (e.g. Merlucciussenegalensis). Thus, these rules must be corrected like this:- "a species reachesits maximal size in high, intermediate or low latitudes of itsarea if it has a boreal, temperate or tropical distribution"; - "the number of vertebrae increases with latitude for borealfish and decreases for tropical ones".     

Fear generalization and behavioral responses to multiple dangers

Animals often exhibit consistent-individual differences (CIDs) in boldness/fearfulness, typically studied in the context of predation risk. We focus here on fear generalization, where fear of one danger (e.g., predators) is correlated with fear of other dangers (e.g., humans, pathogens, moving vehicles, or fire). We discuss why fear generalization should be ecologically important, and why we expect fear to correlate across disparate dangers. CIDs in fear are well studied for some dangers in some taxa (e.g., human fear of pathogens), but not well studied for most dangers. Fear of some dangers has been found to correlate with general fearfulness, but some cases where we might expect correlated fears (e.g., between fear of humans, familiar predators, and exotic predators) are surprisingly understudied.     

Bioinformatic profiling of the transcriptional response of adult rat cardiomyocytes to distinct fatty acids

Diabetes mellitus, obesity, and dyslipidemia increase risk for cardiovascular disease, and expose the heart to high plasma fatty acid (FA) levels. Recent studies suggest that distinct FA species are cardiotoxic (e.g., palmitate), while others are cardioprotective (e.g., oleate), although the molecular mechanisms mediating these observations are unclear. The purpose of the present study was to investigate the differential effects of distinct FA species (varying carbon length and degree of saturation) on adult rat cardiomyocyte (ARC) gene expression. ARCs were initially challenged with 0.4 mM octanoate (8:0), palmitate (16:0), stearate (18:0), oleate (18:1), or linoleate (18:2) for 24 h. Microarray analysis revealed differential regulation of gene expression by the distinct FAs; the order regarding the number of genes whose expression was influenced by a specific FA was octanoate (1,188) > stearate (740) > palmitate (590) > oleate (83) > linoleate (65). In general, cardioprotective FAs (e.g., oleate) increased expression of genes promoting FA oxidation to a greater extent than cardiotoxic FAs (e.g., palmitate), whereas the latter induced markers of endoplasmic reticulum and oxidative stress. Subsequent RT-PCR analysis revealed distinct time- and concentration-dependent effects of these FA species, in a gene-specific manner. For example, stearate- and palmitate-mediated ucp3 induction tended to be transient (i.e., initial high induction, followed by subsequent repression), whereas oleate-mediated induction was sustained. These findings may provide insight into why diets high in unsaturated FAs (e.g., oleate) are cardioprotective, whereas diets rich in saturated FAs (e.g., palmitate) are not.     

Critical evaluation of α1- and β2-microglobulins in urine as markers of cadmium-induced tubular dysfunction

The purpose of the study was to examine the validity of alpha1-microglobulin (alpha1-MG) in comparison with popularly used beta2-microglobulin (beta2-MG). A database was revisited to select ca. 7,500 spot urine samples (of adequate urine density) from non-pregnant, non-lactating and never-smoking adult women. The validity of the MGs was examined in terms of stability of the MG-uria prevalence in urine samples of various creatinine (CR or cr) concentration or specific gravity (SG or sg). Comparisons were made for MGs as observed (e.g., alpha1-MGob), as corrected for CR (e.g., alpha1-MGcr) and as corrected for SG of 1.016 (e.g., alpha1-MGsg). A cut-off value of 5.7 mg/g cr (or mg/l) for alpha1-MG was deduced from a cut-off value of 400 microg/g cr (or mcirog/l) for beta2-MG, because the correlation between alpha1-MGcr and beta2-MGcr was statistically significant. The prevalence of a 1-MGsg-uria was essentially unchanged (i.e., from a low of 13.6% to a high of 17.0%, or 1.2 times) except for in very dense or very thin urine samples, in contrast, beta2-MGcr-uria showed a substantial increase (from 0.0% to 2.8% with an infinite rate) as a reverse function of a decrease in CR in urine. The prevalence of uncorrected markers, i.e., alpha1-MGob-uria and beta2-MGob-uria, showed even greater CR- or SG-dependent changes. Thus, it appeared prudent to consider a alpha-MGsg rather than beta2-MGcr as a marker of tubular dysfunction among a general population with various urine density.