Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation

With rising energy prices and concern over the environmental impact of fossil fuel consumption, the push to develop biomass derived fuels has increased significantly. Although most global carbon fixation occurs via the Calvin Benson Bassham cycle, there are currently five other known pathways for carbon fixation; the goal of this study was to determine the thermodynamic efficiencies of all six carbon fixation pathways for the production of biomass using flux balance analysis. The three chemotrophic pathways, the reductive acetyl-CoA pathway, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, were found to be more efficient than photoautotrophic carbon fixation pathways. However, as hydrogen is not freely available, the energetic cost of hydrogen production from sunlight was calculated and included in the overall energy demand, which results in a 5 fold increase in the energy demand of chemoautotrophic carbon fixation. Therefore, when the cost of hydrogen production is included, photoautotrophic pathways are more efficient. However, the energetic cost for the production of 12 metabolic precursors was found to vary widely across the different carbon fixation pathways; therefore, different pathways may be more efficient at producing products from a single precursor than others. The results of this study have significant impact on the selection or design of autotrophic organisms for biofuel or biochemical production. Overall biomass production from solar energy is most efficient in organisms using the reductive TCA cycle, however, products derived from one metabolic precursor may be more efficiently produced using other carbon fixation pathways.     

Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women

Increased values of multiple adiposity-related anthropometric traits are important risk factors for many common complex diseases. We performed a genome-wide association (GWA) study for four quantitative traits related to body size and adiposity (BMI, weight, waist circumference, and height) in a cohort of 1,792 adult Filipino women from the Cebu Longitudinal Health and Nutrition Survey (CLHNS). This is the first GWA study of anthropometric traits in Filipinos, a population experiencing a rapid transition into a more obesogenic environment. In addition to identifying suggestive evidence of additional single-nucleotide polymorphism (SNP) association signals (P < 10(-5)), we replicated (P < 0.05, same direction of additive effect) associations previously reported in European populations of both BMI and weight with MC4R and FTO, of BMI with BDNF, and of height with EFEMP1, ZBTB38, and NPPC, but none with waist circumference. We also replicated loci reported in Japanese or Korean populations as associated with BMI (OTOL1) and height (HIST1H1PS2, C14orf145, GPC5). A difference in local linkage disequilibrium (LD) between European and Asian populations suggests a narrowed association region for BDNF, while still including a proposed functional nonsynonymous amino acid substitution variant (rs6265, Val66Met). Finally, we observed significant evidence (P < 0.0042) for age-by-genotype interactions influencing BMI for rs17782313 (MC4R) and rs9939609 (FTO), and for a study year-by-genotype interaction for rs4923461 (BDNF). Our results show that several genetic risk factors are associated with anthropometric traits in Filipinos and provide further insight into the effects of BDNF, FTO, and MC4R on BMI.     

Ammonia flux,physiological parameters,and <Emphasis Type="Italic">Symbiodinium</Emphasis> diversity in the anemonefish symbiosis on Red Sea coral reefs

Despite the ecological importance of anemonefish symbioses, little is known about how nutritional contributions from anemonefish interact with sea anemone physiology and Symbiodinium (endosymbiotic dinoflagellate) genetic identity under field conditions. On Red Sea coral reefs, we measured variation in ammonia concentrations near anemones, excretion rates of anemonefish, physiological parameters of anemones and Symbiodinium, and genetic identity of Symbiodinium within anemones. Ammonia concentrations among anemone tentacles were up to 49% above background levels, and anemonefish excreted ammonia significantly more rapidly after diurnal feeding than they did after nocturnal rest, similar to their excretion patterns under laboratory conditions. Levels of 4 physiological parameters (anemone protein content, and Symbiodinium abundance, chlorophyll a concentration, and division rate) were similar to those known for laboratory-cultured anemones, and in the field did not depend on the number of anemonefish per anemone or depth below sea surface. Symbiodinium abundance varied significantly with irradiance in the shaded reef microhabitats occupied by anemones. Most anemones at all depths harbored a novel Symbiodinium 18S rDNA variant within internal transcribed spacer region 2 (ITS2) type C1, while the rest hosted known ITS2 type C1. Association with Symbiodinium Clade C is consistent with the symbiotic pattern of these anemones on other Indo-Pacific reefs, but the C1 variant of Symbiodinium identified here has not been described previously. We conclude that in the field, anemonefish excrete ammonia at rapid rates that correlate with elevated concentrations among host anemone tentacles. Limited natural variation in anemonefish abundance may contribute to consistently high levels of physiological parameters in both anemones and Symbiodinium, in contrast to laboratory manipulations where removal of fish causes anemones to shrink and Symbiodinium to become less abundant.     

A Theoretical Approach to Study the Evolution of Aggregation Behavior by Larval Codling Moth, <Emphasis Type="BoldItalic">Cydia pomonella</Emphasis> (Lepidoptera: Tortricidae)

Pupation site-seeking larvae of the codling moth, Cydia pomonella, aggregate in response to aggregation pheromone produced by cocoon-spinning conspecific larvae. Larvae that pupate in an aggregation rather than in solitude may experience a lower rate of parasitism by the parasitoid Mastrus ridibundus. Additionally, adults eclosing from a larval aggregation may encounter mates more rapidly at the site of eclosion (on-site) than away from that site (off-site). We employed an evolutionary simulation to determine the effect of several ecological parameters on the evolution of larval aggregation behavior. These parameters included (i) the probability of mate encounter off-site; (ii) the time available for finding a mate; and (iii) the population density of parasitoids and their rate of larval parasitism. The model predicts that larval aggregation behavior is selected for when the probability of off-site mate encounter is low, the time to locate mates is short, and egg-limited parasitoids are at high population levels. We also show that aggregations reduce the risk of parasitism through dilution effects. The parameters found to favour the evolution of larval aggregation behavior are consistent with life history traits exhibited by C. pomonella.     

Inter‐kingdom signaling — symbiotic yeasts produce semiochemicals that attract their yellowjacket hosts

In recent studies, the yeast species Hanseniaspora uvarum and Lachancea thermotolerans were isolated from the digestive tract of four North American yellowjacket species (Hymenoptera: Vespidae), and attraction of yellowjackets to brewer's yeast, Saccharomyces cerevisiae (all Saccharomycetaceae), growing on fruit powder was demonstrated. We tested the hypothesis that Vespula spp. are attracted to cultures of H. uvarum and L. thermotolerans and their respective volatiles. In field experiments, we found that H. uvarum and L. thermotolerans are attractive to three species of yellowjacket, but only when grown on grape juice‐infused yeast peptone dextrose (YPD) agar. Using gas chromatography‐mass spectrometry, we analyzed the headspace volatiles produced by these yeasts, and field tested an 18‐component yeast synthetic semiochemical blend. This synthetic blend attracted western yellowjackets, Vespula pensylvanica (Saussure), but no other yellowjacket species. Acetic acid or ethanol added to the synthetic blend at biologically relevant doses either had no effect or significantly lowered trap captures. Our results demonstrate that yeast symbionts isolated from the digestive tract of yellowjackets are attractive to their hosts. Further research is needed to identify the volatiles mediating attraction of species other than V. pensylvanica to the yeast cultures.     

Bimodal cue complex signifies suitable oviposition sites to gravid females of the common green bottle fly

Gravid females of the common green bottle fly, Lucilia sericata Meigen (Diptera: Calliphoridae), readily locate recently deceased vertebrates as oviposition sites, particularly when these animals have been injured. We investigated semiochemical and visual cues that mediate attraction of gravid females to fresh rat carrion. Female flies were more strongly attracted to incised rat carrion than to intact carrion. They were also attracted to Porapak Q headspace volatile (HSV) extract of incised rat carrion. Analyzing aliquots of Porapak Q HSV extract by gas chromatographic‐electroantennographic detection revealed nine components [phenol, para‐ and/or meta‐cresol (could not be separated), guaiacol, dimethyl trisulfide (DMTS), phenylacetaldehyde, (E)‐2‐octenal, nonanal, and tetramethyl pyrazine] that consistently elicited responses from blow fly antennae. In laboratory experiments, a synthetic blend of these nine components was as attractive to gravid females as Porapak Q HSV extract, but blend attractiveness was due entirely to DMTS. In both laboratory and field experiments, increasing doses of DMTS attracted increasingly more flies. Coupled with DMTS, carrion‐type color cues (dark red, black) were more effective than bright color cues (white, yellow) in attracting flies. In field experiments, dark traps baited with DMTS captured a total of 214 calliphorid flies (200 L. sericata, 10 Lucilia illustris Meigen, three Calliphora vicina Robineau‐Desvoidy, one Calliphora vomitoria L.), all of which were gravid females. These results support the conclusion that DMTS and dark color represent a bimodal cue complex that signifies suitable oviposition sites to gravid calliphorid females, particularly L. sericata.     

The extracellular calcium-sensing receptor (CaSR) on human esophagus and evidence of expression of the CaSR on the esophageal epithelial cell line (HET-1A)

Gastrointestinal reflux disease and eosinophilic esophagitis are characterized by basal cell hyperplasia. The extracellular calcium-sensing receptor (CaSR), a G protein-coupled receptor, which may be activated by divalent agonists, is expressed throughout the gastrointestinal system. The CaSR may regulate proliferation or differentiation, depending on cell type and tissue. The current experiments demonstrate the expression of the CaSR on a human esophageal epithelial cell line (HET-1A) and the location and expression of the CaSR in the human esophagus. CaSR immunoreactivity was seen in the basal layer of normal human esophagus. CaSR expression was confirmed in HET-1A cells by RT-PCR, immunocytochemistry, and Western blot analysis. CaSR stimulation by extracellular calcium or agonists, such as spermine or Mg(2+), caused ERK1 and 2 activation, intracellular calcium concentration ([Ca(2+)](i)) mobilization (as assessed by microspecfluorometry using Fluo-4), and secretion of the multifunctional cytokine IL-8 (CX-CL8). HET-1A cells transiently transfected with small interfering (si)RNA duplex against the CaSR manifested attenuated responses to Ca(2+) stimulation of phospho- (p)ERK1 and 2, [Ca(2+)](i) mobilization, and IL-8 secretion, whereas responses to acetylcholine (ACh) remained sustained. An inhibitor of phosphatidylinositol-specific phospholipase C (PI-PLC) (U73122) blocked CaSR-stimulated [Ca(2+)](i) release. We conclude that the CaSR is present on basal cells of the human esophagus and is present in a functional manner on the esophageal epithelial cell line, HET-1A.     

Modulation of cellular protein trafficking by human immunodeficiency virus type 1 Nef: role of the acidic residue in the ExxxLL motif

The nef gene contributes to the replication of primate lentiviruses by altering the trafficking of cellular proteins involved in adaptive immunity (class I and II major histocompatibility complex [MHC]) and viral transmission (CD4 and DC-SIGN). A conserved acidic leucine-based sequence (E(160)xxxLL) within human immunodeficiency virus type 1 (HIV-1) Nef binds to the cellular adaptor protein (AP) complexes, which mediate protein sorting into endosomal vesicles. The leucine residues in this motif are required for the down-regulation of CD4 and for the up-regulation of DC-SIGN and the invariant chain of MHC class II, but the role of the acidic residue is unclear. Here, substitution of E160 with uncharged residues impaired the ability of Nef to up-regulate the expression of the invariant chain and DC-SIGN at the cell surface, whereas substitution with a basic residue was required for a similar effect on the down-regulation of CD4. All substitutions of E160 relieved the Nef-mediated block to transferrin uptake. E160 was required for the efficient interaction of Nef with AP-1 and AP-3 and for the stabilization of these complexes on endosomal membranes in living cells. Systematic mutation of the ExxxLL sequence together with correlation of binding and functional data leads to the hypotheses that AP-1 and AP-3 are major cofactors for the effect of Nef on the trafficking of transferrin, are less important but contribute to the modulation of the invariant chain and DC-SIGN, and are least critical for the modulation of CD4. The data suggest that the E160 residue plays a differential role in the modulation of leucine-dependent Nef-targets and support a model in which distinct AP complexes are used by Nef to modulate different cellular proteins.