Assembly of local communities: consequences of an optimal body size for the organization of competitively structured communities

Much empirical evidence suggests that there is an optimal body size for mammals and that this optimum is in the vicinity of l00g. This presumably reflects an underlying fitness function that is greatest at this mass. Here, I combine such a fitness function with an equilibrium model of competitive character displacement to assess the potential influence of a globally optimal body size in structuring local ecological communities. The model accurately predicts the range of body sizes and the average difference in size for species in communities of varying species richness. The model also predicts a uniform spacing of body sizes, rather than the gaps and clumps in the sizes of coexisting species observed in real communities. Alternative explanations for this phenomenon are discussed. The allometric relationships that result in a body size optimum subsume a large number of characteristics associated with the physiological, behavioral, demographic, and evolutionary dynamics of the species. Further integration of the underlying dynamics (e.g. individual energetics) of these relationships into all hierarchical levels of ecology will have to incorporate multiple interactive sites, spatial heterogeneity, and phylogenetic structure, but it has the potential to provide important discoveries into the means by which natural selection operates.     

Reproductive systems in conifer seed orchards

Summary In order to quantify female and male fitness values of clones in a Pinus sylvestris L. seed orchard, multilocus-genotypes of parental clones were compared with those of open pollinated seeds in the bulked orchard crop. Female and male contributions to individual seeds were distinguished by observing enzyme gene loci active in both endosperm and embryo tissue. Seed probes from two successive flowering periods were surveyed. The female and male fitnesses of five parental clones measured relative to the population mean were derived. The contributions of four clones were found to be sexually asymmetric. One clone, for instance, made exclusively female contributions in one flowering period. Variations existed in fitness values between clones. Deviations in sex specificity occurred between flowering periods: one clone contributed asymmetrically in both periods, but in sexually reversed proportions. A method to comprehensively quantify and illustrate the observed phenomena is proposed.     

Regulation of growth in larvae of the crab : The effect of cyclic temperatures

Experiments were designed to demonstrate that growth is precisely regulated in crustacean larvae and that cyclic temperatures act as a perturbation on growth regulation. Newly hatched larvae were exposed to either the specific a cyclic temperature, cumulative growth was significantly inhibited. Also, the specific growth rate ( ) of larvae in the cyclic temperature regime was found to oscillate with decreasing amplitude around the of the larvae exposed to constant temperature. This oscillatory pattern has been observed in a wide variety of self-regulating systems. Evidence is presented to demonstrate that this regulatory mechanism also adapts to long-term exposure to cyclic temperatures. These findings increase our understanding of how larvae cope with and adapt to changing environmental temperatures. More significantly, the mechanism could provide a sensitive tool for estimating the effects of specific environmental disturbances on fitness.     

A new DNA profiling system for cell line identification for use in cell banks in Japan

Summary Using the polymorphic DNA probes, ChdTC-15, ChdTC-114, pYNH24, and λTM-18, a DNA profiling system was developed that verified identities of individual cultured cell lines collected in the Japanese cell banks, JCRB, RCB, and IFO. These highly polymorphic DNA probes include both VNTR (Variable Number of Tandem Repeats) sequences and substantial lengths of unique regions. In the mixed probe system, several distinct bands from four to eight can be used for cell line identification. These bands were widely spread in a range of molecular sizes, and were stable and reproducible under stringent conditions of Southern blot hybridization. Because the DNA profile was specific for each individual human cell line, it is useful not only to authenticate many existing cultured cell lines but also to monitor their identity during propagation in a laboratory, and to confirm newly established lines as unique.     

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Simultaneous tissue profiling of eicosanoid and endocannabinoid lipid families in a rat model of osteoarthritis

We describe a novel LC method for the simultaneous and quantitative profiling of 43 oxylipins including eicosanoids, endocannabinoids, and structurally related bioactive lipids with modified acyl groups. The LC-MS/MS method uses switching at a defined time between negative and positive electrospray ionization modes to achieve optimal detection sensitivity for all the lipids. The validated method is linear over a range of 0.01–5 nmol/g (0.1–50 nmol/g for 2-arachidonoyl glycerol) with intra- and interday precision and accuracy between 1.38 and 26.76% and 85.22 and 114.3%, respectively. The method successfully quantified bioactive lipids in different tissue types in the rat, including spinal cord, dorsal root ganglia (DRGs), knee joint, brain, and plasma. Distinct regional differences in the pattern of lipid measured between tissue types were observed using principle component analysis. The method was applied to analyze tissue samples from an established preclinical rat model of osteoarthritis (OA) pain and showed that levels of 12-hydroxyeicosatetraenoic acid were significantly increased in the OA rat knee joint compared with controls, and that 15-hydroxyeicosatetraenoic acid was significantly increased in the DRGs in the model of OA compared with controls. The developed LC-MS/MS method has the potential to provide detailed pathway profiling in tissues and biofluids where the disruption of bioactive oxylipins may be involved in disease states.     

Battling for Ribosomes: Translational Control at the Forefront of the Antiviral Response

In the early stages of infection, gaining control of the cellular protein synthesis machinery including its ribosomes is the ultimate combat objective for a virus. To successfully replicate, viruses unequivocally need to usurp and redeploy this machinery for translation of their own mRNA. In response, the host triggers global shutdown of translation while paradoxically allowing swift synthesis of antiviral proteins as a strategy to limit collateral damage. This fundamental conflict at the level of translational control defines the outcome of infection. As part of this special issue on molecular mechanisms of early virus–host cell interactions, we review the current state of knowledge regarding translational control during viral infection with specific emphasis on protein kinase RNA-activated and mammalian target of rapamycin-mediated mechanisms. We also describe recent technological advances that will allow unprecedented insight into how viruses and host cells battle for ribosomes.     

Effect of the preweaning nutritional state on the cardiac protein profile and functional performance of the rat heart

The aim of the study was to find out whether the changes in nutritional status induced by different litter size during early postnatal development can influence quantitative and qualitative protein remodeling and contractile performance of the myocardium. Male Wistar rats born at the same day were pooled together at 2 days postbirth and assigned by random selection to dams in groups of 4, 8 or 16 rats/litter. The animals were investigated at the age of 4 and 16 weeks. The results revealed that the early postnatal nutritional modification altered weight parameters: whereas lower heart weight persisted in slow-growing rats until 16 weeks, higher body weight of fast-growing rats returned to the control level at the age of 16 weeks. Altered nutritional status influenced also protein remodeling of the myocardium: the concentration of all noncollagenous proteins (fractions of metabolic and contractile proteins) significantly increased in slow-growing rats, on the other hand, the concentration of collagenous proteins (pepsin-soluble and -insoluble fractions) was higher in fast-growing animals. The changes were, however, only transitional: three months after the end of the weaning period most protein changes returned to the control level. However, higher concentration of total blood lipids and triglycerides in fast-growing rats persisted until adulthood. Nutritional changes had, however, only minor effect on ventricular performance. No differences among groups were observed in basal values of the left ventricular pressure, while the maximum pressure attained after an acute ventricular loading and the contractile reserve were significantly decreased in slowgrowing 4 week old rats. The functional consequence of altered nutritional status during weaning was only transitional, in agreement with the transient character of most structural and biochemical markers of myocardial remodeling.     

Cell‐mediated immunity and multi‐locus heterozygosity in bluethroat nestlings

Recent evidence suggests that marker‐based heterozygosity‐fitness correlations may be driven by only one or a few markers, indicating local heterozygosity effects caused by linkage disequilibrium with functional genes. In this study, we investigated the relationship between microsatellite heterozygosity and a measure of cell‐mediated immunity (phytohaemagglutinin; PHA) in bluethroat (Luscinia s. svecica) nestlings using a full‐sibling design. We found significant positive associations between PHA response and two different indices of microsatellite heterozygosity, i.e. multi‐locus heterozygosity and mean d². However, model comparisons disclosed that both associations were more likely caused by local effects rather than general effects and that the two local effects appeared to be realized through two different genetic mechanisms. Our results indicate that both the random assortment of parental chromosomes during meiosis as well as inbreeding can drive heterozygosity‐fitness correlations.