Peroxisome Size Provides Insights into the Function of Autophagy-related Proteins

Autophagy is a major pathway of intracellular degradation mediated by formation of autophagosomes. Recently, autophagy was implicated in the degradation of intracellular bacteria, whose size often exceeds the capacity of normal autophagosomes. However, the adaptations of the autophagic machinery for sequestration of large cargos were unknown. Here we developed a yeast model system to study the effect of cargo size on the requirement of autophagy-related (Atg) proteins. We controlled the size of peroxisomes before their turnover by pexophagy, the selective autophagy of peroxisomes, and found that peroxisome size determines the requirement of Atg11 and Atg26. Small peroxisomes can be degraded without these proteins. However, Atg26 becomes essential for degradation of medium peroxisomes. Additionally, the pexophagy-specific phagophore assembly site, organized by the dual interaction of Atg30 with functionally active Atg11 and Atg17, becomes essential for degradation of large peroxisomes. In contrast, Atg28 is partially required for all autophagy-related pathways independent of cargo size, suggesting it is a component of the core autophagic machinery. As a rule, the larger the cargo, the more cargo-specific Atg proteins become essential for its sequestration.     

Using Quantitative Structure–Activity Relationships to Support the Assessment of the Environmental Fate and Aquatic Toxicity of a Series of Methacrylic Acid Esters

Methacrylic acid esters or methacrylates (with C1 to 8 alkyl side-chains) are a group of compounds used in the manufacture of resins and plastics. Releases to the atmosphere, surface waters, or soil can come about during manufacturing, use, transport, and storage activities. Given the potential for environmental exposures, an examination into factors that control the distribution, fate, and toxicity of methacrylates is warranted. Methacrylates are relatively volatile compounds that are easily and rapidly degraded in the atmosphere and in oxic surface waters and sediments, and so are not considered persistent. Aquatic organisms are also able to metabolize methacrylates as demonstrated by estimated bioconcentration factors of < 45 for the acid and the C1-4 esters, and a measured bioconcentration factor (BCF) for 2-EHMA. Thus, the methacrylates are not considered bioaccumulative. Acute and chronic aquatic toxicity data for the methacrylates were assembled. Quantitative structure–activity relationships (QSARs) were developed with the acute and chronic fish, invertebrate, and algal datasets to support the toxicity assessment of the methacrylates (with log octanol-water partition coefficients used as surrogates for structures). The data show the methacrylates to be of low to moderate toxicity with all acute LC/EC50 values and chronic no observed effect concentrations ranging from about 2 to 170 mg/l for the acid and C1-4 esters, and 0.1 mg/l up to the aqueous solubility limit (about 2 mg/l) for the C8 ester. The measured toxicity data and the data estimated from the QSARs were used to develop predicted no effect concentrations in water and sediment for methacrylic acid and the C1-C8 esters.     

Nitric oxide is a central component in neuropeptide regulation of appetite

In recent years, there have been a large number of neuropeptides discovered that regulate food intake. Many of these peptides regulate food intake by increasing or decreasing nitric oxide (NO). In the current study, we compared the effect of the food modulators ghrelin, NPY and CCK in NOS KO mice. Satiated homozygous and heterozygous NOS KO mice and their wild type controls were administered ghrelin ICV. Food intake was measured for 2 h post injection. Ghrelin did not increase food intake in the homozygous NOS KO mice compared to vehicle treated NOS KO mice, whereas food intake was increased in the wild type controls compared to vehicle treated wild type controls. NPY was administered ICV and food intake measured for 2 h. Homozygous NOS KO mice showed no increase in food intake after NPY administration, whereas the wild type controls did. In our final study, we administered CCK intraperitoneally to homozygous and heterozygous NOS KO mice and their wild type controls after overnight food deprivation. Food intake was measured for 1 h after injection. CCK inhibited food intake in wild type mice after overnight food deprivation, however, CCK failed to inhibit food intake in the NOS KO mice. The heterozygous mice showed partial food inhibition after the CCK. The current results add further support to the theory that NO is a central mediator in food intake.     

The α isoform of topoisomerase II is required for hypercompaction of mitotic chromosomes in human cells

As proliferating cells transit from interphase into M-phase, chromatin undergoes extensive reorganization, and topoisomerase (topo) IIα, the major isoform of this enzyme present in cycling vertebrate cells, plays a key role in this process. In this study, a human cell line conditional null mutant for topo IIα and a derivative expressing an auxin-inducible degron (AID)-tagged version of the protein have been used to distinguish real mitotic chromosome functions of topo IIα from its more general role in DNA metabolism and to investigate whether topo IIβ makes any contribution to mitotic chromosome formation. We show that topo IIβ does contribute, with endogenous levels being sufficient for the initial stages of axial shortening. However, a significant effect of topo IIα depletion, seen with or without the co-depletion of topo IIβ, is the failure of chromosomes to hypercompact when delayed in M-phase. This requires much higher levels of topo II protein and is impaired by drugs or mutations that affect enzyme activity. A prolonged delay at the G2/M border results in hyperefficient axial shortening, a process that is topo IIα-dependent. Rapid depletion of topo IIα has allowed us to show that its function during late G2 and M-phase is truly required for shaping mitotic chromosomes.     

Reconstruction of gross avian genome structure,organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

Background

The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.

Results

Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.

Conclusions

Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1060) contains supplementary material, which is available to authorized users.     

Validity and reliability of two brief physical activity questionnaires among Spanish-speaking individuals of Mexican descent

Background

Klebsiella pneumoniae is a leading cause of hospital-acquired urinary tract infections and pneumonia worldwide, and is responsible for many cases of pyogenic liver abscess among diabetic patients in Asia. A defining characteristic of this pathogen is the presence of a thick, exterior capsule that has been reported to play a role in biofilm formation and to protect the organism from threats such antibiotics and host immune challenge.

Findings

We constructed two knockout mutants of K. pneumoniae to investigate how perturbations to capsule biosynthesis alter the cellular phenotype. In the first mutant, we deleted the entire gene cluster responsible for biosynthesis of the extracellular polysaccharide capsule. In the second mutant, we deleted the capsule export subsystem within this cluster. We find that both knockout mutants have lower amounts of capsule but produce greater amounts of biofilm. Moreover, one of the two mutants abolishes fimbriae expression as well.

Conclusions

These results are expected to provide insight into the interaction between capsule biosynthesis, biofilm formation, and fimbriae expression in this organism.     

Changes in floral bouquets from compound‐specific responses to increasing temperatures

We addressed the potential effects of changes in ambient temperature on the profiles of volatile emissions from flowers and tested whether warming could induce significant quantitative and qualitative changes in floral emissions, which would potentially interfere with plant–pollinator chemical communication. We measured the temperature responses of floral emissions of various common species of Mediterranean plants using dynamic headspace sampling and used GC‐MS to identify and quantify the emitted terpenes. Floral emissions increased with temperature to an optimum and thereafter decreased. The responses to temperature modeled here predicted increases in the rates of floral terpene emission of 0.03–1.4‐fold, depending on the species, in response to an increase of 1 °C in the mean global ambient temperature. Under the warmest projections that predict a maximum increase of 5 °C in the mean temperature of Mediterranean climates in the Northern Hemisphere by the end of the century, our models predicted increases in the rates of floral terpene emissions of 0.34–9.1‐fold, depending on the species. The species with the lowest emission rates had the highest relative increases in floral terpene emissions with temperature increases of 1–5 °C. The response of floral emissions to temperature differed among species and among different compounds within the species. Warming not only increased the rates of total emissions, but also changed the ratios among compounds that constituted the floral scents, i.e. increased the signal for pollinators, but also importantly altered the signal fidelity and probability of identification by pollinators, especially for specialists with a strong reliance on species‐specific floral blends.     

Effects of light and circadian clock on growth and chlorophyll accumulation of Nannochloropsis gaditana

Circadian clocks synchronize various physiological, metabolic and developmental processes of organisms with specific phases of recurring changes in their environment (e.g. day and night or seasons). Here, we investigated whether the circadian clock plays a role in regulation of growth and chlorophyll (Chl) accumulation in Nannochloropsis gaditana, an oleaginous marine microalga which is considered as a potential feedstock for biofuels and for which a draft genome sequence has been published. Optical density (OD) of N. gaditana culture was monitored at 680 and 735 nm under 12:12 h or 18:6 h light‐dark (LD) cycles and after switching to continuous illumination in photobioreactors. In parallel, Chl fluorescence was measured to assess the quantum yield of photosystem II. Furthermore, to test if red‐ or blue‐light photoreceptors are involved in clock entrainment in N. gaditana, some of the experiments were conducted by using only red or blue light. Growth and Chl accumulation were confined to light periods in the LD cycles, increasing more strongly in the first half than in the second half of the light periods. After switching to continuous light, rhythmic oscillations continued (especially for OD₆₈₀) at least in the first 24 h, with a 50% decrease in the capacity to grow and accumulate Chl during the first subjective night. Pronounced free‐running oscillations were induced by blue light, but not by red light. In contrast, the photosystem II quantum yield was determined by light conditions. The results indicate interactions between circadian and light regulation of growth and Chl accumulation in N. gaditana.     

Otolith shape lends support to the sensory drive hypothesis in rockfishes

The sensory drive hypothesis proposes that environmental factors affect both signalling dynamics and the evolution of signals and receivers. Sound detection and equilibrium in marine fishes are senses dependent on the sagittae otoliths, whose morphological variability appears intrinsically linked to the environment. The aim of this study was to understand if and which environmental factors could be conditioning the evolution of this sensory structure, therefore lending support to the sensory drive hypothesis. Thus, we analysed the otolith shape of 42 rockfish species (Sebastes spp.) to test the potential associations with the phylogeny, biological (age), ecological (feeding habit and depth distribution) and biogeographical factors. The results showed strong differences in the otolith shapes of some species, noticeably influenced by ecological and biogeographical factors. Moreover, otolith shape was clearly conditioned by phylogeny, but with a strong environmental effect, cautioning about the use of this structure for the systematics of rockfishes or other marine fishes. However, our most relevant finding is that the data supported the sensory drive hypothesis as a force promoting the radiation of the genus Sebastes. This hypothesis holds that adaptive divergence in communication has significant influence relative to other life history traits. It has already been established in Sebastes for visual characters and organs; our results showed that it applies to otolith transformations as well (despite the clear influence of feeding and depth), expanding the scope of the hypothesis to other sensory structures.