Functions of restored wetlands for juvenile salmon in an industrialized estuary

The Duwamish estuary is an industrialized waterway located in Seattle, WA, USA. Despite a history of habitat loss, naturally produced juvenile Chinook salmon use the estuary. In addition to experiencing degraded habitat in the estuary, wild salmon growth may be affected by competition with more than three million hatchery fish released yearly into the river. Restoring habitat to benefit salmon in the Duwamish River is a priority for trustees of public resources, and a number of wetland restoration sites have been created there. We tested the function of restored sites in the Duwamish estuary for juvenile Chinook salmon by comparing fish densities from enclosure nets or beach seines at three paired restored/un-restored sites and by applying environmental and diet data to a bioenergetics model. We also examined temporal and diet overlap of wild juvenile Chinook salmon with other salmon species and with hatchery-reared Chinook salmon using non-metric multidimensional scaling (NMDS). At a brackish upstream site with a relatively large opening to the river, we found higher densities of juvenile Chinook salmon at the restored site. NMDS results indicated that juvenile Chinook salmon fed on different taxa at the restored sites than at the reference sites. However, modeled growth was similar at restored and reference sites. Co-occurring juvenile chum and Chinook salmon fed differently, with chum eating smaller prey, and Chinook salmon eating larger prey. Co-occurring hatchery and wild juvenile Chinook salmon had similar diets, indicating that they may compete for prey. However, modeled growth was positive and did not differ between hatchery and wild fish, suggesting that food was not limiting. Bioenergetics models indicated that overall juvenile Chinook salmon growth potential at the brackish water site was consistently higher than at more saline sites. Our results suggest that restoration sites in the Duwamish estuary that have larger access openings and are located in brackish water may have increased function over other configurations.     

Pleiotropic and age-dependent effects of decreased protein modification by O-linked N-acetylglucosamine on pancreatic β-cell function and vascularization

The hexosamine biosynthesis pathway (HBP) regulates the post-translational modification of nuclear and cytoplasmic protein by O-linked N-acetylglucosamine (O-GlcNAc). Numerous studies have demonstrated increased flux through this pathway contributes to the development of β-cell dysfunction. The effect of decreased O-GlcNAc on the maintenance of normal β-cell function, however, is not well understood. We studied transgenic mice that over express β-N-acetylglucosaminidase (O-GlcNAcase), an enzyme that catalyzes the removal of O-GlcNAc from proteins, in the pancreatic β-cell under control of the rat insulin promoter. 3-4-Month-old O-GlcNAcase transgenic mice have higher glucose excursions with a concomitant decrease in circulating insulin levels, insulin mRNA levels, and total islet insulin content. In older (8-9-month-old) O-GlcNAcase transgenic mice glucose tolerance is no longer impaired. This is associated with increased serum insulin, islet insulin content, and insulin mRNA in the O-GlcNAcase transgenic mice. These improvements in β-cell function with aging are associated with increased angiogenesis and increased VEGF expression, with parallel increases in activation of Akt and expression of PGC1α. The biphasic effects as a function of age are consistent with published observations of mice with increased O-GlcNAc in islets and demonstrate that O-GlcNAc signaling exerts multiple effects on both insulin secretion and islet survival.     

Characterization of regulatory pathways in Xylella fastidiosa: genes and phenotypes controlled by algU

Many virulence genes in plant bacterial pathogens are coordinately regulated by "global" regulatory genes. Conducting DNA microarray analysis of bacterial mutants of such genes, compared with the wild type, can help to refine the list of genes that may contribute to virulence in bacterial pathogens. The regulatory gene algU, with roles in stress response and regulation of the biosynthesis of the exopolysaccharide alginate in Pseudomonas aeruginosa and many other bacteria, has been extensively studied. The role of algU in Xylella fastidiosa, the cause of Pierce's disease of grapevines, was analyzed by mutation and whole-genome microarray analysis to define its involvement in aggregation, biofilm formation, and virulence. In this study, an algU::nptII mutant had reduced cell-cell aggregation, attachment, and biofilm formation and lower virulence in grapevines. Microarray analysis showed that 42 genes had significantly lower expression in the algU::nptII mutant than in the wild type. Among these are several genes that could contribute to cell aggregation and biofilm formation, as well as other physiological processes such as virulence, competition, and survival.     

Quirks of dye nomenclature. 3. Trypan blue

Trypan blue is colorant from the 19^th century that has an association with Africa as a chemotherapeutic agent against protozoan (Trypanosomal) infections, which cause sleeping sickness. The dye still is used for staining biopsies, living cells and organisms, and it also has been used as a colorant for textiles.     

Impact of the Genetic Background on the Composition of the Chicken Plasma MiRNome in Response to a Stress

Circulating extra-cellular microRNAs (miRNAs) have emerged as promising minimally invasive markers in human medicine. We evaluated miRNAs isolated from total plasma as biomarker candidates of a response to an abiotic stress (feed deprivation) in a livestock species. Two chicken lines selected for high (R+) and low (R−) residual feed intake were chosen as an experimental model because of their extreme divergence in feed intake and energy metabolism. Adult R+ and R− cocks were sampled after 16 hours of feed deprivation and again four hours after re-feeding. More than 292 million sequence reads were generated by small RNA-seq of total plasma RNA. A total of 649 mature miRNAs were identified; after quality filtering, 148 miRNAs were retained for further analyses. We identified 23 and 19 differentially abundant miRNAs between feeding conditions and between lines respectively, with only two miRNAs identified in both comparisons. We validated a panel of six differentially abundant miRNAs by RT-qPCR on a larger number of plasma samples and checked their response to feed deprivation in liver. Finally, we evaluated the conservation and tissue distribution of differentially abundant miRNAs in plasma across a variety of red jungle fowl tissues. We show that the chicken plasma miRNome reacts promptly to the alteration of the animal physiological condition driven by a feed deprivation stress. The plasma content of stress-responsive miRNAs is strongly influenced by the genetic background, with differences reflecting the phenotypic divergence acquired through long-term selection, as evidenced by the profiles of conserved miRNAs with a regulatory role in energy metabolism (gga-miR-204, gga-miR-let-7f-5p and gga-miR-122-5p). These results reinforce the emerging view in human medicine that even small genetic differences can have a considerable impact on the resolution of biomarker studies, and provide support for the emerging interest in miRNAs as potential novel and minimally invasive biomarkers for livestock species.     

Transcriptome-based differentiation of closely-related Miscanthus lines

Background

Distinguishing between individuals is critical to those conducting animal/plant breeding, food safety/quality research, diagnostic and clinical testing, and evolutionary biology studies. Classical genetic identification studies are based on marker polymorphisms, but polymorphism-based techniques are time and labor intensive and often cannot distinguish between closely related individuals. Illumina sequencing technologies provide the detailed sequence data required for rapid and efficient differentiation of related species, lines/cultivars, and individuals in a cost-effective manner. Here we describe the use of Illumina high-throughput exome sequencing, coupled with SNP mapping, as a rapid means of distinguishing between related cultivars of the lignocellulosic bioenergy crop giant miscanthus (Miscanthus × giganteus). We provide the first exome sequence database for Miscanthus species complete with Gene Ontology (GO) functional annotations.

Results

A SNP comparative analysis of rhizome-derived cDNA sequences was successfully utilized to distinguish three Miscanthus × giganteus cultivars from each other and from other Miscanthus species. Moreover, the resulting phylogenetic tree generated from SNP frequency data parallels the known breeding history of the plants examined. Some of the giant miscanthus plants exhibit considerable sequence divergence.

Conclusions

Here we describe an analysis of Miscanthus in which high-throughput exome sequencing was utilized to differentiate between closely related genotypes despite the current lack of a reference genome sequence. We functionally annotated the exome sequences and provide resources to support Miscanthus systems biology. In addition, we demonstrate the use of the commercial high-performance cloud computing to do computational GO annotation.     

Time of Flight-Secondary Ion Mass Spectrometry on isolated extracellular fractions and intact biofilms of three species of benthic diatoms

Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) was used to study compositional characteristics of Extracellular Polymeric Substances (EPS) and compared these to characteristics of the EPS-matrix of intact diatom biofilms. Three benthic diatoms species were investigated, Cylindrotheca closterium, Navicula mutica and Nitzschia cf. brevissima. Comparison of the ToF-SIMS spectra of sequentially extracted EPS-fractions by cluster analysis and multidimensional scaling analysis (MDS) indicated that soluble and bound EPS were not distinguishable based on their ion spectra. On the contrary the water insoluble bicarbonate soluble (WIBS)-EPS-fraction formed a distinct cluster showing that this material was compositionally different from the other EPS-fractions. Ion spectra of the EPS-fractions were dissimilar to results obtained from intact biofilms. This suggested that during the extraction procedure, the structure of the EPS irreversibly changed, which alters the fragmentation patterns of the extracellular surface layer. Furthermore, from the examination of the positive ion spectra it was shown that the overall composition of EPS in the intact biofilms was different between diatom species. In spite of these differences, several common peak patterns were shared between different species. This suggests the presence of common structural components in the EPS of these diatoms that may play a role in building the surface EPS-layer.     

Iron-mediated inhibition of mitochondrial manganese uptake mediates mitochondrial dysfunction in a mouse model of hemochromatosis

Previous phenotyping of glucose homeostasis and insulin secretion in a mouse model of hereditary hemochromatosis (Hfe(-/-)) and iron overload suggested mitochondrial dysfunction. Mitochondria from Hfe(-/-) mouse liver exhibited decreased respiratory capacity and increased lipid peroxidation. Although the cytosol contained excess iron, Hfe(-/-) mitochondria contained normal iron but decreased copper, manganese, and zinc, associated with reduced activities of copper-dependent cytochrome c oxidase and manganese-dependent superoxide dismutase (MnSOD). The attenuation in MnSOD activity was due to substantial levels of unmetallated apoprotein. The oxidative damage in Hfe(-/-) mitochondria is due to diminished MnSOD activity, as manganese supplementation of Hfe(-/-) mice led to enhancement of MnSOD activity and suppressed lipid peroxidation. Manganese supplementation also resulted in improved insulin secretion and glucose tolerance associated with increased MnSOD activity and decreased lipid peroxidation in islets. These data suggest a novel mechanism of iron-induced cellular dysfunction, namely altered mitochondrial uptake of other metal ions.     

Cardiac hypertrophy: synergistic effects of pericardiectomy and mild exercise in rats.

Removal of the pericardium in combination with a mild exercise program of swimming resulted in a significant increase in heart weight and heart weight/body weight ratio of young rats. Either exercise or pericardiectomy alone did not significantly alter these parameters as compared to the control group of rats. This finding further substantiates the pericardium's physiologic effect on the heart. The effects of pericardiectomy should be considered in experimental studies of cardiac hypertrophy and in clinical studies involving cardiac surgery.     

Copper Hypersensitivity and Uptake in Pseudomonas syringae Containing Cloned Components of the Copper Resistance Operon

Copper resistance in Pseudomonas syringae carrying the copABCD operon is associated with accumulation of copper in the periplasm and outer membrane, apparently as a function of the copper-binding activities of the copABC gene products. However, no specific function for copD has been determined. In this study, P. syringae cells containing copCD or copBCD cloned behind the lac promoter were hypersensitive to copper. An increased accumulation of copper was measured in cells containing several combinations of cop genes that included copC and copD. Our data suggest that CopC, a periplasmic copper-binding protein, and CopD, a probable inner membrane protein, may function together in copper uptake.