Stream Aufwuchs accumulation processes: Effects of ecosystem depopulation

The influence of ecosystem depopulation on the Aufwuchs accumulation process was studied in experimental stream ecosystems during fall, spring, and summer 1977–1978. Aufwuchs biomass (chlorophyll a, ATP, and ash-free dry weight) accumulated slower in the depopulated streams than in the reference streams. The influence of depopulation on Aufwuchs accumulation in spring and summer disappeared in less than two weeks suggesting how rapidly stream Aufwuchs may recover from short-term catastrophes. Variability among replicate ATP measurements was less after one or two days of accumulation than after longer accumulation times.     

The impact of the unfolded protein response on human disease

A central function of the endoplasmic reticulum (ER) is to coordinate protein biosynthetic and secretory activities in the cell. Alterations in ER homeostasis cause accumulation of misfolded/unfolded proteins in the ER. To maintain ER homeostasis, eukaryotic cells have evolved the unfolded protein response (UPR), an essential adaptive intracellular signaling pathway that responds to metabolic, oxidative stress, and inflammatory response pathways. The UPR has been implicated in a variety of diseases including metabolic disease, neurodegenerative disease, inflammatory disease, and cancer. Signaling components of the UPR are emerging as potential targets for intervention and treatment of human disease.     

Fast Carbon Footprinting for Large Product Portfolios

Publicly Available Specification 2050‐2011 (PAS 2050), the Green House Gas Product Protocol (GHGPP) standard and forthcoming guideline 14067 from the International Organization for Standardization (ISO) have helped to propel carbon footprinting from a subdiscipline of life cycle assessment (LCA) to the mainstream. However, application of carbon footprinting to large portfolios of many distinct products and services is immensely resource intensive. Even if achieved, it often fails to inform company‐wide carbon reduction strategies because footprint data are disjointed or don't cover the whole portfolio. We introduce a novel approach to generate standard‐compliant product carbon footprints (CFs) for companies with large portfolios at a fraction of previously required time and expertise. The approach was developed and validated on an LCA dataset covering 1,137 individual products from a global packaged consumer goods company. Three novel techniques work in concert in a single approach that enables practitioners to calculate thousands of footprints virtually simultaneously: (i) a uniform data structure enables footprinting all products and services by looping the same algorithm; (ii) concurrent uncertainty analysis guides practitioners to gradually improve the accuracy of only those data that materially impact the results; and (iii) a predictive model generates estimated emission factors (EFs) for materials, thereby eliminating the manual mapping of a product or service's inventory to EF databases. These autogenerated EFs enable non‐LCA experts to calculate approximate CFs and alleviate resource constraints for companies embarking on large‐scale product carbon footprinting. We discuss implementation roadmaps for companies, including further road‐testing required to evaluate the effectiveness of the approach for other product portfolios, limitations, and future improvements of the fast footprinting methodology.     

The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome

Background

Chromosomal deletions are used extensively in Drosophila melanogaster genetics research. Deletion mapping is the primary method used for fine-scale gene localization. Effective and efficient deletion mapping requires both extensive genomic coverage and a high density of molecularly defined breakpoints across the genome.

Results

A large-scale resource development project at the Bloomington Drosophila Stock Center has improved the choice of deletions beyond that provided by previous projects. FLP-mediated recombination between FRT-bearing transposon insertions was used to generate deletions, because it is efficient and provides single-nucleotide resolution in planning deletion screens. The 793 deletions generated pushed coverage of the euchromatic genome to 98.4%. Gaps in coverage contain haplolethal and haplosterile genes, but the sizes of these gaps were minimized by flanking these genes as closely as possible with deletions. In improving coverage, a complete inventory of haplolethal and haplosterile genes was generated and extensive information on other haploinsufficient genes was compiled. To aid mapping experiments, a subset of deletions was organized into a Deficiency Kit to provide maximal coverage efficiently. To improve the resolution of deletion mapping, screens were planned to distribute deletion breakpoints evenly across the genome. The median chromosomal interval between breakpoints now contains only nine genes and 377 intervals contain only single genes.

Conclusions

Drosophila melanogaster now has the most extensive genomic deletion coverage and breakpoint subdivision as well as the most comprehensive inventory of haploinsufficient genes of any multicellular organism. The improved selection of chromosomal deletion strains will be useful to nearly all Drosophila researchers.     

Leaf-Associated Bacterial and Fungal Taxa Shifts in Response to Larvae of the Tree Hole Mosquito, <Emphasis Type="Italic">Ochlerotatus triseriatus</Emphasis>

Larvae of the eastern tree hole mosquito, Ochlerotatus triseriatus (Say), and related container-breeding species are known to feed upon substrate-associated microorganisms. Although the importance of these microbial resources to larval growth has been established, almost nothing is known about the taxonomic composition and dynamics of these critical microbial food sources. We examined bacterial and fungal community compositional changes on oak leaves tethered in natural tree hole habitats of O. triseriatus. We eliminated larvae experimentally in a subset of the tree holes and examined 16S rDNA gene sequences for bacteria and ergosterol concentrations and 18S rRNA gene sequences for fungi collected from leaf material subsamples. Leaf ergosterol content varied significantly with time, but not treatment. Principal component analysis (PCA) was used to compare microbial taxonomic patterns found in leaves incubated with or without larvae present, and we found that larval presence affected both bacterial and fungal groups, either from loosely attached or strongly adherent categories. Bacterial communities generally grouped more tightly when larvae were present, and class level taxa proportions changed when larvae were present, suggesting selection by larval feeding or activities for particular taxa such as members of the Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria classes. Fungal taxa composite scores also separated along PC axes related to the presence of larvae and indicated larval feeding effects on several higher taxonomic groups, including Saccharomycetes, Dothideomycetes, and Chytridiomycota. These results support the hypothesis that larval mosquito feeding and activities altered microbial communities associated with substrate surfaces, potentially leading to decreased food value of the resource and affecting decomposition of particulate matter in the system.     

Adaptation of endoplasmic reticulum exit sites to acute and chronic increases in cargo load

The biogenesis of endoplasmic reticulum (ER) exit sites (ERES) involves the formation of phosphatidylinositol-4 phosphate (PI4) and Sec16, but it is entirely unknown how ERES adapt to variations in cargo load. Here, we studied acute and chronic adaptive responses of ERES to an increase in cargo load for ER export. The acute response (within minutes) to increased cargo load stimulated ERES fusion events, leading to larger but less ERES. Silencing either PI4-kinase IIIα (PI4K-IIIα) or Sec16 inhibited the acute response. Overexpression of secretory cargo for 24 h induced the unfolded protein response (UPR), upregulated COPII, and the cells formed more ERES. This chronic response was insensitive to silencing PI4K-IIIα, but was abrogated by silencing Sec16. The UPR was required as the chronic response was absent in cells lacking inositol-requiring protein 1. Mathematical model simulations further support the notion that increasing ERES number together with COPII levels is an efficient way to enhance the secretory flux. These results indicate that chronic and acute increases in cargo load are handled differentially by ERES and are regulated by different factors.