Aerobic biodegradation of chiral phenoxyalkanoic acid derivatives during incubations with activated sludge

The aerobic biodegradation of racemic mixtures of five chiral phenoxyalkanoic acids was studied according to a biodegradation test that was complemented with enantiomer-specific analysis. Both enantiomers of (RS)-2-phenoxypropanoic acid, (RS)-2-(3-chlorophenoxy)propanoic acid, and (RS)-2-(4-chlorophenoxy)propanoic acid, were completely degraded within 25 days when aerobically incubated with activated sludge. During incubations of (RS)-2-phenoxypropanoic acid, the (R) enantiomer was degraded before the (S) enantiomer, whereas during incubations of (RS)-2-(3-chlorophenoxy)propanoic acid the (S) enantiomer was preferentially degraded. The (R) enantiomer of (RS)-2-(2-chlorophenoxy)propanoic acid was removed after 24 days while only 30% of the (S) enantiomer was degraded within 47 days of incubation. (RS)-2-(2,4,5-Trichlorophenoxy)propanoic acid was the most persistent of all the racemic mixtures tested. After 47 days, the concentration of the (S) enantiomer was nearly unchanged, and the concentration of (R)-2-(2,4,5-trichlorophenoxy)propanoic acid had decreased only by about 40%. The differences observed in the length of the lag phases and in the degradation rates of individual enantiomers can lead to accumulations of the more recalcitrant enantiomer in aquatic or terrestrial ecosystem

Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis

A stringent control of homeostasis is critical for functional maintenance and survival of neurons. In the mammalian retina, the basic motif leucine zipper transcription factor NRL determines rod versus cone photoreceptor cell fate and activates the expression of many rod-specific genes. Here, we report an integrated analysis of NRL-centered gene regulatory network by coupling chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–Seq) data from Illumina and ABI platforms with global expression profiling and in vivo knockdown studies. We identified approximately 300 direct NRL target genes. Of these, 22 NRL targets are associated with human retinal dystrophies, whereas 95 mapped to regions of as yet uncloned retinal disease loci. In silico analysis of NRL ChIP–Seq peak sequences revealed an enrichment of distinct sets of transcription factor binding sites. Specifically, we discovered that genes involved in photoreceptor function include binding sites for both NRL and homeodomain protein CRX. Evaluation of 26 ChIP–Seq regions validated their enhancer functions in reporter assays. In vivo knockdown of 16 NRL target genes resulted in death or abnormal morphology of rod photoreceptors, suggesting their importance in maintaining retinal function. We also identified histone demethylase Kdm5b as a novel secondary node in NRL transcriptional hierarchy. Exon array analysis of flow-sorted photoreceptors in which Kdm5b was knocked down by shRNA indicated its role in regulating rod-expressed genes. Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s) for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis

Nos2 Inactivation Promotes the Development of Medulloblastoma in Ptch1+/− Mice by Deregulation of Gap43–Dependent Granule Cell Precursor Migration

Medulloblastoma is the most common malignant brain tumor in children. A subset of medulloblastoma originates from granule cell precursors (GCPs) of the developing cerebellum and demonstrates aberrant hedgehog signaling, typically due to inactivating mutations in the receptor PTCH1, a pathomechanism recapitulated in Ptch1+/− mice. As nitric oxide may regulate GCP proliferation and differentiation, we crossed Ptch1+/− mice with mice lacking inducible nitric oxide synthase (Nos2) to investigate a possible influence on tumorigenesis. We observed a two-fold higher medulloblastoma rate in Ptch1+/− Nos2−/− mice compared to Ptch1+/− Nos2+/+ mice. To identify the molecular mechanisms underlying this finding, we performed gene expression profiling of medulloblastomas from both genotypes, as well as normal cerebellar tissue samples of different developmental stages and genotypes. Downregulation of hedgehog target genes was observed in postnatal cerebellum from Ptch1+/+ Nos2−/− mice but not from Ptch1+/− Nos2−/− mice. The most consistent effect of Nos2 deficiency was downregulation of growth-associated protein 43 (Gap43). Functional studies in neuronal progenitor cells demonstrated nitric oxide dependence of Gap43 expression and impaired migration upon Gap43 knock-down. Both effects were confirmed in situ by immunofluorescence analyses on tissue sections of the developing cerebellum. Finally, the number of proliferating GCPs at the cerebellar periphery was decreased in Ptch1+/+ Nos2−/− mice but increased in Ptch1+/− Nos2−/− mice relative to Ptch1+/− Nos2+/+ mice. Taken together, these results indicate that Nos2 deficiency promotes medulloblastoma development in Ptch1+/− mice through retention of proliferating GCPs in the external granular layer due to reduced Gap43 expression. This study illustrates a new role of nitric oxide signaling in cerebellar development and demonstrates that the localization of pre-neoplastic cells during morphogenesis is crucial for their malignant progression

Quantifying Earth system interactions for sustainable food production via expert elicitation

Several safe boundaries of critical Earth system processes have already been crossed due to human perturbations; not accounting for their interactions may further narrow the safe operating space for humanity. Using expert knowledge elicitation, we explored interactions among seven variables representing Earth system processes relevant to food production, identifying many interactions little explored in Earth system literature. We found that green water and land system change affect other Earth system processes strongly, while land, freshwater and ocean components of biosphere integrity are the most impacted by other Earth system processes, most notably blue water and biogeochemical flows. We also mapped a complex network of mechanisms mediating these interactions and created a future research prioritization scheme based on interaction strengths and existing knowledge gaps. Our study improves the understanding of Earth system interactions, with sustainability implications including improved Earth system modelling and more explicit biophysical limits for future food production

Tracking Water Molecules on Protein Surfaces

この論文は国立情報学研究所の電子図書館事業により電子化されました。研究会報告Water is recognized to have many important roles in influencing protein structure, folding and function. Understanding protein hydration requires the elucidation of the effects of both the solvent and the protein. While a variety of physical techniques (e.g., X-ray crystallography, small-angle X-ray scattering (SAXS), electron microscopy, NMR spectroscopy, computer simulations) are available for the characterization of protein structures in the solid state and in solution, the description of the behavior of water molecules around proteins is much more problematic, owing to the peculiarities of preferentially bound waters (short residence times, higher average density than bulk water, etc.). Localizing water molecules on protein surfaces or in crevices requires the determination of anhydrous and hydrated protein volumes and surfaces, on the one hand, and elucidation of exact topographies of protein envelopes and possible (hydrophilic) water binding sites, on the other. The latter aspect requires knowledge of the 3D structure of proteins and of the amino acid (AA) building blocks