Impact of Intestinal Microbiota on Intestinal Luminal Metabolome

Low–molecular-weight metabolites produced by intestinal microbiota play a direct role in health and disease. In this study, we analyzed the colonic luminal metabolome using capillary electrophoresis mass spectrometry with time-of-flight (CE-TOFMS) —a novel technique for analyzing and differentially displaying metabolic profiles— in order to clarify the metabolite profiles in the intestinal lumen. CE-TOFMS identified 179 metabolites from the colonic luminal metabolome and 48 metabolites were present in significantly higher concentrations and/or incidence in the germ-free (GF) mice than in the Ex-GF mice (p < 0.05), 77 metabolites were present in significantly lower concentrations and/or incidence in the GF mice than in the Ex-GF mice (p < 0.05), and 56 metabolites showed no differences in the concentration or incidence between GF and Ex-GF mice. These indicate that intestinal microbiota highly influenced the colonic luminal metabolome and a comprehensive understanding of intestinal luminal metabolome is critical for clarifying host-intestinal bacterial interactions

Dynamic Replacement of Histone H3 Variants Reprograms Epigenetic Marks in Early Mouse Embryos

Upon fertilization, reprogramming of gene expression is required for embryo development. This step is marked by DNA demethylation and changes in histone variant composition. However, little is known about the molecular mechanisms causing these changes and their impact on histone modifications. We examined the global deposition of the DNA replication-dependent histone H3.1 and H3.2 variants and the DNA replication-independent H3.3 variant after fertilization in mice. We showed that H3.3, a euchromatic marker of gene activity, transiently disappears from the maternal genome, suggesting erasure of the oocyte-specific modifications carried by H3.3. After fertilization, H3.2 is incorporated into the transcriptionally silent heterochromatin, whereas H3.1 and H3.3 occupy unusual heterochromatic and euchromatin locations, respectively. After the two-cell stage, H3.1 and H3.3 variants resume their usual respective locations on heterochromatin and euchromatin. Preventing the incorporation of H3.1 and H3.2 by knockdown of the histone chaperone CAF-1 induces a reciprocal increase in H3.3 deposition and impairs heterochromatin formation. We propose that the deposition of different H3 variants influences the functional organization of chromatin. Taken together, these findings suggest that dynamic changes in the deposition of H3 variants are critical for chromatin reorganization during epigenetic reprogramming

The Specification and Global Reprogramming of Histone Epigenetic Marks during Gamete Formation and Early Embryo Development in C. elegans

In addition to the DNA contributed by sperm and oocytes, embryos receive parent-specific epigenetic information that can include histone variants, histone post-translational modifications (PTMs), and DNA methylation. However, a global view of how such marks are erased or retained during gamete formation and reprogrammed after fertilization is lacking. To focus on features conveyed by histones, we conducted a large-scale proteomic identification of histone variants and PTMs in sperm and mixed-stage embryo chromatin from C. elegans, a species that lacks conserved DNA methylation pathways. The fate of these histone marks was then tracked using immunostaining. Proteomic analysis found that sperm harbor ?2.4 fold lower levels of histone PTMs than embryos and revealed differences in classes of PTMs between sperm and embryos. Sperm chromatin repackaging involves the incorporation of the sperm-specific histone H2A variant HTAS-1, a widespread erasure of histone acetylation, and the retention of histone methylation at sites that mark the transcriptional history of chromatin domains during spermatogenesis. After fertilization, we show HTAS-1 and 6 histone PTM marks distinguish sperm and oocyte chromatin in the new embryo and characterize distinct paternal and maternal histone remodeling events during the oocyte-to-embryo transition. These include the exchange of histone H2A that is marked by ubiquitination, retention of HTAS-1, removal of the H2A variant HTZ-1, and differential reprogramming of histone PTMs. This work identifies novel and conserved features of paternal chromatin that are specified during spermatogenesis and processed in the embryo. Furthermore, our results show that different species, even those with diverged DNA packaging and imprinting strategies, use conserved histone modification and removal mechanisms to reprogram epigenetic information

Probabilistic active filtering for object search in clutter

© 2019 IEEE. This paper proposes a probabilistic approach for object search in clutter. Due to heavy occlusions, it is vital for an agent to be able to gradually reduce uncertainty in observations of the objects in its workspace by systematically rearranging them. Probabilistic methodologies present a promising sample-efficient alternative to handle the massively complex state-action space that inherently comes with this problem, avoiding the need for both exhaustive training samples and the accompanying heuristics for traversing a large-scale model during runtime. We approach the object search problem by extending a Gaussian Process active filtering strategy with an additional model for capturing state dynamics as the objects are moved over the course of the activity. This allows viable models to be built upon relatively scarce training data, while the complexity of the action space is also reduced by shifting objects over relatively short distances. Validation in both simulation and with a real Baxter robot with a limited number of training samples demonstrates the efficacy of the proposed approach

Myxomycetes of the Kyushu University Forests (1)

九州大学農学部福岡演習林の照葉樹林において,2004年7月から11月にかけて広葉樹とスギ(Cryhptomeria japonica)の腐朽木に発生する変形菌類の生態を調査した.その結果,321個のコロニーが確認され,6目17属47種に分類された.樹種に対する選択性では,Cribraria tenella(アミホコリ)でスギを選択する傾向が推測された.発生の季節性に関しては,夏にはムラサキホコリ目(Stemonitales),秋にはケホコリ目(Trichiales)の割合がそれぞれ高くなった.木材の腐朽度との関連では,C.tenellaやArcyria cinerea(シロウツボホコリ)は腐朽が進んだ木材に選択性を持つが,Physarum viride(アオモジホコリ)やP.nutans(シロモジホコリ)などは腐朽が進んでいない木材に選択性を持っていた.これらのことから,腐朽木上に確認される変形菌類には,木材の種類と腐朽程度,および季節に依存した発生傾向があることが示された.Survey on the ecology of Lignicoulous Myxomycetes, occurring on a decaying wood of broadleaved tree and \u22sugi\u22 (Cryhptomeria japonica), was carried out in the evergreen broadleaved forest of the Kyushu University Forests form July to November in 2004.47 taxa belonging to 17 genera were found in 147 colonies. Investigation about the kind of wood shows Cribraria tenella preferred to \u22sugi\u22. About seasonal occurrence, Stemonitales had a high rate in summer, otherwise, Trichiales in autumn. On the degree of decaying state, C.tenella and Arcyria cinerea preferred to the strongly decayed wood. On the other hand, Physarum viride and P.nutans prefered to the slightly decayed wood. Thus, it is suggested that the tendency of appearance of Lignicolous Myxomycetes depends on the kind of wood, the seasons and the degree of decaying state of wood