TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription

Peer reviewedPublisher PD

Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach

<p>Abstract</p> <p>Background</p> <p>Cichlid fishes in Lake Tanganyika exhibit remarkable diversity in their feeding habits. Among them, seven species in the genus <it>Perissodus </it>are known for their unique feeding habit of scale eating with specialized feeding morphology and behaviour. Although the origin of the scale-eating habit has long been questioned, its evolutionary process is still unknown. In the present study, we conducted interspecific phylogenetic analyses for all nine known species in the tribe Perissodini (seven <it>Perissodus </it>and two <it>Haplotaxodon </it>species) using amplified fragment length polymorphism (AFLP) analyses of the nuclear DNA. On the basis of the resultant phylogenetic frameworks, the evolution of their feeding habits was traced using data from analyses of stomach contents, habitat depths, and observations of oral jaw tooth morphology.</p> <p>Results</p> <p>AFLP analyses resolved the phylogenetic relationships of the Perissodini, strongly supporting monophyly for each species. The character reconstruction of feeding ecology based on the AFLP tree suggested that scale eating evolved from general carnivorous feeding to highly specialized scale eating. Furthermore, scale eating is suggested to have evolved in deepwater habitats in the lake. Oral jaw tooth shape was also estimated to have diverged in step with specialization for scale eating.</p> <p>Conclusion</p> <p>The present evolutionary analyses of feeding ecology and morphology based on the obtained phylogenetic tree demonstrate for the first time the evolutionary process leading from generalised to highly specialized scale eating, with diversification in feeding morphology and behaviour among species.</p

Long-term continuous degradation of carbon nanotubes by a bacteria-driven Fenton reaction

Very few bacteria are known that can degrade carbon nanotubes (CNTs), and the only known degradation mechanism is a Fenton reaction driven by Labrys sp. WJW with siderophores, which only occurs under iron-deficient conditions. No useful information is available on the degradation rates or long-term stability and continuity of the degradation reaction although several months or more are needed for CNT degradation. In this study, we investigated long-term continuous degradation of oxidized (carboxylated) single-walled CNTs (O-SWCNTs) using bacteria of the genus Shewanella. These bacteria are widely present in the environment and can drive the Fenton reaction by alternating anaerobic-aerobic growth conditions under more general environmental conditions. We first examined the effect of O-SWCNTs on the growth of S. oneidensis MR-1, and it was revealed that O-SWCNTs promote growth up to 30 μg/mL but inhibit growth at 40 μg/mL and above. Then, S. oneidensis MR-1 was subjected to incubation cycles consisting of 21-h anaerobic and 3-h aerobic periods in the presence of 30 μg/mL O-SWCNTs and 10 mM Fe(III) citrate. We determined key factors that help prolong the bacteria-driven Fenton reaction and finally achieved long-term continuous degradation of O-SWCNTs over 90 d. By maintaining a near neutral pH and replenishing Fe(III) citrate at 60 d, a degraded fraction of 56.3% was reached. S. oneidensis MR-1 produces Fe(II) from Fe(III) citrate, a final electron acceptor for anaerobic respiration during the anaerobic period. Then, ·OH is generated through the Fenton reaction by Fe(II) and H2O2 produced by MR-1 during the aerobic period. ·OH was responsible for O-SWCNT degradation, which was inhibited by scavengers of H2O2 and ·OH. Raman spectroscopy and X-ray photoelectron spectroscopy showed that the graphitic structure in O-SWCNTs was oxidized, and electron microscopy showed that long CNT fibers initially aggregated and became short and isolated during degradation. Since Shewanella spp. and iron are ubiquitous in the environment, this study suggests that a Fenton reaction driven by this genus is applicable to the degradation of CNTs under a wide range of conditions and will help researchers develop novel methods for waste treatment and environmental bioremediation against CNTs

Contribution of the Fenton reaction to the degradation of carbon nanotubes by enzymes

The widespread use of carbon nanotubes (CNTs) has raised concerns about the human health and ecological effects of CNTs released into the environment. Bacteria play an important role in bioremediation and waste treatment, and their enzymes are mostly responsible for the degradation of contaminants. However, there are still only a few reports about the bacterial degradation of CNTs, and evidence showing the involvement of bacterial enzymes in CNT degradation with their mechanisms has never been reported. The purpose of this study is to clarify whether CNTs can be degraded by bacterial enzymes. In this study, the degradation of oxidized (carboxylated) single-walled CNTs (O-SWCNTs) by mt2DyP, a dye-decolorizing peroxidase of Pseudomonas putida mt-2, a common soil bacterium, was investigated. After incubation of O-SWCNTs with recombinant mt2DyP and its substrate H2O2 for 30 d, the optical absorbance and Raman spectra revealed the degradation of O-SWCNTs. However, inactivation of the enzyme was observed within 60 min of the start of incubation, suggesting that the degradation of O-SWCNTs occurred nonenzymatically. The inactivation of mt2DyP was accompanied by the release of iron, the active center metal, and degradation of O-SWCNTs was significantly inhibited in the presence of diethylenetriamine pentaacetic acid, a chelating agent, indicating that O-SWCNTs were degraded by the Fenton reaction with iron released from mt2DyP and H2O2. The same phenomenon was observed with P450, which is also a heme enzyme. Furthermore, we investigated the contribution of the Fenton reaction to the O-SWCNT degradation by horseradish peroxidase (HRP), which was reported to enzymatically and rapidly degrade O-SWCNTs. Our results revealed that the degradation of O-SWCNTs in the presence of HRP is also mainly due to the Fenton reaction, with negligible enzymatic degradation. This contradicts the report showing enzymatic degradation of O-SWCNTs by HRP but supports the subsequent report quantitatively showing very slow transformation of O-SWCNTs by HRP. The current results emphasize that the Fenton reaction, which has received little attention in CNT degradation by heme enzymes, must be taken into consideration and will contribute to the development of a simple disposal method for CNTs, utilizing the Fenton reaction with bacteria/bacterial enzymes and H2O2

T1強調像での信号強度が出生後日数と負の相関性を示す新生児・乳児期の脳構造

Purpose: Although the neonatal and infantile brain typically shows sequential T1 shortening according to gestational age as a result of myelination, several structures do not follow this rule. We evaluated the relationship between the signal intensity of various structures in the neonatal and infantile brain on T1-weighted imaging (T1WI) and either postnatal or gestational age. Materials and Methods: We examined magnetic resonance images from 120 newborns and infants without any abnormalities in the central nervous system. Written informed consent was obtained from all parents and the institutional review board approved the study. Gestational age at examination ranged from 35 weeks, 3 days to 46 weeks, 6 days, and postnatal age ranged from 7 days to 127 days. Signal intensity on T1WI was evaluated on a scale from Grade 1 (indistinguishable from surrounding structures) to Grade 4 (higher than cortex and close to fat). We evaluated relationships between the T1 signal grades of various structures in the neonatal brain and postnatal or gestational age using Spearman’s correlation analysis. Results: Significant positive correlations were identified between T1 signal grade and gestational age in the pyramidal tract (P < 0.001). Conversely, significant negative correlations were evident between T1 signal grade and postnatal age (P < 0.001), in structures including the stria medullaris thalami, fornix cerebellar vermis, dentate nucleus and anterior pituitary gland. Conclusion: Significant negative correlations exist between signal intensity on T1WI and postnatal age in some structures of the neonatal and infantile brain. Some mechanisms other than myelination might play roles in the course of signal appearance.博士（医学）・乙第1405号・平成29年6月28日Copyright © 2017 by Japanese Society for Magnetic Resonance in Medicine : This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives International License(https://creativecommons.org/licenses/by-nc-nd/4.0/deed.ja)

Extracellular Electron Transfer via Outer Membrane Cytochromes in a Methanotrophic Bacterium Methylococcus capsulatus (Bath)

Electron exchange reactions between microbial cells and solid materials, referred to as extracellular electron transfer (EET), have attracted attention in the fields of microbial physiology, microbial ecology, and biotechnology. Studies of model species of iron-reducing, or equivalently, current-generating bacteria such as Geobacter spp. and Shewanella spp. have revealed that redox-active proteins, especially outer membrane c-type cytochromes (OMCs), play a pivotal role in the EET process. Recent (meta)genomic analyses have revealed that diverse microorganisms that have not been demonstrated to have EET ability also harbor OMC-like proteins, indicating that EET via OMCs could be more widely preserved in microorganisms than originally thought. A methanotrophic bacterium Methylococcus capsulatus (Bath) was reported to harbor multiple OMC genes whose expression is elevated by Cu starvation. However, the physiological role of these genes is unknown. Therefore, in this study, we explored whether M. capsulatus (Bath) displays EET abilities via OMCs. In electrochemical analysis, M. capsulatus (Bath) generated anodic current only when electron donors such as formate were available, and could reduce insoluble iron oxides in the presence of electron donor compounds. Furthermore, the current-generating and iron-reducing activities of M. capsulatus (Bath) cells that were cultured in a Cu-deficient medium, which promotes high levels of OMC expression, were higher than those cultured in a Cu-supplemented medium. Anodic current production by the Cu-deficient cells was significantly suppressed by disruption of MCA0421, a highly expressed OMC gene, and by treatment with carbon monoxide (CO) gas (an inhibitor of c-type cytochromes). Our results provide evidence of EET in M. capsulatus (Bath) and demonstrate the pivotal role of OMCs in this process. This study raises the possibility that EET to solid compounds is a novel survival strategy of methanotrophic bacteria

Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing

© 2020 The Author(s) Macaque monkeys are an important animal model where invasive investigations can lead to a better understanding of the cortical organization of primates including humans. However, the tools and methods for noninvasive image acquisition (e.g. MRI RF coils and pulse sequence protocols) and image data preprocessing have lagged behind those developed for humans. To resolve the structural and functional characteristics of the smaller macaque brain, high spatial, temporal, and angular resolutions combined with high signal-to-noise ratio are required to ensure good image quality. To address these challenges, we developed a macaque 24-channel receive coil for 3-T MRI with parallel imaging capabilities. This coil enables adaptation of the Human Connectome Project (HCP) image acquisition protocols to the in-vivo macaque brain. In addition, we adapted HCP preprocessing methods to the macaque brain, including spatial minimal preprocessing of structural, functional MRI (fMRI), and diffusion MRI (dMRI). The coil provides the necessary high signal-to-noise ratio and high efficiency in data acquisition, allowing four- and five-fold accelerations for dMRI and fMRI. Automated FreeSurfer segmentation of cortex, reconstruction of cortical surface, removal of artefacts and nuisance signals in fMRI, and distortion correction of dMRI all performed well, and the overall quality of basic neurobiological measures was comparable with those for the HCP. Analyses of functional connectivity in fMRI revealed high sensitivity as compared with those from publicly shared datasets. Tractography-based connectivity estimates correlated with tracer connectivity similarly to that achieved using ex-vivo dMRI. The resulting HCP-style in vivo macaque MRI data show considerable promise for analyzing cortical architecture and functional and structural connectivity using advanced methods that have previously only been available in studies of the human brain