Typical Catalases: Function and Structure

Catalase (EC 1.11.1.6) is a heme-containing enzyme ubiquitously present in most aerobic organisms. Although the full range of biological functions of catalase still remains unclear, its main function is the decomposition of hydrogen peroxide into water and oxygen. Catalases have been studied for over 100 years, with examples of the enzyme isolated, purified, and characterized from many different organisms. The crystal structures of 16 heme-containing catalases have now been solved, revealing a common, highly conserved core in all enzymes. The active center consists of a heme with a tyrosine ligand on the proximal side and a conserved histidine and an aspartate on the distal side. Although catalases have been studied for many years, additional functions of catalases have recently been recognized. For example, Scytalidium thermophilum catalase (CATPO) has been shown to oxidize o-diphenolic and some p-diphenolic compounds in the absence of hydrogen peroxide. This and other studies have led to the proposal that this secondary oxidative activity may be a general characteristic of catalases. The present chapter will focus on the function and structure of monofunctional heme catalases, emphasizing the information obtained in the last few years mainly in relation to the secondary activity of these enzymes

The Advanced Energy Initiative: Challenges, Progress, and Opportunities

This talk will address hybrid vehicles and battery technology, ethanol as a fuel, and hydrogen fuel cells, the ability of these technologies to reduce oil dependence and the challenges for each approach, and the progress made. Stationary power generation, solar buildings, and portable power fuel cells will also be discussed. The presentation will be at a programmatic level and will touch on the applied research and technology development opportunities under the Advanced Energy Initiative

Regression based polynomial chaos expansion for crop phenology estimation coupled with polsar imagery

Crop phenology monitoring using Synthetic Aperture Radar(SAR) data is gaining popularity within the remote sensing community due to SAR’s all weather and large coverage imaging capability. This paper introduces a polynomial chaos expansion (PCE) based regression algorithm to retrieve BBCH scale of crops, which identifies the phenology of crops in a standardized system. The impact and applicability of the proposed methodology is successfully illustrated using the TerraSAR-X dual-pol imagery that was acquired over the cultivation period of paddy-rice fields located in Turkey. To assess the applicability of the methodology, root mean square and correlation analysis were performed under different amount of training data and number of inputs

Polarization Impact in TanDEM-X Data Over Vertical-Oriented Vegetation: The Paddy-Rice Case Study

It has been recently shown that the TanDEM-X mission is capable of tracking the plant growth of rice paddies. The precision of the elevation measure depends on the physical interaction between the synthetic aperture radar (SAR) signal and the canopy. In this letter, this interaction is studied by considering the signal polarization. In particular, the vertical and horizontal wave polarizations are compared, and their performance in the temporal mapping of the crop height is analyzed. The temporal elevation difference analysis shows a monotonically increasing trend within the reproductive stage of the canopy, with maximum height discrepancies between polarizations of about 9 cm. From an operational point of view of InSAR-based vegetation height measurements, this letter demonstrates that the oriented structure of the canopy shall be considered not only in polarimetric InSAR studies but also in the interpretation of bistatic spaceborne interferometric elevation models

Assessment of Paddy Rice Height: Sequential Inversion of Coherent and Incoherent Model

This paper investigates the evolution of canopy height of rice fields for a complete growth cycle. For this purpose, copolar interferometric Synthetic Aperture Radar (Pol-InSAR) time series data were acquired during the large across-track baseline (>1 km) science phase of the TanDEM-X mission. The height of rice canopies is estimated by three different model-based approaches. The first approach evaluates the inversion of the Random Volume over Ground (RVoG) model. The second approach evaluates the inversion of a metamodel-driven electromagnetic backscattering model by including a priori morphological information. The third approach combines the previous two processes. The validation analysis was carried out using the Pol-InSAR and ground measurement data acquired between May and September in 2015 over rice fields located in Ipsala district of Edirne, Turkey. The results of presented height estimation algorithms demonstrated the advantage of Pol-InSAR data. The combined RvoG model and EM metamodel height estimation approach provided rice canopy heights with errors less than 20 cm for the complete growth cycle

Role of Active Site Residues on Catalytic Activity of Catalase with Oxidase Activity from Scytalidium Thermophilum

AbstractScytalidium thermophilum produces a catalase with phenol oxidase activity (CATPO) that catalyses the dismutation of hydrogen peroxide (H2O2) to dioxygen and water and also oxidizes several phenolic compounds in the absence of hydrogen peroxide. It comprises 717 amino acids with a 19 amino acid signal sequence, and a 17 amino acid prosequence. It is a homotetrameric protein of molecular mass 320 kDa and subunit molecular mass 80 kDa. Although catalases have been studied for many years, a peroxide independent oxidative activity of catalases has recently been recognized. There are a great number of reports available describing the structural and biochemical characterization of catalases. However basic questions related to substrate and product flow remain unanswered, particularly related to the oxidase activity. The goals of our current studies are to investigate the main and lateral channels known that connect the deeply buried active site to the exterior of the enzyme. We have introduced a number of mutations into these regions and analyzed their specific activities

Senescence and immortality in hepatocellular carcinoma

Cataloged from PDF version of article.Cellular senescence is a process leading to terminal growth arrest with characteristic morphological features. This process is mediated by telomere-dependent, oncogene-induced and ROS-induced pathways, but persistent DNA damage is the most common cause. Senescence arrest is mediated by p16(INK4a)- and p21(Cip1)-dependent pathways both leading to retinoblastoma protein (pRb) activation. p53 plays a relay role between DNA damage sensing and p21(Cip1) activation. pRb arrests the cell cycle by recruiting proliferation genes to facultative heterochromatin for permanent silencing. Replicative senescence that occurs in hepatocytes in culture and in liver cirrhosis is associated with lack of telomerase activity and results in telomere shortening. Hepatocellular carcinoma (HCC) cells display inactivating mutations of p53 and epigenetic silencing of p16(INK4a). Moreover, they re-express telomerase reverse transcriptase required for telomere maintenance. Thus, senescence bypass and cellular immortality is likely to contribute significantly to HCC development. Oncogene-induced senescence in premalignant lesions and reversible immortality of cancer cells including HCC offer new potentials for tumor prevention and treatment. (C) 2008 Elsevier Ireland Ltd. All rights reserved

Spatially restricted loading of BRD2 at DNA double-strand breaks protects H4 acetylation domains and promotes DNA repair

The n-terminal tail of histone H4 recruits repair proteins, including 53BP1, to DNA double-strand breaks (DSB) and undergoes dynamic acetylation during DSB repair. However, how H4 acetylation (H4Ac) recruits repair proteins and reorganizes chromatin during DNA repair is unclear. Here, we show that the bromodomain protein BRD2 is recruited to DSBs. This recruitment requires binding of BRD2’s tandem bromodomains to H4Ac, which is generated at DSBs by the Tip60/KAT5 acetyltransferase. Binding of BRD2 to H4Ac protects the underlying acetylated chromatin from attack by histone deacetylases and allows acetylation to spread along the flanking chromatin. However, BRD2 recruitment is spatially restricted to a chromatin domain extending only 2 kb either side of the DSB, and BRD2 does not spread into the chromatin domains flanking the break. Instead, BRD2 facilitates recruitment of a second bromodomain protein, ZMYND8, which spreads along the flanking chromatin, but is excluded from the DSB region. This creates a spatially restricted H4Ac/BRD2 domain which reorganizes chromatin at DSBs, limits binding of the L3MBTL1 repressor and promotes 53BP1 binding, while limiting end-resection of DSBs. BRD2 therefore creates a restricted chromatin environment surrounding DSBs which facilitates DSB repair and which is framed by extensive ZMYND8 domains on the flanking chromatin

Genome-Wide Transcriptional Reorganization Associated with Senescence-to-Immortality Switch during Human Hepatocellular Carcinogenesis

Cataloged from PDF version of article.Senescence is a permanent proliferation arrest in response to cell stress such as DNA damage. It contributes strongly to tissue aging and serves as a major barrier against tumor development. Most tumor cells are believed to bypass the senescence barrier (become "immortal") by inactivating growth control genes such as TP53 and CDKN2A. They also reactivate telomerase reverse transcriptase. Senescence-to-immortality transition is accompanied by major phenotypic and biochemical changes mediated by genome-wide transcriptional modifications. This appears to happen during hepatocellular carcinoma (HCC) development in patients with liver cirrhosis, however, the accompanying transcriptional changes are virtually unknown. We investigated genome-wide transcriptional changes related to the senescence-to-immortality switch during hepatocellular carcinogenesis. Initially, we performed transcriptome analysis of senescent and immortal clones of Huh7 HCC cell line, and identified genes with significant differential expression to establish a senescence-related gene list. Through the analysis of senescence-related gene expression in different liver tissues we showed that cirrhosis and HCC display expression patterns compatible with senescent and immortal phenotypes, respectively; dysplasia being a transitional state. Gene set enrichment analysis revealed that cirrhosis/senescence-associated genes were preferentially expressed in non-tumor tissues, less malignant tumors, and differentiated or senescent cells. In contrast, HCC/immortality genes were up-regulated in tumor tissues, or more malignant tumors and progenitor cells. In HCC tumors and immortal cells genes involved in DNA repair, cell cycle, telomere extension and branched chain amino acid metabolism were up-regulated, whereas genes involved in cell signaling, as well as in drug, lipid, retinoid and glycolytic metabolism were down-regulated. Based on these distinctive gene expression features we developed a 15-gene hepatocellular immortality signature test that discriminated HCC from cirrhosis with high accuracy. Our findings demonstrate that senescence bypass plays a central role in hepatocellular carcinogenesis engendering systematic changes in the transcription of genes regulating DNA repair, proliferation, differentiation and metabolism