Technological Applications of Porphyrins and Related Compounds: Spintronics and Micro-/Nanomotors

The vital role played by porphyrins in cells and their use in therapeutic processes are well known. More recently, the technological applications of porphyrins have attracted the attention of researchers. Porphyrins have the property of half-metallic material, i.e., molecules that can host transition metals making feasible the production of spin-polarized electronic states at different channels. Therefore, porphyrins and hemeproteins are among the materials that have spin-filtering property to be applied in spintronics. Molecular spintronics is an emerging and highly relevant field due to their applications to the development of high-capacity information-storage devices and quantum computers. The catalytic properties of porphyrins and related compounds such as the hemeproteins are also applicable in the fabrication of micro-/nanomotors (MNMs). In this chapter, we describe the advances and future perspectives in the technological applications of porphyrins and related compounds in spintronic devices and micro-/nanomotors

Indexing Strategies for Rapid Searches of Short Words in Genome Sequences

Searching for matches between large collections of short (14–30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile tool for rapidly searching multiple genomes, whose performance is limited in most cases by the speed of access to the filesystem. We have made publicly available a Web interface for searching the human, mouse, and several other genomes and transcriptomes with oligonucleotide queries

Untersuchung von Renaturierungskonzepten am Seeufer Gals, Bielersee

Analyse des ökologischen Aufwertungspotentials am Seeufer Gals (Bielersee, Schweiz), welche mithilfe einer hydrodynamisch- numerischen Modellierung mit der Software MIKE 21 und Bestimmung von Makrophyten vorgenommen wurde. Unter der Annahme von zwei unterschiedlich starken Windszenarien wurden die windinduzierten signifikanten Wellenhöhen und die welleninduzierten Strömungen für verschiedene Varianten simuliert. Die Ergebnisse der Modellierungen zeigten, ob die in den Varianten geplanten Massnahmen eine Reduzierung der Wellenhöhen und der Strömungen verursachen. Das Hauptziel war, Bedingungen zu schaffen, welche den Habitatsansprüchen von Makrophyten zusagen und somit eine Neuansiedlung von Makrophytenarten an dem Seeufer Gals möglich machen und gleichzeitig die Wellenbelastung auf das Ufer zu verringern, um eine fortschreitende Erosion zu vermeiden. Mithilfe einiger Massnahmen konnten erfolgsversprechende Ergebnisse erzielt werden, die zu einer Verbesserung der aktuellen Situation führen würden. Es wurde ebenfalls gezeigt, dass Makrophyten für die Beurteilung eine bedeutende Rolle spielen, doch eine Bewertung nur anhand von ihnen sehr schwierig ist, da sie nicht nur auf Wellen- und Strömungsbedingungen, sondern auf weitere Faktoren und zudem extrem schnell auf deren Veränderungen reagieren. Die Studie wurde im Rahmen einer Masterarbeit an der TU Dresden im Landschaftswerk Biel-Seeland durchgeführt

Rapid evolution of cancer/testis genes on the X chromosome

BACKGROUND: Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated in the cancer state. This unusual property, together with the finding that many CT proteins elicit an antigenic response in cancer patients, has established a role for this class of genes as targets in immunotherapy regimes. Many families of CT genes have been identified in the human genome, but their biological function for the most part remains unclear. While it has been shown that some CT genes are under diversifying selection, this question has not been addressed before for the class as a whole. RESULTS: To shed more light on this interesting group of genes, we exploited the generation of a draft chimpanzee (Pan troglodytes) genomic sequence to examine CT genes in an organism that is closely related to human, and generated a high-quality, manually curated set of human:chimpanzee CT gene alignments. We find that the chimpanzee genome contains homologues to most of the human CT families, and that the genes are located on the same chromosome and at a similar copy number to those in human. Comparison of putative human:chimpanzee orthologues indicates that CT genes located on chromosome X are diverging faster and are undergoing stronger diversifying selection than those on the autosomes or than a set of control genes on either chromosome X or autosomes. CONCLUSION: Given their high level of diversifying selection, we suggest that CT genes are primarily responsible for the observed rapid evolution of protein-coding genes on the X chromosome

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.

The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus

Baccharis dracunculifolia, the main source of green propolis, exhibits potent antioxidant activity and prevents oxidative mitochondrial damage

Baccharis dracunculifolia DC (Asteraceae) is the main botanical source used by honeybees to produce Brazilian green propolis whose hepatoprotective properties have been already described. in this work we investigated the protective effects of the glycolic extract of B. dracunculifolia (GEBd) against oxidative stress in isolated rat liver mitochondria (RLM). the GEBd was prepared by fractionated percolation using propylene glycol as solvent. the total phenols and flavonoids, which are substances with recognized antioxidant action, were quantified in GEBd and the phytochemical analysis was carried out by HPLC. GEBd exhibited significant scavenger activity towards DPPH radicals and superoxide anions in a concentration-dependent manner, and also a Fe2+ chelating activity. GEBd decreased the basal H2O2 generation and the Fe2+- or t-BuOOH-induced ROS production in isolated mitochondria. Lipid oxidation of mitochondrial membranes, protein thiol groups and GSH oxidation were also prevented by GEBd. This shows that B. dracunculifolia exhibit potent antioxidant activity protecting liver mitochondria against oxidative damage and such action probably contribute to the antioxidant and hepatoprotective effects of green propolis. (C) 2011 Elsevier B.V. All rights reserved.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Mogi das Cruzes UMC, Ctr Interdisciplinar Invest Bioquim CIIB, Mogi Das Cruzes, SP, BrazilUniv Estadual Paulista UNESP, Inst Quim, São Paulo, BrazilFac Ciencias Farmaceut Ribeirao Preto FCFRP USP, São Paulo, BrazilUniversidade Federal de São Paulo UNIFESP, Dept Bioquim, São Paulo, BrazilUniv Fed ABC UFABC, Ctr Ciencias Nat & Humanas CCNH, Santo Andre, SP, BrazilUniversidade Federal de São Paulo UNIFESP, Dept Bioquim, São Paulo, BrazilFAPESP: 2008/01724-4FAPESP: 2008/07246-7CNPq: 301672/2009-1CNPq: 136255/2009-4Web of Scienc

Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

Hen egg-white lysozyme has long been the paradigm for enzymatic glycosyl hydrolysis with retention of configuration, with a protonated carboxylic acid and a deprotonated carboxylate participating in general acid-base catalysis. In marked contrast, the retaining chitin degrading enzymes from glycosyl hydrolase families 18 and 20 all have a single glutamic acid as the catalytic acid but lack a nucleophile on the enzyme. Both families have a catalytic (βα)8-barrel domain in common. X-ray structures of three different chitinolytic enzymes complexed with substrates or inhibitors identify a retaining mechanism involving a protein acid and the carbonyl oxygen atom of the substrate’s C2 N-acetyl group as the nucleophile. These studies unambiguously demonstrate the distortion of the sugar ring toward a sofa conformation, long postulated as being close to that of the transition state in glycosyl hydrolysis.