PHOTOCHEMISTRY OF PHYCOBILIPROTEINS

Native PEC from the cyanobacterium, Mastigocladus laminosus, and its isolated α-subunit show photoreversibly photochromic reactions with difference-maxima around 502 and 570 nm in the spectral region of the α-84 phycoviolobilin chromophore. (b) Native PEC and its β-subunit show little if any reversible photochemistry in the 600–620 nm region, where the phycocyanobilin chromophores on the β-subunit absorb maximally, (c) Reversible photochemistry is retained in ureadenatured PEC at pH = 7.0 or pH ≤ 3. The difference maxima are shifted to 510 and 600 nm, and the amplitudes are decreased. An irreversible absorbance increase occurs around 670 nm (pH ≤ 3). (d) The amplitude of the reversible photoreaction difference spectrum is maximum in the presence of 4–5 M urea or 1 M KSCN, conditions known to dissociate phycobiliprotein aggregates into monomers. At the same time, the phycocyanobilin chromophore(s) are bleached irreversibly, (e) The amplitude becomes very small in high aggregates, e.g. in phycobilisomes. (f) In a reciprocal manner, the phototransformation of native PEC leads to a reversible shift of its aggregation equilibrium between trimer and monomer. The latter is favored by orange, the former by green light, (g) It is concluded that the phycoviolobilin chromophore of PEC is responsible for reversible photochemistry in PEC, and that there is not only an influence of aggregation state on photochemistry, but also vice versa an effect of the status of the chromophore on aggregation state. This could constitute a primary signal in the putative function as sensory pigment, either directly, or indirectly via the release of other polypeptides, via photodynamic effects, or the like

Simcluster: clustering enumeration gene expression data on the simplex space

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space.

Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster.

Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data

Influence of chromophores on quarternary structure of phycobiliproteins from the cyanobacterium, Mastigocladus laminosus

Chromophores of C-phycocyanin and phycoerythrο-cyanin have been chemically modified by reduction to rubins , bleaching , photoisomerization , or perturbation with bulky substituents. Pigments containing modified chromophores, or hybrids containing modified and unmodified chromophores in individual protomers have been prepared. All modifications inhibit the association of the (aß)-protomers of these pigments to higher aggregates. The results demonstrate a pronounced effect of the state of the chromophores on biliprotein quaternary structure. It may be important in phycobi1isome assembly , and also in the dual function of biliproteins as (i) antenna pigments for photosynthesis and (ii) reaction centers for photomor-phogenesis

Characteristics of Liver Transplantation in Argentina: A Multicenter Study

Introduction: There is a lack of information regarding outcomes after liver transplant in Latin America. Objectives: This study sought to describe outcomes after liver transplant in adult patients from Argentina. Methods: We performed an ambispective cohort study of adult patients transplanted between June 2010 and October 2012 in 6 centers from Argentina. Only patients who survived after the first 48 hours postransplantation were included. Pretransplantation and posttransplantation data were collected. Results: A total of 200 patients were included in the study. Median age at time of transplant was 50 (interquartile range [IQR] 26 to 54) years. In total, 173 (86%) patients had cirrhosis, and the most frequent etiology in these patients was hepatitis C (32%). A total of 35 (17%) patients were transplanted with hepatocellular carcinoma. In patients with cirrhosis, the median Model for End-Stage Liver Disease (MELD) score at time of liver transplant was 25 (IQR 19 to 30). Median time on the waiting list for elective patients was 101 (IQR 27 to 295) days, and 3 (IQR 2 to 4) days for urgent patients. Almost 40% of the patients were readmitted during the first 6 months after liver transplant. Acute rejection occurred in 27% of the patients. Biliary and vascular complications were reported in 39 (19%) and 19 (9%) patients, respectively. Renal failure, diabetes, and dyslipidemia were present in 40 (26%), 87 (57%), and 77 (50%) at 2 years, respectively. Conclusions: We believe the information contained in this article might be of value for reviewing current practices and developing local policies.Fil: Haddad, L.. Instituto Universitario del Hospital Italiano de Buenos Aires; ArgentinaFil: Marciano, S.. Instituto Universitario del Hospital Italiano de Buenos Aires; ArgentinaFil: Cleres, M.. Fundación Favaloro; ArgentinaFil: Zerega, A.. Sanatorio Allende; ArgentinaFil: Piñero, F.. Hospital Universitario Austral; ArgentinaFil: Orozco, F.. Hospital Aleman; ArgentinaFil: Braslavsky, G.. Hospital General de Agudos Cosme Argerich; ArgentinaFil: Mendizabal, M.. Hospital Universitario Austral; ArgentinaFil: Gondolesi, Gabriel Eduardo. Fundación Favaloro; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Medicina Traslacional, Trasplante y Bioingeniería. Fundación Favaloro. Instituto de Medicina Traslacional, Trasplante y Bioingeniería; ArgentinaFil: Gil, O.. Sanatorio Allende; ArgentinaFil: Silva, M.. Hospital Universitario Austral; ArgentinaFil: Mastai, Ricardo. Hospital Aleman; ArgentinaFil: Imvertaza, O.. Hospital General de Agudos Cosme Argerich; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Medicina Traslacional, Trasplante y Bioingeniería. Fundación Favaloro. Instituto de Medicina Traslacional, Trasplante y Bioingeniería; ArgentinaFil: Descalzi, V.. Fundación Favaloro; ArgentinaFil: Gadano, A.. Instituto Universitario del Hospital Italiano de Buenos Aires; Argentin

A kinetic study on the photodynamic properties of the xanthene dye merbromin (mercurochrome) and its aggregates with amino acids in aqueous solution

The photophysical properties and the photobleaching of the xanthene dye merbromin(MR), as well as the production and quenching of singlet molecular oxygen, O₂(¹∆g), were investigated in aqueous solutions, in comparison with the xanthene dyes eosine (Eos) and rose bengal (RB). MR photobleaches in the absence of O₂ in a process involving the solvent (H₂O or alcohols). No participation of O₂ or O₂(¹∆g) could be established in the presence of O₂, although O₂ Is consumed. In aqueous and alcoholic solutions, MR forms ground state charge transfer (CT) complexes with biologically relevant electron donor amino acids, such as histidine, thyptophan, and other indolic derivatives. These complexes are formed with relatively high association constants (3 x 10³ - 5 x 10³) and are mainly responsible for the photobleaching of MR and the amino acids in these solutions by a mechanism involving O₂(¹∆g) generated probably by an excited state of the CT complex. MR generates O₂(¹∆g) with a relatively high yield (Φ ∆= 0.23 ± 0.04) and quenches O₂(¹∆g) only physically with = (2.3 ± 0.05) 108 M⁻¹ s⁻¹. This process does not affect the photosensitizing ability of MR under the low concentrations needed for its action. Non-donor compounds like the amino acid methionine and linoleic acid methyl ester are photodegraded by a Type II mechanism without implication of a dye CT complex.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Infrared spectroscopy of phytochrome and model pigments

Fourier-transform infrared difference spectra between the red-absorbing and far-red-absorbing forms of oat phytochrome have been measured in H2O and 2H2O. The difference spectra are compared with infrared spectra of model compounds, i.e. the (5Z,10Z,15Z)- and (5Z,10Z,15E)-isomers of 2,3,7,8,12,13,17,18-octaethyl-bilindion (Et8-bilindion), 2,3-dihydro-2,3,7,8,12,13,17,18-octaethyl-bilindion (H2Et8-bilindion), and protonated H2Et8-bilindion in various solvents. The spectra of the model compounds show that only for the protonated forms can clear differences between the two isomers be detected. Since considerable differences are present between the spectra of Et8-bilindion and H2Et8-bilindion, it is concluded that only the latter compound can serve as a model system of phytochrome. The 2H2O effect on the difference spectrum of phytochrome supports the view that the chromophore in red-absorbing phytochrome is protonated and suggests, in addition, that it is also protonated in far-red-absorbing phytochrome. The spectra show that protonated carboxyl groups are influenced. The small amplitudes in the difference spectra exclude major changes of protein secondary structure

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Photochemistry and photophysics of thienocarbazoles

Two methylated thienocarbazoles and two of their synthetic nitro-precursors have been examined by absorption, luminescence, laser flash photolysis and photoacoustic techniques. Their spectroscopic and photophysical characterization involves fluorescence spectra, fluorescence quantum yields and lifetimes, and phosphorescence spectra and phosphorescence lifetimes for all the compounds. Triplet-singlet difference absorption spectra, triplet molar absorption coefficients, triplet lifetimes, intersystem crossing S-1 similar tosimilar to--> T-1 and singlet molecular oxygen yields were obtained for the thienocarbazoles. In the case of the thienocarbazoles it was found that the lowest-lying singlet and triplet excited states, S, and T-1, are of pi,pi* origin, whereas for their precursors S-1 is n,pi*, and T-1 is pi,pi*. In both thienocarbazoles it appears that the thianaphthene ring dictates the S, T, yield, albeit there is less predominance of that ring in the triplet state of the linear thienocarbazole, which leads to a decrease in the observed Phi(T) value.info:eu-repo/semantics/publishedVersio

Connector Inversion Probe Technology: A Powerful One-Primer Multiplex DNA Amplification System for Numerous Scientific Applications

We combined components of a previous assay referred to as Molecular Inversion Probe (MIP) with a complete gap filling strategy, creating a versatile powerful one-primer multiplex amplification system. As a proof-of-concept, this novel method, which employs a Connector Inversion Probe (CIPer), was tested as a genetic tool for pathogen diagnosis, typing, and antibiotic resistance screening with two distinct systems: i) a conserved sequence primer system for genotyping Human Papillomavirus (HPV), a cancer-associated viral agent and ii) screening for antibiotic resistance mutations in the bacterial pathogen Neisseria gonorrhoeae. We also discuss future applications and advances of the CIPer technology such as integration with digital amplification and next-generation sequencing methods. Furthermore, we introduce the concept of two-dimension informational barcodes, i.e. “multiplex multiplexing padlocks” (MMPs). For the readers' convenience, we also provide an on-line tutorial with user-interface software application CIP creator 1.0.1, for custom probe generation from virtually any new or established primer-pairs