The BioSample Database (BioSD) at the European Bioinformatics Institute.

ABSTRACT The BioSample Databas

SAIL—a software system for sample and phenotype availability across biobanks and cohorts

Summary: The Sample avAILability system—SAIL—is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables

Ultrafast Quenching of Excitons in the ZnxCd1−xS/ZnS Quantum Dots Doped with Mn2+ through Charge Transfer Intermediates Results in Manganese Luminescence

For the first time, a specific time-delayed peak was registered in the femtosecond transient absorption (TA) spectra of ZnxCd1−xS/ZnS (x~0.5) alloy quantum dots (QDs) doped with Mn2+, which was interpreted as the electrochromic Stark shift of the band-edge exciton. The time-delayed rise and decay kinetics of the Stark peak in the manganese-doped QDs significantly distinguish it from the kinetics of the Stark peak caused by exciton–exciton interaction in the undoped QDs. The Stark shift in the Mn2+-doped QDs developed at a 1 ps time delay in contrast to the instantaneous appearance of the Stark shift in the undoped QDs. Simultaneously with the development of the Stark peak in the Mn2+-doped QDs, stimulated emission corresponding to 4T1-6A1 Mn2+ transition was detected in the subpicosecond time domain. The time-delayed Stark peak in the Mn2+-doped QDs, associated with the development of an electric field in QDs, indicates the appearance of charge transfer intermediates in the process of exciton quenching by manganese ions, leading to the ultrafast Mn2+ excitation. The usually considered mechanism of the nonradiative energy transfer from an exciton to Mn2+ does not imply the development of an electric field in a QD. Femtosecond TA data were analyzed using a combination of empirical and computational methods. A kinetic scheme of charge transfer processes is proposed to explain the excitation of Mn2+. The kinetic scheme includes the reduction of Mn2+ by a 1Se electron and the subsequent oxidation of Mn1+ with a hole, leading to the formation of an excited state of manganese

Water-Soluble Products of Photooxidative Destruction of the Bisretinoid A2E Cause Proteins Modification in the Dark

Aging of the retina is accompanied by a sharp increase in the content of lipofuscin granules and bisretinoid A2E in the cells of the retinal pigment epithelium (RPE) of the human eye. It is known that A2E can have a toxic effect on RPE cells. However, the specific mechanisms of the toxic effect of A2E are poorly understood. We investigated the effect of the products of photooxidative destruction of A2E on the modification of bovine serum albumin (BSA) and hemoglobin from bovine erythrocytes. A2E was irradiated with a blue light-emitting diode (LED) source (450 nm) or full visible light (400–700 nm) of a halogen lamp, and the resulting water-soluble products of photooxidative destruction were investigated for the content of carbonyl compounds by mass spectrometry and reaction with thiobarbituric acid. It has been shown that water-soluble products formed during A2E photooxidation and containing carbonyl compounds cause modification of serum albumin and hemoglobin, measured by an increase in fluorescence intensity at 440–455 nm. The antiglycation agent aminoguanidine inhibited the process of modification of proteins. It is assumed that water-soluble carbonyl products formed as a result of A2E photodestruction led to the formation of modified proteins, activation of the inflammation process, and, as a consequence, to the progression of various senile eye pathologies

Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein

Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion

Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein

Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion