Influence of the heterointerface sharpness on exciton recombination dynamics in an ensemble of (In,Al)As/AlAs quantum dots with indirect band-gap

The dynamics of exciton recombination in an ensemble of indirect band-gap (In,Al)As/AlAs quantum dots with type-I band alignment is studied. The lifetime of confined excitons which are indirect in momentum-space is mainly influenced by the sharpness of the heterointerface between the (In,Al)As quantum dot and the AlAs barrier matrix. Time-resolved photoluminescence experiments and theoretical model calculations reveal a strong dependence of the exciton lifetime on the thickness of the interface diffusion layer. The lifetime of excitons with a particular optical transition energy varies because this energy is obtained for quantum dots differing in size, shape and composition. The different exciton lifetimes, which result in photoluminescence with non-exponential decay obeying a power-law function, can be described by a phenomenological distribution function, which allows one to explain the photoluminescence decay with one fitting parameter only.Comment: 10 pages, 7 figure

Potential functions of LEA proteins from the brine shrimp Artemia franciscana - Anhydrobiosis meets bioinformatics.

Late embryogenesis abundant (LEA) proteins are a large group of anhydrobiosis-associated intrinsically disordered proteins (IDP), which are commonly found in plants and some animals. The brine shrimp Artemiafranciscana is the only known animal that expresses LEA proteins from three, and not only one, different groups in its anhydrobiotic life stage. The reason for the higher complexity in the A. franciscana LEA proteome (LEAome), compared with other anhydrobiotic animals, remains mostly unknown. To address this issue, we have employed a suite of bioinformatics tools to evaluate the disorder status of the ArtemiaLEAome and to analyze the roles of intrinsic disorder in functioning of brine shrimp LEA proteins. We show here that A. franciscanaLEA proteins from different groups are more similar to each other than one originally expected, while functional differences among members of group 3 are possibly larger than commonly anticipated. Our data show that although these proteins are characterized by a large variety of forms and possible functions, as a general strategy, A. franciscana utilizes glassy matrix forming LEAs concurrently with proteins that more readily interact with binding partners. It is likely that the function(s) of both types, the matrix-forming and partner-binding LEA proteins, are regulated by changing water availability during desiccation

Uniaxial stress and Zeeman spectroscopy of the 3.324 eV Ge-related photoluminescence in ZnO

Recently observed photoluminescence (PL) in ZnO, positioned at 3.324 eV and known to be related to Ge impurities, is investigated here by uniaxial stress and Zeeman spectroscopy measurements. The 3.324 eV PL line shifts but does not split under uniaxial stress both parallel and perpendicular to the c-axis, indicating trigonal defect symmetry. This reinforces the findings of prior work that the defect centre is related to a substitutional Ge impurity in ZnO. Applied magnetic fields result in linear splittings of the line into two components for fields parallel and perpendicular to the c-axis. This result combined with the temperature dependence of the Zeeman spectra enables the line to be assigned to neutral donor bound exciton recombination. Some possible models for the defect are considered

The Hg isoelectronic defect in ZnO

We report a study of the luminescence due to Hg in ZnO, concentrating on the main zero phonon line (ZPL) at 3.2766(1) eV and its associated phonon sidebands. For a sample implanted with radioactive 192Hg, the ZPL intensity, normalised to that of shallow bound exciton emission, is observed to decrease with an equivalent half-life of 4.5(1) h, very close to the 4.85(20) h half-life of 192Hg. ZnO implanted with stable Hg impurities produces the same luminescence spectrum. Temperature dependent measurements confirm that the zero phonon line is a thermalizing doublet involving one allowed and one largely forbidden transition from excited states separated by 0.91(1)meV to a common ground state. Uniaxial stress measurements show that the allowed transition takes place from an orbitally degenerate excited state to a non-degenerate ground state in a centre of trigonal (C3v) symmetry while the magneto-optical properties are characteristic of electron-hole pair recombination at an isoelectronic defect. The doublet luminescence is assigned to bound exciton recombination involving exchange-split gamma5 and gamma1,2 excited states (using C6v symmetry labels; gamma3 and gamma1,2 using C3v labels) at isoelectronic Hg impurities substituting for Zn in the crystal. The electron and hole g values deduced from the magneto-optical data indicate that this Hg impurity centre in ZnO is hole-attractive

Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins

Many large-scale studies on intrinsically disordered proteins are implicitly based on the structural models deposited in the Protein Data Bank. Yet, the static nature of deposited models supplies little insight into variation of protein structure and function under diverse cellular and environmental conditions. While the computational predictability of disordered regions provides practical evidence that disorder is an intrinsic property of proteins, the robustness of disordered regions to changes in sequence or environmental conditions has not been systematically studied. We analyzed intrinsically disordered regions in the same or similar proteins crystallized independently and studied their sensitivity to changes in protein sequence and parameters of crystallographic experiments. The observed changes in the existence, position, and length of disordered regions indicate that their appearance in X-ray structures dramatically depends on changes in amino acid sequence and peculiarities of the crystallographic experiment. Our study also raises general questions regarding protein evolution and the regulation of protein structure, dynamics, and function via variations in cellular and environmental conditions

Bayesian statistical modelling of human protein interaction network incorporating protein disorder information

<p>Abstract</p> <p>Background</p> <p>We present a statistical method of analysis of biological networks based on the exponential random graph model, namely p2-model, as opposed to previous descriptive approaches. The model is capable to capture generic and structural properties of a network as emergent from local interdependencies and uses a limited number of parameters. Here, we consider one global parameter capturing the density of edges in the network, and local parameters representing each node's contribution to the formation of edges in the network. The modelling suggests a novel definition of important nodes in the network, namely <it>social</it>, as revealed based on the local <it>sociality </it>parameters of the model. Moreover, the sociality parameters help to reveal organizational principles of the network. An inherent advantage of our approach is the possibility of hypotheses testing: <it>a priori </it>knowledge about biological properties of the nodes can be incorporated into the statistical model to investigate its influence on the structure of the network.</p> <p>Results</p> <p>We applied the statistical modelling to the human protein interaction network obtained with Y2H experiments. Bayesian approach for the estimation of the parameters was employed. We deduced <it>social </it>proteins, essential for the formation of the network, while incorporating into the model information on protein disorder. <it>Intrinsically disordered </it>are proteins which lack a well-defined three-dimensional structure under physiological conditions. We predicted the fold group (ordered or disordered) of proteins in the network from their primary sequences. The network analysis indicated that protein disorder has a positive effect on the connectivity of proteins in the network, but do not fully explains the interactivity.</p> <p>Conclusions</p> <p>The approach opens a perspective to study effects of biological properties of individual entities on the structure of biological networks.</p

ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats’ corresponding codons

Free Cysteine Modulates the Conformation of Human C/EBP Homologous Protein

The C/EBP Homologous Protein (CHOP) is a nuclear protein that is integral to the unfolded protein response culminating from endoplasmic reticulum stress. Previously, CHOP was shown to comprise extensive disordered regions and to self-associate in solution. In the current study, the intrinsically disordered nature of this protein was characterized further by comprehensive in silico analyses. Using circular dichroism, differential scanning calorimetry and nuclear magnetic resonance, we investigated the global conformation and secondary structure of CHOP and demonstrated, for the first time, that conformational changes in this protein can be induced by the free amino acid l-cysteine. Addition of l-cysteine caused a significant dose-dependent decrease in the protein helicity – dropping from 69.1% to 23.8% in the presence of 1 mM of l-cysteine – and a sequential transition to a more disordered state, unlike that caused by thermal denaturation. Furthermore, the presence of small amounts of free amino acid (80 µM, an 8∶1 cysteine∶CHOP ratio) during CHOP thermal denaturation altered the molecular mechanism of its melting process, leading to a complex, multi-step transition. On the other hand, high levels (4 mM) of free l-cysteine seemed to cause a complete loss of rigid cooperatively melting structure. These results suggested a potential regulatory function of l-cysteine which may lead to changes in global conformation of CHOP in response to the cellular redox state and/or endoplasmic reticulum stress

Total Laparoscopic Restorative Proctocolectomy: Are There Advantages Compared with the Open and Hand-Assisted Approaches?

PURPOSE: A randomized, controlled trial comparing hand-assisted laparoscopic restorative proctocolectomy with open surgery did not show an advantage for the laparoscopic approach. The trial was criticized because hand-assisted laparoscopic restorative proctocolectomy was not considered a true laparoscopic proctocolectomy. The objective of the present study was to assess whether total laparoscopic restorative proctocolectomy has advantages over hand-assisted laparoscopic restorative proctocolectomy with respect to early recovery. METHODS: Thirty-five patients underwent total laparoscopic restorative proctocolectomy and were compared to 60 patients from a previously conducted randomized, controlled trial comparing hand-assisted laparoscopic restorative proctocolectomy and open restorative proctocolectomy. End points included operating time, conversion rate, reoperation rate, hospital stay, morbidity, quality of life, and costs. The Medical Outcomes Study Short Form 36 and the Gastrointestinal Quality of Life Index were used to evaluate general and bowel-related quality of life. RESULTS: Groups were comparable for patient characteristics, such as sex, body mass index, preoperative disease duration, and age. There were neither conversions nor intraoperative complications. Median operating time was longer in the total laparoscopic compared with the hand-assisted laparoscopic group (298 vs. 214 minutes; P < 0.001). Morbidity and reoperation rates in the total laparoscopic, hand-assisted laparoscopic, and open groups were comparable (29 vs. 20 vs. 23 percent and 17 vs.10 vs. 13 percent, respectively). Median hospital-stay was 9 days in the total laparoscopic group compared with 10 days in the hand-assisted laparoscopic group and 11 days in the open group (P = not significant). There were no differences in quality of life and total costs. CONCLUSIONS: There were no significant short-term benefits for total laparoscopic compared with hand-assisted laparoscopic restorative proctocolectomy with respect to early morbidity, operating time, quality of life, costs, and hospital sta

Comparing Models of Evolution for Ordered and Disordered Proteins

Most models of protein evolution are based upon proteins that form relatively rigid 3D structures. A significant fraction of proteins, the so-called disordered proteins, do not form rigid 3D structures and sample a broad conformational ensemble. Disordered proteins do not typically maintain long-range interactions, so the constraints on their evolution should be different than ordered proteins. To test this hypothesis, we developed and compared models of evolution for disordered and ordered proteins. Substitution matrices were constructed using the sequences of putative homologs for sets of experimentally characterized disordered and ordered proteins. Separate matrices, at three levels of sequence similarity (>85%, 85–60%, and 60–40%), were inferred for each type of protein structure. The substitution matrices for disordered and ordered proteins differed significantly at each level of sequence similarity. The disordered matrices reflected a greater likelihood of evolutionary changes, relative to the ordered matrices, and these changes involved nonconservative substitutions. Glutamic acid and asparagine were interesting exceptions to this result. Important differences between the substitutions that are accepted in disordered proteins relative to ordered proteins were also identified. In general, disordered proteins have fewer evolutionary constraints than ordered proteins. However, some residues like tryptophan and tyrosine are highly conserved in disordered proteins. This is due to their important role in forming protein–protein interfaces. Finally, the amino acid frequencies for disordered proteins, computed during the development of the matrices, were compared with amino acid frequencies for different categories of secondary structure in ordered proteins. The highest correlations were observed between the amino acid frequencies in disordered proteins and the solvent-exposed loops and turns of ordered proteins, supporting an emerging structural model for disordered proteins