Pokefind: a novel topological filter for use with protein structure prediction

Motivation: Our focus has been on detecting topological properties that are rare in real proteins, but occur more frequently in models generated by protein structure prediction methods such as Rosetta. We previously created the Knotfind algorithm, successfully decreasing the frequency of knotted Rosetta models during CASP6. We observed an additional class of knot-like loops that appeared to be equally un-protein-like and yet do not contain a mathematical knot. These topological features are commonly referred to as slip-knots and are caused by the same mechanisms that result in knotted models. Slip-knots are undetectable by the original Knotfind algorithm. We have generalized our algorithm to detect them, and analyzed CASP6 models built using the Rosetta loop modeling method

Variation in OPA1 does not explain the incomplete penetrance of Leber hereditary optic neuropathy

Purpose: Leber hereditary optic neuropathy (LHON) is a common cause of inherited blindness, primarily due to one of three mitochondrial DNA (mtDNA) mutations. These mtDNA pathogenic mutations have variable clinical penetrance. Recent linkage evidence raised the possibility that the nuclear gene optic atrophy 1 (OPA1) determines whether mtDNA mutation carriers develop blindness. To validate these findings we studied OPA1 in three independent LHON cohorts: sequencing the gene in discordant male sib pairs, carrying out a family-based association study of common functional genetic variants, and carrying out a population-based association study of the same genetic variants.Methods: We tested 3 hypothesis in three separate study groups. Study group 1: Direct sequencing of OPA1 coding regions was performed using sequencing methodologies (Applied Biosystems, Foster City, CA). Chromatograms were compared with the GenBank reference sequence NM_015560.1. Splice-site prediction was performed using GeneSplicer. Study group 2: Genotyping for rs166850 and rs10451941 was performed by restriction fragment length polymorphism (RFLP) analysis with specific primers for both genotypes, using The restriction enzymes RsaI and FspBI to discriminate genotypes. Study group 3: Genotyping for rs166850 and rs10451941 was performed by primer extension of allele-specific extensions products by matrix-associated laser desorption/ionisation time-of-flight (MALDI-TOF, Seqeunom, San Diego, CA) mass spectrometry. Allele and genotype frequencies were compared using Pearson's chi-square test. Multiple logistic regression was performed to look for interactions between the variables. All analyses were performed using SPSS software version 17.0 (SPSS Inc.).Results: In all three groups we were unable to find an association between OPA1 genetic variation and visual failure in LHON mtDNA mutation carriers.Conclusions: Our findings suggest that genetic variation in OPA1 is unlikely to make a major contribution to the risk of blindness in LHON mutation carriers.Medical Research Council (UK)UK Parkinson Disease SocietyUK NIHR Biomedical Research Centre for Aging and AgeTelethon-ItalyNewcastle Univ, Inst Human Genet, Newcastle Upon Tyne NE1 3BZ, Tyne & Wear, EnglandRoyal Victoria Infirm, Dept Ophthalmol, Newcastle Upon Tyne NE1 4LP, Tyne & Wear, EnglandUniv Bologna, Dept Neurol Sci, Bologna, ItalyUniv Fed Sao Paulo, UNIFESP, Dept Oftalmol, Sao Paulo, BrazilFdn Neurol Inst C Besta, Unit Mol Neurogenet, Milan, ItalyUniv Fed Sao Paulo, UNIFESP, Dept Oftalmol, Sao Paulo, BrazilTelethon-Italy: GGP06233Web of Scienc

Организация СРС в рамках модульно-рейтинговой системы

Показан подход к организации самостоятельной работы студентов (СРС) в рамках модульно-рейтинговой системы. Представлена модель организации СРС, анализируется содержание ее элементов. Отмечаются организационно-методические трудности, которые могут возникнуть при ее внедрении

Strong extinction of a far-field laser beam by a single quantum dot

Through the utilization of index-matched GaAs immersion lens techniques we demonstrate a record extinction (12%) of a far-field focused laser by a single InAs/GaAs quantum dot. This contrast level enables us to report for the first time resonant laser transmission spectroscopy on a single InAs/GaAs quantum dot without the need for phase-sensitive lock-in detection

Ultrafast optical rotations of electron spins in quantum dots

Coherent manipulation of quantum bits (qubits) on time scales much shorter than the coherence time is a key prerequisite for quantum information processing. Electron spins in quantum dots (QDs) are particularly attractive for implementations of qubits. Efficient optical methods for initialization and readout of spins have been developed in recent years. Spin coherence times in the microsecond range have been demonstrated, so that spin control by picosecond optical pulses would be highly desirable. Then a large number of spin rotations could be performed while coherence is maintained. A major remaining challenge is demonstration of such rotations with high fidelity. Here we use an ensemble of QD electron spins focused into a small number of precession modes about a magnetic field by periodic optical pumping. We demonstrate ultrafast optical rotations of spins about arbitrary axes on a picosecond time scale using laser pulses as control fields.Comment: 10 pages, 4 figure

Quantum computing with defects

Identifying and designing physical systems for use as qubits, the basic units of quantum information, are critical steps in the development of a quantum computer. Among the possibilities in the solid state, a defect in diamond known as the nitrogen-vacancy (NV-1) center stands out for its robustness - its quantum state can be initialized, manipulated, and measured with high fidelity at room temperature. Here we describe how to systematically identify other deep center defects with similar quantum-mechanical properties. We present a list of physical criteria that these centers and their hosts should meet and explain how these requirements can be used in conjunction with electronic structure theory to intelligently sort through candidate defect systems. To illustrate these points in detail, we compare electronic structure calculations of the NV-1 center in diamond with those of several deep centers in 4H silicon carbide (SiC). We then discuss the proposed criteria for similar defects in other tetrahedrally-coordinated semiconductors.Comment: 31 pages, 7 figures, 2 table

Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response

Dramatic rise of mutators has been found to accompany adaptation of bacteria in response to many kinds of stress. Two views on the evolutionary origin of this phenomenon emerged: the pleiotropic hypothesis positing that it is a byproduct of environmental stress or other specific stress response mechanisms and the second order selection which states that mutators hitchhike to fixation with unrelated beneficial alleles. Conventional population genetics models could not fully resolve this controversy because they are based on certain assumptions about fitness landscape. Here we address this problem using a microscopic multiscale model, which couples physically realistic molecular descriptions of proteins and their interactions with population genetics of carrier organisms without assuming any a priori fitness landscape. We found that both pleiotropy and second order selection play a crucial role at different stages of adaptation: the supply of mutators is provided through destabilization of error correction complexes or fluctuations of production levels of prototypic mismatch repair proteins (pleiotropic effects), while rise and fixation of mutators occur when there is a sufficient supply of beneficial mutations in replication-controlling genes. This general mechanism assures a robust and reliable adaptation of organisms to unforeseen challenges. This study highlights physical principles underlying physical biological mechanisms of stress response and adaptation

Quantum Computing

Quantum mechanics---the theory describing the fundamental workings of nature---is famously counterintuitive: it predicts that a particle can be in two places at the same time, and that two remote particles can be inextricably and instantaneously linked. These predictions have been the topic of intense metaphysical debate ever since the theory's inception early last century. However, supreme predictive power combined with direct experimental observation of some of these unusual phenomena leave little doubt as to its fundamental correctness. In fact, without quantum mechanics we could not explain the workings of a laser, nor indeed how a fridge magnet operates. Over the last several decades quantum information science has emerged to seek answers to the question: can we gain some advantage by storing, transmitting and processing information encoded in systems that exhibit these unique quantum properties? Today it is understood that the answer is yes. Many research groups around the world are working towards one of the most ambitious goals humankind has ever embarked upon: a quantum computer that promises to exponentially improve computational power for particular tasks. A number of physical systems, spanning much of modern physics, are being developed for this task---ranging from single particles of light to superconducting circuits---and it is not yet clear which, if any, will ultimately prove successful. Here we describe the latest developments for each of the leading approaches and explain what the major challenges are for the future.Comment: 26 pages, 7 figures, 291 references. Early draft of Nature 464, 45-53 (4 March 2010). Published version is more up-to-date and has several corrections, but is half the length with far fewer reference

Random Amino Acid Mutations and Protein Misfolding Lead to Shannon Limit in Sequence-Structure Communication

The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions) and in structure (structural defects) trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a) sensitive to random errors and (b) restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials