Protein and DNA sequence determinants of thermophilic adaptation

Prokaryotes living at extreme environmental temperatures exhibit pronounced signatures in the amino acid composition of their proteins and nucleotide compositions of their genomes reflective of adaptation to their thermal environments. However, despite significant efforts, the definitive answer of what are the genomic and proteomic compositional determinants of Optimal Growth Temperature of prokaryotic organisms remained elusive. Here the authors performed a comprehensive analysis of amino acid and nucleotide compositional signatures of thermophylic adaptation by exhaustively evaluating all combinations of amino acids and nucleotides as possible determinants of Optimal Growth Temperature for all prokaryotic organisms with fully sequences genomes.. The authors discovered that total concentration of seven amino acids in proteomes, IVYWREL, serves as a universal proteomic predictor of Optimal Growth Temperature in prokaryotes. Resolving the old-standing controversy the authors determined that the variation in nucleotide composition (increase of purine load, or A+G content with temperature) is largely a consequence of thermal adaptation of proteins. However, the frequency with which A and G nucleotides appear as nearest neighbors in genome sequences is strongly and independently correlated with Optimal Growth Temperature. as a result of codon bias in corresponding genomes. Together these results provide a complete picture of proteomic and genomic determinants of thermophilic adaptation.Comment: in press PLoS Computational Biology; revised versio

Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins

The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design sequences with selected thermal properties. Compositional analysis of designed model sequences and natural proteomes reveals a specific trend in amino acid compositions in response to the requirement of stability at elevated environmental temperature: the increase of fractions of hydrophobic and charged amino acid residues at the expense of polar ones. We show that this “from both ends of the hydrophobicity scale” trend is due to positive (to stabilize the native state) and negative (to destabilize misfolded states) components of protein design. Negative design strengthens specific repulsive non-native interactions that appear in misfolded structures. A pressure to preserve specific repulsive interactions in non-native conformations may result in correlated mutations between amino acids that are far apart in the native state but may be in contact in misfolded conformations. Such correlated mutations are indeed found in TIM barrel and other proteins

Entropic stabilization of proteins and its proteomic consequences

We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in folded states of proteins. This finding suggests that Lysines would preferentially entropically stabilize the native state. Indeed we show in computational experiments that Arginine-to-Lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize that if evolution uses this physical mechanisms in its strategies of thermophilic adaptation then hyperthermostable organisms would have much greater content of Lysines in their proteomes than of comparable in size and similarly charged Arginines.. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias towards Arginine-to-Lysine replacement in hyperthermophilic organisms and overall much greater content of Lysines than Arginines in hyperthermophiles. This finding cannot be explained by GC compositional biases. Our study provides an example of how analysis of a delicate physical mechanism of thermostability helps to resolve a puzzle in comparative genomics as to why aminoacid compositions of hyperthermophilic proteomes are significantly biased towards Lysines but not Arginine

Spin dynamics and level structure of quantum-dot quantum wells

We have characterized CdS/CdSe/CdS quantum-dot quantum wells using time-resolved Faraday rotation (TRFR). The spin dynamics show that the electron g-factor varies as a function of quantum well width and the transverse spin lifetime of several nano-seconds is robust up to room temperature. As a function of probe energy, the amplitude of the TRFR signal shows pronounced resonances, which allow one to identify individual exciton transitions. While the TRFR data are inconsistent with the conduction and valence band level scheme of spherical quantum-dot quantum wells, a model in which broken spherical symmetry is taken into account captures the essential features.Comment: 5 pages, 3 figure

ИСПОЛЬЗОВАНИЕ ВТОРИЧНЫХ ГОРЮЧИХ ЭНЕРГЕТИЧЕСКИХ РЕСУРСОВ ДЛЯ ПРОИЗВОДСТВА КОММУНАЛЬНО-БЫТОВОГО ТОПЛИВА

The paper shows an advantage to utilize secondary power resources (lignin, wastes of fine coal with its dressing, sawdust) in mixture with local types of fuel (peat) in order to fulfill power supply purpose, namely: obtaining hot water in boilers of small capacity and obtaining household fuel.Показано преимущество использования вторичных энергоресурсов (лигнин, отходы мелких углей при их обогащении, опилки) в смеси с местными видами топлива (торф) в энергетических целях, в частности при получении горячей воды в котлах малой производительности и при получении бытового топлива.

РАЗРАБОТКА ИМПОРТОЗАМЕЩАЮЩИХ ТЕХНОЛОГИЙ ПРИ ПРОИЗВОДСТВЕ СТРОИТЕЛЬНЫХ МАТЕРИАЛОВ

The paper presents results of investigations on rational usage of mineral resources. In particular, it has shown the possibility to increase a period of raw material serviceability and its application for production of building products depending on chemical and mineralogical composition of the waste. Analysis of the executed investigations shows that import substitution of anthracite, lignite and black coal for local fuels (milled peat and its sub-standard product) is possible in the production technology of porous building materials.A mathematical model for drying process has been developed in the paper. Technology for thermal performance of a sintering machine with calculation of its length at the given pallet speed has been proposed on the basis of the developed model. Once-through circulation of flue gases and heated materials is the main specific feature of belt sintering machines being used in production. In such a case the whole drying process can be divided into two periods: a period of constant drying rate and a period of falling drying rate. Calculations have shown that the drying rate depends on moisture content but it does not depend on heat exchange Bio-criteria, however, heating rate is a function of temperature and Biq. A mechanism of moisture transfer using various drying methods is the same as in an environment with constant temperature and so in an environment with variable temperature. Application of the mathematical model provides the possibility to save significantly power resources expended for drying process.The paper gives description of methodology for calculation of technologically important optimum parameters for sintering processes of agglomeration while using milled peat.Представлены результаты исследований по проблеме рационального использования минеральных ресурсов, в частности показана возможность расширения интервала пригодности сырья и его использования для получения строительных продуктов в зависимости от химического и минералогического состава отходов. Анализ проведенных исследований показывает, что в технологии производства пористых строительных материалов возможно импортозамещение антрацита, бурого и каменного угля на местные виды топлива - фрезерный торф и его некондиционный продукт.Разработана математическая модель процесса сушки и на основе ее решения предложена технология тепловой работы агломерационной машины с расчетом ее длины при заданных скоростях движения палет. Прямоточное движение дымовых газов и нагреваемых материалов является основной особенностью применяемых в производстве ленточных агломерационных машин. При этом весь процесс сушки можно разделить на два периода: постоянной и падающей скорости сушки. Результаты вычислений показали, что скорость сушки зависит от влагосодержания, но не зависит от теплообменного критерия Био. Однако скорость нагревания является функцией и температуры, и Biq. Механизм переноса влаги при различных методах сушки один и тот же в среде как с постоянной, так и с переменной температурами. Применение данной математической модели дает возможность значительной экономии энергоресурсов, затрачиваемых на сушку.Приведены методики расчета технологически важных оптимальных параметров процессов агломерации с применением фрезерного торфа

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

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

<p>Abstract</p> <p>Background</p> <p>By using a standard Support Vector Machine (SVM) with a Sequential Minimal Optimization (SMO) method of training, Naïve Bayes and other machine learning algorithms we are able to distinguish between two classes of protein sequences: those folding to highly-designable conformations, or those folding to poorly- or non-designable conformations.</p> <p>Results</p> <p>First, we generate all possible compact lattice conformations for the specified shape (a hexagon or a triangle) on the 2D triangular lattice. Then we generate all possible binary hydrophobic/polar (H/P) sequences and by using a specified energy function, thread them through all of these compact conformations. If for a given sequence the lowest energy is obtained for a particular lattice conformation we assume that this sequence folds to that conformation. Highly-designable conformations have many H/P sequences folding to them, while poorly-designable conformations have few or no H/P sequences. We classify sequences as folding to either highly – or poorly-designable conformations. We have randomly selected subsets of the sequences belonging to highly-designable and poorly-designable conformations and used them to train several different standard machine learning algorithms.</p> <p>Conclusion</p> <p>By using these machine learning algorithms with ten-fold cross-validation we are able to classify the two classes of sequences with high accuracy – in some cases exceeding 95%.</p

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