Transcription factor binding distribution and properties in prokaryotes

The canonical model of transcriptional regulation in prokaryotes restricted binding site locations to promoter regions and suggested that the binding sequences serve as the main determinants of binding. In this dissertation, I challenge these assumptions. As a member of the TB Systems Biology Consortium, I analyzed and validated ChIP-Seq and microarray experiments for over 100 transcription factors (TFs). In order to study the transcriptional functions of predicted binding sites, I integrated binding and expression data and assigned potential regulatory roles to 20% of the binding sites. Stronger binding sites were more often associated with regulation than weaker sites, suggesting a correlation between binding strength and regulatory impact. Seventy-six percent of the sites fell into annotated coding regions and a significant proportion was assigned to regulatory functions. To study the importance of binding sequences, I compared experimental sites with computational motif predictions. Although a conservative binding motif was found for most TFs, only a fraction of the observed motifs appeared bound in the experiment. Some low-affinity binding sites appeared occupied by the corresponding TF while many high-affinity binding sites were not. Interestingly, I found exactly the same nucleotide sequences (up to 15 residues long) bound in one area of the genome but not bound in another area, pointing to DNA accessibility as an important factor for in vivo binding. To investigate the evolutionary conservation of binding-site occupancy, sequence, and transcriptional impact, I analyzed ChIP-Seq and expression experiments for five conserved TFs for two-to-four Mycobacterial relatives. The regulon composition showed significantly less conservation than expected from the overall gene conservation level across Mycobacteria. Despite expectations, sequence conservation did not serve as a good indicator of whether or not a computationally predicted motif was bound experimentally; and in some cases, a fully conserved motif was bound in one relative but not in the other. Conservation of genic binding sites was higher than expected from the random model, adding to the evidence that at least some genic sites are functional. Understanding the evolutionary story of binding sites allowed me to explain unusual site configurations, some of which indicated a role for DNA looping

Optimization of structural solutions of reinforcement cages of bendable reinforced concrete elements

This article discusses the comparison of the design solutions of welded and knitted reinforcement cages used for reinforcement of concrete structures and evaluated their advantages and disadvantage

Optimization of structural solutions of reinforcement cages of bendable reinforced concrete elements

This article discusses the comparison of the design solutions of welded and knitted reinforcement cages used for reinforcement of concrete structures and evaluated their advantages and disadvantage

Geo-neutrinos and Silicate Earth Enrichment of U and Th

The terrestrial distribution of U, Th, and K abundances governs the thermal evolution, traces the differentiation, and reflects the bulk composition of the earth. Comparing the bulk earth composition to chondritic meteorites estimates the net amounts of these radiogenic heat-producing elements available for partitioning to the crust, mantle, and core. Core formation enriches the abundances of refractory lithophile elements, including U and Th, in the silicate earth by ~1.5. Global removal of volatile elements potentially increases this enrichment to ~2.8. The K content of the silicate earth follows from the ratio of K to U. Variable enrichment produces a range of possible heat-producing element abundances in the silicate earth. A model assesses the essentially fixed amounts of U, Th, and K in the approximately closed crust reservoir. Subtracting these sequestered crustal amounts from the variable amounts in the silicate earth results in a range of possible mantle allocations, leaving global dynamics and thermal evolution poorly constrained. Terrestrial antineutrinos from {\beta}-emitting daughter nuclei in the U and Th decay series traverse the earth with negligible attenuation. The rate at which large subsurface instruments observe these geo-neutrinos depends on the distribution of U and Th relative to the detector. Geo-neutrino observations with sensitivity to U and Th in the mantle are able to estimate silicate earth enrichment, leading to a more complete understanding of the origin, accretion, differentiation, and thermal history of the planet.Comment: published version: 21 pages, 3 figures, 5 table

40Ar–39Ar ages and isotope geochemistry of Cretaceous basalts in northern Madagascar: Refining eruption ages, extent of crustal contamination and parental magmas in a flood basalt province

The Madagascar Cretaceous igneous province exposed in the Mahajanga basin is represented by basalt and basaltic andesite lavas. New 40Ar–39Ar plateau ages (92.3 ± 2.0 Ma and 91.5 ± 1.3 Ma) indicate that the magmatism in the Mahajanga basin started about 92 Ma ago. Four geochemically distinct magma types (Groups A–D) are present. Group A and C rocks have low to moderate TiO2 (1.2–2.6 wt%), Nb (3–9 μg g−1) and Zr (82–200 μg g−1), and show large variations in ɛNdi (+0.1 to −10.8), 206Pb/204Pb (15.28 to 16.33) and γOs (+11.4 to +7378). The large isotopic variations, particularly in Os, Nd and Pb isotopic compositions, are likely due to crustal contamination. The low Pb isotope ratios observed in the Group A and C rocks suggest involvement of continental crust with low μ (238U/204Pb). Group B and D rocks have moderate to high TiO2 (2.2–4.9 wt%), Nb (8–24 μg g−1) and Zr (120–327 μg g−1). Age-corrected isotopes of Group B and D lavas show a small range in ɛNdi (+1.0 to +4.0) and a wide range in γOs (+128 to +1182). Values of 207Pb/204Pb are within the range for Groups A and C, but the Group D 206Pb/204Pb (16.52–17.08) and 208Pb/204Pb (37.51–38.01) values are higher, indicating a different crustal contaminant. Pb isotopic values of the Group B rocks seem to reflect the isotopic features of their mantle source. The magma groups of Mahajanga display a wide range of trace element and isotopic compositions that cannot be explained only by open-system crystallization processes but, rather, by distinct mantle sources

A Study of the Residual 39Ar Content in Argon from Underground Sources

The discovery of argon from underground sources with significantly less 39Ar than atmospheric argon was an important step in the development of direct-detection dark matter experiments using argon as the active target. We report on the design and operation of a low background detector with a single phase liquid argon target that was built to study the 39Ar content of the underground argon. Underground argon from the Kinder Morgan CO2 plant in Cortez, Colorado was determined to have less than 0.65% of the 39Ar activity in atmospheric argon.Comment: 21 pages, 10 figure

Dnmt3a is an epigenetic mediator of adipose insulin resistance

Insulin resistance results from an intricate interaction between genetic make-up and environment, and thus may be orchestrated by epigenetic mechanisms like DNA methylation. Here, we demonstrate that DNA methyltransferase 3a (Dnmt3a) is both necessary and sufficient to mediate insulin resistance in cultured mouse and human adipocytes. Furthermore, adipose-specific Dnmt3a knock-out mice are protected from diet-induced insulin resistance and glucose intolerance without accompanying changes in adiposity. Unbiased gene profiling studies revealed Fgf21 as a key negatively regulated Dnmt3a target gene in adipocytes with concordant changes in DNA methylation at the Fgf21 promoter region. Consistent with this, Fgf21 can rescue Dnmt3a-mediated insulin resistance, and DNA methylation at the FGF21 locus was elevated in human subjects with diabetes and correlated negatively with expression of FGF21 in human adipose tissue. Taken together, our data demonstrate that adipose Dnmt3a is a novel epigenetic mediator of insulin resistance in vitro and in vivo

Вероятностная оценка пригодности судебно-экспертной методики «Микроскопическое исследование текстильных волокон»

 The results of validation of the method “Microscopic analysis of textile fibers” used in forensic fiber examination are presented. An attempt is made to estimate reliability of testing of this method numerically by the proportions of right and false results and credibility ratio.The testing method under consideration consists in establishing a set of external characteristics of natural and chemical textile fibers: color, peculiarities of coloration, morphological features, presence/absence of a matting agent. These generic characteristics are used in forensic textile analysis. As the objects of testing fiber samples from comparative collection of a forensic fiber laboratory were used. Four experts participated in the experiment independently examining eleven fiber samples by eleven external characteristics for a week.A low (2,2 %) rate of false results in relation to the total number of tests was established as well as the low (less than 3,0 %) rate of each expert’s false results. The probability of the right results of characteristics’ assessment is 30 times higher than the probability of false results.The results of the experiment permit the conclusion that the method is suitable to be used in forensic fiber examination when dealing with various tasks: classification, identification, situational and diagnostic.  Представлены результаты валидации методики «Микроскопическое исследование текстильных волокон», применяемой при судебно-экспертном исследовании волокнистых материалов. Предпринята попытка определить надежность тестирования этой методики численно: по значениям долей ложных и правильных результатов и отношению правдоподобия.Рассматриваемая методика тестирования заключается в установлении комплекса внешних признаков природных и химических текстильных волокон: цвета, особенности окраски, морфологических особенностей, наличия/отсутствия матирующего агента. Данные родовые признаки используются при судебно-экспертном исследовании текстильных волокон.Объектами тестирования являлись образцы волокон из сравнительной коллекции лаборатории криминалистической экспертизы волокнистых материалов. В эксперименте участвовали четыре эксперта, которые в течение недели независимо исследовали одиннадцать образцов волокон по одиннадцати внешним признакам.Установлен низкий (2,2 %) уровень ложных результатов по отношению к общему числу тестирований, а также низкий (менее 3,0 %) уровень ложных результатов у каждого из экспертов. Вероятность правильных результатов оценки совокупности признаков в 30 раз выше вероятности ложных результатов.Результаты эксперимента позволяют сделать вывод о том, что методика пригодна для использования в судебной экспертизе волокнистых материалов при решении разнообразных задач: классификационных, идентификационных, ситуационно-диагностических.

Методологические особенности валидации судебно-экспертных методик

The article reviews and summarizes the experience of validating forensic expert techniques in the Russian Federal Centre of Forensic Science of the Ministry of Justice of the Russian Federation. The authors point out the methodological features of practical implementation of the validation procedure. They demonstrate that the specificity, diversity, and complexity of the objects of expert study require the classification of the applied methods in terms of metrology, identification of the main validation parameters of quantitative and qualitative methods, organization of experiments, and evaluation of validation parameters using mathematical analysis methods. They also propose to divide methods into two types: forensic expert measurement methods (FMT) and forensic expert testing methods (FTT). Based on the generalization of information presented in several regulatory documents and scientific publications, the following parameters are identified for FMT: metrological characteristics or properties of the method (specificity, linearity, sensitivity, range of determined values, detection limit, quantitative determination limit) and quality indicators of the method (precision, correctness, accuracy of the analysis result, or uncertainty). When validating FTT, it is proposed to evaluate the reliability of the method and the competence of the expert.An experiment to assess validation parameters is performed using enough control samples with established characteristics of controlled indicators and with the participation of a sufficient number of experts. Requirements for control samples are provided.The authors also give examples of probabilistic evaluation of validation parameters for two qualitative testing methods: microscopic examination of textile fibers and detection of gunshot residue using scanning electron microscopy and X-ray microanalysis. The reliability of these methods is assessed by calculating the likelihood ratio, and the specificity of interpreting the results of FMT and FTT validation is noted.The decision on compliance with the requirements is made if the interval of the established extended uncertainty for the obtained result does not exceed the tolerance field. In the absence of tolerances, FMT is considered suitable for solving forensic expert tasks if the values of the extended uncertainty of the measurement results of the controlled indicator do not exceed the values established during validation. For FTT, a low probabilistic proportion of false positive and false negative results in determining the presence/absence of controlled indicators, as well as experimentally confirmed competence of the expert during validation, are indicators of the suitability of the method for its intended useВ статье представлен обзор и обобщение опыта валидации судебно-экспертных методик (СЭМ) в ФБУ РФЦСЭ при Минюсте России. Отмечены методологические особенности практической реализации процедуры валидации. Показано, что специфичность, разнообразие и сложность объектов экспертного исследования требуют классификации используемых методик в метрологическом плане, выявления основных параметров валидации количественных и качественных методик, организации эксперимента и оценки параметров валидации с применением математических методов анализа. Предлагается разделять методики на два типа: судебноэкспертные методики измерения (СЭМИ) и судебно-экспертные методики тестирования (СЭМТ). На основании обобщения сведений, представленных в ряде нормативных документов и научных публикаций, для СЭМИ выделены следующие параметры: метрологические характеристики или свойства методики (специфичность, линейность, чувствительность, диапазон определяемых величин, предел обнаружения, предел количественного определения) и показатели качества методики (прецизионность, правильность, точность результата анализа или неопределенность). При валидации СЭМТ предложено оценивать надежность методики и компетентность эксперта.Эксперимент по оценке параметров валидации выполняют с использованием достаточного количества контрольных образцов с установленными характеристиками контролируемых показателей и с участием достаточного числа экспертов. Приведены требования, предъявляемые к контрольным образцам.Разобраны примеры вероятностной оценки параметров валидации для двух качественных методик тестирования: по микроскопическому исследованию текстильных волокон и по обнаружению следов продуктов выстрела с помощью сканирующей электронной микроскопии и рентгеноспектрального микроанализа. Дана оценка надежности этих методик с помощью расчета отношения правдоподобия, отмечена специфика интерпретации результатов валидации СЭМИ и СЭМТ.Решение о соответствии СЭМИ предъявленным требованиям принимается, если интервал установленной расширенной неопределенности для полученного результата не выходит за пределы поля допуска. При отсутствии допусков СЭМИ считается пригодной для решения судебноэкспертных задач, если значения расширенной неопределенности результатов измерений контролируемого показателя не превышают значений, установленных при валидации. Для СЭМТ низкая вероятностная доля ложноположительных и ложноотрицательных результатов установления наличия/отсутствия контролируемых показателей, а также экспериментально подтвержденная компетентность эксперта в ходе валидации являются показателями пригодности методики для цели использовани