Development of method of matched morphological filtering of biomedical signals and images

Formalized approach to the analysis of biomedical signals and images with locally concentrated features is developed on the basis of matched morphological filtering taking into account the useful signal models that allowed generalizing the existing methods of digital processing and analysis of biomedical signals and images with locally concentrated features. The proposed matched morphological filter has been adapted to solve such problems as localization of the searched structural elements on biomedical signals with locally concentrated features, estimation of the irregular background aimed at the visualization quality improving of biological objects on X-ray biomedical images, pathologic structures selection on mammogram. The efficiency of the proposed methods of matched morphological filtration of biomedical signals and images with locally concentrated features is proved by experiments

The Phyre2 web portal for protein modeling, prediction and analysis

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission

Solving the tasks of subsurface resources management in GIS RAPID environment

Purpose. Solving the tasks of subsurface resources management based on the created GIS RAPID geoinformation technology. Methods. Close spatial relationships of lineament network characteristics and earthquake epicenters were detected in 3 seismically active areas located in the mountainous regions of Central Europe. Digital elevation models (DEM) based on ASTER satellite surveys and earthquake epicenter data were used. The nature of spatial relationship of lineament network and vein ore objects was studied in the territory of Congo DR, in the Lake Kivu area using space imagery. Gold ore objects were searched and forecasted in Uzbekistan in the site of Jamansai Mountains. High- resolution imagery from QuickBird 2 satellite, geophysical field surveys, geological and geochemical data were used. Findings. It was found that a significant number of epicenters are located in areas of high concentration of “non-standard” azimuths lineaments – from 27 to 34% of the total number of lineaments. It was revealed that 59.6% of the epicenters are located within 10% of sites with the highest values of complex deformation maps; 50% of the areas with the highest values of these maps contain, on average, 89% of all earthquake epicenters. It was found that satellite image lineament concentration maps with “non-standard” azimuths reflect the spatial relationship with known deposits much better than the concentration map of all lineaments. It was detected that the total area of gold ore objects perspective sites is about 20 km2. Originality. The use of GIS RAPID in a number of earth’s crust areas has allowed to establish new regularities linking the networks of physical field and landscape lineament characteristics with ore bodies and earthquake epicenters localization. Practical implications. A new technology has been developed for solving geological forecasting and prospecting problems. The technology can be used to solve a wide range of practical problems, especially in difficult geological conditions when searching for deep objects weakly presented in external fields and landscape.Мета. Рішення задач надрокористування на базі створеної геоінформаційної технології ГІС РАПІД. Методика. Виявлення тісних просторових взаємозв’язків різноманітних характеристик мереж лінеаментів і епіцентрів землетрусів проводилося у 3 сейсмоактивних ділянках, розташованих в гірських районах Центральної Європи. Використовувалися цифрові моделі рельєфу (DEM), побудовані за зйомками зі супутника ASTER і дані по епіцентрах землетрусів. Дослідження характеру просторового взаємозв’язку мережі лінеаментів і жильних рудних об’єктів проводилися на території Демократичної Республіки Конго, в районі озера Ківу із використанням космічних зйомок. Дослідження пошуку та прогнозу золоторудних об’єктів виконувалися в Узбекистані на ділянці Джамансайскіх гір. Використовувалися високоточні космічні зйомки зі супутника QuickBird 2, зйомки геофізичних полів, геологічні та геохімічні дані. Результати. Виявлено, що значна частина епіцентрів приурочена саме до ділянок підвищеної концентрації лінеаментів “нестандартних” азимутів, складаючи від 27 до 34% загального числа лінеаментів. Встановлено, що 59.6% епіцентрів знаходяться всередині 10% території ділянок, що володіють найвищими значеннями комплексних карт деформацій; 50% території з найвищими значеннями цих карт вміщають, в середньому, 89% усіх епіцентрів землетрусів. Визначено, що карти концентрації лінеаментів космознімків з “нестанартними” азимутами значно краще відображають просторовий взаємозв’язок з відомими родовищами у порівнянні з картою концентрації всіх лінеаментів. Встановлено, що сумарна площа перспективних ділянок золоторудних об’єктів склала близько 20 км2. Наукова новизна. Застосування ГІС РАПІД на ряді ділянок земної кори дозволило встановити нові закономірності, що зв’язують характеристики мережі лінеаментів фізичних полів і ландшафту з локалізацією рудних тіл та епіцентрів землетрусів. Практична значимість. Розроблено нову технологію рішення прогнозних і пошукових геологічних завдань, яка може застосовуватися для вирішення широкого кола практичних задач, особливо у складних геологічних умовах при пошуках глибокозалягаючих об’єктів, що слабо виявляються в зовнішніх полях і ландшафті.Цель. Решения задач недропользования на базе созданной геоинформационной технологии ГИС РАПИД. Методика. Выявление тесных пространственных взаимосвязей разнообразных характеристик сетей линеаментов и эпицентров землетрясений проводилось в 3 сейсмоактивных участках, расположенных в горных районах Центральной Европы. Использовались цифровые модели рельефа (DEM), построенные по съемкам со спутника ASTER, и данные об эпицентрах землетрясений. Исследования характера пространственной взаимосвязи сети линеаментов и жильных рудных объектов проводились на территории Демократической Республики Конго, в районе озера Киву с использованием космических съемок. Исследования поиска и прогноза золоторудных объектов выполнялись в Узбекистане на участке Джамансайских гор. Использовались высокоточные космические съемки со спутника QuickBird 2, съемки геофизических полей, геологические и геохимические данные. Результаты. Выявлено, что значительная часть эпицентров приурочена именно к участкам повышенной концентрации линеаментов “нестандартных” азимутов, составляя от 27 до 34% общего числа линеаментов. Установлено, что 59.6% эпицентров находятся внутри 10% территории участков, обладающих наивысшими значениями комплексных карт деформаций; 50% территории с наивысшими значениями этих карт вмещают, в среднем, 89% всех эпицентров землетрясений. Определено, что карты концентрации линеаментов космоснимков с “нестанартными” азимутами значительно лучше отражают пространственную взаимосвязь с известными месторождениями по сравнению с картой концентрации всех линеаментов. Установлено, что суммарная площадь перспективных участков золоторудных объектов составила около 20 км2. Научная новизна. Применение ГИС РАПИД на ряде участков земной коры позволило установить новые закономерности, связывающие характеристики сети линеаментов физических полей и ландшафта с локализацией рудных тел и эпицентров землетрясений. Практическая значимость. Разработана новая технология решения прогнозных и поисковых геологических задач, которая может применяться для решения широкого круга практических задач, особенно в сложных геологических условиях при поисках глубокозалегающих объектов, слабо проявляющихся во внешних полях и ландшафте.The work is performed as a part of planned research of the geoinformation systems department of the Dnipro University of Technology. The results are obtained without any financial support of grants and research projects. The authors express appreciation to reviewers and editors for their valuable comments, recommendations, and attention to the work

Multimedia information technology and the annotation of video

The state of the art in multimedia information technology has not progressed to the point where a single solution is available to meet all reasonable needs of documentalists and users of video archives. In general, we do not have an optimistic view of the usability of new technology in this domain, but digitization and digital power can be expected to cause a small revolution in the area of video archiving. The volume of data leads to two views of the future: on the pessimistic side, overload of data will cause lack of annotation capacity, and on the optimistic side, there will be enough data from which to learn selected concepts that can be deployed to support automatic annotation. At the threshold of this interesting era, we make an attempt to describe the state of the art in technology. We sample the progress in text, sound, and image processing, as well as in machine learning

Structural alphabets derived from attractors in conformational space

Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis.Results: A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.Conclusions: The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. © 2010 Pandini et al; licensee BioMed Central Ltd

How to perform RT-qPCR accurately in plant species?: a case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population

Background: Flower colour variation is one of the most crucial selection criteria in the breeding of a flowering pot plant, as is also the case for azalea (Rhododendron simsii hybrids). Flavonoid biosynthesis was studied intensively in several species. In azalea, flower colour can be described by means of a 3-gene model. However, this model does not clarify pink-coloration. The last decade gene expression studies have been implemented widely for studying flower colour. However, the methods used were often only semi-quantitative or quantification was not done according to the MIQE-guidelines. We aimed to develop an accurate protocol for RT-qPCR and to validate the protocol to study flower colour in an azalea mapping population. Results: An accurate RT-qPCR protocol had to be established. RNA quality was evaluated in a combined approach by means of different techniques e.g. SPUD-assay and Experion-analysis. We demonstrated the importance of testing noRT-samples for all genes under study to detect contaminating DNA. In spite of the limited sequence information available, we prepared a set of 11 reference genes which was validated in flower petals; a combination of three reference genes was most optimal. Finally we also used plasmids for the construction of standard curves. This allowed us to calculate gene-specific PCR efficiencies for every gene to assure an accurate quantification. The validity of the protocol was demonstrated by means of the study of six genes of the flavonoid biosynthesis pathway. No correlations were found between flower colour and the individual expression profiles. However, the combination of early pathway genes (CHS, F3H, F3'H and FLS) is clearly related to co-pigmentation with flavonols. The late pathway genes DFR and ANS are to a minor extent involved in differentiating between coloured and white flowers. Concerning pink coloration, we could demonstrate that the lower intensity in this type of flowers is correlated to the expression of F3'H. Conclusions: Currently in plant research, validated and qualitative RT-qPCR protocols are still rare. The protocol in this study can be implemented on all plant species to assure accurate quantification of gene expression. We have been able to correlate flower colour to the combined regulation of structural genes, both in the early and late branch of the pathway. This allowed us to differentiate between flower colours in a broader genetic background as was done so far in flower colour studies. These data will now be used for eQTL mapping to comprehend even more the regulation of this pathway

Advancing transcriptome platforms

During the last decade of years, remarkable technological innovations have emerged that allow the direct or indirect determination of the transcriptome at unprecedented scale and speed. Studies using these methods have already altered our view of the extent and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome. Here, we outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based platform, the well accepted tag-based sequencing platform, and the recently developed RNA-Seq (RNA sequencing) based platform. Importantly, these next-generation technologies revolutionize assessing the entire transcriptome via the recent RNA-Seq technology

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression