5 research outputs found
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments
Get PDFHybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized
Assessment of the content of metals and metalloids in the snow cover at the oil production sites (Middle River Ob region)
Get PDFThis article presents results of investigation of dust load and content of metals and metalloids (MMs) in the snow samples taken at the Vatinskoye oil field (Khanty-Mansi Autonomous District - Yugra). Concentrations of dissolved and suspended forms of MMs in 20 samples collected in March 2021 were determined by the ICP-MS and ICP-AES methods. Eighteen elements (Ag, Ba, Bi, Cd, Cr, Cu, Fe, Hg, Li, Mn, Ni, Pb, Sb, Sn, Sr, Ti, W, and Zn) indicating various sources of emissions were selected for further analysis. Filters with a pore diameter of 0.45 μm were used to separate dissolved and suspended forms. Enrichment of the suspension with chalcophile elements (Ag, Cu, Zn, Sn, Sb, Pb) was noted in the background areas. Calculations of enrichment coefficients (CO) using Li as a reference element demonstrated that Cu, Mn and Ni come from natural sources (rocks and soils), while the others have a mixed natural-anthropogenic origin. It was noted also that the mass fraction of a number of metals (Cr, Cu, Ni, Zn) increases in solid-phase deposits. The metals Zn, Cu and Cr are mainly contained in snow in suspended form, and Ni - both in dissolved and suspended forms. As a result of calculations of the total Cr pollution index, most of the deposit is classified as "low, non-hazardous" pollution areas. The highest concentrations of MMs in the snow were found in the southern part of the deposit, where the main infrastructure facilities and the communications lines are concentrated, including roads, railways and pipelines. They were specified as "average, moderately dangerous" level of pollution. To determine sources of pollution, the factor analysis was applied, and as a result of which two main factors were identified: 1) the background pollution, which is indicative of deposition of Cu, Sn, Sb, Ag; 2) the anthropogenic one, corresponding to high levels of Cr, Ni, Zn. Spatial analysis of the MMs distribution showed that the deposition of Ni, Cr is associated with drilling operations, while Zn - with the presence of transport. The data obtained can be used to understand the processes of atmospheric deposition of potentially toxic metals and metalloids, as well as to assess the quality of the environment at oil and gas fields
Molecular detection of bacteria from a possible material oral origin in neonatal gastric aspirates obtained from complicated pregnancies
No full textPhDIt has been suggested that periodontal disease, a disease that affects the supporting
tissues of the teeth, represents a risk factor for adverse pregnancy outcomes. Certain
oral pathogens possess a demonstrated ability to translocate and invade the amniotic
tissues. Once in the amniotic environment, these opportunistic colonisers could then
initiate or contribute to a perinatal infection, and in this way be involved in the
complications. The overall aim of this study was to determine the presence, and
confirm the origin, of suspected maternal oral microbiota in neonatal gastric
aspirates (swallowed amniotic fluid) collected due to complications during
pregnancy and/or evidence of neonatal sepsis.
Non-cultural PCR-based methods directed to the ribosomal encoding genes (rDNA)
were applied to analyse neonatal and maternal samples. The use of universal and
species-specific primers that target the bacterial 16S rRNA gene allowed
identification and quantification of broad-range and specific bacteria to the species
level. Sequence comparative analysis of a more variable fragment, the intergenic
spacer region located between the 16S and the 23S rDNA, was finally used to
compare strains obtained from the neonates and their counterparts in the respective
mother’s oral and vaginal samples.
Data analysis allowed identification of a range of potential confounding factors for
presence of bacteria in the infants, such as vaginal delivery and prolonged rupture of
membranes. However, bacteria with a possible oral origin were mostly identified in
the neonatal samples in low prevalence and not associated with any particular
variable. Quantitative analysis of potential periodontal pathogens demonstrated the
presence of Porphyromonas gingivalis (1%) and Fusobacterium nucleatum (16%) in
the neonates. F. nucleatum was detected at relatively high levels (mean=4.41E+02
cells/ml); representing up to 50% of the total bacterial load, which strongly supports
its possible role in pregnancy complications. Also, F. nucleatum subspecies analysis
and comparisons at the strain level suggest the oral cavity as the most likely origin of
this infectious agent. This study supports the need for further studies.UNESCO / OREAL Partnership Co-Sponsored fellowships for young women in Life Science 200
Оценка содержания металлов и металлоидов в снежном покрове на участках нефтедобычи Среднего Приобья
Get PDFThis article presents results of investigation of dust load and content of metals and metalloids (MMs) in the snow samples taken at the Vatinskoye oil field (Khanty-Mansi Autonomous District - Yugra). Concentrations of dissolved and suspended forms of MMs in 20 samples collected in March 2021 were determined by the ICP-MS and ICP-AES methods. Eighteen elements (Ag, Ba, Bi, Cd, Cr, Cu, Fe, Hg, Li, Mn, Ni, Pb, Sb, Sn, Sr, Ti, W, and Zn) indicating various sources of emissions were selected for further analysis. Filters with a pore diameter of 0.45 μm were used to separate dissolved and suspended forms. Enrichment of the suspension with chalcophile elements (Ag, Cu, Zn, Sn, Sb, Pb) was noted in the background areas. Calculations of enrichment coefficients (CO) using Li as a reference element demonstrated that Cu, Mn and Ni come from natural sources (rocks and soils), while the others have a mixed natural-anthropogenic origin. It was noted also that the mass fraction of a number of metals (Cr, Cu, Ni, Zn) increases in solid-phase deposits. The metals Zn, Cu and Cr are mainly contained in snow in suspended form, and Ni - both in dissolved and suspended forms. As a result of calculations of the total Cr pollution index, most of the deposit is classified as "low, non-hazardous" pollution areas. The highest concentrations of MMs in the snow were found in the southern part of the deposit, where the main infrastructure facilities and the communications lines are concentrated, including roads, railways and pipelines. They were specified as "average, moderately dangerous" level of pollution. To determine sources of pollution, the factor analysis was applied, and as a result of which two main factors were identified: 1) the background pollution, which is indicative of deposition of Cu, Sn, Sb, Ag; 2) the anthropogenic one, corresponding to high levels of Cr, Ni, Zn. Spatial analysis of the MMs distribution showed that the deposition of Ni, Cr is associated with drilling operations, while Zn - with the presence of transport. The data obtained can be used to understand the processes of atmospheric deposition of potentially toxic metals and metalloids, as well as to assess the quality of the environment at oil and gas fields.Проведена оценка уровня загрязнения снежного покрова потенциально токсичными металлами и металлоидами на территории Ватинского нефтяного месторождения (Ханты-Мансийский автономный округ - Югра). В результате исследования фильтрата талого снега и твёрдофазных выпадений (частиц крупнее 0,45 мкм) отмечено увеличение концентрации Ni и Cr, связанное с ведением буровых работ, а также Zn за счёт работы транспорта. Уровень загрязнения возрастает на участках с повышенной концентрацией промышленных объектов
Полициклические ароматические углеводороды в снежном покрове Ямало-Ненецкого автономного округа как индикаторы влияния источников техногенных эмиссий
Get PDFA study of the content and composition of polycyclic aromatic hydrocarbons (PAHs) in the solid fraction of the snowpack is carried out on the territory of the Yamal-Nenetz Autonomous region, the north of Western Siberia. The total content of ten three-six nucleus PAHs was determined in the 51 samples collected at various distances from oil and gas producers and roads, near settlements, and in remote Arctic areas. The total PAH content varies from the lowest 0.3 ng/mg on the Bely Island, increasing to ~ 5 ng/mg in areas of new gas fields, and up to high 15 ng/mg in cities. Characteristic features of PAHs composition under the influence of gas flares emissions in central areas of high technogenic load are identified; they are a total content of up to 144 ng/mg and enrichment with low- molecular weight PAHs. In remote Arctic regions, high-molecular weight 5–6 nucleus PAHs dominate. Profiles of individual PAHs near gas flares, roads and residential sector facilities have been determined. The percentage contribution of the sum of 3, 4 and 5, 6-nucleus PAHs to the total PAH content indicates the gas flaring impact. Ratios of fluorantene to pyrene and benzene(b)fluorantene to benzene(ghi)perylene indicate changes in the snow PAHs composition with a decrease in the gas flaring contribution. The data obtained for the assessment of gas flaring emission impact on the PAHs composition in the snowpack are relevant to polar areas where new fields are being developed.Проведен анализ содержания и состава полициклических ароматических углеводородов (ПАУ) в твердой фракции снежного покрова Ямало-Ненецкого автономного округа (ЯНАО). Определено суммарное содержание десяти 3–6-ядерных ПАУ в 51 пробе, отобранной на различных расстояниях от объектов топливно-энергетического комплекса, у автодорог, вблизи населенных пунктов и в удаленных арктических районах. Суммарное содержание ПАУ варьирует от 0,3 нг/мг на о. Белый, повышенного ~5 нг/мг в районах разработки новых газовых месторождений до высоких 15 нг/мг в городах ЯНАО. Выделены характерные черты состава ПАУ под влиянием эмиссий газовых факелов в центральных районах высокой техногенной нагрузки при содержании до 144 нг/мг и обогащение низкомолекулярными ПАУ. В удаленных арктических регионах доминируют высокомолекулярные 5-, 6-ядерные ПАУ. Определены профили индивидуальных ПАУ вблизи факельных установок сжигания природного газа, транспортных магистралей и объектов жилого сектора. Процентный вклад суммы 3-, 4- и 5–6-ядерных ПАУ в суммарное содержание ПАУ указывает на степень влияния эмиссий факельных установок. Индикаторные показатели: отношения флуорантена к пирену и бенз(b)флуорантена к бенз(ghi)перилену — описывают изменение состава ПАУ в твердой фракции снега при снижении вклада факельных эмиссий. Полученные данные о влиянии эмиссий на состав ПАУ снежного покрова в зонах действия техногенных источников актуальны для полярных районов освоения новых месторождений
