Vertical stratification of the air microbiome in the lower troposphere

The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface

ВЛИЯНИЕ ИМПУЛЬСНЫХ МАГНИТНЫХ ПОЛЕЙ НА ЭКСПРЕССИЮ ГЕНОВ ОНКОСУПРЕССОРОВ В ЭКСПЕРИМЕНТЕ НА КУЛЬТУРЕ КЛЕТОК ГЛИОБЛАСТОМЫ ЧЕЛОВЕКА T98G

Aim: to study the effect of a pulsed magnetic field (PMF) on the expression of key tumor suppressor genes, such as aPc, MLH, and MGMt in human t98G glioblastoma cell line. material and methods. the PMF with the intensity of 15 and 300 mt was used alone and in combination with ionizing radiation at a single dose of 10 Gy. to perform ionizing radiation, theratron Equinox 60co unit Best theratronics Ltd., Ottawa, canada) was used. the source of the pulsed magnetic field was Neuro-Ms / D therapeutic advanced device of the Neurosoft company. Live and dead cells were determined in NanoEntekJuliFl cell counter (Korea) using a 0.4 % trypan blue solution to stain dead cells. total RNa was extracted according to the protocol of the manufacturer trizol with changes: the aqueous phase was separated with trizol reagent twice. the quantitative measurement of the isolated RNa was carried out on a Qubit 2.0 fluorimeter using a kit of reagents with the Quant-it RNa assayKit RNa intercalating dye (Life technologies, usa). the expression of MLH, aPc, and MGMt genes was evaluated by Rt-PcR using a cFx96 amplifier (BioRad, usa). Data were analyzed using the cycle threshold (ct) method with normalization for tBP gene expression in each sample. Relative expression of the genetic locus (Exp) was calculated by the 2-Δct method. statistical analysis of the results was carried out using the statictica v10 software package. Results. One day after exposure to PMF, significant differences in the MGMt expression level compared to the control were found (p<0.05). a significant decrease in the transcriptional activity of the MGMt gene in glioblastoma cells was observed with PMF intensity of 15 mt, and correlated with the cell mortality rate. No changes in the mortality rate were observed after radiation exposure combined with 15 mt PMF. However, the mortality rate decreased from 18.7 % to 15 % after radiation exposure combined with 300 mt PMF. Conclusion. the effect of reduction in the transcriptional activity of MGMt in t98G glioblastoma cells and the effect of PMF as a monofactor on their viability characterize the magnetic susceptibility of tumor cell mechanisms. Given the multidirectional nature of the combined interaction of ionizing radiation and PMF, it is necessary to emphasize the importance of choosing and justifying the role of biotropic parameters of PMF in order to exclude a negative effect on the treatment.Цель исследования – изучить влияние импульсного магнитного поля (ИМП) на экспрессию ключевых генов онкосупрессоров aPc, MLH, MGMt клеточной линии глиобластомы человека t98G. Материал и методы. На культуре клеток t98G проведено воздействие ИМП с параметрами индукции 15 и 300 mt как самостоятельно, так и в сочетании с воздействием ионизирующего излучения (РОД 10 Гр). Ионизирующее излучение проводилось на аппарате theratronEquinox фирмы Besttheratronics, где в качестве источника излучения использовался 60Со. Источником импульсного магнитного поля служил аппарат «Нейро-МС/Д терапевтический расширенный» компании «Нейрософт». Определение живых/мертвых клеток проводили в счетчике клеток NanoEntekJuliFl (Корея) с использованием 0,4 % раствора трипанового синего для окраски мертвых клеток. Экстракцию тотальной РНК проводили по протоколу изготовителя trizol с изменениями: водную фазу сепарировали с реагентом trizol дважды. Количественное измерение выделенной РНК проводили на флюориметре Qubit 2.0 с использованием набора реактивов с РНК-интеркалирующим красителем Quant-it RNa assayKit (Lifetechnologies, США). Оценку экспрессии генов MLH, aPc, MGMt проводили методом Rt-PcR на амплификаторе cFx96 (BioRad, США). Данные анализировали с использованием метода порогового значения цикла (ct) с нормализацией по экспрессии гена tBP в каждом образце. Относительную экспрессию генетического локуса (Еxp) рассчитывали по методу 2-Δct. Статистический анализ результатов осуществляли с помощью пакета программ statictica v10. Результаты. Установлено, что через сутки после воздействия ИМП индукцией 15 mt и 300 mt отношение уровня экспрессии MGMt к контролю имело значимые различия (p<0,05). Наиболее выраженное снижение транскрипционной активности гена MGMt в клетках глиобластомы отмечалось при ИМП 15 mt и коррелировало с показателем летальности клеток. Уровень летальности, достигнутый после лучевого воздействия и ИМП 15 mt, не изменялся, а при сочетании с ИМП 300 mt снижался с 18,7 до 15 %. Заключение. Эффекты снижения транскрипционной активности MGMt в клетках глиобластомы t98G и способность влияния ИМП как монофактора на их жизнеспособность характеризуют магнитовосприимчивость клеточных механизмов опухоли. При сочетании ИМП с ионизирующим излучением характер их взаимовлияния меняется от индифферентного до антагонистического, что указывает на необходимость подбора и обоснования ключевых биотропных параметров

Genome-wide association interaction analysis for complex diseases: an example on Alzheimer’s disease.

Objectives: Common genetic mutations that can be detected via a genome-wide association (GWA) study and at the same time have a strong contribution to disease risk are fairly limited. Some of the genetic variants in humans are either rare, thus more difficult to be identified, or they are common, but exert relatively small or even no individual effects that are masked or enhanced by one or several genes. The discovery of interacting genetic variants, possibly explaining part of the hidden genetic heritability, requires the development of sophisticated strategies and bioinformatics tools. Methods: In the present study, we propose a minimal protocol for genome-wide association interaction (GWAI) analysis that involves screening over large-scale genomic data in the search for epistatic or synergetic effects. The different steps of this minimal protocol are illustrated on a real-life data application for Alzheimer disease (AlzD) (large human cohort of 2,259 cases and 6,017 controls from France) and the pros and cons of the approaches are discussed. Results: Using the protocol, we identified two pairs of AlzD-associated interacting SNPs: from chromosome 6q11.1 and 13q12.11 and male-specific epistasis between SNPs from chromosome 5q34 and 15q22.2. Conclusion: In the present work we developed and applied an epistasis detection protocol to perform a comprehensive genome-wide search for AlzD-associated epistatic effects, hereby combining the strengths of different strategies, methods and statistical tools. It is the first time an epistasis study of this magnitude has been conducted in the context of AlzD. We show the advantages of viewing and analyzing data from different angles. A replication analysis strategy adapted to the epistasis detection context, as well as a meta-analytic approach confirmed effects of the discovered interactions. Apart from the biological and clinical importance, the present work offers a roadmap for future investigations in the field of epistasis detection and interpretation

EFFECT OF PULSED MAGNETIC FIELDS ON THE EXPRESSION LEVELS OF TUMOR SUPPRESSOR GENES IN HUMAN T98G GLYOBLASTOMA CELL LINE

Aim: to study the effect of a pulsed magnetic field (PMF) on the expression of key tumor suppressor genes, such as aPc, MLH, and MGMt in human t98G glioblastoma cell line. material and methods. the PMF with the intensity of 15 and 300 mt was used alone and in combination with ionizing radiation at a single dose of 10 Gy. to perform ionizing radiation, theratron Equinox 60co unit Best theratronics Ltd., Ottawa, canada) was used. the source of the pulsed magnetic field was Neuro-Ms / D therapeutic advanced device of the Neurosoft company. Live and dead cells were determined in NanoEntekJuliFl cell counter (Korea) using a 0.4 % trypan blue solution to stain dead cells. total RNa was extracted according to the protocol of the manufacturer trizol with changes: the aqueous phase was separated with trizol reagent twice. the quantitative measurement of the isolated RNa was carried out on a Qubit 2.0 fluorimeter using a kit of reagents with the Quant-it RNa assayKit RNa intercalating dye (Life technologies, usa). the expression of MLH, aPc, and MGMt genes was evaluated by Rt-PcR using a cFx96 amplifier (BioRad, usa). Data were analyzed using the cycle threshold (ct) method with normalization for tBP gene expression in each sample. Relative expression of the genetic locus (Exp) was calculated by the 2-Δct method. statistical analysis of the results was carried out using the statictica v10 software package. Results. One day after exposure to PMF, significant differences in the MGMt expression level compared to the control were found (p<0.05). a significant decrease in the transcriptional activity of the MGMt gene in glioblastoma cells was observed with PMF intensity of 15 mt, and correlated with the cell mortality rate. No changes in the mortality rate were observed after radiation exposure combined with 15 mt PMF. However, the mortality rate decreased from 18.7 % to 15 % after radiation exposure combined with 300 mt PMF. Conclusion. the effect of reduction in the transcriptional activity of MGMt in t98G glioblastoma cells and the effect of PMF as a monofactor on their viability characterize the magnetic susceptibility of tumor cell mechanisms. Given the multidirectional nature of the combined interaction of ionizing radiation and PMF, it is necessary to emphasize the importance of choosing and justifying the role of biotropic parameters of PMF in order to exclude a negative effect on the treatment

A genome-wide linkage study of individuals with high scores on NEO personality traits

The NEO-Five-Factor Inventory divides human personality traits into five dimensions: neuroticism, extraversion, openness, conscientiousness and agreeableness. In this study, we sought to identify regions harboring genes with large effects on the five NEO personality traits by performing genome-wide linkage analysis of individuals scoring in the extremes of these traits (90th percentile). Affected-only linkage analysis was performed using an Illumina 6K linkage array in a family-based study, the Erasmus Rucphen Family study. We subsequently determined whether distinct, segregating haplotypes found with linkage analysis were associated with the trait of interest in the population. Finally, a dense single-nucleotide polymorphism genotyping array (Illumina 318K) was used to search for copy number variations (CNVs) in the associated regions. In the families with extreme phenotype scores, we found significant evidence of linkage for conscientiousness to 20p13 (rs1434789, log of odds (LOD)5.86) and suggestive evidence of linkage (LOD 2.8) for neuroticism to 19q, 21q and 22q, extraversion to 1p, 1q, 9p and12q, openness to 12q and 19q, and agreeableness to 2p, 6q, 17q and 21q. Further analysis determined haplotypes in 21q22 for neuroticism (P-values0.009, 0.007), in 17q24 for agreeableness (marginal P-value0.018) and in 20p13 for conscientiousness (marginal P-values0.058, 0.038) segregating in families with large contributions to the LOD scores. No evidence for CNVs in any of the associated regions was found. Our findings imply that there may be genes with relatively large effects involved in personality traits, which may be identified with next-generation sequencing techniques

Genome-wide association interaction analysis for Alzheimer’s disease.

Identification of epistasis is a challenging task that when successful gives new clues to systems-level genetics where the complexity of underling biology of human disease can be better understood. Though many novel methods for detecting epistasis have been proposed and many studies for epistasis detection have been conducted, so far few studies can demonstrate replicable epistasis. In the present work, we propose a minimal protocol for exhaustive genome-wide association interaction (GWAI) analysis that involves screening for epistasis over large-scale genomic data combining strengths of different methods and statistical tools. The different steps of this protocol are illustrated on a real-life data application for Alzheimer’s disease (a large cohort of 2259 patients and 6017 controls from France). Using this protocol, we identified AD-associated interacting SNPs-pair from chromosome 6q11.1 (rs6455128, the KHDRBS2 gene) and 13q12.11 (rs7989332, the CRYL1 gene) and male-specific epistasis between SNPs from chromosome 5q34 (rs729149 and rs3733980, the WWC1 gene) and 15q22.2 (rs9806612, rs9302230 and rs7175766, the TLN2 gene). The transcriptome analysis revealed negative correlation between expression levels of KHDRBS2 and CRYL1 in both the temporal cortex and cerebellum brain regions and positive correlation between the expression levels of CRYL1 and WWC1 in the temporal cortex brain region. A replication analysis strategy and a meta-analysis approach in independent data confirmed effects of some of the discovered interactions

Genome-Wide Association Interaction Analysis for Alzheimer’s Disease

We propose a minimal protocol for exhaustive genome-wide association interaction analysis that involves screening for epistasis over large-scale genomic data combining strengths of different methods and statistical tools. The different steps of this protocol are illustrated on a real-life data application for Alzheimer's disease (AD) (2259 patients and 6017 controls from France). Particularly, in the exhaustive genome-wide epistasis screening we identified AD-associated interacting SNPs-pair from chromosome 6q11.1 (rs6455128, the KHDRBS2 gene) and 13q12.11 (rs7989332, the CRYL1 gene) (p = 0.006, corrected for multiple testing). A replication analysis in the independent AD cohort from Germany (555 patients and 824 controls) confirmed the discovered epistasis signal (p = 0.036). This signal was also supported by a meta-analysis approach in 5 independent AD cohorts that was applied in the context of epistasis for the first time. Transcriptome analysis revealed negative correlation between expression levels of KHDRBS2 and CRYL1 in both the temporal cortex (β = -0.19, p = 0.0006) and cerebellum (β = -0.23, p < 0.0001) brain regions. This is the first time a replicable epistasis associated with AD was identified using a hypothesis free screening approach

Complete genome sequence of bacillus altitudinis type strain SGAir0031 isolated from tropical air collected in Singapore

Bacillus altitudinis strain SGAir0031 (Firmicutes) was isolated from tropical air samples collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb and one plasmid with 32 kb. The genome consists of 3,820 protein-coding genes, 81 tRNAs, and 24 rRNAs.MOE (Min. of Education, S’pore)Published versio