More Like this

1. High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils

   https://doi.org/10.1128/AEM.01383-21  

   Zhang, Si-Yu; Xiao, Xiao; Chen, Song-Can; Zhu, Yong-Guan; Sun, Guo-Xin; Konstantinidis, Konstantinos T. (September 2021, Applied and Environmental Microbiology)

   Cann, Isaac (Ed.)

   ABSTRACT Arsenic (As) metabolism genes are generally present in soils, but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes ( ars ) including arsR , acr3 , arsB , arsC , arsM , arsI , arsP , and arsH as well as energy-generating As respiratory oxidation ( aioA ) and reduction ( arrA ) genes. Somewhat unexpectedly, the relative DNA abundances and diversities of ars , aioA , and arrA genes were not significantly different between low and high (∼10 versus ∼100 mg kg −1 ) As soils. Compared to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars gene abundance only when its concentration was higher than 410 mg kg −1 . In contrast, metatranscriptomics revealed that relative to low-As soils, high-As soils showed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community wide as opposed to taxon specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil or other environments should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level; thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems. 

   more » « less
2. Possibilities of applying the concept of “winter city” in the Russian Arctic (on the example of the city of Nadym).

   https://doi.org/10.25283/2223-4594-2021-2-291-303  

   Fedorov, Roman Y; Sizov, Oleg S; Kuklina, Vera V; Lobanov, Andrei A; Soromotin, Andrei V; Pechkin, Alexander S; Pechkina, Yulia A; Esau, Igor N (April 2021, Arctica)

   null (Ed.)

   On example of the city of Nadym, located in the Yamalo-Nenets Autonomous Area, the authors consider the socio-ecological problems of the development of green, blue and white open urban spaces. The research approach presented in the article is based on the study of a multifaceted complex of urban social and natural systems in their integrated unity, not just as public places, but as biomes — highly integrated urban ecosystems. A posteriori the researchers based on the materials of interviews conducted in 2020 with experts who in different years took part in the study or planned the development of the open urban spaces in Nadym, as well as on the analysis of available publications on this topic and publicly available data. The study found that factors such as the short summer, during which many residents leave the city, as well as the prevalence of freezing temperatures for almost eight months, in fact, transform the green and blue spaces of Nadym into white. This situation indicates the advisability of a more active appeal to the concept of a “winter city” in the development of the city urban environment. The application of the concept principles can be in demand in the process of creating more comfortable living conditions and spatial mobility of the Nadym residents, as well as for developing the recreational opportunities of the city open spaces and integrating them into the natural environment surrounding the city, which in general can be considered as one of the factors for the sustainable development of the city and the formation of post-industrial features in its socio-economic life. 

   more » « less
3. Mineralogical Associations of Sedimentary Arsenic within a Contaminated Aquifer Determined through Thermal Treatment and Spectroscopy

   https://doi.org/10.3390/min13070889  

   Varner, Thomas S.; Kulkarni, Harshad V.; Bhuiyan, Mesbah Uddin; Cardenas, M. Bayani; Knappett, Peter S.; Datta, Saugata (July 2023, Minerals)

   Sedimentary arsenic (As) in the shallow aquifers of Bangladesh is enriched in finer-grained deposits that are rich in organic matter (OM), clays, and iron (Fe)-oxides. In Bangladesh, sediment color is a useful indicator of pore water As concentrations. The pore waters of orange sediments are usually associated with lower As concentrations (<50 µg/L) owing to abundant Fe-oxides which sorb As. Using this color signal as a guide, spectroscopic measurements alongside thermal treatment were extensively utilized for analyzing the properties of both Fe-oxides and clay minerals. This study uses Fourier transform infrared (FTIR) and diffuse reflectance (DR) measurements along with thermal treatment to evaluate the solid-phase associations of As from sediment collected along the Meghna River in Bangladesh. The samples analyzed in this study were chosen to represent the various lithologies present at the study site and included riverbank sands (1 m depth), silt (6 m depth), aquifer sand (23 m depth), and a clay aquitard (37 m depth). The concentrations of sedimentary As and Fe were measured by X-ray fluorescence, and the spectroscopic measurements were taken on the samples prior to the thermal treatment. For the thermal treatment, sediment samples were placed in a preheated furnace at 600 °C for 3 h. The thermal treatment caused a deepening of reddish-brown hues in all samples, and the greatest change in color was observed in the finer-grained samples. The FTIR spectral analysis revealed that the clay minerals were composed primarily of illite, smectite, and kaolinite. The DR results indicate that the majority of Fe in sands was present as goethite; however, in the clay and silt samples, Fe was incorporated into the structure of clay minerals as Fe(II). The amount of structural Fe(II) was strongly positively correlated with the sedimentary As concentrations, which were highest in the finer-grained samples. After thermal treatment, the concentrations of As in the finer-grained samples decreased by an average of 40%, whereas the change in the As concentrations of the sand samples was negligible. These findings indicate that significant proportions of solid-phase As may be retained by OM and Fe(II)-bearing clay minerals. 

   more » « less
4. Mineralogical Associations of Sedimentary Arsenic within a Contaminated Aquifer Determined through Thermal Treat-ment and Spectroscopy

   Thomas S. Varner, Harshad V. (September 2023, Minerals)

   Sedimentary arsenic (As) in the shallow aquifers of Bangladesh is enriched in finer-grained de-posits rich in organic matter, clays, and iron (Fe)-oxides. In Bangladesh, sediment color is a use-ful indicator of pore-water As concentrations. The pore-waters of orange sediments are usually associated with lower As concentrations (<50 µg/L) owing to abundant Fe-oxides which sorb As. Using this color signal as a guide, spectroscopic measurements alongside thermal treatment have been extensively utilized for analyzing the properties of both Fe-oxides and clay minerals. This study uses Fourier transform infrared (FTIR) and diffuse reflectance (DR) measurements along with thermal treatment to evaluate the solid-phase associations of As from sediment col-lected along the Meghna River in Bangladesh. The samples analyzed in this study were chosen to represent the various lithologies present at the study site and included riverbank sands (1 m depth), silt (6 m depth), aquifer sand (23 m depth), and a clay aquitard (37 m depth). The concen-trations of sedimentary As and Fe were measured by X-Ray Fluorescence and the spectroscopic measurements were taken on the samples prior to the thermal treatment. For the thermal treat-ment, sediment samples were placed in a preheated furnace at 600C for 3 hours. The thermal treatment caused a deepening of reddish-brown hues in all samples, and the greatest change of color was observed in the finer-grained samples. The FTIR spectral analysis revealed that the clay minerals were composed primarily of illite, smectite, and kaolinite. The DR results indicat-ed that the majority of Fe in sands was present as goethite; however, in the clay and silt samples, Fe was incorporated into the structure of clay minerals as Fe(II). The amount of structural Fe(II) was strongly positively correlated with the sedimentary As concentrations, which were highest in the finer-grained samples. After thermal treatment, the concentrations of As in the finer-grained samples decreased by an average of 40% whereas the change in the As concentrations of the sand samples was negligible. These findings indicate that significant proportions of solid-phase As may be retained by OM and Fe(II)-bearing clay minerals. 

   more » « less
5. Identification of differential alternative splicing events with an adjusted beta-distribution model

   https://doi.org/10.1109/EIT.2017.8053369  

   Liu, Kan; Du, Qian; Ren, Guodong; Yu, Bin; Zhang, Chi (May 2017, IEEE International Conference on Electro Information Technology (EIT))

   High-throughput next generation sequencing of cDNA, i.e. RNA-Seq, presents an unprecedented resource for characterizing the alternative splicing (AS) in complex eukaryotic transcriptomes. Accumulating evidences indicate that AS is developmentally regulated, but the precise responses of AS event to development is not well understood. Here, we describe a new method, based on an adjusted beta-distribution model, for detection of differential AS patterns from RNA-Seq data comparisons. Applying our method to two datasets of RNA-Seq for zika infection in human cells and pollen tissue in Arabidopsis thaliana, we identified 1,871 differentially AS events for 1,394 protein-coding genes in human and 496 differentially AS events for 358 protein-coding genes in Arabidopsis, respectively. The results included known AS events reported before as well as novel events, which demonstrate that the biological replicates are important in the effective identification using β-distribution. With a high accurate rate, our new method in differential AS identification will facilitate future investigation on transcriptomic annotation. 

   more » « less