Metatranscriptome analysis of microbial communities in rice microcosms

Metatranscriptomics is a state-of-the-art technique to elucidate the functional activities of microbial communities, but its application is still limited to marine microbial assemblages. In my PhD project, we established the complete approach of soil metatranscriptomics, involving RNA extraction, cDNA library preparation by random priming, 454-pyrosequencing, and bioinformatic data analysis. The approach was tested on microbial communities in the oxic surface layer and the anoxic bulk soil of flooded rice paddy soil microcosms. Total RNA was recovered in high integrity and purity by low-pH phenol extraction (pH 5.0) followed by Q-Sepharose column chromatography. We were able to enrich mRNA sequences up to 50-70% in the metatranscriptome libraries using Ribo-Zero™ rRNA removal kit (Meta-Bacteria). All the 454 reads obtained were preprocessed prior to data analysis to minimize sequence ambiguities. A total of 10,000 SSU-ribotags (total RNA) were analyzed to elucidate community composition in the oxic and anoxic zones at three different incubation time points (25, 45 and 90 days after transplantation of rice seedlings). Additionally, about 45,000 and 12,000 mRNA-tags (enriched mRNA) were obtained for the analysis of functional activities in, respectively, the oxic and anoxic zone of 90-day-old rice microcosms. SSU-ribotag data analysis revealed no major temporal changes in community composition except for Geobacter, Clostridia and methanogens in the anoxic bulk soil. However, the taxonomic composition of microbial communities was clearly distinct between the oxic and anoxic zones, with cyanobacteria being the dominant group in the surface layer. Although mRNA-tags related to basic cellular functions were most abundant in both mRNA datasets, the expression of specific functions in response to different oxygen conditions was observed such as, for example, methane oxidation in the oxic zone and methanogenesis in the anoxic zone. Our metatranscriptomic approach provides a means to analyze the composition and functional gene expression of complex soil microbial communities while avoiding the limitations of PCR-based approaches

Relationship between sleep and obesity among U.S. and South Korean college students

Background Little is known about the relationship between sleep and obesity in young adults, particularly college students. This study examined the relationship between sleep (i.e., sleep duration and quality) and obesity in a large and diverse binational sample of college students. Methods Analyses were based on a 40-item paper survey from 2016/2017 to 2017/2018 academic years, with a 72% response rate. The samples were 1578 college students aged 18–25 years from five universities (two in the U.S. and three in South Korea). Weight and height were measured objectively; other measures (e.g., health behaviors) were self-reported. Multinomial logistic regression was used to assess the association between sleep duration and independent variables (race/nationality, gender, and BMI). Poisson regression was used to examine the relationship between sleep quality and independent variables. Results Overall, blacks had a higher adjusted odds ratio (AOR) of short sleep (\u3c 7 h/night) than whites (AOR = 1.74, P \u3c .01); overweight participants had a higher AOR of short sleep than normal weight participants (AOR = 1.52, P \u3c .01); and obese participants had a higher AORs of both short and long sleep (\u3e 9 h/night) (AOR = 1.67, P \u3c .01; AOR = 1.79, P \u3c .05, respectively). Among men, being black, overweight, and obesity were associated with short sleep (P \u3c .05), whereas only obesity was related to short sleep among women (P \u3c .05). In analyses stratified by race and nationality, overweight and obesity were related to short sleep among blacks only (P \u3c .05). Overall, sleep quality (getting enough sleep to feel rested in the morning in the past 7 days) was worse in blacks and South Koreans than whites (P \u3c .05), worse in women than men (P \u3c .05), and worse in participants with obesity than normal weight participants (P \u3c .05). Conclusions Obesity was associated with both short (\u3c 7 h/night) and long sleep duration (\u3e 9 h/night) and poor sleep quality among all participants. In comparison with whites, blacks were more like to have short sleep, and blacks and South Koreans had worse sleep quality. Further investigations using a larger sample of college students in multiple countries may be helpful to identify target populations who are at a greater risk of obesity and sleep problems

Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands

Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T = VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (≤0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1ω5c, C18:1ω5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (ω-1) hydroxy fatty acids. The G + C content of the DNA is 58.5–59.0 mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov

Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion.

Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness-costly metabolites through natural selection. In this strategy, metabolic cross-feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co-evolved wild-type lactic acid bacteria and engineered auxotrophic Saccharomyces cerevisiae in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B-group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange

Development and Implementation of a High-Pressure, Double-Acting, Bi-Directional Loading Cell for Drilled Shafts

Drilled shaft foundation elements provide a cost-effective foundation alternative for the support of building and bridge superstructure loads. Bi-directional pile loading tests (BDPLTs) to evaluate the capacity of drilled shafts have become popular owing to their capacity to save time and effort as compared to the use of top-down loading tests. However, the use of BDPLTs requires that production shafts be post-grouted following testing in order to assure appropriate in-service performance. Commonly used single-acting loading cells and/or loading cell construction details can pose the potential for the development of voids following post-grouting due to their monotonic jacking action and large footprint. This paper described the development and use of high pressure bi-directional loading cells intended to minimize the possibility of post-test construction defects. First, a comparison was made between the single-acting and double-acting loading cells. Second, the results of laboratory calibrations on the pressurized loading cells were performed, as were component testing of the pumps, hoses, and hydraulic fluid synchronization lines. Then, the use of the new high pressure double-acting loading cells in production testing of instrumented shafts was described, and the efficacy of the new loading cells was illustrated. The new loading cells provided the profession with a load cell alternative for conducting BDLTs and should serve to help reduce the risk of post-test grouting defects in drilled shaft foundations.Keywords: field testing, cementing/grouting, deep foundations, site infrastructure and constructio

Relationship between sleep and obesity among U.S. and South Korean college students

Background Little is known about the relationship between sleep and obesity in young adults, particularly college students. This study examined the relationship between sleep (i.e., sleep duration and quality) and obesity in a large and diverse binational sample of college students. Methods Analyses were based on a 40-item paper survey from 2016/2017 to 2017/2018 academic years, with a 72% response rate. The samples were 1578 college students aged 18–25 years from five universities (two in the U.S. and three in South Korea). Weight and height were measured objectively; other measures (e.g., health behaviors) were self-reported. Multinomial logistic regression was used to assess the association between sleep duration and independent variables (race/nationality, gender, and BMI). Poisson regression was used to examine the relationship between sleep quality and independent variables. Results Overall, blacks had a higher adjusted odds ratio (AOR) of short sleep ( 9 h/night) (AOR = 1.67, P < .01; AOR = 1.79, P < .05, respectively). Among men, being black, overweight, and obesity were associated with short sleep (P < .05), whereas only obesity was related to short sleep among women (P < .05). In analyses stratified by race and nationality, overweight and obesity were related to short sleep among blacks only (P < .05). Overall, sleep quality (getting enough sleep to feel rested in the morning in the past 7 days) was worse in blacks and South Koreans than whites (P < .05), worse in women than men (P < .05), and worse in participants with obesity than normal weight participants (P < .05). Conclusions Obesity was associated with both short ( 9 h/night) and poor sleep quality among all participants. In comparison with whites, blacks were more like to have short sleep, and blacks and South Koreans had worse sleep quality. Further investigations using a larger sample of college students in multiple countries may be helpful to identify target populations who are at a greater risk of obesity and sleep problems

On the Estimation of an Almost Ideal Demand System with Autoregressive Errors

A new GLS estimation procedure is employed in the estimation of a dynamic version of Almost Ideal Demand System with vector autoregressive errors. The procedure enables us to have more natural form of autoregressive parameters. Also, a new habit formation specification obeying the adding up restriction is proposed. In an application for four categories of food in the U.S., test results show that the error process is a first order vector autoregressive process and that the demand system is characterized by habit formation