Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice

Background: The daily cycling of plant physiological processes is speculated to arise from the coordinated rhythms of gene expression. However, the dynamics of diurnal 3D genome architecture and their potential functions underlying the rhythmic gene expression remain unclear. Results: Here, we reveal the genome-wide rhythmic occupancy of RNA polymerase II (RNAPII), which precedes mRNA accumulation by approximately 2 h. Rhythmic RNAPII binding dynamically correlates with RNAPII-mediated chromatin architecture remodeling at the genomic level of chromatin interactions, spatial clusters, and chromatin connectivity maps, which are associated with the circadian rhythm of gene expression. Rhythmically expressed genes within the same peak phases of expression are preferentially tethered by RNAPII for coordinated transcription. RNAPII-associated chromatin spatial clusters (CSCs) show high plasticity during the circadian cycle, and rhythmically expressed genes in the morning phase and non-rhythmically expressed genes in the evening phase tend to be enriched in RNAPII-associated CSCs to orchestrate expression. Core circadian clock genes are associated with RNAPII-mediated highly connected chromatin connectivity networks in the morning in contrast to the scattered, sporadic spatial chromatin connectivity in the evening; this indicates that they are transcribed within physical proximity to each other during the AM circadian window and are located in discrete “transcriptional factory” foci in the evening, linking chromatin architecture to coordinated transcription outputs. Conclusion: Our findings uncover fundamental diurnal genome folding principles in plants and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation

The correlation of the intestinal with pharyngeal microbiota in early neonates

IntroductionThe gut-lung axis has long been recognized as an important mechanism affecting intestinal and lung immunity. Still, few studies have examined the correlation between the intestinal and pharyngeal microbiota in early neonates, especially when feeding patterns are one of the main drivers of microbiota development.MethodsTo explore the composition and function of intestinal and pharyngeal microbiota and to analyze the effect of limited formula feeding on the initial microbiota colonization in early full-term neonates, we characterized the stool and oropharyngeal microbiota of 20 healthy full-term newborns sampled on days 0 and 5–7 after birth using 16S rRNA gene sequencing. Based on the sequencing results, a comparison was made of the compositions and functions of the intestinal and oropharyngeal microbiota for analysis.Results and discussionAt the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most abundant in both niches. At the genus level, the species of pioneer bacteria were rich in the intestine and oropharynx but low in abundance on day 0. On days 5–7, Bifidobacterium (25.40%) and Escherichia-Shigella (22.16%) were dominant in the intestine, while Streptococcus (38.40%) and Staphylococcus (23.13%) were dominant in the oropharynx. There were eight core bacteria genera in the intestine and oropharynx on days 5–7, which were Bifidobacterium, Escherichia-Shigella, Staphylococcus, Streptococcus, Bacteroides, Parabacteroides, Rothia, and Acinetobacter. As indicated by PICRUSt analysis, on days 5–7, the intestinal microbiota was more predictive than the oropharyngeal microbiota in transcription, metabolism, cell motility, cellular processes and signaling, and organismal system function in the KEGG pathway. Compared to exclusive breastfeeding, limited formula feeding (40–60%) had no significant effect on the neonatal intestinal and oropharyngeal microbiota composition during the initial colonization period. Our results suggest that the initial colonization of microbiota is closely related to the ecological niche environment in the intestine and oropharynx, with their core microbiota being closely correlated. We found that early limited formula feeding could not significantly affect the initial colonization of microbiota in the intestine and oropharynx

A Comparative Analysis of Technical Efficiency and Input Allocation Decisions of Farm Lenders in the Commercial Banking Industry and the Farm Credit System during the Late 2000s Recession

This paper applies the stochastic Translog input distance function and stochastic frontier analysis (SFA) method to evaluate the operational efficiency of farm lenders in the commercial banking industry and the Farm Credit System (FCS). This paper uses the late 2000s recession as a backdrop for scrutinizing the operating decisions of commercial banks and FCS lending units. The model is applied as a comparative analytical frame work to analyze the operating strategies and efficiencies of commercial banks and FCS lending units. Moreover, under the same efficiency analytical framework, this study investigates the effect of the size of lending operations on the lenders’ efficiency and input allocation decisions. This study also adopts an intertemporal perspective by looking at comparative commercial banks and FCS efficiency before and after the most recent financial crisis. The study’s analyses of changes in both technical efficiency (TE) and allocative efficiency (AE) will help clarify the contributions of different factors to total factor productivity change and, thus help commercial banks and FCS make future operating adjustments to maximize total factor productivity. This analysis may clarify any differences in input allocations and other operating decisions that define small and large lenders’ strategies to survive the tight financial conditions of the late 2000s

Report on Global Environmental Competitiveness (2013)

This book explores the environmental competitiveness of 133 countries around the world, presenting an index evaluation system to facilitate a comparative analysis of environmental competitiveness on a global scale. This is a new way to measure competitiveness in the light of the contradiction between world economic development and environmental protection. Global environmental competitiveness covers five aspects: the ecological environment, resources environment, environmental management, environmental impacts and environmental coordination. The authors use longitudinal study and horizontal analysis, combining qualitative and quantitative analysis methods so as to conduct an in-depth study of theoretical, empirical and methodological issues of global environmental competitiveness.The work is presented here in three main parts beginning with the theory, technical road-map and analytical approach used. The second part reports on the countries as evaluation objects, analyzing the development status of global environmental competitiveness as a whole and revealing the strengths and weaknesses of each country's environmental competitiveness. Basic paths and strategies to enhance the competitiveness level are presented. In the third part the reader will discover a sub-report and evaluation of the environmental competitiveness for 133 countries around the world, revealing the characteristics and relative differences of countries representing different levels of development, in order to provide an important decision-making reference to those considering environmental economic policies, especially those considering accelerating a green economic transformation and enhancing environmental competitiveness.This book will appeal to scholars and professionals with an interest in environmental issues and environmental competitiveness at a global level, as well as those with an interest in each of the 133 countries analyzed in this text, including environmental policy makers in those countries