Metacommunity ecology meets bioassessment : Assessing spatio-temporal variation in multiple facets of macroinvertebrate diversity in human-influenced large lakes

Highlights • We examined drivers of 6 biotic metrics in a metacommunity context in two large lakes. • The relative roles of spatial, human-induced and natural factors were quantified. • The roles of spatial variables are comparable with local environmental conditions. • The relative roles of different drivers varied substantially among seasons. • Spatial processes, natural conditions and temporal variation should be considered.Metacommunity theory emphasizes that local communities are jointly affected by environmental filtering and spatial processes. However, the roles of spatial processes are often given insufficient attention in bioassessment practices, which may bias the assessments of ecological status based on biotic metrics. Here, we quantified the relative importance and the seasonal stability of spatial processes, natural conditions and human-induced factors in structuring variation in different bioassessment metrics based on macroinvertebrate communities. Our study systems were two extensively sampled large and shallow lakes with strong nutrient gradients related to human disturbance. The roles of different drivers were examined for three kinds of indicators: general diversity, trait-based and taxonomic distinctness metrics, and their performance in characterizing human disturbance was evaluated. Overall, human-induced and spatial factors were all important in explaining variation in the three types of bioassessment metrics. Contrary to our expectations, however, we found that the importance of spatial processes on bioassessment metrics can be comparable to the effects of local environmental conditions at the within-lake scale. Furthermore, the results showed substantial seasonal variability in the relative roles of different drivers, which might be linked to life-cycle seasonality of macroinvertebrates. As expected, trait-based metrics generally were best associated with human-induced variables in both lakes, whereas general diversity and taxonomic distinctness metrics performed poorly. The low effectiveness of taxonomic distinctness metrics might due to low species richness associated with high nutrient levels. To conclude, our results suggest that bioassessment cannot exclusively rely on the idea of environmental filtering even if we focus on fine spatial scales. We hence strongly urge that spatial processes, natural drivers and temporal variability should be better considered in combination in the development and application of bioassessment approaches. In addition, taxonomic distinctness measures should be used with caution, especially for the ecosystems and organism groups typically characterized by low species richness

Tet and TDG Mediate DNA Demethylation Essential for Mesenchymal-to-Epithelial Transition in Somatic Cell Reprogramming

SummaryTet-mediated DNA oxidation is a recently identified mammalian epigenetic modification, and its functional role in cell-fate transitions remains poorly understood. Here, we derive mouse embryonic fibroblasts (MEFs) deleted in all three Tet genes and examine their capacity for reprogramming into induced pluripotent stem cells (iPSCs). We show that Tet-deficient MEFs cannot be reprogrammed because of a block in the mesenchymal-to-epithelial transition (MET) step. Reprogramming of MEFs deficient in TDG is similarly impaired. The block in reprogramming is caused at least in part by defective activation of key miRNAs, which depends on oxidative demethylation promoted by Tet and TDG. Reintroduction of either the affected miRNAs or catalytically active Tet and TDG restores reprogramming in the knockout MEFs. Thus, oxidative demethylation to promote gene activation appears to be functionally required for reprogramming of fibroblasts to pluripotency. These findings provide mechanistic insight into the role of epigenetic barriers in cell-lineage conversion

Use of a Generalized Additive Model to Investigate Key Abiotic Factors Affecting Microcystin Cellular Quotas in Heavy Bloom Areas of Lake Taihu

Lake Taihu is the third largest freshwater lake in China and is suffering from serious cyanobacterial blooms with the associated drinking water contamination by microcystin (MC) for millions of citizens. So far, most studies on MCs have been limited to two small bays, while systematic research on the whole lake is lacking. To explain the variations in MC concentrations during cyanobacterial bloom, a large-scale survey at 30 sites across the lake was conducted monthly in 2008. The health risks of MC exposure were high, especially in the northern area. Both Microcystis abundance and MC cellular quotas presented positive correlations with MC concentration in the bloom seasons, suggesting that the toxic risks during Microcystis proliferations were affected by variations in both Microcystis density and MC production per Microcystis cell. Use of a powerful predictive modeling tool named generalized additive model (GAM) helped visualize significant effects of abiotic factors related to carbon fixation and proliferation of Microcystis (conductivity, dissolved inorganic carbon (DIC), water temperature and pH) on MC cellular quotas from recruitment period of Microcystis to the bloom seasons, suggesting the possible use of these factors, in addition to Microcystis abundance, as warning signs to predict toxic events in the future. The interesting relationship between macrophytes and MC cellular quotas of Microcystis (i.e., high MC cellular quotas in the presence of macrophytes) needs further investigation

Two ultraviolet radiation datasets that cover China

Ultraviolet (UV) radiation has significant effects on ecosystems, environments, and human health, as well as atmospheric processes and climate change. Two ultraviolet radiation datasets are described in this paper. One contains hourly observations of UV radiation measured at 40 Chinese Ecosystem Research Network stations from 2005 to 2015. CUV3 broadband radiometers were used to observe the UV radiation, with an accuracy of 5%, which meets the World Meteorology Organization's measurement standards. The extremum method was used to control the quality of the measured datasets. The other dataset contains daily cumulative UV radiation estimates that were calculated using an all-sky estimation model combined with a hybrid model. The reconstructed daily UV radiation data span from 1961 to 2014. The mean absolute bias error and root-mean-square error are smaller than 30% at most stations, and most of the mean bias error values are negative, which indicates underestimation of the UV radiation intensity. These datasets can improve our basic knowledge of the spatial and temporal variations in UV radiation. Additionally, these datasets can be used in studies of potential ozone formation and atmospheric oxidation, as well as simulations of ecological processes

Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

Abstract Background Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. Results We perform single-cell RNA sequencing analysis of 1916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. Based on the regulatory activities rather than the expression patterns, all cells analyzed can be well classified into four major groups with epithelial, mesodermal, hematopoietic, and neuronal identities. For different organs within the same group, the similarities and differences of their features and developmental paths are revealed and reconstructed. Conclusions We identify mutual interactions between epithelial and mesenchymal cells and detect epithelial cells with prevalent mesenchymal features during organogenesis, which are similar to the features of intermediate epithelial/mesenchymal cells during tumorigenesis. The comprehensive transcriptome at single-cell resolution profiled in our study paves the way for future mechanistic studies of the gene-regulatory networks governing mammalian organogenesis

Climate Change Causes Salinity To Become Determinant in Shaping the Microeukaryotic Spatial Distribution among the Lakes of the Inner Mongolia-Xinjiang Plateau

ABSTRACT Climate change greatly affects lake microorganisms in arid and semiarid zones, which alters ecosystem functions and the ecological security of lakes. However, the responses of lake microorganisms, especially microeukaryotes, to climate change are poorly understood. Here, using 18S ribosomal RNA (rRNA) high-throughput sequencing, we investigated the distribution patterns of microeukaryotic communities and whether and how climate change directly or indirectly affected the microeukaryotic communities on the Inner Mongolia-Xinjiang Plateau. Our results showed that climate change, as the main driving force of lake change, drives salinity to become a determinant of the microeukaryotic community among the lakes of the Inner Mongolia-Xinjiang Plateau. Salinity shapes the diversity and trophic level of the microeukaryotic community and further affects lake carbon cycling. Co-occurrence network analysis further revealed that increasing salinity reduced the complexity but improved the stability of microeukaryotic communities and changed ecological relationships. Meanwhile, increasing salinity enhanced the importance of deterministic processes in microeukaryotic community assembly, and the dominance of stochastic processes in freshwater lakes transformed into deterministic processes in salt lakes. Furthermore, we established lake biomonitoring and climate sentinel models by integrating microeukaryotic information, which would provide substantial improvements to our predictive ability of lake responses to climate change. IMPORTANCE Our findings have important implications for understanding the distribution patterns and the driving mechanisms of microeukaryotic communities among the lakes of the Inner Mongolia-Xinjiang Plateau and whether and how climate change directly or indirectly affects microeukaryotic communities. Our study also establishes the groundwork to use the lake microbiome for the assessment of aquatic ecological health and climate change, which is critical for ecosystem management and for projecting the ecological consequences of future climate warming

Clinical significance of tumor deposits in gastric cancer after radical gastrectomy: a propensity score matching study

Abstract Objective The value of tumor deposits (TDs) in the prognosis and staging of gastric cancer (GC) is still under debate. This study aims to evaluate the prognostic value of TDs and the best ways to incorporate TDs in the TNM classification of GC. Methods Patients (n = 3460) undergoing curative gastrectomy for GC in the West China Hospital from 2005 to 2017 were retrospectively reviewed and divided into two groups according to the TD status (positive vs. negative). Later, clinicopathological features and overall survival (OS) between the two groups were compared. Thereafter, the associations between the presence of TD and other clinicopathological factors were evaluated through logistic regression. In addition, univariate and multivariate Cox regression were conducted for determining prognostic factors. The possibility of selection bias was reduced through conducting the 1:1 propensity score matching (PSM) analysis. The modified classification systems proposed previously that incorporated TDs into the TNM staging system were assessed. Results There were 10.5% of patients (362/3460) diagnosed with TDs. TDs were significantly related to unfavorable factors such as advanced T stage and N stage and independently associated with poor prognosis. The 5-year OS of patients with TDs was significantly lower than that of patients without TDs (31.0% vs. 60.9%, P < 0.001), whereas higher than that of patients with peritoneal metastasis (31.0% vs. 5.0%, P < 0.001). In patients receiving chemotherapy, the 5-year OS of patients with TDs was also significantly lower than that of patients without TDs (42.0% vs. 50.9%, P = 0.026). Moreover, the system incorporating TDs in the TNM classification as metastatic lymph nodes outperformed others. Conclusions TDs are related to the aggressive characteristics and are an independent prognostic factor for GC. Incorporating TDs in the TNM classification as the metastatic lymph nodes increases the accuracy in predicting prognosis