Effects of the herbicides metazachlor and flufenacet on phytoplankton communities - A microcosm assay

Agrochemicals are the main pollutants in freshwater ecosystems. Metazachlor and flufenacet are two common herbicides applied in fall (i.e., August-October) to agricultural fields in Northern Germany. High concentrations of these herbicides are often found in adjacent aquatic ecosystems. Phytoplankton are one of the highly susceptible non-targeted aquatic organismal groups for herbicides and effects on phytoplankton may initiate a chain of consequences in meta communities through trophic interactions. Few studies have focused on responses of the phytoplankton community for metazachlor and, no studies have focused on flufenacet. We studied the effects of metazachlor and flufenacet on the phytoplankton community by conducting a microcosm experiment exposing natural fall phytoplankton communities to environmentally realistic concentrations as 0 (control), 0.5, 5 and 50 µg L-1 of metazachlor and flufenacet treatments over a 4-week period. We measured changes in density, composition (i.e., in phyla and species level), taxonomic diversity indices, and functional features of phytoplankton communities as a response to herbicides. A reduction in the density of Chlorophyta species (e.g., Koliella longiseta, Selenastrum bibraianum) and Cyanobacteria species (e.g., Merismopedia tenuissima and Aphanocapsa elegans) was observed in herbicide treatments compared to controls. The phytoplankton community shifted towards a high density of species from Bacillariophyta (e.g., Nitzschia fonticola and Cyclotella meneghiniana), Miozoa (i.e., Peridinium willei), and Euglenozoa (i.e., Trachelomonas volvocina) in herbicide treatments compared to controls. Metazachlor and flufenacet showed significant negative effects on taxonomic diversity indices (e.g., species richness, the Shannon-Wiener index) and functional features (e.g., functional dispersion and redundancy) of the phytoplankton communities, with increasing herbicide concentrations. Our study provides insights into direct, selective, and irrecoverable effects of metazachlor and flufenacet on phytoplankton communities in the short-term. The comprehensive understanding of these effects of environmentally realistic herbicide concentrations on aquatic biota is essential for a sustainable management of aquatic ecosystems in agricultural areas.

Planning actions with a magnetic tool: how initial tool orientation and number of functional ends influence motor planning abilities in capuchin monkeys (Sapajus spp.)

The way in which animals grasp objects to perform subsequent action execution allows studying their anticipatory abilities. We examined whether 11 capuchin monkeys (Sapajus spp.) were able to prospectively grasp a magnetic dowel to use it as a tool to retrieve a baited metallic container from a plexiglas box placed in front of them. We investigated whether and how initial dowel orientation (horizontal vs vertical) affected grasping and using the dowel to retrieve the container in two testing conditions: (1) 2-FE condition in which the dowel had two functional magnetic ends; (2) 1-FE condition in which the dowel had only one functional magnetic end. In the 2-FE condition, capuchins had to take into account the initial dowel orientation since both ends were functional, whereas in the 1-FE condition capuchins had also to take into account the initial functional end position when grasping the dowel. Capuchins were trained to grasp the dowel to put one functional end in contact with the metallic container. However, they did not learn to associate the functional end of the 1-FE dowel to successful retrieval. Capuchins showed better anticipatory planning (1) in 2-FE than in 1-FE condition and (2) when the dowel was initially positioned on the horizontal plane than on the vertical one. Moreover, hand preferences affected planning in the 1-FE condition. Results were discussed within the frameworks of primates' abilities to use abstract cues and on their abilities to process functional features and spatial cues and to perform mental rotations.

A multiparametric MRI-based CAD system for accurate diagnosis of bladder cancer staging

Appropriate treatment of bladder cancer (BC) is widely based on accurate and early BC staging. In this paper, a multiparametric computer-aided diagnostic (MP-CAD) system is developed to differentiate between BC staging, especially T1 and T2 stages, using T2-weighted (T2W) magnetic resonance imaging (MRI) and diffusion-weighted (DW) MRI. Our framework starts with the segmentation of the bladder wall (BW) and localization of the whole BC volume (V_t) and its extent inside the wall (V_w). Our segmentation framework is based on a fully connected convolution neural network (CNN) and utilized an adaptive shape model followed by estimating a set of functional, texture, and morphological features. The functional features are derived from the cumulative distribution function (CDF) of the apparent diffusion coefficient. Texture features are radiomic features estimated from T2W-MRI, and morphological features are used to describe the tumors' geometric. Due to the significant texture difference between the wall and bladder lumen cells, V_t is parcelled into a set of nested equidistance surfaces (i.e., iso-surfaces). Finally, features are estimated for individual iso-surfaces, which are then augmented and used to train and test machine learning (ML) classifier based on neural networks. The system has been evaluated using 42 data sets, and a leave-one-subject-out approach is employed. The overall accuracy, sensitivity, specificity, and area under the receiver operating characteristics (ROC) curve (AUC) are 95.24%, 95.24%, 95.24%, and 0.9864, respectively. The advantage of fusion multiparametric iso-features is highlighted by comparing the diagnostic accuracy of individual MRI modality, which is confirmed by the ROC analysis. Moreover, the accuracy of our pipeline is compared against other statistical ML classifiers (i.e., random forest (RF) and support vector machine (SVM)). Our CAD system is also compared with other techniques (e.g., end-to-end convolution neural networks (i.e., ResNet50).

Coupled photocatalytic-bacterial degradation of pyrene: Removal enhancement and bacterial community responses

Polycyclic aromatic hydrocarbons (PAHs) are a class of pollutants that ubiquitously present in environment and hard to be degraded by microorganisms. Herein, we reported a novel photocatalytic-bacterial coupled removal system to treat PAH-polluted water. Using pyrene as the model pollutant, we demonstrated that the removal percentage of different groups was in order: 63.89% ± 1.03% (Vis-Biological) > 61.27% ± 1.08% (UV-Biological) > 59.58% ± 1.15% (UV) > 57.41% ± 1.13% (Vis) > 6.65% ± 0.72% (Biological) > 1.70% ± 0.34% (Control), showing the coupled system significantly improved the removal percentage of pyrene. Additionally, we observed that the coupled system driven by visible light showed higher removal percentage than UV light, exhibiting a good potential for future application. Sequencing analysis of 16S rRNA genes showed that alpha diversity (richness, evenness and diversity) got promoted and data of the relative abundance showed that Pseudomonadaceae was substituted as the dominant bacteria for Planococcaceae, with some other functional bacteria quickly acclimatizing in the bacterial community. Difference analysis indicated that over half of top fifteen genera were generally different significantly (p < 0.001) among two different samples, and UV light altered structure and composition of bacterial community more than visible light. Functional features' change suggested that the bacterial community not only protected itself but also participated in degrading pyrene. Overall, our study offered a new method for PAH degradation and contributed to further understanding of coupled catalytic-bacterial degradation processes.

Phenanthrene removal and response of bacterial community in the combined system of photocatalysis and PAH-degrading microbial consortium in laboratory system

This work aimed to study the removal of phenanthrene, change of bacterial community and microbial functions through combined photocatalysis and biodegradation under ultraviolet (UV) and visible light illumination. Results showed that phenanthrene removal was enhanced in combined system irradiated by UV and visible light. High-throughput sequencing of 16S rRNA gene manifested that alpha diversity (richness, evenness and diversity) got promoted and data of relative abundance reported that Planococcaceae as the dominant bacteriawas replaced by Pseudomonadaceae, with some other functional bacteria quickly acclimatizing. Difference analysis indicated that top fifteen genera were generally different significantly (p < 0.001) among two distinct samples, particularly for Pseudomonas on relative abundance. Functional features' regulation suggested that the bacterial community not only protected itself well but also participated in degrading phenanthrene. Selecting suitable degrading microbial consortium from natural environment and understanding deeply on performance of bacterial community contribute to assemble effective and directional combined system.

Flow regimes filter species traits of benthic diatom communities and modify the functional features of lowland streams - a nationwide scale study

Changes in land use, climate and flow diversion are key drivers of river flow regime change that may eventually affect freshwater biodiversity and ecosystem functions. However, our knowledge is limited on how the functional features of stream organisms vary along the gradient of hydrological disturbance (i.e. flow regime changes) and how flow regimes mediate the functional features in lowland streams. We analyzed the functional traits of benthic diatoms (unicellular siliceous algae) that are most sensitive and tolerant to flow regime changes along a nationwide scale of 246 sites in Denmark. We combined RLQ and fourth-corner analyses to explore the co-variation between hydrological variables (R table) and species traits (Q table), constrained by the relative abundance of each species (L table) as observed in each of the sampling sites. Further, we examine the relationships between functional features (i.e., functional redundancy and diversity) and hydrological variables by multivariate statistical analyses. Results show that species turnover with displacement of sensitive species by tolerant species was the dominating process in benthic diatom communities during high flow disturbances. Functional features, as indicated by functional diversity and redundancy indices, were mediated mainly by high and low flow magnitude. Median daily flow magnitude shows a consistent positive relationship with functional redundancy and richness indices indicating that larger streams are more resilient to flow perturbations. In addition flow regime changes are less important than median daily flow magnitude and show inconsistent correlation to functional features likely due to the interaction of multiple environmental stressors. Our study highlights the robustness of trait-based approaches for identifying flow regime changes in streams, and strongly suggests that biodiversity conservation and water resource management should focus on protecting natural base flow in headwater streams and generally reduce flow regulation for sustaining stream ecosystems under future global changes.

The granulocytes are the main immunocompetent hemocytes in Crassostrea gigas

Hemocytes comprise diverse cell types with morphological and functional heterogeneity and play indispensable roles in immunological homeostasis of invertebrates. The morphological classification of different hemocytes in mollusk has been studied since the 1970's, yet the involvement of the different sub-populations in immune functions is far from clear. In the present study, three types of hemocytes were morphologically identified and separated as agranulocytes, semi-granulocytes and granulocytes by flow cytometry and Percoll^® density gradient centrifugation. The granulocytes were characterized functionally as the main phagocytic and encapsulating population, while semi-granulocytes and agranulocytes exhibited low or no such capacities, respectively. Meanwhile, the lysosome activity and the productions of ROS and NO were all mainly concentrated in granulocytes under both normal and immune-activated situations. Further, the mRNA transcripts of some immune related genes, including CgTLR, CgClathrin, CgATPeV, CgLysozyme, CgDefensin and CgIL-17, were mainly expressed in granulocytes, lower in semi-granulocytes and agranulocytes. These results collectively suggested that the granulocytes were the main immunocompetent hemocytes in oyster C. gigas, and a differentiation relationship among these three sub-population hemocytes was inferred based on the gradual changes in morphological, functional and molecular features.

Demystifying the mechanistic and functional aspects of p21 gene activation with double-stranded RNAs in human cancer cells

BACKGROUND

The recently identified phenomenon of double-stranded RNA (dsRNA)-mediated gene activation (RNAa) has been studied extensively, as it is present in humans, mice, and Caenorhabditis elegans, suggesting that dsRNA-mediated RNAa is an evolutionarily conserved mechanism. Previous studies have shown that dsP21-322 can induce tumor suppressor gene p21 expression in several human cancer cells. Nonetheless, the role of dsRNAs in the activation of gene expression, including their target molecules and associated key factors, remains poorly understood.

METHODS

Oligonucleotides were used to overexpress dsRNAs and dsControl. Real-time PCR and Western blotting were used to detect corresponding mRNA and protein expression, respectively. Fluorescence microscopy was used to examine the kinetics of dsRNA subcellular distribution. Luciferase reporter assays were performed to verify dsRNA target molecules. Chromatin immunoprecipitation (ChIP) assays were carried out to determine whether histone modification and other associated key factors are involved in saRNA-mediated p21 expression.

RESULTS

We demonstrated that dsRNA-mediated p21 induction in human cell lines is a common phenomenon. This process occurs at the transcriptional level, and the complementary p21 promoter is the intended dsRNA target. Additionally, ChIP assays indicated that p21 activation was accompanied by an increased enrichment of AGO1 and the trimethylation of histone H3K4 at dsRNA-targeted genomic sites.

CONCLUSION

These data systematically reveal the mechanistic and functional aspects of ncRNA-mediated p21 activation in human cancer cells, which may be a useful tool to analyze gene function and aid in the development of novel drug targets for cancer therapeutics.

How the sourdough may affect the functional features of leavened baked goods

Sourdough fermentation is one of the oldest food biotechnologies, which has been studied and recently rediscovered for its effect on the sensory, structural, nutritional and shelf life properties of leavened baked goods. Acidification, proteolysis and activation of a number of enzymes as well as the synthesis of microbial metabolites cause several changes during sourdough fermentation, which affect the dough and baked good matrix, and influence the nutritional/functional quality. Currently, the literature is particularly rich of results, which show how the sourdough fermentation may affect the functional features of leavened baked goods. In the form of pre-treating raw materials, fermentation through sourdough may stabilize or to increase the functional value of bran fractions and wheat germ. Sourdough fermentation may decrease the glycaemic response of baked goods, improve the properties and bioavailability of dietary fibre complex and phytochemicals, and may increase the uptake of minerals. Microbial metabolism during sourdough fermentation may also produce new nutritionally active compounds, such as peptides and amino acid derivatives (e.g., γ-amino butyric acid) with various functionalities, and potentially prebiotic exo-polysaccharides. The wheat flour digested via fungal proteases and selected sourdough lactobacilli has been demonstrated to be probably safe for celiac patients.