Fungal Community as a Bioindicator to Reflect Anthropogenic Activities in a River Ecosystem

The fungal community interacts with the ambient environment and can be used as a bioindicator to reflect anthropogenic activities in aquatic ecosystems. Several studies have investigated the impact of anthropogenic activities on the fungal community and found that community diversity and composition are influenced by such activities. Here we combined chemical analysis of water properties and sequencing of fungal internal transcribed spacer regions to explore the relationship between water quality indices and fungal community diversity and composition in three river ecosystem areas along a gradient of anthropogenic disturbance (i.e., less-disturbed mountainous area, wastewater-discharge urban area, and pesticide and fertilizer used agricultural area). Results revealed that the level of anthropogenic activity was strongly correlated to water quality and mycoplankton community. The increase in organic carbon and nitrogen concentrations in water improved the relative abundance of Schizosaccharomyces, which could be used as a potential biomarker to reflect pollutant and nutrient discharge. We further applied a biofilm reactor using water from the three areas as influent to investigate the differences in fungal communities in the formed biofilms. Different community compositions were observed among the three areas, with the dominant fungal phyla in the biofilms found to be more sensitive to seasonal effects than those found in water. Finally, we determined whether the fungal community could recover following water quality restoration. Our biofilm reactor assay revealed that the recovery of fungal community would occur but need a long period of time. Thus, this study highlights the importance of preserving the original natural aquatic ecosystem

Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

The investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today.We have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets.Our work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis

Multi-ancestry genome-wide association meta-analysis of Parkinson?s disease

Although over 90 independent risk variants have been identified for Parkinson’s disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson’s disease with 49,049 cases, 18,785 proxy cases and 2,458,063 controls including individuals of European, East Asian, Latin American and African ancestry. In a meta-analysis, we identified 78 independent genome-wide significant loci, including 12 potentially novel loci (MTF2, PIK3CA, ADD1, SYBU, IRS2, USP8, PIGL, FASN, MYLK2, USP25, EP300 and PPP6R2) and fine-mapped 6 putative causal variants at 6 known PD loci. By combining our results with publicly available eQTL data, we identified 25 putative risk genes in these novel loci whose expression is associated with PD risk. This work lays the groundwork for future efforts aimed at identifying PD loci in non-European populations

Directed evolution of a β-N-acetylhexosaminidase from Haloferula sp. for lacto-N-triose II and lacto-N-neotetraose synthesis from chitin

In our previous study, a β-N-acetylhexosaminidase (HaHex74) from Haloferula sp. showing high human milk oligosaccharides (HMOs) synthesis ability was identified and characterized. In this study, HaHex74 was further engineered by directed evolution and site-saturation mutagenesis to improve its transglycosylation activity for HMOs synthesis. A mutant (mHaHex74) with improved transglycosylation activity (HaHex74-Asn401Ile/His394Leu) was obtained and characterized. mHaHex74 exhibited maximal activity at pH 5.5 and 35 °C, respectively, which were distinct from that of HaHex74 (pH 6.5 and 45 °C). Moreover, mHaHex74 showed the highest LNT2 conversion ratio of 28.2% from N,N’-diacetyl chitobiose (GlcNAc2), which is 2.2 folds higher than that of HaHex74. A three-enzyme cascade reaction for the synthesis of LNT2 and LNnT from chitin was performed in a 5–L reactor, and the contents of LNT2 and LNnT reached up to 15.0 g Lsingle bond1 and 4.9 g Lsingle bond1, respectively. Therefore, mHaHex74 maybe a good candidate for enzymatic synthesis of HMOs

Recovery trajectories and community resilience of biofilms in receiving rivers after wastewater treatment plant upgrade.

Wastewater treatment plant (WWTP) upgrades can reduce both nutrient and micropollutant emissions into receiving rivers, thus modifying the composition and function of biological communities. However, how microbial communities vary and whether they can be restored to levels found in less-polluted rivers remains uncertain. Aquatic biofilms are sensitive to environmental change and respond rapidly to bottom-up pressure. Thus, we used 12 flumes configured in three experimental treatments to mimic the dynamic processes of biofilm microbial communities occurring in a wastewater-receiving river following WWTP upgrade, with rivers containing two levels of nutrients and micropollutants used as references. We compared the biofilm microbial biomass, carbon source utilization, and community composition among the three "blocks". Results showed that the metabolic patterns of the carbon sources and composition of the biofilm bacterial communities in the flumes mimicking a receiving river with WWTP upgrade recovered over time to those mimicking a less-disturbed river. The restoration of potential carboxylic acid-consuming denitrifying bacteria (i.e., Zoogloea, Comamonas, Dechloromonas, and Acinetobacter) likely played a significant role in this process. Combining quantitative analysis of the denitrification genes nirS and nosZ, we confirmed that the denitrification function of the river biofilms recovered after WWTP upgrade, consistent with our previous field investigation

Novel Latex Microsphere Immunochromatographic Assay for Rapid Detection of Cadmium Ion in Asparagus

Recently, concerns about heavy metal cadmium ion (Cd2+) residue in asparagus have been frequently reported, and there is an urgent need to develop an effective, sensitive, and rapid detection method for Cd2+. In this study, we innovatively combined molecular microbiology to carry out the comparative screening of Cd2+ chelators in a green, efficient, and specific way. The knock-out putative copper-transporter gene (pca1Δ) yeast strain with high sensitivity to Cd2+ was first used to screen the Cd2+ chelator, and the optimum chelator 1-(4-Isothiocyanatobenzyl)ethylenediamine-N,N,N,N′-tetraacetic acid (ITCBE) was obtained. Additionally, a rapid latex microsphere immunochromatographic assay (LMIA) was developed, based on the obtained monoclonal antibody (mAb) with high specificity and high affinity (affinity constant Ka = 1.83 × 1010 L/mol), to detect Cd2+ in asparagus. The 50% inhibitive concentration (IC50) of test strip was measured to be 0.2 ng/mL, and the limit of detection (IC10) for qualitative (LOD, for visual observation) and quantitative detection (LOQ, for data simulation) of the test strip was 2 ng/mL and 0.054 ng/mL, respectively. In all, the developed mAb-based LMIA shows a great potential for monitoring Cd2+ in asparagus, even in vegetable samples

Investigations on the interactions between plasma proteins and magnetic iron oxide nanoparticles with different surface modifications

Three types of magnetic iron oxide nanoparticles with various kinds of surface modifications were synthesized, and the interactions between the nanoparticles and two types of high abundant plasma proteins were investigated by isothermal titration calorimetry and dynamic light scattering (DLS) methods. It was found that these interactions were strongly dependent on the surface properties of the nanoparticles. Enthalpy-entropy analysis suggested that poly(ethylene glycol) (PEG) modification on the particle surface could effectively reduce the interactions between the magnetic nanoparticles and the plasma proteins. DLS investigations further implied that electrostatic attractions could either increase or decrease the colloidal stability of the nanoparticles, depending on the particle surface properties, which will give rise to different in vivo biodistributions for the intravenously injected nanoparticles, according to literature reports. Proper surface modifications, upon the use of PEG in combination with various types of small molecules for reducing surface charges, were found to be effective for eliminating the strong interactions between nanoparticles and proteins, which is of the utmost importance for developing iron oxide magnetic nanoparticles with long blood circulation time for in vivo applications

Modified Ni-carbonate interfaces for enhanced CO₂ methanation activity: tuned reaction pathway and reconstructed surface carbonates

A Ni/Zr-La2O2CO3 catalyst with interfaces between Ni metal and Zr-modified carbonate support was used for atmospheric CO2 methanation reaction, exhibiting 81% conversion and 99.6% CH4 selectivity at 300 °C. The Zr4+ ions incorporated in La2O2CO3 lattices properly strengthened the Ni-carbonate interaction for enhancing the Ni dispersion and hydrogen activation ability of the catalyst. The Zr-modification could also tune the surface basic property for promoting the adsorptive dissociation of CO2. In-situ DRIFT spectra demonstrated that only the hydrogenation reaction pathway of formate intermediates was proceeded in Ni/La2O2CO3-catalyzed CO2 methanation. As a contrast, the hydrogenation pathways of CO and formate intermediates with relatively high activity were co-existed at the modified Ni-Zr-La2O2CO3 interfaces. Furthermore, the isotopic data evidenced that dynamic reconstruction and interconversion of the surface carbonate species occurred in the reaction, which might contribute to the key steps of CO2 dissociation and intermediates transformation.We thank National Natural Science Foundation of China (22178161) and National Key R&D Program of China (2018YFE0122600) for financial support