Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.

Variability of the structure of winter microbial communities in Chelyabinsk lakes

Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.

Metabolic Profiling of Rhizobacteria Serratia plymuthica and Bacillus subtilis Revealed Intra- and Interspecific Differences and Elicitation of Plipastatins and Short Peptides Due to Co-cultivation

Rhizobacteria live in diverse and dynamic communities having a high impact on plant growth and development. Due to the complexity of the microbial communities and the difficult accessibility of the rhizosphere, investigations of interactive processes within this bacterial network are challenging. In order to better understand causal relationships between individual members of the microbial community of plants, we started to investigate the inter- and intraspecific interaction potential of three rhizobacteria, the S. plymuthica isolates 4Rx13 and AS9 and B. subtilis B2g, using high resolution mass spectrometry based metabolic profiling of structured, low-diversity model communities. We found that by metabolic profiling we are able to detect metabolite changes during cultivation of all three isolates. The metabolic profile of S. plymuthica 4Rx13 differs interspecifically to B. subtilis B2g and surprisingly intraspecifically to S. plymuthica AS9. Thereby, the release of different secondary metabolites represents one contributing factor of inter- and intraspecific variations in metabolite profiles. Interspecific co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g showed consistently distinct metabolic profiles compared to mono-cultivated species. Thereby, putative known and new variants of the plipastatin family are increased in the co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g. Interestingly, intraspecific co-cultivation of S. plymuthica 4Rx13 and S. plymuthica AS9 revealed a distinct interaction zone and showed distinct metabolic profiles compared to mono-cultures. Thereby, several putative short proline-containing peptides are increased in co-cultivation of S. plymuthica 4Rx13 with S. plymuthica AS9 compared to mono-cultivated strains. Our results demonstrate that the release of metabolites by rhizobacteria alters due to growth and induced by social interactions between single members of the microbial community. These results form a basis to elucidate the functional role of such interaction-triggered compounds in establishment and maintenance of microbial communities and can be applied under natural and more realistic conditions, since rhizobacteria also interact with the plant itself and many other members of plant and soil microbiota.

Salivary protein glycopatterns for natural regulation of oral microbiota

Background：Little is known about the relationship between salivary protein glycopatterns and oral microbial communities in the patients of gastric cancer (GC) and type 2 diabetes mellitus (T2DM).Methods：In this study, the oral microbiome of healthy volunteers (HVs) and GC patients were detected using 16S rDNA sequencing. The Fucose-neoglycoproteins were synthesized and used to explore the effects of Fucose moiety against Aggregatibacter segnis (A. segnis). The sialoglycoproteins were isolated and used to assess the role of the Siaα2-3/6Gal-linked glycans against Candida albicans (C. albicans).Findings：The results showed that five species (e.g. A. segnis, Megasphaera micronuciformis) were significantly increased (p<0.05) while two species (Streptococcus salivarius and Oral taxon 870) were significantly decreased (p<0.01) in the saliva of GC patients compared to HVs. The adhesion of A. segnis could be inhibited by 30 μg/mL of fucose-neoglycoproteins. The growth and adhesion of C. albicans could be inhibited gradually by 50-400 μg/mL sialoglycoproteins. And Siaα2-3Gal moieties played a major role against the growth and adhesion of C. albicans.Interpretation：These findings provide a novel theory that dynamic communities of oral microbiota are regulated naturally by host salivary protein glycopatterns, having important implications for developing new carbohydrate drugs for oral and body health. Funding：This study was supported by the National Natural Science Foundation of China (Grant No. 81871955), the China Postdoctoral Science Foundation (Grant No. 2020M673628XB), and the Natural Science Foundation of Shaanxi Province (Grant No. 2021JQ-446).

Salivary protein glycopatterns for natural regulation of oral microbiota

The oral microbiota is the direct precursor of dental caries and periodontitis, which are the most common microbial-induced diseases worldwide. The distinct microenvironment at the oral barrier breeds unique microbial communities, which are regulated by host factors (inflammation or dietary sugars)1. Increasing evidence indicates that dysbiosis of oral microbial communities is associated with many human diseases2-5. Our studies demonstrated that human disease could induce different alterations in salivary protein glycopatterns6. However, the relationship between salivary protein glycopatterns and oral microbial communities is unknown. Here, we report that altered salivary protein glycopatterns, namely, fucosylated or sialylated structures induced by gastric cancer (GC) or type 2 diabetes mellitus (T2DM), respectively, are also drivers of dysbiosis of oral microbial communities and ultimately dental caries and periodontitis. The fucosylated neoglycoproteins and sialic acid (SA) α2-3 galactose (Gal) structure can inhibit the growth or/and adhesion of Aggregatibacter segnis and Candida albicans from the oral cavity of patients with GC and T2DM, respectively. These findings provide a novel theory that dynamic communities of oral microbiota are regulated naturally by host salivary protein glycopatterns, having important implications for developing new carbohydrate drugs for oral and body health.

Modeling the trophic impacts of invasive zooplankton in a highly invaded river

The lower Columbia River (Washington and Oregon, USA) has been heavily invaded by a large number of planktonic organisms including the invasive copepod Pseudodiaptomus forbesi and the planktonic juveniles of the invasive clam, Corbicula fluminea. In order to assess the ecological impacts of these highly abundant invaders, we developed a multivariate auto-regressive (MAR) model of food web dynamics based upon a 12-year time-series of plankton community and environmental data from the Columbia River. Our model results indicate that plankton communities in the lower Columbia River are strongly impacted by the copepod P. forbesi at multiple trophic levels. We observed different ecological effects across different life stages of P. forbesi, with nauplii negatively impacting ciliates and autotrophs, and copepodite stages negatively impacting Daphnia and cyclopoid copepods. Although juvenile C. fluminea were highly abundant in the summer and autumn of each year, our best fit MAR model did not show significant C. fluminea impacts. Our results illustrate the strong ecological impact that some zooplankton invaders may cause within rivers and estuarine systems, and highlight the need for further research on the feeding ecology of the planktonic life-stage of C. fluminea. Overall, our study demonstrates the manner in which long-term, high resolution data sets can be used to better understand the ecological impacts of invasive species among complex and highly dynamic communities.

Research on peasants poverty alleviation under ecological constraint based on neural network algorithm and network features

Aiming at the actual problems encountered in the specific poverty alleviation work, this article designs a management system specifically designed for poverty alleviation workers to solve poverty alleviation data sharing and online editing and uploading of poverty alleviation logs. Based on the neural network and network characteristics, a system model is constructed, and the application of structural disturbance theory in dynamic networks is studied. Moreover, in this study, the dynamic change information between time-series networks is taken into account for structural disturbances. By combining structural disturbances and local topology, a new similarity measurement method suitable for dynamic networks is proposed. In addition, this study proposes an algorithm based on evolutionary clustering and density clustering to detect the structure of dynamic communities. Finally, this study compares the proposed method with the classic method in the artificial network and the real network and analyzes the performance of the research model through data analysis. The research results show that the model constructed in this paper has good performance.

LinkZoo

This article presents LinkZoo, a web-based, linked data enabled tool that supports collaborative management of information resources. LinkZoo addresses the modern needs of information-intensive collaboration environments to publish, manage, and share heterogeneous resources within user-driven contexts. Users create and manage diverse types of resources into common spaces such as files, web documents, people, datasets, and calendar events. They can interlink them, annotate them, and share them with other users, thus enabling collaborative editing, as well as enrich them with links to externally linked data resources. Resources are inherently modeled and published as resource description framework (RDF) and can be explicitly interlinked and dereferenced by external applications. LinkZoo supports creation of dynamic communities that enable web-based collaboration through resource sharing and annotating, exposing objects on the linked data Cloud under controlled vocabularies and permissions. The authors demonstrate the applicability of the tool on a popular collaboration use case scenario for sharing and organizing research resources.