RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements

Improving the framework for assessment of ecological change in the Arctic: A circumpolar synthesis of freshwater biodiversity

1. Climate warming and subsequent landscape transformations result in rapid ecological change in Arctic freshwaters. Here we provide a synthesis of the diversity of benthic diatoms, plankton, macrophytes, macroinvertebrates, and fish in Arctic freshwaters.2. We developed a multi-organism measure of alpha diversity to characterise circumpolar spatial patterns and their environmental correlates, and we assessed ecoregion-level beta diversity for all organism groups across the Arctic.3. Alpha diversity was lowest at high latitudes and elevations and where dispersal barriers exist. Diversity was positively related to temperature, and both temperature and connectivity limited diversity on high latitude islands. Beta diversity was highly variable among ecoregions for most organism groups, ranging from 0 (complete similarity) to 1 (complete dissimilarity). The high degree of dissimilarity within many ecoregions illustrates the uniqueness of many Arctic freshwater communities.4. Northward range expansion of freshwater taxa into Arctic regions may lead to increased competition for cold-stenothermic and cold-adapted species, and ultimately lead to the extinction of unique Arctic species. Societal responses to predicted impacts include: (1) actions to improve detection of changes (e.g., harmonised monitoring, remote sensing) and engagement with Arctic residents and Indigenous Peoples; and (2) actions to reduce the impact of unwanted changes (e.g., reductions of CO2 emissions, action against the spread of invasive species).5. Current Arctic freshwater monitoring shows large gaps in spatial coverage, while time series data are scarce. Arctic countries should develop an intensified, long-term monitoring programme with routine reporting. Such an approach will allow detection of long-term changes in water quality, biodiversity, and ecosystem services of Arctic freshwaters

First circumpolar assessment of Arctic freshwater phytoplankton and zooplankton diversity : Spatial patterns and environmental factors

Arctic freshwaters are facing multiple environmental pressures, including rapid climate change and increasing land-use activities. Freshwater plankton assemblages are expected to reflect the effects of these stressors through shifts in species distributions and changes to biodiversity. These changes may occur rapidly due to the short generation times and high dispersal capabilities of both phyto- and zooplankton. Spatial patterns and contemporary trends in plankton diversity throughout the circumpolar region were assessed using data from more than 300 lakes in the U.S.A. (Alaska), Canada, Greenland, Iceland, the Faroe Islands, Norway, Sweden, Finland, and Russia. The main objectives of this study were: (1) to assess spatial patterns of plankton diversity focusing on pelagic communities; (2) to assess dominant component of beta diversity (turnover or nestedness); (3) to identify which environmental factors best explain diversity; and (4) to provide recommendations for future monitoring and assessment of freshwater plankton communities across the Arctic region. Phytoplankton and crustacean zooplankton diversity varied substantially across the Arctic and was positively related to summer air temperature. However, for zooplankton, the positive correlation between summer temperature and species numbers decreased with increasing latitude. Taxonomic richness was lower in the high Arctic compared to the sub- and low Arctic for zooplankton but this pattern was less clear for phytoplankton. Fennoscandia and inland regions of Russia represented hotspots for, respectively, phytoplankton and zooplankton diversity, whereas isolated regions had lower taxonomic richness. Ecoregions with high alpha diversity generally also had high beta diversity, and turnover was the most important component of beta diversity in all ecoregions. For both phytoplankton and zooplankton, climatic variables were the most important environmental factors influencing diversity patterns, consistent with previous studies that examined shorter temperature gradients. However, barriers to dispersal may have also played a role in limiting diversity on islands. A better understanding of how diversity patterns are determined by colonisation history, environmental variables, and biotic interactions requires more monitoring data with locations dispersed evenly across the circumpolar Arctic. Furthermore, the importance of turnover in regional diversity patterns indicates that more extensive sampling is required to fully characterise the species pool of Arctic lakes.Peer reviewe

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes ∼11 500 candidate binding sites for ∼400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genome-wide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes

Figure 3 in Fauna of microcrustaceans (Cladocera: Copepoda) of shallow freshwater ecosystems of Wrangel Island (Russian Far East)

Figure 3. Simplified map of the compared regions.Published as part of Novichkova, Anna A. & Chertoprud, Elena S., 2015, Fauna of microcrustaceans (Cladocera: Copepoda) of shallow freshwater ecosystems of Wrangel Island (Russian Far East), pp. 2955-2968 in Journal of Natural History 49 (45) on page 2961, DOI: 10.1080/00222933.2015.1056269, http://zenodo.org/record/400237

Figure 4 in Fauna of microcrustaceans (Cladocera: Copepoda) of shallow freshwater ecosystems of Wrangel Island (Russian Far East)

Figure 4. Dendrogram for hierarchical clustering (group average) of faunas of different arctic regions.Published as part of Novichkova, Anna A. & Chertoprud, Elena S., 2015, Fauna of microcrustaceans (Cladocera: Copepoda) of shallow freshwater ecosystems of Wrangel Island (Russian Far East), pp. 2955-2968 in Journal of Natural History 49 (45) on page 2962, DOI: 10.1080/00222933.2015.1056269, http://zenodo.org/record/400237

Crustaceans in the Meiobenthos and Plankton of the Thermokarst Lakes and Polygonal Ponds in the Lena River Delta (Northern Yakutia, Russia): Species Composition and Factors Regulating Assemblage Structures

Information about invertebrates in the low-flow water bodies of northeastern Siberia is far from complete. In particular, little is known about crustaceans—one of the main components of meiobenthic and zooplanktonic communities. An open question is which environmental factors significantly affect the crustaceans in different taxonomic and ecological groups? Based on the data collected on the zooplankton and meiobenthos in the tundra ponds in the southern part of the Lena River Delta, analysis of the crustacean taxocene structure was performed. In total, 59 crustacean species and taxa were found. Five of these are new for the region. The species richness was higher in the large thermokarst lakes than in the small water bodies, and the abundance was higher in small polygonal ponds than in the other water bodies. Variations in the Cladocera assemblages were mainly affected by the annual differences in the water temperature; non-harpacticoid copepods were generally determined by hydrochemical factors; and for Harpacticoida, the macrophyte composition was significant. Three types of the crustacean assemblages characteristic of different stages of tundra lake development were distinguished. The hypothesis that the formation of crustacean taxocenes in the Lena River Delta is mainly determined by two types of ecological filters, temperature and local features of the water body, was confirmed

A new species of honeycombed Chydorus Leach, 1816 (Cladocera: Anomopoda Chydoridae) from tundra of North-East Russia

Sinev, Artem Y., Novichkova, Anna A., Chertoprud, Elena S. (2022): A new species of honeycombed Chydorus Leach, 1816 (Cladocera: Anomopoda Chydoridae) from tundra of North-East Russia. Zootaxa 5154 (2): 198-210, DOI: https://doi.org/10.11646/zootaxa.5154.2.

Compositionı characteristics and long-term variability of the freshwater microcrustacean fauna of the Faroe Islands

Chertoprud, Anna A. Novichkova ı Elena S., Azovsky, Andrey I. (2019): Compositionı characteristics and long-term variability of the freshwater microcrustacean fauna of the Faroe Islands. Journal of Natural History 53 (39): 2449-2465, DOI: 10.1080/00222933.2019.170458