We study ciliates and their symbiotic events with bacteria. We have different research lines, including taxonomic characterization of holobionts using the NGTax workflow. We have expertise in morphological, ultrastructural, molecular, and  genomics  applied to ciliates (common and rare species).

Our main research interest is the study of associations between living beings from different species in the broadest sense, especially from an evolutionary perspective. These are mostly focused on the study of bacteria interacting with eukaryotes, including mutualists, parasites, and pathogens. In particular, the Unit Coordinator for the present project has a strong experience in ciliates and their associated bacteria, in particular those belonging to the order Rickettsiales. 
In terms of study approaches, a major expertise of the research unit is on bioinformatics and genome/transcriptome analyses, including assembly, metabolic prediction, and comparative analyses. Moreover, “wet lab” research activities are carried out as well, including in particular molecular biology, light and transmission electron microscopy. 

Cuoiodepur is a jointstock company by large majority private. Cuoiodepur operates near Pisa (Italy) in one of the largest tannery wastewater treatment plants in Europe. At present, the plant employs about 33 people and hosts a public-private research and development laboratory (CER2CO “Centro Ricerca Reflui Conciari”). 

GENEWIZ, a Brooks Life Sciences Company, provides a suite of genomic services including Sanger and NGS, Gene and Oligo Synthesis as well as GLP / CLIA regulatory services. With European Headquarters in Germany and a global network of laboratories across Europe, USA and Asia, GENEWIZ is easily accessible around the world. Our unique, proprietary sequencing solutions and automation technologies puts us at the forefront of the life science technology curve making us the preferred partner for academia, pharma, biotechnology, agriculture and clinical institutions.

Aquatic Sciences, Fisheries and Aquaculture Stream is within the Department of Zoological Sciences, Addis Ababa University. Within the stream, we conduct  research and teaching in aquatic sciences, aquatic biodiversity and conservation, limnology, wetlands, fisheries, and aquaculture.

Our work focuses on the biodiversity and taxonomy of ciliated protists. We are conversant with the classic morphospecies concept but also interested in the application of molecular methods in the taxonomy of ciliates and their symbionts especially in tropical aquatic ecosystems including lakes, wetlands and coastal marine ecosystems.

We focus on the fundamental research of ciliates, including species diversity and taxonomy, morphogenesis during reproduction, phylogenetics and systematics, epigenetic regulatory mechanisms of gene expression and DNA replication, gene functions and molecular mechanisms in important physiological processes using model organisms such as Tetrahymena, Paramecium, Euplotes.

Our research group focuses on the ecology, diversity and taxonomy of ciliates mainly in lakes. We have a strong background on unicellular eukaryotic organisms, especially ciliates, in limnology and the microbial food web. In detail, our best skills are in microscopic techniques (light and epifluorescence techniques), cultivation (batch and continuous cultures), experimental design (lab and in situ), image analysis, HPLC, complete field trip logistics etc. To understand the autecology of ciliates in planktonic food webs, we study these protists on an alpha-taxonomic level including morphological and molecular state-of-the-art methods (from single-cell sequencing to high-throughput sequencing). Moreover, we are interested in symbiotic and other mutualistic relationships, especially on the green algal diversity found in freshwater ciliates. Recently, we investigated co-occurrence networks in the aquatic microbial food web and observed the key role of specific ciliate species. Finally, we consequently transfer knowledge on basic research to pupils, laymen and the interested public. 

Symbiotic ciliates (commensals, mutualists and/or parasites) are very common in the aquatic environment, where these are associated with a wide range of organisms, from sponges to vertebrates. Our laboratory concentrates specifically on the taxonomy of peritrichs, particularly those from natural populations of freshwater (copepods, amphibians and fish) and marine (fish and a variety of invertebrates) hosts, incorporating ultrastructure and molecular techniques.

We are primarily interested in genomics and molecular biology of ciliates. Our lab is currently investigating chromatin-related proteins in the model ciliate Paramecium using: functional genomics coupled to gene knockdowns by RNAi; localization of fluorescent fusion-proteins expressed from DNA constructs microinjected into macronuclei; pull-down assays (and ChIP-seq); PCR analyses of IES retention, etc. We’ve also been sequencing, assembling, annotating and analysing the genomes (macronuclear and micronuclear) of non-model freshwater ciliate species (heterotrichs and karyorelicts), all of which uses bioinformatics extensively. We’ve also performed RNA-seq, sRNA-seq for developmental time courses, and tRNA-seq to investigate tRNAs. We’ve done a little prototyping of ribosome profiling in Paramecium, and plan to do some of this for the non-model ciliates later this year. Our lab is also busy with in vitro assays of ciliate proteins expressed in and purified from E. coli. We are also involved in producing new software tackling ciliate-specific issues (e.g. relating to gene prediction and IES identification, some of which is publicly available: https://github.com/Swart-lab).

The New Lineages of Life Group (PI Dr Schulz) at the Joint Genome Institute (JGI) focuses on the discovery of novel bacterial, archaeal and eukaryotic microbes and viruses in environmental sequence data. We use multi-omics (metagenomics, metatranscriptomics, single cell genomics and phylogenomics) and machine learning to identify new divergent lineages and expand the Tree of Life. We then investigate the coding potential to find novel functions that may impact microbiome structure and biogeochemical cycles. Currently funded projects in the group aim to 1) develop unbiased (without primers) strain-resolved sequencing of RNA viruses from complex environmental samples and 2) establish a single-cell-based discovery pipeline for terrestrial protists.

Our company has equipment for field research and sampling, including soil corers. Through long-term collaborations the company has access to field sites relating to both constructed water treatment facilities and natural wetland areas with available background field research. The company staff designed water treatment wetlands include long-term monitoring data (e.g. continuously monitored water quality data from the past ten years), which can be used to assess the impact of site characteristics to the sampled and identified ciliates.
The company collaborates with other companies, municipalities, water protection associations, universities, and research institutions in Finland, through which the company has access to laboratory facilities as well as to supporting applied and scientific knowledge. Guesthouse and laboratory available at Kilpisjärvi Biological Station. 

Our research focuses on basic understanding of genetic and epigenetic mechanisms involving ribonucleic acid (RNA) as key regulator in terms of gene-expression, development, epigenetic inheritance and evolution. 
In our work we aim to understand the various mechanisms in which small RNAs mediate epigentic information. Using molecular genetic methods in combination with NGS, we analyze sRNA, long RNA and chromatin modification on the genome wide level integrating data to understand cellular and systemic genome regulation and virus defense.