Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages

Abstract Background Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. Results We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100–10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Conclusions Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.http://deepblue.lib.umich.edu/bitstream/2027.42/111733/1/12864_2015_Article_1570.pd

Biodiversity of cryopegs in permafrost

Abstract This study describes the biodiversity of the indigenous microbial community in the sodium-chloride water brines (cryopegs) derived from ancient marine sediments and sandwiched within permafrost 100-120,000 years ago after the Arctic Ocean regression. Cryopegs remain liquid at the in situ temperature of À9 to À11°C and make up the only habitat on the Earth that is characterized by permanently subzero temperatures, high salinity, and the absence of external influence during geological time. From these cryopegs, anaerobic and aerobic, spore-less and spore-forming, halotolerant and halophilic, psychrophilic and psychrotrophic bacteria, mycelial fungi and yeast were isolated and their activity was detected below 0°C

Fungi in Microbial Culture Collections and Their Metabolites

This study presents the results of a comparative analysis of the fungal diversity in the world system of microbial culture collections on one side with a variety of known fungal producers on the other side. The main VKM databases used are FungalDC and Metabolites of Fungi and the central point of analysis is the fungal ability to synthesize promising metabolites for applied use. It indicates that the option of obtaining new promising strains from the collection funds is still underestimated by the scientific community. In particular, it is shown that no more than 3% of the total fungal species fund contained in culture collections are used practically. It is possible that their use will considerably expand the range of studied strains and lead to the acquisition of new scientifically significant data

Life Science—Microbial Culture Collections Data Integration Tasks

This paper presents interconnections between catalogs of microbial culture collections and biological databases inspected. Microbial Biological Resources Centers (mBRCs) provide Life Science (LS) and biotechnology with fit-for-use microbiological resources and related data of consistent quality. To optimize the services, facilitate cumulative research, make crosschecks, and avoid duplication of efforts, must ensure that the databases developed and maintained are interconnected with mBRC data. This research shows that, at present, connections are minimal. It proposes ways to plug the mBRC databases into the Life Science community. Such connections could open dialogue by making the mBRC data visible and accessible from the Life Science databases, and reciprocally making the Life Science database records visible and accessible from the mBRC-aggregated catalog. For this purpose, we inspected most of the databases discovered on the Internet. Each database was characterized by name, acronym, year of the last correction, uniform resource location (URL), area of practical use (health system, agriculture, etc.), presence of microbial data and database producer. The databases with microbial data were inspected in more detail in terms of the lists of the partner databases, the lists of ontologies used, the access format from computer programs, and database subjects. Our new metabase has collected 2667 Life Science databases, from which 1123 databases have microbial data

The Use of Mycelial Fungi to Test the Fungal Resistance of Polymeric Materials

There are two main themes in the research on the biodegradation of industrial materials by mycelial fungi. The challenge of reducing environmental pollution necessitates the creation of biodegradable polymers that allow microorganisms, including mycelial fungi, to degrade them to low-molecule soluble substances. Additionally, to minimize the biodegradation of industrial materials while they are operating in the environment, there is a need to produce fungi-resistant polymer compositions. The fungal resistance of industrial materials and products can be assessed using a specific set of mycelial fungi cultures. Test cultures selected for this purpose are supported in the All-Russian Collection of Microorganisms (VKM). This review addresses the principle of culture selection to assess the fungal resistance of industrial materials and evaluates the results of the tests using these cultures

The Use of Mycelial Fungi to Test the Fungal Resistance of Polymeric Materials

There are two main themes in the research on the biodegradation of industrial materials by mycelial fungi. The challenge of reducing environmental pollution necessitates the creation of biodegradable polymers that allow microorganisms, including mycelial fungi, to degrade them to low-molecule soluble substances. Additionally, to minimize the biodegradation of industrial materials while they are operating in the environment, there is a need to produce fungi-resistant polymer compositions. The fungal resistance of industrial materials and products can be assessed using a specific set of mycelial fungi cultures. Test cultures selected for this purpose are supported in the All-Russian Collection of Microorganisms (VKM). This review addresses the principle of culture selection to assess the fungal resistance of industrial materials and evaluates the results of the tests using these cultures

Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells

Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.peerReviewe