The Genomics of Isolated Populations of Gampsocleis glabra (Orthoptera: Tettigoniidae) in Central and Western Europe

Habitat destruction and fragmentation are among the major current threats to global biodiversity. Fragmentation may also affect species with good dispersal abilities. We study the heath bushcricket Gampsocleis glabra, a specialist of steppe-like habitats across Europe that are highly fragmented, investigating if these isolated populations can be distinguished using population genomics and if there are any traces of admixture or dispersal among them. We try to answer these questions using genome-wide SNP data generated with ddRAD sequencing. We calculated F-statistics and visualized differentiation using STRUCTURE plots. While limited by the difficulty of sampling this threatened species, our results show that all populations except one that was represented by a singleton were clearly distinct, with pairwise FST values between 0.010 and 0.181. STRUCTURE indicated limited but visible admixture across most populations and probably also an exchange of individuals between populations of Germany and The Netherlands. We conclude that in G. glabra, a certain amount of gene flow has persisted, at least in the past, also among populations that are isolated today. We also detect a possibly more recent dispersal event between a population in The Netherlands and one in Germany, which may be human aided. We suggest that the conservation of larger populations should be maintained, that efforts should be taken to restore abandoned habitat, that the preservation even of small habitat fragments may be beneficial for the conservation of this species, and that these habitats should be regularly monitored for possible (re-)colonization

Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse Large B-Cell Lymphoma

Background: As microRNA-142 (miR-142) is the only human microRNA gene where mutations have consistently been found in about 20% of all cases of diffuse large B-cell lymphoma (DLBCL), we wanted to determine the impact of miR-142 inactivation on protein expression of DLBCL cell lines. Methods: miR-142 was deleted by CRISPR/Cas9 knockout in cell lines from DLBCL. Results: By proteome analyses, miR-142 knockout resulted in a consistent up-regulation of 52 but also down-regulation of 41 proteins in GC-DLBCL lines BJAB and SUDHL4. Various mitochondrial ribosomal proteins were up-regulated in line with their pro-tumorigenic properties, while proteins necessary for MHC-I presentation were down-regulated in accordance with the finding that miR-142 knockout mice have a defective immune response. CFL2, CLIC4, STAU1, and TWF1 are known targets of miR-142, and we could additionally confirm AKT1S1, CCNB1, LIMA1, and TFRC as new targets of miR-142-3p or -5p. Conclusions: Seed-sequence mutants of miR-142 confirmed potential targets and novel targets of miRNAs can be identified in miRNA knockout cell lines. Due to the complex contribution of miRNAs within cellular regulatory networks, in particular when miRNAs highly present in RISC complexes are replaced by other miRNAs, primary effects on gene expression may be covered by secondary layers of regulation

The Genomics of Isolated Populations of Gampsocleis glabra (Orthoptera : Tettigoniidae) in Central and Western Europe

Habitat destruction and fragmentation are among the major current threats to global biodiversity. Fragmentation may also affect species with good dispersal abilities. We study the heath bushcricket Gampsocleis glabra, a specialist of steppe-like habitats across Europe that are highly fragmented, investigating if these isolated populations can be distinguished using population genomics and if there are any traces of admixture or dispersal among them. We try to answer these questions using genome-wide SNP data generated with ddRAD sequencing. We calculated F-statistics and visualized differentiation using STRUCTURE plots. While limited by the difficulty of sampling this threatened species, our results show that all populations except one that was represented by a singleton were clearly distinct, with pairwise FST values between 0.010 and 0.181. STRUCTURE indicated limited but visible admixture across most populations and probably also an exchange of individuals between populations of Germany and The Netherlands. We conclude that in G. glabra, a certain amount of gene flow has persisted, at least in the past, also among populations that are isolated today. We also detect a possibly more recent dispersal event between a population in The Netherlands and one in Germany, which may be human aided. We suggest that the conservation of larger populations should be maintained, that efforts should be taken to restore abandoned habitat, that the preservation even of small habitat fragments may be beneficial for the conservation of this species, and that these habitats should be regularly monitored for possible (re-)colonization

The Genomics of Isolated Populations of Gampsocleis glabra (Orthoptera : Tettigoniidae) in Central and Western Europe

Habitat destruction and fragmentation are among the major current threats to global biodiversity. Fragmentation may also affect species with good dispersal abilities. We study the heath bushcricket Gampsocleis glabra, a specialist of steppe-like habitats across Europe that are highly fragmented, investigating if these isolated populations can be distinguished using population genomics and if there are any traces of admixture or dispersal among them. We try to answer these questions using genome-wide SNP data generated with ddRAD sequencing. We calculated F-statistics and visualized differentiation using STRUCTURE plots. While limited by the difficulty of sampling this threatened species, our results show that all populations except one that was represented by a singleton were clearly distinct, with pairwise FST values between 0.010 and 0.181. STRUCTURE indicated limited but visible admixture across most populations and probably also an exchange of individuals between populations of Germany and The Netherlands. We conclude that in G. glabra, a certain amount of gene flow has persisted, at least in the past, also among populations that are isolated today. We also detect a possibly more recent dispersal event between a population in The Netherlands and one in Germany, which may be human aided. We suggest that the conservation of larger populations should be maintained, that efforts should be taken to restore abandoned habitat, that the preservation even of small habitat fragments may be beneficial for the conservation of this species, and that these habitats should be regularly monitored for possible (re-)colonization

Long time persistence and evolution of carbapenemase-producing Enterobacterales in the wastewater of a tertiary care hospital in Germany

Background: Worldwide observations revealed increased frequencies of multi-resistant Enterobacterales and resistance genes in hospital wastewater compared to any other type of wastewater. Despite the description of clonal lineages possibly adapted to hospital wastewater, little is known about long term persistence as well as evolution of these lineages. Methods: In this study, wastewater isolates of different Enterobacterales species from a tertiary care hospital were investigated with 2.5 years distance. Whole Genome Sequencing (WGS) and resistance gene identification were performed for E. coli, C. freundii, S. marcescens, K. pneumoniae, K. oxytoca, and E. cloacae isolates (n = 59), isolated in 2022 and compared with strains isolated from the same wastewater pipeline in 2019 (n = 240). Results: Individual clonal lineages with highly related isolates could be identified in all species identified more than once in 2022 that appear to persist in the wastewater drainage. A common motif of all persistent clonal lineages was the carriage of mobile genetic elements encoding carbapenemase genes with hints for horizontal gene transfer in persistent clones in this environment observed over the 2.5-year period. Multiple plasmid replicons could be detected in both years. In 2022 isolates blaVIM-1 replaced blaOXA-48 as the most common carbapenemase gene compared to 2019. Interestingly, despite a similar abundance of carbapenemase genes (>80% of all isolates) at both time points genes encoding extended spectrum β-lactamases decreased over time. Conclusions: This data indicates that hospital wastewater continuously releases genes encoding carbapenemases to the urban wastewater system. The evolution of the resident clones as well as the reasons for the selection advantage in this specific ecological niche needs to be further investigated in the future

Host KIR/HLA-C Genotypes Determine HIV-Mediated Changes of the NK Cell Repertoire and Are Associated With Vpu Sequence Variations Impacting Downmodulation of HLA-C

NK cells play a pivotal role in viral immunity, utilizing a large array of activating and inhibitory receptors to identify and eliminate virus-infected cells. Killer-cell immunoglobulin-like receptors (KIRs) represent a highly polymorphic receptor family, regulating NK cell activity and determining the ability to recognize target cells. Human leukocyte antigen (HLA) class I molecules serve as the primary ligand for KIRs. Herein, HLA-C stands out as being the dominant ligand for the majority of KIRs. Accumulating evidence indicated that interactions between HLA-C and its inhibitory KIR2DL receptors (KIR2DL1/L2/L3) can drive HIV-1-mediated immune evasion and thus may contribute to the intrinsic control of HIV-1 infection. Of particular interest in this context is the recent observation that HIV-1 is able to adapt to host HLA-C genotypes through Vpu-mediated downmodulation of HLA-C. However, our understanding of the complex interplay between KIR/HLA immunogenetics, NK cell-mediated immune pressure and HIV-1 immune escape is still limited. Therefore, we investigated the impact of specific KIR/HLA-C combinations on the NK cell receptor repertoire and HIV-1 Vpu protein sequence variations of 122 viremic, untreated HIV-1(+) individuals. Compared to 60 HIV-1(-) controls, HIV-1 infection was associated with significant changes within the NK cell receptor repertoire, including reduced percentages of NK cells expressing NKG2A, CD8, and KIR2DS4. In contrast, the NKG2C(+) and KIR3DL2(+) NK cell sub-populations from HIV-1(+) individuals was enlarged compared to HIV-1(-) controls. Stratification along KIR/HLA-C genotypes revealed a genotype-dependent expansion of KIR2DL1(+) NK cells that was ultimately associated with increased binding affinities between KIR2DL1 and HLA-C allotypes. Lastly, our data hinted to a preferential selection of Vpu sequence variants that were associated with HLA-C downmodulation in individuals with high KIR2DL/HLA-C binding affinities. Altogether, our study provides evidence that HIV-1-associated changes in the KIR repertoire of NK cells are to some extent predetermined by host KIR2DL/HLA-C genotypes. Furthermore, analysis of Vpu sequence polymorphisms indicates that differential KIR2DL/HLA-C binding affinities may serve as an additional mechanism how host genetics impact immune evasion by HIV-1