Do pheromone traps help to reduce new attacks of Ips typographus at the local scale after a sanitary cut?

The spruce bark beetle, Ips typographus, is causing severe economic losses during epidemic phases triggered by droughts and/or windstorms. Sanitation felling and salvage logging are usually the most recommended strategies to limit the damages. However, any additional control method to limit the economic impact of an outbreak would be welcome. In this respect, the efficiency of pheromone trapping is still controversial or poorly documented. In this 2-year study (2020-2021), at the peak of a severe outbreak in Belgium, we quantified the wood volume and presence/absence of new attacks at 126 sites attacked during the previous year and within 100 m from the initial attack. Each site was randomly allocated to one of three treatments: (1) three crosstraps baited with pheromones, (2) one tree-trap baited with pheromones and treated with an insecticide and (3) control sites with no trapping device. The attacked trees of the previous year were all cut and removed before the start of the experiment and newly attacked trees were removed as they were detected. The trapping devices were only active during spring to target overwintering bark beetles that might have escaped the sanitation cuts and to limit the risk of attracting dispersing beetles from outside the patch during the summer. We found a strong decrease of the attacks relative to the previous year in all treatments, including the controls (more than 50% of the control sites had no new attacks). There was no relationship between the new attacks and the attacks of the previous year. In both years, new attacks were more frequent (presence/absence) in sites with crosstraps (95% Confidence Interval [56-84%] of the sites with new attacks) than in sites with a tree-trap (26-57% - p = 0.02) and to a lesser extent than in control sites (32-63%, p = 0.08). In 2020, the attacked volumes were slightly higher in sites with crosstraps (95% Confidence Interval [3.4-14.2 m³]) than in control sites (0.2-3.5 m³, p = 0.04) and no significant difference was found with tree-trap sites (1.1-6.2 m³, p = 0.38). In 2021, there were no significant differences between the volumes attacked in the control sites (1.8-9.4 m³), crosstraps sites (0.9-6.4 m³) and tree-trap sites (0-2.5 m³). Overall, we found no evidence in favor of the efficacy of pheromone trapping during spring to reduce economic damages at the local scale when combined with sanitation felling and during a severe outbreak. The use of baited crosstraps could even be hazardous as it seemed to increase the occurrence of new attacks probably by attracting bark beetles but failing to neutralize them.

Digitalization in Processes.

Digitalization is having an increasing impact on all industrial sectors, including the chemical and biotechnological industries. Aiming for innovative research and development, the Swiss Universities of Applied Sciences play a pivotal role in transferring academic knowledge and know-how to industrial practice. We review selected examples of projects related to the digitalization of processes and bioprocesses at four different institutions across Switzerland. These developments cover the whole spectrum of digital technologies, including big data, connectivity, analytics and automation. They are conducted in close collaboration with industrial partners and aim to support the growth of this important industrial sector.

Evolutionary history of inquiline social parasitism in Plagiolepis ants.

Social parasitism, i.e. the parasitic dependence of a social species on another free-living social species, is one of the most intriguing phenomena in social insects. It has evolved to various levels, the most extreme form being inquiline social parasites which have lost the worker caste, and produce only male and female sexual offspring that are reared by the host worker force. The inquiline syndrome has been reported in 4 species within the ant genus Plagiolepis, in Europe. Whether inquiline social parasitism evolved once or multiple times within the genus remains however unknown. To address this question, we generated data for 5 inquiline social parasites - 3 species previously described and 2 unidentified species - and their free-living hosts from Europe, and we inferred their phylogenetic relationships. We tested Emery's rule, which predicts that inquiline social parasites and their hosts are close relatives. Our results show that inquiline parasitism evolved independently at least 5 times in the genus. Furthermore, we found that all inquilines were associated with one of the descendants of their most related free-living species, suggesting sympatric speciation is the main process leading to the emergence of the parasitic species, consistent with the stricter version of Emery's rule.

Genome-wide analysis of single nucleotide variants allows for robust and accurate assessment of clonal derivation in cell lines used to produce biologics.

A clonally derived (or "monoclonal") cell line is a cell population derived from a single progenitor cell. Clonally derived cell lines are required for many biotechnological applications. For instance, recombinant mammalian cells used to produce therapeutic proteins are expected by regulatory authorities to be clonally derived. Assurance of clonal derivation (or "clonality") is usually obtained from the characterization of the procedure used for cell cloning, for instance by assessing the success rate of single-cell sorting but not by assessing the cell line itself. We have developed a method to assess clonal derivation directly from the genetic makeup of cells. The genomic test of clonality is based on whole-genome sequencing and statistical analysis of single nucleotide variants. This approach quantifies the clonal fractions present in nonclonal samples and it provides a measure of the probability that a cell line is derived from a single cell. Upon experimental validation of the test, we show that it is highly accurate and that it can robustly detect minor clonal fractions of as little as 1% of the cell population. Moreover, we find that it is applicable to various cell line development protocols. This approach can simplify development protocols and shorten timelines while ensuring clonal derivation with high confidence.

Repeated evolution of queen parthenogenesis and social hybridogenesis in Cataglyphis desert ants.

Over the last decade, genetic studies on social insects have revealed a remarkable diversity of unusual reproductive strategies, such as male clonality, female clonality, and social hybridogenesis. In this context, Cataglyphis desert ants are useful models because of their unique reproductive systems. In several species, queens conditionally use sexual reproduction and parthenogenesis to produce sterile workers and reproductive queens, respectively. In social hybridogenesis, two distinct genetic lineages coexist within a population, and workers result from mating between partners of different lineages; in contrast, queens and males are both produced asexually by parthenogenesis. Consequently, nonreproductive workers are all interlineage hybrids, whereas reproductives are all pure lineage individuals. Here, we characterized the reproductive systems of 11 species to investigate the distribution of the conditional use of sex and social hybridogenesis in Cataglyphis. We identified one new case in which sexual reproduction was conditionally used in the absence of dependent-lineage reproduction. We also discovered five new instances of social hybridogenesis. Based on our phylogenetic analyses, we inferred that both the conditional use of sex and social hybridogenesis independently evolved multiple times in the genus Cataglyphis.

Evolution of hybridogenetic lineages in Cataglyphis ants.

In most social Hymenoptera, a diploid egg develops into either a queen or a worker depending on environmental conditions. Hybridogenetic Cataglyphis ants display a bizarre genetic system, where queen-worker caste determination is primarily determined by genetic factors. In hybridogenetic populations, all workers are F1 hybrids of two distinct lineages, whereas new queens are nearly always pure-lineage individuals produced by clonal reproduction. The distribution and evolutionary history of these hybridogenetic populations have not yet been thoroughly analysed. Here, we studied the phylogeographic distribution of hybridogenetic populations in two closely related Spanish species: Cataglyphis humeya and Cataglyphis velox. Hybridogenesis has been previously documented in a locality of C. velox, but whether this system occurs elsewhere within the range of the two species was yet unknown. Queens and workers from 66 localities sampled across the range of the species were genotyped at 18 microsatellite markers to determine whether queens were produced by parthenogenesis and whether workers were hybrids of divergent lineages. Populations with F1 hybrid workers were identified by combining genetic, geographical and mating assortments data. In most populations of C. velox, workers were found to be hybrids of two divergent lineages. Workers were however produced via random mating in two marginal populations of C. velox, and in all populations studied of its sister species C. humeya. High-throughput sequencing data were obtained to confirm inferences based on microsatellites and to characterize relationships between populations. Our results revealed a complicated history of reticulate evolution that may account for the origin of hybridogenetic lineages in Cataglyphis.

Detecting topological variations of DNA at single-molecule level.

In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electrophoretic forces, translocate through a narrow orifice, transient residings of edited segments inside the orifice modulate the ionic flow. Here we utilize two programmable barcoding methods based on base-pairing, namely forming a gap in dsDNA and creating protrusion sites in ssDNA for generating a hybrid DNA complex. We integrate a discriminative noise analysis for ds and ss DNA topologies into the threshold detection, resulting in improved multi-level signal detection and consequent extraction of reliable information about topological variations. Moreover, the positional information of the barcode along the template sequence can be determined unambiguously. All methods may be further modified to detect nicks in DNA, and thereby detect DNA damage and repair sites.

Phenotypic plasticity in an ant with strong caste-genotype association.

Caste determination in social Hymenoptera (whether a female egg develops into a reproductive queen or a sterile worker) is a remarkable example of phenotypic plasticity where females with highly similar genomes exhibit striking differences in morphology and behaviour. This phenotypic dichotomy is typically influenced by environmental factors. However, recent studies have revealed a strong caste-genotype association in hybridogenetic ants: workers are all interlineage hybrids while queens are all purebred, suggesting that female caste fate is genetically determined. Using the hybridogenetic ant Cataglyphis mauritanica, we show that under laboratory conditions, purebred offspring develop into reproductive queens but occasionally give rise to workers. Moreover, while hybrids typically become workers, juvenile hormone treatment can switch their developmental pathway to the reproductive caste. These results indicate that phenotypic plasticity has been retained in an ant with a strong caste-genotype association, despite its lack of expression in natural conditions.

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

BACKGROUND: Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. RESULTS: We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. CONCLUSIONS: This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89.

Computational expression deconvolution aims to estimate the contribution of individual cell populations to expression profiles measured in samples of heterogeneous composition. Zhong et al. recently proposed Digital Sorting Algorithm (BMC Bioinformatics 2013 Mar 7;14:89) and showed that they could accurately estimate population-specific expression levels and expression differences between two populations. They compared DSA with Population-Specific Expression Analysis (PSEA), a previous deconvolution method that we developed to detect expression changes occurring within the same population between two conditions (e.g. disease versus non-disease). However, Zhong et al. compared PSEA-derived specific expression levels across different cell populations. Specific expression levels obtained with PSEA cannot be directly compared across different populations as they are on a relative scale. They are accurate as we demonstrate by deconvolving the same dataset used by Zhong et al. and, importantly, allow for comparison of population-specific expression across conditions.

Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome.

Insertions of the human-specific subfamily of LINE-1 (L1) retrotransposon are highly polymorphic across individuals and can critically influence the human transcriptome. We hypothesized that L1 insertions could represent genetic variants determining important human phenotypic traits, and performed an integrated analysis of L1 elements and single nucleotide polymorphisms (SNPs) in several human populations. We found that a large fraction of L1s were in high linkage disequilibrium with their surrounding genomic regions and that they were well tagged by SNPs. However, L1 variants were only partially captured by SNPs on standard SNP arrays, so that their potential phenotypic impact would be frequently missed by SNP array-based genome-wide association studies. We next identified potential phenotypic effects of L1s by looking for signatures of natural selection linked to L1 insertions; significant extended haplotype homozygosity was detected around several L1 insertions. This finding suggests that some of these L1 insertions may have been the target of recent positive selection.

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

Genome-wide increase in histone H2A ubiquitylation in a mouse model of Huntington's disease.

BACKGROUND: Huntington's disease (HD) is a neurodegenerative disorder with selective vulnerability of striatal neurons and involves extensive transcriptional dysregulation early in the disease process. Previous work in cell and mouse models has shown that histone modifications are altered in HD. Specifically, monoubiquitylated histone H2A (uH2A) is present at the promoters of downregulated genes which led to the hypothesis that uH2A plays a role in transcriptional silencing in HD. OBJECTIVE: To broaden our view of uH2A function in transcription in HD, we examined genome-wide binding sites of uH2A in 12-week old striatal tissue from R6/2 transgenic HD mouse model. METHODS: We used chromatin immunoprecipitation followed by genomic promoter microarray hybridization (ChIP-chip) and then interrogated how these binding sites correlate with transcribed genes. RESULTS: Our analysis reveals that, while uH2A levels are globally increased at the genome in the transgenic (TG) striatum, uH2A localization at a gene did not strongly correlate with the absence of its transcript. Furthermore, analysis of differential ubiquitylation in wild-type (WT) and TG striata did not reveal the expected enrichment of uH2A at genes with decreased expression in the TG striatum. CONCLUSIONS: This first description of genome-wide localization of uH2A in an HD model reveals that monoubiquitylation of histone H2A may not function at the level of the individual gene but may rather influence transcription through global chromatin structure.

Cell population-specific expression analysis of human cerebellum.

BACKGROUND: Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types expressing genes of interest and achieves quantitative estimates of cell type-specific expression levels. This procedure makes use of marker gene expression and circumvents the need for additional experimental information like tissue composition. RESULTS: To systematically assess the performance of statistical deconvolution, we applied PSEA to gene expression profiles from cerebellum tissue samples and compared with parallel, experimental separation methods. Owing to the particular histological organization of the cerebellum, we could obtain cellular expression data from in situ hybridization and laser-capture microdissection experiments and successfully validated computational predictions made with PSEA. Upon statistical deconvolution of whole tissue samples, we identified a set of transcripts showing age-related expression changes in the astrocyte population. CONCLUSIONS: PSEA can predict cell-type specific expression levels from tissues homogenates on a genome-wide scale. It thus represents a computational alternative to experimental separation methods and allowed us to identify age-related expression changes in the astrocytes of the cerebellum. These molecular changes might underlie important physiological modifications previously observed in the aging brain.

Comparative analyses of Purkinje cell gene expression profiles reveal shared molecular abnormalities in models of different polyglutamine diseases.

Polyglutamine (PolyQ) diseases have common features that include progressive selective neurodegeneration and the formation of protein aggregates. There is growing evidence to suggest that critical nuclear events lead to transcriptional alterations in PolyQ diseases such as spinocerebellar ataxia type 7 (SCA7) and Huntington's disease (HD), conditions which share a cerebellar degenerative phenotype. Taking advantage of laser capture microdissection technique, we compared the Purkinje cell (PC) gene expression profiles of two transgenic polyQ mouse models (HD: R6/2; SCA7: P7E) by microarray analysis that was validated by real time quantitative PCR. A large number of transcriptional alterations were detected in the R6/2 transgenic model of HD. Similar decreases in the same mRNAs, such as phospholipase C, ß 3, purkinje cell protein 2 (Pcp2) and aldolase C, were found in both models. A decrease in aldolase C and phospholipase C, ß 3, may lead to an increase in the vulnerability of PCs to excitotoxic events. Furthermore, downregulation of mRNAs mediated by the Pcp2-promoter is common in both models. Thus, our data reveal shared molecular abnormalities in different polyQ disorders.

Genome-wide histone acetylation is altered in a transgenic mouse model of Huntington's disease.

In Huntington's disease (HD; MIM ID #143100), a fatal neurodegenerative disorder, transcriptional dysregulation is a key pathogenic feature. Histone modifications are altered in multiple cellular and animal models of HD suggesting a potential mechanism for the observed changes in transcriptional levels. In particular, previous work has suggested an important link between decreased histone acetylation, particularly acetylated histone H3 (AcH3; H3K9K14ac), and downregulated gene expression. However, the question remains whether changes in histone modifications correlate with transcriptional abnormalities across the entire transcriptome. Using chromatin immunoprecipitation paired with microarray hybridization (ChIP-chip), we interrogated AcH3-gene interactions genome-wide in striata of 12-week old wild-type (WT) and transgenic (TG) R6/2 mice, an HD mouse model, and correlated these interactions with gene expression levels. At the level of the individual gene, we found decreases in the number of sites occupied by AcH3 in the TG striatum. In addition, the total number of genes bound by AcH3 was decreased. Surprisingly, the loss of AcH3 binding sites occurred within the coding regions of the genes rather than at the promoter region. We also found that the presence of AcH3 at any location within a gene strongly correlated with the presence of its transcript in both WT and TG striatum. In the TG striatum, treatment with histone deacetylase (HDAC) inhibitors increased global AcH3 levels with concomitant increases in transcript levels; however, AcH3 binding at select gene loci increased only slightly. This study demonstrates that histone H3 acetylation at lysine residues 9 and 14 and active gene expression are intimately tied in the rodent brain, and that this fundamental relationship remains unchanged in an HD mouse model despite genome-wide decreases in histone H3 acetylation.

Gene expression analysis on a single cell level in Purkinje cells of Huntington's disease transgenic mice.

Ataxia is a clinical feature of most polyglutamine disorders. Cerebellar neurodegeneration of Purkinje cells (PCs) in Huntington's Disease (HD) brain was described in the 1980s. PC death in the R6/2 transgenic model for HD was published by Turmaine et al. So far, PCs have not been examined on a single cell level. In order to begin to understand PC dysfunction and degeneration in HD we performed a gene expression study on laser-dissected PC based on a DNA microarray screening and quantitative real time PCR (Q-PCR). We demonstrate downregulation of the retinoid acid receptor-related orphan receptor (ROR) mRNA and ROR-mediated mRNAs, also seen by immunofluorescent staining. As ROR and ROR-dependent transcriptional dysregulation is not only found in the R6/2 model for HD but also in a model for spinocerebellar ataxia type 1 (SCA1) (Serra et al.) the data suggest common pathogenic mechanisms for both polyglutamine diseases.

Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain.

Human diseases are often accompanied by histological changes that confound interpretation of molecular analyses and identification of disease-related effects. We developed population-specific expression analysis (PSEA), a computational method of analyzing gene expression in samples of varying composition that can improve analyses of quantitative molecular data in many biological contexts. PSEA of brains from individuals with Huntington's disease revealed myelin-related abnormalities that were undetected using standard differential expression analysis.

Combined transcriptome analysis of fetal human and mouse cerebral cortex exposed to alcohol.

Fetal exposure to environmental insults increases the susceptibility to late-onset neuropsychiatric disorders. Alcohol is listed as one of such prenatal environmental risk factors and known to exert devastating teratogenetic effects on the developing brain, leading to complex neurological and psychiatric symptoms observed in fetal alcohol spectrum disorder (FASD). Here, we performed a coordinated transcriptome analysis of human and mouse fetal cerebral cortices exposed to ethanol in vitro and in vivo, respectively. Up- and down-regulated genes conserved in the human and mouse models and the biological annotation of their expression profiles included many genes/terms related to neural development, such as cell proliferation, neuronal migration and differentiation, providing a reliable connection between the two species. Our data indicate that use of the combined rodent and human model systems provides an effective strategy to reveal and analyze gene expression changes inflicted by various physical and chemical environmental exposures during prenatal development. It also can potentially provide insight into the pathogenesis of environmentally caused brain disorders in humans.