Isolation and characterization of SPOROMUSA ACIDOVORANS sp. nov., a methylogrophic homoacetogenic bacterium

SPOROMUSA ACIDOVORANS sp. nov. was isolated from a pilot fermenter inoculated with effluent sample from the alcohol distillation industry. The isolate was a Gram-negative, motile, curved, spore-forming rod. The DNA base composition was 42 % G+C. The temperature range for growth was 20 to 40°C, with an optimum at 35°C ; growth occurred within a pH range of 5.4 to 7.5, with an optimum at pH 6.5. Growth substrates included methanol, H2-CO2, formate, fructose, ribose, fumarate, succinate and glycerol. Yeast extract was required for growth. The organism performed the homoacetogenic reaction. (Résumé d'auteur

Combining remote sensing, habitat suitability models and cellular automata to model the spread of the invasive shrub Ulex europaeus

Modeling the past or future spread patterns of invasive plant species is challenging and in an ideal case requires multi-temporal and spatially explicit data on the occurrences of the target species as well as information on the habitat suitability of the areas at risk of being invaded. Most studies either focus on modeling the habitat suitability of a given area for an invasive species or try to model the spreading behavior of an invasive species based on temporally or spatially limited occurrence data and some environmental variables. Here we suggest a workflow that combines habitat suitability maps, occurrence data from multiple time steps collected from remote sensing data, and cellular automata models to first reconstruct the spreading patterns of the invasive shrub Ulex europaeus on the island Chiloé in Chile and then make predictions for the future spread of the species. First, U. europaeus occurrences are derived for four time steps between 1988 and 2020 using remote sensing data and a supervised classification. The resulting occurrence data is combined with occurrence data of the native range of U. europaeus from the GBIF database and selected environmental variables to derive habitat suitability maps using Maxent. Then, cellular automata models are calibrated using the occurrence estimates of the four time steps, the suitability map, and some additional geo-layer containing information about soils and human infrastructure. Finally, a set of calibrated cellular automata models are used to predict the potential spread of U. europaeus for the years 2070 and 2100 using climate scenarios. All individual steps of the workflow where reference data was available led to sufficient results (supervised classifications Overall Accuracy > 0.97; Maxent AUC > 0.85; cellular automata Balanced Accuracy > 0.91) and the spatial patterns of the derived maps matched the experiences collected during the field surveys. Our model predictions suggest a continuous expansion of the maximal potential range of U. europaeus, particularly in the Eastern and Northern part of Chiloé Island. We deem the suggested workflow to be a good solution to combine the static habitat suitability information—representing the environmental constraints—with a temporally and spatially dynamic model representing the actual spreading behavior of the invasive species. The obtained understanding of spreading patterns and the information on areas identified to have a high invasion probability in the future can support land managers to plan prevention and mitigation measures

A large deletion in the COL2A1 gene expands the spectrum of pathogenic variants causing bulldog calf syndrome in cattle.

BACKGROUND Congenital bovine chondrodysplasia, also known as bulldog calf syndrome, is characterized by disproportionate growth of bones resulting in a shortened and compressed body, mainly due to reduced length of the spine and the long bones of the limbs. In addition, severe facial dysmorphisms including palatoschisis and shortening of the viscerocranium are present. Abnormalities in the gene collagen type II alpha 1 chain (COL2A1) have been associated with some cases of the bulldog calf syndrome. Until now, six pathogenic single-nucleotide variants have been found in COL2A1. Here we present a novel variant in COL2A1 of a Holstein calf and provide an overview of the phenotypic and allelic heterogeneity of the COL2A1-related bulldog calf syndrome in cattle. CASE PRESENTATION The calf was aborted at gestation day 264 and showed generalized disproportionate dwarfism, with a shortened compressed body and limbs, and dysplasia of the viscerocranium; a phenotype resembling bulldog calf syndrome due to an abnormality in COL2A1. Whole-genome sequence (WGS) data was obtained and revealed a heterozygous 3513 base pair deletion encompassing 10 of the 54 coding exons of COL2A1. Polymerase chain reaction analysis and Sanger sequencing confirmed the breakpoints of the deletion and its absence in the genomes of both parents. CONCLUSIONS The pathological and genetic findings were consistent with a case of "bulldog calf syndrome". The identified variant causing the syndrome was the result of a de novo mutation event that either occurred post-zygotically in the developing embryo or was inherited because of low-level mosaicism in one of the parents. The identified loss-of-function variant is pathogenic due to COL2A1 haploinsufficiency and represents the first structural variant causing bulldog calf syndrome in cattle. Furthermore, this case report highlights the utility of WGS-based precise diagnostics for understanding congenital disorders in cattle and the need for continued surveillance for genetic disorders in cattle

Applying generic landscape-scale models of natural pest control to real data: Associations between crops, pests and biocontrol agents make the difference

Managing agricultural land to maximize the supply of natural pest control can help reduce pesticide use. Tools that are able to represent the relationship between landscape structure, field management and natural pest control can help in deciding which management practices should be used and where. However, the reliability and the predictive power of generic models of natural pest control is largely unknown. We applied an existing generic model of natural pest control potential based on landscape structure to nine sites in five European countries and tested the resulting values against field measurements of natural pest control. Subsequently, we added information on local level factors to test the possibility of improving model performance and predictive power. The results showed that there is generally little or no evidence of correlation between modeled and field-measured values of natural pest control. Moreover, we found high variability in the results, depending on the associations of crops, pests and biocontrol agents considered (e.g. Oilseed rape-Pollen beetle-Parasitoids) and on the different case studies. Factors at the local level, such as conservation tillage, had an overall positive effect on natural pest control, and their inclusion in the models typically increased their predictive power. Our results underline the importance of developing predictive models of natural pest control which are tailored towards specific associations between crops, pests and biocontrol agents, consider local level factors and are trained using field measurements. They would serve as important tools within farmers' decision making, ultimately supporting the shift toward a low-pesticide agriculture

Modelling Distributions of Rove Beetles in Mountainous Areas Using Remote Sensing Data

Mountain ecosystems are biodiversity hotspots that are increasingly threatened by climate and land use/land cover changes. Long-term biodiversity monitoring programs provide unique insights into resulting adverse impacts on plant and animal species distribution. Species distribution models (SDMs) in combination with satellite remote sensing (SRS) data offer the opportunity to analyze shifts of species distributions in response to these changes in a spatially explicit way. Here, we predicted the presence probability of three different rove beetles in a mountainous protected area (Gran Paradiso National Park, GPNP) using environmental variables derived from Landsat and Aster Global Digital Elevation Model data and an ensemble modelling approach based on five different model algorithms (maximum entropy, random forest, generalized boosting models, generalized additive models, and generalized linear models). The objectives of the study were (1) to evaluate the potential of SRS data for predicting the presence of species dependent on local-scale environmental parameters at two different time periods, (2) to analyze shifts in species distributions between the years, and (3) to identify the most important species-specific SRS predictor variables. All ensemble models showed area under curve (AUC) of the receiver operating characteristics values above 0.7 and true skills statistics (TSS) values above 0.4, highlighting the great potential of SRS data. While only a small proportion of the total area was predicted as highly suitable for each species, our results suggest an increase of suitable habitat over time for the species Platydracus stercorarius and Ocypus ophthalmicus, and an opposite trend for Dinothenarus fossor. Vegetation cover was the most important predictor variable in the majority of the SDMs across all three study species. To better account for intra- and inter-annual variability of population dynamics as well as environmental conditions, a continuation of the monitoring program in GPNP as well as the employment of SRS with higher spatial and temporal resolution is recommended

DYRK1B haploinsufficiency in a Holstein cattle with epilepsy.

In this study, epilepsy with focal seizures progressing to generalized seizures was diagnosed in a 6-month-old Holstein heifer. The seizures were characterized by a brief pre-ictal phase with depression and vocalization. During the ictal phase eyelid spasms, tongue contractions, nodding and abundant salivation were observed, rapidly followed by a convulsive phase with bilateral tonic, clonic or tonic-clonic activity and loss of consciousness. Finally, during the postictal phase the heifer was obtunded and disorientated, unable to perceive obstacles and hypermetric, and pressed its head against objects. In the inter-seizure phase, the heifer was clinically normal. Neuropathology revealed axonal degeneration in the brainstem and diffuse astrocytic hypertrophic gliosis. Whole genome sequencing of the affected heifer identified a private heterozygous splice-site variant in DYRK1B (NM_001081515.1: c.-101-1G>A), most likely resulting in haploinsufficiency owing to loss-of-function. This represents a report of a DYRK1B-associated disease in cattle and adds DYRK1B to the candidate genes for epilepsy

Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution

<p>Abstract</p> <p>Background</p> <p>New high-throughput sequencing technologies promise a very sensitive and high-resolution analysis of DNA methylation patterns in quantitative terms. However, a detailed and comprehensive comparison with existing validated DNA methylation analysis methods is not yet available. Therefore, a systematic cross-validation of 454 sequencing and conventional pyrosequencing, both of which offer exact quantification of methylation levels with a single CpG dinucleotide resolution, was performed.</p> <p>Results</p> <p>To this end the methylation patterns of 12 loci (<it>GSTπ1, p16</it>^{<it>INK4a</it>}<it>, RASSF1A, SOCS1, MAL, hsa-mir-1-1, hsa-mir-9-3, hsa-mir-34a, hsa-mir-596, hsa-mir-663, MINT31</it>, and <it>LINE-1</it>) were analyzed in ten primary hepatocellular carcinoma specimens. After applying stringent quality control criteria, 35749 sequences entered further analysis. The methylation level of individual CpG dinucleotides obtained by 454 sequencing was systematically compared with the corresponding values obtained by conventional pyrosequencing. Statistical analyses revealed an excellent concordance of methylation levels for all individual CpG dinucleotides under study (r²= 0.927).</p> <p>Conclusions</p> <p>Our results confirm that 454 sequencing of bisulfite treated genomic DNA provides reliable high quality quantitative methylation data and identify <it>MAL, hsa-mir-9-3, hsa-mir-596, and hsa-mir-663 </it>as new targets of aberrant DNA methylation in human hepatocelluar carcinoma. In addition, the single molecule resolution of 454 sequencing provides unprecedented information about the details of DNA methylation pattern heterogeneity in clinical samples.</p

Correction to: Genomic diversity and population structure of the Leonberger dog breed.

An amendment to this paper has been published and can be accessed via the original article

A cross-regional analysis of red-backed shrike responses to agri-environmental schemes in Europe

Agri-Environmental Schemes (AES) are the main policy tool to counteract farmland biodiversity declines in Europe, but their biodiversity benefit varies across sites and is likely moderated by landscape context. Systematic monitoring of AES outcomes is lacking, and AES assessments are often based on field experiments encompassing one or few study sites. Spatial analysis methods encompassing broader areas are therefore crucial to better understand the context dependency of species' responses to AES. Here, we quantified red-backed shrike (Lanius collurio) occurrences in relation to AES adoption in three agricultural regions: Catalonia in Spain, the Mulde River Basin in Germany, and South Moravia in the Czech Republic. We used pre-collected biodiversity datasets, comprising structured and unstructured monitoring data, to compare empirical evidence across regions. Specifically, in each region we tested whether occurrence probability was positively related with the proportion of grassland-based AES, and whether this effect was stronger in simple compared to complex landscapes. We built Species Distribution Models using existing field observations of the red-backed shrike, which we related to topographic, climatic, and field-level land-use information complemented with remote sensing-derived land-cover data to map habitats outside agricultural fields. We found a positive relationship between AES area and occurrence probability of the red-backed shrike in all regions. In Catalonia, the relationship was stronger in structurally simpler landscapes, but we found little empirical support for similar landscape-moderated effects in South Moravia and the Mulde River Basin. Our results highlight the complexity of species' responses to management across different regional and landscape contexts, which needs to be considered in the design and spatial implementation of future conservation measures

Multiple FGF4 retrocopies recently derived within canids

Two transcribed retrocopies of the fibroblast growth factor 4 (FGF4) gene have previously been described in the domestic dog. An FGF4 retrocopy on chr18 is associated with disproportionate dwarfism, while an FGF4 retrocopy on chr12 is associated with both disproportionate dwarfism and intervertebral disc disease (IVDD). In this study, whole-genome sequencing data were queried to identify other FGF4 retrocopies that could be contributing to phenotypic diversity in canids. Additionally, dogs with surgically confirmed IVDD were assayed for novel FGF4 retrocopies. Five additional and distinct FGF4 retrocopies were identified in canids including a copy unique to red wolves (Canis rufus). The FGF4 retrocopies identified in domestic dogs were identical to domestic dog FGF4 haplotypes, which are distinct from modern wolf FGF4 haplotypes, indicating that these retrotransposition events likely occurred after domestication. The identification of multiple, full length FGF4 retrocopies with open reading frames in canids indicates that gene retrotransposition events occur much more frequently than previously thought and provide a mechanism for continued genetic and phenotypic diversity in canids