A5036927183- Virus-based gene therapy research
- Dermatology and Skin Diseases
- Cancer Genomics and Diagnostics
- Animal Genetics and Reproduction
- Genetic and phenotypic traits in livestock
- Sarcoma Diagnosis and Treatment
- Machine Learning in Bioinformatics
- Genetic Associations and Epidemiology
- Veterinary Oncology Research
- Environmental DNA in Biodiversity Studies
- Genetic diversity and population structure
- Asthma and respiratory diseases
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Plant Pathogens and Fungal Diseases
- T-cell and B-cell Immunology
- Bioinformatics and Genomic Networks
- Plant and animal studies
- Cancer-related gene regulation
- FOXO transcription factor regulation
- Plant and Fungal Interactions Research
- Glycosylation and Glycoproteins Research
- Insect and Pesticide Research
- Insect and Arachnid Ecology and Behavior
- HIV Research and Treatment
Science for Life Laboratory
2015-2023
Uppsala University
2010-2023
Swedish University of Agricultural Sciences
2009-2015
Instytut Biologii Doświadczalnej im. Marcelego Nenckiego
2003
Abstract Osteosarcoma is a debilitating bone cancer that affects humans, especially children and adolescents. A homologous form of osteosarcoma spontaneously occurs in dogs, its differential incidence observed across breeds allows for the investigation tumor mutations context multiple genetic backgrounds. Using whole-exome sequencing dogs from three susceptible (22 golden retrievers, 21 Rottweilers, 23 greyhounds), we found tumors show high frequency somatic copy-number alterations (SCNA),...
Abstract Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted small isolated on Sumatra Borneo, most likely extinct Malay Peninsula. Here, we analyse 5 historical 16 modern genomes from these investigate genomic consequences recent decline, such as increased load. We find Peninsula population experienced shortly before extirpation, which possibly...
Ancient DNA has significantly improved our understanding of the evolution and population history extinct megafauna. However, few studies have used complete ancient genomes to examine species responses climate change prior extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during Late Pleistocene became approximately 14 thousand years before present (ka BP). While humans been proposed as potential causes...
Humans and dogs are both affected by the allergic skin disease atopic dermatitis (AD), caused an interaction between genetic environmental factors. The German shepherd dog (GSD) is a high-risk breed for canine AD (CAD). In this study, we used Swedish cohort of GSDs as model human AD. Serum IgA levels known to be lower in compared other breeds. We detected significantly CAD cases controls (p = 1.1×10−5) our study population. also separation within GSD cohort, where could grouped into two...
Protein–protein interactions are important for the majority of biological processes. A significant number computational methods have been developed to predict protein–protein using protein sequence, structural and genomic data. Vast experimental data is publicly available on Internet, but it scattered across numerous databases. This fact motivated us create evaluate new high-throughput datasets interacting proteins. We extracted interaction from DIP, MINT, BioGRID IntAct Then we constructed...
Background Measurement of plasma concentration natriuretic peptides ( NP s) is suggested to be value in diagnosis cardiac disease dogs, but many factors other than status may influence their concentrations. Dog breed potentially 1 such factor. Objective To investigate variation concentrations pro‐atrial peptide 31‐67 (pro ANP 31‐67) and N‐terminal B‐type NT ‐pro BNP ) healthy dogs. Animals 535 healthy, privately owned dogs 9 breeds were examined at 5 centers as part the European Union EU...
Abstract Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to in their genomes. However, we still know little about what regions genome become and how such form. Here, compare genetic differentiation across genomes bumblebee species living sympatry allopatry reveal potential impact during divergence uncover barrier loci. We first compared alpine Bombus sylvicola a previously unidentified sister Rocky Mountains,...
Many wild species have suffered drastic population size declines over the past centuries, which led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates modern-day populations often lack concordance with dwindling sizes conservation status threatened species. One way directly quantify consequences is compare genome-wide data from pre-decline museum samples modern samples....
Abstract Adaptive ecological differentiation among sympatric populations is promoted by environmental heterogeneity, strong local selection and restricted gene flow. High flow, on the other hand, expected to homogenize genetic variation therefore prevent adaptation. Understanding how adaptation can persist at spatial scale which flow occurs has remained an elusive goal, especially for wild vertebrate populations. Here, we explore roles of natural nonrandom (isolation breeding time habitat...
Abstract Despite the success of genome-wide association studies, much genetic contribution to complex traits remains unexplained. Here, we analyse high coverage whole-genome sequencing data, evaluate rare variants 414 plasma proteins. The frequency distribution is skewed towards spectrum, and damaging are more often rare. We estimate that less than 4.3% narrow-sense heritability expected be explained by in our cohort. Using a gene-based approach, identify Cis -associations for 237 proteins,...
Mapping of chromosomal regions harboring genetic polymorphisms that regulate complex traits is usually followed by a search for the causative mutations underlying observed effects. This often challenging task even after fine mapping, as millions base pairs including many genes will typically need to be investigated. Thus trace mutation(s) there great efficient bioinformatic strategies. Here, we searched and regulating growth in Virginia chicken lines - an experimental population comprising...
Abstract The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts cryptic complex life cycles, thus representing suitable model system method development. Here, report scale, unbiased...
Reverse transcriptase (RT) is a viral enzyme crucial for HIV-1 replication. Currently, 12 drugs are targeted against the RT. The low fidelity of RT-mediated transcription leads to quick accumulation drug-resistance mutations. sequence-resistance relationship remains only partially understood. Using publicly available data collected from over 15 years HIV proteome research, we have created general and predictive rule-based model resistance eight RT inhibitors. Our rough set-based considers...
Chronic kidney disease (CKD) affects 10% of the human population, with only a small fraction genetically defined. CKD is also common in dogs and has been diagnosed nearly all breeds, but its genetic basis remains unclear. Here, we performed Bayesian mixed model genome-wide association analysis for canine boxer population 117 cases 137 controls, identified 21 regions associated disease. At top markers from each region, carried an average 20.2 risk alleles, significantly higher than controls...
Crosslinking of immunoglobulin E antibodies (IgE) bound at the surface mast cells and subsequent mediator release is considered most important trigger for allergic reactions. Therefore, genetic control IgE levels studied in context diseases, such as asthma, atopic rhinitis, or dermatitis (AD). We performed genome-wide association studies 161 Labrador Retrievers with regard to total allergen-specific levels. identified a significant on CFA 5 antigen-specific responsiveness Acarus siro....
Immunoglobulin A deficiency (IgAD) is the most common primary immune disorder in both humans and dogs, characterized by recurrent mucosal tract infections a predisposition for allergic other mediated diseases. In several dog breeds, low IgA levels have been observed at high frequency with clinical resemblance to human IgAD. this study, we used genome-wide association studies (GWAS) identify genomic regions associated dogs as comparative model We novel percentile groups-approach establish...
Hypothyroidism is a complex clinical condition found in both humans and dogs, thought to be caused by combination of genetic environmental factors. In this study we present multi-breed analysis predisposing risk factors for hypothyroidism dogs using three high-risk breeds—the Gordon Setter, Hovawart the Rhodesian Ridgeback. Using genome-wide association approach meta-analysis, identified major locus shared these breeds on chromosome 12 (p = 2.1x10-11). Further characterisation candidate...
Non-synonymous single-nucleotide polymorphisms (nsSNPs) within the coding regions of genes causing amino acid substitutions (AASs) may have a large impact on protein function. The possibilities to identify nsSNPs across genomes increased notably with advent next-generation sequencing technologies. Thus, there is strong need for efficient bioinformatics tools predict functional effect AASs. Such can be used most promising candidate mutations further experimental validation.Here we present...
Abstract Pyometra is one of the most common diseases in female dogs, presenting as purulent inflammation and bacterial infection uterus. On average 20% intact dogs are affected before 10 years age, a proportion that varies greatly between breeds (3–66%). The clear breed predisposition suggests genetic risk factors involved disease development. To identify associated with disease, we performed genome-wide association study (GWAS) golden retrievers, increased developing pyometra (risk ratio:...
Autoinflammatory disease (AID) manifests from the dysregulation of innate immune system and is characterised by systemic persistent inflammation. Clinical heterogeneity leads to patients presenting with one or a spectrum phenotypic signs, leading difficult diagnoses in absence clear genetic cause. We used separate genome-wide SNP analyses investigate five signs AID (recurrent fever, arthritis, breed specific secondary dermatitis, otitis reactive amyloidosis) canine comparative model, pure...
Over the last six decades, populations of bumblebees Bombus sylvicola and balteatus in Colorado have experienced decreases tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts floral composition under climate change. Here we used morphometrics population genomics to determine whether morphological change is ongoing, investigate genetic basis variation, analyse structure these populations. We...
Abstract Summary: High-throughput genotyping and sequencing technologies facilitate studies of complex genetic traits provide new research opportunities. The increasing popularity genome-wide association (GWAS) leads to the discovery associated loci a better understanding architecture underlying not only diseases, but also other monogenic phenotypes. Several softwares are available for performing GWAS analyses, R environment being one them. Results: We present cgmisc, an package that enables...