Effects of larval crowding on the transcriptome of .

Larval crowding is one common ecological stressor for many insect species. In , high larval density alters multiple widely-studied phenotypes including life-history traits, morphology and behavior. Nevertheless, we still miss a holistic view of the full range of phenotypic changes and the underlying molecular mechanisms.

A window into local adaptation.

How organisms adapt to their environment is not only a central topic of evolutionary biology but also a pressing question in the light of recent global change. Unravelling the genetic basis of these local adaptations can help to predict the response of a population to an increase in temperature or the more frequent occurrence of droughts. A popular approach to study the genes that drive local adaptation is the analysis of genotype-environment associations (GEA), testing the correlation of genomic features (typically single-nucleotide polymorphisms, SNPs) and environmental conditions.

Evolution of Metabolome and Transcriptome Supports a Hierarchical Organization of Adaptive Traits.

Most organismal phenotypes have a polygenic basis, which enables adaptive phenotypic responses on ecological time scales. While adaptive phenotypic changes are highly parallel in replicate populations, this does not apply to the contributing loci. In particular for small populations, the same phenotypic shift can be fueled by different sets of alleles at alternative loci (genetic redundancy).

Phenotypic convergence in a natural population acclimated to low temperature.

Fluidity of a given membrane decreases at lower ambient temperatures, whereas it rises at increasing temperatures, which is achieved through changes in membrane lipid composition. In consistence with homeoviscous adaptation theory, lower temperatures result in increased tissue concentrations of polyunsaturated fatty acids (PUFAs) in , suggesting a higher PUFA requirement at lower temperatures. However, so far homeoviscous adaptation has been suggested for single or geographically separated genotypes only.

The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime.

Background: Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence, which combines advantages of experimental evolution such as time series, replicate populations, and controlled environmental conditions, with whole genome sequencing. Recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures-either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates.

Detecting selected haplotype blocks in evolve and resequence experiments.

Shifting from the analysis of single nucleotide polymorphisms to the reconstruction of selected haplotypes greatly facilitates the interpretation of evolve and resequence (E&R) experiments. Merging highly correlated hitchhiker SNPs into haplotype blocks reduces thousands of candidates to few selected regions. Current methods of haplotype reconstruction from Pool-seq data need a variety of data-specific parameters that are typically defined ad hoc and require haplotype sequences for validation.

Neuronal Function and Dopamine Signaling Evolve at High Temperature in Drosophila.

Neuronal activity is temperature sensitive and affects behavioral traits important for individual fitness, such as locomotion and courtship. Yet, we do not know enough about the evolutionary response of neuronal phenotypes in new temperature environments. Here, we use long-term experimental evolution of Drosophila simulans populations exposed to novel temperature regimes.

Genetic redundancy fuels polygenic adaptation in Drosophila.

The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic-i.e.

A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment.

Gene expression profiling is one of the most reliable high-throughput phenotyping methods, allowing researchers to quantify the transcript abundance of expressed genes. Because many biotic and abiotic factors influence gene expression, it is recommended to control them as tightly as possible. Here, we show that a 24 h age difference of females that were subjected to RNA sequencing (RNA-Seq) five and six days after eclosure resulted in more than 2000 differentially expressed genes.

Polymorphism-aware protein databases - a prerequisite for an unbiased proteomic analysis of natural populations.

Recent technological advances have increased the throughput of proteomics, facilitating the characterization of molecular phenotypes on the population level, thus bearing the potential to complement transcriptomic analyses. Reference protein databases are crucial for the analysis and quantification, because only peptides in the protein database can be identified. Any peptide carrying an amino acid variant cannot be identified.

Progressive muscle proteome changes in a clinically relevant pig model of Duchenne muscular dystrophy.

Duchenne muscular dystrophy (DMD) is caused by genetic deficiency of dystrophin and characterized by massive structural and functional changes of skeletal muscle tissue, leading to terminal muscle failure. We recently generated a novel genetically engineered pig model reflecting pathological hallmarks of human DMD better than the widely used mdx mouse. To get insight into the hierarchy of molecular derangements during DMD progression, we performed a proteome analysis of biceps femoris muscle samples from 2-day-old and 3-month-old DMD and wild-type (WT) pigs.

Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data.

The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and widespread use of this method for many research questions, ranging from unraveling the genetic basis of complex traits, to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies have determined, for example, the influence of sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated.

The influence of simulated microgravity on the proteome of .

Background: The waterflea is an interesting candidate for bioregenerative life support systems (BLSS). These animals are particularly promising because of their central role in the limnic food web and its mode of reproduction. However, the response of to altered gravity conditions has to be investigated, especially on the molecular level, to evaluate the suitability of for BLSS in space.

Proteomic analysis of extracellular medium of cryopreserved carp (Cyprinus carpio L.) semen.

During freezing and thawing, spermatozoa are exposed to physical and chemical stressors that result in adverse changes in sperm structures and physiological functions. The present study provides, for the first time, a comprehensive description of protein changes in the extracellular medium of cryopreserved semen. Using 2D-DIGE and a combination of protein fractionation by one-dimensional gel electrophoresis and high performance liquid chromatography electrospray ionization tandem mass spectrometry, 183 proteins released from sperm to an extracellular medium were identified.

Interclonal proteomic responses to predator exposure in Daphnia magna may depend on predator composition of habitats.

Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterizing the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the water flea, is a textbook example for predator-induced phenotypic plastic defences; however, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages. We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation.

Stage-specific proteome signatures in early bovine embryo development.

Development of early embryonic stages before activation of the embryonic genome depends on sufficiently stored products of the maternal genome, adequate recruitment and degradation of mRNAs, as well as activation, deactivation, and relocation of proteins. By application of an isobaric tagging for relative and absolute quantification (iTRAQ)-based approach, the proteomes of bovine embryos at the zygote and 2-cell and 4-cell stage with MII oocytes as a reference were quantitatively analyzed. Of 1072 quantified proteins, 87 differed significantly in abundance between the four stages.

Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses.

Background: Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. However, molecular mechanisms underlying this plasticity are poorly understood so far.