On the inverse association between the number of QTL and the trait-specific genomic relationship of a candidate to the training set.

Background: Accuracy of genomic prediction depends on the heritability of the trait, the size of the training set, the relationship of the candidates to the training set, and the , where is the number of QTL and is the number of independently segregating chromosomal segments. Due to LD, the number of independently segregating QTL (effective QTL) can be lower than . In this paper, we show that is inversely associated with the trait-specific genomic relationship of a candidate to the training set.

Genomic prediction in hybrid breeding: I. Optimizing the training set design.

Training sets produced by maximizing the number of parent lines, each involved in one cross, had the highest prediction accuracy for H0 hybrids, but lowest for H1 and H2 hybrids. Genomic prediction holds great promise for hybrid breeding but optimum composition of the training set (TS) as determined by the number of parents (n) and crosses per parent (c) has received little attention. Our objective was to examine prediction accuracy ([Formula: see text]) of GCA for lines used as parents of the TS (I1 lines) or not (I0 lines), and H0, H1 and H2 hybrids, comprising crosses of type I0 × I0, I1 × I0 and I1 × I1, respectively, as function of n and c.

Spontaneous and action potential-evoked Ca release from endoplasmic reticulum in neocortical synaptic boutons.

Although the endoplasmic reticulum (ER) is present throughout axons, and IP and ryanodine receptors are widely expressed in nerve terminals, whether Ca release from presynaptic stores contributes to action potential (AP)-evoked Ca transients remains controversial. We investigated the release of Ca from ER stores in boutons en passant of neocortical layer 5 pyramidal neurons. A hallmark of these stores is that they spontaneously release Ca at a low frequency.

Serotonergic Modulation of Spontaneous and Evoked Transmitter Release in Layer II Pyramidal Cells of Rat Somatosensory Cortex.

As axons from the raphe nuclei densely innervate the somatosensory cortex, we investigated how serotonin (5-HT) modulates transmitter release in layer II pyramidal cells of rat barrel cortex. In the presence of tetrodotoxin and gabazine, 10 μM 5-HT caused a waxing and waning in the frequency of miniature excitatory postsynaptic currents (mEPSC) with no effect on amplitude. Specifically, within 15 min of recording the mEPSC frequency initially increased by 28 ± 7%, then dropped to below control (-15 ± 3%), before resurging back to 27 ± 7% larger than control.

Diffusion of Ca from Small Boutons en Passant into the Axon Shapes AP-Evoked Ca Transients.

Not only the amplitude but also the time course of a presynaptic Ca transient determine multiple aspects of synaptic transmission. In small bouton-type synapses, the mechanisms underlying the Ca decay kinetics have not been fully investigated. Here, factors that shape an action-potential-evoked Ca transient were quantitatively studied in synaptic boutons of neocortical layer 5 pyramidal neurons.

Noradrenaline Increases mEPSC Frequency in Pyramidal Cells in Layer II of Rat Barrel Cortex via Calcium Release From Presynaptic Stores.

Somatosensory cortex is innervated by afferents originating from the which typically release noradrenaline. We tested if activation of presynaptic α-adrenoceptors (AR) coupled to a G-mediated signaling cascade resulted in calcium (Ca) release from stores and thereby increased spontaneous transmitter release in rat barrel cortex. Adding 1-100 μM noradrenaline (NA) or 5 μM cirazoline (CO), a α-AR specific agonist, to the standard artificial cerebrospinal fluid increased the frequency of miniature excitatory postsynaptic currents (mEPSC) by 64 ± 7% in 51% of pyramidal cells in layer II (responders) with no effect on the amplitude.

An improved measurement of the Ca-binding affinity of fluorescent Ca indicators.

Fluorescent Ca indicators are widely used to measure the intracellular Ca concentration ([Ca]) in living cells, including neurons. By calibrating an indicator in solutions that mimic the main ionic constituents of the actual cytoplasm, [Ca] can be determined from the measured fluorescence intensity. However, different studies have reported considerably different Ca-binding affinities (K) for the same indicator, even though they used calibrating solutions with similar compositions.

Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle.

Background: Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required.

Genome-wide association studies of fertility and calving traits in Brown Swiss cattle using imputed whole-genome sequences.

Background: The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic data available. Functional traits such as fertility and calving traits have been included in routine genomic estimation of breeding values making large quantities of phenotypic data available for these traits.

Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle.

The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle.

Improving Focal Photostimulation of Cortical Neurons with Pre-derived Wavefront Correction.

Recent progress in neuroscience to image and investigate brain function has been made possible by impressive developments in optogenetic and opto-molecular tools. Such research requires advances in optical techniques for the delivery of light through brain tissue with high spatial resolution. The tissue causes distortions to the wavefront of the incoming light which broadens the focus and consequently reduces the intensity and degrades the resolution.

Targeted pruning of a neuron's dendritic tree via femtosecond laser dendrotomy.

Neurons are classified according to action potential firing in response to current injection. While such firing patterns are shaped by the composition and distribution of ion channels, modelling studies suggest that the geometry of dendritic branches also influences temporal firing patterns. Verifying this link is crucial to understanding how neurons transform their inputs to output but has so far been technically challenging.

Improved two-photon imaging of living neurons in brain tissue through temporal gating.

We optimize two-photon imaging of living neurons in brain tissue by temporally gating an incident laser to reduce the photon flux while optimizing the maximum fluorescence signal from the acquired images. Temporal gating produces a bunch of ~10 femtosecond pulses and the fluorescence signal is improved by increasing the bunch-pulse energy. Gating is achieved using an acousto-optic modulator with a variable gating frequency determined as integral multiples of the imaging sampling frequency.

Low-cost photo-responsive nanocarriers by one-step functionalization of flame-made titania agglomerates with l-Lysine.

A novel versatile photo-responsive nanocarrier that is able to load and release several functional molecules is obtained by one-step conjugation of scalable flame-made titania agglomerates. Highly crystalline anatase nano-crystals are synthesized by scalable flame spray pyrolysis of organometallic precursor solutions. Nanocarriers are self-assembled by adsorption of lysine molecules on the photocatalytic nanoparticles' surface leading to a minimal flocculation and highly reactive amine terminations.

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle.

Background: Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less well documented. We explored the consequences of commonly recommended preparatory steps and the effects of single and multi sample variant identification methods using four publicly available software applications (Platypus, HaplotypeCaller, Samtools and UnifiedGenotyper) on whole genome sequence data of 65 key ancestors of Swiss dairy cattle populations.

Four-dimensional multi-site photolysis of caged neurotransmitters.

Neurons receive thousands of synaptic inputs that are distributed in space and time. The systematic study of how neurons process these inputs requires a technique to stimulate multiple yet highly targeted points of interest along the neuron's dendritic tree. Three-dimensional multi-focal patterns produced via holographic projection combined with two-photon photolysis of caged compounds can provide for highly localized release of neurotransmitters within each diffraction-limited focus, and in this way emulate simultaneous synaptic inputs to the neuron.

Mathematical analysis and algorithms for efficiently and accurately implementing stochastic simulations of short-term synaptic depression and facilitation.

The release of neurotransmitter vesicles after arrival of a pre-synaptic action potential (AP) at cortical synapses is known to be a stochastic process, as is the availability of vesicles for release. These processes are known to also depend on the recent history of AP arrivals, and this can be described in terms of time-varying probabilities of vesicle release. Mathematical models of such synaptic dynamics frequently are based only on the mean number of vesicles released by each pre-synaptic AP, since if it is assumed there are sufficiently many vesicle sites, then variance is small.

Interaction of short-term depression and firing dynamics in shaping single neuron encoding.

We investigated how the two properties short-term synaptic depression of afferent input and postsynaptic firing dynamics combine to determine the operating mode of a neuron. While several computational roles have been ascribed to either, their interaction has not been studied. We considered two types of short-term synaptic dynamics (release-dependent and release-independent depression) and two classes of firing dynamics (regular firing and firing with spike-frequency adaptation).

Quantifying impacts of short-term plasticity on neuronal information transfer.

Short-term changes in efficacy have been postulated to enhance the ability of synapses to transmit information between neurons, and within neuronal networks. Even at the level of connections between single neurons, direct confirmation of this simple conjecture has proven elusive. By combining paired-cell recordings, realistic synaptic modeling, and information theory, we provide evidence that short-term plasticity can not only improve, but also reduce information transfer between neurons.

Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.

Predicting organismal phenotypes from genotype data is important for plant and animal breeding, medicine, and evolutionary biology. Genomic-based phenotype prediction has been applied for single-nucleotide polymorphism (SNP) genotyping platforms, but not using complete genome sequences. Here, we report genomic prediction for starvation stress resistance and startle response in Drosophila melanogaster, using ∼2.

Simultaneous multi-site two-photon photostimulation in three dimensions.

We demonstrate simultaneous multi-site two-photon photolysis of caged neurotransmitters with close to diffraction-limited resolution in all three dimensions (3D). We use holographic projection of multiple focal spots, which allows full control over the 3D positions of uncaging sites with a high degree of localized excitation. Our system incorporates a two-photon imaging setup to visualize the 3D morphology of the neurons in order to accurately determine the photostimulation sites.

Input-rate modulation of γ oscillations is sensitive to network topology, delays and short-term plasticity.

Simulated networks of excitatory and inhibitory neurons have previously been shown to reproduce critical features of experimental data regarding neural coding in V1, such as a positive relationship between thalamic input spike rate and the power of gamma frequency oscillations. This effect, referred to as modulated gamma power, could represent a neural code in V1 for stimulus characteristics that affect thalamic spike rate such as contrast or intensity. The simulated network's assumptions included homogeneous random connectivity, equal synaptic delays after spike arrival, and constant synaptic efficacies.

Involvement of nonselective cation channels in the depolarisation initiating vasomotion.

1. Coordinated oscillations in diameter occur spontaneously in cerebral vessels and depend on the opening of voltage dependent calcium channels. However, the mechanism that induces the initial depolarisation has remained elusive.

Animal navigation: general properties of directed walks.

The ability to locomote is a defining characteristic of all animals. Yet, all but the most trivial forms of navigation are poorly understood. Here we report and discuss the analytical results of an in-depth study of a simple navigation problem.