Characterisation of five candidate genes within the ETEC F4ab/ac candidate region in pigs

BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) that express the F4ab and F4ac fimbriae is a major contributor to diarrhoea outbreaks in the pig breeding industry, infecting both newborn and weaned piglets. Some pigs are resistant to this infection, and susceptibility is inherited as a simple dominant Mendelian trait. Indentifying the genetics behind this trait will greatly benefit pig welfare as well as the pig breeding industry by providing an opportunity to select against genetically susceptible animals, thereby reducing the number of diarrhoea outbreaks. The trait has recently been mapped by haplotype sharing to a 2.5 Mb region on pig chromosome 13, a region containing 18 annotated genes. FINDINGS: The coding regions of five candidate genes for susceptibility to ETEC F4ab/ac infection (TFRC, ACK1, MUC20, MUC4 and KIAA0226), all located in the 2.5 Mb region, were investigated for the presence of possible causative mutations. A total of 34 polymorphisms were identified in either coding regions or their flanking introns. The genotyping data for two of those were found to perfectly match the genotypes at the ETEC F4ab/ac locus, a G to C polymorphism in intron 11 of TFRC and a C to T silent polymorphism in exon 22 of KIAA0226. Transcriptional profiles of the five genes were investigated in a porcine tissue panel including various intestinal tissues. All five genes were expressed in intestinal tissues at different levels but none of the genes were found differentially expressed between ETEC F4ab/ac resistant and ETEC F4ab/ac susceptible animals in any of the tested tissues. CONCLUSIONS: None of the identified polymorphisms are obvious causative mutations for ETEC F4ab/ac susceptibility, as they have no impact on the level of the overall mRNA expression nor predicted to influence the composition of the amino acids composition. However, we cannot exclude that the five tested genes are bona fide candidate genes for susceptibility to ETEC F4ab/ac infection since the identified polymorphism might affect the translational apparatus, alternative splice forms may exist and post translational mechanisms might contribute to disease susceptibility

Detecting controlling nodes of boolean regulatory networks

Boolean models of regulatory networks are assumed to be tolerant to perturbations. That qualitatively implies that each function can only depend on a few nodes. Biologically motivated constraints further show that functions found in Boolean regulatory networks belong to certain classes of functions, for example, the unate functions. It turns out that these classes have specific properties in the Fourier domain. That motivates us to study the problem of detecting controlling nodes in classes of Boolean networks using spectral techniques. We consider networks with unbalanced functions and functions of an average sensitivity less than 23k, where k is the number of controlling variables for a function. Further, we consider the class of 1-low networks which include unate networks, linear threshold networks, and networks with nested canalyzing functions. We show that the application of spectral learning algorithms leads to both better time and sample complexity for the detection of controlling nodes compared with algorithms based on exhaustive search. For a particular algorithm, we state analytical upper bounds on the number of samples needed to find the controlling nodes of the Boolean functions. Further, improved algorithms for detecting controlling nodes in large-scale unate networks are given and numerically studied

Caspase-8 deficiency in epidermal keratinocytes triggers an inflammatory skin disease

Expression of enzymatically inactive caspase-8, or deletion of caspase-8 from basal epidermal keratinocytes, triggers chronic skin inflammation in mice. Unlike similar inflammation resulting from arrest of nuclear factor κB activation in the epidermal cells, the effect induced by caspase-8 deficiency did not depend on TNF, IL-1, dermal macrophage function, or expression of the toll-like receptor adapter proteins MyD88 or TRIF. Both interferon regulatory factor (IRF) 3 and TANK-binding kinase were constitutively phosphorylated in the caspase-8–deficient epidermis, and knockdown of IRF3 in the epidermis-derived cells from these mice abolished the expression of up-regulated genes. Temporal and spatial analyses of the alterations in gene expression that result from caspase-8 deficiency reveal that the changes are initiated before birth, around the time that cornification develops, and occur mainly in the suprabasal layer. Finally, we found that caspase-8–deficient keratinocytes display an enhanced response to gene activation by transfected DNA. Our findings suggest that an enhanced response to endogenous activators of IRF3 in the epidermis, presumably generated in association with keratinocyte differentiation, contributes to the skin inflammatory process triggered by caspase-8 deficiency

Innovative Barcode-Konzepte für DNA-Sequenzierverfahren der zweiten Generation

Die Sequenzierung von DNA wurde zur Jahrtausendwende durch die Entwicklung der Sequenzierverfahren zweiter Generation revolutioniert. Die massive Parallelisierung als Kernkonzept ermöglicht seither eine stetig steigende Effizienz und damit sinkende Kosten für die Analyse von DNA und RNA. Grundlegend für die Parallelisierung ist auch der Einsatz von synthetisch erzeugten DNA-Sequenzen, Oligonukleotide genannt, die im Verbund mit nativen Molekül- Fragmenten eigenständige Einheiten, sogenannte Templates, bilden. Die Einbettung von zusätzlichen Sequenzen zur Markierung der Templates vor der Verarbeitung begründet das Feld der Barcodes. Das Auftreten von Sequenzfehlern und quantitativen Effekten im experimentellen Protokoll der Sequenzierung, wie in der PCR, motivieren die Anwendung von Fehlerkorrekturmechanismen und die Normalisierung von Zählgrößen durch den Einsatz von Barcodes. Die dargelegte Arbeit umfasst zwei unterschiedliche Konzepte zum Einsatz von Barcodes, wobei zwei gänzlich verschiedene Anwendungsgebiete betrachtet werden: Zur gemeinsamen Sequenzierung von unterschiedlichen Proben, Multiplexing genannt, wird das Konzept der Watermark Codes für die Verwendung als Barcodes vorgeschlagen. Basierend auf dem ursprünglichen Prinzip von Davey und MacKay aus dem Jahre 2000 wird das Konzept für die DNA-Sequenzierung angepasst und die Eignung des Verfahrens anhand praxistauglicher Codes gezeigt. Den zweiten Themenkomplex bildet der Einsatz von Zufallsbarcodes. Auf Basis der zufälligen Kombination von speziellen Oligonukleotiden können mit moderatem Aufwand sehr viele unterschiedliche Zufallsbarcodes erzeugt werden, die zur Zählung von Molekülen verwendet werden. Als Erweiterung von zwei bereits bekannten Konzepten wird ein verallgemeinertes Verfahren zur Implementierung von Zufallsbarcodes vorgestellt und experimentell anhand der Illumina Technologie evaluiert.Since the turn of the millennium, DNA-Sequencing has been revolutionised by the upcoming next-generation sequencing methods. The massive parallelisation, as a central concept, provides a steadily increasing efficiency and dropping costs on the analysis of DNA and RNA. For this parallel strategy an integration of synthetic DNA sequences, the oligonucleotides, is essential, which are used to build short separable compounds with native DNA fragments, the so called templates. The concept of barcodes is involved in the embedding of additional sequences into the oligonucleotides to label the compound-molecules prior to experimental processing. The existence of sequence errors and quantitative effects during the sequencing protocol, e.g. the PCR, gives the motivation for the application of error correction and the normalization of molecule-counts via labelling. The presented work includes two diverse concepts for barcoding, within two entirely different tasks: For the joint sequencing of several probes, known as multiplexing, the concept of Watermark Codes is proposed: Based on the original principle given by Davey and MacKay in the year 2000, an adaptation for DNA sequencing is given as a proof of principle study. The second topic is the application of random barcodes. Based on the stochastic combination of welldefined oligonucleotides, random barcodes can give a cost-efficient generation of diverse sequences to be used for counting molecules. As the generalisation of two known concepts, a novel method is proposed to produce random codes, which are evaluated via the Illumina sequencing technology

Data from: Timing of head movements is consistent with energy minimization in walking ungulates

Many ungulates show a conspicuous nodding motion of the head when walking. Until now, the functional significance of this behaviour remained unclear. Combining in vivo kinematics of quadrupedal mammals with a computer model, we show that the timing of vertical displacements of the head and neck is consistent with minimizing energy expenditure for carrying these body parts in an inverted pendulum walking gait. Varying the timing of head movements in the model resulted in increased metabolic cost estimate for carrying the head and neck of up to 63%. Oscillations of the head–neck unit result in weight force oscillations transmitted to the forelimbs. Advantageous timing increases the load in single support phases, in which redirecting the trajectory of the centre of mass (COM) is thought to be energetically inexpensive. During double support, in which—according to collision mechanics—directional changes of the impulse of the COM are expensive, the observed timing decreases the load. Because the head and neck comprise approximately 10% of body mass, the effect shown here should also affect the animals' overall energy expenditure. This mechanism, working analogously in high-tech backpacks for energy-saving load carriage, is widespread in ungulates, and provides insight into how animals economize locomotion

Maple worksheet

The .zip folder contains the Maple worksheet used for the publication "Timing of head movements is consistent with energy minimization in walking ungulates"

spatial representativity - Report of 2013 WG2/SG1 activity

The assessment of spatial representativeness of air quality monitoring stations is an outstanding issue that impinges on several areas relevant to risk assessment and population exposure as well as on the design of monitoring networks, model development, evaluation and data assimilation. There are several approaches proposed in the literature that try to define the area of representativeness of a monitoring station as “a similar area” or “spatial homogeneous field of pollution” (e.g. Bobbia et al., 2008). Such a definition cannot fit the intrinsic anisotropy of the atmospheric flow and dispersion, and is limited in time.JRC.H.2-Air and Climat