Systems biology in animal sciences

Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed ‘omics’ technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A ‘system’ approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with ‘system approaches’ in animal sciences, providing exciting opportunities to predict and modulate animal traits

Gene expression patterns in anterior pituitary associated with quantitative measure of oestrous behaviour in dairy cows

Intensive selection for high milk yield in dairy cows has raised production levels substantially but at the cost of reduced fertility, which manifests in different ways including reduced expression of oestrous behaviour. The genomic regulation of oestrous behaviour in bovines remains largely unknown. Here, we aimed to identify and study those genes that were associated with oestrous behaviour among genes expressed in the bovine anterior pituitary either at the start of oestrous cycle or at the mid-cycle (around day 12 of cycle), or regardless of the phase of cycle. Oestrous behaviour was recorded in each of 28 primiparous cows from 30 days in milk onwards till the day of their sacrifice (between 77 and 139 days in milk) and quantified as heat scores. An average heat score value was calculated for each cow from heat scores observed during consecutive oestrous cycles excluding the cycle on the day of sacrifice. A microarray experiment was designed to measure gene expression in the anterior pituitary of these cows, 14 of which were sacrificed at the start of oestrous cycle (day 0) and 14 around day 12 of cycle (day 12). Gene expression was modelled as a function of the orthogonally transformed average heat score values using a Bayesian hierarchical mixed model on data from day 0 cows alone (analysis 1), day 12 cows alone (analysis 2) and the combined data from day 0 and day 12 cows (analysis 3). Genes whose expression patterns showed significant linear or non-linear relationships with average heat scores were identified in all three analyses (177, 142 and 118 genes, respectively). Gene ontology terms enriched among genes identified in analysis 1 revealed processes associated with expression of oestrous behaviour whereas the terms enriched among genes identified in analysis 2 and 3 were general processes which may facilitate proper expression of oestrous behaviour at the subsequent oestrus. Studying these genes will help to improve our understanding of the genomic regulation of oestrous behaviour, ultimately leading to better management strategies and tools to improve or monitor reproductive performance in bovines

LHC and B physics probes of neutrinoless double beta decay in supersymmetry without R-parity

In the event of an observation of neutrinoless double beta decay, a relevant question would be: what lepton number violating physics is responsible for the decay? The exchange of Majorana neutrinos and/or supersymmetric particles may contribute. We point out that measurements of supersymmetric signals at the LHC, including single slepton production, could be used to help bound some supersymmetric processes contributing to neutrinoless double beta decay. LHC information about the supersymmetric spectrum could be combined with Bd-Bd bar mixing data in order to bound a competing neutrinoless double beta decay process involving sbottom exchange

Localization and Manipulation of Small Parts Using GelSight Tactile Sensing

Robust manipulation and insertion of small parts can be challenging because of the small tolerances typically involved. The key to robust control of these kinds of manipulation interactions is accurate tracking and control of the parts involved. Typically, this is accomplished using visual servoing or force-based control. However, these approaches have drawbacks. Instead, we propose a new approach that uses tactile sensing to accurately localize the pose of a part grasped in the robot hand. Using a feature-based matching technique in conjunction with a newly developed tactile sensing technology known as GelSight that has much higher resolution than competing methods, we synthesize high-resolution height maps of object surfaces. As a result of these high-resolution tactile maps, we are able to localize small parts held in a robot hand very accurately. We quantify localization accuracy in benchtop experiments and experimentally demonstrate the practicality of the approach in the context of a small parts insertion problem.National Science Foundation (U.S.) (NSF Grant No. 1017862)United States. National Aeronautics and Space Administration (NASA under Grant No. NNX13AQ85G)United States. Office of Naval Research (ONR Grant No. N000141410047

Superluminal neutrinos in long baseline experiments and SN1987a

Precise tests of Lorentz invariance in neutrinos can be performed using long baseline experiments such as MINOS and OPERA or neutrinos from astrophysical sources. The MINOS collaboration reported a measurement of the muonic neutrino velocities that hints to super-luminal propagation, very recently confirmed at 6 sigma by OPERA. We consider a general parametrisation which goes beyond the usual linear or quadratic violation considered in quantum-gravitational models. We also propose a toy model showing why Lorentz violation can be specific to the neutrino sector and give rise to a generic energy behaviour E^alpha, where alpha is not necessarily an integer number. Supernova bounds and the preferred MINOS and OPERA regions show a tension, due to the absence of shape distortion in the neutrino bunch in the far detector of MINOS. The energy independence of the effect has also been pointed out by the OPERA results.Comment: 22 pages, 7 figures; comment on Cherenkov emission added, version matching JHEP published pape

Keratinocyte Binding Assay Identifies Anti-Desmosomal Pemphigus Antibodies Where Other Tests Are Negative

The serological diagnosis of pemphigus relies on the detection of IgG autoantibodies directed against the epithelial cell surface by indirect immunofluorescence (IIF) on monkey esophagus and against desmoglein 1 (Dsg1) and Dsg3 by ELISA. Although being highly sensitive and specific tools, discrepancies can occur. It is not uncommon that sera testing positive by ELISA give a negative result by IIF and vice versa. This brings diagnostic challenges wherein pemphigus has to be ascertained or ruled out, especially when no biopsy is available. We utilized the ability of anti-Dsg3 and anti-Dsg1 IgG to bind in specific desmosomal patterns to living cells to investigate these discrepancies between IIF and ELISA. Living cultured primary normal human keratinocytes were grown under differentiating conditions to induce adequate expression of Dsg1 and Dsg3, incubated with patient serum for 1 h, and then stained to visualize bound IgG. We investigated two different groups; sera from patients with a positive direct immunofluorescence (DIF) and inconsistent serological findings (n = 43) and sera with positive ELISA or IIF but with negative DIF (n = 60). As positive controls we used 50 sera from patients who fulfilled all diagnostics criteria, and 10 sera from normal human subjects served as negative controls. In the DIF positive group, IgG from 39 of the 43 sera bound to the cells in a desmosomal pattern while in the DIF negative group none of the 60 sera bound to the cells. This shows that for pemphigus patients, ELISA and IIF can be negative while anti-desmosomal antibodies are present and vice versa that ELISA and IIF can be positive in non-pemphigus cases. In absence of a biopsy for DIF, such findings may lead to misdiagnosis

In Quest of Neutrino Masses at O{\cal{O}}(eV) Scale

Neutrino oscillation and tritium beta decay experiments taken simultaneously into account are able to access the so far imperceptible absolute neutrino masses at the electronvolt level. The neutrino mass spectrum derived in this way is independent of the nature of neutrinos (Dirac or Majorana). Furthermore, the lack of neutrinoless double beta decay gives additional constraints on the Majorana neutrino mass spectrum. A case of three neutrinos is examined. Influence of different solutions to the solar neutrino deficit problem on the results is discussed. Apart from the present situation, four qualitatively distinct experimental situations which are possible in the future are investigated: when the two decay experiments give only upper bounds on effective neutrino masses, when either one of them gives a positive result, and when both give positive results. The discussion is carried out by taking into account the present experimental errors of relevant neutrino parameters as well as their much more precise expected estimations (e.g. by $\nu$ factories). It is shown in which cases the upgraded decay experiments simultaneously with neutrino oscillation data may be able to fix the absolute scale of the neutrino mass spectrum, answer the question of the neutrino nature and put some light on CP phases in the lepton sector.Comment: 30 pages, 6 figs, to appear in PR

On the Quantitative Impact of the Schechter-Valle Theorem

We evaluate the Schechter-Valle (Black Box) theorem quantitatively by considering the most general Lorentz invariant Lagrangian consisting of point-like operators for neutrinoless double beta decay. It is well known that the Black Box operators induce Majorana neutrino masses at four-loop level. This warrants the statement that an observation of neutrinoless double beta decay guarantees the Majorana nature of neutrinos. We calculate these radiatively generated masses and find that they are many orders of magnitude smaller than the observed neutrino masses and splittings. Thus, some lepton number violating New Physics (which may at tree-level not be related to neutrino masses) may induce Black Box operators which can explain an observed rate of neutrinoless double beta decay. Although these operators guarantee finite Majorana neutrino masses, the smallness of the Black Box contributions implies that other neutrino mass terms (Dirac or Majorana) must exist. If neutrino masses have a significant Majorana contribution then this will become the dominant part of the Black Box operator. However, neutrinos might also be predominantly Dirac particles, while other lepton number violating New Physics dominates neutrinoless double beta decay. Translating an observed rate of neutrinoless double beta decay into neutrino masses would then be completely misleading. Although the principal statement of the Schechter-Valle theorem remains valid, we conclude that the Black Box diagram itself generates radiatively only mass terms which are many orders of magnitude too small to explain neutrino masses. Therefore, other operators must give the leading contributions to neutrino masses, which could be of Dirac or Majorana nature.Comment: 18 pages, 4 figures; v2: minor corrections, reference added, matches journal version; v3: typo corrected, physics result and conclusions unchange

Accretion Processes for General Spherically Symmetric Compact Objects

We investigate the accretion process for different spherically symmetric space-time geometries for a static fluid. We analyse this procedure using the most general black hole metric ansatz. After that, we examine the accretion process for specific spherically symmetric metrics obtaining the velocity of the sound during the process and the critical speed of the flow of the fluid around the black hole. In addition, we study the behaviour of the rate of change of the mass for each chosen metric for a barotropic fluid.Comment: 10 pages, 15 figures, v2 accepted for publication in 'European Physical Journal C

Constructible motivic functions and motivic integration

We introduce a direct image formalism for constructible motivic functions. One deduces a very general version of motivic integration for which a change of variables theorem is proved. These constructions are generalized to the relative framework, in which we develop a relative version of motivic integration. These results have been announced in math.AG/0403349 and math.AG/0403350. Main results and statements unchanged. Many minor slips corrected and some details added.Comment: Final versio