A first generation BAC-based physical map of the channel catfish genome

BACKGROUND: Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL) and the effective positional cloning of genes. RESULTS: A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF) of 46,548 Bacterial Artificial Chromosomes (BAC) clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1) anchoring 19 of the largest contigs to the microsatellite linkage map 2) comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP) patterns seen in Southern blots, and 3) contig sequencing. CONCLUSION: This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits

Usability improvements of the Thermipig model for precision pig farming

Pig livestock farming systems encounter several economic and environmental challenges, connected with meat price decrease, sanitary norms, emissions etc. To deal with these issues, methods and models to assess the performance of a pig production system have been developed. For instance, Thermipig model represents the pig fattening room and simulates performances of pigs at the batch level, taking into account interactions between the individual variability of pigs, farmer's practices, room characteristics and outdoor climate conditions. The model requires some static basic inputs fulfilled in several spreadsheets (such as rooms, pigs, and dietary characteristics) but also data files for voluminous variable inputs (such as outdoor temperature or climate control box parameters) for further modelling and outcome producing. This leads to challenges in data providing by the farmers and have to be improved. This paper deals with the implementation of the separate modules of the developed data warehouse system for usability improvements of the Thermipig model. The idea is to substitute input from the data files with online data input and automated variable processing by the model using the python script for connection to the remote data warehouse. The data warehouse system is extended with ‘Property Sets’ section dealing with all the operations that can be performed to a set of input variables. This approach demonstrates the ability of the data warehouse to act as data supplier for the remote model. As well the outcome of the model is also transferable back to the data warehouse for evaluation. This work is done within the Era-Net SuSan PigSys project - Improving pig system performance through a whole system approach

Image resonance in the many-body density of states at a metal surface

The electronic properties of a semi-infinite metal surface without a bulk gap are studied by a formalism that is able to account for the continuous spectrum of the system. The density of states at the surface is calculated within the GW approximation of many-body perturbation theory. We demonstrate the presence of an unoccupied surface resonance peaked at the position of the first image state. The resonance encompasses the whole Rydberg series of image states and cannot be resolved into individual peaks. Its origin is the shift in spectral weight when many-body correlation effects are taken into account

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter

A novel family of diversified immunoregulatory receptors in teleosts is homologous to both mammalian Fc receptors and molecules encoded within the leukocyte receptor complex

Three novel and closely related leukocyte immune-type receptors (IpLITR) have been identified in channel catfish (Ictalurus punctatus). These receptors belong to a large polymorphic and polygenic subset of the Ig superfamily with members located on at least three independently segregating loci. Like mammalian and avian innate immune regulatory receptors, IpLITRs have both putative inhibitory and stimulatory forms, with multiple types coexpressed in various lymphoid tissues and clonal leukocyte cell lines. IpLITRs have an unusual and novel relationship to mammalian and avian innate immune receptors: the membrane distal Ig domains of an individual IpLITR are related to fragment crystallizable receptors (FcRs) and FcR-like proteins, whereas the membrane proximal Ig domains are related to several leukocyte receptor complex encoded receptors. This unique composition of Ig domains within individual receptors supports the hypothesis that functionally and genomically distinct immune receptor families found in tetrapods may have evolved from such ancestral genes by duplication and recombination events. Furthermore, the discovery of a large heterogeneous family of immunoregulatory receptors in teleosts, reminiscent of amphibian, avian, and mammalian Ig-like receptors, suggests that complex innate immune receptor networks have been conserved during vertebrate evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at http://dx.doi.org/10.1007/s00251-006-0134-1 and is accessible for authorized users