Different approaches to identify markers for meat quality and production traits in pigs: analysis of the transcriptome in post mortem skeletal muscle and investigation of candidate genes

Due to the growing attention of consumers towards their food, improvement of quality of animal products has become one of the main focus of research. To this aim, the application of modern molecular genetics approaches has been proved extremely useful and effective. This innovative drive includes all livestock species productions, including pork. The Italian pig breeding industry is unique because needs heavy pigs slaughtered at about 160 kg for the production of high quality processed products. For this reason, it requires precise meat quality and carcass characteristics. Two aspects have been considered in this thesis: the application of the transcriptome analysis in post mortem pig muscles as a possible method to evaluate meat quality parameters related to the pre mortem status of the animals, including health, nutrition, welfare, and with potential applications for product traceability (chapters 3 and 4); the study of candidate genes for obesity related traits in order to identify markers associated with fatness in pigs that could be applied to improve carcass quality (chapters 5, 6, and 7). Chapter three addresses the first issue from a methodological point of view. When we considered this issue, it was not obvious that post mortem skeletal muscle could be useful for transcriptomic analysis. Therefore we demonstrated that the quality of RNA extracted from skeletal muscle of pigs sampled at different post mortem intervals (20 minutes, 2 hours, 6 hours, and 24 hours) is good for downstream applications. Degradation occurred starting from 48 h post mortem even if at this time it is still possible to use some RNA products. In the fourth chapter, in order to demonstrate the potential use of RNA obtained up to 24 hours post mortem, we present the results of RNA analysis with the Affymetrix microarray platform that made it possible to assess the level of expression of more of 24000 mRNAs. We did not identify any significant differences between the different post mortem times suggesting that this technique could be applied to retrieve information coming from the transcriptome of skeletal muscle samples not collected just after slaughtering. This study represents the first contribution of this kind applied to pork. In the fifth chapter, we investigated as candidate for fat deposition the TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) gene. This gene is involved in mechanisms regulating energy homeostasis in skeletal muscle and is associated with predisposition to obesity in humans. By resequencing a fragment of the TBC1D1 gene we identified three synonymous mutations localized in exon 2 (g.40A>G, g.151C>T, and g.172T>C) and 2 polymorphisms localized in intron 2 (g.219G>A and g.252G>A). One of these polymorphisms (g.219G>A) was genotyped by high resolution melting (HRM) analysis and PCR-RFLP. Moreover, this gene sequence was mapped by radiation hybrid analysis on porcine chromosome 8. The association study was conducted in 756 performance tested pigs of Italian Large White and Italian Duroc breeds. Significant results were obtained for lean meat content, back fat thickness, visible intermuscular fat and ham weight. In chapter six, a second candidate gene (tribbles homolog 3, TRIB3) is analyzed in a study of association with carcass and meat quality traits. The TRIB3 gene is involved in energy metabolism of skeletal muscle and plays a role as suppressor of adipocyte differentiation. We identified two polymorphisms in the first coding exon of the porcine TRIB3 gene, one is a synonymous SNP (c.132T> C), a second is a missense mutation (c.146C> T, p.P49L). The two polymorphisms appear to be in complete linkage disequilibrium between and within breeds. The in silico analysis of the p.P49L substitution suggests that it might have a functional effect. The association study in about 650 pigs indicates that this marker is associated with back fat thickness in Italian Large White and Italian Duroc breeds in two different experimental designs. This polymorphisms is also associated with lactate content of muscle semimembranosus in Italian Large White pigs. Expression analysis indicated that this gene is transcribed in skeletal muscle and adipose tissue as well as in other tissues. In the seventh chapter, we reported the genotyping results for of 677 SNPs in extreme divergent groups of pigs chosen according to the extreme estimated breeding values for back fat thickness. SNPs were identified by resequencing, literature mining and in silico database mining. analysis, data reported in the literature of 60 candidates genes for obesity. Genotyping was carried out using the GoldenGate (Illumina) platform. Of the analyzed SNPs more that 300 were polymorphic in the genotyped population and had minor allele frequency (MAF) >0.05. Of these SNPs, 65 were associated (P<0.10) with back fat thickness. One of the most significant gene marker was the same TBC1D1 SNPs reported in chapter 5, confirming the role of this gene in fat deposition in pig. These results could be important to better define the pig as a model for human obesity other than for marker assisted selection to improve carcass characteristics.

Quantifizierung von Steinschlagrisiken an Straßen

Thema: Quantifizierung von Steinschlagrisiken an Straßen Die Einschätzung eines bestehenden Steinschlagrisikos an Verkehrswegen ist in Gebirgs- und Mittelgebirgsregionen seit jeher eine Aufgabe, die mit verschiedensten Methoden und unterschiedlichem Aufwand bearbeitet wird. In der vorliegenden Untersuchung werden die maßgebenden Parameter zur Beschreibung einer Böschung aufgenommen und bewertet. Es wurde ein Arbeitsblatt entwickelt, in dem festgelegte Parameter erfasst werden, die teils mit Ankreuztechnik, teils mit der Eingabe von Daten, im Computer notiert werden. Das Arbeitsblatt umfasst vier Themenbereiche: Allgemeine Daten, Angaben zur Geometrie der Böschung, Angaben zum Verkehr und Angaben zum Gestein und Gebirge. Ein Computerprogramm, das auf der Basis der Software Excel von Microsoft erstellt wurde, vergibt nach der Dateneingabe Bewertungspunkte (1. Bewertungsschritt). Es werden Summen gebildet und die Teilbereiche bewertet (2. Bewertungsschritt). Jeder Teilbereich besitzt drei Bewertungsklassen. Die Verknüpfung der Bewertung der Teilbereiche Geometrische Angaben und Angaben zum Gestein und Gebirge stellt die eigentliche Risikoeinschätzung dar (3. Bewertungsschritt). Es gibt drei Einstufungen zur Beschreibung des Risikos: ð Der Verkehr ist durch Steinschlag sehr gering gefährdet. ð Der Verkehr ist durch Steinschlag gering gefährdet. Eine Detailüberprüfung muss erfolgen, da eine Gefährdung nicht auszuschließen ist. ð Der Verkehr ist gefährdet. Es besteht ein hohes Steinschlagrisiko. Bewertungen und Hinweise zu den Teilbereichen Allgemeine Daten und Angaben zum Verkehr kann der Anwender nach eigenem Ermessen zusätzlich nutzen. Die abschließende Risikoeinschätzung erfolgt durch den Anwender bzw. einen Sachverständigen.

Worldwide Diaspora of Aethina tumida (Coleoptera: Nitidulidae), a Nest Parasite of Honey Bees

Native to sub-Saharan Africa, Aethina tumida Murray (Coleoptera: Nitidulidae) is now an invasive pest of honey bee, Apis mellifera L., colonies in Australia and North America. Knowledge about the introduction (s) of this beetle from Africa into and among the current ranges will elucidate pest populations and invasion pathways and contribute to knowledge of how a parasite expands in new populations. We examined genetic variation in adult beetle samples from the United States, Australia, Canada, and Africa by sequencing a 912-base pair region of the mitochondrial DNA cytochrome c oxidase subunit I gene and screening 10 informative microsatellite loci. One Canadian introduction of small hive beetles can be traced to Australia, whereas the second introduction seems to have come from the United States. Beetles now resident in Australia were of a different African origin than were beetles in North America. North American beetles did not show covariance between two mitochondrial haplotypes and their microsatellite frequencies, suggesting that these beetles have a shared source despite having initial genetic structure within their introduced range. Excellent dispersal of beetles, aided in some cases by migratory beekeeping and the bee trade, seems to lead to panmixis in the introduced populations as well as in Africa.

From Craton to Rift: Empirically Based Ground-Truth Criteria for Local Events Recorded on Regional Networks

Region-specific empirically based ground-truth (EBGT) criteria used to estimate the epicentral-location accuracy of seismic events have been developed for the Main Ethiopian Rift and the Tibetan plateau. Explosions recorded during the Ethiopia-Afar Geoscientific Lithospheric Experiment (EAGLE), the International Deep Profiling of Tibet, and the Himalaya (INDEPTH III) experiment provided the necessary GT0 reference events. In each case, the local crustal structure is well known and handpicked arrival times were available, facilitating the establishment of the location accuracy criteria through the stochastic forward modeling of arrival times for epicentral locations. In the vicinity of the Main Ethiopian Rift, a seismic event is required to be recorded on at least 8 stations within the local Pg/Pn crossover distance and to yield a network-quality metric of less than 0.43 in order to be classified as EBGT5(95%) (GT5 with 95% confidence). These criteria were subsequently used to identify 10 new GT5 events with magnitudes greater than 2.1 recorded on the Ethiopian Broadband Seismic Experiment (EBSE) network and 24 events with magnitudes greater than 2.4 recorded on the EAGLE broadband network. The criteria for the Tibetan plateau are similar to the Ethiopia criteria, yet slightly less restrictive as the network-quality metric needs to be less than 0.45. Twenty-seven seismic events with magnitudes greater than 2.5 recorded on the INDEPTH III network were identified as GT5 based on the derived criteria. When considered in conjunction with criteria developed previously for the Kaapvaal craton in southern Africa, it is apparent that increasing restrictions on the network-quality metric mirror increases in the complexity of geologic structure from craton to plateau to rift. Accession Number: WOS:000322569200012

Effective compression ratio-A new measurement of the quality of thorax compression during CPR

PURPOSE: Computer-based feedback systems for assessing the quality of cardiopulmonary resuscitation (CPR) are widely used these days. Recordings usually involve compression and ventilation dependent variables. Thorax compression depth, sufficient decompression and correct hand position are displayed but interpreted independently of one another. We aimed to generate a parameter, which represents all the combined relevant parameters of compression to provide a rapid assessment of the quality of chest compression-the effective compression ratio (ECR). METHODS: The following parameters were used to determine the ECR: compression depth, correct hand position, correct decompression and the proportion of time used for chest compressions compared to the total time spent on CPR. Based on the ERC guidelines, we calculated that guideline compliant CPR (30:2) has a minimum ECR of 0.79. To calculate the ECR, we expanded the previously described software solution. In order to demonstrate the usefulness of the new ECR-parameter, we first performed a PubMed search for studies that included correct compression and no-flow time, after which we calculated the new parameter, the ECR. RESULTS: The PubMed search revealed 9 trials. Calculated ECR values ranged between 0.03 (for basic life support [BLS] study, two helpers, no feedback) and 0.67 (BLS with feedback from the 6th minute). CONCLUSION: ECR enables rapid, meaningful assessment of CPR and simplifies the comparability of studies as well as the individual performance of trainees. The structure of the software solution allows it to be easily adapted to any manikin, CPR feedback devices and different resuscitation guidelines (e.g. ILCOR, ERC).

Treatment of acute ischaemic stroke with thrombolysis or thrombectomy in patients receiving anti-thrombotic treatment

Systemic thrombolysis with alteplase is the only approved medical treatment for patients with acute ischaemic stroke. Thrombectomy is also increasingly used to treat proximal occlusions of the cerebral arteries, but has not shown superiority over systemic thrombolysis with alteplase. Many patients with acute ischaemic stroke are pretreated with antiplatelet or anticoagulant drugs, which can increase the bleeding risk of thrombolysis or thrombectomy. Pretreatment with aspirin monotherapy increases the bleeding risk of alteplase in both observational and randomised trials with no effect on clinical outcome, and the risk of intracerebral haemorrhage is increased with the combination of aspirin and clopidogrel. Antiplatelet drugs should not be given in the first 24 h after alteplase treatment. Data from pooled randomised trials and a large observational study show that thrombolysis can probably be done safely in patients given vitamin-K antagonists if the international normalised ratio is less than 1·7, although bleeding risk is slightly raised. Almost no data are available for the safety of alteplase in patients with atrial fibrillation who have been given novel oral anticoagulants (NOAC) for stroke prevention. Some coagulation parameters could help to identify patients treated with NOAC who might be eligible for thrombolysis. Thrombectomy can be done in patients given antiplatelets and probably in those given anticoagulants; however, conclusions about anticoagulants are based on findings from observational studies with small patient numbers.

Pancreatic carcinoma, pancreatitis, and healthy controls: metabolite models in a three-class diagnostic dilemma

Metabolomics as one of the most rapidly growing technologies in the "-omics" field denotes the comprehensive analysis of low molecular-weight compounds and their pathways. Cancer-specific alterations of the metabolome can be detected by high-throughput mass-spectrometric metabolite profiling and serve as a considerable source of new markers for the early differentiation of malignant diseases as well as their distinction from benign states. However, a comprehensive framework for the statistical evaluation of marker panels in a multi-class setting has not yet been established. We collected serum samples of 40 pancreatic carcinoma patients, 40 controls, and 23 pancreatitis patients according to standard protocols and generated amino acid profiles by routine mass-spectrometry. In an intrinsic three-class bioinformatic approach we compared these profiles, evaluated their selectivity and computed multi-marker panels combined with the conventional tumor marker CA 19-9. Additionally, we tested for non-inferiority and superiority to determine the diagnostic surplus value of our multi-metabolite marker panels. Compared to CA 19-9 alone, the combined amino acid-based metabolite panel had a superior selectivity for the discrimination of healthy controls, pancreatitis, and pancreatic carcinoma patients [Formula: see text] We combined highly standardized samples, a three-class study design, a high-throughput mass-spectrometric technique, and a comprehensive bioinformatic framework to identify metabolite panels selective for all three groups in a single approach. Our results suggest that metabolomic profiling necessitates appropriate evaluation strategies and-despite all its current limitations-can deliver marker panels with high selectivity even in multi-class settings.

A human-horse comparative map based on equine BAC end sequences

In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E

Seasonal variability in spontaneous cervical artery dissection

We examined the seasonal variability of spontaneous cervical artery dissection (sCAD) by analysing prospectively collected data from 352 patients with 380 sCAD (361 symptomatic sCAD; 305 carotid and 75 vertebral artery dissections) admitted to two university hospitals with a catchment area of 2,200,000 inhabitants between 1985 and 2004. Presenting symptoms and signs of the 380 sCAD were ischaemic stroke in 241 (63%), transient ischaemic attack in 40 (11%), retinal ischemia in seven (2%), and non-ischaemic in 73 (19%) cases; 19 (5%) were asymptomatic sCAD. A seasonal pattern, with higher frequency of sCAD in winter (31.3%; 95% confidence interval (CI): 26.5 to 36.4; p=0.021) compared to spring (25.5%; 95% CI: 21.1 to 30.3), summer (23.5%; 95% CI: 19.3 to 28.3), and autumn (19.7%; 95% CI: 15.7 to 24.1) was observed. Although the cause of seasonality in sCAD is unclear, the winter peaks of infection, hypertension, and aortic dissection suggest common underlying mechanisms.