Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica).

A large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome-wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome-wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small-effect QTL that were not detectable in this study.

A Novel Model to Explain Extreme Feather Pecking Behavior in Laying Hens.

Feather pecking (FP) is a serious economic and welfare problem in the domestic fowl. It has recently been shown that the distribution of FP bouts within groups is heterogeneous and contains a sub-population of extreme feather peckers (EFP). The present study proposed a novel model to detect EFP hens. A mixture of two negative binomial distributions was fitted to FP data of a F2 cross of about 960 hens, and, based on the results, a calculation of the posterior probability for each hen belonging to the EFP subgroup (pEFP) was done. The fit of the mixture distribution revealed that the EFP subgroup made up a proportion of one third of the F2 cross. The EFP birds came more frequently into pecking mood and showed higher pecking intensities compared to the remaining birds. Tonic immobility and emerge box tests were conducted at juvenile and adult age of the hens to relate fearfulness to EFP. After dichotomization, all traits were analyzed in a multivariate threshold model and a genomewide association study was performed. The new trait pEFP has a medium heritability of 0.35 and is positively correlated with the fear traits. Breeding for this new trait could be an interesting option to reduce the proportion of extreme feather peckers. An index of fear related traits might serve as a proxy to breed indirectly for pEFP. GWAS revealed that all traits are typical quantitative traits with many genes and small effects contributing to the genetic variance.

Genomic analysis of perinatal sucking reflex in German Brown Swiss calves.

A healthy sucking reflex is essential for newborn calves to ensure sufficient colostrum intake in the first few hours postpartum. In recent decades, European Brown Swiss breeders have repeatedly reported that some calves lack the ability to consume colostrum directly after birth due to an absent sucking reflex. In this study, we collected the phenotypes of more than 5,500 German Brown Swiss calves and performed variance component estimation with sire threshold models using Markov chain Monte Carlo algorithms. The 50K (777K) genotypes of nearly 2,000 (200) calves were collected, and an imputation was performed for all 50K genotypes up to 777K. Genome-wide association studies (GWAS) for the trait sucking reflex were conducted for all 777K genotypes. Depending on the trait coding, a low heritability was estimated to range from 0.08 to 0.11. The GWAS results identified 34 trait-associated SNP on 6 different chromosomes. Post-GWAS analyses showed significant overrepresentation of Gene Ontologies for central nervous development and several regulative processes. Functional annotation clustering and pathway analysis revealed relations to lipid metabolism, immune and endocrine systems, and signal transduction. The results of this study suggest that breeding for an improved sucking reflex is possible but requires large data sets for the estimation of reliable breeding values (either large progeny testing groups or a large reference genome in a genomic selection program).

Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F2 crosses.

In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.

Mapping QTL for production traits in segregating Piétrain pig populations using genome-wide association study results of F2 crosses.

In this study, genome-wide association study (GWAS) results of porcine F2 crosses were used to map QTL in outcross Piétrain populations. For this purpose, two F2 crosses (Piétrain × Meishan, n = 304; Piétrain × Wild Boar, n = 291) were genotyped with the PorcineSNP60v2 BeadChip and phenotyped for the dressing yield, carcass length, daily gain and drip loss traits. GWASs were conducted in the pooled F2 cross applying single marker mixed linear models. For the investigated traits, between two and five (in total 15) QTL core regions, spanning 250 segregating SNPs around a significant trait-associated peak SNP, were identified. The SNPs within the QTL core regions were subsequently tested for trait association in two outcross Piétrain populations consisting of 771 progeny-tested boars and 210 sows with their own performance records. In the sow (boar) dataset, five (eight) of the 15 mapped QTL were validated. Hence, many QTL mapped in the F2 crosses (with Piétrain as a common founder breed) are still segregating in the current Piétrain breed. This confirms the usefulness of existing F2 crosses for mapping QTL that are still segregating in the recent founder breed generation. The approach utilizes the high power of an F2 cross to map QTL in a breeding population for which it is not guaranteed that they would be found using a GWAS in this population.

[Surgical therapy of lung metastases from head and neck cancer]. / Chirurgische Therapie pulmonaler Metastasen von Kopf-Hals-Tumoren.

Pulmonary metastasectomy is an established procedure in oncological therapeutic concepts. A systematic literature search and an analysis of all studies published since 01.01.2000 should evaluate the advantage of pulmonary metastasectomy for patients with primary head and neck cancer. Lung metastases develop in 1.9-13% of head and neck cancer patients. Following metastasectomy, patients reach a median survival of 9.5-78 months and 5-year survival rates of up to 58% are achieved. Intrathoracic recurrence occurs in 18.4-81.8% of patients, selected instances of which can be successfully treated by remetastasectomy. Patients with squamous cell carcinoma have the worst prognosis, but could also become long-term survivors (≥ 60 months). Pulmonary metastasectomy is frequently the only potentially curative therapeutic approach and offers a better long-term survival than nonsurgical therapies. Lung metastasectomy is thus the treatment of choice in selected patients with pulmonary metastases from primary head and neck cancer.

Genome-wide association analysis for growth, muscularity and meat quality in Piétrain pigs.

Improvement in growth and meat quality is one of the main objectives in sire line pig breeding programmes. Mapping quantitative trait loci for these traits using experimental crosses and a linkage-based approach has been performed frequently in the past. The Piétrain breed often was involved as a founder breed to establish the experimental crosses. This breed was selected for muscularity and leanness but shows relatively poor meat quality. It is frequently used as a sire line breed. With the advent of genome-wide and dense SNP chips in pig genomic research, it is possible to also conduct genome-wide association studies within the Piétrain breed. In this study, around 500 progeny-tested sires were genotyped with 60k SNPs. Data filtering showed that around 48k SNPs were useable in this sample. These SNPs were used to conduct a genome-wide association study for growth, muscularity and meat quality traits. Because it is known that a mutation in the RYR1 gene located on chromosome 6 shows a major effect on meat quality, this mutation was included in the models. Single-marker and multimarker association analyses were performed. The results revealed between zero and eight significant associations per trait with P < 5 × 10(-5) . Of special interest are SNPs located on SSC6, SSC10 and SSC15.

Endoscopic laser-assisted diverticulotomy without versus with wound closure in the treatment of Zenker's diverticulum.

The aim of the present study was to compare the modifications of endoscopic laser-assisted diverticulotomy regarding closure of mucosal wound at the cricopharyngeal bridge. The results of 62 cases after endoscopic laser-assisted diverticulotomy without and with wound closure were retrospectively compared. After laser-assisted transection of the cricopharyngeal bridge, the mucosa wound was left open (OW) in 35 cases (56%), whereas a closure of the mucosa wound (CW) with sutures and fibrin glue was performed in 27 patients (44%). Duration of hospitalization, residual diverticular sac rate and occurrence of complications did not differ significantly between the two groups. Mean surgical time was significantly less in the OW cases. According to these results, it can be assumed that readapting and sealing the wound after transecting the cricopharyngeal bridge does not significantly reduce the complication rate. It does, however, extend the length of surgery and increases the cost of the procedure.

Influence of formalin fixation on tissue dimensions in palatal tonsils.

AIM: To investigate the change of tissue dimensions after formalin fixation, and to determine the optimal time of fixation. HYPOTHESIS: Formalin fixation may lead to shrinkage in tissue dimensions and may thus alter tumor stages. BACKGROUND: It is often observed in tumor surgery that the dimensions in vivo seem larger than after resection, and tissue appears to shrink further after formalin fixation. This might alter dimensions and assessment of spread of the tumor and thus lead to a lesser tumor classification and stage. In cases where the decision for adjuvant chemoradiation is based upon the stage, it may thus be of relevance for the patient to evaluate the pathologic and not the in vivo dimensions of the tumor. MATERIAL AND METHODS: In order to obtain comparable tissues, we investigated 100 palatal tonsils after cold steel dissection tonsillectomy for chronic tonsillitis. There were four time points investigated: directly after excision in the operating room and after four, 24 and 72 h of fixation in formaldehyde (4% Formaldehyde in phosphate buffer pH 7.4). The tissue was measured in the following dimensions: volume (ml), weight (g) and length, broadness and width (mm). RESULTS: The tissue size did not change significantly in dimensions except for an increase in length. The time of fixation did not influence the size. DISCUSSION: Formalin fixation does not significantly influence the tissue dimensions of palatal tonsils in comparison to direct ex vivo measurements. A minimal time of fixation of 20 h is required in order to stop all degenerative processes; however, longer fixation does not change the dimensions of the specimen. CONCLUSION: The null hypothesis has to be withdrawn that tissue dimensions are altered by formalin fixation. Thus, the histopathological measurements do not influence TNM staging.

[Multimorbid patients with poor soft tissue conditions: treatment of distal tibia fractures with retrograde intramedullary nailing]. / Multimorbide Patienten mit schlechten Weichteilverhältnissen: Behandlung distaler Tibiafrakturen mittels retrogradem Tibiamarknagel.

The appropriate treatment of a distal tibia fracture in multimorbid patients with poor soft tissue and skin conditions, poor peripheral blood supply and osteopenic bone is challenging. In this case report we present two patients with these characteristics. Given these exceptional conditions none of the conventional therapies (e.g. cast, internal plate fixation, external fixation, anterograde intramedullary nailing) appeared feasible. To achieve sufficient fracture healing, we chose an unconventional treatment approach of retrograde tibial nailing with inclusion of the ankle and subtalar joint.

A two-step approach to map quantitative trait loci for meat quality in connected porcine F(2) crosses considering main and epistatic effects.

The aim of this study was to map QTL for meat quality traits in three connected porcine F(2) crosses comprising around 1000 individuals. The three crosses were derived from the founder breeds Chinese Meishan, European Wild Boar and Pietrain. The animals were genotyped genomewide for approximately 250 genetic markers, mostly microsatellites. They were phenotyped for seven meat quality traits (pH at 45 min and 24 h after slaughter, conductivity at 45 min and 24 h after slaughter, meat colour, drip loss and rigour). QTL mapping was conducted using a two-step procedure. In the first step, the QTL were mapped using a multi-QTL multi-allele model that was tailored to analyse multiple connected F(2) crosses. It considered additive, dominance and imprinting effects. The major gene RYR1:g.1843C>T affecting the meat quality on SSC6 was included as a cofactor in the model. The mapped QTL were tested for pairwise epistatic effects in the second step. All possible epistatic effects between additive, dominant and imprinting effects were considered, leading to nine orthogonal forms of epistasis. Numerous QTL were found. The most interesting chromosome was SSC6. Not all genetic variance of meat quality was explained by RYR1:g.1843C>T. A small confidence interval was obtained, which facilitated the identification of candidate genes underlying the QTL. Epistasis was significant for the pairwise QTL on SSC12 and SSC14 for pH24 and for the QTL on SSC2 and SSC5 for rigour. Some evidence for additional pairwise epistatic effects was found, although not significant. Imprinting was involved in epistasis.

Mapping quantitative trait loci for metabolic and cytological fatness traits of connected F2 crosses in pigs.

In the present study 3 connected F(2) crosses were used to map QTL for classical fat traits as well as fat-related metabolic and cytological traits in pigs. The founder breeds were Chinese Meishan, European Wild Boar, and Pietrain with to some extent the same founder animals in the different crosses. The different selection history of the breeds for fatness traits as well as the connectedness of the crosses led to a high statistical power. The total number of F(2) animals varied between 694 and 966, depending on the trait. The animals were genotyped for around 250 genetic markers, mostly microsatellites. The statistical model was a multi-allele, multi-QTL model that accounted for imprinting. The model was previously introduced from plant breeding experiments. The traits investigated were backfat depth and fat area as well as relative number of fat cells with different sizes and 2 metabolic traits (i.e., soluble protein content as an indicator for the level of metabolic turnover and NADP-malate dehydrogenase as an indicator for enzyme activity). The results revealed in total 37 significant QTL on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 14, 17, and 18, with often an overlap of confidence intervals of several traits. These confidence intervals were in some cases remarkably small, which is due to the high statistical power of the design. In total, 18 QTL showed significant imprinting effects. The small and overlapping confidence intervals for the classical fatness traits as well as for the cytological and metabolic traits enabled positional and functional candidate gene identification for several mapped QTL.

[Update on HPV-induced oropharyngeal cancer]. / Aktuelles zu HPV-induzierten Oropharynxkarzinomen.

Oropharyngeal squamous cell carcinoma (OSCC) is associated with oncogenic human papillomavirus (HPV) infection in 30-40% of all cases in Germany. The use of PCR and / or in situ hybridisation to detect HPV in tumour tissue is used in combination with p16 immunohistochemistry to reliably distinguish HPV-related and HPV-unrelated OSCC. The distinct biological behaviour of the HPV-related subset of OSCC results in a more favourable prognosis. This might be the result of a greater response to chemotherapy and radiotherapy as seen in recent studies. Ongoing and future clinical trials will stratify for HPV status. If the results of these prospective, randomized trials are consistent with the preliminary results of recent studies, HPV status will be of enormous clinical relevance in the future.

Involvement of multiple loci in quorum quenching of autoinducer I molecules in the nitrogen-fixing symbiont Rhizobium (Sinorhizobium) sp. strain NGR234.

Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. Since we have previously described the complete genome sequence of NGR234, we now report on a genome-wide functional analysis of the genes and enzymes involved in autoinducer I hydrolysis in this microbe. Altogether we identified five cosmid clones that repeatedly gave a positive result in our function-based approach for the detection of autoinducer I hydrolase genes. Of these five cosmid clones, two were located on pNGR234b and three were on cNGR234. Subcloning and in vitro mutagenesis in combination with BLAST analyses identified the corresponding open reading frames (ORFs) of all cosmid clones: dlhR, qsdR1, qsdR2, aldR, and hitR-hydR. Analyses of recombinant DlhR and QsdR1 proteins by using high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrate that these enzymes function as acyl homoserine lactone (AHL) lactonases. Furthermore, we showed that these enzymes inhibited biofilm formation and other quorum-sensing-dependent processes in Pseudomonas aeruginosa, Chromobacterium violaceum, and Agrobacterium tumefaciens. Finally, our experimental data suggest that competitive colonization of roots in the rhizospheres of cowpea plants is affected by DlhR and QsdR1.

Landscape genetics of the key African acacia species Senegalia mellifera (Vahl)- the importance of the Kenyan Rift Valley.

Acacias across Africa have enormous ecological and economic importance, yet their population genetics are poorly studied. We used seven microsatellite loci to investigate spatial genetic structure and to identify potential ecological and geographic barriers to dispersal in the widespread acacia, Senegalia (Acacia) mellifera. We quantified variation among 791 individuals from 28 sampling locations, examining patterns at two spatial scales: (i) across Kenya including the Rift Valley, and (ii) for a local subset of 11 neighbouring locations on Mpala Ranch in the Laikipia plateau. Our analyses recognize that siblings can often be included in samples used to measure population genetic structure, violating fundamental assumptions made by these analyses. To address this potential problem, we maximized genetic independence of samples by creating a sibship-controlled data set that included only one member of each sibship and compared the results obtained with the full data set. Patterns of genetic structure and barriers to gene flow were essentially similar when the two data sets were analysed. Five well-defined geographic regions were identified across Kenya within which gene flow was localized, with the two strongest barriers to dispersal splitting the Laikipia Plateau of central Kenya from the Western and Eastern Rift Valley. At a smaller scale, in the absence of geographic features, regional habitat gradients appear to restrict gene flow significantly. We discuss the implications of our results for the management of this highly exploited species.

[A review of indications for primary surgical care of patients with advanced head and neck cancer]. / Ist die primäre Chirurgie bei fortgeschrittenen Kopf-Hals-Karzinomen noch aktuell?

Organ preservation protocols for advanced head and neck carcinoma have proven to be successful in controlled clinical trials. This has led to an increase in the use of primary chemoradiation for these tumors. However, the intensification of nonoperative treatment protocols has been associated with a dramatic increase in acute treatment-related toxicity and mortality. In this paper, the role of primary surgical care is reviewed. Recent publications in the field and current treatment concepts are discussed.

[Human papillomavirus and cancer of the oropharynx. Molecular interaction and clinical implications]. / Humane Papillomviren und Oropharynxkarzinome. Molekulare Interaktion und klinische Auswirkung.

One-third of the cases of oropharyngeal squamous cell carcinoma (OSCC) contain oncogenic human papillomavirus (HR-HPV). Epidemiologic and molecular evidence underlines the causal role of HR-HPV in these tumors, which can be defined as HPV-related OSCC. These tumors differ from chemical/toxin-induced OSCC in several biological aspects, including specific molecular and genetic alterations. This leads to a characteristic clinical profile of HPV-related OSCC. Sexual risk factors play a role; however, the knowledge about natural infection and the rate of persistence of HR-HPV in the oropharynx is marginal. It is shown that the distinct biological behavior of the HPV-related subset of oropharyngeal tumors results in a more favorable prognosis. This might be the result of a better response to chemotherapy and radiotherapy. However, further studies are needed to show whether it will be possible to reliably select patients for individualized therapy depended on the HPV status of their tumors. Therefore, we think it will be mandatory to consider and stratify HPV status in the design of prospective clinical trials in the future.

Transoral laser surgery for laryngeal cancer: outcome, complications and prognostic factors in 275 patients.

AIM: Curative treatment options for laryngeal carcinoma include primary radiation therapy, open surgical techniques and transoral laser surgery (TLS). In the last decade, TLS has become an important tool in the treatment of laryngeal cancer and has become the standard approach in many institutions. The aim of this study was to review the experience of a single center institution with TLS for early and advanced laryngeal cancer. METHODS: We retrospectively analyzed 275 patients who underwent TLS in regard to the survival outcome and surgical complications. RESULTS: The 5-year disease-free survival estimate was 90.3% and the 10-year disease-free survival estimate was 88.2%. The 5-year larynx preservation rate estimate was 88.2% and the 10-year larynx preservation rate estimate was 87.3%. The disease-free survival was significantly worsened by the variables T and N (p=0.0003; p<0.001, respectively). Two percent of all patients required intraoperative tracheostomy and the rate of minor postoperative complications was 17%. There were no fatal complications. CONCLUSIONS: We conclude that TLS is a valid treatment method for early laryngeal carcinoma. Selected cases of advanced carcinomas may also benefit from TLS.