Id Gene regulation and function in the prosensory domains of the chicken inner ear: a link between Bmp Signaling and Atoh1

Bone morphogenetic proteins (Bmps) regulate the expression of the proneural gene Atoh1 and the generation of hair cells in the developing inner ear. The present work explored the role of Inhibitor of Differentiation genes (Id1-3) in this process. The results show that Id genes are expressed in the prosensory domains of the otic vesicle, along with Bmp4 and Bmp7. Those domains exhibit high levels of the phosphorylated form of Bmp-responding R-Smads (P-Smad1,5,8), and of Bmp-dependent Smad transcriptional activity as shown by the BRE-tk-EGFP reporter. Increased Bmp signaling induces the expression of Id1-3 along with the inhibition of Atoh1. Conversely, the Bmp antagonist Noggin or the Bmp-receptor inhibitor Dorsomorphin elicit opposite effects, indicating that Bmp signaling is necessary for Id expression and Atoh1 regulation in the otocyst. The forced expression of Id3 is sufficient to reduce Atoh1 expression and to prevent the expression of hair cell differentiation markers. Together, these results suggest that Ids are part of the machinery that mediates the regulation of hair cell differentiation exerted by Bmps. In agreement with that, during hair cell differentiation Bmp4 expression, P-Smad1,5,8 levels and Id expression are downregulated from hair cells. However, Ids are also downregulated from the supporting cells which contrarily to hair cells exhibit high levels of Bmp4 expression, P-Smad1,5,8, and BRE-tk-EGFP activity, suggesting that in these cells Ids escape from Bmp/Smad signaling. The differential regulation of Ids in time and space may underlie the multiple functions of Bmp signaling during sensory organ development.

Use of recovered frying oils in chicken and rabbit feeds: effect on the fatty acid and tocol composition and on the oxidation levels of meat, liver and plasma

The addition of some fat co- and by-products to feeds is usual nowadays; however, the regulations of their use are not always clear and vary between countries. For instance, the use of recycled cooking oils is not allowed in the European Union, but they are used in other countries. However, oils recovered from industrial frying processes could show satisfactory quality for this purpose. Here we studied the effects of including oils recovered from the frying industry in rabbit and chicken feeds (at 30 and 60 g/kg, respectively) on the fatty acid (FA) and tocol (tocopherol1tocotrienol) compositon of meat, liver and plasma, and on their oxidative stability. Three dietary treatments (replicated eight times) were compared: fresh non-used oil (LOX); oil discarded from the frying industry, having a high content of secondary oxidation compounds (HOX); and an intermediate level (MOX) obtained by mixing 50 : 50 of LOX and HOX. The FA composition of oil diets and tissues was assessed by GC, their tocol content by HPLC, the thiobarbituric acid value was used to assess tissue oxidation status, and the ferrous oxidation-xylenol orange method was used to assess the susceptibility of tissues to oxidation. Our results indicate that FA composition of rabbit and chicken meat, liver and plasma was scarcely altered by the addition of recovered frying oils to feed. Differences were encountered in the FA composition between species, which might be attributed mainly to differences in the FA digestion, absorption and metabolism between species, and to some physiological dietary factors (i.e. coprophagy in rabbits that involves fermentation with FA structure modification). The a-tocopherol (aT) content of tissues was reduced in response to the lower aT content in the recovered frying oil. Differences in the content of other tocols were encountered between chickens and rabbits, which might be attributable to the different tocol composition of their feeds, as well as to species differences in the digestion and metabolism of tocols. Tissue oxidation and susceptibility to oxidation were in general low and were not greatly affected by the degree of oxidation of the oil added to the feeds. The relative content of polyunsaturated fatty acids/aT in these types of samples would explain the differences observed between species in the susceptibility of each tissue to oxidation. According to our results, oils recovered from the frying industry could be useful for feed uses.

Effect of feed fat by-products with trans fatty acids and heated oil on cholesterol and oxycholesterols in chicken

Chicken is the most widely consumed meat all over the world due to chickens being easy to rear, their fast growth rate and the meat having good nutritional characteristics. The main objective of this paper was to study the effects of dietary fatty by-products in low, medium and high levels of oxidized lipids and trans fatty acids (TFAs) on the contents of cholesterol and oxycholesterols in meat, liver, and plasma of chickens. A palm fatty acid distillate, before and after hydrogenation, and a sunflower-olive oil blend (70/30, v/v) before and after use in a commercial frying process were used in feeding trials after adding 6% of the fats to the feeds. Highly oxidized lipid and TFA feeds significantly increased the contents of cholesterol and oxycholesterols in all tissues of chicken (0.01 < p <= 0.05). The contents of oxycholesterols in chicken meat, liver and plasma obtained from TFA feeding trials varied between 17 and 48 μg/100 g in meat, 19-42 μg/100 g in liver and 105-126 μg/dL in plasma. In contrast, in the oxidized lipid feeding trials, oxycholesterols varied between 13 and 75 μg/100 g in meat, 30-58 μg/100 g in liver and 66-209 μg/dL in plasma. Meat from chickens fed with feeds containing high levels of TFAs or oxidized lipids may contribute to higher ingestion of cholesterol and oxycholesterols by humans.

Metabolomic assays of amoxicillin, cephapirin and ceftiofur in chicken muscle. Application to treated chicken samples by liquid chromatography quadrupole time-of-flight mass spectrometry

The aim of this study was to identity metabolites and transformation products (TPs) in chicken muscle from amoxicillin (AMX), cephapirin (PIR) and ceftiofur (TIO), which are antibiotics of the β-lactam family. Liquid chromatography coupled to quadrupole time-of-flight (QqTOF) mass spectrometry was utilized due to its high resolution, high mass accuracy and MS/MS capacity for elemental composition determination and structural elucidation. Amoxicilloic acid (AMA) and amoxicillin diketopiperazine (DKP) were found as transformation products from AMX. Desacetylcephapirin (DAC) was detected as a metabolite of PIR. Desfuroylceftiofur (DFC) and its conjugated compound with cysteine (DFC-S-Cys) were detected as a result of TIO in contact with chicken muscle tissue. The metabolites and transformation products were also monitored during the in vivo AMX treatment and slaughtering period. It was found that two days were enough to eliminate AMX and associated metabolites/transformation products after the end of administration.

Effect of supplementation with MgCO3 and L-tryptophan on the welfare and on the carcass and meat quality of two halothane pig genotypes (NN and nn)

Sixty-one animals with different Halothane genes (homozygous halothane positive, n=34; and homozygous halothane negative, n=27) were fed with three diets (controlgroup, with no supplement; magnesium (Mg) group with 1.28g MgCO3/kg and tryptophan (Trp) group with 5g L-Trp/kg) during the last 5 days before slaughter. Animals were submitted to minimal stress ante mortem conditions. Pig behaviour was recorded at the experimental farm, raceway to the CO2 stunning system and during the stunning period. Corneal reflexes were recorded after stunning as well. There were no differences in feed intake among diets (p>0.05) during the 5 days of treatment. Thehalothane positive (nn) group had lower intake than the halothane negative (NN) group(p<0.01). The behaviour of the pigs in the raceway did not differ (p>0.05) among treatments or halothane genotype. A significant (p<0.001) interaction diet*halothane was found in the time to appear the first retreat attempt during the exposure to the CO2 system. In the nn group, the time of performing the first retreat attempt was later in the Mg (p<0.05) than the Control group. Moreover, in the Mg group, the nn had a later (p<0.05) first retreat attempt than the NN. Thus, Mg supplementation could have a positive effect on welfare of nn pigs. The nn had a lower proportion of animals thatshowed corneal reflexes after stunning than NN, indicating a higher effectiveness of thestunning method in nn pigs. Neither Mg nor Trp affected carcass quality and meat quality parameters, although significant differences were found between genotypes

Organic chicken product authentication: state-of-the-art and future perspectives

Organic food products are highly susceptible to fraud. Currently, administrative controls are conducted to detect fraud, but having an analytical tool able to verify the organic identity of food would be very supportive. The state-of-the-art in food authentication relies on fingerprinting approaches that find characteristic analytical patterns to unequivocally identify authentic products. While wide research on authentication has been conducted for other commodities, the authentication of organic chicken products is still in its infancy. Challenges include finding fingerprints to discriminate organic from conventional products, and recruiting sample sets that cover natural variability. Future research might be oriented towards developing new authentication models for organic feed, eggs and chicken meat, keeping models updated and implementing them into regulations. Meanwhile, these models might be very supportive to the administrative controls directing inspections towards suspicious fraudulent samples.

Meat quality of ten cattle breeds of the Southwest of Europe

A sample of about 70 young bulls of each of ten beef cattle breeds reared in their typical production systems has been characterised with respect to meat quality traits. Breeds included were Asturiana de los Valles, Asturiana de la Montaña, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica and Retinta from Spain, and Aubrac, Gasconne and Salers from France. As was previously showed regarding carcass traits, there exist large differences both between and within breed – systems. In general, rustic breeds tended to present darker and redder meats with higher haematin contents, whereas less precocious and more specialised breeds showed brighter meats with bigger water losses. Protein content was similar, whereas intramuscular fat presented the larger variations both between and within breeds. ICDH content was higher in the more rustic breeds, showing the predominantly oxidative character of their fibres. Texture measurements showed in general large within breed-system variations, the differences between breeds being less evident. Within breed-system, daily gain weight was positively associated with brighter and tender meats. In the range studied, increasing slaughter weight within breed did not have influence on meat quality. Conformation was related to lower water holding capacity and less dry matter and intramuscular fat, as well as to a lower haematin content giving brighter meats. The increase in fatness scores was related to an augment of toughness in meat specialised breeds, although in Avileña-Negra Ibérica breed fatness carcasses were related to more tender meats. Redness parameter a* was positively related to fatter animals and opposed to conformation, the opposite being true for the L* (lightness) parameter. There was a small trend of fatter carcasses to be related to oxidative fibres, whereas the muscular fibres of the more conformed carcasses were more glycolytic. Texture measurements maximum load, maximum stress and toughness were very closely related. Shear force was opposed to tenderness. Losses at cooking were opposed to juiciness, but only in the Spanish breeds. No consistent trends regarding relationships between carcass characteristics and tenderness could be observed. Overall acceptability was primarily related with tenderness and flavour, and later on juiciness.

Estimation of lean meat content in pig carcasses using X-ray Computed Tomography and PLS regression

Lean meat percentage (LMP) is an important carcass quality parameter. The aim of this work is to obtain a calibration equation for the Computed Tomography (CT) scans with the Partial Least Square Regression (PLS) technique in order to predict the LMP of the carcass and the different cuts and to study and compare two different methodologies of the selection of the variables (Variable Importance for Projection — VIP- and Stepwise) to be included in the prediction equation. The error of prediction with cross-validation (RMSEPCV) of the LMP obtained with PLS and selection based on VIP value was 0.82% and for stepwise selection it was 0.83%. The prediction of the LMP scanning only the ham had a RMSEPCV of 0.97% and if the ham and the loin were scanned the RMSEPCV was 0.90%. Results indicate that for CT data both VIP and stepwise selection are good methods. Moreover the scanning of only the ham allowed us to obtain a good prediction of the LMP of the whole carcass.

Estudio del rendimiento cárnico de reproductores porcinos selectos de razas puras en estación de control

El sistema actual de testajes ofi ciales de porcino selecto en España, con el retorno de los mejores verracos a los núcleos de selección, ha demostrado ser muy efi caz para la selección y promoción de los futuros reproductores de élite. Esta metodología se ha ido mejorando y aproximando a los estándares europeos mediante la complementación de los parámetros de crecimiento, consumo de pienso, efi ciencia alimentaria, con parámetros de calidad de canal, de calidad de carne y de despiece de descendientes o colaterales de reproductores porcinos activos raza pura. En este artículo se presentan los resultados de los primeros 138 animales evaluados con esta nueva metodología. Production, carcass and meat quality of spanish pig pure breeds in Central Test Station The current system of pure breed offi cial tests in Spain, with the return of the best boars to the selection’s nucleus, up to now has proved to be very effective for the selection and the promotion of the future elite pure breed boars. This methodology has been improving and moving to European standards by means of the complementation of the growth, feed consumption, food effi ciency parameters with the quality of carcass, quality of meat and cutting parameters of relatives (sibblings) of active pedigree breeder. This chapter presents the results of fi rst 138 evaluated animals with this new methodology.

Comparison of different devices for predicting the lean meat percentage of pig carcasses

Lean meat percentage (LMP) is the criterion for carcass classification and it must be measured on line objectively. The aim of this work was to compare the error of the prediction (RMSEP) of the LMP measured with the following different devices: Fat-O-Meat’er (FOM), UltraFOM (UFOM), AUTOFOM and -VCS2000. For this reason the same 99 carcasses were measured using all 4 apparatus and dissected according to the European Reference Method. Moreover a subsample of the carcasses (n=77) were fully scanned with a X-ray Computed Tomography equipment (CT). The RMSEP calculated with cross validation leave-one-out was lower for FOM and AUTOFOM (1.8% and 1.9%, respectively) and higher for UFOM and VCS2000 (2.3% for both devices). The error obtained with CT was the lowest (0.96%) in accordance with previous results, but CT cannot be used on line. It can be concluded that FOM and AUTOFOM presented better accuracy than UFOM and VCS2000.

Effect of magnesium sulphate and L-tryptophan and genotype on the feed intake, behaviour and meat quality of pigs

Sixty-nine entire male pigs with different halothane genotype (homozygous halothane positive – nn –, n=36; and homozygous halothane negative – NN-, n=33) were fed with a supplementation of magnesium sulphate (Mg) and/or L-tryptophan (Trp) in the diet for 5 days before slaughter. Animals were housed individually and were submitted to stressful ante mortem conditions (mixed in the lorry according to treatments and transported 1 hour on rough roads). Individual feed intake was recorded during the 5-d treatment. At the abattoir, pig behaviour was assessed in the raceway to the stunning system and during the stunning period by exposure to CO2. Muscle pH, colour, water holding capacity, texture and cathepsin activities were determined to assess meat quality. The number of pigs with an individual feed intake lower than 2 kg/d was significantly different among diets (P&0.05; Control: 8.7 %; Mg&Trp: 43.5 %; Trp: 17.4 %) and they were considered to have inadequate supplement intake. During the ante mortem period, 15.2 % of pigs included in the experiment died, and this percentage decreased to 8.7 % in those pigs with a feed intake & 2kg/day, all of them from the stress-sensitive pigs (nn). In general, no differences were observed in the behaviour of pigs along the corridor leading to the stunning system and inside the CO2 stunning system. During the stunning procedure, Trp diet showed shorter periods of muscular excitation than control and Mg&Trp diets. The combination of a stressful ante mortem treatment and Mg&Trp supplementation led to carcasses with high incidence of severe skin lesions. Different meat quality results were found when considering all pigs or considering only those with adequate supplement intake. In this later case, Trp increased pH45 (6.15) vs Control diet (5.96) in the Longissimus thoracis (LT) muscle (P&0.05) and pH at 24h (Trp: 5.59 vs C: 5.47) led to a higher incidence of dark, firm and exudative (DFD) traits in SM muscle (P&0.05). Genotype affected negatively all the meat quality traits. Seventy-five percent of LT and 60.0 % of the SM muscles from nn pigs were classified as pale, soft and exudative (PSE), while none of the NN pigs showed these traits (P&0.0001). No significant differences were found between genotypes on the incidence of DFD meat. Due to the negative effects observed in the Mg&Trp group in feed intake and carcass quality, the utilization of a mixture of magnesium sulphate and tryptophan is not recommended.

Multiple non-collinear TF-map alignments of promoter regions

Background: The analysis of the promoter sequence of genes with similar expression patterns isa basic tool to annotate common regulatory elements. Multiple sequence alignments are on thebasis of most comparative approaches. The characterization of regulatory regions from coexpressedgenes at the sequence level, however, does not yield satisfactory results in manyoccasions as promoter regions of genes sharing similar expression programs often do not shownucleotide sequence conservation.Results: In a recent approach to circumvent this limitation, we proposed to align the maps ofpredicted transcription factors (referred as TF-maps) instead of the nucleotide sequence of tworelated promoters, taking into account the label of the corresponding factor and the position in theprimary sequence. We have now extended the basic algorithm to permit multiple promotercomparisons using the progressive alignment paradigm. In addition, non-collinear conservationblocks might now be identified in the resulting alignments. We have optimized the parameters ofthe algorithm in a small, but well-characterized collection of human-mouse-chicken-zebrafishorthologous gene promoters.Conclusion: Results in this dataset indicate that TF-map alignments are able to detect high-levelregulatory conservation at the promoter and the 3'UTR gene regions, which cannot be detectedby the typical sequence alignments. Three particular examples are introduced here to illustrate thepower of the multiple TF-map alignments to characterize conserved regulatory elements inabsence of sequence similarity. We consider this kind of approach can be extremely useful in thefuture to annotate potential transcription factor binding sites on sets of co-regulated genes fromhigh-throughput expression experiments.

The evolution of conventions under incomplete information

We formulate an evolutionary learning process in the spirit ofYoung (1993a) for games of incomplete information. The process involves trembles. For many games, if the amount of trembling is small, play will be in accordance with the games' (semi-strict) Bayesian equilibria most of the time. This supports the notion of Bayesian equilibrium. Further, often play will most of the time be in accordance with exactly one Bayesian equilibrium. This gives a selection among the Bayesian equilibria. For two specific games of economic interest wecharacterize this selection. The first is an extension to incomplete information of the prototype strategic conflict known as Chicken. The second is an incomplete information bilateral monopoly, which is also an extension to incompleteinformation of Nash's demand game, or a simple version ofthe so-called sealed bid double auction. For both gamesselection by evolutionary learning is in favor of Bayesianequilibria where some types of players fail to coordinate, such that the outcome is inefficient.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few aminoacids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.