Glycolytic potential and ultimate muscle pH values in red deer (Cervus elaphus) and fallow deer (Dama dama)

The ultimate pH value of meat (measured at approx. 24 hours post slaughter) gives information about the technological quality, i.e. shelf life, colour, water-holding properties and tenderness and is a direct consequence of muscle glycogen (energy) levels at slaughter. It may therefore also indicate whether or not the animal has been exposed to stressful energy depleting events prior to slaughter. In the present study, 141 animals (130 red deer (Cervus elaphus) and 11 fallow deer (Dama dama) were included to investigate the relationship between ultimate pH and residual glycogen concentration in red deer and fallow deer M. longissimus. In addition, the muscle glycogen content and ultimate pH values in three red deer muscles (Mm. triceps brachii, longissimus and biceps femoris) were studied. M. triceps brachii had higher ultimate pH and lower glycogen content compared with the other two studied muscles. The frequency of intermediate DFD (5.8≤ pH<6.2) was 5.4% in red deer M. longissimus, compared with 9.1% in fallow deer, while the frequency of DFD (pH≥ 6.2) was much lower in red deer (3.8%) than in fallow deer (54.5%). A curvilinear relationship between ultimate pH and total glucose concentration (glycogen and glucose) 30 min post slaughter in red deer and fallow deer M. longissimus was found. The relationship between muscle pH and lactic acid concentration however, was indicated to be linear. A significant variation in total glucose concentration at ultimate pH below 5.80 was observed, including values in the range from 18 to 123 mmol/kg wet tissue. It was concluded that further studies are needed to further explore the relationship between muscle glycogen content and technological and sensory quality attributes of meat from different deer species.Abstract in Swedish / Sammanfattning:Köttets pH-värde (mätt ca 24 timmar efter slakt) har stor betydelse för den teknologiska kvaliteten som t. ex. hållbarhet, färg, vattenhållande förmåga och mörhet. Glykogenförrådet (energinivån) i djurens muskulatur vid slakt är helt avgörande för köttets slutliga pH-värde. Därför kan pH-värdet också indikera om hanteringen av slaktdjur varit skonsam eller om stora mängder muskelenergi har förbrukats vid stress. I vår undersökning ingick 141 hjortar (130 kronhjortar (Cervus elaphus) och 11 dovhjortar (Dama dama) för att studera sambandet mellan köttets pH-värde och glykogeninnehållet i M. longissimus. Glykogeninnehåll och pH-värden i 3 muskler från kronhjort (Mm. triceps brachii, longissimus och biceps femoris) undersöktes också. M. triceps brachii hade högre pH-värde och lägre glykogeninnehåll jämfört med de två andra musklerna. Det var inte så stor skillnad i frekvensen av intermediär DFD (pH-värden mellan 5,8 og 6,2) mellan de två hjortarterna (5,4% för kronhjort och 9,1% för dovhjort), däremot var frekvensen av DFD (pH-värden över 6,2) mycket låg hos kronhjort (3,8%) jämfört med dovhjort (54,5%). Det fanns ett kurvlinjärt samband mellan slutligt pH-värde i köttet och total glukoskoncentration (glykogen + glukos) mätt i M. longissimus 30 min efter slakt för både kron- och dovhjort. Ett linjärt samband mellan pH-värde och koncentration av mjölksyra i M. longissimus kunde också visas. Vi fann en mycket stor varitation i glukoskoncentration (18−123 mmol/kg våtvikt) när köttets pH-värdet var 5,8 eller lägre. Det behövs fler undersökningar för att vidare klargöra sambanden mellan glykogeninnehåll i muskulaturen och teknologisk och sensorisk kvalitet i olika typer av hjortkött

A method for the allocation of sequencing resources in genotyped livestock populations

International audienceAbstractBackgroundThis paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population.MethodsWe present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level. We tested the performance of the two algorithms in simulated pedigrees. For each pedigree, we evaluated the proportion of population haplotypes that are carried by the focal individuals and compared our results to a variant of the widely-used key ancestors approach and to two haplotype-based approaches. We calculated the expected phasing accuracy of the haplotypes of a focal individual at the sequence level given the proportion of the fixed sequencing budget allocated to its family.ResultsAlphaSeqOpt maximises the ability to capture and phase the most frequent haplotypes in a population in three ways. First, it selects focal individuals that collectively represent a larger portion of the population haplotype diversity than existing methods. Second, it selects focal individuals from across the pedigree whose haplotypes can be easily phased using family-based phasing and imputation algorithms, thus maximises the ability to impute sequence into the rest of the population. Third, it allocates more of the fixed sequencing budget to focal individuals whose haplotypes are more frequent in the population than to focal individuals whose haplotypes are less frequent. Unlike existing methods, we additionally present an algorithm to allocate part of the sequencing budget to the families (i.e. immediate ancestors) of focal individuals to ensure that their haplotypes can be phased at the sequence level, which is essential for enabling and maximising subsequent sequence imputation.ConclusionsWe present a new method for the allocation of a fixed sequencing budget to focal individuals and their families such that the final sequenced haplotypes, when phased at the sequence level, represent the maximum possible portion of the haplotype diversity in the population that can be sequenced and phased at that budget

Glycolytic potential and ultimate muscle pH values in red deer (Cervus elaphus) and fallow deer (Dama dama)

The ultimate pH value of meat (measured at approx. 24 hours post slaughter) gives information about the technological quality, i.e. shelf life, colour, water-holding properties and tenderness and is a direct consequence of muscle glycogen (energy) levels at slaughter. It may therefore also indicate whether or not the animal has been exposed to stressful energy depleting events prior to slaughter. In the present study, 141 animals (130 red deer (Cervus elaphus) and 11 fallow deer (Dama dama) were included to investigate the relationship between ultimate pH and residual glycogen concentration in red deer and fallow deer M. longissimus. In addition, the muscle glycogen content and ultimate pH values in three red deer muscles (Mm. triceps brachii, longissimus and biceps femoris) were studied. M. triceps brachii had higher ultimate pH and lower glycogen content compared with the other two studied muscles. The frequency of intermediate DFD (5.8≤ pH<6.2) was 5.4% in red deer M. longissimus, compared with 9.1% in fallow deer, while the frequency of DFD (pH≥ 6.2) was much lower in red deer (3.8%) than in fallow deer (54.5%). A curvilinear relationship between ultimate pH and total glucose concentration (glycogen and glucose) 30 min post slaughter in red deer and fallow deer M. longissimus was found. The relationship between muscle pH and lactic acid concentration however, was indicated to be linear. A significant variation in total glucose concentration at ultimate pH below 5.80 was observed, including values in the range from 18 to 123 mmol/kg wet tissue. It was concluded that further studies are needed to further explore the relationship between muscle glycogen content and technological and sensory quality attributes of meat from different deer species. Abstract in Swedish / Sammanfattning: Köttets pH-värde (mätt ca 24 timmar efter slakt) har stor betydelse för den teknologiska kvaliteten som t. ex. hållbarhet, färg, vattenhållande förmåga och mörhet. Glykogenförrådet (energinivån) i djurens muskulatur vid slakt är helt avgörande för köttets slutliga pH-värde. Därför kan pH-värdet också indikera om hanteringen av slaktdjur varit skonsam eller om stora mängder muskelenergi har förbrukats vid stress. I vår undersökning ingick 141 hjortar (130 kronhjortar (Cervus elaphus) och 11 dovhjortar (Dama dama) för att studera sambandet mellan köttets pH-värde och glykogeninnehållet i M. longissimus. Glykogeninnehåll och pH-värden i 3 muskler från kronhjort (Mm. triceps brachii, longissimus och biceps femoris) undersöktes också. M. triceps brachii hade högre pH-värde och lägre glykogeninnehåll jämfört med de två andra musklerna. Det var inte så stor skillnad i frekvensen av intermediär DFD (pH-värden mellan 5,8 og 6,2) mellan de två hjortarterna (5,4% för kronhjort och 9,1% för dovhjort), däremot var frekvensen av DFD (pH-värden över 6,2) mycket låg hos kronhjort (3,8%) jämfört med dovhjort (54,5%). Det fanns ett kurvlinjärt samband mellan slutligt pH-värde i köttet och total glukoskoncentration (glykogen + glukos) mätt i M. longissimus 30 min efter slakt för både kron- och dovhjort. Ett linjärt samband mellan pH-värde och koncentration av mjölksyra i M. longissimus kunde också visas. Vi fann en mycket stor varitation i glukoskoncentration (18−123 mmol/kg våtvikt) när köttets pH-värdet var 5,8 eller lägre. Det behövs fler undersökningar för att vidare klargöra sambanden mellan glykogeninnehåll i muskulaturen och teknologisk och sensorisk kvalitet i olika typer av hjortkött

Colour stability and water-holding capacity of M. Longissimus and carcass characteristics in fallow deer (Dama dama) grazed on natural pasture or fed barley

The effects of feeding regimen on carcass characteristics, meat colour and water-holding capacity of M. liongissimus were studied in 24 female fallow deer (Dama.dama). All animals were farm raised; twelve were grazed on pasture and twelve were fed barley and a small amount of hay prior to slaughter. The animals were slaughtered at two occasions (during the Southern Hemisphere spring); after 19 weeks of feeding (n=12; 6 grazing and 6 barley fed animals; group 1) and after 24 weeks of feeding (n=12; 6 grazing and 6 barley fed animals; group 2). The barley/hay-fed deer had significantly higher body condition scores and carcass weights than the pasture raised group. No difference in meat ultimate pH values between the treatment groups was recorded. The meat from the pasture raised deer had significantly longer colour display life after 2 and 3 weeks of refrigerated storage (+ 2.0 0c) in vacuum bags. There was no difference in drip loss between the two treatment groups. However, significantly lower drip losses wer found in meat from the animals in group 2 compared with the ones in group 1 (P< 0.001). It was concluded that the feeding regimen of the animals is an important factor that contributes to the variation in quality of fresh chilled deer meat (venison), mainly the colour stability and display life of vacuum packaged meat

Influence of level of nutrition during late pregnancy on reproductive productivity of red deer. I. Adult and primiparous hinds gestating red deer calves

The present study aimed to relate feed intake of red deer hinds during late pregnancy to dam body condition, foetal development and calf growth. Across 3 years, multiparous (n = 33) or primiparous (n = 18) hinds with known conception dates were housed in individual pens from days 150–220 of pregnancy, during which time they were each offered one of three daily allowances of pelletised rations (11 MJME/kg DM; 16% CP): high (H; ad libitum), medium (M; 30% less; multiparous hinds only) and low (L; 50% less). Restricted intake levels were retrospectively calculated from the mean intake of H hinds in the previous week. Hinds were returned to pasture at day 220 and calving was closely monitored. Liveweights, body condition score (BCS), and lactation score (LS) of hinds were recorded weekly from day 130 of pregnancy until calves were weaned at 12 weeks of age. Calves were tagged and weighed at birth, and subsequently weighed at 7 and 12 weeks of age. Additionally, hinds in the first year of study underwent CT scans on days 150 and 215 of pregnancy to assess compositional changes of the dam and conceptus. Mean daily ad libitum intakes of H hinds increased from 1.8 to 2.0 kg DM (0.6–0.7 MJME/kg0.75) at around day 150 to 2.8–3.2 kg DM (0.8–0.9 MJME/kg0.75) by day 220. Those of M and L hinds peaked at 1.8 and 1.6 kg DM, respectively, by day 220. This was reflected in significant treatment effects on liveweight gain and change in BCS and LS by the time of calving. CT scans indicated a significant treatment effect by day 215 on the mass of hind tissues (fat and lean) and a non-significant trend on conceptus/foetal weights. Despite apparent differences in foetal growth trajectories, there were no discernable treatment effects on sex-adjusted birth weights. However, there was an unexpectedly wide spread in calving dates that reflected considerable variation in gestation length. Furthermore, gestation length was negatively correlated with change in hind liveweight (but not BCS) between days 150 and 220 of pregnancy for all groups of hinds (P < 0.05). Of three neonatal calf mortalities, none were related to overweight (dystocia) or underweight (non-viability) calves. Subsequent growth rates (g/day) of surviving calves did not reflect prior treatment of their dams, although variation in birth date influenced weights on specific dates. It is concluded from this study that while variation in nutrition to hinds during the last trimester may strongly influence foetal development, under conditions of modest feed imbalance, variation in gestation length compensates to ensure optimisation of birth weight

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume I Introduction to DUNE

International audienceThe preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay—these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. This TDR is intended to justify the technical choices for the far detector that flow down from the high-level physics goals through requirements at all levels of the Project. Volume I contains an executive summary that introduces the DUNE science program, the far detector and the strategy for its modular designs, and the organization and management of the Project. The remainder of Volume I provides more detail on the science program that drives the choice of detector technologies and on the technologies themselves. It also introduces the designs for the DUNE near detector and the DUNE computing model, for which DUNE is planning design reports. Volume II of this TDR describes DUNE's physics program in detail. Volume III describes the technical coordination required for the far detector design, construction, installation, and integration, and its organizational structure. Volume IV describes the single-phase far detector technology. A planned Volume V will describe the dual-phase technology

DUNE Offline Computing Conceptual Design Report

International audienceThis document describes Offline Software and Computing for the Deep Underground Neutrino Experiment (DUNE) experiment, in particular, the conceptual design of the offline computing needed to accomplish its physics goals. Our emphasis in this document is the development of the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes. In this effort, we concentrate on developing the tools and systems thatfacilitate the development and deployment of advanced algorithms. Rather than prescribing particular algorithms, our goal is to provide resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves and to provide computing that achieves the physics goals of the DUNE experiment