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Body conformation comparison of Czech and Polish Hucul horses

Body conformation comparison of Czech and Polish Hucul horses

Measurements of 17 body measures and 11 indices of body conformation on 209 breeding individuals of the Hucul horse were used to analyse the effect of country of origin (Poland and the Czech Republic), sex (stallions and mares), age (5 classes) and sire line (Gurgul, Goral, Oušor, Hroby, Polan, Pietrosu, Prislop). All horses were measured by one person. Measures and indexes were analysed by the GLM procedure. The main effect was the country of origin. Highly significant differences were found be- tween both Polish and Czech horses in two thirds of measurements and in more than half of indices. The Czech Hucul horses are significantly higher, longer, wider in pelvis and have longer head than Polish horses. On the contrary to the Czech horses are Polish horses more compact, massive and have deeper chest. Their cannon bone in relation to height of wither is wider.

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Growth and body conformation responses of genetically divergent Australian sheep to Spirulina (Arthrospira platensis) supplementation

Growth and body conformation responses of genetically divergent Australian sheep to Spirulina (Arthrospira platensis) supplementation

Therefore, we can infer from our result that Spirulina’s growth promoting qualities in non- meat type sheep breeds and in combination with heterosis due to crossbreeding (Leymaster, 2001; Petrovic et al., 2011) does not impact the nutrient use efficiency or partitioning in the first crosses. Furthermore, the result of current study confirmed the widely accepted interaction between sire breed and sex on liveweight and body conformation measurements, the basis of which has been extensively studied in the last decade (Afolayan et al., 2006; Cam et al., 2010; Fogarty et al., 2005a; Fogarty et al., 2005b; Hopkins et al., 2007b; Ponnampalam et al., 2007). Thus, a demonstration of the strong positive correlations between body measurements and liveweight in our present study reaffirms current consensus (Abbasi and Ghafouri-Kesbi, 2011; López-Carlos et al., 2010; Otoikhian et al., 2008; Sowande and Sobola, 2008). Based on previous reports and our current findings, it is therefore imperative to include body conformation measurements in selective breeding programs aimed towards increasing lamb liveweight (Abbasi and Ghafouri-Kesbi, 2011; Afolayan et al., 2006). Additionally, body conformation measurements would allow selection to prioritize growth of particular anatomical areas in lamb which would certainly improve the lamb productivity.

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Analysis of the population of the Old Kladruby horse in point of the body conformation

Analysis of the population of the Old Kladruby horse in point of the body conformation

The objective of the present study was a detailed analysis of the body conformation of the Old Klad- ruby horse in the Stud Farm Kladruby. We applied 26 body dimensions, 9 angles of extremity joints and 12 hippo-metrical indices of 167 breeding horses to analyse the population according to the colou- ration (grey, black), lines (9 lines), sex (stallions and mares) and age categories (4 classes). The resul- ting measures were analysed statistically by means of a linear model with fixed effects (GLM). Most of the statistical highly significant differences were differences detected between stallions and mares and between the Old Kladruby grey and black horses. The stallions have a significantly longer profile of the head (by more than 1 cm) and width of the cheeks. The mares have a highly significantly larger chest (longer by 2.9 cm, more deeply by 3.3 cm), width of coxae and angles of the shoulder and knee joints. The black horses have highly significantly longer profile of the head (by more than 2.5 cm) and width of cheeks, longer the blade-bone and significantly longer the pelvis (by 2.3 cm). The grey horses have highly significantly shorter arm and forearm, longer metacarpus, pastern and shinbone. The differences between age categories are highly significant by heights of body, girth and by hippo-metrical indices. The differences among the lines of the same colouration are minimal. Only white line Rudolfo is signi- ficantly small sized and the least compact.

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Comparison of body conformation of Moravian warm-blooded horse and Sarvar horse

Comparison of body conformation of Moravian warm-blooded horse and Sarvar horse

Measurements of 7 body measures and 6 indices of body conformation on 34 breeding individuals of Moravian warm-blooded horse and 19 of Sarvar horse (Leutstettener) were used to analyse the effect of country of origin (Czech Republik, germany), sire lines or breed (Furioso, Przedswit, English thor- oughbred, Sarvar, Others) and age (4 classes). All horses were measured by one person. Measures and indexes were analysed by gLM procedure. Significant differences were found between both Czech and german population only in index of body frame. Sarvar horses are longer to their height than Moravian warm-blooded horses. The shorter body frame have the horses by English thoroughbred, the longer by Furioso. The younger horses are higher than the older. According to results of Linear Description of Body Conformation we found out, that population of Sarvar horse is more balanced than population of Moravian warm-blooded horse.

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Growth and body conformation responses of genetically divergent Australian sheep to Spirulina (Arthrospira platensis) supplementation

Growth and body conformation responses of genetically divergent Australian sheep to Spirulina (Arthrospira platensis) supplementation

Therefore, we can infer from our result that Spirulina’s growth promoting qualities in non- meat type sheep breeds and in combination with heterosis due to crossbreeding (Leymaster, 2001; Petrovic et al., 2011) does not impact the nutrient use efficiency or partitioning in the first crosses. Furthermore, the result of current study confirmed the widely accepted interaction between sire breed and sex on liveweight and body conformation measurements, the basis of which has been extensively studied in the last decade (Afolayan et al., 2006; Cam et al., 2010; Fogarty et al., 2005a; Fogarty et al., 2005b; Hopkins et al., 2007b; Ponnampalam et al., 2007). Thus, a demonstration of the strong positive correlations between body measurements and liveweight in our present study reaffirms current consensus (Abbasi and Ghafouri-Kesbi, 2011; López-Carlos et al., 2010; Otoikhian et al., 2008; Sowande and Sobola, 2008). Based on previous reports and our current findings, it is therefore imperative to include body conformation measurements in selective breeding programs aimed towards increasing lamb liveweight (Abbasi and Ghafouri-Kesbi, 2011; Afolayan et al., 2006). Additionally, body conformation measurements would allow selection to prioritize growth of particular anatomical areas in lamb which would certainly improve the lamb productivity.

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 Body conformation, carcass composition and physicochemical and sensory properties of meat from pheasants of different origin

 Body conformation, carcass composition and physicochemical and sensory properties of meat from pheasants of different origin

The compared genetic groups were characterized by high dressing percentage. However, the percent- age proportion of eviscerated carcass with neck to the body weight of pheasants before slaughter at 16 weeks of age was lower than in 15-week-old pheasants studied by Sarica et al. (1999). In other studies, 16-week-old pheasants were characterized by the same (Adamski and Kuzniacka, 2006) or low- er (Kuzniacka et al., 2010) dressing percentage as in our study. The dissection analysis showed that the compared groups of pheasants differed significantly only in the content of skin with subcutaneous fat and in the content of abdominal fat. Significantly greater carcass fatness in female Mongolian × Versicolor pheasants makes them more suitable as stewing birds. The content of skin with subcutaneous fat in the analysed males was similar to that obtained by Kokoszyński et al. (2008). The analysed females

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Comparison of Selected Herds of Hutzul Horses Bred in the Czech Republic and Slovakia

Comparison of Selected Herds of Hutzul Horses Bred in the Czech Republic and Slovakia

The objective of the present study was to analyse the eff ect of the age, line, gender and place of measurement on the body dimensions and indices of body conformation of Hutzul horses bred in some herds in the Czech Republic and in Slovakia. The database consisted of 111 horses (81 mares, 16 geldings and 14 stallions) which were measured during fi eld measurements in the individual herds. The data were collected using the Microso Excel 2000 programme and were statistically processed using the statistical programme Unistat version 5.1. The data were evaluated statistically using the general linear model (GLM) and if any eff ect proved to be statistically signifi cant we assessed the respective body dimension and index with a follow-up multiple comparison according to Tukey. The results indicate that there are certain diff erences among the populations of Hutzul horses, but the indisputable diff erence is among the places of measurement. Out of the 14 measured body dimensions 11 were statistically highly signifi cant and one was statistically signifi cant and out of the 4 indices of body conformation 3 were statistically highly signifi cant and one was statistically signifi cant. The eff ect of the gender showed important statistical diff erences. The average values of the CG, WCHSB, DCH and LP were measured in the geldings and the lowest (with the exception of CG where mares showed the lowest average values) in stallions. It can therefore be assumed that mares are deeper and more robust than stallions. Stallions are bonier and a er castration they become considerably stronger but do not increase their height any more. The line has a signifi cant eff ect on the DLB, IBC and IROB and a highly signifi cant eff ect on the WCHSB and FWP. Horses of the Prislop line achieved the highest average values and the Hroby and Gurgul horses the lowest. The eff ect of the age was signifi cant only on WCHSB. The highest average values were achieved by 8-year-old horses and the lowest by 3-year-old and 19 and 20-year-old horses. The herd in Topoľčianky was the most balanced, while the least balanced was the SR Hucul Club herd.

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Detection and mapping of QTL on bovine
chromosomes 2 and 5 segregating for live weight,
average daily gain and body measurements in
Japanese Black Cattle

Detection and mapping of QTL on bovine chromosomes 2 and 5 segregating for live weight, average daily gain and body measurements in Japanese Black Cattle

mation traits in this crossbred population and that ani- mals homozygous for allele 205 gave the best results in terms of linkage with segregating QTL for beef conforma- tion (Napolitano et al., 2001). Their study examined only 7 body conformation measurements–Withers height, bo- dy length, chest width, chest depth, chest girth, rump len- gth and pelvis width. In our present study, we examined 15 body conformation measurements and detected highly significant QTL on chromosome 2 for hip width and chest depth located at 1 cM and 8 cM respectively (Sire Family 1) and for pin bone width at 16cM in Sire Family 3. The implication is that the bracketing microsatellite markers TGLA44 and TGLA431 flanking this interval in Sire Family 1 and BM3627 and BMS803 in Sire Family 3 can be used in marker-assisted selection to introduce or ret- ain the beneficial QTL allele. Our findings in this study clearly demonstrated that the chromosomal interval 1 - 6cM on BTA2 harboured significant QTL (P<0.05) for birth weight, weaning weight, withers height, hip height, body length, shoulder width, lumbar width, thurl width and canon circumference. In other breeds of cattle, Casas et al. (1998) reported that a locus near the centromere of bovine chromosome 2 was responsible for muscle hyper- trophy in two half-sib families of Belgian Blue x MARC III and Piedmontese x Angus and confirmed the location to be 4 cM with a 95% confidence interval between 2 – 6 cM. This interval has been recognised as one harbouring the myostatin gene (Casas et al., 2000). Bovine chromosome 2 has also been shown to harbour QTL significantly lin- ked to carcass quality, for instance, MacNeil and Grosz (2002) detected a significant QTL for marbling in Here- ford x Composite Double backcross cattle located at 122 cM with a 95% confidence interval from 112–132 cM bet- ween the microsatellite markers IDVGA-2 and FCB11. Grosz and Macneil (2001) using this same population, had earlier reported a significant QTL for birth weight on chromosome 2 located at 114 cM in the interval between BM2113 and OarFCB11 microsatellite markers. In a half- sib family of Brahman x Hereford cattle, Casas et al. (2003) reported the detection of putative QTL for birth weight on bovine chromosomes 1, 2 and 3 Kim et al. (2003) also detected a signify-cant QTL for birth weight on bovine chromosome 2 in a cross-bred population of Angus x Brahman. More recently, Li et al. (2004a) iden- tified and fine-mapped QTL for backfat on bovine chro- mosomes 2, 5, 6, 19, 21 and 23 in a commercial line of Beefbooster cattle. Our detection of significant QTL for birth weight on bovine chromosome 2 in this study is in agreement with these reports.

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Mapping the quantitative trait loci (QTL) for body shape and conformation measurements on BTA1 in Japanese Black cattle

Mapping the quantitative trait loci (QTL) for body shape and conformation measurements on BTA1 in Japanese Black cattle

There were significant differences between families in CHESTGTH measurements, for which families 1 and 2 were had higher results than families 3–5, which was not entirely surprising because sires 1 and 2 had been selected for average daily gain (daily gain line) whereas sires 3–5 belonged to the beef marbling score line. Chest girth is an important body conformation measurement that has been reported in Japanese Black cattle. Mukai et al. (1995) studied the genetic relationships between body measurements, growth and field carcass performance traits and reported highly significant and positive genetic correlations between CHESTGTH and carcass weight at the begin- ning, middle and end of performance testing of 0.64, 0.77 and 0.79, respectively. They concluded that it was possible to improve total merit of the carcass by intro- ducing CHESTGTH into performance testing of Japa- nese Black cattle. Other studies (Oyama et al. 1996; Kitamura et al. 1999) on genetic relationships among

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Teaching Animal Science and Genetics To Australian University Undergraduates To Enhance Inquiry Based Student Learning and Research with Sheep: Growth and Conformation Traits in Crossbred Prime Lambs

Teaching Animal Science and Genetics To Australian University Undergraduates To Enhance Inquiry Based Student Learning and Research with Sheep: Growth and Conformation Traits in Crossbred Prime Lambs

The growth of lambs is influenced by a number of factors such as nutrition, health, genetics sex, litter size, season of lambing, age of dam and year of lamb birth (Kuchtik and Dobes, 2006). To enable producers make informed decisions concerning breed, nutrition and management practices, there is a need for greater exploration of these factors including how they interact and influence growth performance in sheep. One way to achieve rapid growth or increase meat output and heavy market weight is by using terminal sire breeds (Mousa et al., 1999). Consequently, this study compares the growth performance and body conformation of Merino crossbred progeny sired by White Suffolk and Poll Dorset rams which are primarily used as terminal sire breeds for prime lamb production in Australia due to their early maturation and rapid growth (Hinton, 2006). The second objective of this study was to evaluate the effects of sire breed and sex on growth and body conformation traits in crossbred prime lambs and quantify their relationships.

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 Genetic correlations between longevity and conformation traits in the Czech Holstein population

 Genetic correlations between longevity and conformation traits in the Czech Holstein population

ABSTRACT: Genetic correlations between longevity and conformation traits were estimated using data on Czech Holstein cows first calved in the years 1993–2008. Longevity traits considered were length of productive life and number of lactations initiated and their functional equivalents (i.e. the longevity traits corrected for milk production). Conformation traits were twenty one linear descriptive type traits, six com- posite traits and height at sacrum measured in cm. A possible nonlinear relationship between conformation and longevity traits was also investigated. The heritabilities ranged from 0.05 to 0.43 for conformation traits and from 0.03 to 0.05 for longevity traits. Low to moderate genetic relationships between conformation and longevity traits were found. The genetic correlations were higher for functional longevity than for direct longevity traits. Negative genetic correlations with all longevity traits were found for height at the sacrum, stature, dairy form, body conformation, and capacity. Final score showed weak genetic correlation with all analyzed longevity traits. Positive genetic correlations occurred between feet and legs and direct longevity and functional longevity (0.19, 0.14) and between udder and direct longevity (0.10). Body condition score and angularity showed strong genetic correlations with functional longevity (body condition score 0.30, angularity –0.31). Foot and leg traits showed weak genetic correlations with longevity traits except rear legs set (side view) (–0.24) and hock quality (0.19). The udder traits showed inconsistent and rather weak genetic correlations with longevity traits, with the exception of a stronger genetic correlation between rear udder width and functional longevity (–0.22) and between central ligament and number of lactations (–0.18, –0.19). The teat traits showed always negative genetic correlations with longevity traits. The strongest correlations were found for rear teat position (–0.28) and the weakest for teat length (–0.03). Some conformation traits showed markedly stronger genetic correlations with functional longevity than with direct longevity (rear udder width and rear udder height, dairy form, body condition score, angularity, rear legs set (side view), rear legs rear view). A quadratic relationship between conformation and longevity traits did exist. Even if the linear relationship generally prevailed, the quadratic relationship should be taken into account.

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Genetic correlations between type traits of young Polish Holstein Friesian bulls and their daughters

Genetic correlations between type traits of young Polish Holstein Friesian bulls and their daughters

ABSTRACT: The objective of this study was to evaluate the usefulness of young bulls’ conformation scores in a national type evaluation system. For this purpose the genetic correlations between conformation traits of sires and the same type traits of their daughters were estimated. Young bulls were evaluated as required for registration in the herd book and for entering progeny testing. Data were 7 linearly scored (1–9 scale) and 3 descriptive (scored from 50 to 100) conformation traits of 933 young bulls born between 2005 and 2008, and the same traits evaluated in their 65 479 daughters. A two-trait animal model was used to estimate genetic correlations between the type traits of bulls and their daughters. (Co)variance components were estimated by a Bayesian method via Gibbs sampling. Two linear models were used: the linear model for bulls included fixed linear regressions on age at evaluation, fixed effects of herd and classifier, and random additive genetic effect; the linear model for cows contained fixed effects of herd-year-season-classifier, lactation stage, fixed linear regression on age at calving, and random additive genetic effect. Estimates of bulls’ heritabilities for all analyzed traits ranged from 0.07 for feet and legs to 0.25 for body depth. Heritabilities of cows were the lowest for rear legs rear view (0.05) and foot angle (0.06), and the highest for size (0.43). The genetic correlations between similarly described traits of bulls and their daughters were moderate to high (0.42–0.91). The lowest genetic correlation (0.42) was for chest width, and the highest (0.91) for rump angle. The magnitude of genetic correla- tions between pairs of type traits of sires and daughters was high enough to suggest that the body conformation of dairy cows can be improved by making use of some measurements taken from young bulls. Including highly correlated bull scores for size, rump angle, and three linear leg traits in the evaluation system could improve the accuracy of type breeding value evaluation.

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Structure and conformation of photosynthetic pigments and related compounds  Conformation analysis of chlorophyll derivatives

Structure and conformation of photosynthetic pigments and related compounds Conformation analysis of chlorophyll derivatives

The oop distortions give a good pictorial overview of how solvent effects influence the tetrapyrrole’s conformation. However, a complete overview of the 3D configuration in TPPs is not obtained without discussing the in-plane (ip) distortion as well. The largest ip contribution to the TPP structure comes from the bre mode of ip distortion. This mode measures the total compression and stretching in the 24-atom tetrapyrrole ring. The TPP series contains a range of bre NSD values between 0.158 – 0.226 Å and from these values, there does not seem to be a correlation associated with the presence of a solvent in the unit cell. Other smaller contributions in this free base TPP series include m-str and N-str with a range of 0.04 – 0.056 Å in m-str and -0.042 to 0.053 Å in N-str (absolute values given). The smallest contribution seen is given by the rot mode. There is little to no trn(x) and trn(y) distortion in these TPP compounds. Therefore, this analysis proves that the small solvents can influence the macrocycle conformation due to intermolecular interactions resulting in a more planar oop conformation. The D oop range is narrow in the TPPs with either no solvent or a

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Thermodynamic capacity of a protein

Thermodynamic capacity of a protein

the target pattern C upon entering the target basin of attraction (funnel). By analogy with pattern associa- tion, this idea may be generalised to the recognition of multiple patterns. This raises the question of how to train the sequence to recognise more than one confor- mation. For lattice models, Shakhnovich and co-workers [7,8] have explored the folding of sequences designed to minimise a conformation’s absolute and relative energies. The essence of the training technique is to embed the protein into the target conformation and optimise sta- bility over sequence space; the resulting (near-optimal) sequence spontaneous folds to the target. The dilute rep- resentation of conformations by contact patterns suggests that we can superimpose p patterns without saturation [9], providing us with a total pattern to which we train in the usual way. This is essentially equivalent to the method used to select bi-stable 36-mers in [10].

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The synthesis of a pyridine : N  oxide isophthalamide rotaxane utilizing supplementary amide hydrogen bond interactions

The synthesis of a pyridine : N oxide isophthalamide rotaxane utilizing supplementary amide hydrogen bond interactions

was undertaken, quantifying the stability of the pseudo-rotax- ane relative to the individual thread and macrocycle, and attempting to quantify the intermolecular interactions in the pseudo-rotaxane. Once again, the syn – syn conformation (depicted in Fig. 6) was the most stable relative to the individ- ual thread and macrocycle, and the least stable was the anti – anti conformation. The relative behaviour of these two confor- mations was essentially the same as observed for pseudo-rotax- ane 1·5, with the latter being 32 kJ mol −1 higher in energy. However, unlike for pseudo-rotaxane 1·5, the syn – anti confor- mation was similar in energy to the anti–anti conformation, rather than the syn – syn conformation, being 30 kJ mol −1 higher in energy than the syn – syn. Importantly, and perhaps counter-intuitively given that pseudo-rotaxane 2·5 is not experi- mentally observed, a similar binding energy for 2·5 to that of 1·5 was calculated. For 2·5, the zero-point corrected binding energy for the most stable conformation (syn–syn) was found to be around 213 kJ mol −1 , only 10 kJ mol −1 smaller than in the case of 1·5.

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Effects of Branching on Conformation, Crystallization, and Self Assembly of Polymers

Effects of Branching on Conformation, Crystallization, and Self Assembly of Polymers

from dilute (Figure 3.1). With increasing concentration, the excluded volume interactions becomes progressively screened resulting in, from a SAW, to a RW of persistence steps, to RW of main-chain monomers, to RW of side-chains. In the melt, they showed the side-chains do not completely penetrate in accord with the highest concentration regime showing screening of side-chains from the same bottlebrush. Although the concentration dependence of the overall and local length scales follow the same qualitative trend for predictions by Borisov and results by Paturej, they do not agree on the mechanism of interaction for side-chains of neighboring bottlebrushes. Borisov predicts a SAW to RW transition (before side-chain interpenetration) due to impermeability of side-chains whereas Paturej et al. claims the side-chains screen the excluded volume interactions through side-chain penetration. Although the discrepancy seems minor, the net effect on the overall conformation can be severe. If Borisov’s predictions are true, the compression of the side-chains results in a further extension of the main-chain where as the interpenetration predicted by Paturej would result in a softening of the main-chain extension. From lyotropic phase observations, Borisov’s analysis seems more validated, but more experiments are required to say anything conclusive.

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Relationships between longevity and conformation traits in Czech Fleckvieh cows

Relationships between longevity and conformation traits in Czech Fleckvieh cows

The following conformation traits were used: ob- jectively scored linear type (LT) traits were height at sacrum, muscularity, rump length, rump width, rump angle, body depth, rear legs side view, hock, pastern, hoof angle, fore udder length, rear udder attachment, central ligament, udder depth, front teat placement, teat length, and teat width. The traits were scored on a nine-point scale. The body measurements (BM) in cm were height at withers, height at sacrum, chest girth, body depth, rump length, rump width. The aggregated traits (AT) scored in the interval between 50 and 100 points were dairy character, muscularity, feet and legs, udder.

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A folded conformation of an ascidiacycl­amide derivative: 3 meth­oxy­sulfoxide (2R,3R) threoninyl desoxazoline ascidiacycl­amide

A folded conformation of an ascidiacycl­amide derivative: 3 meth­oxy­sulfoxide (2R,3R) threoninyl desoxazoline ascidiacycl­amide

Ascidiacyclamide (ASC), (3), is a symmetric cyclic peptide containing unusual amino acids, such as oxazoline (Oxz) and thiazole (Thz) (Hamamoto et al., 1983). Two major confor- mations and their conformational equilibrium have been suggested for ASC (Ishida et al., 1988; In et al., 1993). In our series of studies, the relationships between ASC conformation and symmetry of the chemical structure have been examined; additionally, we have studied the asymmetric modi®cations which disturb the C 2 symmetry of ASC and how this affects

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Enhancer variants: evaluating functions in common disease

Enhancer variants: evaluating functions in common disease

To identity enhancer targets, DNA fluorescence in situ hybridization (FISH) [59,60], as well as chromatin associ- ation methods (chromosome conformation capture (3C)) [61], can be employed. These are powerful approaches for evaluating whether a region of interest interacts with a specific genomic target, but they suffer from the limitation that the regions of interest must be pre-specified, that is, they are ‘one-by-one’ approaches. 4C (circular chromo- some conformation capture), an extension of 3C, can cap- ture all regions that physically contact a site of interest, without prior knowledge of the regions that contact that site being necessary [62] (that is, a ‘one-to-all’ approach). Higher-throughput methods include carbon-copy chro- mosome conformation capture (5C, many-to-many), a high-throughput expansion of 3C, Hi-C (all-to-all) and chromatin interaction analysis by paired-end tag se- quencing (ChIA-PET) (for detailed comparison of these methods, see reviews [63,64]). These global approaches can enable the identification of loci that directly and indir- ectly contact enhancers of interest, and can reveal com- plex interactions in which dozens to hundreds of loci aggregate, so-called transcriptional hubs or enhanceo- somes [65]. These types of high-order interactions have been recently described by several studies [55,56,58]. The extent by which they overlap risk loci remains unexplored. Unfortunately, these approaches tend to be expensive and difficult for most labs to execute, and their resolution often prohibits their use for interrogating GWAS loci. Until recently, for example, the resolution of Hi-C was limited to capturing interactions separated by more than one megabase; 5 to 10 times greater than the distance by which most enhancer-gene interactions occur. Despite the limitations, ‘C’-based methods have been implemented to successfully identify targets of enhancer-risk variants and to quantify their functional effects. For example, Cowper- Sal lari and colleagues utilized 3C and allele-specific ex- pression to demonstrate the impact of the breast cancer risk SNP rs4784227 on expression of TOX3, thought to have a role in chromatin regulation [38]. Bauer and co- workers utilized 3C to identify BCL11A as the gene target of an erythroid enhancer, and then further demonstrated the impact of enhancer variants on transcription factor binding and expression. Gene editing strategies have also been employed to demonstrate that this enhancer is essen- tial for erythroid gene expression [28]. Finally, we highlight

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3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering

3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering

between genomic conformation and function. However, some challenges have been encountered in this process, indicating that resolution can be affected by many factors [120]. The most important limiting factor is the selection of the first restriction enzyme, which determines the max- imum resolution of 3C experiments because contacts be- tween DNA fragments can be detected only at restriction enzyme cut sites. If two restriction enzymes, four-cutter and six-cutter, are compared, the former will yield a 16- fold higher resolution library (256 bp vs. 4096 bp) in humans. However, we should also take into account that the distribution of restriction sites is not uniform in the genome, resulting in different resolutions at different gen- omic regions. A further increase in resolution can be achieved by substituting restriction enzymes with MNase [118] or DNase I [102], which can cut at any site along the genome and can theoretically generate single base pair resolution. After the restriction enzyme to be used in the 3C experiment is chosen, the resolution of the contact maps is further affected by sequencing depth. When it is insufficient to explore contacts at the level of individual restriction fragments, the resolution will be determined by an appropriate bin size. In addition, research on the 3D conformation of repeat regions in the genome is difficult and is mainly because sequence information in this region is often incomplete, and thus sequencing-based 3C methods cannot effectively handle data mapping in this area. Another experimental factor that may impact the output of 3C study is the bias caused potentially by the crosslinking agent. Because crosslinking treatment in- appropriately will crosslink the fibers, which are in close physical proximity rather than directly interacting [121]. Therefore, the consideration that to isolate native nuclei in an isotonic buffer to retain the native chromosome loops will properly present the native chromosome con- formation [121, 122]. Moreover, comparative study of 3C- type experiments with FISH indicated that 3C-type experi- ments or FISH alone must be interpreted with caution when studying chromatin architecture [39], thus cross- validation of Hi-C with FISH [123] or visible data achieved with super-resolution microscope [10, 124] still need to be considered. Resemble the concept of native chromosome loops, that joint assays will present crucial information for fully understanding chromatin organization.

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