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21.
Background
A haplotype approach to genomic prediction using high density data in dairy cattle as an alternative to single-marker methods is presented. With the assumption that haplotypes are in stronger linkage disequilibrium (LD) with quantitative trait loci (QTL) than single markers, this study focuses on the use of haplotype blocks (haploblocks) as explanatory variables for genomic prediction. Haploblocks were built based on the LD between markers, which allowed variable reduction. The haploblocks were then used to predict three economically important traits (milk protein, fertility and mastitis) in the Nordic Holstein population.Results
The haploblock approach improved prediction accuracy compared with the commonly used individual single nucleotide polymorphism (SNP) approach. Furthermore, using an average LD threshold to define the haploblocks (LD≥0.45 between any two markers) increased the prediction accuracies for all three traits, although the improvement was most significant for milk protein (up to 3.1 % improvement in prediction accuracy, compared with the individual SNP approach). Hotelling’s t-tests were performed, confirming the improvement in prediction accuracy for milk protein. Because the phenotypic values were in the form of de-regressed proofs, the improved accuracy for milk protein may be due to higher reliability of the data for this trait compared with the reliability of the mastitis and fertility data. Comparisons between best linear unbiased prediction (BLUP) and Bayesian mixture models also indicated that the Bayesian model produced the most accurate predictions in every scenario for the milk protein trait, and in some scenarios for fertility.Conclusions
The haploblock approach to genomic prediction is a promising method for genomic selection in animal breeding. Building haploblocks based on LD reduced the number of variables without the loss of information. This method may play an important role in the future genomic prediction involving while genome sequences. 相似文献22.
Y Deng J Zhao D Sakurai KM Kaufman JC Edberg RP Kimberly DL Kamen GS Gilkeson CO Jacob RH Scofield CD Langefeld JA Kelly ME Alarcón-Riquelme BIOLUPUS GENLES Networks JB Harley TJ Vyse BI Freedman PM Gaffney KM Sivils JA James TB Niewold RM Cantor W Chen BH Hahn EE Brown PROFILE BP Tsao 《Arthritis research & therapy》2012,14(Z3):A5
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Cloning and sequencing of a cluster of genes encoding branched-chain alpha-keto acid dehydrogenase from Streptomyces avermitilis and the production of a functional E1 [alpha beta] component in Escherichia coli. 总被引:2,自引:2,他引:0
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A cluster of genes encoding the E1 alpha, E1 beta, and E2 subunits of branched-chain alpha-keto acid dehydrogenase (BCDH) of Streptomyces avermitilis has been cloned and sequenced. Open reading frame 1 (ORF1) (E1 alpha), 1,146 nucleotides long, would encode a polypeptide of 40,969 Da (381 amino acids). ORF2 (E1 beta), 1,005 nucleotides long, would encode a polypeptide of 35,577 Da (334 amino acids). The intergenic distance between ORF1 and ORF2 is 73 bp. The putative ATG start codon of the incomplete ORF3 (E2) overlaps the stop codon of ORF2. Computer-aided searches showed that the deduced products of ORF1 and ORF2 resembled the corresponding E1 subunit (alpha or beta) of several prokaryotic and eukaryotic BCDH complexes. When these ORFs were overexpressed in Escherichia coli, proteins of about 41 and 34 kDa, which are the approximate masses of the predicted S. avermitilis ORF1 and ORF2 products, respectively, were detected. In addition, specific E1 [alpha beta] BCDH activity was detected in E. coli cells carrying the S. avermitilis ORF1 (E1 alpha) and ORF2 (E1 beta) coexpressed under the control of the T7 promoter. 相似文献
26.
Stirrett K Denoya C Westpheling J 《Journal of industrial microbiology & biotechnology》2009,36(1):129-137
Polyketide antibiotics are among the most important therapeutics used in human and animal health care. Type II polyketides
are composed primarily of acetate-derived thioesters, and the subunits for the PKS are contained in a single module that includes
a ketosynthase, acyl carrier protein, chain-length factor and sometimes a keto-reductase, aromatase, cyclase and modifying
enzymes, such as glycosylases or hydroxylases. While the enzyme complexes that make up the PKS have been the focus of intense
study (Khosla in Chem Rev 7:2577–2590, 1997), the pathways for precursor synthesis have not been established and predictions
are complicated by the fact that acetate may be derived from a number of metabolic pathways. Here we show that 50% of the
acetate for synthesis of the Type II polyketide, actinorhodin, in Streptomyces coelicolor, is derived from the catabolism of the branched amino acids by pathways that are nutrient dependent. The streptomycetes are
apparently unique in that they contain two BCDH gene clusters, each of which is potentially capable of converting leucine,
valine and isoleucine to the corresponding thioesters, and contain at least three different pathways for valine catabolism
that are differentially used in response to nutrient availability. 相似文献
27.
Mono- and dimethylating activities and kinetic studies of the ermC 23 S rRNA methyltransferase 总被引:6,自引:0,他引:6
The ermC 23 S rRNA methyltransferase converts a single adenine residue to N6,N6-dimethyladenine, both in vivo and in vitro. The ermC methyltransferase was demonstrated to produce both N6-mono and N6,N6-dimethylated adenine residues in Bacillus subtilis 23 S rRNA during the course of the reaction in vitro. An almost total conversion of monomethylated intermediates into dimethylated products was observed upon completion of the reaction. Data presented here demonstrate that the addition of the two methyl groups to each 23 S rRNA molecule takes place through a monomethylated intermediate and suggest that the enzyme dissociates from its RNA substrate between the two consecutive methylation reactions. The enzyme is able to utilize monomethylated RNA as substrate for the addition of a second methyl group with an efficiency approximately comparable to that obtained when unmethylated RNA was the initial substrate. Initial-rate data and inhibition studies suggest that the ermC methylase reaction involves a sequential mechanism occurring by two consecutive Random Bi Bi reactions. 相似文献
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Mário C BarrosoJúnior Guilherme P Esteves Thiago P Nunes Lucia MG Silva Alvaro CD Faria Pedro L Melo 《Biomedical engineering online》2011,10(1):14
Introduction
A novel system that combines a compact mobile instrument and Internet communications is presented in this paper for remote evaluation of tremors. The system presents a high potential application in Parkinson's disease and connects to the Internet through a TCP/IP protocol. Tremor transduction is carried out by accelerometers, and the data processing, presentation and storage were obtained by a virtual instrument. The system supplies the peak frequency (fp), the amplitude (Afp) and power in this frequency (Pfp), the total power (Ptot), and the power in low (1-4 Hz) and high (4-7 Hz) frequencies (Plf and Phf, respectively). 相似文献29.
Saman Bowatte Paul CD Newton Shona Brock Phil Theobald Dongwen Luo 《The ISME journal》2015,9(1):265-267
Nitrous oxide (N2O) emissions from grazed pastures are a product of microbial transformations of nitrogen and the prevailing view is that these only occur in the soil. Here we show this is not the case. We have found ammonia-oxidising bacteria (AOB) are present on plant leaves where they produce N2O just as in soil. AOB (Nitrosospira sp. predominantly) on the pasture grass Lolium perenne converted 0.02–0.42% (mean 0.12%) of the oxidised ammonia to N2O. As we have found AOB to be ubiquitous on grasses sampled from urine patches, we propose a ‘plant'' source of N2O may be a feature of grazed grassland.In terms of climate forcing, nitrous oxide (N2O) is the third most important greenhouse gas (Blunden and Arndt, 2013). Agriculture is the largest source of anthropogenic N2O (Reay et al., 2012) with about 20% of agricultural emissions coming from grassland grazed by animals (Oenema et al., 2005).Grazed grassland is a major source of N2O because grazers harvest nitrogen (N) from plants across a wide area but recycle it back onto the pasture, largely as urine, in patches of very high N concentration. The N in urine patches is often in excess of what can be used by plants resulting in losses through leaching as nitrate, as N2O and through volatilisation as ammonia (NH3) creating a high NH3 environment in the soil and plant canopy; an important point that we will return to later. The established wisdom is that N2O is generated exclusively by soil-based microbes such as ammonia-oxidising bacteria (AOB). This soil biology is represented in models designed to simulate N2O emissions and the soil is a target for mitigation strategies such as the use of nitrification inhibitors.We have previously shown that pasture plants can emit N2O largely through acting as a conduit for emissions generated in the soil, which are themselves controlled to some degree by the plant (Bowatte et al., 2014). In this case the origin of the emission is still the soil microbes. However, AOB have been found on the leaves of plants, for example, Norway spruce (Papen et al., 2002; Teuber et al., 2007) and weeds in rice paddies (Bowatte et al., 2006), prompting us to ask whether AOB might be present on the leaves of pasture species and contribute to N2O emissions as they do in soil.We looked for AOB on plants in situations where NH3 concentrations were likely to be high, choosing plants from urine patches in grazed pastures and plants from pastures surrounding a urea fertiliser manufacturing plant. DNA was extracted from the leaves (including both the surface and apoplast) and the presence of AOB tested using PCR. AOB were present in all the species we examined—the grasses Lolium perenne, Dactylis glomerata, Anthoxanthum odoratum, Poa pratensis, Bromus wildenowii and legumes Trifolium repens and T. subterraneum.To measure whether leaf AOB produce N2O, we used intact plants of ryegrass (L. perenne) lifted as cores from a paddock that had been recently grazed by adult sheep. The cores were installed in a chamber system designed to allow sampling of above- and belowground environments separately (Bowatte et al., 2014). N2O emissions were measured from untreated (control) plants and from plants where NH3 was added to the aboveground chamber and leaves were either untreated or sterilised by wiping twice with paper towels soaked in 1% hypoclorite (Sturz et al., 1997) and then with sterile water. We tested for the presence and abundance of AOB on the leaves by extracting DNA and using PCR and real-time PCR targeting the ammonia monoxygenase A (amoA) gene, which is characteristic of AOB. AOB identity was established using cloning and DNA sequencing. Further details of these experiments can be found in the Supplementary Information.The addition of NH3 to untreated plants significantly stimulated N2O emissions (P<0.001) compared with the controls; by contrast, the plants with sterilised leaves produced significantly less N2O than controls (P<0.001) even with NH3 added (Figure 1) providing strong evidence for emissions being associated with bacteria on the leaves. Control plants did emit N2O suggesting there was either sufficient NH3 available for bacterially generated emissions and/or other plant-based mechanisms were involved (Bowatte et al., 2014).Open in a separate windowFigure 1Effect of an elevated NH3 atmosphere and surface sterilisation of leaves on leaf N2O emissions measured over 1-h periods on three occasions during the day. Values are means (s.e.m.), where n=7.The major AOB species identified was Nitrosospira strain III7 that has been previously shown to produce N2O (Jiang and Bakken, 1999). We measured 109 AOB cells per m2 ryegrass leaf, assuming a specific leaf area of 250 cm2 g−1 leaf.The rate of production of N2O (0.1–0.17 mg N2O-N per m2 leaf area per hour) can be translated to a field situation using the leaf area index (LAI)—1 m2 leaf per m2 ground would be an LAI of 1. LAI in a pasture can vary from <1 to >6 depending on the management (for example, Orr et al., 1988). At LAI of 1, the AOB leaf emission rate would equate to a N2O emission rate of about 0.1–0.3 mg N2O-N per m2 ground per hour. By comparison, the emission rates measured after dairy cattle urine (650 kg N ha−1) was applied to freely and poorly drained soil were 0.024–1.55 and 0.048–3.33 mg N2O-N per m2 ground per hour, respectively (Li and Kelliher, 2005).The fraction of the NH3 that was converted to N2O by the leaf AOB was 0.02–0.42% (mean 0.12%). The mean value is close to that measured for Nitrosospira strains including strain III7 isolated from acidic, loamy and sandy soils where values ranged from 0.07 to 0.10% (Jiang and Bakken, 1999). This is good evidence that the AOB on leaves have the capacity to produce N2O at the same rate as AOB in soils. We do not suggest that leaf AOB will produce as much N2O as soil microbes; however, because leaf AOB have access to a source of substrate—volatilised NH3—that is unavailable to soil microbes and may constitute 26% (Laubach et al., 2013) to 40% (Carran et al., 1982) of the N deposited in the urine, N2O emissions from these aboveground AOB are additional to soil emissions. Further research is required to identify the situations in which leaf AOB contribute to total emissions and to quantify this contribution. 相似文献
30.
Kumaran Kandasamy Sujatha S Mohan Rajesh Raju Shivakumar Keerthikumar Ghantasala S Sameer Kumar Abhilash K Venugopal Deepthi Telikicherla Daniel J Navarro Suresh Mathivanan Christian Pecquet Sashi Kanth Gollapudi Sudhir Gopal Tattikota Shyam Mohan Hariprasad Padhukasahasram Yashwanth Subbannayya Renu Goel Harrys KC Jacob Jun Zhong Raja Sekhar Vishalakshi Nanjappa Lavanya Balakrishnan Roopashree Subbaiah YL Ramachandra Abdul B Rahiman Keshava TS Prasad Jian-Xin Lin Jon CD Houtman Stephen Desiderio Jean-Christophe Renauld Stefan N Constantinescu Osamu Ohara Toshio Hirano Masato Kubo Sujay Singh Purvesh Khatri Sorin Draghici Gary D Bader Chris Sander Warren J Leonard Akhilesh Pandey 《Genome biology》2010,11(1):1-9