Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform     

Robin A Atherton  Bennet J McComish  Lara D Shepherd  Lorraine A Berry  Nick W Albert  Peter J Lockhart 《Plant methods》2010,6(1):22

Background  

Complete chloroplast genome sequences provide a valuable source of molecular markers for studies in molecular ecology and evolution of plants. To obtain complete genome sequences, recent studies have made use of the polymerase chain reaction to amplify overlapping fragments from conserved gene loci. However, this approach is time consuming and can be more difficult to implement where gene organisation differs among plants. An alternative approach is to first isolate chloroplasts and then use the capacity of high-throughput sequencing to obtain complete genome sequences. We report our findings from studies of the latter approach, which used a simple chloroplast isolation procedure, multiply-primed rolling circle amplification of chloroplast DNA, Illumina Genome Analyzer II sequencing, and de novo assembly of paired-end sequence reads.  相似文献   

Identifying and measuring agrarian sentiment in regional Australia     

Helen Louise Berry  Linda Courtenay Botterill  Geoff Cockfield  Ning Ding 《Agriculture and Human Values》2016,33(4):929-941

In common with much of the Western world, agrarianism—valuing farmers and agricultural activity as intrinsically worthwhile, noble, and contributing to the strength of the national character—runs through Australian culture and politics. Agrarian sentiments and attitudes have been identified through empirical research and by inference from analysis of political debate, policy content, and studies of media and popular culture. Empirical studies have, however, been largely confined to the US, with little in the way of recent re-evaluations of, or developments from, early work. This paper reports on research that seeks quantitative empirical evidence for the existence of agrarianism in the Australian community and seeks to identify its core characteristics. Using a purpose-designed sub-set of items within a large, omnibus-style survey of regional and rural Australia, we demonstrate that agrarianism exists as a scientifically quantifiable concept identifiable through responses to four key propositions: that Australians should support policies aimed at improving the position of the agricultural industries; that working in agriculture and associated industries brings out the best in people; that agricultural producers make a major contribution to environmental protection and biodiversity conservation; and that the development of agriculture in Australia contributed to the development of the national character. We found very little variation in the degree to which different demographic groupings agree with agrarianism. Older people, farmers, and non-Indigenous Australian-born respondents were among those who were statistically significantly more likely to agree with the defining propositions of agrarianism, but their scores were only very slightly higher than those of other sub-populations in the sample.  相似文献   

Response of Thawed Epidi dymal Red Deer Spermatozoa to Increasing Concentrations of Hydrogen Peroxide,and Importance of Individual Male Variability     

AE Domínguez‐Rebolledo  F Martínez‐Pastor  AF Bisbal  JL Ros‐Santaella  O García‐Álvarez  A Maroto‐Morales  AJ Soler  JJ Garde  MR Fernández‐Santos 《Reproduction in domestic animals》2011,46(3):393-403

Oxidative stress represents a challenge during sperm manipulation. We have tested the effect of increasing hydrogen peroxide (H₂O₂) levels on red deer spermatozoa after cryopreservation, and the role of male‐to‐male variation in that response. In a first experiment, eight thawed samples were submitted to 0, 25, 50, 100 and 200 μm H₂O₂ for 2 h at 37°C. Intracellular reactive oxygen species (H₂DCFDA‐CM) increased with H₂O₂ concentration, but we only detected a decrease in sperm function (motility by CASA and chromatin damage by sperm chromatin structure assay) with 200 μm . Lipoperoxidation assessed by the thiobarbituric acid reactive substance (TBARS) method increased slightly with 50 μm H₂O₂ and above. In a second experiment, samples from seven males were submitted to 0 and 200 μm H₂O₂ for 2 h, triplicating the experiment within each male. Males differed at thawing and regarding their response to incubation and H₂O₂ presence. We found that the kinematic parameters reflected male‐to‐male variability, whereas the response of the different males was similar for lipid peroxidation and viability. A multiparametric analysis showed that males grouped differently if samples were assessed after thawing, after incubation without H₂O₂ or after incubation with H₂O₂. Red deer spermatozoa are relatively resilient to H₂O₂ after thawing, but it seems to be a great male‐to‐male variability regarding the response to oxidative stress. The acknowledgement of this individual variability might improve the development of optimized sperm work protocols.  相似文献   

Intra- and interobserver variability of board-certified veterinary radiologists and veterinary general practitioners for pulmonary nodule detection in standard and inverted display mode images of digital thoracic radiographs of dogs     

Reese DJ  Green EM  Zekas LJ  Flores JE  Hill LN  Winter MD  Berry CR  Ackerman N 《Journal of the American Veterinary Medical Association》2011,238(8):998-1003

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Genetic associations between feed efficiency measured in a performance test station and performance of growing cattle in commercial beef herds     

Crowley JJ  Evans RD  Mc Hugh N  Pabiou T  Kenny DA  McGee M  Crews DH  Berry DP 《Journal of animal science》2011,89(11):3382-3393

Interest in selection for improved feed efficiency is increasing, but before any steps are taken toward selecting for feed efficiency, correlations with other economically important traits must first be quantified. The objective of this study was to quantify the genetic associations between feed efficiency measured during performance testing and linear type traits, BW, live animal value, and carcass traits recorded in commercial herds. Feed efficiency data were available on 2,605 bulls from 1 performance test station. There were between 10,384 and 93,442 performance records on type traits, BW, animal value, or carcass traits from 17,225 commercial herds. (Co)variance components were estimated using linear mixed animal models. Genetic correlations between the muscular type traits in commercial animals and feed conversion ratio (-0.33 to -0.25), residual feed intake (RFI; -0.33 to -0.22), and residual BW gain (RG; 0.24 to 0.27) suggest that selection for improved feed efficiency should increase muscling. This is further evidenced by the genetic correlations between carcass conformation of commercial animals and feed conversion ratio (-0.46), RFI (-0.37), and residual BW gain (0.35) measured in performance-tested animals. Furthermore, the genetic correlations between RFI and both ultrasonic fat depth and carcass fat score (0.39 and 0.33, respectively) indicated that selection for improved RFI will result in leaner animals. It can be concluded from the genetic correlations estimated in this study that selection for feed efficiency will have no unfavorable effects on the performance traits measured in this study and will actually lead to an improvement in performance for some traits, such as muscularity, animal price, and carcass conformation. Conversely, this suggests that genetic selection for traits such as carcass quality, muscling traits, and animal value might also be indirectly selecting for more efficient animals.  相似文献   

Evaluation of a breast support conveyor to improve poultry welfare on the shackle line     

Lines JA  Jones TA  Berry PS  Cook P  Spence J  Schofield CP 《The Veterinary record》2011,168(5):129

A breast support conveyor has the potential to improve bird welfare by avoiding the need to invert and suspend broilers by their legs as they move from the point of shackling to entry into the electric waterbath. To evaluate its effect on welfare under commercial conditions, a breast support conveyor was installed under the conventional shackle line of a small poultry processing plant. A structured assessment of the behaviour of the birds indicated a significant decrease in struggling and wing flapping at the point of shackling, on the straight conveyor and at entry into the waterbath. This resulted in a lower prevalence of red wing tips and bruising in the first wing joint. The shackle line and conveyor in this installation, however, passed around a 90° corner, which appeared to cause more disturbance to the birds on the conveyor than to comparable birds suspended from shackles in the traditional manner. The results indicate that a breast support conveyor has the potential to improve bird welfare on straight shackle lines and that, because struggling activity and duration following shackling are reduced, the time between shackling and stunning could also be reduced using this method, further improving bird welfare. Breast support conveyors should not be used when the shackle lines have sharp bends.  相似文献   

Genetics of animal health and disease in cattle     

Berry DP  Bermingham ML  Good M  More SJ 《Irish veterinary journal》2011,64(1):5-10

There have been considerable recent advancements in animal breeding and genetics relevant to disease control in cattle, which can now be utilised as part of an overall programme for improved cattle health. This review summarises the contribution of genetic makeup to differences in resistance to many diseases affecting cattle. Significant genetic variation in susceptibility to disease does exist among cattle suggesting that genetic selection for improved resistance to disease will be fruitful. Deficiencies in accurately recorded data on individual animal susceptibility to disease are, however, currently hindering the inclusion of health and disease resistance traits in national breeding goals. Developments in 'omics' technologies, such as genomic selection, may help overcome some of the limitations of traditional breeding programmes and will be especially beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors in adulthood. However, access to large databases of phenotypes on health and disease will still be necessary. This review clearly shows that genetics make a significant contribution to the overall health and resistance to disease in cattle. Therefore, breeding programmes for improved animal health and disease resistance should be seen as an integral part of any overall national disease control strategy.  相似文献   

Management of bovine tuberculosis in Michigan wildlife: current status and near term prospects     

O'Brien DJ  Schmitt SM  Fitzgerald SD  Berry DE 《Veterinary microbiology》2011,151(1-2):179-187

Surveillance and control activities for bovine tuberculosis (bTB) in free-ranging Michigan white-tailed deer (Odocoileus virginianus) have now been underway for over a decade. Significant progress has been made, lowering apparent prevalence in deer in the core area by >60%, primarily via reduction of deer densities through hunting, and restrictions on public feeding and baiting of deer. These broad strategies of the Michigan Department of Natural Resources (MDNR), implemented with the cooperation of Michigan deer hunters, halved the deer population in the bTB endemic area. However, as hunters see fewer deer, their willingness to sustain aggressive harvests has waned, and public resentment of control measures has grown. During the past four years, apparent prevalence in core area deer has held approximately steady just below 2%. After bottoming out in 2004 at an estimated 10-12 deer/km(2), deer numbers have since rebounded by ～ 30%. Public compliance with baiting and feeding restrictions has been variable. In general, hunters in the core area do not perceive bTB as a problem, in spite of 13 years of MDNR outreach. To date, MDNR has expended more than US$23 million on TB-related activities. Of late, a substantial portion of that funding has been diverted to support other programs which have suffered from budget shortfalls. Livestock herd breakdowns continue to occur sporadically, averaging 3-4 per year 2005 to present. In total, 46 cattle and 4 captive deer herds have been diagnosed bTB positive statewide, the majority yielding only 1 positive animal. Five cattle herds were twice infected, one thrice. Michigan Department of Agriculture (MDA) policy emphasis has shifted towards obtaining producer support for wildlife risk mitigation and farm biosecurity. Funding has proven a limiting factor, with the majority of the US$63 million spent to date devoted to whole herd testing. Nevertheless, some initiatives justify cautious optimism. Promising research to support eventual vaccination of wild deer continues. Some hunters and landowners have begun to recognize the costs of high deer densities and supplemental feeding. A peninsula-wide ban on baiting and feeding was enacted. Some cattle producers, recognizing their precarious circumstances, have begun work to change long-held prevailing opinions among their peers about farm biosecurity. Yet formidable challenges remain, and evidence suggests that eradication of bTB, if it can be achieved, will take decades, and will require greater public and political resolve than has been demonstrated thus far.  相似文献   

Computed tomographic findings,surgical management and postoperative outcomes of large intermuscular lipomas in the hindlimb of 11 dogs     

JD Crowley  G Hosgood  NV Crawford  JL Richardson 《Australian veterinary journal》2020,98(4):135-139

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Reproductive success of rose‐ringed parakeets Psittacula krameri in a captive UK population     

Mark S Lambert  Giovanna Massei  Jennifer Bell  Leslie Berry  Carol Haigh  David P Cowan 《Pest management science》2009,65(11):1215-1218

BACKGROUND: Rose‐ringed parakeets Psittacula krameri (Scop.) have recently become established in several European countries, with potential for significant negative economic and ecological impacts. However, in northern Europe the potential for reproductive output is largely unknown. In 2005 the authors established a captive outdoor colony in north‐east England and examined breeding success over 2 years. RESULTS: In 2006 (19 pairs, 15 clutches) the average first clutch size was 3.6 (±0.3) eggs. Six clutches were infertile, and overall the colony produced 1.4 (±0.5) fertile eggs per pair. Eleven pairs produced a second clutch following removal of the first; seven were infertile, and overall productivity was 0.7 (±0.4) fertile eggs per pair. Unsuccessful pairs were rearranged or replaced. In 2007, overall productivity was 2.5 (±0.4) and 1.8 (±0.4) fertile eggs per pair for the first and second attempts respectively. For pairs that remained unchanged through 2006–2007, productivity was consistent between years and breeding attempts. CONCLUSION: Where food and nest sites were not limiting, clutch sizes in north‐east England were similar to those in the native range, and consistent between first and second attempts. This has implications for the future expansion and management of the species. © Crown Copyright 2009. Reproduced with permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.  相似文献