Phylogenomics and molecular evolution of foot-and-mouth disease virus

This report describes the use of Bayesian methods to analyze polyprotein coding region sequences (n = 217) obtained from GenBank to define the genome-wide phylogeny of foot and mouth disease virus (FMDV). The results strongly supported the monophyly of five FMDV serotypes, O, A, Asia 1, C, and SAT 3, while sequences for the two remaining FMDV serotypes, SAT 1 and SAT 2 did not separate into entirely distinct clades. The phylogenomic tree revealed three sister-group relationships, serotype O + Asia 1, A + C, and SAT 1 + 3 + 2, with a new branching pattern: {[(O, Asia 1), (A, C)], (SAT 1, 2, 3)}. Within each serotype, there was no apparent periodic, geographic, or host species influence on the evolution of global FMDVs. Analysis of the polyprotein coding region of these sequences provided evidence for the influence of purifying selection on the evolution of FMDV. Using a Bayesian coalescent approach, the evolutionary rate of FMDV isolates that circulated during the years 1932-2007 was estimated to be 1.46 × 10(-3) substitutions/site/year, and the most recent common ancestor of the virus existed approximately 481 years ago. Bayesian skyline plot revealed a population expansion in the early 20(th) century that was followed by a rapid decline in population size from the late 20(th) century to the present day. These findings provide new insights into the mechanisms that impact on the evolution of this important livestock pathogen.     

畜禽钙磷和微量元素营养研究进展

矿物元素在畜禽生长发育、新陈代谢、神经活动、免疫功能、内分泌等几乎所有的生命活动过程中都发挥着重要的生理作用,分为钙、磷、钠、镁等常量元素和铁、锰、钴、铜等微量元素。某种矿物元素摄入不足或在体内过量蓄积、矿物元素间比例失调,都将引起严重后果。随着畜禽养殖业的集约化规模化发展,饲用矿物元素用量迅速增加,但存在不合理使用的情况,造成了资源浪费和环境污染。因此,在满足畜禽营养需要量的前提下,合理地使用矿物元素剂型及剂量,实现降低矿物元素经畜禽粪污向环境中的排放量,不仅利于集约化畜禽养殖业的发展,同时也能有效降低畜禽粪污中的重金属含量,为种植业提供优良的有机肥来源,维护生态系统的平衡,促进种植业和养殖业的可持续健康发展。基于此,以畜禽体内含量最高的常量元素钙磷和微量元素为切入点,介绍了饲用矿物元素的应用现状、畜禽矿物元素基础需要量及合适的添加范围,着重综述了新型饲用微量元素的开发与应用进展,并探讨了矿物元素动态饲喂模式的可行性及有效性,以期为合理利用矿物元素资源及进一步解决全球生态农业研究的畜禽矿物元素导致的环境污染提供参考。     

Biosensors in the livestock industry: an automated ovulation prediction system for dairy cows

Biosensor technology can offer the livestock industry new types of monitoring and measuring devices of which the specificity, sensitivity, reproducibility, speed and ease of use exceed the current technology. Biosensors can be applied to the detection and identification of infectious diseases in livestock, contaminants and toxins in feed, therapeutic drug residues in animal husbandry and oestrus detection. Our team is applying biosensor technology to the livestock industry by developing a fully automated ovulation prediction system for dairy cows. The results from field-tests show that the progesterone biosensor can characterize the ovulation cycles of cows and detect pregnancy.     

The development of China's medical biotech industry needs to be driven by innovation

The Chinese biotech industry is going through a period of fast growth, and with its huge population, China is predicted to be the biggest single-country market in the world. However, the Chinese biotech industry has to tackle the critical issue of innovation, which should be the driving force for China's development into an advanced and responsible country. Here, in this article, the authors review the history of the Chinese biotech industry, exemplified by the development of genetically engineered drugs during the last 20 years, and also point out its the future.     

Review: Use of human-edible animal feeds by ruminant livestock

The drive to increase the output of animal product in some sectors of ruminant livestock production has led to greater use of feeds such as cereal grains and soyabean meal that are potentially human-edible. This trend has caused concern since, by so doing, ruminants compete not only with monogastric livestock but also with the human population for a limited global area of cultivatable land on which to produce grain crops. Reasons for using potentially human-edible feeds in ruminant diets include increased total daily energy intake, greater supply of essential amino acids and improved ruminal balance between fermentable energy and degradable protein. Soyabean meal, produced on land that has been in arable cultivation for many years can fulfil a useful role as a supplier of undegraded dietary protein in diets for high-yielding dairy cows. However, in the context of sustaining the production of high-quality foods from livestock to meet the demands of a growing human population, the use of potentially human-edible feed resources by livestock should be restricted to livestock with the highest daily nutrient requirements; that is, potentially human-edible feed inputs should be constrained to meeting requirements for energy and protein and to rectifying imbalances in nutrient supply from pastures and forage crops such as high concentrations of nitrogen (N). There is therefore a role for human-edible feeds in milk production because forage-only systems are associated with relatively low output per head and also low N use efficiency compared with systems with greater reliance on human-edible feeds. Profitability on farm is driven by control of input costs as well as product value and examples are given of low-cost bovine milk and meat production with little or no reliance on potentially human-edible feeds. In beef production, the forage-only systems currently under detailed real-time life-cycle analysis at the North Wyke Farm Platform, can sustain high levels of animal growth at low feed cost. The potential of all-forage diets should be demonstrated for a wide range of ruminant milk and meat production systems. The challenge for the future development of ruminant systems is to ensure that potentially human-edible feeds, or preferably human-inedible by-products if available locally, are used to complement pastures and forage crops strategically rather than replace them.     

The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks,effects of interventions and the way forward

The purpose of this review was to provide an updated overview on the use of antimicrobial agents in livestock, the associated problems for humans and current knowledge on the effects of reducing resistance in the livestock reservoir on both human health and animal production. There is still limiting data on both use of antimicrobial agents, occurrence and spread of resistance as well as impact on human health. However, in recent years, emerging issues related to methicillin-resistant Staphylococcus aureus, Clostridium difficile, Escherichia coli and horizontally transferred genes indicates that the livestock reservoir has a more significant impact on human health than was estimated 10 years ago, where the focus was mainly on resistance in Campylobacter and Salmonella. Studies have indicated that there might only be a marginal if any benefit from the regular use of antibiotics and have shown that it is possible to substantially reduce the use of antimicrobial agents in livestock production without compromising animal welfare or health or production. In some cases, this should be done in combination with other measures such as biosecurity and use of vaccines. To enable better studies on both the global burden and the effect of interventions, there is a need for global harmonized integrated and continuous surveillance of antimicrobial usage and antimicrobial resistance, preferably associated with data on production and animal diseases to determine the positive and negative impact of reducing antimicrobial use in livestock.     

Effects of Remedial Sport Hunting on Cougar Complaints and Livestock Depredations

Remedial sport hunting of predators is often used to reduce predator populations and associated complaints and livestock depredations. We assessed the effects of remedial sport hunting on reducing cougar complaints and livestock depredations in Washington from 2005 to 2010 (6 years). The number of complaints, livestock depredations, cougars harvested, estimated cougar populations, human population and livestock populations were calculated for all 39 counties and 136 GMUs (game management units) in Washington. The data was then analyzed using a negative binomial generalized linear model to test for the expected negative relationship between the number of complaints and depredations in the current year with the number of cougars harvested the previous year. As expected, we found that complaints and depredations were positively associated with human population, livestock population, and cougar population. However, contrary to expectations we found that complaints and depredations were most strongly associated with cougars harvested the previous year. The odds of increased complaints and livestock depredations increased dramatically (36 to 240%) with increased cougar harvest. We suggest that increased young male immigration, social disruption of cougar populations, and associated changes in space use by cougars - caused by increased hunting resulted in the increased complaints and livestock depredations. Widespread indiscriminate hunting does not appear to be an effective preventative and remedial method for reducing predator complaints and livestock depredations.     

农牧交错带系统生产力概念及其对生态重建的意义

论证了黄土高原农牧交错带在全球所有同纬度(39°～41°N)地区中是作物生长盛期内光、温及降水条件组合最好的地带,并以初步的实证和观测支持了这一论点,阐述了通过开发能很好地适应自然条件,特别是能扬长避短,充分利用总体上虽较严酷而局部具有优势的气候资源的“系统生产力”的新思路;中心选择和应用生物量高、水分效率高、覆盖作用好的新作物和相应的种植制度,围绕生物量“为牧而农”式地实行农牧结合;重“料”于粮草,相应改变传统农业的格局,以大幅度地提高黄土高原地区的系统生产力,探索走出一条生态重建和支柱产业协调发展新路的可能性。     

聚焦糖尿病治疗药物

糖尿病药物市场是当前制药行业最具价值和发展最快的市场之一,拥有大量需要药物干预的糖尿病患者。自从胰岛素被发现以来,制药公司研发了一大批具有数十亿美元销售额的药物。由于人们更倾向于久坐的生活习惯,世界卫生组织预测糖尿病患者数量将呈爆炸性增加,也极大地提高了大批新型重磅炸弹级抗糖尿病药物问世的几率。在新型药物（包括传统的胰岛素类似物）稳固地位的驱动下,糖尿病药物市场被预测将在未来5 年内翻倍。本综述分析了当前市场动态,以及越来越不利于市场发展的管理环境对产品发展的影响。当创新药物面临着国家监管部门越来越多的审查,胰岛素类生物仿制药的法规也即将颁布,从长远来看,将在无形中削弱糖尿病市场。此外,还讨论了胰岛素仿制药进入市场带来的重要挑战,并对其治疗作用进行了评价。     

From microbes to fish the next revolution in food production

Increasing global population and the consequent increase in demand for food are not a new story. Agroindustrial activities such as livestock help meet this demand. Aquaculture arose decades ago and revolutionized the agroindustrial activity as a significant food generator. However, like livestock, aquaculture is based on finite resources and has been accused of being unsustainable. Abandoning aquaculture is not an option considering the food, foreign exchange, and employment it generates, and therefore must be reinvented. Among the many alternatives suggested to make aquaculture more sustainable, microorganisms have been highlighted as a direct food source for cultured fish and crustaceans, a strategy that promises to revolutionize aquaculture by eliminating waste. Considering waste, as part of a cycle, it can increase stock densities and reduce emissions of contaminants and operational costs.     

Seasonality constraints to livestock grazing intensity

Increasing food production is essential to meet the future food demand of a growing world population. In light of pressing sustainability challenges such as climate change and the importance of the global livestock system for food security as well as GHG emissions, finding ways to increasing food production sustainably and without increasing competition for food crops is essential. Yet, many unknowns relate to livestock grazing, in particular grazing intensity, an essential variable to assess the sustainability of livestock systems. Here, we explore ecological limits to grazing intensity (GI; i.e. the fraction of net primary production consumed by grazing animals) by analysing the role of seasonality in natural grasslands. We estimate seasonal limitations to GI by combining monthly net primary production data and a map of global livestock distribution with assumptions on the length of nonfavourable periods that can be bridged by livestock (e.g. by browsing dead standing biomass, storage systems or biomass conservation). This allows us to derive a seasonality‐limited potential GI, which we compare with the GI prevailing in 2000. We find that GI in 2000 lies below its potential on 39% of the total global natural grasslands, which has a potential for increasing biomass extraction of up to 181 MtC/yr. In contrast, on 61% of the area GI exceeds the potential, made possible by management. Mobilizing this potential could increase milk production by 5%, meat production by 4% or contribute to free up to 2.8 Mio km² of grassland area at the global scale if the numerous socio‐ecological constraints can be overcome. We discuss socio‐ecological trade‐offs, which may reduce the estimated potential considerably and require the establishment of sound monitoring systems and an improved understanding of livestock system's role in the Earth system.     

Environmental changes impacting Echinococcus transmission: research to support predictive surveillance and control

Echinococcosis, resulting from infection with tapeworms Echinococcus granulosus and E. multilocularis, has a global distribution with 2–3 million people affected and 200,000 new cases diagnosed annually. Costs of treatment for humans and economic losses to the livestock industry have been estimated to exceed $2 billion. These figures are likely to be an underestimation given the challenges with its early detection and the lack of mandatory official reporting policies in most countries. Despite this global burden, echinococcosis remains a neglected zoonosis. The importance of environmental factors in influencing the transmission intensity and distribution of Echinococcus spp. is increasingly being recognized. With the advent of climate change and the influence of global population expansion, food insecurity and land‐use changes, questions about the potential impact of changing temperature, rainfall patterns, increasing urbanization, deforestation, grassland degradation and overgrazing on zoonotic disease transmission are being raised. This study is the first to comprehensively review how climate change and anthropogenic environmental factors contribute to the transmission of echinococcosis mediated by changes in animal population dynamics, spatial overlap of competent hosts and the creation of improved conditions for egg survival. We advocate rigorous scientific research to establish the causal link between specific environmental variables and echinococcosis in humans and the incorporation of environmental, animal and human data collection within a sentinel site surveillance network that will complement satellite remote‐sensing information. Identifying the environmental determinants of transmission risk to humans will be vital for the design of more accurate predictive models to guide cost‐effective pre‐emptive public health action against echinococcosis.     

Impact of drug discovery on stem cell biology

Despite the rapid technical progress in pharmaceutical industry in the past decade, it is still a great challenge to find new drugs and the situation seems more and more serious. However, the history of pharmaceutical industry clearly indicated that the significance of drug discovery went far beyond providing new drugs. For instance, drugs or candidates could be used as selective probes to reveal novel cellular mechanisms, which is a fundamental tenet of chemical biology. More interestingly, accumulating evidence indicates that drugs and candidates can find important use in stem cell biology. Not only approved drugs but also undeveloped pharmacological agents could serve as efficient agents to regulate stem cell fate. Moreover, the target and activity knowledge accumulated during the drug discovery process will help select the stem cell fate modulators in a rational manner. As the progress in stem cell biology will bring positive influence to drug discovery, it can be expected that the current drug discovery efforts will finally bear great fruits in the future.     

Mitigating climate change: the role of domestic livestock

Livestock contribute directly (i.e. as methane and nitrous oxide (N2O)) to about 9% of global anthropogenic greenhouse gas (GHG) emissions and around 3% of UK emissions. If all parts of the livestock production lifecycle are included (fossil fuels used to produce mineral fertilizers used in feed production and N2O emissions from fertilizer use; methane release from the breakdown of fertilizers and from animal manure; land-use changes for feed production and for grazing; land degradation; fossil fuel use during feed and animal production; fossil fuel use in production and transport of processed and refrigerated animal products), livestock are estimated to account for 18% of global anthropogenic emissions, but less than 8% in the UK. In terms of GHG emissions per unit of livestock product, monogastric livestock are more efficient than ruminants; thus in the UK, while sheep and cattle accounted for 32% of meat production in 2006, they accounted for 48% of GHG emissions associated with meat production. More efficient management of grazing lands and of manure can have a direct impact in decreasing emissions. Improving efficiency of livestock production through better breeding, health interventions or improving fertility can also decrease GHG emissions through decreasing the number of livestock required per unit product. Increasing the energy density of the diet has a dual effect, decreasing both direct emissions and the numbers of livestock per unit product, but, as the demands for food increase in response to increasing human population and a better diet in some developing countries, there is increasing competition for land for food v. energy-dense feed crops. Recalculating efficiencies of energy and protein production on the basis of human-edible food produced per unit of human-edible feed consumed gave higher efficiencies for ruminants than for monogastric animals. The policy community thus have difficult decisions to make in balancing the negative contribution of livestock to the environment against the positive benefit in terms of food security. The animal science community have a responsibility to provide an evidence base which is objective and holistic with respect to these two competing challenges.     

Towards a rational policy for dealing with tsetse

The past 20 years have seen the development of bait technologies that enable livestock keepers to control tsetse flies and, hence, African trypanosomiasis. The techniques have, however, often been applied on too small a scale, without due regard to the realities of tsetse population dynamics. The consequent lack of progress has led to calls for a return to large-scale operations. Analysis of successful programmes to control or eliminate tsetse in southern Africa suggests that the combined use of recently improved bait methods and insecticide spraying will provide the building blocks for achieving the wider objective of the African Union, which is to create large tsetse-free zones.     

Global Material Flows and Resource Productivity: Forty Years of Evidence

The international industrial ecology (IE) research community and United Nations (UN) Environment have, for the first time, agreed on an authoritative and comprehensive data set for global material extraction and trade covering 40 years of global economic activity and natural resource use. This new data set is becoming the standard information source for decision making at the UN in the context of the post‐2015 development agenda, which acknowledges the strong links between sustainable natural resource management, economic prosperity, and human well‐being. Only if economic growth and human development can become substantially decoupled from accelerating material use, waste, and emissions can the tensions inherent in the Sustainable Development Goals be resolved and inclusive human development be achieved. In this paper, we summarize the key findings of the assessment study to make the IE research community aware of this new global research resource. The global results show a massive increase in materials extraction from 22 billion tonnes (Bt) in 1970 to 70 Bt in 2010, and an acceleration in material extraction since 2000. This acceleration has occurred at a time when global population growth has slowed and global economic growth has stalled. The global surge in material extraction has been driven by growing wealth and consumption and accelerating trade. A material footprint perspective shows that demand for materials has grown even in the wealthiest parts of the world. Low‐income countries have benefited least from growing global resource availability and have continued to deliver primary materials to high‐income countries while experiencing few improvements in their domestic material living standards. Material efficiency, the amount of primary materials required per unit of economic activity, has declined since around 2000 because of a shift of global production from very material‐efficient economies to less‐efficient ones. This global trend of recoupling economic activity with material use, driven by industrialization and urbanization in the global South, most notably Asia, has negative impacts on a suite of environmental and social issues, including natural resource depletion, climate change, loss of biodiversity, and uneven economic development. This research is a good example of the IE research community providing information for evidence‐based policy making on the global stage and testament to the growing importance of IE research in achieving global sustainable development.     

Modeling linkage disequilibrium in natural populations: the example of the Soay sheep population of St. Kilda, Scotland

The use of linkage disequilibrium to localize the genes underlying quantitative traits has received considerable attention in the livestock genetics community over the past few years. This has resulted in the investigation of linkage disequilibrium structures of several domestic livestock populations to assess their potential use in fine-mapping efforts. However, the linkage disequilibrium structure of free-living populations has been less well investigated. As the direct evaluation of linkage disequilibrium can be both time consuming and expensive the use of simulations that include as many aspects of population history as possible is advocated as an alternative. A simulation of the linkage disequilibrium structure of the Soay sheep population of St. Kilda, Scotland, is provided as an example. The simulated population showed significant decline of linkage disequilibrium with genetic distance and low levels of background linkage disequilibrium, indicating that the Soay sheep population is a viable resource for linkage disequilibrium fine mapping of quantitative trait loci.     

The resumption of consumption -- a review on tuberculosis

Among all infectious diseases that afflict humans, tuberculosis (TB) remains the deadliest. At present, epidemiologists estimate that one-third of the world population is infected with tubercle bacilli, which is responsible for 8 to 10 million new cases of TB and 3 million deaths annually throughout the world. Approximately 95% of new cases and 98% of deaths occur in developing nations, generally due to the few resources available to ensure proper treatment and where human immunodeficiency virus (HIV) infections are common. In 1882, Dr Robert Koch identified an acid-fast bacterium, Mycobacterium tuberculosis, as the causative agent of TB. Thirty-nine years later, BCG vaccine was introduced for human use, and became the most widely used prophylactic strategy to fight TB in the world. The discovery of the properties of first-line antimycobacterial drugs in the past century yielded effective chemotherapies, which considerably decreased TB mortality rates worldwide. The later introduction of some additional drugs to the arsenal used to treat TB seemed to provide an adequate number of effective antimicrobial agents. The modern, standard short-course therapy for TB recommended by the World Health Organization is based on a four-drug regimen that must be strictly followed to prevent drug resistance acquisition, and relies on direct observation of patient compliance to ensure effective treatment. Mycobacteria show a high degree of intrinsic resistance to most antibiotics and chemotherapeutic agents due to the low permeability of its cell wall. Nevertheless, the cell wall barrier alone cannot produce significant levels of drug resistance. M. tuberculosis mutants resistant to any single drug are naturally present in any large bacterial population, irrespective of exposure to drugs. The frequency of mutants resistant to rifampicin and isoniazid, the two principal antimycobacterial drugs currently in use, is relatively high and, therefore, the large extra-cellular population of actively metabolizing and rapidly growing tubercle bacilli in cavitary lesions will contain organisms which are resistant to a single drug. Consequently, monotherapy or improperly administered two-drug therapies will select for drug-resistant mutants that may lead to drug resistance in the entire bacterial population. Thereby, despite the availability of effective chemotherapy and the moderately protective vaccine, new anti-TB agents are urgently needed to decrease the global incidence of TB. The resumption of TB, mainly caused by the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains and HIV epidemics, led to an increased need to understand the molecular mechanisms of drug action and drug resistance, which should provide significant insight into the development of newer compounds. The latter should be effective to combat both drug-susceptible and MDR/XDR-TB.     

Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland

Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land‐use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH₄⁺‐N. In‐depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N‐reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land‐use and/or climate changes.     

Comparison and evaluation of lupus nephritis response criteria in lupus activity indices and clinical trials

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with diverse manifestations. Although the approval of new therapies includes only one agent in 50 years, a number of promising new drugs are in development. Lupus nephritis is a dreaded complication of SLE as it is associated with significant morbidity and mortality. Advancing the treatment of lupus nephritis requires well-designed clinical trials and this can be challenging in SLE. The major obstacles involve identifying the correct population of patients to enroll and ensuring that a clinically appropriate and patient-centered endpoint is being measured. In this review, we will first discuss the clinical utility of endpoints chosen to represent lupus nephritis in global disease activity scales. Second, we will review completed and active trials focused on lupus nephritis and discuss the endpoints chosen. There are many important lessons to be learned from existing assessment tools and clinical trials. Reviewing these points will help ensure that future efforts will yield meaningful disease activity measures and well-designed clinical trials to advance our understanding of lupus management.