Direct and indirect impacts of crop–livestock organization on mixed crop–livestock systems sustainability: a model-based study

Crop–livestock production is claimed more sustainable than specialized production systems. However, the presence of controversial studies suggests that there must be conditions of mixing crop and livestock productions to allow for higher sustainable performances. Whereas previous studies focused on the impact of crop–livestock interactions on performances, we posit here that crop–livestock organization is a key determinant of farming system sustainability. Crop–livestock organization refers to the percentage of the agricultural area that is dedicated to each production. Our objective is to investigate if crop–livestock organization has both a direct and an indirect impact on mixed crop–livestock (MC–L) sustainability. In that objective, we build a whole-farm model parametrized on representative French sheep and crop farming systems in plain areas (Vienne, France). This model permits simulating contrasted MC–L systems and their subsequent sustainability through the following indicators of performance: farm income, production, N balance, greenhouse gas (GHG) emissions (/kg product) and MJ consumption (/kg product). Two MC–L systems were simulated with contrasted crop–livestock organizations (MC₂₀–L₈₀: 20% of crops; MC₈₀–L₂₀: 80% of crops). A first scenario – constraining no crop–livestock interactions in both MC–L systems – permits highlighting that crop–livestock organization has a significant direct impact on performances that implies trade-offs between objectives of sustainability. Indeed, the MC₈₀–L₂₀ system is showing higher performances for farm income (+44%), livestock production (+18%) and crop GHG emissions (−14%) whereas the MC₂₀–L₈₀ system has a better N balance (−53%) and a lower livestock MJ consumption (−9%). A second scenario – allowing for crop–livestock interactions in both MC₂₀–L₈₀ and MC₈₀–L₂₀ systems – stated that crop–livestock organization has a significant indirect impact on performances. Indeed, even if crop–livestock interactions permit improving performances, crop–livestock organization influences the capacity of MC–L systems to benefit from crop–livestock interactions. As a consequence, we observed a decreasing performance trade-off between MC–L systems for farm income (−4%) and crop GHG emissions (−10%) whereas the gap increases for nitrogen balance (+23%), livestock production (+6%) – MJ consumption (+16%) – GHG emissions (+5%) and crop MJ consumption (+5%). However, the indirect impact of crop–livestock organization doesn’t reverse the trend of trade-offs between objectives of sustainability determined by the direct impact of crop–livestock organization. As a conclusion, crop–livestock organization is a key factor that has to be taken into account when studying the sustainability of mixed crop–livestock systems.     

系统生物学与细胞发生系统动力学

系统生物学是系统理论和实验生物技术、计算机数学模型等方法整合的生物系统研究,系统遗传学研究基因组的稳态与进化、功能基因组和生物性状等复杂系统的结构、动态与发生演变等。合成生物学是系统生物学的工程应用,采用工程学方法、基因工程和计算机辅助设计等研究人工生物系统的生物技术。系统与合成生物学的结构理论,序列标志片段显示分析与微流控生物芯片,广泛用于研究细胞代谢、繁殖和应激的自组织进化、生物体形态发生等细胞分子生物系统原理等。     

Modeling and simulation of biological systems from image data

This essay provides an introduction to the terminology, concepts, methods, and challenges of image‐based modeling in biology. Image‐based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like “what is the functional role of shape” or “how are biological shapes generated and regulated” can be addressed in the framework of image‐based systems biology. The combination of image quantification, model building, and computer simulation is illustrated here using the example of diffusion in the endoplasmic reticulum.     

Improved understanding of gene expression regulation using systems biology

This article reviews the current state of systems biology approaches, including the experimental tools used to generate ‘omic’ data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.     

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

Large‐scale proteomic approaches have been used to study signaling pathways. However, identification of biologically relevant hits from a single screen remains challenging due to limitations inherent in each individual approach. To overcome these limitations, we implemented an integrated, multi‐dimensional approach and used it to identify Wnt pathway modulators. The LUMIER protein–protein interaction mapping method was used in conjunction with two functional screens that examined the effect of overexpression and siRNA‐mediated gene knockdown on Wnt signaling. Meta‐analysis of the three data sets yielded a combined pathway score (CPS) for each tested component, a value reflecting the likelihood that an individual protein is a Wnt pathway regulator. We characterized the role of two proteins with high CPSs, Ube2m and Nkd1. We show that Ube2m interacts with and modulates β‐catenin stability, and that the antagonistic effect of Nkd1 on Wnt signaling requires interaction with Axin, itself a negative pathway regulator. Thus, integrated physical and functional mapping in mammalian cells can identify signaling components with high confidence and provides unanticipated insights into pathway regulators.     

Vaccinology in the era of high-throughput biology

Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced ‘experimental challenge models'' in humans.     

系统生物学——生命科学的新领域

系统生物学是继基因组学、蛋白质组学之后一门新兴的生物学交叉学科,代表21世纪生物学的未来.最近,系统生物学研究机构纷纷成立.在研究上,了解一个复杂的生物系统需要整合实验和计算方法.基因组学和蛋白质组学中的高通量方法为系统生物学发展提供了大量的数据.计算生物学通过数据处理、模型构建和理论分析,成为系统生物学发展的一个必不可缺、强有力的工具.在应用上,系统生物学代表新一代医药开发和疾病防治的方向.     

Quality control of mitochondria during aging: Is there a good and a bad side of mitochondrial dynamics?

Maintenance of functional mitochondria is essential in order to prevent degenerative processes leading to disease and aging. Mitochondrial dynamics plays a crucial role in ensuring mitochondrial quality but may also generate and spread molecular damage through a population of mitochondria. Computational simulations suggest that this dynamics is advantageous when mitochondria are not or only marginally damaged. In contrast, at a higher degree of damage, mitochondrial dynamics may be disadvantageous. Deceleration of fusion‐fission cycles could be one way to adapt to this situation and to delay a further decline in mitochondrial quality. However, this adaptive response makes the mitochondrial network more vulnerable to additional molecular damage. The “mitochondrial infectious damage adaptation” (MIDA) model explains a number of inconsistent and counterintuitive data such as the “clonal expansion” of mutant mitochondrial DNA. We propose that mitochondrial dynamics is a double‐edged sword and suggest ways to test this experimentally.     

Differential expression of the GTL2 gene within the callipyge region of ovine chromosome 18

The inheritance pattern of the skeletal muscle hypertrophy phenotype caused by the callipyge gene has been characterized as polar overdominance. We hypothesized that this trait may be caused by a gain or loss of gene expression because of the reversible nature of the phenotype in paternal vs. maternal inheritance. Suppression subtraction cDNA probes were made from skeletal muscle mRNA of normal (NN) and callipyge (C(Pat)N(Mat)) animals and hybridized to Southern blots containing bacterial artificial chromosomes (BACs) that comprise a physical contig of the callipyge region. The CN-NN probes hybridized to two ovine and seven bovine BACs. Sequence analysis of fragments within those BACs indicated short regions of similarity to mouse gene trap locus (gtl2). Northern blots analysis of RNA from hypertrophy-responsive muscles show a population of GTL2 mRNA centred around 2.4 kb that were abundantly expressed in 14-day prenatal NN and C(Pat)N(Mat) lambs but were down-regulated in day 14 and day 56 postnatal NN lambs. The expression of GTL2 remained elevated in 14- and 56-day-old C(Pat)N(Mat) lambs as well as in 56-day-old N(Pat)C(Mat) and CC lambs. Expression of GTL2 in the supraspinatus, which does not undergo hypertrophy, was very low for all genotypes and ages. Isolation of cDNA sequences show extensive alternative splicing and a lack of codon bias suggesting that GTL2 does not encode a protein. The mutation of the callipyge allele has altered postnatal expression of GTL2 in muscles that undergo hypertrophy and will help identify mechanisms involved in growth, genomic imprinting and polar overdominance.