Predicted avian responses to bioenergy development scenarios in an intensive agricultural landscape

Conversion of native prairie to agriculture has increased food and bioenergy production but decreased wildlife habitat. However, enrollment of highly erodible cropland in conservation programs has compensated for some grassland loss. In the future, climate change and production of second-generation perennial biofuel crops could further transform agricultural landscapes and increase or decrease grassland area. Switchgrass (Panicum virgatum) is an alternative biofuel feedstock that may be economically and environmentally superior to maize (Zea mays) grain for ethanol production on marginally productive lands. Switchgrass could benefit farmers economically and increase grassland area, but there is uncertainty as to how conversions between rowcrops, switchgrass monocultures and conservation grasslands might occur and affect wildlife. To explore potential impacts on grassland birds, we developed four agricultural land-use change scenarios for an intensively cultivated landscape, each driven by potential future climatic changes and ensuing irrigation limitations, ethanol demand, commodity prices, and continuation of a conservation program. For each scenario, we calculated changes in area for landcover classes and predicted changes in grassland bird abundances. Overall, birds responded positively to the replacement of rowcrops with switchgrass and negatively to the conversion of conservation grasslands to switchgrass or rowcrops. Landscape context and interactions between climate, crop water use, and irrigation availability could influence future land-use, and subsequently, avian habitat quality and quantity. Switchgrass is likely to provide higher quality avian habitat than rowcrops but lower quality habitat than conservation grasslands, and therefore, may most benefit birds in heavily cultivated, irrigation dependent landscapes under warmer and drier conditions, where economic profitability may also encourage conversions to drought tolerant bioenergy feedstocks.     

Competing to coordinate cell fate decisions: the MST2-Raf-1 signaling device

How do biochemical signaling pathways generate biological specificity? This question is fundamental to modern biology, and its enigma has been accentuated by the discovery that most proteins in signaling networks serve multifunctional roles. An answer to this question may lie in analyzing network properties rather than individual traits of proteins in order to elucidate design principles of biochemical networks that enable biological decision-making. We discuss how this is achieved in the MST2/Hippo-Raf-1 signaling network with the help of mathematical modeling and model-based analysis, which showed that competing protein interactions with affinities controlled by dynamic protein modifications can function as Boolean computing devices that determine cell fate decisions. In addition, we discuss areas of interest for future research and highlight how systems approaches would be of benefit.     

Systems genetic analysis of hippocampal neuroanatomy and spatial learning in mice

Variation in hippocampal neuroanatomy correlates well with spatial learning ability in mice. Here, we have studied both hippocampal neuroanatomy and behavior in 53 isogenic BXD recombinant strains derived from C57BL/6J and DBA/2J parents. A combination of experimental, neuroinformatic and systems genetics methods was used to test the genetic bases of variation and covariation among traits. Data were collected on seven hippocampal subregions in CA3 and CA4 after testing spatial memory in an eight‐arm radial maze task. Quantitative trait loci were identified for hippocampal structure, including the areas of the intra‐ and infrapyramidal mossy fibers (IIPMFs), stratum radiatum and stratum pyramidale, and for a spatial learning parameter, error rate. We identified multiple loci and gene variants linked to either structural differences or behavior. Gpc4 and Tenm2 are strong candidate genes that may modulate IIPMF areas. Analysis of gene expression networks and trait correlations highlight several processes influencing morphometrical variation and spatial learning.     

植物重金属胁迫耐受机制

重金属是一类会对植物产生毒害作用的污染物,植物在长期进化过程中演变出耐受重金属胁迫的相关机制。以植物重金属耐受性为基础,对近几年来国内外植物响应重金属胁迫的耐受机制研究作一简要综述。主要概述了重金属对植物的胁迫影响及植物抗氧化系统,脯氨酸、可溶性糖、可溶性蛋白等渗透调节物质和不同类型基因家族等方面对植物耐受重金属胁迫机制的研究进展。以期为提高植物耐重金属胁迫能力及研究植物修复重金属污染土壤的应用奠定一定的基础。     

Automixis in Artemia: solving a century‐old controversy

Parthenogenesis (reproduction through unfertilized eggs) encompasses a variety of reproduction modes with (automixis) or without (apomixis) meiosis. Different modes of automixis have very different genetic and evolutionary consequences but can be particularly difficult to tease apart. In this study, we propose a new method to discriminate different types of automixis from population‐level genetic data. We apply this method to diploid Artemia parthenogenetica, a crustacean whose reproductive mode remains controversial despite a century of intensive cytogenetic observations. We focus on A. parthenogenetica from two western Mediterranean populations. We show that they are diploid and that markers remain heterozygous in cultures maintained up to ~36 generations in the laboratory. Moreover, parallel patterns of population‐wide heterozygosity levels between the two natural populations strongly support the conclusion that diploid A. parthenogenetica reproduce by automictic parthenogenesis with central fusion and low, but nonzero recombination. This settles a century‐old controversy on Artemia, and, more generally, suggests that many automictic organisms harbour steep within‐chromosome gradients of heterozygosity due to a transition from clonal transmission in centromere‐proximal regions to a form of inbreeding similar to self‐fertilization in centromere‐distal regions. Such systems therefore offer a new avenue for contrasting the genomic consequences of asexuality and inbreeding.     

不同放牧制度下呼伦湖流域草原植被冠层截留

冠层截留是降雨过程中的水量分配和流域水平衡的一个重要组成部分,通过水浸泡法和降雨模拟实验研究呼伦湖流域草原3种放牧制度下(休牧、轮牧、自由放牧(超载放牧))植被冠层截留量的变化规律,并利用遥感解译植被归一化指数(NDVI),确定3种放牧制度下草原面积,估算呼伦湖流域草原降雨截留量。研究表明:在休牧、轮牧、自由放牧3种制度下,水浸泡法测定的截留量分别是0.468、0.320、0.271 mm。降雨模拟实验法测得的结果分别是0.957、0.613、0.431 mm。休牧、轮牧、自由放牧草场叶面积指数、盖度、容重、生物量等指标差异显著(P0.05),且单株植被高度、鲜重对截留量影响显著呈线性正相关关系。呼伦湖流域草原一次降雨量为大于等于30 mm全流域降雨,其植被截留量为6.462×106m3。     

Lipid metabolism and Type VII secretion systems dominate the genome scale virulence profile of Mycobacterium tuberculosis in human dendritic cells

Background

Mycobacterium tuberculosis continues to kill more people than any other bacterium. Although its archetypal host cell is the macrophage, it also enters, and survives within, dendritic cells (DCs). By modulating the behaviour of the DC, M. tuberculosis is able to manipulate the host’s immune response and establish an infection. To identify the M. tuberculosis genes required for survival within DCs we infected primary human DCs with an M. tuberculosis transposon library and identified mutations with a reduced ability to survive.

Results

Parallel sequencing of the transposon inserts of the surviving mutants identified a large number of genes as being required for optimal intracellular fitness in DCs. Loci whose mutation attenuated intracellular survival included those involved in synthesising cell wall lipids, not only the well-established virulence factors, pDIM and cord factor, but also sulfolipids and PGL, which have not previously been identified as having a direct virulence role in cells. Other attenuated loci included the secretion systems ESX-1, ESX-2 and ESX-4, alongside many PPE genes, implicating a role for ESX-5. In contrast the canonical ESAT-6 family of ESX substrates did not have intra-DC fitness costs suggesting an alternative ESX-1 associated virulence mechanism. With the aid of a gene-nutrient interaction model, metabolic processes such as cholesterol side chain catabolism, nitrate reductase and cysteine-methionine metabolism were also identified as important for survival in DCs.

Conclusion

We conclude that many of the virulence factors required for survival in DC are shared with macrophages, but that survival in DCs also requires several additional functions, such as cysteine-methionine metabolism, PGLs, sulfolipids, ESX systems and PPE genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1569-2) contains supplementary material, which is available to authorized users.