HiCdat: a fast and easy-to-use Hi-C data analysis tool

Background

The study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists.

Results

HiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq).

Conclusions

HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0678-x) contains supplementary material, which is available to authorized users.     

Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity

In light of rising energy costs, lignocellulosic ethanol has been identified as a renewable alternative to petroleum-based transportation fuels. In an attempt to reach government mandated ethanol production levels, potential plant biofeedstock candidates have been investigated, and cold-tolerant, perennial accessions within the C₄ grass genus Miscanthus have been identified as leading contenders in the Midwestern US. To facilitate the development of improved cultivars through marker-assisted breeding, a quantitative trait locus (QTL) study was conducted on a full-sib, F₁ mapping population segregating for flowering time, height, leaf width, and yield using a genetic map consisting of 846 segregating SNP and SSR markers. This was a 3 year study investigating the genetic architecture underlying traits important to biomass production in a population of 221 progeny from a cross between M. sinensis ‘Grosse Fountaine’ and M. sinensis ‘Undine’ established in the spring of 2010; 72 QTLs with LOD scores above the genome-wide, permuted threshold equivalent to a P-value of 0.05 were identified across 13 traits. Of the 36 QTLs identified in 2011, 22 were detected again the following year. Both the use of spring emergence and vigor rating as a covariate to account for variation related to differences in establishment increased the power to detect QTLs in the 2 year establishment period. Finally, a dry period in the middle of the 2012 growing season suggested that yield declines were due to a decrease in tiller diameter.     

Complementarity in root architecture for nutrient uptake in ancient maize/bean and maize/bean/squash polycultures

Background and Aims

During their domestication, maize, bean and squash evolved in polycultures grown by small-scale farmers in the Americas. Polycultures often overyield on low-fertility soils, which are a primary production constraint in low-input agriculture. We hypothesized that root architectural differences among these crops causes niche complementarity and thereby greater nutrient acquisition than corresponding monocultures.

Methods

A functional–structural plant model, SimRoot, was used to simulate the first 40 d of growth of these crops in monoculture and polyculture and to determine the effects of root competition on nutrient uptake and biomass production of each plant on low-nitrogen, -phosphorus and -potassium soils.

Key Results

Squash, the earliest domesticated crop, was most sensitive to low soil fertility, while bean, the most recently domesticated crop, was least sensitive to low soil fertility. Nitrate uptake and biomass production were up to 7 % greater in the polycultures than in the monocultures, but only when root architecture was taken into account. Enhanced nitrogen capture in polycultures was independent of nitrogen fixation by bean. Root competition had negligible effects on phosphorus or potassium uptake or biomass production.

Conclusions

We conclude that spatial niche differentiation caused by differences in root architecture allows polycultures to overyield when plants are competing for mobile soil resources. However, direct competition for immobile resources might be negligible in agricultural systems. Interspecies root spacing may also be too large to allow maize to benefit from root exudates of bean or squash. Above-ground competition for light, however, may have strong feedbacks on root foraging for immobile nutrients, which may increase cereal growth more than it will decrease the growth of the other crops. We note that the order of domestication of crops correlates with increasing nutrient efficiency, rather than production potential.     

荒漠河岸林植物木质部导水与栓塞特征及其对干旱胁迫的响应

 以同处于干旱区的塔里木河下游(铁干里克)和黑河下游(乌兰图格)断面为研究区, 比较了荒漠河岸林主要建群种胡杨(Populus euphratica)、柽柳(Tamarix spp.)、疏叶骆驼刺(Alhagi sparsifolia)和花花柴(Karelinia caspia)在长期遭受不同干旱胁迫下的根、枝条木质部导水力和栓塞化程度的变化特征, 并分析了木质部导水对干旱胁迫的响应及适应策略。结果表明: 1) 黑河下游荒漠河岸林植物的导水能力显著高于塔里木河下游, 其中柽柳、胡杨、疏叶骆驼刺和花花柴根木质部的初始比导率(K_s0)分别高11.97、6.74、7.10和3.73倍, 枝条的K_s0分别高9.48、3.65、2.07和1.88倍, 地下水埋深导致的干旱胁迫程度不同是诱发荒漠植物导水能力差异的根本原因; 2)柽柳耐干旱能力最强, 适应范围较宽, 而花花柴、疏叶骆驼刺的耐旱性相对较弱, 适生范围较窄, 这可能与植物的根系分布有关; 3)干旱胁迫较轻时, 枝条木质部是荒漠河岸林植物水分传输的主要阻力部位, 干旱胁迫严重时, 根木质部是限制植株水流的最大阻碍部位; 4)荒漠河岸林植物主要通过调节枝条木质部的水流阻力来适应干旱胁迫, 且其适应策略与干旱胁迫程度有关, 干旱胁迫轻时, 植物通过限制枝条木质部水流来协调整株植物的均匀生长; 干旱胁迫严重时, 植物通过牺牲劣势枝条、增强优势枝条水流来提高植株整体生存的机会。     

城市公园中慢行系统的选线与设计研究

城市公园作为城市中自然景观的重要组成部分,发挥着为人们提供散步漫游、休憩交往场所的重要作用,其内部慢行系统的研究对提升城市公园整体景观品质和游览体验有着重要的意义。以城市公园慢行系统为研究对象,通过实地调研和理论研究相结合的方法,从选线和设计两大方面探讨了城市公园慢行系统的构建。最后以黄山市滨江游园慢行系统为例,对其内部慢行系统的选线规划、景观规划和细节设计进行了具体的规划和设计,对理论研究结果进行验证和反馈,以期为同类型项目提供指导和借鉴。     

城市绿地中的声景观对精神复愈的作用

当前针对声景观的研究多数是以探索人们喜好的声音为主,而很少考虑声景观与视觉景观的相互作用。为探讨城市绿地中声景观与视觉景观相互作用对于精神复愈的作用,选取了8个具有代表性的城市绿地。以能够反映样地景观特点的视频作为复愈能力评测的媒介,通过计算机技术将选取的5种声音（单一鸟鸣声、多种鸟鸣声、蛙叫声、流水声和中国古典音乐）与在所选样地上录制的8段视频进行组合,选择191位大学生作为评价人员,对城市绿地的精神复愈性能力进行评价;并邀请5位景观专业的研究生对城市绿地的景观特征进行定量分析。结果显示：城市绿地中存在水流声或蛙叫声会降低绿地的精神复愈能力;把单一鸟鸣声和多种鸟类鸟鸣声设置在地形起伏较平坦的环境中能够更加有效地提高精神复愈能力。     

Dendrochronological analysis of the ancient architecture of Kingdom of Lo. Upper Mustang,Nepal

Upper Mustang is a land of extraordinary, precious, tangible and intangible cultural heritage deeply rooted in the Tibetan culture and tradition of Buddhism as well as the Bön religion. The unique architecture provides a great source of timber suitable for dendrochronological research. Century-old fortresses, palaces, Buddhist monasteries and temples, houses and chörtens reflect the great importance of wood as a building material (used alongside clay and stone). We present pioneering research on historical wood from Upper Mustang. The objectives of the study were to determine the wood species used in the traditional architecture of the region, to make an attempt to date materials from Upper Mustang using existing tree-ring chronologies developed for neighbouring geographical regions and to determine the need and the chance of creating separate tree-ring chronologies for Upper Mustang. For the presented study we collected 191 samples from the oldest buildings preserved in Upper Mustang. Anatomical studies of samples resulted in the identification of four species of conifer wood: Himalayan pine – Pinus wallichiana A.B. Jacks, Himalayan fir – Abies spectabilis D.Don, Juniperus spp. and Larix spp. The main achievement of our research was the development of an Upper Mustang master chronology covering the period from 1317 to 1943. The chronology is based on data derived from Pinus wallichiana A.B. Jacks.     

Biophysical properties and functional significance of stem water storage tissues in Neotropical savanna trees

Biophysical characteristics of sapwood and outer parenchyma water storage compartments were studied in stems of eight dominant Brazilian Cerrado tree species to assess the impact of differences in tissue capacitance on whole-plant water relations. The rate of decline in tissue water potential with relative water content (RWC) was greater in the outer parenchyma than in the sapwood for most of the species, resulting in tissue-and species-specific differences in capacitance. Sapwood capacitance on a tissue volume basis ranged from 40 to 160 kg m-3 MPa-1, whereas outer parenchyma capacitance ranged from 25 to only 60 kg m-3 MPa-1. In addition, osmotic potentials at full turgor and at the turgor loss point were more negative for the outer parenchyma compared with the sapwood, and the maximum bulk elastic modulus was higher for the outer parenchyma than for the sapwood. Sapwood capacitance decreased linearly with increasing sapwood density across species, but there was no significant correlation between outer parenchyma capacitance and tissue density. Midday leaf water potential, the total hydraulic conductance of the soil/leaf pathway and stomatal conductance to water vapour (gs) all increased with stem volumetric capacitance, or with the relative contribution of stored water to total daily transpiration. However, the difference between the pre-dawn water potential of non-transpiring leaves and the weighted average soil water potential, a measure of the water potential disequilibrium between the plant and soil, increased asymptotically with total stem capacitance across species, implying that overnight recharge of water storage compartments was incomplete in species with greater capacitance. Overall, stem capacitance contributes to homeostasis in the diurnal and seasonal water balance of Cerrado trees.     

Regulation and function of root exudates

Root-secreted chemicals mediate multi-partite interactions in the rhizosphere, where plant roots continually respond to and alter their immediate environment. Increasing evidence suggests that root exudates initiate and modulate dialogue between roots and soil microbes. For example, root exudates serve as signals that initiate symbiosis with rhizobia and mycorrhizal fungi. In addition, root exudates maintain and support a highly specific diversity of microbes in the rhizosphere of a given particular plant species, thus suggesting a close evolutionary link. In this review, we focus mainly on compiling the information available on the regulation and mechanisms of root exudation processes, and provide some ideas related to the evolutionary role of root exudates in shaping soil microbial communities.