扁蓿豆叶绿体基因组密码子偏好性分析

为阐明扁蓿豆(Medicago ruthenica)叶绿体基因组密码子使用模式,以其50条蛋白编码序列(CDS)为对象,利用软件CodonW 1.4.2、Excel以及在线程序对其ENC,RSCU,GC含量、中性绘图、PR2-plot、最优密码子等进行分析得到以下结果:基因组平均GC含量为40.58％,其中GC1＞ G...     

Evaluation of Breeding Value and Selection of Bull Dams in the Danish Dairy Breeds: I. Studies on Realized Efficiency of Bull Dam and Bull Sire Selection

Abstract

The relationship between twice the adjusted daughter yield deviation (DYD) of the son and the average of the estimated breeding values (EBV) of his parents was investigated for milk and fat yield. Deviations from expectations of DYD minus the pedigree index and the regression of DYD on the EBV for each of the parents were estimated. The EBV of each bull dam was calculated in several ways using different combinations of pedigree information and their own records. In all, 1693 bulls (880 Black and White (BW), 418 Red Danish (RD) and 395 Danish Jersey (DJ)) with Direct Updating indices for milk and fat yield were included in the investigation. Mean discrepancies between estimated and observed genetic merit for kg of milk yield were ?348 for BW, ?213 for RD and ?228 for DJ, when all of the bull dams' individual records were utilized in breeding value estimation. The corresponding mean discrepancies for kg of fat yield were ?14.7, ?11.5 and ?11.9, respectively. The discrepancies were positively correlated with the number of lactation records included in the dams' EBVs. Regression coefficients of bull DYDs on bull dam breeding values were significantly lower than expected for RD and BW regardless of the number of individual lactation records included in the dams' indexes for milk and fat yield. For all three breeds, the regression coefficients were lowest for fat yield. The most probable cause of overestimation in bull dam EBVs is preferential treatment, particularly in second and later lactations. To avoid this bias, estimation of a bull dam's breeding value should be based on pedigree information and on records from only her first lactation.     

Can plot edge bias be reduced by means of airborne laser scanning?

This paper presents new methods for plot edge bias (PEB) correction of individual tree competition indices (CIs) using airborne laser scanning (ALS) as auxiliary information in multivariate ratio and multivariate regression models. I applied the methods to 557 plots from the Norwegian National Forest Inventory located in Hedmark County in South East Norway and compared them to the benchmarks methods linear expansion and simulated annealing by studying the individual tree growth predictions before and after PEB correction. Generally, the simulated annealing method seemed to improve growth prediction most and overall the existing methods performed better than those based on ALS. All PEB-correction methods tested gave minor changes in growth predictions and the absolute change in percent in adj. R² and Akaike's Information Criterion (AIC) was numerically small, with an average percentage change for the tested CIs between 1.8 for adj. R² and 0.6 for AIC of the observed values in the original data. The small differences in the results between the original data and the PEB-corrected data show that on average PEB remains a minor problem for individual tree growth prediction. Whether the results are valid for forests with significantly different spatial composition than that of this database remains to be confirmed.     

曲线连续箱梁桥支座设置的比较

以实际工程为例,对采用MIDAS空间梁单元小半径曲线梁桥支座的布置进行计算和比较分析,并通过掌握小半径曲线梁桥支座受力特点,从而确定出适合该桥的支座布置形式。     

The occurrence of primary burrowing crayfish in terrestrial habitat

A researcher’s perception of a target species’ landscape strongly influences the design of habitat studies conducted at broad spatial scales. Consequently, researcher-dependent perceptions may misguide conservation efforts. Although the life histories of some crayfish (i.e., primary burrowers) are centered on a fossorial existence independent of surface water, all North American crayfish are viewed in an aquatic context. This paradigm restricts the range of habitats that are typically sampled and managed for crayfish conservation. This study used presence/absence of the primary burrower Distocambarus crockeri at 137 locations within the Long Cane Ranger District of the Sumter National Forest, South Carolina, USA, to model the habitat association of the species across a GIS-based landscape. Logistic regression indicated that D. crockeri presence was most strongly associated with a terrestrial habitat defined by a set of morphologically similar soils located along ridge tops. Furthermore, the species was negatively associated with aquatic habitats such as streams and floodplains. The results indicate that D. crockeri is a terrestrial habitat specialist and should be modeled and managed at the landscape as a terrestrial organism. When viewed as a subset of the total United States cambarid fauna, primary burrowers are disproportionately imperiled. Primary burrowers comprise only 15% of the total crayfish fauna, while they account for 32% of those crayfish ranked critically imperiled. Habitat loss and an aquatic bias that restricted sampling to aquatic and semi-aquatic habitats might explain the group’s disproportionate imperilment.     

Assessing eddy-covariance flux tower location bias across the Fluxnet-Canada Research Network based on remote sensing and footprint modelling

We describe an approach for evaluating the representativeness of eddy covariance flux measurements and assessing sensor location bias (SLB) based on footprint modelling and remote sensing. This approach was applied to the 12 main sites of the Fluxnet-Canada Research Network (FCRN)/Canadian Carbon Program (CCP) located along an east-west continental-scale transect, covering grassland, forest, and wetland biomes. For each site, monthly and annual footprint climatologies (i.e. monthly or annual cumulative footprints) were calculated using the Simple Analytical Footprint model on Eulerian coordinates (SAFE). The resulting footprint climatologies were then overlaid on to images of the Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) derived from LANDSAT Thematic Mapper (TM) imagery, which were used as surrogates of land surface fluxes to estimate SLB. Results indicate that (i) the sizes of annual footprint climatology increased exponentially with increasing cumulative footprint percentages and, for a given percentage of footprint climatology, the footprint areas were significantly different among the sites. Typically, the 90% annual footprint climatology areas varied from 1.1 km² to 5.0 km²; (ii) using either NDVI or EVI as the flux surrogate, the SLB was less than 5% for most sites with respect to the reference area of interest (A_r) at 90% annual footprint climatology (scenario A) and a circular area with radius of 1 km centred at the individual tower (scenario B), with several exceptions; (iii) the SLB decreased with increasing size of footprint climatology for all sites for both scenarios A and B; (iv) out of 12, eight flux towers represented most of the ecosystem surrounding the towers for an area of 0.3 km² up to 10 km² with a satisfactorily low bias of <5%, whereas four towers represented areas ranging from only 0.75 to 4 km²; and (v) the seasonal differences in monthly SLB using NDVI as a flux surrogate were about 1-4% for most sites for both scenarios A and B.     

大肠杆菌基因中密码对使用的规律

为了探讨基因组序列的非随机性对密码对使用的影响程度,揭示依赖上下文的密码对偏爱性(CDCB)可能存在的规律,本文主要对大肠杆菌基因组中密码子及其紧邻密码子(密码对)偏爱作了全面的统计分析。结果发现85%的密码子在其紧邻密码子位点有显著依赖上下文的密码对偏爱性,通过密码对与全序列六联体(三联体对)的相对丰度比较发现,大约35%的密码对偏好性不能用基因组的序列组分来解释。当密码子第二和第三位点核苷酸相同,且紧邻密码子相同时,它们的相对丰度有显著相关性。结果表明我们的数据支持依赖上下文的密码子偏好的主要原因是蛋白质合成精确性选择的假设,即本文结果揭示了依赖上下文的密码对偏好性可能存在的规律,从而为今后进一步研究大肠杆菌基因组中密码对使用偏好性提供参考。     

独行菜LaBBX基因低温表达响应与密码子偏性分析

BBX是调控植物非生物胁迫相关基因表达,响应植物逆境胁迫的重要锌指蛋白类转录因子。为探究BBX在独行菜(Lepidium apetalum)幼苗耐受低温生长中的表达响应及其密码子偏好性,本研究基于独行菜转录组数据,筛选独行菜BBX编码基因的cDNA序列,并从独行菜幼苗中克隆获得全长733 bp的基因编码区序列,命名为LaBBX。序列分析表明,LaBBX由242个氨基酸组成,包含2个B-box锌指蛋白结构域,蛋白分子量为61.66 kDa,等电点为5.09,无信号肽和跨膜区。独行菜幼苗受低温胁迫时,LaBBX基因显著上调表达,6 h上调表达至21倍,且24 h内均呈现高水平表达,说明该转录因子可能在独行菜幼苗受低温胁迫时起重要作用。偏好性分析结果显示,独行菜LaBBX基因的ENc、CAI值和GC含量分别为55.453、0.244和46.78%,其密码子使用偏性较弱,相对偏好使用AT,高频密码子有8个,CDS序列及RSCU聚类分析中与十字花科植物最相近;其偏好性的形成与突变和自然选择等诸多因素相关,酵母菌表达系统更适合作为LaBBX基因的异源表达受体,拟南芥是适宜LaBBX基因的遗传转化受体。本研究为了解独行菜LaBBX基因的异源表达及基因功能提供了重要参考。     

蒺藜苜蓿WRKY转录因子密码子使用偏好性分析

密码子使用偏好性普遍存在于各种生物中,但突变和自然选择压力对每种生物密码子使用偏好性不同.WRKY基因家族是一类只存在于植物的转录因子,主要参与植物体内转录调控和信号转导过程.本研究以蒺藜苜蓿(Medicago truncatula)WRKY转录因子(MtWRKY)为研究对象,揭示Mt WRKY基因密码子使用偏好性形成的主要因素,并筛选最优密码子.研究结果表明,代表MtWRKY基因的点均分布在有效密码子数(effective number of codons,ENC)标准曲线以下,表明密码子受自然选择压力或突变选择压力或其他因素影响;密码子第1、2位平均GC含量(GC12)与密码子第3位GC含量(GC3)相关性分析发现,GC12与GC3呈显著正相关(r=0.34,P＜0.01),表明突变压力导致密码子3个位点具有相似的GC含量;GC3s值分布在0.2～0.5之间,表明密码子使用偏好性主要受突变压力影响.奇偶偏好分析表明,MtWRKY基因第3位密码子CT含量＞AG含量.G和C(或者A和T)不成比例分布在密码子第3位上,表明密码子使用偏好性受到自然选择压力影响,但很可能突变压力仍起主要作用.最优密码子使用频率(frequency of optimal codons,Fop)与GC含量以及序列长度相关性分析发现,Fop与外显予GC含量呈显著正相关(r=0.57,P＜0.01),而与内含子GC含量呈较弱正相关(r=0.09,P＞0.05);Fop与外显子序列的长度呈正相关(r=0.28,P＜0.05),而与内含子长度呈负相关(r=-0.01,P＞0.05).表明MtWRKY基因外显子和内含子序列的形成受不同选择压力影响;外显子密码子使用偏好性受突变压力影响,而内含子可能是由于自然选择压力作用于突变选择形成的.确定了4个以G或C结尾的最优密码子.研究结果为WRKY转基因研究过程中密码子优化提供了理论支持.     

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.