MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom‐up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R² = 0.997). When compared with previous developed software with similar features (BRAT and EZ‐Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high‐throughput root length measurements while saving both labor and time.     

X-ray sterilization of biopharmaceutical manufacturing equipment—Extractables profile of a film material and copolyester Tritan™ compared to gamma irradiation

The biopharmaceutical industry gains enormous flexibility in production processes by using sterilized preassembled single-use devices. Gamma irradiation is an established sterilization technology that may be restricted in the future by the availability of ⁶⁰Co as irradiation source and irradiation capacities. X-ray technology is considered an alternative type of radiation for sterilizing SU equipment. In the context of extractables and leachables—one concern connected with the use of single-use process equipment—the effect of X-ray irradiation on the extractables profile of the materials needs to be compared to established gamma irradiation to qualify this alternative technology. An approach is presented to obtain robust and comprehensive extractables data for materials used in SU devices after sterilization either using X-ray or gamma irradiation. A careful selection of the test items and the test design allows a one-to-one comparison of data obtained from a combination of orthogonal analytical techniques. The extractables of a modern SU film material and the copolyester Tritan™ are evaluated. The data presented allow a risk evaluation on the safety of this new sterilization modality for biopharmaceutical applications. It is demonstrated that the extractables profile of a polymer is not affected by the type of irradiation used for sterilization.     

Ephedra sinica Stapf (Ephedraceae): The fleshy bracts of seed cones used in Mongolian food and its nutritional components

Ephedra sinica Stapf (commonly, Chinese ephedra) grows mainly in Mongolia, Inner Mongolia, and other regions of northern China. The stems of Chinese ephedra have been called the world’s oldest medicine; other uses remain to be reported. Among the Mongolian people, in addition to medical applications, the fleshy bracts of the seed cones (or “fruit”) are traditionally used as food, fresh or dried, in several ways; for example, the fruit is used as a refined sugar, a cheese condiment, and a tea substitute. In this paper, we analyze the fruit’s nutritional components: moisture, crude protein, crude fat, crude fiber, carbohydrate, ash, pectin, vitamins, fatty acids, mineral elements, and amino acids. Ethnobotanical and nutritional component information may indicate that the plant has potential for development as a special food plant     

Describing maize (Zea Mays L.) landrace persistence in the Bajío of Mexico: A survey of 1940s and 1950s collection locations

Passport data for Mexico’s Guanajuato State were used to locate the sites where maize was collected in the 1940s and 1950s in an effort to document and conserve diversity. A map presenting survey points illustrates that collections have occurred repeatedly in the same locations. Observations of these locations reveal that urbanization and industrialization, not high yielding varieties, are displacing traditional varieties. Non-linear principal components analysis was used to assess associations between variables in areas where maize persists. Landraces appear to be associated with mountains and mesas, mixed cropping, little or no access to irrigation and areas classified as having low agricultural capacity; conversely, landraces have more commonly been replaced in areas of high agricultural capacity. The areas of high agriculture capacity, located in the riparian areas and plains, also have been the easiest to develop for urban and industrial use. Increasingly high rates of urbanization and development in areas of high agriculture capacity will impede the conservation of crop diversity in these areas.     

Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population

We searched for quantitative trait loci (QTL) underlying fitness-related traits in a free-living pedigree of 588 Soay sheep in which a genetic map using 251 markers with an average spacing of 15 cM had been established previously. Traits examined included birth date and weight, considered both as maternal and offspring traits, foreleg length, hindleg length, and body weight measured on animals in August and jaw length and metacarpal length measured on cleaned skeletal material. In some cases the data were split to consider different age classes separately, yielding a total of 15 traits studied. Genetic and environmental components of phenotypic variance were estimated for each trait and, for those traits showing nonzero heritability (N= 12), a QTL search was conducted by comparing a polygenic model with a model including a putative QTL. Support for a QTL at genome-wide significance was found on chromosome 11 for jaw length; suggestive QTL were found on chromosomes 2 and 5 (for birth date as a trait of the lamb), 8 (birth weight as a trait of the lamb), and 15 (adult hindleg length). We discuss the prospects for refining estimates of QTL position and effect size in the study population, and for QTL searches in free-living pedigrees in general.     

红籽瓜数量性状分析软件的设计与实现

主要介绍了如何使用面向对象技术对红籽瓜数量性状分析软件的设计,阐述了软件的设计过程,代码的编写。实现了对红籽瓜数量性状的分析。     

大鼠尿激酶SYBR Green I real time RT-PCR引物的设计

设计用于SYBR Green I法实时定量逆转录多聚酶链反应(QRT-PCR)检测大鼠尿激酶型纤溶酶原激活因子(uPA)mRNA的引物。从基因库获取靶基因及相关序列,充分收集争分析相关生物信息学数据,应用Oligo 6.22设计出一对长度为21bp的引物,其GG含量为52.4%;上下游引物3’最稳定二聚体和及发夹结构的能量分别为-1.5、-0.40 kcal/mol和-3.5、-O.90 kcal/mol,引物间最稳定二聚体为-3.1 kcal/mol。5’端和中间△G值较高,高于3’端△G;引发效率分别455和403。实验证明,该引物能够高效、特异地实现对靶序列的检测,适用于SYBR Green I法实时定量检测(uPA)mRNA。     

花生抗青枯病种质脂肪酸组成的遗传多样性

通过对123份不同类型抗青枯病花生种质种子脂肪酸的鉴定测试,分析了抗青枯病花生种质在这些性状方面的遗传分化,并与6006份资源组成的花生基础收集品进行了比较。研究结果表明,我国抗青枯病花生资源的油酸含量平均为51.78%,显著高于基础收集品的对应值(45.64%);亚油酸含量平均为28.88%,显著低于基础收集品的对应值(34.36%);高油酸种质较多,油酸含量达61%以上的资源23份,所占比重为18.7%,显著高于基础品中的相应比重(2.65%)。标准差、变异系数以及遗传多样性指数的分析结果表明,抗青枯病资源在油酸和亚油酸含量方面的遗传分化程度高。     

ProSight Annotator: Complete control and customization of protein entries in UniProt XML files

The effectiveness of any proteomics database search depends on the theoretical candidate information contained in the protein database. Unfortunately, candidate entries from protein databases such as UniProt rarely contain all the post-translational modifications (PTMs), disulfide bonds, or endogenous cleavages of interest to researchers. These omissions can limit discovery of novel and biologically important proteoforms. Conversely, searching for a specific proteoform becomes a computationally difficult task for heavily modified proteins. Both situations require updates to the database through user-annotated entries. Unfortunately, manually creating properly formatted UniProt Extensible Markup Language (XML) files is tedious and prone to errors. ProSight Annotator solves these issues by providing a graphical interface for adding user-defined features to UniProt-formatted XML files for better informed proteoform searches. It can be downloaded from http://prosightannotator.northwestern.edu .