Microsatellite‐enriched genomic libraries as a source of polymorphic loci for Schistosoma mansoni

Microsatellite markers for Schistosoma mansoni were developed using four genomic microsatellite‐enriched libraries. Microsatellites were observed in 65.4% of all sequences. Primer pairs were designed and tested for 23 loci. Eighteen loci produced amplification products, out of which 11 were polymorphic and were further characterized on 100 individuals of S. mansoni. Two to 19 alleles per locus were detected. The average values of expected and observed heterozygosities among the 11 loci were 0.79 and 0.59, respectively.     

Method for generation of human hyperdiversified antibody fragment library

The selection of antibody fragments from libraries using in vitro screening technologies has proven to be a very good alternative to the classical hybridoma technology, and has overcome the laborious process of antibody humanization. However, the complexity of the library is critical in the probability of being able to directly isolate a high affinity antibody specific to a target. We report a method to make hyperdiversified antibody fragment libraries, based on human immunoglobulin variable genes mimicking the somatic hypermutation process. This mutagenesis technology, MutaGen, was used for the first time on the entire variable domain (frameworks and CDRs) of large repertoires of human variable antibody domains. Our MutaGen process uses low-fidelity human polymerases, known as mutases, suggested to be involved in the somatic hypermutation process of immunoglobulin genes. Depending on the mutases used, we generated complementary mutation patterns with randomly distributed mutations. The libraries were generated with an average of 1.8 mutations per 100 amino acids. The hyperdiversified antibody fragment libraries constructed with our process should enable the selection of antibody fragments specific to virtually any target.     

Characteristics of the microbial community in rhizosphere of Camptotheca acuminata cultured with exotic invasive plant Eupatorium adenophorum

The traditional culture-dependent plate counting and culture-independent small-subunit-ribosomal RNA gene-targeted molecular techniques, Single-Strand Conformation Polymorphism (SSCP) and ter-minal Restriction Fragment Length Polymorphism (tRFLP) combined with 16S rDNA clone library were adopted to investigate the impacts of secretion from Camptotheca acuminata (abbreviated to Ca) roots on the quantities and structure of eukaryotic microbes and bacteria in the rhizosphere, and the possi-bility that Ca controls exotic invasive plant Eupatorium adenophorum (Ea). The counting results indi-cated that the number of bacteria increased in turn in rhizospheres of Ea, Ca-Ea mixed culture and Ca, while that of eukaryotic microbes decreased. PCR-SSCP profiles showed eukaryotic microbial bands (corresponding to biodiversity) in rhizosphere of Ea were more complex than those of Ca and CE. Meristolohmannia sp., Termitomyces sp. and Rhodophyllus sp. were the dominant populations in the rhizosphere of Ca. Bacterial terminal restriction fragments (TRFs) profiles showed no difference among three kinds of rhizospheres, and the sequences of the 16S rDNA clone library from Ca rhizospheres were distributed in 10 known phyla, in which phylum Proteobacteria were the absolute dominant group and accounted for 24.71% of the cloned sequences (δ-Proteobacteria accounted for up to 17.65%), and phyla Acidobacteria and Bacteroidetes accounted for 16.47% and 10.59% of the cloned sequences, respectively. In addition, high performance liquid chromatography detected a trace amount of camp-tothecin and hydroxycamptothecin in the rhizospheric soil of Ca and CE, but examined neither camp-tothecin nor hydroxycamptothecin in rhizospheric soil of Ea. Therefore, invasion and diffusion of Ea evidently depended on distinguishing the eukaryotic community structure, but not on that of the bac-terial pattern. Ca was able to alter the eukaryotic community structure of invasive Ea by secreting camptothecin and hydroxycamptothecin into rhizospheres, and may benefit the control of overspread of Ea. This study provided theoretical evidence for rhizospheric microbial aspects on substituting Ca for Ea.     

Automated work-flow for processing high-resolution direct infusion electrospray ionization mass spectral fingerprints

The use of mass spectrometry (MS) is pivotal in analyses of the metabolome and presents a major challenge for subsequent data processing. While the last few years have given new high performance instruments, there has not been a comparable development in data processing. In this paper we discuss an automated data processing pipeline to compare large numbers of fingerprint spectra from direct infusion experiments analyzed by high resolution MS. We describe some of the intriguing problems that have to be addressed, starting with the conversion and pre-processing of the raw data to the final data analysis. Illustrated on the direct infusion analysis (ESI-TOF-MS) of complex mixtures the method exploits the full quality of the high-resolution present in the mass spectra. Although the method is illustrated as a new library search method for high resolution MS, we demonstrate that the output of the preprocessing is applicable to cluster-, discriminant analysis, and related multivariate methods applied directly to mass spectra from direct infusion analysis of crude extracts. This is done to find the relationship between several terverticillate Penicillium species and identify the ions responsible for the segregation.     

Isolation and characterization of microsatellites in Primula glaucescens Moretti and their cross-species amplification in P. spectabilis Tratt.

The hexaploid herbaceous species Primula glaucescens Moretti and Primula spectabilis Tratt. (2n = 6x = 66) are two endemics of the Italian Pre-Alps protected by national and international laws. In order to plan conservation strategies for natural populations and to study the influence of the latest glaciation on them we developed a set of microsatellites markers for the endangered Primula species: ten primer pairs allowed analysis of polymorphic disomic loci in P. glaucescens samples and seven of them also amplified polymorphic disomic markers in P. spectabilis. Kirsten Wolff and Giorgio Binelli contributed equally to the paper     

图书馆开展大学生信息素养教育的优势与途径

论述了对大学生进行信息素养教育的意义,阐明了图书馆在开展大学生信息素养教育过程中起到的优势作用,提出了利用图书馆进行大学生信息素养教育的6种途径。     

高校图书馆中文图书采访的质量控制

分析了高校图书馆中文图书采访工作中的制约因素,并从采购制度、人员素质、采访方式、质量分析等方面阐述了控制图书采访质量的措施。     

A prostate cancer tissue specific spectral library for targeted proteomic analysis

Prostate cancer is the most common cancer in males worldwide. Mass spectrometry-based targeted proteomics has demonstrated great potential in quantifying proteins from formalin-fixed paraffin-embedded (FFPE) and (fresh) frozen biopsy tissues. Here we provide a comprehensive tissue-specific spectral library for targeted proteomic analysis of prostate tissue samples. Benign and malignant FFPE prostate tissue samples were processed into peptide samples by pressure cycling technology (PCT)-assisted sample preparation, and fractionated with high-pH reversed phase liquid chromatography (RPLC). Based on data-dependent acquisition (DDA) MS analysis using a TripleTOF 6600, we built a library containing 108,533 precursors, 84,198 peptides and 9384 unique proteins (1% FDR). The applicability of the library was demonstrated in prostate specimens.     

Cover Image,Volume 116, Number 2, February 2019

A key point of protein stability engineering is to identify specific target residues whose mutations can stabilize the protein structure without negatively affecting the function or activity of the protein. Here, we propose a method called RiSLnet (Rapid i dentification of Smart mutant Library using residue network) to identify such residues by combining network analysis for protein residue interactions, identification of conserved residues, and evaluation of relative solvent accessibility. To validate its performance, the method was applied to four proteins, that is, T4 lysozyme, ribonuclease H, barnase, and cold shock protein B. Our method predicted beneficial mutations in thermal stability with ~62% average accuracy when the thermal stability of the mutants was compared with the ones in the Protherm database. It was further applied to lysine decarboxylase (CadA) to experimentally confirm its accuracy and effectiveness. RiSLnet identified mutations increasing the thermal stability of CadA with the accuracy of ~60% and significantly reduced the number of candidate residues (~99%) for mutation. Finally, combinatorial mutations designed by RiSLnet and in silico saturation mutagenesis yielded a thermally stable triple mutant with the half-life (T _1/2) of 114.9 min at 58°C, which is approximately twofold higher than that of the wild-type.