VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding the clonal composition changes that occur within a tumor in response to certain micro-environment or treatments may lead to the design of more sophisticated and effective approaches to eradicate tumor cells. However, tracking tumor clonal sub-populations has been challenging due to the lack of distinguishable markers. To address this problem, a VDJ-seq protocol was created to trace the clonal evolution patterns of diffuse large B cell lymphoma (DLBCL) relapse by exploiting VDJ recombination and somatic hypermutation (SHM), two unique features of B cell lymphomas.In this protocol, Next-Generation sequencing (NGS) libraries with indexing potential were constructed from amplified rearranged immunoglobulin heavy chain (IgH) VDJ region from pairs of primary diagnosis and relapse DLBCL samples. On average more than half million VDJ sequences per sample were obtained after sequencing, which contain both VDJ rearrangement and SHM information. In addition, customized bioinformatics pipelines were developed to fully utilize sequence information for the characterization of IgH-VDJ repertoire within these samples. Furthermore, the pipeline allows the reconstruction and comparison of the clonal architecture of individual tumors, which enables the examination of the clonal heterogeneity within the diagnosis tumors and deduction of clonal evolution patterns between diagnosis and relapse tumor pairs. When applying this analysis to several diagnosis-relapse pairs, we uncovered key evidence that multiple distinctive tumor evolutionary patterns could lead to DLBCL relapse. Additionally, this approach can be expanded into other clinical aspects, such as identification of minimal residual disease, monitoring relapse progress and treatment response, and investigation of immune repertoires in non-lymphoma contexts.     

Occurrence of Phyllodistomum folium (Olfers) (Digenea) in the eel, Anguilla anguilla (Linnaeus), in a small river

The occurrence of Phyllodistomum folium in a population of eels was studied throughout one year. Abundance exhibited a summer peak. Gravid adults were found in all months, indicating that eels can serve as a definitive host for this parasite.     

华北晚古生代煤中一种科达叶的角质层研究

江苏徐州煤田太原组２０号煤层中一种分散角质层,根据其表皮构造特征及其它证据,认为是科达叶的角质层。利用光学显微镜和扫描电镜对这种角质层进行了详细研究,并与国内外研究较详细的几种科达叶的表皮构造进行了比较,表明当前标本是一种新和产达叶表皮构造类型。     

预测鼻咽癌放射敏感性的CB微核法

本文介绍一种预测鼻咽癌放射敏感性的方法——CB微核法。以该法评介了鼻咽癌细胞株及20例鼻咽癌患者活检标本的放射敏感性,随着剂量增加,微核率也明显增加。CB微核的剂量-效应与克隆法的剂量效应呈高度负相关(r=-0.970)。活检标本微核实验表明,20例中8例反应较高,7例中等,5例反应偏 低;随访表明,反应偏低者中已有2例有复发倾向。由于CB微核法具有简便、快速、正确性较高等优点,适于临床应用。     

中国东北落叶松属植物分类学特征的分析Ⅱ：———种鳞及针叶的地理变异

中国东北部的落叶松属植物,在分类学上常被视为２个种＾［２,３］。然而对其种鳞的形态、正常种鳞的数量及针叶长度的研究统计结果表明,以上性状存在地理处的差异,然而又有明显的连续变异特性,证明长白山及东北东部分布的落叶松,在起源上晚于兴安落叶松（Ｌｉｘ ｇｍｅｌｉｎｉｉ）,应是兴安落叶松在东北东部的地理变异种。     

Near-infrared Fourier transform Raman and conventional Raman studies of calf gamma-crystallins in the lyophilized state and in solution.

We present in this report a detailed structural study of calf gamma-crystallins both in the solid state and in solution by the newly developed technique of near-infrared (IR) Fourier transform (FT)-Raman spectroscopy as well as by the conventional Raman method. In comparison with conventional laser Raman spectroscopy, the near-IR FT-Raman approach exhibits several attractive features such as fluorescence rejection capability, frequency accuracy, and the FT's multiplex and throughput advantages. These distinct characteristics combined form the basis for the particular suitability of FT-Raman in crystallin structural analysis and elucidation. We have thus obtained evidence in support of the view that native calf gamma-II crystallin does not contain a disulfide bond either in the lyophilized state or in solution. In addition, conventional Raman spectra are examined for all four gamma-crystallin fractions. gamma-S, gamma-II, gamma-III, and gamma-IV, and the results indicate a high degree of structural similarities among them. It is also found that the sulfhydryl groups in all four gamma-crystallins are highly resistant to air oxidation and are capable of maintaining their reduced state during isolation in the absence of added reductants or such chelating agents as EDTA.     

Enhanced intracellular glutathione synthesis and excretion capability of Candida utilis by using a low pH-stress strategy

AIMS: To study the effect of low pH stress on glutathione (GSH) synthesis and excretion capability of GSH fermentation production in Candida utilis. METHODS AND RESULTS: When C. utilis WSH 02-08 was cultivated in a glucose-ammonium sulfate medium without pH control, GSH leakage occurred when the pH of the medium decreased to 1.5. However, analysis of the cell viability indicated that the cells were not lysed. To further study the effect of low pH stress on GSH production, pH-controlled batch cultures were conducted, where the pH was switched from 5.5 to 1.2 at 24 h and maintained at 1.2 for 6 h. Nearly all intracellular GSH was leaked into the medium and the cell viability decreased dramatically, conceiving a long-term exposure of strain WSH 02-08 at low pH environment led to a complete cell lysis. A critical point (treated at pH 1.2 for 3 h) was experimentally determined, where most cells were alive but suffering a low pH stress. Low pH-stressed C. utilis cells displayed an increased intracellular GSH synthesis and export capability, which protected the cells against short-term low pH treatment. CONCLUSIONS: Using this knowledge, a low pH-stress strategy was developed and applied in fed-batch production of GSH and 197.3 mg l-1 of GSH was secreted into the medium. The GSH-specific production yield could be increased from 2.11 to 2.67% (w/w), and the total GSH concentration could reach 737.1 mg l-1 and increased by 24.9%. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of GSH secretion of C. utilis at low pH. This study demonstrated the importance of the physiology-based fermentation strategy in the production of useful metabolites.