A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

Microdissection has been used for the examination of tissues at DNA, RNA, and protein levels for over a decade. Laser capture microscopy (LCM) is the most common microdissection technique used today. In this technique, a laser is used to focally melt a thermoplastic membrane that overlies a dehydrated tissue section¹. The tissue section composite is then lifted and separated from the membrane. Although this technique can be used successfully for tissue examination, it is time consuming and expensive. Furthermore, the successful completion of procedures using this technique requires the use of a laser, thus limiting its use. A new more affordable and practical microdissection approach called mesodissection is a possible solution to the pitfalls of LCM. This technique employs the MESO-1/MeSectr system to mill the desired tissue from a slide mounted tissue sample while concurrently dispensing and aspirating fluid to recover the desired tissue sample into a consumable mill bit. Before the dissection process begins, the user aligns the formalin fixed paraffin embedded (FFPE) slide with a hematoxylin and eosin stained (H&E) reference slide. Thereafter, the operator annotates the desired dissection area and proceeds to dissect the appropriate segment. The program generates an archived image of the dissection. The main advantage of mesodissection is the short duration needed to dissect a slide, taking an average of ten minutes from set up to sample generation in this experiment. Additionally, the system is significantly more cost effective and user friendly. A slight disadvantage is that it is not as precise as laser capture microscopy. In this article we demonstrate how mesodissection can be used to extract RNA from slides from FFPE granulomas caused by Mycobacterium tuberculosis (Mtb).     

利用激光显微切割与microarray 技术对恒河猴脑中白质与 灰质基因表达的差异性的研究

目的:利用激光显微切割技术和microarray技术比较恒河猴脑组织中前额叶皮质(prefontal cortex,PFC)与小脑皮质(cere-bellar cortex,CBC)的灰质与白质基因表达的差异。方法:利用激光显微切割技术(laser capture dissection,LCM)与microarray技术的有效结合,提取恒河猴PFC与CBC的白质与灰质,分别提取RNA,合成cDNA文库。最后利用GeneChip 1.0 ST芯片技术,分析得出大脑与小脑中灰质与白质的表达差异性。结果:无论是灰质还是白质,在PFC中的高表达基因都要远远多于在CBC中的高表达基因。结论:使用LCM可以提取单一的细胞群,从而用于要求更为精确的实验当中。     

Prediction of the in planta Phakopsora pachyrhizi secretome and potential effector families

Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, can cause losses greater than 80%. Despite its economic importance, there is no soybean cultivar with durable ASR resistance. In addition, the P. pachyrhizi genome is not yet available. However, the availability of other rust genomes, as well as the development of sample enrichment strategies and bioinformatics tools, has improved our knowledge of the ASR secretome and its potential effectors. In this context, we used a combination of laser capture microdissection (LCM), RNAseq and a bioinformatics pipeline to identify a total of 36 350 P. pachyrhizi contigs expressed in planta and a predicted secretome of 851 proteins. Some of the predicted secreted proteins had characteristics of candidate effectors: small size, cysteine rich, do not contain PFAM domains (except those associated with pathogenicity) and strongly expressed in planta. A comparative analysis of the predicted secreted proteins present in Pucciniales species identified new members of soybean rust and new Pucciniales‐ or P. pachyrhizi‐specific families (tribes). Members of some families were strongly up‐regulated during early infection, starting with initial infection through haustorium formation. Effector candidates selected from two of these families were able to suppress immunity in transient assays, and were localized in the plant cytoplasm and nuclei. These experiments support our bioinformatics predictions and show that these families contain members that have functions consistent with P. pachyrhizi effectors.     

Eco-efficiency analysis by basf: the method

Intention, Goal, Scope, Background  BASF has developed the tool of eco-efficiency analysis to address not only strategic issues, but also issues posed by the marketplace, politics and research. It was a goal to develop a tool for decision-making processes which is useful for a lot of applications in chemistry and other industries. Objectives. The objectives were the development of a common tool, which is usable in a simple way by LCA-experts and understandable by a lot of people without any experience in this field. The results should be shown in such a way that complex studies are understandable in one view. Methods  The method belongs to the rules of ISO 14040 ff. Beyond these life cycle aspect costs, calculations are added and summarized together with the ecological results to establish an eco-efficiency portfolio. Results and Discussion  The results of the studies are shown in a simple way, the eco-efficiency portfolio. Therefore, ecological data are summarized in a special way as described in this paper. It could be shown that the weighting factors, which are used in our method, have a negligible impact on the results. In most cases, the input data have an important impact on the results of the study. Conclusions. It could be shown that the newly developed eco-efficiency analysis is a new tool, which is usable for a lot of problems in decision-making processes. It is a tool which compares different alternatives of a defined customer benefit over the whole life cycle. Recommendations and Outlook  This new method can be a helpful tool in different fields of the evaluation of product or process alternatives. It can be used in research and development as well as in the optimization of customer processes and products. It is an analytical tool for getting more sustainable processes and products in the future     

SIVQ-LCM Protocol for the ArcturusXT Instrument

SIVQ-LCM is a new methodology that automates and streamlines the more traditional, user-dependent laser dissection process. It aims to create an advanced, rapidly customizable laser dissection platform technology. In this report, we describe the integration of the image analysis software Spatially Invariant Vector Quantization (SIVQ) onto the ArcturusXT instrument. The ArcturusXT system contains both an infrared (IR) and ultraviolet (UV) laser, allowing for specific cell or large area dissections. The principal goal is to improve the speed, accuracy, and reproducibility of the laser dissection to increase sample throughput. This novel approach facilitates microdissection of both animal and human tissues in research and clinical workflows.     

哺乳动物单细胞研究技术的现状与未来

近年来,生命科学和医学的基础研究已深入到单细胞阶段。单细胞研究为揭示生命活动的基本规律、探索细胞异质性、提高对疾病发病机制的认识等提供了重要的线索和依据,同时,单细胞技术已被应用于日常实践中,如法医学和临床生殖医学。单细胞研究中使用的技术也在不断变化,并越来越复杂。文中主要介绍单细胞分离技术,包括手工挑取、激光捕获显微切割和微流控技术,以及单细胞中DNA、RNA和蛋白质分析方法的各种技术。此外,文中总结了近年来生命科学和医学领域的主要单细胞研究成果,讨论了单细胞相关技术和研究的不足,并介绍了其未来的发展方向。     

Long-chain metabolites of vitamin E: Interference with lipotoxicity via lipid droplet associated protein PLIN2

The long-chain metabolites of vitamin E (LCM) emerge as a new class of regulatory metabolites and have been considered as the active compounds formed during vitamin E metabolism. The bioactivity of the LCM is comparable to the already established role of other fat-soluble vitamins. The biological modes of action of the LCM are far from being unraveled, but first insights pointed to distinct effects and suggested a specific receptor, which in turn lead to the aforementioned hypothesis. Here, a new facet on the interaction of LCM with foam cell formation of THP-1 macrophages is presented. We found reduced levels of mRNA and protein expression of lipid droplet associated protein PLIN2 by α-tocopherol (α-TOH), whereas the LCM and the saturated fatty acid, stearic acid, increased expression levels of PLIN2. In a lipotoxic setup (0–800?μM stearic acid and 0–100?μM α-TOH or 0–5?μM α-13′-COOH) differences in cellular viability were found. A reduced viability was observed for cells under co-treatment of α-TOH and stearic acid, whereas an increased viability for stearic acid incubation in combination with α-13′-COOH was observed. The striking similarity of PLIN2 expression levels and worsened or mitigated lipotoxicity, respectively, revealed a protective effect of PLIN2 on basal stearic acid-induced lipotoxic conditions in PLIN2 knockdown experiments. Based on our results, we conclude that α-13′-COOH protects cells from lipotoxicity, at least partially via PLIN2 regulation.Herewith another facet of LCM functionality was presented and their reputation as regulatory metabolites was further established.     

Developing Effective Product Panel Methodology Through Practice

Product forums are a cooperative approach to integrated product policy. These forums, also referred to as product panels, are an effective platform for bringing together actors from all of the life cycle stages of a product. The Spanish experience in conducting a product panel for electrical and electronic toys identified key factors that are needed for ensuring success. Setting specific goals that are applicable to the actors involved was found to be vital, as were timing and the provision of adequate facilities. The chairperson also played an important role in facilitating discussion and opinion sharing among members.