Ice-cap. A high-throughput method for capturing plant tissue samples for genotype analysis

High-throughput genotype screening is rapidly becoming a standard research tool in the post-genomic era. A major bottleneck currently exists, however, that limits the utility of this approach in the plant sciences. The rate-limiting step in current high-throughput pipelines is that tissue samples from living plants must be collected manually, one plant at a time. In this article I describe a novel method for harvesting tissue samples from living seedlings that eliminates this bottleneck. The method has been named Ice-Cap to reflect the fact that ice is used to capture the tissue samples. The planting of seeds, growth of seedlings, and harvesting of tissue are all performed in a 96-well format. I demonstrate the utility of this system by using tissue harvested by Ice-Cap to genotype a population of Arabidopsis seedlings that is segregating a previously characterized mutation. Because the harvesting of tissue is performed in a nondestructive manner, plants with the desired genotype can be transferred to soil and grown to maturity. I also show that Ice-Cap can be used to analyze genomic DNA from rice (Oryza sativa) seedlings. It is expected that this method will be applicable to high-throughput screening with many different plant species, making it a useful technology for performing marker assisted selection.     

A novel minimally invasive method for monitoring oxygen in microbial fuel cells

Oxygen availability is a potential rate-limiting step in the bioelectrochemical process catalyzed by microbes in microbial fuel cells (MFC). Determination of oxygen availability using a minimally invasive oxygen sensor is advantageous in terms of ease of usage, maintenance and cost-effectiveness as compared to using conventional probe-type oxygen sensors. The utility of this method is substantiated by using this sensor to demonstrate the relationship between oxygen availability and current density. 10 % drop in oxygen concentration resulted in a concomitant drop in current density by about 36 %, further establishing the criticality of monitoring oxygen levels in the MFC. The detachable sensor membrane of the minimally invasive sensor confers multiple advantages. The novel method would enable real-time monitoring of oxygen in MFCs, simplify process optimization and validation and more importantly, provide an impetus for development of more efficient MFC designs.     

A novel method for the transport and long-term storage of cultures and samples in an anaerobic atmosphere

Nylon-aluminium-polyethylene laminated, sealable bags provided a more economical and flexible method of transportation, incubation and storage than anaerobic jars. The bags were used with a special heat sealer and 'Anaerocult-A' sachets to remove oxygen. The environment inside the bags remained oxygen-free for at least 3 years.     

A method for preparing freeze-clamped tissue samples for metabolite analyses

A rapid and simple method for preparing freeze-clamped tissue samples for metabolite determinations is described. Freeze-clamped rat heart tissue samples weighing from 0.8 to 1.0 g were homogenized directly in an Ultra-Turrax homogenizer for 60 s in 3.5 ml of ice-cold 0.6 M HClO4 without pulverizing them in liquid nitrogen. After centrifugation, the pellet was rehomogenized in the Ultra-Turrax homogenizer for 30 s in 1.5 ml of HClO4. Following a further centrifugation the extracts were combined and the pH was adjusted to 7.0 by adding 5 M K2CO3. The neutralized supernatant was used for the desired assays. The analyses of the tissue extracts obtained from isolated perfused rat hearts by the present method give similar results for different kinds of metabolites than those processed according to the previous classical method. Moreover, the values of the various parameters determined from the tissue extracts prepared according to the method described here are similar to the data reported in literature. The method can be readily applied to any other freeze-clamped tissue. The greatest improvement obtained is that the homogenization procedure can be accomplished easily and conveniently in about one-tenth of the time required for the earlier classical method without the time-consuming and unpleasant tissue grinding in liquid nitrogen.     

A minimally invasive approach for correction of chin ptosis

Although ptosis of the tip of the chin is common and can be seen in persons of any age, it is frequently seen in older patients seeking facial rejuvenation. A variety of techniques have been described to correct ptosis of the chin. The authors describe a minimally invasive method that can be used correct chin ptosis. This technique uses a small intraoral incision to place a U-shaped Prolene suture that gathers the soft tissue of the chin and elevates it above the lower border of the mandibular symphysis. A retrospective review of 314 cases performed in conjunction with face lifts between January of 1994 and January of 2000 was performed to evaluate this technique. There were no significant complications, and long-term results have been very satisfactory and lasting.     

A novel, inexpensive, and sensitive method for analysis of tyrosine hydroxylase activity in tissue samples.

Tyrosine hydroxylase activity in whole mouse brains was measured $\text{in v}\text{vitro}$. The L-dihydroxyphenylaline (L-DOPA) formed by the enzyme was quantitated by liquid chromatography with electrochemical detection (LCEC). An investigation of the incubation factors (added Fe⁺², DOPA decarboxylase inhibitor concentration, substrate concentration, amount of tissue, time of incubation) is reported. Under optimal conditions the activity was found to be 15.1 ± 0.6 (S.E.M.) nmol DOPA formed/hr./g. tissue.     

外来物种入侵大数据采集方法的建立与应用

为准确、快速地获取入侵生物野外调查数据, 我们基于全球卫星导航系统、地理信息系统、移动互联网等现代信息技术提出了外来物种入侵大数据采集方法, 设计并研发了数据表单可自定义的野外调查工具软件——云采集。该系统以Android手机为数据采集终端, 采用C#和Java语言设计开发, 运用卫星导航定位技术实现野外调查发生位置的快速采集, 通过定义9种调查指标的数据类型及指标(列值)默认值、图像拍摄、语音录入、排序等4个辅助属性, 建立调查指标与手机客户端数据录入界面的关联, 实现用户界面可定制的数据录入模式。该系统在国家重点研发项目、福建省科技重大专项及福建省红火蚁(Solenopsis invicta)疫情普查等项目的调查任务中予以应用。实践检验表明: 该系统实现了野外调查数据的离线采集、数据同步、数据查询与输出管理, 将移动智能终端采集取代传统的纸笔记录, 简化了野外调查的流程, 提高了入侵生物野外调查的数据质量, 为外来生物入侵野外调查大数据采集提供了信息化支持。     

A rapid method for tissue collection and high-throughput isolation of genomic DNA from mature trees

Collection of tissue and subsequent isolation of genomic DNA from mature tree species often proves difficult. DNA extraction from needles, leaves, or buds is recommended in many protocols. Collecting these tissues from mature trees generally requires the use of firearms or climbing if sampling is to be nondestructive. As a result, sample collection is a major expense of many tree-based projects. Tree (and plant) tissues generally contain large amounts of polysaccharides and phenolic compounds that are difficult to separate from DNA. Many methods aim to overcom these problems, with most involving extraction in buffers containing the nonionic detergent cetyltrimethyl-ammonium bromide (CTAB), followed by numerous steps to clean contaminants from the DNA, using organic solvents and differential salt precipitation. These steps are time-consuming, such that isolation of DNA becomes the bottleneck in many molecular studies. This paper presents a new, efficient, cambium collection method for tree species and a DNA extraction protocol based on that of Doyle and Doyle (1987), with follow-up purification using the Wizard nuclei lysis and protein precipitation solutions (Promega). Results show a significant improvement in yield and DNA purity compared with other published methods, with consistently high yields of pure genomic DNA and high sample throughput. The relatively low cost per extraction, no requirement for use of liquid nitrogen, no requirement for freezer storage, and long-term sample stability after collection are important additional benefits.     

A method for branched-chain amino acid aminotransferase activity in microgram and nanogram tissue samples

A method for branched-chain amino acid aminotransferase is described which is based on running the reaction in the reverse of the usual direction with glutamate and alpha-ketoisocaproate as substrates. The alpha-ketoglutarate generated is reduced with glutamate dehydrogenase and NADH. For sensitivity in the nanomole range, the NAD+ generated is measured directly by converting to the highly fluorescent strong alkali product. For smaller samples, down to the 0.2- to 2-pmol range, the NAD+ is amplified by enzymatic cycling.     

A cut-off based approach for gene expression analysis of formalin-fixed and paraffin-embedded tissue samples

Microarray analysis of formalin-fixed and paraffin-embedded (FFPE) tissue seems to be of importance for the detection of molecular marker sets in prostate cancer (PC). The compromised RNA integrity of FFPE tissue results in a high degree of variability at the probe level of microarray data as shown by degradation plot. We tested methods that reduce the variability by including all probes within 300 nucleotides, within 600 nucleotides, or up to a calculated breakpoint with reference to the 3'-end. Accepted PC pathways such as the Wnt signaling pathway could be observed to be significantly regulated within FFPE microarray datasets. The best representation of PC gene expression, as well as better comparability to meta-analysis and fresh-frozen microarray data, could be obtained with a 600-nucleotide cutoff. Beyond the specific impact for PC microarray data analysis we propose a cutoff of 600 nucleotides for samples for which the integrity of the RNA cannot be guaranteed.     

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

Next-generation sequencing has proven an extremely effective technology for molecular counting applications where the number of sequence reads provides a digital readout for RNA-seq, ChIP-seq, Tn-seq and other applications. The extremely large number of sequence reads that can be obtained per run permits the analysis of increasingly complex samples. For lower complexity samples, however, a point of diminishing returns is reached when the number of counts per sequence results in oversampling with no increase in data quality. A solution to making next-generation sequencing as efficient and affordable as possible involves assaying multiple samples in a single run. Here, we report the successful 96-plexing of complex pools of DNA barcoded yeast mutants and show that such ‘Bar-seq’ assessment of these samples is comparable with data provided by barcode microarrays, the current benchmark for this application. The cost reduction and increased throughput permitted by highly multiplexed sequencing will greatly expand the scope of chemogenomics assays and, equally importantly, the approach is suitable for other sequence counting applications that could benefit from massive parallelization.     

A technique for long-term collection of uterine contents from mares

A technique for collection of uterine contents from mares is described: it uses a purse-string suture of the cervix to retain a collecting device. Its use during collection of uterine fluids in various experiments is evaluated. The procedure was satisfactory for at least eight-hour collection periods.