When the caps fall off: Responses to telomere uncapping in yeast

Telomeres protect the ends of linear chromosomes from activities that cause sequence losses or challenge chromosome integrity. Furthermore, these ends must be hidden from detection by the DNA damage recognition and response pathways. In particular, they must not fuse with each other. These fundamental and very first functions attributed to telomeres are also summarized with the term ‘chromosome capping’. However, telomeres can become uncapped and the foremost cellular responses to such events aim to restore genome stability in the most conservative fashion possible. I will provide an outline of cellular responses to uncapping in budding yeast and briefly discuss the reverse, namely avoidance mechanisms that prevent telomere formation at inappropriate places.     

An establishment of the procedures to eliminate incorrect blood due to non-matched or mislabeled tubes

This study aims to establish a set of procedures to eliminate incorrect blood due to non-matched tubes or mislabeled tubes. The errors such as these are suspected to have occurred when upon first and second-detection. Under the identical laboratory conditions, the results of re-detection of blood bag samples and rare type antigen samples, as well as re-collected samples from donor, and plasma diluted are not consistent with the original results. Here, 20 antigen erythrocytes were detected for blood bag samples and original samples, in which no incorrect blood was mistakenly administered or mislabeled. Samples taken under identical laboratory conditions were not found to have incorrect blood administered to a non-matched tube. The results showed nonlinear changes by HBsAg ELSIA after plasma dilution. The study suggests that the second-detection taken shortly after first detection is the most appropriate method to detect errors at the earliest time point. Blood bag samples are identical to those of the original antigen identification group, which means that the probability of the samples coming from the same donor is extremely highly. At same time, space and plasma diluted, re-detection can effectively exclude incorrect blood being added to a non-matched tube.     

An automated sample preparation system with mini-reactor to isolate and process submegabase fragments of bacterial DNA

Existing methods for extraction and processing of large fragments of bacterial genomic DNA are manual, time-consuming, and prone to variability in DNA quality and recovery. To solve these problems, we have designed and built an automated fluidic system with a mini-reactor. Balancing flows through and tangential to the ultrafiltration membrane in the reactor, cells and then released DNA can be immobilized and subjected to a series of consecutive processing steps. The steps may include enzymatic reactions, tag hybridization, buffer exchange, and selective removal of cell debris and by-products of the reactions. The system can produce long DNA fragments (up to 0.5 Mb) of bacterial genome restriction digest and perform DNA tagging with fluorescent sequence-specific probes. The DNA obtained is of high purity and floating free in solution, and it can be directly analyzed by pulsed-field gel electrophoresis (PFGE) or used in applications requiring submegabase DNA fragments. PFGE-ready samples of DNA restriction digests can be produced in as little as 2.1 h and require less than 10⁸ cells. All fluidic operations are automated except for the injection of the sample and reagents.     

An establishment of the procedures to eliminate incorrect blood due to non-matched or mislabeled tubes

This study aims to establish a set of procedures to eliminate incorrect blood due to non-matched tubes or mislabeled tubes. The errors such as these are suspected to have occurred when upon first and second-detection. Under the identical laboratory conditions, the results of re-detection of blood bag samples and rare type antigen samples, as well as re-collected samples from donor, and plasma diluted are not consistent with the original results. Here, 20 antigen erythrocytes were detected for blood bag samples and original samples, in which no incorrect blood was mistakenly administered or mislabeled. Samples taken under identical laboratory conditions were not found to have incorrect blood administered to a non-matched tube. The results showed nonlinear changes by HBsAg ELSIA after plasma dilution. The study suggests that the second-detection taken shortly after first detection is the most appropriate method to detect errors at the earliest time point. Blood bag samples are identical to those of the original antigen identification group, which means that the probability of the samples coming from the same donor is extremely highly. At same time, space and plasma diluted, re-detection can effectively exclude incorrect blood being added to a non-matched tube.     

An automated method for the quasi-continuous analysis of degradation and transfer products during the enzymatic hydrolysis of oligosaccharides

A method is presented which allows for the automated quasi-continuous analysis of the degradation and transfer products developing during the enzymatic hydrolysis of oligosaccharides. A liquid chromatographic system is integrated into the bypass of a small batch reactor which makes it possible to take oligomer spectra without any manual sample processing being necessary. The time intervals between analyses are substantially reduced by making use of an overlapping analysis technique. Postcolumn derivatization with an orcinol sulfuric acid reagent gives a high sensitivity for carbohydrates. The great potential of this method is demonstrated for the characterization of a beta-glucosidase (pI 8.4) from Trichoderma reesei QM 9414 and an alpha 1,4-glucan glucohydrolase from Aspergillus niger with cellotetraose and maltohexaose as examplary substrates.     

An extended boiling method for small-scale preparation of plasmid DNA tailored to long-range automated sequencing

Automated fluorescence sequencing depends on high-quality plasmid DNA, which is conveniently prepared by minipreparation procedures. While those procedures are effective for high-copy number plasmids, purity and yields of low-copy number plasmids are often not sufficient to achieve reasonable sequencing results. Here, we describe a reproducible and cheap procedure for the small-scale preparation of plasmid DNA, which is based on the original Holmes and Quigley protocol, comprising a boiling and two selective precipitation steps. Besides various other modifications, this procedure utilizes polyethylene glycol (PEG) precipitation as a key step to further purify plasmid DNA tailored to automated fluorescence sequencing. Independent of the plasmid size and copy number, the modified procedure yields plasmid DNA, which gives average reading lengths of 800 and more bases with a standard fluorescence cycle sequencing protocol. To demonstrate the efficiency and reproducibility of the method, sequencing data of various human interleukin-6 gene variants cloned in different vectors are presented. This procedure offers an economical alternative to commercial miniprep kits, utilizing silica resins or anion-exchanger matrices and, moreover, is more reliable and consistent with respect to reading lengths and accuracy in automated fluorescence sequencing.     

An automated method for DNA preparation from thousands of YAC clones.

We describe an automated method for the preparation of yeast genomic DNA capable of preparing thousands of DNAs in parallel from a YAC library. Briefly, the protocol involves four steps: (1) Yeast clones are grown in the wells of 96-well microtiter plates with filter (rather than plastic) well-bottoms, which are embedded in solid growth media; (2) These yeast cultures are resuspended and their concentrations determined by optical density measurement; (3) Equal numbers of cells from each well are embedded in low-melting temperature agarose blocks in fresh 96-well plates, again with filter bottoms; and (4) DNA is prepared in the agarose blocks by a protocol similar to that used for preparing DNA for pulsed-field gels, with the reagents being dialyzed through the (filter) bottoms of the microtiter plate. The DNA produced by this method is suitable for pulsed-field gel electrophoresis, for restriction enzyme digestion, and for the polymerase chain reaction (PCR). Using this protocol, we produced 3000 YAC strain DNAs in three weeks. This automated procedure should be extremely useful in many genomic mapping projects.     

Electron cryotomography sample preparation using the Vitrobot

Electron cryotomography is the highest-resolution structural technique currently available that can be applied to unique objects such as flexible large protein complexes, irregular viruses, organelles and small cells. Specimens are preserved in a near-native, 'frozen-hydrated' state by vitrification. The thickness of the vitreous ice must be optimized for each specimen, and gold fiducials are typically added to facilitate image alignment. Here, we describe in detail our protocols for electron cryotomography sample preparation including (i) introduction of fiducial markers into the sample and (ii) sample vitrification. Because we almost exclusively use an automated, climate-controlled plunge-freezing device (the FEI Vitrobot) to vitrify our samples, we discuss its operation and parameters in detail. A session in which eight grids are prepared takes 1.5-2 h.     

High-throughput bioanalytical method using automated sample preparation and liquid chromatography-atmospheric pressure ionspray mass spectrometry for quantitative determination of glybenclamide in human serum

A liquid chromatographic-mass spectrometric (LC-MS) method with rapid automated sample preparation was developed and validated for determination of glybenclamide in human serum. Glybenclamide and its deuterated labelled internal standard were extracted from human serum samples by automated solid-phase extraction. The extract was injected into the LC-MS system for analysis. Glybenclamide and its internal standard were measured in multiple ion monitoring mode. The method was validated over a range of 10-1000 ng/ml with good accuracy and precision and was applicable for pharmacokinetic studies.     

Rapid and efficient FBN1 mutation detection using automated sample preparation and direct sequencing as the primary strategy

Mutations in the fibrillin-1 (FBN1) gene cause Marfan syndrome (MFS) and the other type-1 fibrillinopathies. Finding these mutations is a major challenge considering that the FBN1 gene has a coding region of 8,600 base pairs divided into 65 exons. Most of the more than 600 known mutations have been identified using a mutation scanning method prior to sequencing of fragments with a suspected mutation. However, it is not obvious that these screening methods are ideal, considering cost, efficiency, and sensitivity. We have sequenced the entire FBN1 coding sequence and flanking intronic sequences in samples from 105 patients with suspected MFS, taking advantage of robotic devices, which reduce the cost of supplies and the quantity of manual work. In addition, automation avoids many tedious steps, thus reducing the opportunity for human error. Automated assembling of PCR, purification of PCR products, and assembly of sequencing reactions resulted in completion of the FBN1 sequence in half of the time needed for the manual protocol. Mutations were identified in 69 individuals. The mutation detection rate (76%), types, and genetic distribution of mutations resemble the findings in other MFS populations. We conclude that automated sequencing using the robotic systems is well suited as a primary strategy for diagnostic mutation identification in FBN1.     

An improved sample preparation method for analyzing mycobacterial proteins in two-dimensional gels

Two-dimensional gel electrophoresis (2-DE) is currently a widely used analytical method for resolving complex mixtures of proteins. Sample preparation has a marked influence on 2-DE pattern. To reduce impurities and to increase the low-abundance proteins, protein precipitation is often used for the preparation of samples before 2-DE. In this study, we revealed that addition of SDS prior to TCA precipitation of mycobacterial cell extract proteins increases the resolution of the 2-D gel pattern.     

An automated method for consistent helix assignment using turn information

A new automated helix assignment method is presented that leads to a more consistent definition of the helix termini, especially of the helix C-terminus. The method assigns a helix to segments of protein chain where adjacent helical turn structures are observed, capped by specific distorted turn types (e.g., open helical turns without a hydrogen bond) or capping motifs (e.g., the Schellman motif). Helix termini are detected by observing the behavior of the NH group in N-termini and the CO group in C-termini; in each case, the respective group must be free to interact with hydrogen bonding partners outside of the putative helix for a helix terminus to be assigned. The presented assignment method and SHAFT-assigned helices are part of Secbase and are made available with Relibase+ 3.0 and the free web version of Relibase 3.0. The method can also be used for the helix assignments of additional protein structures.     

An automated method for the fluorescamine reaction using a peristaltic pump.

An automated method is described for the measurement of amino acids and proteins by the fluorescamine reaction. Isopropanol is used as solvent for the fluorescamine, and all reagents are pumped by a peristaltic pump.     

MALDI sample preparation: the ultra thin layer method

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) (1, 2). The ultra-thin layer method involves the production of a substrate layer of matrix crystals (alpha-cyano-4-hydroxycinnamic acid) on the sample plate, which serves as a seeding ground for subsequent crystallization of a matrix/analyte mixture. Advantages of the ultra-thin layer method over other sample deposition approaches (e.g. dried droplet) are that it provides (i) greater tolerance to impurities such as salts and detergents, (ii) better resolution, and (iii) higher spatial uniformity. This method is especially useful for the accurate mass determination of proteins. The protocol was initially developed and optimized for the analysis of membrane proteins and used to successfully analyze ion channels, metabolite transporters, and receptors, containing between 2 and 12 transmembrane domains (2). Since the original publication, it has also shown to be equally useful for the analysis of soluble proteins. Indeed, we have used it for a large number of proteins having a wide range of properties, including those with molecular masses as high as 380 kDa (3). It is currently our method of choice for the molecular mass analysis of all proteins. The described procedure consistently produces high-quality spectra, and it is sensitive, robust, and easy to implement.     

An automated device for the preparation of complex reagent mixtures

A microcomputer-controlled device was built that automatically prepares small volumes of mixtures of up to eight reagents. The operation of the system is fast, flexible, and reliable, thus making possible the routine use of experimental protocols that require large numbers of small volume reagent samples, each having a different composition. In particular, the software we developed for this device handles the preparation of three-antibody staining solutions to be used in triple labeling immunofluorescent flow cytometry experiments that involve only two fluorochromes. In this role, the device is known as an “Immunofluorescence Tomograph.”     

Sensitive high-performance liquid chromatographic determination of nifedipine in dog plasma using an automated sample preparation system with laboratory robot

Nifedipine, a calcium-channel blocking drug was analysed in dog plasma after oral dosing with two different formulations. Sample preparation was automated with a laboratory robot. Quantitative determination of the drug was performed on a reversed-phase HPLC system with electrochemical detection (ED) using an internal standard. Validation of the analytical method showed that the system is well suited for pharmacokinetic studies on dogs. The assay was linear in the range 1–50 ng/ml. Inter-day and intra-day variability were between 6.43–18.15% C.V. and 1.57–5.53% C.V., respectively.