Sequential V(A)/Q distributions in the normal rabbit by micropore membrane inlet mass spectrometry.

We developed micropore membrane inlet mass spectrometer (MMIMS) probes to rapidly measure inert-gas partial pressures in small blood samples. The mass spectrometer output was linearly related to inert-gas partial pressure (r(2) of 0.996-1.000) and was nearly independent of large variations in inert-gas solubility in liquid samples. We infused six inert gases into five pentobarbital-anesthetized New Zealand rabbits and used the MMIMS system to measure inert-gas partial pressures in systemic and pulmonary arterial blood and in mixed expired gas samples. The retention and excretion data were transformed into distributions of ventilation-to-perfusion ratios (V(A)/Q) with the use of linear regression techniques. Distributions of V(A)/Q were unimodal and broad, consistent with prior reports in the normal rabbit. Total blood sample volume for each VA/Q distribution was 4 ml, and analysis time was 8 min. MMIMS provides a convenient method to perform the multiple inert-gas elimination technique rapidly and with small blood sample volumes.     

NMR observation of selected segments in a larger protein: central-segment isotope labeling through intein-mediated ligation

Peptide segments in a protein, which can include an active site of interest or be a series of parts constituting the entire structure, are now selectively observed by nuclear magnetic resonance (NMR) spectroscopy using samples prepared by the intein-mediated ligation method. Two separate inteins were used to ligate NMR-transparent segments to both the ends of an NMR-visible segment, producing a partly visible intact protein molecule. The (15)N-(1)H correlation spectrum of a 370-residue maltose binding protein labeled with (15)N at a continuous segment comprising residues Gly(101)-Ser(238) showed the essential elimination of signal overlapping, the signals being at the same positions as for the uniformly labeled sample. This method will allow structural analysis by NMR of over 50-kDa proteins in combination with contemporary NMR techniques suppressing the signal decays of larger proteins.     

The technology of the Global HIV Vaccine Research Cryorepository

This paper gives an overview of our developments in the fields of cryotechnology and cryoelectronics for managing biological samples stored over liquid nitrogen, fields that are essential to a central cryostorage facility for AIDS related material used in worldwide collaborative research. As a fundamental part of this project we have developed new electronic cryovials and carrier plates attached to Flash memory chips, so that a redundant and portable set of data is present with each sample. The recovery of peripheral blood mononuclear cells (PBMCs) after cryopreservation in the new cryosubstrates showed, especially for small sample volumes (0.1 ml), an increased viability in comparison to the preservation in standard cryovials. The electronic cryosubstrates interface with a dedicated laboratory workflow management system for reproducible and standardized sample processing. This system can read standard operating procedures (SOPs) stored on each sample's memory chip. Finally, we have developed a polymorphic cryoelectronic infrastructure for sample storage tanks. This cryoelectronic system has been integrated in a hermetic storage and semiautomatic handling environment. The new technologies provide state‐of‐the‐art sample identification, documentation and tracking that brings added value to each sample. The first application of these technologies is in a worldwide collaborative research towards the production of an AIDS vaccine. The functionality and versatility of the technologies will lead to an essential optimization of sample and data exchange for global clinical studies by ensuring a high degree of standardization between laboratories.     

Studies on Destabilization of Caseinate Complex during Frozen Storage of Milk

Unpasteurized skim milk was storaged in a frozen state at ?7°C or ?20°C for up to several months. There was no increase of non casein and non protein nitrogens, but a slight increase of free tyrosine and a slight decrease of alkaline phosphatase activity were detected when storage period was prolonged. Destabilization occurred solely in caseinate complex, but non micellar casein appeared to be stable.

The contents of calcium and inorganic phosphate in the caseinate complex separated by ultracentrifugation were increased appreciably after frozen storage. The viscosity characteristics of frozen storaged skim milk was also investigated.

Caseinate complex was ultracentrifugally separated from skim milk before and after frozen storage, and then lyophilized. Skim milk itself was also lyophilized before and after frozen storage. Dispersibility was examined on the reconstituted suspension of the lyophilized samples.

The lyophilized sample from frozen storaged milk was much less dispersible than the lyophilized control sample prepared before frozen storage. However, when lyophilized samples were once resolved with reagents such as urea and potassium oxalate and then dialyzed against fresh milk, stable micelle resulted in both samples prepared before and after frozen storage.

Some reduction of dispersibility occurred during lyophilization and subsequent storage in a dried state in the caseinate complex prepared before frozen storage. This reduction was small when skim milk was lyophilized and stored.     

The physical dimensions of the human neonatal cardiovascular system

To establish a data base for studies which seek to model and simulate the human perinatal cardiovascular system, we dissected three stillborn, full-term infants and measured the length, internal diameter, and wall thickness of over 1000 blood vessel segments. Cumulatively, these segments represent the major and minor vessels of the systemic and pulmonary circulation at birth. Statistical analysis showed that the methods used to obtain these physical dimensions were highly consistent and that storage of tissue samples in 10 percent formaldehyde solution caused a linear shrinkage of approximately 6.3 percent. A topological code was developed to illustrate the network relationships of blood vessel segments. An example of data utilization based on the topological code is presented and discussed.     

Direct analysis by small-pool PCR of MS205 minisatellite mutation rates in sperm after mutagenic therapies.

We have used small-pool PCR to analyse mutation in samples of sperm taken from men after mutagenic therapy. Small-pool PCR uses direct analysis of germline DNA at a highly unstable tandem-repeated "minisatellite" locus to measure rates of length-change mutation in individual sperm samples. The advantages of this approach are that the normal mutation rate is extremely high (about 0.4% per gamete at the locus analysed here), so that relatively small increases in mutation rate can be detectable in individual samples. It is known from work on sperm from untreated individuals that different alleles at this locus have different mutation rates. For this reason, we have analysed the germline mutation rates in sperm samples from two men, in each case comparing a post-treatment sample with a pre-treatment sample from the same individual. We find no evidence for altered mutation in the post-treatment sample, suggesting that the repopulation of the germ-cell compartment after treatment may be subject to stringent mechanisms for the detection and elimination of germ-cell damage.     

Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data

Background  

Classification studies using gene expression datasets are usually based on small numbers of samples and tens of thousands of genes. The selection of those genes that are important for distinguishing the different sample classes being compared, poses a challenging problem in high dimensional data analysis. We describe a new procedure for selecting significant genes as recursive cluster elimination (RCE) rather than recursive feature elimination (RFE). We have tested this algorithm on six datasets and compared its performance with that of two related classification procedures with RFE.     

Cavitation and water storage capacity in bole xylem segments of mature and young Douglas-fir trees

Hydraulic specific conductivity, vulnerability to cavitation and water storage capacity of Douglas-fir sapwood was determined for samples from six young (1.0-1.5 m tall) and six mature trees (41-45 m tall). Measurements on samples from young trees showedthere were no effects of two contrasting sample types (entire stem segments vs sectors chiseled out of entire stems) on any of the calculated hydraulic parameters, for vulnerability to cavitation and water storage capacity. Measurements on mature trees were made on wood from four heights on the bole and from two sapwood depths. Outer and inner sapwood at the base of the tree had higher water storage capacities and were more vulnerable to cavitation than was sapwood from the tree top. At every height, old trees were more vulnerable to cavitation than at 1.0 m from the ground in young trees. The water storage capacities showed three distinct phases at the base of the trunk. Young trees had similar water storage capacity (per unit volume of sapwood) to the topof the mature trees, which was lower than the water storage capacity throughout the rest of the bole xylem. The way in which capacitance was calculated (on a volumetric basis vs a relative water content basis) affected the conclusion one would draw at the low water potentials (<-3 MPa). Within a tree, we found an apparent trade-off between having both hydraulic specific conductivity and stem water storage, and vulnerability to cavitation.     

Measurement of porosity in very small samples of plant tissue

The relative volume of internal gas spaces (i.e., porosity) of the shoot and roots of a plant largely determines its resistance to flooding, as oxygen may diffuse through these cavities from non-flooded parts of the plant into the submerged tissues. The current techniques to measure porosity either need relatively large amounts of plant tissue (200 mg per sample), or are time-consuming and not sufficiently accurate for specific types of plant material. These limitations were the reason to develop a new method of porosity measurement. Small segments of roots were taken from freshly harvested plants, placed in a two-piece hard gelatin capsule and weighed on a microbalance. The root segments were subsequently infiltrated with water under vacuum, blotted carefully and weighed again. Using the increase in weight and the specific weight of infiltrated tissue, derived from a larger sample of roots, it was possible to calculate the porosity of individual root segments as small as 3–5 mg with a length of 5 mm. The new method combines this use of small samples with a high accuracy, and proved useful for a variety of plant species. Porosity data obtained with this method will improve our knowledge of small-scale processes such as aerenchyma development in root tips.     

A Magnetic Bead-Based Method for Concentrating DNA from Human Urine for Downstream Detection

Due to the presence of PCR inhibitors, PCR cannot be used directly on most clinical samples, including human urine, without pre-treatment. A magnetic bead-based strategy is one potential method to collect biomarkers from urine samples and separate the biomarkers from PCR inhibitors. In this report, a 1 mL urine sample was mixed within the bulb of a transfer pipette containing lyophilized nucleic acid-silica adsorption buffer and silica-coated magnetic beads. After mixing, the sample was transferred from the pipette bulb to a small diameter tube, and captured biomarkers were concentrated using magnetic entrainment of beads through pre-arrayed wash solutions separated by small air gaps. Feasibility was tested using synthetic segments of the 140 bp tuberculosis IS6110 DNA sequence spiked into pooled human urine samples. DNA recovery was evaluated by qPCR. Despite the presence of spiked DNA, no DNA was detectable in unextracted urine samples, presumably due to the presence of PCR inhibitors. However, following extraction with the magnetic bead-based method, we found that ∼50% of spiked TB DNA was recovered from human urine containing roughly 5×10³ to 5×10⁸ copies of IS6110 DNA. In addition, the DNA was concentrated approximately ten-fold into water. The final concentration of DNA in the eluate was 5×10⁶, 14×10⁶, and 8×10⁶ copies/µL for 1, 3, and 5 mL urine samples, respectively. Lyophilized and freshly prepared reagents within the transfer pipette produced similar results, suggesting that long-term storage without refrigeration is possible. DNA recovery increased with the length of the spiked DNA segments from 10±0.9% for a 75 bp DNA sequence to 42±4% for a 100 bp segment and 58±9% for a 140 bp segment. The estimated LOD was 77 copies of DNA/µL of urine. The strategy presented here provides a simple means to achieve high nucleic acid recovery from easily obtained urine samples, which does not contain inhibitors of PCR.     

Changes in Bacteria Recoverable from Subsurface Volcanic Rock Samples during Storage at 4 degrees C

The abundance of viable microorganisms recovered from deep subsurface volcanic rock samples increased after rock perturbation and storage for 1 week at 4 degrees C, while the diversity and evenness of recoverable heterotrophic bacterial communities generally decreased. One sample of each morphologically distinct colony type, recovered both before and after storage of U12n rock samples, was purified and characterized by fatty acid methyl ester (MIDI) and API rapid NFT strips. As determined by MIDI cluster analysis, the composition of the recoverable microbial communities changed with storage of rock samples; some groups of organisms were recovered only before, only after, or at both sample times. In general, the isolates recovered only after storage of rock samples had a greater ability to utilize the carbohydrates included in API test strips and had faster generation times than isolates recovered only on initial plating. The nutritional versatility and faster growth rates of organisms recovered in higher proportions after sample storage provide evidence that some microbial community changes may be due to the proliferation of a few bacterial types. However, because some new genera are recovered only after storage, the possibility also exists that dormant bacterial types are resuscitated during sample perturbation and storage.     

Changes in Bacteria Recoverable from Subsurface Volcanic Rock Samples during Storage at 4°C

The abundance of viable microorganisms recovered from deep subsurface volcanic rock samples increased after rock perturbation and storage for 1 week at 4°C, while the diversity and evenness of recoverable heterotrophic bacterial communities generally decreased. One sample of each morphologically distinct colony type, recovered both before and after storage of U12n rock samples, was purified and characterized by fatty acid methyl ester (MIDI) and API rapid NFT strips. As determined by MIDI cluster analysis, the composition of the recoverable microbial communities changed with storage of rock samples; some groups of organisms were recovered only before, only after, or at both sample times. In general, the isolates recovered only after storage of rock samples had a greater ability to utilize the carbohydrates included in API test strips and had faster generation times than isolates recovered only on initial plating. The nutritional versatility and faster growth rates of organisms recovered in higher proportions after sample storage provide evidence that some microbial community changes may be due to the proliferation of a few bacterial types. However, because some new genera are recovered only after storage, the possibility also exists that dormant bacterial types are resuscitated during sample perturbation and storage.     

新鲜土壤样品储存温度和时间对不同形态氮素的影响

土壤氮素形态及含量具有重要的生态学研究意义,而土壤样品的储存对土壤氮素含量的准确测定有很大影响.为了选择合理的土壤样品储存方法,本研究以福建省建瓯市万木林保护区罗浮栲林土壤为研究对象,测定在不同温度(25、4和-20 ℃)、不同储存时间(0、7和30 d)下土壤铵态氮、硝态氮、总氮、可溶性有机氮、氨基酸氮含量和微生物生物量氮,以及冷冻后常温培养过程中的氮素含量.结果表明: 在7 d的储存时间内,除氨基酸氮以外,常温培养样品下其余的氮素含量均有所增加;与新鲜样品相比,冷藏、冷冻样品的所有氮素含量之间均无显著性差异,且氮素含量变化较常温培养下更加稳定.因低温储存样品有刺激氮矿化的效果,在30 d储存时间内,与新鲜样品相比,除可溶性有机氮外,冷藏、冷冻样品的所有氮素含量均显著升高;两种冷储存方法之间无显著差异.因此,新鲜样品带回实验室后应及时处理;如需要冷储藏,时间不要超过半个月.如果需要较长的储存时间,则需将样品放置于更低的温度(-40或-80 ℃).在对储存土壤样品进行培养试验之前,需要进行预培养处理.在预培养过程中,除硝态氮含量呈现先下降再迅速升高的趋势外,其余氮素均随着培养时间逐渐趋近于新鲜土壤样品含量,在培养一周左右恢复到与新鲜土壤样品氮含量最为接近的状态.结合已有研究,对野外取样和风干样品需要5～14 d的预培养,冷储存样品预培养时间不应少于一周.     

Synergism of capillary isotachophoresis and capillary zone electrophoresis

The combination of capillary isotachophoresis and capillary zone electrophoresis may enhance greatly the performance of analytical capillary electrophoresis with respect to both separation power and the concentration sensitivity. The concentrating effects and the separation power of isotachophoresis allow the analysis of diluted samples and the elimination of interferences due to bulk components. The separation process of zone electrophoresis enables one to resolve the stack of trace analytes and detect the resulting individual zones with high sensitivity. The transition of isotachophoresis into zone electrophoresis plays the key role in the overall performance of this hyphenated technique. This article describes the dynamics of the conversion of isotachophoresis into zone electrophoretic mode and shows that the key role is played by the segments of the leading and terminating zones from the isotachophoretic stage. The magnitude of these segments directly effects the detection time as well as the separation width of the peaks of analytes. It is shown that these effects are also important in the analyses by capillary zone electrophoresis where isotachophoresis is induced by the sample itself. Finally, the paper presents a list of recommended, user-friendly, electrolyte systems which enable one to simply predict the performance of the combination isotachophoresis-zone electrophoresis.     

Simultaneous loading of 200 sample lanes for DNA sequencing on vertical and horizontal, standard and ultrathin gels.

We have developed a simple and efficient technique for automated parallel loading of >/=200 lanes on a 30 cm-wide gel in automated DNA sequencing, using porous filter materials and an associated manual or robotic system. The samples are loaded onto the teeth of a comb made of the porous material. The comb, with samples, is inserted directly above the straight edge of the polymerized gel. The samples are driven from the comb into the gel by the applied electrical field. A particularly advantageous aspect of this method is the elimination of the thin gel walls separating the sample wells in the standard gel loading technique. The time for sample loading is significantly reduced to a few minutes. The loading technique is applicable to horizontal or vertical systems, with standard or ultrathin gels.     

Sample storage for soil enzyme activity and bacterial community profiles

Storage of samples is often an unavoidable step in environmental data collection, since available analytical capacity seldom permits immediate processing of large sample sets needed for representative data. In microbiological soil studies, sample pretreatments may have a strong influence on measurement results, and thus careful consideration is required in the selection of storage conditions. The aim of this study was to investigate the suitability of prolonged (up to 16 weeks) frozen or air-dried storage for divergent soil materials. The samples selected to this study were mineral soil (clay loam) from an agricultural field, humus from a pine forest and compost from a municipal sewage sludge composting field. The measured microbiological parameters included functional profiling with ten different hydrolysing enzyme activities determined by artificial fluorogenic substrates, and structural profiling with bacterial 16S rDNA community fingerprints by amplicon length heterogeneity analysis (LH-PCR). Storage of samples affected the observed fluorescence intensity of the enzyme assay's fluorophor standards dissolved in soil suspension. The impact was highly dependent on the soil matrix and storage method, making it important to use separate standardisation for each combination of matrix type, storage method and time. Freezing proved to be a better storage method than air-drying for all the matrices and enzyme activities studied. The effect of freezing on the enzyme activities was small (< 20%) in clay loam and forest humus and moderate (generally 20-30%) in compost. The most dramatic decreases (> 50%) in activity were observed in compost after air-drying. The bacterial LH-PCR community fingerprints were unaffected by frozen storage in all matrices. The effect of storage treatments was tested using a new statistical method based on showing similarity rather than difference of results.     

A validated method for the detection and quantitation of 50 drugs of abuse and medicinal drugs in oral fluid by gas chromatography-mass spectrometry

Oral fluid is of increasing interest as an alternative sample matrix in drugs of abuse analysis. Compared to the conventional sample matrix blood, sample volumes of oral fluid are smaller and the concentrations of some drugs can be much lower. This imposes some restrictions on the analysis method, which has to be able to detect and quantify multiple analytes from a small sample volume at low concentrations. A sensitive multi-component method for quantitative determination of 50 drug compounds from oral fluid samples collected with the StatSure SalivaSampler? device was developed. The compounds analysed include cannabis, cocaine, amphetamines, opioids, benzodiazepines and other psychoactive medicines. Both liquid–liquid-extraction (LLE) and solid-phase-extraction (SPE) are employed in the sample pre-treatment and the samples are analysed using gas chromatography–mass spectrometry (GC–MS) with the mass selective detector (MSD) operating in either electron ionization (EI) or negative-ion chemical ionization (NICI) mode. The method was fully validated, and the validated parameters included linearity, selectivity, accuracy, precision, and extraction efficiency. Stability of the collected samples during storage at ?18 °C was also studied, and even after over a year's storage all analyte concentrations were more than 60% of the original concentrations. The described method is suitable for routine analysis of oral fluid samples and it has been applied to analysis of more than 4000 oral fluid samples collected anonymously from volunteer road users in Finland during 2007–2009 as a part of the EU project DRUID (Driving under the Influence of Drugs, Alcohol and Medicines). At the moment the developed method is the most comprehensive validated analysis method for oral fluid samples.     

Orientation of Small Specimens for Cryosectioning

A simple technique is introduced to achieve symmetrically oriented frozen sections of small specimens such as young fish or frog larvae. Small samples are especially difficult to orient if they are already frozen to the chuck in a freezing microtome. Orientation of the sample in a mold filled with embedding medium prior to freezing permits sectioning as well as easy labeling and storage of the specimens. The use of a stereo microscope during orientation is optional.     

Automated sample mounting and alignment system for biological crystallography at a synchrotron source

High-throughput data collection for macromolecular crystallography requires an automated sample mounting and alignment system for cryo-protected crystals that functions reliably when integrated into protein-crystallography beamlines at synchrotrons. Rapid mounting and dismounting of the samples increases the efficiency of the crystal screening and data collection processes, where many crystals can be tested for the quality of diffraction. The sample-mounting subsystem has random access to 112 samples, stored under liquid nitrogen. Results of extensive tests regarding the performance and reliability of the system are presented. To further increase throughput, we have also developed a sample transport/storage system based on "puck-shaped" cassettes, which can hold sixteen samples each. Seven cassettes fit into a standard dry shipping Dewar. The capabilities of a robotic crystal mounting and alignment system with instrumentation control software and a relational database allows for automated screening and data collection to be developed.     

Different chromosomal distribution patterns of radiation-induced interchange breakpoints in barley: first post-treatment mitosis versus viable offspring.

Translocation breakpoints (TBs) induced by ionizing radiation are nonrandomly distributed along barley chromosomes. When first post-treatment mitoses were evaluated, centromeres and the heterochromatin-containing proximal segments tended to be more than randomly involved, and terminal segments to be less than randomly involved in translocations. Contrary to this, small chromosomal regions in median and distal arm positions, characterized by high recombination rates and high gene density, were identified as preferred sites for the origination of viable translocations, probably due to deviations in chromatin organization. Apparently, the position of a TB has an influence on the rate of viability versus elimination of the carrier cells. Surprisingly, TBs within centromeres and heterochromatin-containing segments seem to be more harmful for survival than those induced in gene-rich regions.