BrdU-33258 Hoechst analysis of DNA replication in human lymphocytes with supernumerary or structurally abnormal X chromosomes

BrdU-33258 Hoechst techniques have been used to characterize DNA replication patterns in lymphocytes from human females with supernumerary or structurally abnormal X chromosomes. Fluorescence analysis permits identification of late replicating X chromosomes in a very high proportion of cells and affords a high resolution method for determining the interchange points of X-X and X-autosome translocations. Asynchrony among terminal replication patterns of multiple late replicating X chromosomes within an individual cell can occasionally be demonstrated. The arms of isochromosomes usually exhibit symmetrical fluorescence patterns, with replication terminating in bands Xq21 and Xq23 (predominant pattern) or in bands Xq25 and Xq27 (alternative pattern) in both arms. In the vast majority of lymphocytes containing a balanced X-13 or X-19 translocation, the normal X is late replicating. However, DNA synthesis in the translocation products occasionally appears somewhat delayed relative to that expected for an early replicating X, consistent with possible position effects on replication kinetics.     

Three interesting cases of Down's syndrome

The results of the cytogenetic study of three families that have children affected by Down's syndrome are presented. The karyotype of case 1 was 48,XY,+21,22s+,+mar; the marker chromosome had been produced "de novo". Case 2 was: 47,X,t(Xq21q), +t(21qXq); the abnormality had been produced "de novo". Case 3 was carrier of a homogeneous trisomy 21 (47,XY,+21), where the mother was carrier of a balanced translocation 13q14q. CBG, GTG, Ag-NOR, QFQ and FPG banding techniques were used to determine the origin and importance of these anomalies.     

Endonuclease-mediated long PCR and its application to restriction mapping

The polymerase chain reaction (PCR) is the most widely used technique for the study of DNA. Applications for PCR have been extended significantly by the development of "long" PCR, a technique that makes it possible to amplify DNA fragments up to 40 kb in length. This article describes two novel applications of the long PCR technique, one which simplifies restriction mapping and another which enhances amplification specificity and yield. The same primers used to perform the long PCR amplification can be used as probes to perform restriction mapping of the DNA fragment amplified. Restriction digestion performed prior to long PCR amplification can be used to selectively suppress the amplification of members of families of closely related DNA sequences, thereby making it possible to selectively amplify one of a group of highly homologous sequences. These two complimentary techniques, both involving use of the long PCR paired with restriction digestion, have potential application in any laboratory in which PCR is performed.     

Two-year death prediction models among patients with Chagas Disease using machine learning-based methods

Chagas disease (CD) is recognized by the World Health Organization as one of the thirteen most neglected tropical diseases. More than 80% of people affected by CD will not have access to diagnosis and continued treatment, which partly supports the high morbidity and mortality rate. Machine Learning (ML) can identify patterns in data that can be used to increase our understanding of a specific problem or make predictions about the future. Thus, the aim of this study was to evaluate different models of ML to predict death in two years of patients with CD. ML models were developed using different techniques and configurations. The techniques used were: Random Forests, Adaptive Boosting, Decision Tree, Support Vector Machine, and Artificial Neural Networks. The adopted settings considered only interview variables, only complementary exam variables, and finally, both mixed. Data from a cohort study with CD patients called SaMi-Trop were analyzed. The predictor variables came from the baseline; and the outcome, which was death, came from the first follow-up. All models were evaluated in terms of Sensitivity, Specificity and G-mean. Among the 1694 individuals with CD considered, 134 (7.9%) died within two years of follow-up. Using only the predictor variables from the interview, the different techniques achieved a maximum G-mean of 0.64 in predicting death. Using only the variables from complementary exams, the G-mean was up to 0.77. In this configuration, the protagonism of NT-proBNP was evident, where it was possible to observe that an ML model using only this single variable reached G-mean of 0.76. The configuration that mixed interview variables and complementary exams achieved G-mean of 0.75. ML can be used as a useful tool with the potential to contribute to the management of patients with CD, by identifying patients with the highest probability of death.Trial Registration: This trial is registered with ClinicalTrials.gov, Trial ID: {"type":"clinical-trial","attrs":{"text":"NCT02646943","term_id":"NCT02646943"}}NCT02646943.     

Apoptosis can be detected in attached colonic adenocarcinoma HT29 cells using annexin V binding, but not by TUNEL assay or sub-G0 DNA content

BACKGROUND: Induction of apoptosis in adherent cell lines is associated with cell loss from the substratum. In this study the adenocarcinoma cell line, HT29, treated with indomethacin (400microM) has been employed as a model system to demonstrate how flow cytometric analysis can be used to quantify the changes that occur during this process. METHODS: Adherent and floating cell populations have been analyzed independently for effects on cell number, cell cycle characteristics and apoptosis using TUNEL assay and Annexin V binding. In addition apoptosis has been assessed using DNA laddering and morphology. RESULTS: Apoptosis was detected in adherent cells treated with indomethacin using Annexin V binding but not by other techniques employed in this study. In contrast, analysis of "floating" cells revealed the presence of apoptotic cells both in control and indomethacin treated cells using all the techniques employed. However quantification by flow cytometry showed that a significantly higher proportion of control "floaters" were late apoptotic/necrotic rather than apoptotic. DISCUSSION: The data here illustrate the need to interpret measures of apoptosis in adherent cell lines with care and the value of using flow cytometric techniques in the quantitative evaluation of the process.     

An industrial application of multiparameter flow cytometry: assessment of cell physiological state and its application to the study of microbial fermentations.

BACKGROUND: When using traditional microbiological techniques to monitor cell proliferation and viability, stressed, sublethally injured, or otherwise "viable but nonculturable" cells often go undetected. Because of this, such cells often are not considered by mathematical models used to predict bioprocess performance on scale-up and inaccuracies result. Therefore, analytical techniques, decoupled from postsampling growth, are desirable to rapidly monitor individual cell physiologic states during microbial fermentations. METHODS: Microbial cells, including Escherichia coli, Rhodococus sp., and Sacharomyces cerevisiae, were taken at various stages from a range of fermentation processes and stained with one of three mixtures of fluorescent stains: rhodamine 123/propidium iodide, bis-oxonol/propidium iodide, or bis-oxonol/ethidium bromide/propidium iodide. An individual cell's physiologic state was assessed with a Coulter Epics Elite analyzer based on the differential uptakes of these fluorescent stains. RESULTS: It was possible to resolve an individual cell's physiologic state beyond culturability based on the functionality of dye extrusion pumps and the presence or absence of an intact polarized cytoplasmic membrane, enabling assessment of population heterogeneity. This approach allows the simultaneous differentiation of at least four functional subpopulations in microbial populations. CONCLUSIONS: Fluorescent staining methods used in our laboratories have led to a functional classification of the physiological state of individual microbial cells based on reproductive activity, metabolic activity, and membrane integrity. We have used these techniques extensively for monitoring the stress responses of microorganisms in such diverse areas as bioremediation, biotransformation, food processing, and microbial fermentation; microbial fermentation is discussed in this article.     

Determination of tularemia antibodies by an immunoenzyme method on a solid-phase carrier (ELISA)

ELISA "sandwich" techniques have been developed and the optimum assay conditions for detecting specific antibodies in human serum samples have been determined. The possibility of using these techniques for the determination of the level of antibodies to tularemia antigens in the sera of persons immunized with live tularemia vaccine has been shown. Statistically significant differences in the level of antibodies to tularemia antigen in the sera of immunized and nonimmunized persons have been established. The comparative study of five serological methods - ELISA, the agglutination test, the passive hemagglutination test, the immunofluorescence test and the defined antigen substrate sera ( DASS ) techniques - has revealed the advantage of ELISA, whose sensitivity has proved to be considerably higher than that of all other methods used in our work.     

Spectral analysis and fingerprinting for biomedia characterisation

Classical culture media, as well as domestic and/or industrial wastewater treated by biological processes, have a complex composition. The on-line and/or in situ determination of some substances is possible, but expensive, as sample collection and pre-treatment are often necessary with strict rules of sterility. More global methods can be used to detect rapidly "accidents" such as the appearance of an undesirable by-product in a fermentation broth or of a toxic substance in wastewater. These methods combine a "hard" part, for sensing, and a "soft" part, for data treatment. Among potential "hard" candidates, spectroscopy can be the basis for non-invasive and non-destructive measuring systems. Some of them have been already tested in situ: ultra-violet-visible, infra-red (mid or near), fluorescence (mono-dimensional, two-dimensional or synchronous), dielectric, while others, more sophisticated, such as mass spectrometry, coupled or not to pyrolysis, nuclear magnetic resonance and Raman spectroscopy, have been proposed. All these methods provide spectra, i.e. large sets of data, from which meaningful information should be rapidly extracted, either for analysis or fingerprinting. The recourse to data-mining techniques (the "soft" part) such as principal components analysis, projection on latent structures or artificial neural networks, is a necessary step for that task. A review of techniques, mostly based on spectroscopy, with examples taken in the bioengineering field in general is proposed.     

Ability of static and statistical mechanics posturographic measures to distinguish between age and fall risk

Traditional posturographic analysis and four statistical mechanics techniques were applied to center-of-pressure (COP) trajectories of young, older "low-fall-risk" and older "high-fall-risk" individuals. Low-fall-risk older adults were active 3 days per week in a cardiac rehabilitation program, while high-fall-risk older adults were diagnosed with perilymph fistula. Subjects diagnosed with perilymph fistula must have experienced two of the following vestibular findings: constant disequilibrium, positional vertigo and/or a positive fistula test. Non-parametric statistical tests were used to determine whether the posturographic measures could detect differences between the young and older "low-fall-risk" groups (age comparison) and between the older "low-" and "high-risk" groups (risk of falling comparison). The statistical mechanics techniques were more sensitive than the traditional measures: detecting significant differences between the young and older "low-risk" groups, while none of the traditional measures were significantly different. In addition, interpretation of the statistical mechanics techniques may offer more insight into the nature of the process controlling the COP trajectories. However, the methods offered slightly different explanations. For instance, the Hurst rescaled range analysis suggests that the movement of the COP is governed solely by anti-persistent behavior, whereas the stabilogram diffusion analysis suggests a short-term persistence balanced by a long-term anti-persistence. These discrepancies highlight the need for a model that incorporates the biological systems responsible for maintaining balance and experimental methods to directly quantify their status and roles. Until such a model exists, however, the statistical mechanics techniques appear to have some advantages over traditional posturographic measures for studying balance control.     

Videomicroscopy in the study of protoplasmic streaming and cell movement

Summary Various types of cell motility have been observed and analyzed with techniques of increasing sensitivity and sophistication. Photokymography, cinemicrography and laser-Doppler spectroscopy have all made important contributions to our knowledge of cytoplasmic streaming and cell movement.Now videomicroscopy is finding applications in recording and analyzing two different kinds of images. Video intensification microscopy by image intensifiers and silicon intensified target (SIT) video cameras is used to intensify images too dim to be viewed by eye or photographed. On the other hand, video enhanced microscopy uses a less sensitive chalnicon or other vidicon camera with adjustable amplification and offset to enhance the contrast and improve the resolution of microscopes that employ instrumental compensators.Both of these videotechniques have greatly extended the usefulness of the optical microscope: image intensification to brighten dim images and video enhancement to improve the contrast and resolution so that even submicroscopic structures and events can be recorded. These video techniques can both be further extended by a frame memory, with which images can be further enhanced by computer processing. Still to be developed, however, are appropriate methods for automatic tracking of particle motions.     

An overview of the assessment of aquatic ecosystem health using benthic invertebrates

Community structure or species composition of benthic invertebrates has frequently been used in environmental monitoring and assessment of aquatic systems. Three general approaches have been taken: the saprobic approach, which requires detailed knowledge of taxonomy and is most effective in measuring impacts from sewage effluents; diversity indices, which do not require detailed knowledge of species requirements but ignore information provided by important species and tend to lose information; and biotic indices, which combine both approaches. In the past few years considerable advances have been made by applying multivariate statistical techniques to large data matrices and relating benthic community structure to key environmental variables. Using these techniques it is possible to establish reference communities for a set of environmental conditions, to predict the benthic community that should occur at new sites and thus measure deviation from an expected community type. This suggests that environmental criteria and objectives can be established based on biological variables as opposed to the more traditional chemical approach.Measurement of ecosystem health using functional attributes of benthic invertebrates is generally in the development stage. In the future, functional measures of ecosystem health, such as chronic measures of toxicity or stress, should be incorporated into any assessment process.     

Relationships between genomic base content and distribution of mass in coded proteins

The aim of this research was to examine the possible significance of genome/protein relationships in terms of effects on distribution of mass, especially in proteins. Amino acid residues in proteins have side-chains and polypeptide segments. We use "SCM" (side-chain mass), "MCM" (main-chain mass), and "deltaM" (SCM-MCM) as the deviation from "mass balance." Total MCM of the 61 amino acids in the standard code, 3412, equals total SCM: they form a mass balanced set (mean deltaM = 0). Of 14 natural variants of the code, seven have slightly positive mean deltaM values and seven have slightly negative values. Codes with the standard amino acids assigned randomly to the 20 codon sets of the standard code have about one chance in 3,300 of producing a mass balanced set. In natural proteins, as %A + T increases, the proportion of the mass in the side-chains also increases, by about half the amount calculated for standard genes with various AT/GC ratios, partly due to selection of codons with greater variability in composition at synonymous sites. For 203 representative species (including organelles), the total protein mass is distributed approximately equally between SCM and MCM (overall mean deltaM/amino acid residue, -0.06). The attainment of some overall macromolecular mass balance may have been a criterion for selecting the codon/amino acid pairs. When both structural and dynamic requirements are considered, a genetic code based on hydrophobicity and mass balance as key properties seems likely.     

Comparison of a culture‐based and a PCR‐based methods for estimating bacterial abundance on eggshells,with comments on statistical analyses

Field ornithologists have used traditional culture‐based techniques to determine the presence and abundance of microbes on surfaces such as eggshells, but culture‐independent PCR‐based methods have recently been introduced. We compared the traditional culture‐based and the real‐time PCR‐based methods for detecting and quantifying Escherichia coli on the eggshells of Eurasian Magpies (Pica pica). PCR estimates of bacterial abundance were ～10 times higher than culture‐based estimates, and the culture‐based technique failed to detect bacteria at lower densities. When both methods detected bacteria, bacterial densities determined by the two methods were positively correlated, indicating that both methods can be used to study factors affecting bacterial densities. The difference between the two methods is consistent with generally acknowledged higher sensitivity of the PCR method, but the extent of the difference in our study (10×) may have been influenced by both a PCR‐based overestimation and culture‐based underestimation of bacterial densities. Our results also illustrate that bacterial counts may sometimes produce left‐censored data (i.e., we did not detect E. coli in 62% of our samples using the culture‐based method). Specific statistical methods have been developed for analyzed left‐censored data, but, to our knowledge, have not been used by ornithologists. In future studies, investigators studying bacterial loads should provide information about the possible degree of left censoring and should justify their choice of statistical methods from the broad set of available methods, including those explicitly designed for censored data.     

Analysis of the HLA-DRw8 haplotype: Recognition by HTC typing of three distinct antigen complexes in Caucasians,Native Americans,and Orientals

We have used seven HLA-D homozygous typing cells (HTC) in a comparative study of the DRw8 antigen complex in three racial groups. Three distinct HLA-D specificities were recognized, each associated with HLA-DRw8. Four of the HTC defined a DRw8-associated HLA-D specificity designated 8.1, one defined a specificity designated 8.2, and two defined a specificity designated 8.3. Each of the three specificities showed an association with a distinct racial group: Dw"8.1" in Caucasians, Dw"8.2" in Pacific Northwest Indians, and Dw"8.3" in Orientals. An informative primed lymphocyte (PLT) cell generated against a Dw"8.1" haplotype was able to distinguish 8.1 from 8.2 and 8.3. Using selected anti-DRw8 sera, a serologic distinction between 8.1 and 8.3 could also be made. It was thus possible, by using both cellular and serologic techniques in a comparative population study, to recognize at least three HLA-D-defined splits of the DRw8 haplotype.     

Single-molecule studies of complex systems: the replisome

A complete, system-level understanding of biological processes requires comprehensive information on the kinetics and thermodynamics of the underlying biochemical reactions. A wide variety of structural, biochemical, and molecular biological techniques have led to a quantitative understanding of the molecular properties and mechanisms essential to the processes of life. Yet, the ensemble averaging inherent to these techniques limits us in understanding the dynamic behavior of the molecular participants. Recent advances in imaging and molecular manipulation techniques have made it possible to observe the activity of individual enzymes and record "molecular movies" that provide insight into their dynamics and reaction mechanisms. An important future goal is extending the applicability of single-molecule techniques to the study of larger, more complex multi-protein systems. In this review, the DNA replication machinery will be used as an example to illustrate recent progress in the development of various single-molecule techniques and its contribution to our understanding of the orchestration of multiple enzymatic processes in large biomolecular systems.     

Structural principles governing domain motions in proteins.

With the use of a recently developed method, twenty-four proteins for which two or more X-ray conformers are known have been analyzed to reveal structural principles that govern domain motions in proteins. In all 24 cases, the domain motion is a rotation about a physical axis created through local interactions both covalent and noncovalent. In many cases, two or more mechanical hinges separated in space create a stable hinge axis for precise control of the domain closure. The terminal regions of alpha-helices and beta-sheets have been found to act as mechanical hinges in a significant number of cases. In some cases, the two terminal regions of neighboring strands of a single beta-sheet can create a hinge axis, as can the two termini of a single alpha-helix. These two structures have been termed the "double-hinged beta-sheet" and "double-hinged alpha-helix," respectively. A flexible loop that attaches one domain to another and through which the effective hinge axis passes is another construct that is used to create a hinge. Noncovalent interactions between segments remote along the polypeptide chain can also form hinges. In addition alpha-helices that preserve their hydrogen bonding structure when bent have been found to behave as mechanical hinges. It is suggested that these alpha-helices act as a store of elastic energy that drives the closing of domains for rapid capture of the substrate. If the repertoire of possible interdomain structures is as limited as this study suggests, the dynamic behavior of proteins could soon be predicted using bioinformatics techniques. Proteins 1999;36:425-435.     

Simultaneous X-ray imaging of plant root growth and water uptake in thin-slab systems

Direct and simultaneous observation of root growth and plant water uptake is difficult because soils are opaque. X-ray imaging techniques such as projection radiography or Computer Tomography (CT) offer a partial alternative to such limitations. Nevertheless, there is a trade-off between resolution, large field-of-view and 3-dimensionality: With the current state of the technology, it is possible to have any two. In this study, we used X-ray transmission through thin-slab systems to monitor transient saturation fields that develop around roots as plants grow. Although restricted to 2-dimensions, this approach offers a large field-of-view together with high spatial and dynamic resolutions. To illustrate the potential of this technology, we grew peas in 1 cm thick containers filled with soil and imaged them at regular intervals. The dynamics of both the root growth and the water content field that developed around the roots could be conveniently monitored. Compared to other techniques such as X-ray CT, our system is relatively inexpensive and easy to implement. It can potentially be applied to study many agronomic problems, such as issues related to the impact of soil constraints (physical, chemical or biological) on root development.     

Isolation, stages of differentiation, and long term maintenance of adult rat myocytes

Although a variety of techniques have been developed to isolate myocytes from adult hearts, the long term viability of such cells has only recently been investigated. In addition, relatively little is known about the stages of differentiation such cells proceed through following isolation. In the present study myocytes were isolated using two techniques, one involving retrograde perfusion via the aorta, and the other involving mechanical "shearing." In addition, several modifications were made to minimize the trauma normal associated with isolating myocytes from adult hearts. Both techniques yielded a high percentage of rod-shaped, quiescent myocytes, although myocytes isolated using the "shearing" method were less likely to remain viable for more than 24 hours. With both techniques those cells which remained viable for more than 24 hours proceeded through an identical pattern of differentiation leading to stable, attached cells which remained viable for up to four weeks. These results demonstrate that with the appropriate isolation techniques it is possible to maintain adult myocardial cells in culture for lengthy periods of time.     

Low impedance walking robots

For both historical and technological reasons, most robots,including those meant to mimic animals or operate in naturalenvironments,³ use actuators and control systems that have high(stiff) mechanical impedance. By contrast, most animals exhibitlow (soft) impedance. While a robot's stiff joints may be programmedto closely imitate the recorded motion of an animal's soft joints,any unexpected position disturbances will generate reactiveforces and torques much higher for the robot than for the animal.The dual of this is also true: while an animal will react toa force disturbance by significantly yielding position, a typicalrobot will greatly resist. These differences cause three deleterious effects for high impedancerobots. First, the higher forces may cause damage to the robotor to its environment (which is particularly important if thatenvironment includes people). Second, the robot must acquirevery precise information about its position relative to theenvironment so as to minimize its velocity upon impact. Third,many of the self-stabilizing effects of natural dynamics are"shorted out"⁴ by the robot's high impedance, so that stabilizationrequires more effort from the control system. Over the past 5 yr, our laboratory has designed a series ofwalking robots based on "Series-Elastic Actuators" and "VirtualModel Control." Using these two techniques, we have been ableto build low-impedance walking robots that are both safe androbust, that operate blindly without any model of upcoming terrain,and that add minimal control effort in parallel to their self-stabilizingpassive dynamics. We have discovered that it is possible toachieve surprisingly effective ambulation from rather simplemechanisms and control systems. After describing the historicaland technological motivations for our approach, this paper givesan overview of our methods and shows some of the results wehave obtained.