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PubMed1999

Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.

Animals↗

PubMedDate not supplied

Tomato root growth, gravitropism, and lateral development: correlation with auxin transport.

Tomato (Lycopersicon esculentum, Mill.) roots were analyzed during growth on agar plates. Growth of these roots was inhibited by the auxin transport inhibitors naphthylphthalamic acid (NPA) and semicarbazone derivative I (SCB-1). The effect of auxin transport inhibitors on root gravitropism was analyzed by measurement of the angle of gravitropic curvature after the roots were reoriented 90 degrees from the vertical. NPA and SCB-1 abolished both the response of these roots to gravity and the formation of lateral roots, with SCB-1 being the more effective at inhibition. Auxins also inhibited root growth. Both auxins tested has a slight effect on the gravity response, but this effect is probably indirect, since auxins reduced the growth rate. Auxins also stimulated lateral root growth at concentration where primary root growth was inhibited. When roots were treated with both IAA and NPA simultaneously, a cumulative inhibition of root growth was found. When both compounds were applied together, analysis of gravitropism and lateral root formation indicated that the dominant effect was exerted by auxin transport inhibitors. Together, these data suggest a model for the role of auxin transport in controlling both primary and lateral root growth.

Biological Transport↗

PubMed1987

Observations of HCN in comet P/Halley.

We present observations of the HCN J = 1-0 rotational transition at 3.4 mm wavelength in comet P/Halley. The data were obtained during a total of 56 individual observing sessions between November 1985 and May 1986 and represent the first time that a cometary parent molecule has been so extensively monitored. The HCN production rate is well correlated with the total visual magnitude of the comet, and comparison of the HCN production to the total gas production of the comet indicates that it is a relatively minor constituent with 0.1% the abundance of H2O. Comparison of HCN and CN production suggests that HCN is a major parent molecule of CN, but probably not the sole parent. HCN spectra obtained by binning the data with heliocentric distance show that the line width, and thus the parent outflow velocity, increases with decreasing heliocentric distance, and that there is a tendency for the lines to be blue shifted due to anisotropic outgassing from the nucleus. Finally, there is evidence of day-to-day time variability in the total HCN emission and in the hyperfine ratios. The time variation of the total emission is consistent with the known time variable behavior of the comet, and detailed comparisons to optical data, where possible, confirm this interpretation. However, non-LTE values of the hyperfine ratios are not consistent with theoretical modeling of the excitation of these transitions.

Astronomical Phenomena↗

PubMed1996

Sequence of the bchG gene from Chloroflexus aurantiacus: relationship between chlorophyll synthase and other polyprenyltransferases.

The sequence of the Chloroflexus aurantiacus open reading frame thought to be the C. aurantiacus homolog of the Rhodobacter capsulatus bchG gene is reported. The BchG gene product catalyzes esterification of bacteriochlorophyllide a by geranylgeraniol-PPi during bacteriochlorophyll a biosynthesis. Homologs from Arabidopsis thaliana, Synechocystis sp. strain PCC6803, and C. aurantiacus were identified in database searches. Profile analysis identified three related polyprenyltransferase enzymes which attach an aliphatic alcohol PPi to an aromatic substrate. This suggests a broader relationship between chlorophyll synthases and other polyprenyltransferases.

Amino Acid Sequence↗

PubMed1996

Two-stage model of radon-induced malignant lung tumors in rats: effects of cell killing.

A two-stage stochastic model of carcinogenesis is used to analyze lung tumor incidence in 3750 rats exposed to varying regimens of radon carried on a constant-concentration uranium ore dust aerosol. New to this analysis is the parameterization of the model such that cell killing by the alpha particles could be included. The model contains parameters characterizing the rate of the first mutation, the net proliferation rate of initiated cells, the ratio of the rates of cell loss (cell killing plus differentiation) and cell division, and the lag time between the appearance of the first malignant cell and the tumor. Data analysis was by standard maximum likelihood estimation techniques. Results indicate that the rate of the first mutation is dependent on radon and consistent with in vitro rates measured experimentally, and that the rate of the second mutation is not dependent on radon. An initial sharp rise in the net proliferation rate of initiated cell was found with increasing exposure rate (denoted model I), which leads to an unrealistically high cell-killing coefficient. A second model (model II) was studied, in which the initial rise was attributed to promotion via a step function, implying that it is due not to radon but to the uranium ore dust. This model resulted in values for the cell-killing coefficient consistent with those found for in vitro cells. An "inverse dose-rate" effect is seen, i.e. an increase in the lifetime probability of tumor with a decrease in exposure rate. This is attributed in large part to promotion of intermediate lesions. Since model II is preferable on biological grounds (it yields a plausible cell-killing coefficient), such as uranium ore dust. This analysis presents evidence that a two-stage model describes the data adequately and generates hypotheses regarding the mechanism of radon-induced carcinogenesis.

Animals↗

PubMed2005

A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data.

Analysis of large-scale gene expression studies usually begins with gene clustering. A ubiquitous problem is that different algorithms applied to the same data inevitably give different results, and the differences are often substantial, involving a quarter or more of the genes analyzed. This raises a series of important but nettlesome questions: How are different clustering results related to each other and to the underlying data structure? Is one clustering objectively superior to another? Which differences, if any, are likely candidates to be biologically important? A systematic and quantitative way to address these questions is needed, together with an effective way to integrate and leverage expression results with other kinds of large-scale data and annotations. We developed a mathematical and computational framework to help quantify, compare, visualize and interactively mine clusterings. We show that by coupling confusion matrices with appropriate metrics (linear assignment and normalized mutual information scores), one can quantify and map differences between clusterings. A version of receiver operator characteristic analysis proved effective for quantifying and visualizing cluster quality and overlap. These methods, plus a flexible library of clustering algorithms, can be called from a new expandable set of software tools called CompClust 1.0 (http://woldlab.caltech.edu/compClust/). CompClust also makes it possible to relate expression clustering patterns to DNA sequence motif occurrences, protein-DNA interaction measurements and various kinds of functional annotations. Test analyses used yeast cell cycle data and revealed data structure not obvious under all algorithms. These results were then integrated with transcription motif and global protein-DNA interaction data to identify G1 regulatory modules.

Algorithms↗

PubMed1987

Design of an elemental analysis system for CELSS research.

The results of experiments conducted with higher plants in tightly sealed growth chambers provide definite evidence that the physical closure of a chamber has significant effects on many aspects of a plant's biology. One of these effects is seen in the change in rates of uptake, distribution, and re-release of nutrient elements by the plant (mass balance). Experimental data indicates that these rates are different from those recorded for plants grown in open field agriculture, or in open growth chambers. Since higher plants are a crucial component of a CELSS, it is important that the consequences of these rate differences be understood with regard to the growth and yield of the plants. This paper will focus on the description of a system for elemental analysis which can be used to monitor the mass balance of nutrient elements in CELSS experiments. Additionally, data on the uptake of nutrient elements by higher plants grown in a growth chamber will be presented.

Anions↗

PubMed1998

Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds.

A new bacterial species belonging to the genus Shewanella is described on the basis of phenotypic characterization and sequence analysis of its 16S rRNA-encoding and gyrase B (gyrB) genes. This organism, isolated from shallow-water marine sediments derived from the Amazon River delta, is a Gram-negative, motile, polarly flagellated, facultatively anaerobic, rod-shaped eubacterium and has a G&C content of 51.7 mol%. Strain SB2BT is exceptionally active in the anaerobic reduction of iron, manganese and sulfur compounds. SB2BT grows optimally at 35 degrees C, with 1-3% NaCl and over a pH range of 7-8. Analysis of the 16S rDNA sequence revealed a clear affiliation between strain SB2BT and members of the gamma subclass of the class Proteobacteria. High similarity values were found with certain members of the genus Shewanella, especially with Shewanella putrefaciens, and this was supported by cellular fatty acid profiles and phenotypic characterization. DNA-DNA hybridization between strain SB2BT and its phylogenetically closest relatives revealed low similarity values (24.6-42.7%) which indicated species status for strain SB2BT. That SB2BT represents a distinct bacterial species within the genus Shewanella is also supported by gyrB sequence analysis. Considering the source of the isolate, the name Shewanella amazonensis sp. nov. is proposed and strain SB2BT (= ATCC 700329T) is designated as the type strain.

Base Sequence↗

PubMed1994

Galactic cosmic ray abundances and spectra behind defined shielding.

LET spectra have been measured for lunar missions and for several near Earth orbits ranging from 28 degrees to 83 degrees inclination. In some of the experiments the flux of GCR was determined separately from contributions caused by interactions in the detector material. Results of these experiments are compared to model calculations. The general agreement justifies the use of the model to calculate GCR fluxes. The magnitude of variations caused by solar modulation, geomagnetic shielding, and shielding by matter determined from calculated LET spectra is generally in agreement with experimental data. However, more detailed investigations show that there are some weak points in modeling solar modulation and shielding by material. These points are discussed in more detail.

Cosmic Radiation↗

PubMed1997

Assessment of a portable clinical blood analyzer during space flight.

This study was designed to validate the utility of a commercial portable clinical blood analyzer (PCBA) in ground-based studies and on the space shuttle. Ionized calcium, pH, electrolytes, glucose, and hematocrit were determined. Results agreed well with those from traditional laboratory methods, and the PCBA demonstrated good between-day precision for all analytes. In-flight analysis of control samples revealed differences in one analyte (sodium). There were few changes in crew members' results during flight, and these were expected. Potassium increased in flight compared with before flight, and potassium, pH, and hematocrit decreased after flight. Ionized calcium was decreased in flight and on landing day. Changes during flight were likely related to sample collection technique. Postflight changes likely reflected the fluid redistribution that occurs after exposure to weightlessness. These data confirm that the PCBA is a reliable instrument for most analytes, and can provide important medical data in remote locations, such as orbiting spacecraft.

Adult↗

PubMed2003

A statistical model of diurnal variation in human growth hormone.

The diurnal pattern of growth hormone (GH) serum levels depends on the frequency and amplitude of GH secretory events, the kinetics of GH infusion into and clearance from the circulation, and the feedback of GH on its secretion. We present a two-dimensional linear differential equation model based on these physiological principles to describe GH diurnal patterns. The model characterizes the onset times of the secretory events, the secretory event amplitudes, as well as the infusion, clearance, and feedback half-lives of GH. We illustrate the model by using maximum likelihood methods to fit it to GH measurements collected in 12 normal, healthy women during 8 h of scheduled sleep and a 16-h circadian constant-routine protocol. We assess the importance of the model components by using parameter standard error estimates and Akaike's Information Criterion. During sleep, both the median infusion and clearance half-life estimates were 13.8 min, and the median number of secretory events was 2. During the constant routine, the median infusion half-life estimate was 12.6 min, the median clearance half-life estimate was 11.7 min, and the median number of secretory events was 5. The infusion and clearance half-life estimates and the number of secretory events are consistent with current published reports. Our model gave an excellent fit to each GH data series. Our analysis paradigm suggests an approach to decomposing GH diurnal patterns that can be used to characterize the physiological properties of this hormone under normal and pathological conditions.

Adult↗

PubMed1995

A study of the radiation environment on board the Space Shuttle flight STS-57.

A joint NASA-Russian study of the radiation environment inside a SPACEHAB 2 locker on Space Shuttle flight STS-57 was conducted. The Shuttle flew in a nearly circular orbit of 28.5 degrees inclination and 462 km altitude. The locker carried a charged particle spectrometer, a tissue equivalent proportional counter (TEPC), and two area passive detectors consisting of combined NASA plastic nuclear track detectors (PNTDs) and thermoluminescent detectors (TLDs), and Russian nuclear emulsions, PNTDs and TLDs. All the detector systems were shielded by the same Shuttle mass distribution. This makes possible a direct comparison of the various dose measurement techniques. In addition, measurements of the neutron energy spectrum were made using the proton recoil technique. The results show good agreement between the integral LET spectrum of the combined galactic and trapped particles using the tissue equivalent proportional counter and track detectors between about 15 keV/micrometers and 200 keV/micrometers. The LET spectrum determined from nuclear emulsions was systematically lower by about 50%, possibly due to emulsion fading. The results show that the TEPC measured an absorbed dose 20% higher than the TLDs, due primarily to an increased TEPC response to neutrons and a low sensitivity of TLDs to high LET particles under normal processing techniques. There is a significant flux of high energy neutrons that is currently not taken into consideration in dose equivalent calculations. The results of the analysis of the spectrometer data will be reported separately.

Cosmic Radiation↗

PubMed2003

Mortality of atomic bomb survivors predicted from laboratory animals.

Exposure, pathology and mortality data for mice, dogs and humans were examined to determine whether accurate interspecies predictions of radiation-induced mortality could be achieved. The analyses revealed that (1) days of life lost per unit dose can be estimated for a species even without information on radiation effects in that species, and (2) accurate predictions of age-specific radiation-induced mortality in beagles and the atomic bomb survivors can be obtained from a dose-response model for comparably exposed mice. These findings illustrate the value of comparative mortality analyses and the relevance of animal data to the study of human health effects.

Age Factors↗

PubMed2002

Alteration of gene expression profiles in skeletal muscle of rats exposed to microgravity during a spaceflight.

To clarify the mechanism of skeletal muscle wasting during spaceflights, we investigated whether intramuscular gene expression profiles are affected, by using DNA microarray methods. Male rats sent on the 17-day NASA STS-90 Neurolab spaceflight were sacrificed 24 hours after return to earth (MG group). Ground control rats were maintained for 17 days in flight-simulated cages (CS group). Spaceflight induced a 19% and 23% loss of tibialis anterior and gastrocnemius muscle mass, respectively, as compared to ground controls. Muscle RNA was analyzed by the Clontech Atlas DNA expression array in four rats, with two MG/ CS pairs for the tibialis anterior, and one pair for the gastrocnemius. Alterations in gene expression were verified for selected genes by reverse-transcription PCR. In both muscles of MG rats, mRNAs for 12 genes were up-regulated by over 2-fold, and 38 were down-regulated compared to controls. There was inhibition of genes for cell proliferation and growth factor cascades, including cell cycle genes and signal transduction proteins, such as p21 Cip1, retinoblastoma (Rb), cyclins G1/S, -E and -D3, MAP kinase 3, MAD3, and ras related protein RAB2. These data indicate that following exposure to microgravity, there is downregulation of genes involved in regulation of muscle satellite cell replication.

Animals↗

PubMedDate not supplied

Adaptation of SUBSTOR for controlled-environment potato production with elevated carbon dioxide.

The SUBSTOR crop growth model was adapted for controlled-environment hydroponic production of potato (Solanum tuberosum L. cv. Norland) under elevated atmospheric carbon dioxide concentration. Adaptations included adjustment of input files to account for cultural differences between the field and controlled environments, calibration of genetic coefficients, and adjustment of crop parameters including radiation use efficiency. Source code modifications were also performed to account for the absorption of light reflected from the surface below the crop canopy, an increased leaf senescence rate, a carbon (mass) balance to the model, and to modify the response of crop growth rate to elevated atmospheric carbon dioxide concentration. Adaptations were primarily based on growth and phenological data obtained from growth chamber experiments at Rutgers University (New Brunswick, N.J.) and from the modeling literature. Modified-SUBSTOR predictions were compared with data from Kennedy Space Center's Biomass Production Chamber for verification. Results show that, with further development, modified-SUBSTOR will be a useful tool for analysis and optimization of potato growth in controlled environments.

Biomass↗

PubMed1998

Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber.

A new method was used to probe the conformation of chromatin in living mammalian cells. The method employs ionizing radiation and is based on the concept that such radiation induces correlated breaks in DNA strands that are in spatial proximity. Human dermal fibroblasts in G0 phase of the cell cycle and Chinese hamster ovary cells in mitosis were irradiated by X-rays or accelerated ions. Following lysis of the cells, DNA fragments induced by correlated breaks were end-labeled and separated according to size on denaturing polyacrylamide gels. A characteristic peak was obtained for a fragment size of 78 bases, which is the size that corresponds to one turn of DNA around the nucleosome. Additional peaks between 175 and 450 bases reflect the relative position of nearest-neighbor nucleosomes. Theoretical calculations that simulate the indirect and direct effect of radiation on DNA demonstrate that the fragment size distributions are closely related to the chromatin structure model used. Comparison of the experimental data with theoretical results support a zig-zag model of the chromatin fiber rather than a simple helical model. Thus, radiation-induced damage analysis can provide information on chromatin structure in the living cell.

Animals↗

PubMed1988

Band structure of the solar system: an objective test of the grouping of planets and satellites.

Alfvén in his early work on the origin of the solar system (1942-1946) noted a pronounced band structure in the gravitational potential distribution of secondary bodies, and suggested this feature to be directly related to the formation process. When the critical velocity phenomenon was later discovered, a close agreement was found between the planet-satellite bands on one hand, and the critical velocity limits of the major compound elements in the interstellar medium on the other, suggesting a specific emplacement mechanism for the dusty plasma which presumably constituted the solar nebula. Since the originally perceived band structure was outlined in a qualitative fashion, an attempt is made here to analyze the distribution by a statistical technique, testing the significance of clustering of the observational data in the bands. The results show that, with proper scaling of the parameters, such a band structure indeed appears, with features closely similar to those originally conceived. Some deviations are indicated by the cluster analysis, however; their significance is discussed in terms of process involved in the formation of the solar system.

Astronomical Phenomena↗

PubMed1996

Neutron yields from interactions of GCR-like beams in stopping targets.

In order to accurately determine the radiation risk to astronauts from GCR, the nature of the secondary radiation field created by the fragmentation of GCR in shielding and tissue must be understood. Due to the their high penetrabilities, neutrons are an important component of the secondary radiation field, especially for astronauts protected by thick shielding on lunar or Martian bases. Neutron yields from 435A MeV and 272A MeV Nb stopping in Nb and Al targets are presented, along with some preliminary analysis of neutron yields from 155A MeV C stopping in Al. Energy spectra and angular distributions are shown for neutron energies above 20 MeV. The data provides some information about the dependence of the neutron yield on projectile energy and target mass. Comparisons of the data with BUU calculations are also shown.

Aluminum↗