An improved method for assaying pyrophosphate exchange measuring Cerenkov radiation

The determination of the amount of radioactivity in ³²P-labeled nucleotides absorbed to charcoal is greatly simplified when the same medium is used for extraction and for counting the secondary Cerenkov radiation. Addition of 4-methylumbelliferone increases the efficiency and decreases quenching caused by charcoal particles. With regard to reproducibility and amount of background the method is comparable to other published methods. Its application in a pyrophosphate exchange assay is described.     

Human body area factors for radiation exchange analysis: standing and walking postures

Effective radiation area factors (f _eff) and projected area factors (f _p) of unclothed Caucasians’ standing and walking postures used in estimating human radiation exchange with the surrounding environment were determined from a sample of adults in Canada. Several three-dimensional (3D) computer body models were created for standing and walking postures. Only small differences in f _eff and f _p values for standing posture were found between gender (male or female) and body type (normal- or over-weight). Differences between this study and previous studies were much larger: ≤0.173 in f _p and ≤0.101 in f _eff. Directionless f _p values for walking posture also had only minor differences between genders and positions in a stride. However, the differences of mean directional f _p values of the positions dependent on azimuth angles were large enough, ≤0.072, to create important differences in modeled radiation receipt. Differences in f _eff values were small: 0.02 between the normal-weight male and female models and up to 0.033 between positions in a stride. Variations of directional f _p values depending on solar altitudes for walking posture were narrower than those for standing posture. When both standing and walking postures are considered, the mean f _eff value, 0.836, of standing (0.826) and walking (0.846) could be used. However, f _p values should be selected carefully because differences between directional and directionless f _p values were large enough that they could influence the estimated level of human thermal sensation.     

A method of factor analysis for shape coordinates

Currently the most common reporting style for a geometric morphometric (GMM) analysis of anthropological data begins with the principal components of the shape coordinates to which the original landmark data have been converted. But this focus often frustrates the organismal biologist, mainly because principal component analysis (PCA) is not aimed at scientific interpretability of the loading patterns actually uncovered. The difficulty of making biological sense of a PCA is heightened by aspects of the shape coordinate setting that further diverge from our intuitive expectations of how morphometric measurements ought to combine. More than 50 years ago one of our sister disciplines, psychometrics, managed to build an algorithmic route from principal component analysis to scientific understanding via the toolkit generally known as factor analysis. This article introduces a modification of one standard factor‐analysis approach, Henry Kaiser's varimax rotation of 1958, that accommodates two of the major differences between the GMM context and the psychometric context for these approaches: the coexistence of “general” and “special” factors of form as adumbrated by Sewall Wright, and the typical loglinearity of partial warp variance as a function of bending energy. I briefly explain the history of principal components in biometrics and the contrast with factor analysis, introduce the modified varimax algorithm I am recommending, and work three examples that are reanalyses of previously published cranial data sets. A closing discussion emphasizes the desirability of superseding PCA by algorithms aimed at anthropological understanding rather than classification or ordination.     

An improved method for the analysis of sister-chromatid exchange in vivo

A single injection method of halogenated nucleosides for analysis in vivo of SCE is reported. Halogenated nucleosides were suspended in plant oils, such as peanut oil, and injected into mice subcutaneously. When the dosage of halogenated nucleosides reached 500 mg/kg, satisfactory differential sister chromatid staining of bone marrow cells was obtained. This technique was simple, neither special equipment nor surgical procedure was needed, and the dosage of halogenated nucleosides was relatively low.     

Advanced method for oligonucleotide deprotection

A new procedure for rapid deprotection of synthetic oligodeoxynucleotides has been developed. While all known deprotection methods require purification to remove the residual protective groups (e.g. benzamide) and insoluble silicates, the new procedure based on the use of an ammonia-free reagent mixture allows one to avoid the additional purification steps. The method can be applied to deprotect the oligodeoxynucleotides synthesized by using the standard protected nucleoside phosphoramidites dG^iBu, dC^Bz and dA^Bz.     

GrpE, a nucleotide exchange factor for DnaK

The cochaperone GrpE functions as a nucleotide exchange factor to promote dissociation of adenosine 5'-diphosphate (ADP) from the nucleotide-binding cleft of DnaK. GrpE and the DnaJ cochaperone act in concert to control the flux of unfolded polypeptides into and out of the substrate-binding domain of DnaK by regulating the nucleotide-bound state of DnaK. DnaJ stimulates nucleotide hydrolysis, and GrpE promotes the exchange of ADP for adenosine triphosphate (ATP) and also augments peptide release from the DnaK substrate-binding domain in an ATP-independent manner. The eukaryotic cytosol does not contain GrpE per se because GrpE-like function is provided by the BAG1 protein, which acts as a nucleotide exchange factor for cytosolic Hsp70s. GrpE, which plays a prominent role in mitochondria, chloroplasts, and bacterial cytoplasms, is a fascinating molecule with an unusual quaternary structure. The long alpha-helices of GrpE have been hypothesized to act as a thermosensor and to be involved in the decrease in GrpE-dependent nucleotide exchange that is observed in vitro at temperatures relevant to heat shock. This review describes the molecular biology of GrpE and focuses on the structural and kinetic aspects of nucleotide exchange, peptide release, and the thermosensor hypothesis.     

An improved method for analysis of biomass sugars and galacturonic acid by anion exchange chromatography

The most accurate analysis method for sugars in biomass, based on gas chromatography, requires a time consuming and laborious sample derivatation to trimethylsilanes or alditol acetates. In comparison, sample preparations for sugar analysis by liquid chromatography are simple water dilutions. However, HPLC methods either require long analysis times, use of expensive solvents, or do not give good resolution of sugars. A gradient method developed previously using a Dionex PA-1 column and pulsed-amperometric detection was modified to reduce analysis time from 75 to less than 40?min and provide good resolution of arabinose, rhamnose, galactose, xylose, glucose, fructose, sucrose, cellobiose, and galacturonic acid in both standards and hydrolyzed citrus waste biomass.     

Animal exchange ratios: an alternative point of view

An alternative interpretation is provided of the concepts of carrying capacity and exchange ratios, particularly suitable for game animal species, based on management models for a given area of rangeland or pasture. It involves modelling animal population dynamics as discrete‐time logistic equations. Carrying capacity is then generated endogenously using rainfall as a proxy. The model interaction parameters, also generated endogenously, represent the animal exchange ratios. Because these two parameters are generated endogenously, this approach takes into account all the animals' habitat requirements (food, cover, water and space) simultaneously, unlike other approaches that tend to consider food requirements only. This makes the approach amenable to multi‐species situations. It also captures the ecological definition of population growth models where the realized rather than the theoretical carrying capacity is determined endogenously.     

Evaluation of microwave radiation method for sample preparation of pine needles and wood for carbohydrate analysis

The aim of the current study was to test the suitability of microwave heating for stopping carbohydrate transformations in plant material. Needles and branches of Pinus sylvestris were treated in microwave oven (2.45 GHz, 800W) and compared to the samples treated in boiling ethanol (96 %). In extracts obtained from the microwaved material the ratio of sucrose to hexoses (glucose and fructose) decreased, while ethanol treatment resulted in stable extracts. The carbohydrate composition in dry samples estimated after a month of storage was persistent. The boiling of needles in ethanol in microwave oven gave the same results as boiling on a heating plate. In the woody material, differently from the needles, the total concentration of measured carbohydrates depended significantly on the preparation method. In the case of needles, the treatment of plant material in ethanol was better suited for the determination of carbohydrate levels than the microwave treatment.     

A model method for testing cosmic radiation

The experiments showed that after gamma irradiation as well as after irradiation by secondary cosmic rays (hard component)Equisetum arvense spores produce in the first developmental phases prothalia at a changed rate,i.e. in favour of the females. This effect being specific for radiation cannot be produced by heat, pressure or changes of electric and magnetic field (i.e. factors appearing in higher sea levels with a stronger intensity of cosmic rays). It will be possible to apply the sensitivity of the mentioned method for investigating the problems of testing cosmic ray variations. The possibility of its application in spontaneous variability research is not less important.     

P-Rex2, a new guanine-nucleotide exchange factor for Rac

We have identified a new guanine-nucleotide exchange factor, P-Rex2, and cloned it from human skeletal muscle and brain libraries. It has widespread tissue distribution but is not expressed in neutrophils. P-Rex2 is a 183 kDa protein that activates the small GTPase Rac and is regulated by phosphatidylinositol (3,4,5)-trisphosphate and the beta gamma subunits of heterotrimeric G proteins in vitro and in vivo. P-Rex2 has structure, activity and regulatory properties similar to P-Rex1 but has divergent tissue distribution, as P-Rex1 is mainly expressed in neutrophils. Together, they form an enzyme family capable of mediating Rac signalling downstream of G protein-coupled receptors and phosphoinositide 3-kinase.     

Hsp110 is a nucleotide-activated exchange factor for Hsp70

Hsp110 proteins constitute a subfamily of the Hsp70 chaperones and are potent nucleotide exchange factors (NEFs) for canonical Hsp70s of the eukaryotic cytosol. Here, we show that the NEF activity of the yeast Hsp110 homologue Sse1 itself is controlled by nucleotide. Nucleotide binding results in formation of a stabilized conformation of Sse1 that is required for association with the yeast Hsp70 Ssa1. The interaction triggers release of bound ADP from Ssa1, but nucleotide persists bound to Sse1 in the complex. Surprisingly, removal of this nucleotide does not affect the integrity of the complex. Instead, rebinding of ATP to the Hsp70 prompts the dissociation of the complex. Our data demonstrate that in contrast to previously characterized NEFs for Hsp70 chaperones, the NEF activity of Sse1 requires nucleotide binding and let us propose a new model for Hsp110 function.     

New perspectives in radiation oncology: Young radiation oncologist point of view and challenges

AimTo assess the role of the young radiation oncologist in the context of important recent advancements in the field of radiation oncology, and to explore new perspectives and competencies of the young radiation oncologist.BackgroundRadiation oncology is a field that has rapidly advanced over the last century. It holds a rich tradition of clinical care and evidence-based practice, and more recently has advanced with revolutionary innovations in technology and computer science, as well as pharmacology and molecular biology.Materials and methodsSeveral young radiation oncologists from different countries evaluated the current status and future directions of radiation oncology.ResultsFor young radiation oncologists, it is important to reflect on the current practice and future directions of the specialty as it relates to the role of the radiation oncologist in the comprehensive management of cancer patients. Radiation oncologists are responsible for the radiation treatment provided to patients and its subsequent impact on patients’ quality of life. Young radiation oncologists must proactively master new clinical, biological and technical information, as well as lead radiation oncology teams consisting of physicists, dosimetrists, nurses and technicians.ConclusionsThe role of the young radiation oncologist in the field of oncology should be proactive in developing new competencies. Above all, it is important to remember that we are dealing with the family members and loved ones of many individuals during the most difficult part of their lives.     

Biochemical analysis of SopE from Salmonella typhimurium, a highly efficient guanosine nucleotide exchange factor for RhoGTPases.

RhoGTPases are key regulators of eukaryotic cell physiology. The bacterial enteropathogen Salmonella typhimurium modulates host cell physiology by translocating specific toxins into the cytoplasm of host cells that induce responses such as apoptotic cell death in macrophages, the production of proinflammatory cytokines, the rearrangement of the host cell actin cytoskeleton (membrane ruffling), and bacterial entry into host cells. One of the translocated toxins is SopE, which has been shown to bind to RhoGTPases of the host cell and to activate RhoGTPase signaling. SopE is sufficient to induce profuse membrane ruffling in Cos cells and to facilitate efficient bacterial internalization. We show here that SopE belongs to a novel class of bacterial toxins that modulate RhoGTPase function by transient interaction. Surface plasmon resonance measurements revealed that the kinetics of formation and dissociation of the SopE.CDC42 complex are in the same order of magnitude as those described for complex formation of GTPases of the Ras superfamily with their cognate guanine nucleotide exchange factors (GEFs). In the presence of excess GDP, dissociation of the SopE.CDC42 complex was accelerated more than 1000-fold. SopE-mediated guanine nucleotide exchange was very efficient (e.g. exchange rates almost 10(5)-fold above the level of the uncatalyzed reaction; substrate affinity), and the kinetic constants were similar to those described for guanine nucleotide exchange mediated by CDC25 or RCC1. Far-UV CD spectroscopy revealed that SopE has a high content of alpha-helical structure, a feature also found in Dbl homology domains, Sec7-like domains, and the Ras-GEF domain of Sos. Despite the lack of any obvious sequence similarity, our data suggest that SopE may closely mimic eukaryotic GEFs.