Genetic determination of ploidy level in Xanthophyllomyces dendrorhous

Xanthophyllomyces dendrorhous (formely Phaffia rhodozyma) is a basidiomycetous yeast-like fungus that produces carotenoids useful for the food industry. Recently, its sexual cycle was reported but little is known about its genetic constitution. To inquire into the ploidy state of X. dendrorhous, biased mutant spectrum, genetic complementation and mitotic recombination analysis were used. A wild-type strain was subjected to N-methyl-N′-nitro-N-nitrosoguanidine mutagenic treatment. Auxotrophic and carotene mutants were forced to revert to the wild-type phenotype. Pigment producing and prototroph revertants behaved as diploid except for adenine less mutants. These results are in agreement with the limited spectrum of auxotrophs obtained in this strain for the ADE1 locus. To analyze the genetic characteristic of the adenine genetic marker of X. dendrorhous, protoplast fusion experiments with several adenine less mutants were performed. The experiments presented in this work suggest that the ATCC 2430 (UDC 67-385) strain of X. dendrorhous is diploid and a heterozygous constitution is proposed for the ADE1 locus. This revised version was published online in June 2006 with corrections to the Cover Date.     

Variations with position of replication errors due to exonuclease warm-up

A.A mismatch errors occurring during poly(dA) replication with the Klenow fragment of E. coli DNA polymerase I have been quantified. The A/T ratio measured for chains extended by 1-25 nucleotides decreases by a factor of at least 15 from beginning to end. The deduced true error rate may decrease by a factor of 2.5 at each successive nucleotide addition. When ddATP is used instead of dATP, the ddA/T ratio indicates little variation of the misincorporation probability with position. Thus, the accuracy improvement in the first case is due to a warm-up of the proofreading function.     

Systematic errors in data evaluation due to ethanol stripping and water vaporization

Systematic errors due to the neglect of water and/or ethanol partition between liquid and gaseous phases are discussed for bioreactors equipped with or without a condenser. Both water vapor and ethanol vapor are present in the off-gas leaving the condenser. Presence of residual water vapor largely influences the gas measurements by dilution. As a consequence, the oxygen consumption rate can be overestimated by a factor of 3 if calculations are not corrected for water vapor content or if no additional device is implemented after the condenser to completely dry the off-gases. The mass balance and partition equations predict that the condenser has only a small effect on reduction of the ethanol vapor content of the off-gas. The reason is the high ethanol concentration of the condensate droplets on the condenser wall in contact with the off-gases. Model predictions as well as experimental results show that ethanol evaporation represents a large fraction of the ethanol production rate and influences greatly the elemental recoveries. For a reactor working at 30 degrees C without condensation of the vapors and for a volumetric aeration rate of 0.63vvm, stripping of ethanol resulted in a gaseous dilution rate of 0.016 h-1 for ethanol. The dilution rate by stripping was reduced to 0.014 h-1 when a condenser at 12 degrees C was implemented. The fraction of ethanol that is stripped is mainly dependent on the ratio D/vvm (liquid to gaseous flow rates), and the effect is only slightly influenced by low condenser temperature. The evaporation of ethanol may account for more than 20% of the ethanol formation rate. Therefore, the condenser does not succeed to reflux all ethanol to the reactor broth. In terms of a unit operation, ethanol vapor can be efficiently reduced by absorption instead of condensation. To demonstrate the feasibility, a simple modification of the reactor was tested for continuous cultures: the feed port was changed from the top-plate to the top of the condenser, which was used as an absorption column. Ethanol stripping was reduced by a factor of 4 as compared to the condensation setup (at 12 degrees C): it accounted for 2% of the ethanol production rate as compared to 8.2% at D = 0.19 h-1 and 0.63vvm.     

Biases in RCS tree ring chronologies due to sampling heights of trees

The Regional Curve Standardization (RCS) is one of the most employed standardization methods to remove biological signals in long tree ring chronologies. The approach assumes that an overall age-related growth trend typify all tree ring series to be included in a standardized tree ring chronology. Although several potential problems of the method have been examined, the influence of varying the sampling height along tree stems has not been evaluated. Considering that age-related growth trends may vary with stem height, biases may arise when combining samples from unknown or variable sampling heights, a frequent situation with subfossil logs. In this study we perform a detailed stem analysis of 15 lakeshore black spruce (Picea mariana Mill. B.S.P.) trees in the taiga of eastern Canada to describe how the age-related growth trend varies with stem height and evaluate associated biases in RCS chronologies built from living and subfossil trees. Results show that the age-related growth trends vary markedly and systematically along stems, potentially generating large methodological biases in RCS chronologies, especially near the recent chronology end. These biases may lead to erroneous reconstructions of recent climatic trends and cause false divergence between tree ring and climate series. We have developed a correction procedure that appears efficient in removing these biases from chronologies built with the lakeshore trees and associated subfossil logs.     

Evaluation of counting error due to colony masking in bioaerosol sampling.

Colony counting error due to indistinguishable colony overlap (i.e., masking) was evaluated theoretically and experimentally. A theoretical model to predict colony masking was used to determine colony counting efficiency by Monte Carlo computer simulation of microorganism collection and development into CFU. The computer simulation was verified experimentally by collecting aerosolized Bacillus subtilis spores and examining micro- and macroscopic colonies. Colony counting efficiency decreased (i) with increasing density of collected culturable microorganisms, (ii) with increasing colony size, and (iii) with decreasing ability of an observation system to distinguish adjacent colonies as separate units. Counting efficiency for 2-mm colonies, at optimal resolution, decreased from 98 to 85% when colony density increased from 1 to 10 microorganisms cm-2, in contrast to an efficiency decrease from 90 to 45% for 5-mm colonies. No statistically significant difference (alpha = 0.05) between experimental and theoretical results was found when colony shape was used to estimate the number of individual colonies in a CFU. Experimental colony counts were 1.2 times simulation estimates when colony shape was not considered, because of nonuniformity of actual colony size and the better discrimination ability of the human eye relative to the model. Colony surface densities associated with high counting accuracy were compared with recommended upper plate count limits and found to depend on colony size and an observation system's ability to identify overlapped colonies. Correction factors were developed to estimate the actual number of collected microorganisms from observed colony counts.(ABSTRACT TRUNCATED AT 250 WORDS)     

The calculation of errors and the choice of sampling times in the determination of irreversible disposal rates in vivo by isotope experiments

In well-known methods of estimating rates of irreversible disposal (utilization) in vivo the rates are calculated from the areas to infinity under specific radioactivity-time (S-t) or quantity-of-label-time (q-t) curves obtained by measurements on samples of plasma after intravenous injection of labelled substrate. The errors in the calculated rates are mostly those of the estimates of the areas. These errors are of two kinds: random, caused by the variances of the values of S or q, and systematic, caused by differences between the curves used to interpolate between these values and the true curves. A rigorous method is given for calculating the random errors from the variances of the values of S or q, and is applied to choosing the best times to sample the plasma from small animals from which few plasma samples can be taken. A procedure for estimating systematic errors is also given. Programs in BASIC language to carry out the calculations are deposited as Supplementary Publication SUP 50058 (5 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms given in Biochem. J. (1975) 145, 5.     

Estimation of sampling errors in a high-resolution TV microscope image-processing system

The basic postulate of this paper is that the commonly accepted sampling density of 2-4 pixels/micron in a high-resolution TV microscope system is too low to digitize exactly and analyze the complex cellular detail found in stained cell images. Depending on the specific microscope system, the required sampling density is much higher, lying between 15 and 30 pixels/micron. This sampling density is derived from the aliasing error, the resolution loss, and computational limitations. The mathematical and optical methods and equipment used to obtain these results are described in detail.     

Evidence for bias in estimates of local genetic structure due to sampling scheme

Traditional population genetic analyses typically seek to characterize the genetic substructure caused by the nonrandom distribution of individuals. However, the genetic structuring of adult populations often does not remain constant over time, and may vary relative to season or life-history stages. Estimates of genetic structure may be biased if samples are collected at a single point in time, and will reflect the social organization of the species at the time the samples were collected. The complex population structures exhibited by many migratory species, where temporal shifts in social organization correspond to a large-scale shift in geographic distribution, serve as examples of the importance that time of sampling can have on estimates of genetic structure. However, it is often fine-scale genetic structure that is crucial for defining practical units for conservation and management and it is at this scale that distributional shifts of organisms relative to the timing of sampling may have a profound yet unrecognized impact on our ability to interpret genetic data. In this study, we used the wild turkey to investigate the effects of sampling regime on estimates of genetic structure at local scales. Using mitochondrial sequence data, nuclear microsatellite data and allozyme data, we found significant genetic structuring among localized winter flocks of wild turkeys. Conversely, we found no evidence for genetic structure among sampling locations during the spring, when wild turkeys exist in mixed assemblages of genetically differentiated winter flocks. If the lack of detectable genetic structure among individuals is due to an admixture of social units as in the case of wild turkeys during the spring, then the F _IS value rather than the F _ST value may be the more informative statistic in regard to the levels of genetic structure among population subunits.