Homozygosity in a population of variable size and mutation rate

A formula is obtained for the probability that two genes at a single locus, sampled at random from a population at time t, are of particular types. The model assumed is a diffusion approximation to a neutral Wright-Fisher model in which mutation is not necessarily symmetric and the population size is a function of time. It is shown that for symmetric mutation in a population undergoing a step-function type bottleneck, homozygosity increases with decreasing population size. A formula is given for the distribution of the number of segregating sites occurring in two randomly sampled sequences of completely linked sites, with general mutation at a site and identical mutation structure between sites.We give similar results for a population of fixed size but for which the mutation rate is a function of time, and not necessarily symmetric. We confirm the intuitively clear effect that increasing the mutation rate decreases homozygosity.     

Estimating effective population size or mutation rate with microsatellites

Microsatellites are short tandem repeats that are widely dispersed among eukaryotic genomes. Many of them are highly polymorphic; they have been used widely in genetic studies. Statistical properties of all measures of genetic variation at microsatellites critically depend upon the composite parameter theta = 4Nmicro, where N is the effective population size and micro is mutation rate per locus per generation. Since mutation leads to expansion or contraction of a repeat number in a stepwise fashion, the stepwise mutation model has been widely used to study the dynamics of these loci. We developed an estimator of theta, theta; (F), on the basis of sample homozygosity under the single-step stepwise mutation model. The estimator is unbiased and is much more efficient than the variance-based estimator under the single-step stepwise mutation model. It also has smaller bias and mean square error (MSE) than the variance-based estimator when the mutation follows the multistep generalized stepwise mutation model. Compared with the maximum-likelihood estimator theta; (L) by, theta; (F) has less bias and smaller MSE in general. theta; (L) has a slight advantage when theta is small, but in such a situation the bias in theta; (L) may be more of a concern.     

Effect of nitrogen supply rate on disease resistance in tomato depends on the pathogen

The aim of this study was to investigate the effect of tissue nitrogen concentration, as a consequence of nitrogen supply rate, on the susceptibility of tomato plants to three pathogens. We varied tissue N concentration by supplying N at different rates by adding nitrate in different, exponentially increasing amounts to the nutrient solution on which the tomato plants were grown. Separate experiments were carried out to test susceptibility of tomato plants to the bacterial speck-causing Pseudomonas syringae pv tomato, to the wilt agent Fusarium oxysporum f.sp. lycopersici and to tomato powdery mildew caused by Oidium lycopersicum. The effect of tissue N concentration appeared to be highly pathogen-dependent: there was no effect on susceptibility to F. oxysporum, but susceptibility to P. syringae and O. lycopersicum increased significantly with increasing N concentration. We have previously demonstrated the opposite for susceptibility to Botrytis cinerea: decreasing susceptibility with increasing N concentration. The apparent contradictory effects are discussed in relation to the effect of N supply on both the nutritional value of the plant tissue to the pathogen and on the concentration of resistance-related compounds. We conclude that the effect of changing both characteristics on disease susceptibility is highly pathogen-specific and is probably dependent on differences in resource requirements of the pathogen or the sensitivity of the pathogen to plant resistance reactions or on both these factors. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effect of particle size on the rate of enzymatic hydrolysis of cellulose

The effect of particle size on enzymatic hydrolysis of cellulose has been investigated. The average size of microcrystalline cotton cellulose has been reduced to submicron scale by using a media mill. The milled products were further subjected to hydrolysis using cellulase. High cellulose concentration (7%) appeared to retard the size reduction and resulted in greater particles and smaller specific surface areas than those at low concentration (3%) with the same milling time. Initial rate method was employed to explore the rate of enzymatic hydrolysis of cellulose. The production rate of cellobiose was increased at least 5-folds due to the size reduction. The yield of glucose was also significantly increased depending upon the ratio of enzyme to substrate. A high glucose yield (60%) was obtained in 10-h hydrolysis when the average particle size was in submicron scale.     

Haldane and the mutation rate

Based on a talk given at the Haldane Centenary Symposium held on 6 November 1992 at Ahmedabad as part of the 58th Annual Meeting of the Indian Academy of Sciences.     

The effect of straw size, freezing rate and thawing rate upon post-thaw quality of dog semen

Optimal freeze-thaw processes for dog semen will yield a maximal number of insemination doses from an ejaculate. The objectives of this study were to compare the effects of two straw sizes (0.25- and 0.5-mL French), two freezing rates (straws suspended 3.5 and 8 cm above liquid nitrogen) and two thawing rates (in water at 37 and 70 degrees C) upon post-thaw quality of dog semen, and to determine the best treatment combination. Quality was expressed in terms of the percentage progressively motile sperm 5 and 60 min after thawing and the percentage of abnormal acrosomes 5 min after thawing. One ejaculate from each of eight dogs was frozen. Two straws from each ejaculate were exposed to each of the eight treatment combinations. Data were analyzed by means of a repeated measures factorial analysis of variance and means compared using Bonferroni's test. Dog affected each response variable (P < 0.01). Neither straw size, nor freezing rate, nor thawing rate affected motility 5 min after thawing (P > 0.05). Half-milliliter straws resulted in 5.7% more progressively motile sperm 60 min after thawing and 6.5% fewer abnormal acrosomes than 0.25-mL straws (P < 0.05, n = 64). The percentage progressively motile sperm 60 min after thawing tended to be higher for semen thawed at 70 degrees C compared to 37 degrees C (P < 0.06, n = 64). Semen thawed in water at 70 degrees C had 6.6% fewer abnormal acrosomes than semen thawed in water at 37 degrees C (P < 0.05, n = 64). Freezing rate interacted with thawing rate (P < 0.05) in their effects upon acrosomal morphology and freezing 8 cm above liquid nitrogen and thawing in water at 70 degrees C was best. Dog semen should be frozen in 0.5-mL straws, 8 cm above liquid nitrogen and thawed in water at 70 degrees C.     

Clone selection and the mutation rate

A statistical model for mutation and selection is formulated for organisms that reproduce by division. The mutation rate that optimizes the probability of clone survival is approximated using the theory of branching processes. However, it is shown by example that this optimizing mutation rate need not be the most advantageous mutation rate. The principle that selection favors those modifying features that optimize the probability of clone survival is thereby shown to be of limited applicability.     

Exhaustive computational identification of pathogen sequences far-distant from background genomes: Identification and experimental verification of human-blind dengue PCR primers

We recently developed novel algorithms for exhaustive identification of all nucleotide subsequences present in a pathogen genome which differ by at least a chosen number of mismatches from the sequences of host/background organisms. This type of exhaustive computational analysis will be useful in reducing false positives and cross-reactivity in PCR and hybridization assays. We present the first experimental test of the method by showing that the subsequences identified when used as 18-mer PCR primers can detect the presence of dengue virus (DENV) even in the presence of a large excess of complex human genomic DNA. From our computations, 715 serotype-specific primer pairs were identified for three different DENV serotypes in which each primer sequence lies at least two mismatches from the nearest human sequence. DNA clones of representative strains of DENV-1, DENV-2, and DENV-4 viruses were subjected to real-time PCR testing using eight primer pairs each. Efficiencies were uniformly very high (mean+/-S.D.=99.6+/-3%), and amplification of human DNA was never observed within 35 cycles, even at a 5.5-fold molar excess of human DNA. Exhaustive primer/probe screening can potentially produce more selective and sensitive diagnostic assays for pathogens, especially in the presence of complex backgrounds.     

Mammalian DNA replication: mutation biases and the mutation rate

Experimental studies have shown that the fidelity of DNA replication can be affected by the concentrations of free deoxyribonucleotides present in the cell. Replication of mammalian chromosomes is achieved using pools of newly-synthesized deoxyribonucleotides which fluctuate during the cell cycle. Since regions of mammalian chromosomes are replicated sequentially, there is the potential for differences among mammalian loci in both the relative and absolute frequencies of the various transitional and transversional mutations which may occur. Where these mutations are effectively neutral, at silent sites in genes and in non-coding sequences, this may result in different rates of evolution and in different base compositions, as have been observed in data from mammalian genes. A simple model of the DNA replication process is developed to describe how the mutation rate could be affected by the G + C contents of the deoxyribonucleotide pools and of the replicating DNA. Mutation rates are predicted to vary from locus to locus; only in the particular case of identical G + C contents in the DNA locus and the deoxyribonucleotide pools, and no proofreading, will the mutation rate be uniform over all loci.     

Difference between evolutionarily effective and germ line mutation rate due to stochastically varying haplogroup size

Within a Y-chromosome haplogroup defined by unique event mutations, variation in microsatellites can accumulate due to their rapid mutation. Estimates based on pedigrees for the Y-chromosome microsatellite mutation rate are 3 or more times greater than the same estimates from evolutionary considerations. We show by simulation that the haplogroups that survive the stochastic processes of drift and extinction accumulate microsatellite variation at a lower rate than predicted from corresponding pedigree estimates; in particular, under constant total population size, the accumulated variance is on average 3-4 times smaller.     

The impact of cross-immunity, mutation and stochastic extinction on pathogen diversity

We examine the dynamics of antigenically diverse infectious agents using a mathematical model describing the transmission dynamics of arbitrary numbers of pathogen strains, interacting via cross-immunity, and in the presence of mutations generating new strains and stochastic extinctions of existing ones. Equilibrium dynamics fall into three classes depending on cross-immunity, transmissibility and host population size: systems where global extinction is likely, stable single-strain persistence, and multiple-strain persistence with stable diversity. Where multi-strain dynamics are stable, a diversity threshold region separates a low-prevalence, low-diversity region of parameter space from a high-diversity, high-prevalence region. The location of the threshold region is determined by the reproduction number of the pathogen and the intensity of cross-immunity, with the sharpness of the transition being determined by the manner in which immunity accrues with repeated infections. Host population size and cross-immunity are found to be the most decisive factors in determining pathogen diversity. While the model framework developed is simplified, we show that it can capture essential aspects of the complex evolutionary dynamics of pathogens such as influenza.     

Molecular identification of the turf grass rapid blight pathogen

Rapid blight is a newly described disease on turf grasses, primarily found on golf courses using suboptimal water for irrigation purposes. On the basis of shared morphological characteristics, it has been proposed that the rapid blight pathogen belongs to a genus of stramenopiles, Labyrinthula, which had been known to cause disease of marine plants only. We have collected 10 isolates from four species of turf grass in five states and sequenced portions of the SSU (18S) rDNA gene from each to provide a definitive taxonomic placement for rapid blight pathogens. We also included sequences from Labyrinthuloides yorkensis, Schizochytrium aggregatum, Aplanochytrium sp., Thraustochytrium striatum, Achlya bisexualis and several nonturf-grass isolates of Labyrinthula. We found that rapid blight isolates indeed are placed firmly within the genus Labyrinthula and that they lack detectable genetic diversity in the 18S rDNA region. We propose that the rapid blight pathogens share a recent common ancestor and might have originated from a single, infected population.     

Effect of growth rate and incC mutation on symmetric plasmid distribution by the IncP-1 partitioning apparatus

The incC and korB genes of IncP-1 plasmid RK2 encode homologues of ubiquitous ParA and ParB partitioning proteins of bacterial plasmids and chromosomes. Using immunofluorescence microscopy, we found that KorB, which binds to 12 widely distributed sites on the genome, is located in symmetrically placed foci in cells containing IncP-1 plasmids. When maintained by the low-copy-number P7 replicon, an RK2 segment including incC, korB and the kla, kle and korC regions encodes an efficient partitioning system that gives a pattern of foci similar to RK2 itself. Symmetrical distribution of KorB foci correlates with segregational stability conferred by either the IncP-1 or P7 partitioning systems; KorB distribution follows plasmid distribution. In the absence of a second partitioning system, incC inactivation resulted in paired or clumped foci that were not symmetrically distributed. At a slow growth rate, position analysis of foci showed a cycle from one central focus to two foci (at one- and three-quarter positions) and back, and at a high growth rate it showed a cycle from two foci to four and back. This pattern fits with the plasmid being coupled to the replication zones in the cell and being moved to successively younger zones by active partitioning, indicating a tight association between replication and partitioning.     

Effect of dietary protein on embryo recovery rate and quality in superovulated heifers

For almost 3 decades, superovulation and embryo transfer have been used in cattle breeding to increase the number of offspring from genetically superior female animals. Several factors including nutrition affect the number of transferable embryos recovered. We compared the effects of two different dietary protein levels easily achieved in practical conditions on embryo number and quality in superovulated heifers. Finnish Ayrshire heifers (n = 37) were allocated to isoenergic diets containing either 14% (D14) or 18% (D18) crude protein (CP). Estruses were synchronized, and the heifers were subsequently superovulated and inseminated using a standard FSH-protocol. Embryos were collected 7 days after inseminations (71-72 days after the beginning of the treatment period) by uterine flushing. The number of corpora lutea, and the number and quality of embryos were determined. Protein feeding did not affect superovulatory response, the number of embryos or the number of transferable embryos recovered. Proportionally more poor-quality embryos were found in group D14 than in group D18 (20.2% versus 13.2%, respectively, P = 0.053). It is concluded that a long-term moderate increase in the content of crude protein fed to energy-adequate heifers does not seem to affect superovulatory response and the number of embryos recovered, but it may be advantageous to the quality of embryos.