Pericentric inversions of chromosome number 9: benign or harmful?

Pericentric inversions of chromosome number 9 have been studied in 4 different probands: a normal female with designation 46,XX,inv(9)(p12q13); a male with Down syndrome designated as 47,XY,+21,inv(9))p13q13); a premature infant with multiple, congenital malformations who was 46,XX,inv(9)(p12q21), and a Down syndrome proband with 47,XYqs,+21,inv(9)(p13q21). All 4 cases were shown to be inherited based on family studies. These families are discussed with reference to the literature as to what possible effect this structural change could have on the reproductive capability of a normal carrier and what guidelines are available for counseling such a carrier.     

Molecular genetics of radiation-induced chromosome breaks in a gene area in Drosophila: "position" effect of gene mutation?

On the sample of 43 gamma-ray and neutron-induced inversion or translocation exchanges with the vestigial (vg) phenotype, the molecular cytogenetic analysis of distribution of exchange breakpoints on the molecular map of Drosophila vg region (subsection 49D3-4 on the polytene chromosome 2R) was performed using hybridisation in situ technique. Simultaneously, PCR-assay of DNA alterations in all exons and introns (except for intron 4) of the vg gene for 18 mutants with exchange breakpoints outside of the gene was carried out. The results obtained by these molecular genetic techniques have shown that 1) radiation-induced breaks under chromosome exchanges with the vg phenotype were regularly located inside of the vg gene (19 cases out of 43 studied ones or 44.2%) passing through the large introns; 2) breakpoints were frequently flanked by deletions of the gene as whole (3 exchanges) or of its major part (3 exchanges); 3) many of the breaks (18/43 or 41.8%) are situated outside (distal or proximal) of the gene although such mutants have got the vg phenotype; 4) 2/3 (12/18 or 66.7%) vg mutants with the breakpoint outside of gene show the intragenic DNA lesions (microdeletions, microinversions) occurring obviously independently and simultaneously with the neighbor chromosome breaks; 5) only each third vg mutant with break outside of the gene (6/18 or 33.3%) have the unchanged gene subregions under study and presents obviously the result of "position effect" which appear to manifest itself for a distance of 2-30 kb (more near and farther locations of the proximal and distal breakpoints, respectively, relative to the vg gene). Our findings showing regular induction of the multiple genetic lesions (chromosome breaks and mutations of the adjacent genes) on the both ends of chromosome exchange induced by single track produced by gamma-rays or neutrons were discussed as a scientific basis for the conceptually new approaches to the assessment of both genetic damage numbers in the cell genome with chromosome exchange (the multiple genetic lesions) and radiation genetic risk (our molecular genetic approach showing the need for an increase of risk levels at least on a factor of 3 for the heritable chromosome alterations detected by the ordinary cytogenetic monitoring).     

Can occupancy patterns be used to predict distributions in widely separated geographic regions?

Occupancy models, that describe the presence and absence patterns of a species in a given area, are increasingly being used to predict the occurrence of the species in unsurveyed sites, as an aid to conservation planning. In this paper, we consider whether conclusions about local distributions derived from one landscape can be extrapolated to others. We found that habitat patchiness influenced the distribution and abundance of the host-specific moth Wheeleria spilodactylus in a similar way in two landscapes widely separated geographically. In both geographic regions, the spatial location (positive effect of connectivity), and quantity of resource (positive effect of host plant density) increased the likelihood that the moth would be present, consistent with the expectations of metapopulation dynamics. Though some biological attributes of the species appeared to be slightly different, including population density and the timing of the life cycle (phenology), occupancy patterns in one landscape accurately predict occupancy in the other landscape. Our results suggest that it maybe possible to make predictions from one landscape to another, even when the landscapes are widely separated.     

Can zebra mussels change stratification patterns in a small reservoir?

Colonization and proliferation of zebra mussel (Dreissena polymorpha) population in Hargus lake, a small thermally stratified reservoir in Ohio, U.S.A., caused a significant increase in water clarity and a remarkable decrease in phytoplankton biomass during the period from 1993 to 1995. Increased light penetration and reduced organic matter loading to the meta-and hypolimnion were reflected in the lake stratification patterns, particularly in the temperature and oxygen profiles in the metalimnion. The meta- and hypolimnetic water temperature increased significantly over three years, irrespective of variation in surface water temperature. The epilimnion depth (mixing depth) increased by about the same magnitude as did the average Secchi depth. However, the total heat content of the lake did not show a consistent trend to increasing zebra mussel abundance, as it was largely influenced by the temperature of the large water volumes near the surface, which were in turn affected by weather conditions. Concurrent with the thermal structure change, the dissolved oxygen structure also changed over three years, though to a lesser extent. The changes in oxygen stratification pattern were reflected by increased oxygen concentrations in the metalimnion and a lowered depth of 3 mg l^–1 DO isopleth. These observed changes were likely attributed to increased water mixing depth, metalimnion photosynthesis and reduced oxygen consumption by organic matter. With increased epilimnion thickness and improved oxygen conditions in the metalimnion, the habitable space for aquatic macro-organisms (including fish) expanded substantially. Our results suggest that the indirect impacts of zebra mussels on small lake stratification patterns may have much broader implications than do the direct trophic interactions to the whole ecosystem.     

Sequence variation patterns along a latitudinal cline in Scots pine (Pinus sylvestris): signs of clinal adaptation?

Adaptive clinal variation is abundant in nature, and its genetic basis is of great interest. The polygenic nature of this variation poses a challenge for identifying the causative loci underlying these adaptations. Here, we have examined the patterns of sequence variation in ten candidate genes for timing of bud set and cold tolerance, traits that form strong latitudinal clines in Scots pine (Pinus sylvestris). A set of reference genes was used for comparison and to infer a simplified demographic background model with approximate Bayesian computation methods. Against the resulting bottleneck model, the neutrality tests show little signs for local adaptation, but species-wide selection is suggested in some of the studied genes. In line with the theoretical expectations, we see little evidence for adaptive differentiation with F _ST methods. Instead, allele frequency clines were found in three genes (dhn1, ftl2, and prr1). Our results add to the discussion on which molecular signals best characterize a gene subject to clinally varying selection. This will be especially relevant when these kinds of observations can be examined in parallel with association study results.     

Induction of premature chromosome condensation in Drosophila melanogaster — rat heterokaryons

Summary After fusion mediated by polyethylene glycol (PEG) plus dimethyl sulfoxide (DMSO) between rat and Drosophila melanogaster cells cultured in vitro, the phenomenon of premature chromosome condensation (PCC) induced by mitotic rat chromosomes was detected in Drosophila nuclei. Exceptionally PCC was induced in rat nuclei but only in the presence of a very high ploidy level of Drosophila mitotic chromosomes. This provides further evidence of the lack of species specificity and of the effect of dosage of the PCC inducing factors, even among very distant species.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

Can root traits predict communities of soil nematodes in restored northern prairies?

Plant and Soil - We examined how restoration affects the structure and function of grasslands belowground by relating changes in the morphology and architecture of root systems of dominant plants...     

Can contact potentials reliably predict stability of proteins?

The simplest approximation of interaction potential between amino acid residues in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation. Finding a contact potential capable of predicting free energies of protein states across a variety of protein families will aid protein folding and engineering in silico on a computationally tractable time-scale. We test the ability of contact potentials to accurately and transferably (across various protein families) predict stability changes of proteins upon mutations. We develop a new methodology to determine the contact potentials in proteins from experimental measurements of changes in protein's thermodynamic stabilities (DeltaDeltaG) upon mutations. We apply our methodology to derive sets of contact interaction parameters for a hierarchy of interaction models including solvation and multi-body contact parameters. We test how well our models reproduce experimental measurements by statistical tests. We evaluate the maximum accuracy of predictions obtained by using contact potentials and the correlation between parameters derived from different data-sets of experimental (DeltaDeltaG) values. We argue that it is impossible to reach experimental accuracy and derive fully transferable contact parameters using the contact models of potentials. However, contact parameters may yield reliable predictions of DeltaDeltaG for datasets of mutations confined to the same amino acid positions in the sequence of a single protein.     

Cytogenetic analysis of variegation suppressors and a dominant temperature-sensitive lethal in region 23–26 of chromosome 2L in Drosophila melanogaster

Three suppressor loci for position-effect variegation, one dominant temperature-sensitive (DTS), three Minute genes, and two recessive visible mutants (ed, tkv) have been cytogenetically localized by using duplications and deficiencies in regions 23-25 of chromosome arm 2L of Drosophila melanogaster. Two of the suppressor loci studied proved to represent haplo-abnormal genes localized in regions 23A6-23F6 and 24E2-25A1, respectively. The third one is a strong triplo-abnormal suppressor mapping in 25F4-26B9 which affects white variegation in wm4h when present in three doses. The l(2)2DTS mutation, which belongs to a group of noncomplementing dominant temperature-sensitive mutations, is localized in the 25A4-B1 region. Furthermore, two Minute genes have been localized in region 24 that are included in Df(2L)M11 and can be separated employing translocation (Y;2)P8 (24E2-4): M(2)LS2 in 24D3-4-24E2-4, and M(2)z in 24E4-5-24F5-7. A third Minute gene (M(2)S1) is localized in 25C3-8-25C9-D1. The usefulness of the isolated chromosomal rearrangements for further genetic studies of region 23-26 is discussed.     

Adaptive changes in bacteria: a consequence of nonlinear transitions in chromosome topology?

Adaptive changes in bacteria are generally considered to result from random mutations selected by the environment. This interpretation is challenged by the non-randomness of genomic changes observed following ageing or starvation in bacterial colonies. A theory of adaptive targeting of sequences for enzymes involved in DNA transactions is proposed here. It is assumed that the sudden leakage of cAMP consecutive to starvation induces a rapid drop in the ATP/ADP ratio that inactivates the homeostasis in control of the level of DNA supercoiling. This phase change enables the emergence of local modifications in chromosome topology in relation to the missing metabolites, a first stage in expression of an adaptive status in which DNA transactions are induced. The nonlinear perspective proposed here is homologous to that already suggested for adaptation of pluricellular organisms during their development. In both cases, phases of robustness in regulation networks for genetic expression are interspaced by critical periods of breakdown of the homeostatic regulations during which, through isolation of nodes from a whole network, specific changes with adaptive value may locally occur.     

Can paternal effects via seminal fluid contribute to the evolution of polyandry?

Genetic benefits from mating with multiple males are thought to favour the evolution of polyandry. However, recent evidence suggests that non-genetic paternal effects via seminal fluid might contribute to the observed effects of polyandry on offspring performance. Here, we test this hypothesis using the field cricket Teleogryllus oceanicus. Using interference RNA, we first show that at least one seminal fluid protein is essential for embryo survival. We then show that polyandrous females mated to three different males produced embryos with higher pre-hatching viability than did monandrous females mated with the same male three times. Pseudo-polyandrous females that obtained sperm and seminal fluid from a single male and seminal fluid from two additional males had embryos with viabilities intermediate between monandrous and polyandrous females. Our results suggest either that ejaculate mediated paternal effects on embryo viability have both genetic and non-genetic components, or that seminal fluids transferred by castrated males provide only a subset of proteins contained within the normal ejaculate, and are unable to exert their full effect on embryo viability.     

Are dicentric anaphase bridges formed by somatic recombination in X chromosome inversion heterozygotes of Drosophila melanogaster?

Summary Mitotic recombination has been induced with X-rays in Drosophila melanogaster larvae and assayed later as twin mosaic spots on the adult tergites. With the use of the In(1)sc ^4L sc ^8R chromosome which lacks the nucleolar organizer and is marked with yellow (y) indirect evidence was obtained that mitotic recombination between ring and rod chromosomes results, in a majority of cases, in XO spots, bearing the rod-X only. This was concluded from the relative scarcity and small sizes of y NO^- spots (uncovering the sc ⁴ sc ⁸ chromosome), compared to control sisters bearing an extra Y chromosome with its NO locus. Thus, dicentric chromatid bridges formed by mitotic recombination between the ring and rod chromosomes are probably eliminated at the next division.In In(1)sc ⁴ sc ⁸/f^36a (rod/rod) females, no effect of the Y chromosome on the frequency and sizes of cross-over spots was observed. Either any dicentric chromatid bridges formed by recombination between inverted rod chromosomes fragment at division, with a centromeric piece going to each pole, or such bridges are not usually formed by recombination. The latter case would indicate that somatic pairing of homologues is not accurate in X chromosome inversion heterozygotes and consequently, that recombination yields aneuploid cells.Additional studies are cited which indicate that X chromosome heterozygotes for entire arm inversions may not pair in the typical loop at the time of mitotic recombination.Supported in part by U.S.P.H.S. Grant GM 17096 to J.R.M., and the Kredit zur Förderung des akademischen Nachwuchses an der Universität Zürich to R.N.     

Can a simple algebraic analysis predict markers-genome heterozygosity correlations?

A current algebraic analysis on genome-wide heterozygosity estimates suggests that correlations between molecular markers and genome-wide heterozygosity, rho, depend on the ratio between the number of markers used, r, and the number of genome loci, n; that is: rho approximately square root r/n. Hence, it is unfeasible to obtain reliable estimates of genome-wide heterozygosity in species of large genome using a few markers. We cast some doubts about this analysis as it assumed that the probability that an individual was heterozygous at a locus is equal to the average heterozygosity of this locus in the population. However, we believe that individual heterozygosity at a given locus depends on individual pedigree. Because the pedigree is common for all loci of an individual, their probabilities of heterozygosity are not independent within the genome. We first performed simulations generating random genomes for 100 individuals. Among these individuals, markers and genome-wide heterozygosities correlated as expected from the above equation. However, when we simulated random mating among these individuals and in successive generations including their descendents, as occur in real populations, the correlations between markers and genome-wide heterozygosity were much higher than those predicted from algebraic analyses, and estimates of genome-wide heterozygosity improved slightly with the increment of the number of loci in the genome.     

Can we predict nutrient limitation in streams and rivers?

1. Anthropogenic impacts on the biogeochemical cycles of nitrogen (N) and phosphorus (P) affect natural ecosystems worldwide. Modelling is required to predict where and when these key nutrients limit primary production in freshwaters. 2. We reviewed 382 nutrient‐enrichment experiments to examine which factors promote limitation of microphytobenthos biomass by N or P in streams and rivers. Using regression models, we examined whether the response of microphytobenthos biomass to N and P additions could be predicted by the absolute N and P concentrations in the water, the water N:P ratio or a combination of the two. 3. The absolute N concentration in the water was the best predictor of the magnitude of the response of microphytobenthos biomass to N additions. In comparison, the N:P ratio was the best predictor of whether or not N was limiting. However, predictions were uncertain except at extreme N:P ratios <1 : 1 and >100 : 1. 4. The absolute P concentration in the water was the best predictor of the magnitude of the response of microphytobenthos biomass to P additions. Neither the absolute nor the relative N and P concentrations predicted whether or not P was limiting. 5. The absolute and the relative N and P water concentrations contribute significant and complementary insights into the responses of microphytobenthos biomass to nutrient enrichment in running waters. However, ability to predict nutrient limitation from these concentrations is constrained by substantial error in the models. In the future, the prediction ability of models of nutrient limitation might be improved by focussing on regional scales and accounting for additional factors such as light and disturbance.