Chloroplast genome organisation in sugar beet and maize

Summary The XhoI and SmaI restriction map of the chloroplast genome from the fertile cytoplasm of sugar beet has been constructed from overlapping cosmid clones. The genome was found to be typical of that of a dicotyledonous species, being 147.3 kb in size and having an inverted repeat. RbcL for the large subunit of ribulose-1,5-bisphosphate carboxylase, psbA for the 32 kD protein of the photosystem II reaction centre, and the 16S ribosomal RNA were located using heterologous probes. In both sugar beet and maize the inverted repeats recombine giving two isomeric forms of the genome.     

Saccharomyces genome database: underlying principles and organisation

A scientific database can be a powerful tool for biologists in an era where large-scale genomic analysis, combined with smaller-scale scientific results, provides new insights into the roles of genes and their products in the cell. However, the collection and assimilation of data is, in itself, not enough to make a database useful. The data must be incorporated into the database and presented to the user in an intuitive and biologically significant manner. Most importantly, this presentation must be driven by the user's point of view; that is, from a biological perspective. The success of a scientific database can therefore be measured by the response of its users - statistically, by usage numbers and, in a less quantifiable way, by its relationship with the community it serves and its ability to serve as a model for similar projects. Since its inception ten years ago, the Saccharomyces Genome Database (SGD) has seen a dramatic increase in its usage, has developed and maintained a positive working relationship with the yeast research community, and has served as a template for at least one other database. The success of SGD, as measured by these criteria, is due in large part to philosophies that have guided its mission and organisation since it was established in 1993. This paper aims to detail these philosophies and how they shape the organisation and presentation of the database.     

Spontaneous mutation and parental age in humans.

A statistical analysis of parental age and the incidence of new mutation has been performed. Some new data on Apert, Crouzon, and Pfeiffer syndromes is presented and combined with all available data from the literature on parental age and new mutation. Significant heterogeneity among syndromes for the rate of increase in incidence with parental age was found. A parsimonious conclusion is that mutations fall into two groups, one with a high rate of increase with age and the other with a low rate of increase with age. For the high-rate-of-increase group, a linear model relating incidence to age is rejected, while an exponential model is not. In addition, for this group, increased paternal age cannot account for the observed increase in maternal age--that is, increased maternal age also contributes to the incidence of new mutations. For the low-rate-of-increase group, increased paternal age alone can account for the observed increase in maternal ages; also, either a linear or exponential model is acceptable. In addition, there is no evidence for a mixture of parental age-independent cases with parental age-dependent cases for any of the syndromes examined. The curves reflecting incidence of new mutation and paternal age for two syndromes, Apert and neurofibromatosis, have an anomalous shape. In both cases the curve increases up to age 37 and drops at age 42 before increasing again at age 47. The usual explanation for the effect of parental age on new mutations is the mechanism of "copy-error" at mitotic division in male sperone that specifies an increased probability of mutation with time spent by a spermatozoon or ovum in a haploid state, a period of time that may also increase with age of the parent. A firm answer to the question of parental age and new mutation awaits identification of the molecular defect underlying some of these syndromes; we will then be in a position to determine in which parent the mutation occurred and at what age it did so.     

Mammalian chromodomain proteins: their role in genome organisation and expression

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in the regulation of gene expression and genome organisation. BioEssays 22:124-137, 2000.     

Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella

Genome colinearity has been studied for two closely related diploid species of the Brassicaceae family, Arabidopsis thaliana and Capsella rubella. Markers mapping to chromosome 4 of A. thaliana were found on two linkage groups in Capsella and colinear segments spanning more than 10 cM were revealed. Detailed analysis of a 60 kbp region in A. thaliana and its counterpart in C. rubella showed virtually complete conservation of gene repertoire, order and orientation. The comparison of orthologous genes revealed very similar exon-intron structures and sequence identities of 90% or more were found for exon sequences. This extensive genome colinearity at the genetic and molecular level allows the efficient transfer of data from the well-studied A. thaliana genome to other species in the Brassicaceae family, substantially facilitating genome analysis studies for species of this family.     

Distribution of parental genome blocks in recombinant inbred lines

We consider recombinant inbred lines obtained by crossing two given homozygous parents and then applying multiple generations of self-crossings or full-sib matings. The chromosomal content of any such line forms a mosaic of blocks, each alternatively inherited identically by descent from one of the parents. Quantifying the statistical properties of such mosaic genomes has remained an open challenge for many years. Here, we solve this problem by taking a continuous chromosome picture and assuming crossovers to be noninterfering. Using a continuous-time random walk framework and Markov chain theory, we determine the statistical properties of these identical-by-descent blocks. We find that successive block lengths are only very slightly correlated. Furthermore, the blocks on the ends of chromosomes are larger on average than the others, a feature understandable from the nonexponential distribution of block lengths.     

The parental investment model and minimum mate choice criteria in humans

Trivers' parental investment model states that individuals facinghigher levels of parental investment will become increasinglychoosy in their choice of mates. For humans, this leads to twopredictions. First, both males and females will be choosierin relationships more likely to lead to the production of children.Second, females will be choosier than are males, because theirminimum risk of parental investment is higher. Previous studiesof human mate choice found support for these predictions, withone curious exception: male choosiness was lower for short-termsexual relationships involving no relationship commitment (one-nightstands) than for short-term relationships involving no sexualactivity (single dates). Because the risk of parental investmentwould be higher in a one-night stand, this suggests that truerisk of parental investment was not the underlying factor governingchoosiness levels, either because study subjects assigned differentlevels of sexual activity to the relationships than were intendedby the investigators of the study or because perceived riskis more important in human mate choice than real risk. To confirmthat male/female differences in choosiness criteria exist inhumans, and to evaluate the effect that different expected levelsof real or perceived parental investment may have on choosiness,we studied mate choosiness in the context of five types of relationshipsthat reflected explicitly defined, increasing levels of riskof parental investment for both males and females. The subjectswere 468 undergraduate students, mostly between the ages of18–24. By using questionnaires, male and female participantsrated their minimum requirements in a potential mate for 29personal characteristics with respect to level of relationship.Our results confirm the major predictions of the parental investmentmodel for humans but suggest that sex differences in choosinessare better explained by perceived rather than real risk of parentalinvestment.     

Chromatin complexes as aperiodic microcrystalline arrays that regulate genome organisation and expression

The current understanding of chromatin-mediated repression in Metazoa stems largely from work on two systems in Drosophila: heterochromatin-induced position-effect variegation and repression of the homeotic genes by the Polycomb-group of genes. A common feature of these two systems is the cooperative assembly of multimeric complexes which can epigenetically silence gene activity. Moreover, both older and more recent work has suggested that these complexes can themselves associate to give rise to larger complexes: The specificity of the association is likely to be determined by complementarity of the structural components of the complexes. Here, we aim to accommodate these, and other, features of chromatin-mediated repression in a single hypothesis, namely the crystallisation hypothesis. This hypothesis views the nucleus as being an environment that favours the formation of chromatin complexes which behave as aperiodic microcrystalline arrays constructed through the cooperative assembly of different types of lattice unit. The lattice units possess regions of structural complementarity that allow interactions between complexes. Aperiodicity confers specificity on the complexes and is a key feature of the model which, we suggest, provides a gene with a “chromosomal address.” The chromosomal address allows the side-by-side alignment of homologous chromosomal regions, a property that may be important in a variety of biologically relevant situations. Aperiodicity is also a feature of the hypothesis that is directly testable. Dev. Genet. 22:85–99, 1998. © 1998 Wiley-Liss, Inc.     

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

Increasing access to plant genome sequences as well as high resolution gene-based genetic maps have recently offered the opportunity to compare modern genomes and model their evolutionary history from their reconstructed founder ancestors on an unprecedented scale. In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day genomes and allowed us to gain insight into how they are organised and regulated today.     

Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees

Restriction mapping and sequencing have shown that humans have substantially lower levels of mitochondrial genome diversity (d) than chimpanzees. In contrast, humans have substantially higher levels of heterozygosity (H) at protein-coding loci, suggesting a higher level of diversity in the nuclear genome. To investigate the discrepancy further, we sequenced a segment of the mitochondrial genome control region (CR) from 49 chimpanzees. The majority of these were from the Pan troglodytes versus subspecies, which was underrepresented in previous studies. We also estimated the average heterozygosity at 60 short tandem repeat (STR) loci in both species. For a total sample of 115 chimpanzees, d = 0.075 +/0 0.037, compared to 0.020 +/- 0.011 for a sample of 1,554 humans. The heterozygosity of human STR loci is significantly higher than that of chimpanzees. Thus, the higher level of nuclear genome diversity relative to mitochondrial genome diversity in humans is not restricted to protein-coding loci. It seems that humans, not chimpanzees, have an unusual d/H ratio, since the ratio in chimpanzees is similar to that in other catarrhines. This discrepancy in the relative levels of nuclear and mitochondrial genome diversity in the two species cannot be explained by differences in mutation rate. However, it may result from a combination of factors such as a difference in the extent of sex ratio disparity, the greater effect of population subdivision on mitochondrial than on nuclear genome diversity, a difference in the relative levels of male and female migration among subpopulations, diversifying selection acting to increase variation in the nuclear genome, and/or directional selection acting to reduce variation in the mitochondrial genome.      

Plant genome organisation and diversity: the year of the junk!

Having gained a thorough understanding of the structure and organization of model plant genomes, such as those of Arabidopsis thaliana and rice, we have now started to investigate the most interesting aspect of genome structure - its variations. Variation in DNA sequence is responsible for the genetic component of phenotypic variation (i.e. the component upon which both natural and artificial selection act). Recent studies have started to shed light on sequence variation outside of the genic regions, owing mainly to large insertion/deletion (indel) polymorphisms caused by the presence or absence of transposable elements of different classes. In addition to long terminal repeat retrotransposons, DNA transposons have been shown to be responsible for these polymorphisms. These comprise Helitrons, CACTA and Mu-like elements that are capable of acquiring and piecing together fragments of plant genes and are often expressed. Future analyses of the functional roles of intergenic sequence variation will tell us if we will need to pay more attention not only to genes, but also to the 'junk' DNA surrounding them.     

Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts

Petite-positive Saccharomyces yeasts can be roughly divided into the sensu stricto, including Saccharomyces cerevisiae, and sensu lato group, including Saccharomyces castellii; the latter was recently studied for transmission and the organisation of its mitochondrial genome. S. castellii mitochondrial molecules (mtDNA) carrying point mutations, which confer antibiotic resistance, behaved in genetic crosses as the corresponding point mutants of S. cerevisiae. While S. castellii generated spontaneous petite mutants in a similar way as S. cerevisiae, the petites exhibited a different inheritance pattern. In crosses with the wild type strains a majority of S. castellii petites was neutral, and the suppressivity in suppressive petites was never over 50%. The two yeasts also differ in organisation of their mtDNA molecules. The 25,753 bp sequence of S. castellii mtDNA was determined and the coding potential of both yeasts is similar. However, the S. castellii intergenic sequences are much shorter and do not contain sequences homologous to the S. cerevisiae biologically active intergenic sequences, as ori/rep/tra, which are responsible for the hyper-suppressive petite phenotype found in S. cerevisiae. The structure of one suppressive S. castellii mutant, CA38, was also determined. Apparently, a short direct intergenic repeat was involved in the generation of this petite mtDNA molecule.     

Microtubules in ascidian eggs during meiosis, fertilization, and mitosis

The sequential changes in the distribution of microtubules during germinal vesicle breakdown (GVBD), fertilization, and mitosis were investigated with antitubulin indirect immunofluorescence microscopy in several species of ascidian eggs (Molgula occidentalis, Ciona savignyi, and Halocynthia roretzi). These alterations in microtubule patterns were also correlated with observed cytoplasmic movements. A cytoplasmic latticework of microtubules was observed throughout meiosis. The unfertilized egg of M. occidentalis had a small meiotic spindle with wide poles; the poles became focused after egg activation. The other two species had more typical meiotic spindles before fertilization. At fertilization, a sperm aster first appeared near the cortex close to the vegetal pole. It enlarged into an unusual asymmetric aster associated with the egg cortex. The sperm aster rapidly grew after the formation of the second polar body, and it was displaced as far as the equatorial region, corresponding to the site of the myoplasmic crescent, the posterior half of the egg. The female pronucleus migrated to the male pronucleus at the center of the sperm aster. The microtubule latticework and the sperm aster disappeared towards the end of first interphase with only a small bipolar structure remaining until first mitosis. At mitosis the asters enlarged tremendously, while the mitotic spindle remained remarkably small. The two daughter nuclei remained near the site of cleavage even after division was complete. These results document the changes in microtubule patterns during maturation in Ascidian oocytes, demonstrate that the sperm contributes the active centrosome at fertilization, and reveal the presence of a mitotic apparatus at first division which has an unusually small spindle and huge asters.     

Microtubules during formation of the micropylar canal in Drosophila melanogaster

The micropylar apparatus in Drosophila melanogaster contains a 0,8μm wide canal through which sperm entry occurs. During oogenesis the canal is formed by deposition of extracellular material (chorion) around long cellular processes filled with microtubules.     

Endogenous regulation of environmentally induced sexuality in a rotifer: a multigenerational parental effect induced by fertilisation

SUMMARY 1. Sexual reproduction in the heterogonic life cycle of many rotifers occurs when amictic females, which produce diploid eggs developing parthenogenetically into females, are environmentally induced to produce mictic females. Mictic females produce haploid eggs which develop parthenogenetically into males or, if fertilised, into resting eggs – encysted embryos which develop into amictic females after an obligatory diapause. 2. A Florida strain of Brachionus calyciflorus was used to test the prediction that amictic females hatching from resting eggs (Generation 1), and those from the next few parthenogenetic generations, have a lower propensity to produce mictic daughters in response to crowding than those from later parthenogenetic generations. In 10 replicate clones, populations initiated by amictic females from generations 1, 5, 8, 12 and 18 were exposed to a standardised crowding stimulus, and the proportion of mictic females in the populations was determined. These proportions varied significantly across generations and clones. They were very low in the early generations and gradually increased to a mean of about 0.5 at Generation 12. 3. The mechanism for the transgenerational plasticity in response to crowding is not known. One possibility is that resting eggs contain an agent from their fertilised mictic mother's yolk gland that prevents development into mictic females and is transmitted in increasingly low concentrations through successive parthenogenetic generations of amictic females. 4. This parental effect may contribute to clonal fitness by ensuring that a clone developing from a resting egg will attain a higher population size through female parthenogenesis before maximising its commitment to sexual reproduction, even in the presence of a crowding stimulus from a high population density of other clones. Therefore, the number of resting eggs to which a clone contributes its genes should be maximised. 5. The clonal variation in propensity to produce mictic females in this strain indicates genetic variation in the trade‐off between maximising population growth via female parthenogenesis and increasing the probability of producing at least some resting eggs before local extinction from the plankton.     

Microtubules mediate changes in membrane cortical elasticity during contractile activation

The mechanical properties of living cells are highly regulated by remodeling dynamics of the cytoarchitecture, and are linked to a wide variety of physiological and pathological processes. Microtubules (MT) and actomyosin contractility are both involved in regulating focal adhesion (FA) size and cortical elasticity in living cells. Although several studies have examined the effects of MT depolymerization or actomyosin activation on biological processes, very few have investigated the influence of both on the mechanical properties, FA assembly, and spreading of fibroblast cells. Here, we examine how activation of both processes modulates cortical elasticity as a function of time. Enhancement of contractility (calyculin A treatment) or the depolymerization of MTs (nocodazole treatment) individually caused a time-dependent increase in FA size, decrease in cell height and an increase in cortical elasticity. Surprisingly, sequentially stimulating both processes led to a decrease in cortical elasticity, loss of intact FAs and a concomitant increase in cell height. Our results demonstrate that loss of MTs disables the ability of fibroblast cells to maintain increased contractility and cortical elasticity upon activation of myosin-II. We speculate that in the absence of an intact MT network, a large amount of contractile tension is transmitted directly to FA sites resulting in their disassembly. This implies that tension-mediated FA growth may have an upper bound, beyond which disassembly takes place. The interplay between cytoskeletal remodeling and actomyosin contractility modulates FA size and cell height, leading to dynamic time-dependent changes in the cortical elasticity of fibroblast cells.