Maternal influence on blood pressure suggests involvement of mitochondrial DNA in the pathogenesis of hypertension: the Framingham Heart Study

OBJECTIVE

To investigate the contribution of the mitochondrial genome to hypertension and quantitative blood pressure (BP) phenotypes in the Framingham Heart Study cohort, a randomly ascertained, community-based sample.

METHODS

Longitudinal BP values of 6421 participants (mean age, 53 years; 46% men) from 1593 extended families were used for analyses. In analyses of BP as a continuous trait, a variance components model with a variance component for maternal effects was used to estimate the mitochondrial heritability of the long-term average BP adjusted for age, sex, body mass index, and hypertension treatment. For analyses of BP as a categorical trait, a nonparametric test sensitive to excessive maternal inheritance was used to test for mitochondrial effect on long-term hypertension, defined as systolic BP of at least 140 mmHg or diastolic BP of at least 90 mmHg or use of antihypertensive medication in one-half or more of qualifying examinations. This test was based on 353 pedigrees comprised of 403 individuals informative for mitochondrial DNA contribution.

RESULTS

The estimated fraction of hypertensive pedigrees potentially due to mitochondrial effects was 35.2% (95% confidence interval, 27-43%, P < 10). The mitochondrial heritabilities for multivariable-adjusted long-term average systolic BP and diastolic BP were, respectively, 5% (P < 0.02) and 4% (P = 0.11).

CONCLUSION

Our data provide support for a maternal effect on hypertension status and quantitative systolic BP, consistent with mitochondrial influence. Additional studies are warranted to identify mitochondrial DNA variant(s) affecting BP.

Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications

Mitochondrial DNA translocations to the nucleus (numt pseudogenes) are pervasive among eukaryotes, but copy number within the nuclear genome varies widely among taxa. As an increasing number of genomes are sequenced in their entirety, the origins, transfer mechanisms and insertion sites of numts are slowly being characterized. We investigated mitochondrial transfers within a genetically diverse rodent lineage and here report 15 numts totaling 21.8 kb that are harbored within the nuclear genome of the vole Microtus rossiaemeridionalis. The 15 numts total 21.8 kb and range from 0.39 to over 3.0 kb in length. Phylogenetic analyses revealed that these numts resulted from three independent insertions to the nucleus, two of which were followed by subsequent nuclear duplication events. The dates of the two translocations that led to subsequent duplications were estimated at 1.97 and 1.19 MYA, which coincide with the origin and radiation of the genus Microtus. Numt sequence data from five Microtus species were used to estimate an average rate of nucleotide substitution as 2.6x10(-8) subs/site/yr. This substitution rate is higher than in many other mammals, but is concordant with the elevated rate of mtDNA substitution in this lineage. Our data suggest that numt translocation in Microtus is more extensive than in either Mus or in Rattus, consistent with the elevated rate of speciation, karyotypic rearrangement, and mitochondrial DNA evolution in Microtus.

Diabetic larvae and obese flies-emerging studies of metabolism in Drosophila

The past few years have seen a shift in the use of Drosophila, from studies of growth and development toward genetic characterization of carbohydrate, sterol, and lipid metabolism. This research, reviewed below, establishes a new foundation for using this simple genetic model system to define the basic regulatory mechanisms that underlie metabolic homeostasis and holds the promise of providing new insights into the causes and treatments of critical human disorders such as diabetes and obesity.

Centrin controls the activity of the ciliary reversal-coupled voltage-gated Ca2+ channels Ca2+-dependently

In Paramecium, ciliary reversal is coupled with voltage-gated Ca(2+) channels on the ciliary membrane. We previously isolated a P. caudatum mutant, cnrC, with a malfunction of the Ca(2+) channels and discovered that the channel activity of cnrC was restored by transfection of the P. caudatum centrin (Pccentrin1p) gene, which encodes a member of the Ca(2+)-binding EF-hand protein family. In this study, we injected various mutated Pccentrin1p genes into cnrC and investigated whether these genes restore the Ca(2+) channel activity of cnrC. A Pccentrin1p mutant gene lacking Ca(2+) sensitivity of the third and fourth EF-hands lost the ability to restore the channel function of cnrC, and mutation of the fourth EF-hand caused more serious impairment than mutation of the third EF-hand. Moreover, a Pccentrin1p gene lacking the N-terminal 34-amino acid sequence also lost the ability to restore the channel activity. Native-PAGE analysis demonstrated that the N-terminal sequence is important for the Ca(2+)-dependent structural change of Pccentrin1p. These results demonstrate that Pccentrin1p Ca(2+)-dependently regulates the Ca(2+) channel activity in vivo.

Virulence genes and the evolution of host specificity in plant-pathogenic fungi

In the fungal kingdom, the ability to cause disease in plants appears to have arisen multiple times during evolution. In many cases, the ability to infect particular plant species depends on specific genes that distinguish virulent fungi from their sometimes closely related nonvirulent relatives. These genes encode host-determining "virulence factors," including small, secreted proteins and enzymes involved in the synthesis of toxins. These virulence factors typically are involved in evolutionary arms races between plants and pathogens. We briefly summarize current knowledge of these virulence factors from several fungal species in terms of function, phylogenetic distribution, sequence variation, and genomic location. Second, we address some issues that are relevant to the evolution of virulence in fungi toward plants; in particular, horizontal gene transfer and the genomic organization of virulence genes.

Mutations affecting a putative MutLalpha endonuclease motif impact multiple mismatch repair functions

Mutations in DNA mismatch repair (MMR) lead to increased mutation rates and higher recombination between similar, but not identical sequences, as well as resistance to certain DNA methylating agents. Recently, a component of human MMR machinery, MutLalpha, has been shown to display a latent endonuclease activity. The endonuclease active site appears to include a conserved motif, DQHA(X)(2)E(X)(4)E, within the COOH-terminus of human PMS2. Substitution of the glutamic acid residue (E705) abolished the endonuclease activity and mismatch-dependent excision in vitro. Previously, we showed that the PMS2-E705K mutation and the corresponding mutation in Saccharomyces cerevisiae were both recessive loss of function alleles for mutation avoidance in vivo. Here, we show that mutations impacting this endonuclease motif also significantly affect MMR-dependent suppression of homeologous recombination in yeast and responses to S(n)1-type methylating agents in both yeast and mammalian cells. Thus, our in vivo results suggest that the endonuclease activity of MutLalpha is important not only in MMR-dependent mutation avoidance but also for recombination and damage response functions.

Activation of the Diguanylate Cyclase PleD by Phosphorylation-mediated Dimerization

Diguanylate cyclases (DGCs) are key enzymes of second messenger signaling in bacteria. Their activity is responsible for the condensation of two GTP molecules into the signaling compound cyclic di-GMP. Despite their importance and abundance in bacteria, catalytic and regulatory mechanisms of this class of enzymes are poorly understood. In particular, it is not clear if oligomerization is required for catalysis and if it represents a level for activity control. To address this question we perform in vitro and in vivo analysis of the Caulobacter crescentus diguanylate cyclase PleD. PleD is a member of the response regulator family with two N-terminal receiver domains and a C-terminal diguanylate cyclase output domain. PleD is activated by phosphorylation but the structural changes inflicted upon activation of PleD are unknown. We show that PleD can be specifically activated by beryllium fluoride in vitro, resulting in dimerization and c-di-GMP synthesis. Cross-linking and fractionation experiments demonstrated that the DGC activity of PleD is contained entirely within the dimer fraction, confirming that the dimer represents the enzymatically active state of PleD. In contrast to the catalytic activity, allosteric feedback regulation of PleD is not affected by the activation status of the protein, indicating that activation by dimerization and product inhibition represent independent layers of DGC control. Finally, we present evidence that dimerization also serves to sequester activated PleD to the differentiating Caulobacter cell pole, implicating protein oligomerization in spatial control and providing a molecular explanation for the coupling of PleD activation and subcellular localization.

Functional characterization, sequence comparisons and distribution of a polyketide synthase gene required for perithecial pigmentation in someFusariumspecies

Polyketides are a structurally diverse class of secondary metabolites produced by bacteria, fungi, plants and animals. The fungal genus Fusarium includes agronomically important plant pathogenic and mycotoxin-producing species and produces numerous polyketides. The study further characterized a polyketide synthase-encoding gene (PKS3 = PGL1) that was previously identified in F. graminearum and F. verticillioides. Disruption of the F. verticillioides PGL1 indicated that it is required for the production of the dark pigment in perithecial walls, as previously shown in F. graminearum. A third PGL1 orthologue was identified in the genomic sequence of N. haematococca (anamorph F. solani f. sp. pisi). Analysis of the carboxy-terminal end of the deduced PGL1 protein indicated that it had a functional domain related to dehydrogenases/reductases that is sometimes present in non-ribosomal peptide synthetases. Comparison of the genomic regions flanking PGL1 in F. graminearum, F. verticillioides and N. haematococca revealed that the extent of gene synteny in this region was greater between F. graminearum and F. verticillioides than between either of these species and N. haematococca. Southern blot analysis indicated that PGL1 occurs widely within the genus Fusarium including species with no known sexual stage.

Exploring Fast Computational Strategies for Probabilistic Phylogenetic Analysis

In recent years, the advent of Markov chain Monte Carlo (MCMC) techniques, coupled with modern computational capabilities, has enabled the study of evolutionary models without a closed form solution of the likelihood function. However, current Bayesian MCMC applications can incur significant computational costs, as they are based on a full sampling from the posterior probability distribution of the parameters of interest. Here, we draw attention as to how MCMC techniques can be embedded within normal approximation strategies for more economical statistical computation. The overall procedure is based on an estimate of the first and second moments of the likelihood function, as well as a maximum likelihood estimate. Through examples, we review several MCMC-based methods used in the statistical literature for such estimation, applying the approaches to constructing posterior distributions under non-analytical evolutionary models relaxing the assumptions of rate homogeneity, and of independence between sites. Finally, we use the procedures for conducting Bayesian model selection, based on Laplace approximations of Bayes factors, which we find to be accurate and computationally advantageous. Altogether, the methods we expound here, as well as other related approaches from the statistical literature, should prove useful when investigating increasingly complex descriptions of molecular evolution, alleviating some of the difficulties associated with nonanalytical models.

QTL ANALYSIS OF FLORAL TRAITS IN LOUISIANA IRIS HYBRIDS

The formation of hybrid zones between nascent species is a widespread phenomenon. The evolutionary consequences of hybridization are influenced by numerous factors, including the action of natural selection on quantitative trait variation. Here we examine how the genetic basis of floral traits of two species of Louisiana Irises affects the extent of quantitative trait variation in their hybrids. Quantitative trait locus (QTL) mapping was used to assess the size (magnitude) of phenotypic effects of individual QTL, the degree to which QTL for different floral traits are colocalized, and the occurrence of mixed QTL effects. These aspects of quantitative genetic variation would be expected to influence (1) the number of genetic steps (in terms of QTL substitutions) separating the parental species phenotypes; (2) trait correlations; and (3) the potential for transgressive segregation in hybrid populations. Results indicate that some Louisiana Iris floral trait QTL have large effects and QTL for different traits tend to colocalize. Transgressive variation was observed for six of nine traits, despite the fact that mixed QTL effects influence few traits. Overall, our QTL results imply that the genetic basis of floral morphology and color traits might facilitate the maintenance of phenotypic divergence between Iris fulva and Iris brevicaulis, although a great deal of phenotypic variation was observed among hybrids.

Toxicogenetics of Antiretroviral Therapy: Genetic Factors that Contribute to Metabolic Complications

Metabolic complications of antiretroviral therapy (ART) have emerged as a major concern for long-term, successful management of HIV infection. Variability in the response to ART between individuals has been increasingly linked to the genetic background of patients, as regards efficacy and susceptibility to adverse reactions (toxicogenetics). This review summarizes the biological and methodological background for the genetic prediction of metabolic toxicity of ART. Recent studies are discussed which suggest that single-nucleotide polymorphisms (SNPs) in several genes involved in lipid metabolism and lipid transport in the general population (ABCA1, APOA5, APOC3, APOE, CETP) might modulate plasma triglyceride and high-density lipoprotein cholesterol levels in HIV-infected patients. At present, genetic prediction of lipodystrophy is not possible. Lipodystrophy has been linked to an accumulation of mtDNA mutations, a finding causally associated with ageing phenotypes in animal models. No mutations in LMNA, a gene linked to rare, inherited forms of lipodystrophy, have been identified in small studies of patients with lipodystrophy, and a possible link to a TNF promoter SNP remains to be confirmed. With the rapidly decreasing cost of genetic testing, the main issues that need to be addressed prior to introduction of toxicogenetic prediction in HIV clinical practice include reproducibly high predictive values of SNP associations with clinically relevant and well defined metabolic outcomes, studies that evaluate the contribution of SNPs in the context of multi-SNP and haplotype analysis, and the validation of genetic markers in independent, large patient cohorts. Comprehensive, whole genome approaches are increasingly being used.

Alternatively Spliced T-cell Receptor Transcripts Are Up-regulated in Response to Disruption of Either Splicing Elements or Reading Frame

Nonsense mutations create premature termination codons (PTCs), leading to the generation of truncated proteins, some of which have deleterious gain-of-function or dominant-negative activity. Protecting cells from such aberrant proteins is non-sense-mediated decay (NMD), an RNA surveillance pathway that degrades transcripts harboring PTCs. A second response to nonsense mutations is the up-regulation of alternatively spliced transcripts that skip the PTC. This nonsense-associated altered splicing (NAS) response has the potential to rescue protein function, but the mechanism by which it is triggered has been controversial. Some studies suggest that, like NMD, NAS is triggered as a result of nonsense mutations disrupting reading frame, whereas other studies suggest that NAS is triggered when nonsense mutations disrupt exonic splicing enhancers (ESEs). Using T-cell receptor-beta (TCRbeta), which naturally acquires PTCs at high frequency, we provide evidence that both mechanisms act on a single type of mRNA. Mutations that disrupt consensus ESE sites up-regulated an alternatively spliced TCRbeta transcript that skipped the mutations independently of reading frame disruption and the NMD factor UPF1. In contrast, reading frame-disrupting mutations that did not disrupt consensus ESE sites elicited UPF1-dependent up-regulation of the alternatively spliced TCRbeta transcript. Restoration of reading frame prevented this up-regulation. Our results suggest that the response of an mRNA to a nonsense mutation depends on its context.

Root system architecture: opportunities and constraints for genetic improvement of crops

Abiotic stresses increasingly curtail crop yield as a result of global climate change and scarcity of water and nutrients. One way to minimize the negative impact of these factors on yield is to manipulate root system architecture (RSA) towards a distribution of roots in the soil that optimizes water and nutrient uptake. It is now established that most of the genetic variation for RSA is driven by a suite of quantitative trait loci. As we discuss here, marker-assisted selection and quantitative trait loci cloning for RSA are underway, exploiting genomic resources, candidate genes and the knowledge gained from Arabidopsis, rice and other crops. Nonetheless, efficient and accurate phenotyping, modelling and collaboration with breeders remain important challenges, particularly when defining ideal RSA for different crops and target environments.

Mixed infections, cryptic diversity, and vector-borne pathogens: evidence from Polygenis fleas and Bartonella species

Coinfections within hosts present opportunities for horizontal gene transfer between strains and competitive interactions between genotypes and thus can be a critical element of the lifestyles of pathogens. Bartonella spp. are Alphaproteobacteria that parasitize mammalian erythrocytes and endothelial cells. Their vectors are thought to be various biting arthropods, such as fleas, ticks, mites, and lice, and they are commonly cited as agents of various emerging diseases. Coinfections by different Bartonella strains and species can be common in mammals, but little is known about specificity and coinfections in arthropod vectors. We surveyed the rate of mixed infections of Bartonella in flea vectors (Polygenis gwyni) parasitizing cotton rats (Sigmodon hispidus) in which previous surveys indicated high rates of infection. We found that nearly all fleas (20 of 21) harbored one or more strains of Bartonella, with rates of coinfection approaching 90%. A strain previously identified as common in cotton rats was also common in their fleas. However, another common strain in cotton rats was absent from P. gwyni, while a rare cotton rat strain was quite common in P. gwyni. Surprisingly, some samples were also coinfected with a strain phylogenetically related to Bartonella clarridgeiae, which is typically associated with felids and ruminants. Finally, a locus (pap31) that is characteristically borne on phage in Bartonella was successfully sequenced from most samples. However, sequence diversity in pap31 was novel in the P. gwyni samples, relative to other Bartonella previously typed with pap31, emphasizing the likelihood of large reservoirs of cryptic diversity in natural populations of the pathogen.

Is transplanting an effective means of preserving vegetation?

Transplantation to new locations is used widely to propagate horticultural and agricultural species but is also promoted as a means of relocating whole communities that stand in the way of development. It may be used as well to move vegetation from the field for experimentation under controlled conditions. Transplantation has not in the past been considered a reliable means of conserving threatened species or reproducing functional characteristics of natural communities, and has been regarded by many as highly ineffective. However, its potential must now be re-examined because of the many recent transplant attempts as well as advances in related fields. Recent trials illustrate that individual endangered species are still particularly difficult to transplant and displaced multi-species sods are almost always changed in the process. Exact reconstruction of communities from individual components is next to impossible because the full complement of species, including critical microbial components, is almost never known. Owing to a limited understanding of phenology, reproduction, functional roles, and interrelationships among constituent microbes, cryptogams, vascular plants, and fauna, transplants may be placed into sites with both biological and physical insufficiencies. Genetic diversity may be lost or, if genotypes from diverse sources are mixed, outbreeding depression may result. Recent advances in soil science, microbial ecology, and population genetics have in some cases improved the effectiveness of transplantation, but new insights mainly permit a fuller appreciation of the causes of failure. Home-site advantage has been demonstrated, and habitat protection appears to be the best and perhaps only reliable way of preserving intact natural communities and rare species. Furthermore, experimentation with vegetational mats under controlled conditions may have little relevance to natural ecosystems.

From circadian rhythms to clock genes in depression

Depression, particularly unipolar depression, has often been linked to circadian (i.e. approximately 24-h) rhythm abnormalities. The observation that many diverse rhythms are disrupted in depressed patients indicates that such disturbances are not unique to specific rhythms, but instead are of a more central origin (i.e. involve the central circadian pacemaker and/or the molecular circadian clock core machinery). One rhythm that is often disrupted in depression is the sleep-wake cycle - a disruption that, in turn, might lead to other rhythm disturbances. Thus, there are two general ways in which disrupted circadian rhythms could lead to depression: (i) disorganization within the circadian system could itself lead to neurobiological dysfunction and (ii) a circadian disturbance of the normal sleep-wake cycle could facilitate or exacerbate the depressed state. The recent discovery of the molecular clock responsible for the generation of circadian rhythms provides novel mechanistic insights into how rhythm abnormalities might lead to disrupted behavioural states, and offers new therapeutic avenues for the treatment of the timing abnormalities that might underlie depression. The finding that the molecular circadian clock is present in many cells in the central nervous system and regulates the timing of the expression of at least 10% of the transcripts in many tissues emphasizes how circadian dysfunction could have drastic consequences for normal physiological function in the brain.

Chaperone effects on prion and nonprion aggregates

Exposure to high temperature or other stresses induces a synthesis of heat shock proteins. Many of these proteins are molecular chaperones, and some of them help cells to cope with heat-induced denaturation and aggregation of other proteins. In the last decade, chaperones have received increased attention in connection with their role in maintenance and propagation of the Saccharomyces cerevisiae prions, infectious or heritable agents transmitted at the protein level. Recent data suggest that functioning of the chaperones in reactivation of heat-damaged proteins and in propagation of prions is based on the same molecular mechanisms but may lead to different consequences depending on the type of aggregate. In both cases the concerted and balanced action of "chaperones' team," including Hsp104, Hsp70, Hsp40 and possibly other proteins, determines whether a misfolded protein is to be incorporated into an aggregate, rescued to the native state or targeted for degradation.

Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1

The IncP-7 plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon transfer to the recipient strain P. putida KT2440. We designed a customized whole-genome oligonucleotide microarray to study the coordinated expression of pCAR1 and the chromosome in the transconjugant strain KT2440(pCAR1). First, the transcriptome of KT2440(pCAR1) during growth with carbazole as the sole carbon source was compared to that during growth with succinate. The carbazole catabolic car and ant operons were induced, along with the chromosomal cat and pca genes involved in the catechol branch of the beta-ketoadipate pathway. Additionally, the regulatory gene antR encoding the AraC/XylS family transcriptional activator specific for car and ant operons was upregulated. The characterization of the antR promoter revealed that antR is transcribed from an RpoN-dependent promoter, suggesting that the successful expression of the carbazole catabolic operons depends on whether the chromosome contains the specific RpoN-dependent activator. Next, to analyze whether the horizontal transfer of a plasmid alters the transcription network of its host chromosome, we compared the chromosomal transcriptomes of KT2440(pCAR1) and KT2440 under the same growth conditions. Only subtle changes were caused by the transfer of pCAR1, except for the significant induction of the hypothetical gene PP3700, designated parI, which encodes a putative ParA-like ATPase with an N-terminal Xre-type DNA-binding motif. Further transcriptional analyses showed that the parI promoter was positively regulated by ParI itself and the pCAR1-encoded protein ParA.

Genetic interaction between glabra3-shapeshifter and siamese in Arabidopsis thaliana converts trichome precursors into cells with meristematic activity

The identity of many genes required for trichome differentiation is known. This paper describes a novel interaction between mutant alleles of two such genes. One of the alleles, called gl3-sst, is derived from the GL3 locus, which encodes a basic helix-loop-helix type transcription factor. The mutation in the gl3-sst protein modifies its ability to form a complex with the GL1 protein (a MYB transcription factor required for trichome formation), leading to changes in gene expression compared with wild type during gl3-sst mutant trichome development. The other mutant allele, sim, is a likely loss of function allele derived from the SIM locus, which is predicted to encode a negative regulator of D-type cyclin activity. The gl3-sst sim double mutant exhibits mounds of cells derived from the proliferation of single trichome precursors. The ectopic expression of a D-type cyclin gene in gl3-sst mimics the double mutant phenotype. Thus, an interaction between altered trichome gene expression caused by the gl3-sst mutation and relaxed regulation of D-type cyclin activity in the double mutant converted a non-dividing cell into a novel highly proliferating cell type.

The function of Dmrt genes in vertebrate development: It is not just about sex

The Dmrt genes encode a large family of transcription factors whose function in sexual development has been well studied in invertebrates and vertebrates. Their expression pattern is not restricted to the developing gonads, indicating that Dmrt genes might regulate other developmental processes. Here we review the expression pattern of several members of this family across species and summarize recent findings on the function of a subset of these genes in non-gonadal tissues.

Mitochondrial dysfunction: the first domino in brain aging and Alzheimer's disease?

With the increasing average life span of humans and with decreasing cognitive function in elderly individuals, age-related cognitive disorders including dementia have become a major health problem in society. Aging-related mitochondrial dysfunction underlies many common neurodegenerative disorders diseases, including Alzheimer's disease (AD). AD is characterized by two major histopathological hallmarks, initially intracellular and with the progression of the disease extracellular accumulation of oligomeric and fibrillar beta-amyloid (Abeta) peptides and intracellular neurofibrillary tangles (NFT) composed of hyperphosphorylated tau protein. In this review, the authors focus on the latest findings in AD animal models indicating that these histopathological alterations induce deficits in the function of the complexes of the respiratory chain and therefore consecutively result in mitochondrial dysfunction. This parameter is intrinsically tied to oxidative stress. Both are early events in aging and especially in the pathogenesis of aging-related severe neurodegeneration. Ginkgo biloba extract seems to be of therapeutic benefit in the treatment of mild to moderate dementia of different etiology, although the data are quite heterogeneous. Herein, the authors suggest that mitochondrial protection and subsequent reduction of oxidative stress are important components of the neuroprotective activity of Ginkgo biloba extract.

Sex-dependent up-regulation of two splicing factors, Psf and Srp20, during hippocampal memory formation

Gene transcription is required for long-term memory (LTM) formation. LTM formation is impaired in a male-specific manner in mice lacking either of the two Ca(2+)/calmodulin-dependent kinase kinase (Camkk) genes. Since altered transcription was suggested to cause these impairments in LTM formation, we used microarrays to screen for CaMKKbeta-dependent gene expression changes. Here we show that the hippocampal mRNA expression of two splicing factors, splicing factor arginine/serine-rich 3 (Sfrs3/Srp20) and polypyrimidine tract-binding protein-associated splicing factor (Psf), is altered in CaMKKbeta-deficient males. In wild-type (WT) mice, the basal expression level in the hippocampus is higher in males than in females, and the sex difference in Srp20 expression is detectable before puberty. Training in two hippocampus-dependent learning tasks, the spatial version of the Morris water maze (MWM) and background contextual fear conditioning, increases the hippocampal mRNA expression of both splicing factors in WT males. However, the increase in Srp20 mRNA expression occurs only in males and not in females, whereas the up-regulation of Psf expression occurs in both sexes. Importantly, control experiments demonstrate that the up-regulation of both splicing factors is specific for the learned associations after contextual fear conditioning. In summary, we provide the first evidence for a regulation of splicing factors during LTM formation and we suggest that alternative splicing contributes to sex differences in LTM formation.

Transposable element fragments in protein-coding regions and their contributions to human functional proteins

Transposable elements (TEs) and their contributions to protein-coding regions are of particular interest. Here we searched for TE fragments in Homo sapiens at both the transcript and protein levels. We found evidence in support of TE exonization and its association with alternative splicing. Despite recent findings that long evolutionary times are required to incorporate TE into proteins, we found many functional proteins with translated TE cassettes derived from young TEs. Analyses of two Bcl-family proteins and Alu-encoded segments suggest the coding and functional potential of TE sequences.

RecBCD and RecJ/RecQ Initiate DNA Degradation on Distinct Substrates in UV-Irradiated Escherichia coli

After UV irradiation, recA mutants fail to recover replication, and a dramatic and nearly complete degradation of the genomic DNA occurs. Although the RecBCD helicase/nuclease complex is known to mediate this catastrophic DNA degradation, it is not known how or where this degradation is initiated. Previous studies have speculated that RecBCD targets and initiates degradation from the nascent DNA at replication forks arrested by DNA damage. To test this question, we examined which enzymes were responsible for the degradation of genomic DNA and the nascent DNA in UV-irradiated recA cells. We show here that, although RecBCD degrades the genomic DNA after UV irradiation, it does not target the nascent DNA at arrested replication forks. Instead, we observed that the nascent DNA at arrested replication forks in recA cultures is degraded by RecJ/RecQ, similar to what occurs in wild-type cultures. These findings indicate that the genomic DNA degradation and nascent DNA degradation in UV-irradiated recA mutants are mediated separately through RecBCD and RecJ/RecQ, respectively. In addition, they demonstrate that RecBCD initiates degradation at a site(s) other than the arrested replication fork directly.

Biological roles of prion domains

In vivo amyloid formation is a widespread phenomenon in eukaryotes. Self-perpetuating amyloids provide a basis for the infectious or heritable protein isoforms (prions). At least for some proteins, amyloid-forming potential is conserved in evolution despite divergence of the amino acid (aa) sequences. In some cases, prion formation certainly represents a pathological process leading to a disease. However, there are several scenarios in which prions and other amyloids or amyloid-like aggregates are either shown or suspected to perform positive biological functions. Proven examples include self/nonself recognition, stress defense and scaffolding of other (functional) polymers. The role of prion-like phenomena in memory has been hypothesized. As an additional mechanism of heritable change, prion formation may in principle contribute to heritable variability at the population level. Moreover, it is possible that amyloid-based prions represent by-products of the transient feedback regulatory circuits, as normal cellular function of at least some prion proteins is decreased in the prion state.

Functional analysis of N-terminal domains of Arabidopsis chlorophyllide a oxygenase

Higher plants acclimate to various light environments by changing the antenna size of a light-harvesting photosystem. The antenna size of a photosystem is partly determined by the amount of chlorophyll b in the light-harvesting complexes. Chlorophyllide a oxygenase (CAO) converts chlorophyll a to chlorophyll b in a two-step oxygenation reaction. In our previous study, we demonstrated that the cellular level of the CAO protein controls accumulation of chlorophyll b. We found that the amino acids sequences of CAO in higher plants consist of three domains (A, B, and C domains). The C domain exhibits a catalytic function, and we demonstrated that the combination of the A and B domains regulates the cellular level of CAO. However, the individual function of each of A and B domain has not been determined yet. Therefore, in the present study we constructed a series of deleted CAO sequences that were fused with green fluorescent protein and overexpressed in a chlorophyll b-less mutant of Arabidopsis thaliana, ch1-1, to further dissect functions of A and B domains. Subsequent comparative analyses of the transgenic plants overexpressing B domain containing proteins and those lacking the B domain determined that there was no significant difference in CAO protein levels. These results indicate that the B domain is not involved in the regulation of the CAO protein levels. Taken together, we concluded that the A domain alone is involved in the regulatory mechanism of the CAO protein levels.

Anthraquinones as defensive compounds in eggs of Galerucini leaf beetles: biosynthesis by the beetles?

Eggs of leaf beetles of the tribe Galerucini, subfamily Galerucinae, contain polyketides that are unusual in insects: 1,8-dihydroxylated anthraquinones (chrysazin, chrysophanol) and anthrones (dithranol, chrysarobin) deterring predators. The host plants do not contain these compounds. In the present study, we tested the hypothesis that the beetles, but not bacterial or fungal microorganisms living as endosymbionts within the beetles, produce the anthraquinones. The tansy leaf beetle Galeruca tanaceti was used as Galerucini model organism. It was treated with antimicrobial substances to eradicate the microorganisms and inhibit the hypothesised endosymbiotic anthraquinone production. Despite treatment, female G. tanaceti laid eggs containing anthraquinones. Although broad spectrum antimicrobials were used, it cannot be excluded that the potential endosymbiotic microorganisms are resistant. Given that the hypothesised endosymbionts are transferred via the eggs from one generation to the next, bacterial or fungal DNA was expected to be present in the eggs. With the exception of Wolbachia pipientis, however, no further 16S rDNA from bacteria responsible for anthraquinone biosynthesis was detected in eggs of untreated beetles. Because Wolbachia were also found in closely related anthraquinone-free insects, we exclude these bacteria as producers of the defensive polyketides. Nor was any 18S rDNA from fungi with anthraquinone biosynthetic abilities detected. Our results indicate that anthraquinones and anthrones in eggs of Galerucini are produced by beetle enzymes and not by endosymbiotic microorganisms within the eggs.

Human NEIL1 localizes with the centrosomes and condensed chromosomes during mitosis

The DNA glycosylase hNEIL1 initiates base excision repair (BER) of a number of oxidized purines and pyrimidines in cellular DNA and is one of three mammalian orthologs of the Escherichia coli Nei/Fpg enzymes. Human NEIL1 has been purified and extensively characterized biochemically, however, not much is known about its intracellular distribution. In the present work, we have studied the cellular localization of hNEIL1 using both antibodies raised against the full-length recombinant protein and a stable HeLa cell line expressing hNEIL1 fused N-terminal to EGFP. The results presented reveal an intricate mitotic distribution of hNEIL1. Centrosomal localization of hNEIL1 was observed when mitotic HeLa cells were immunostained with hNEIL1 antibodies. This localization was confirmed when Western blots of isolated centrosomes from stably expressing hNEIL1-EGFP HeLa cells were probed with GFP or hNEIL1 antibodies, even though a fluorescent signal could not be detected in the centrosomes of these cells. Human NEIL1 was also shown to be associated with mitotic condensed chromosomes. Notably, the interaction of hNEIL1 with condensed chromatin was disrupted when cells were fixed with chemical fixatives that are regularly used in immunodetection techniques.

A Serratia marcescens OxyR homolog mediates surface attachment and biofilm formation

OxyR is a conserved bacterial transcription factor with a regulatory role in oxidative stress response. From a genetic screen for genes that modulate biofilm formation in the opportunistic pathogen Serratia marcescens, mutations in an oxyR homolog and predicted fimbria structural genes were identified. S. marcescens oxyR mutants were severely impaired in biofilm formation, in contrast to the hyperbiofilm phenotype exhibited by oxyR mutants of Escherichia coli and Burkholderia pseudomallei. Further analysis revealed that OxyR plays a role in the primary attachment of cells to a surface. Similar to what is observed in other bacterial species, S. marcescens OxyR is required for oxidative stress resistance. Mutations in oxyR and type I fimbrial genes resulted in severe defects in fimbria-associated phenotypes, revealing roles in cell-cell and cell-biotic surface interactions. Transmission electron microscopy revealed the absence of fimbria-like surface structures on an OxyR-deficient strain and an enhanced fimbrial phenotype in strains bearing oxyR on a multicopy plasmid. The hyperfimbriated phenotype conferred by the multicopy oxyR plasmid was absent in a type I fimbrial mutant background. Real-time reverse transcriptase PCR indicated an absence of transcripts from a fimbrial operon in an oxyR mutant that were present in the wild type and a complemented oxyR mutant strain. Lastly, chromosomal P(lac)-mediated expression of fimABCD was sufficient to restore wild-type levels of yeast agglutination and biofilm formation to an oxyR mutant. Together, these data support a model in which OxyR contributes to early stages of S. marcescens biofilm formation by influencing fimbrial gene expression.

The promoter of the TLC1.1 retrotransposon from Solanum chilense is activated by multiple stress-related signaling molecules

The LTR retrotransposons are the most abundant mobile elements in the plant genome and seem to play an important role in genome reorganization induced by environmental challenges. Their success in this function depends on the ability of their promoters to respond to different signaling pathways that regulate plant adaptation to biotic and abiotic stresses. The promoter of the TLC1.1 retrotransposon from Solanum chilense contains two primary ethylene-responsive elements (PERE boxes) that are essential for its response to ethylene and for the stress-induced expression. Here, we describe that a 270 bp fragment (P270), derivative of this retroelement promoter, is also able to activate the transcription of the GUS reporter gene in transgenic plants in response to salicylic acid (SA), abscisic acid (ABA), methyl jasmonate (MeJA), hydrogen peroxide (H2O2) and the synthetic auxin 2,4-D. PERE box-dependent and independent routes are involved in the response of P270 to these signal molecules. MeJA, H2O2 and 2,4-D activate this promoter through cis-acting elements other than PERE boxes, whereas ABA and SA act via a PERE box-independent pathway but require this element for maximal activation. Three putative cis-acting elements MRE, GCN4 and GT1/TCA identified in the P270 promoter may be involved in the PERE box-independent activation pathway. These results suggest that the promoter of TLC1.1 may act as an integrator of different signal transduction pathways, allowing this member of the TLC1 retrotransposon family to be activated in response to multiples challenges.

Downregulation of terpenoid indole alkaloid biosynthetic pathway by low temperature and cloning of a AP2 type C-repeat binding factor (CBF) from Catharanthus roseus (L). G. Don

Plants produce secondary metabolites in response to various external signals. Coordinated transcriptional control of biosynthetic genes emerges as a major mechanism dictating the accumulation of secondary metabolites in plant cells. However, information about stress regulation of secondary metabolites and the molecular mechanisms regulating these specialized pathways are poorly understood. Here, we show that terpenoid indole alkaloid (TIA) biosynthetic pathway is differentially regulated in response to different abiotic stresses in Catharanthus roseus, a model medicinal plant producing important anticancer and antihypertensive drugs. Semiquantitative RT-PCR analysis of TIA and related primary pathway genes in response to dehydration, low temperature, salinity, UV-light and wounding revealed their negative regulation in response to low temperature. HPLC analysis further supports the notion that TIA biosynthetic pathway is negatively controlled by low temperature stress. Furthermore, we report the cloning of a C-repeat binding transcription factor from C. roseus (CrCbf), belonging to AP2 class of transcription factor and possessed the NLS and CBF signature sequence characteristic of CBFs. CrCbf was found to be similar to Brassica Cbfs, whereas it was distant to monocot Cbfs. Southern analysis of CrCbf revealed the presence of more than one copy of CrCbf gene or other Cbf homologues in C. roseus genome. The transcription of CrCbf was found to be constitutive in response to low temperature but it showed differential distribution. The need for identifying novel transcription factors in understanding secondary metabolite biosynthesis is discussed.

Shared quantitative trait loci underlying the genetic correlation between continuous traits

We review genetic correlations among quantitative traits in light of their underlying quantitative trait loci (QTL). We derive an expectation of genetic correlation from the effects of underlying loci and test whether published genetic correlations can be explained by the QTL underlying the traits. While genetically correlated traits shared more QTL (33%) on average than uncorrelated traits (11%), the actual number of shared QTL shared was small. QTL usually predicted the sign of the correlation with good accuracy, but the quantitative prediction was poor. Approximately 25% of trait pairs in the data set had at least one QTL with antagonistic effects. Yet a significant minority (20%) of such trait pairs have net positive genetic correlations due to such antagonistic QTL 'hidden' within positive genetic correlations. We review the evidence on whether shared QTL represent single pleiotropic loci or closely linked monotropic genes, and argue that strict pleiotropy can be viewed as one end of a continuum of recombination rates where r=0. QTL studies of genetic correlation will likely be insufficient to predict evolutionary trajectories over long time spans in large panmictic populations, but will provide important insights into the trade-offs involved in population and species divergence.

A simple array platform for microRNA analysis and its application in mouse tissues

MicroRNAs (miRNAs) are a novel class of small noncoding RNAs that regulate gene expression at the post-transcriptional level and play a critical role in many important biological processes. Most miRNAs are conserved between humans and mice, which makes it possible to analyze their expressions with a set of selected array probes. Here, we report a simple array platform that can detect 553 nonredundant miRNAs encompassing the entire set of miRNAs for humans and mice. The platform features carefully selected and designed probes with optimized hybridization parameters. Potential cross-reaction between mature miRNAs and their precursors was investigated. The array platform was used to analyze miRNAs in the mouse central nervous system (CNS, spinal cord and brain), and two other non-CNS organs (liver and heart). Two types of miRNAs, differentially expressed organ/tissue-associated miRNAs and ubiquitously expressed miRNAs, were detected in the array analysis. In addition to the previously reported neuron-related miR-124a, liver-related miR-122a, and muscle-related miR-133a, we also detected new tissue-associated miRNAs (e.g., liver-associated miR-194). Interestingly, while the majority of pre-miRNAs were undetectable, miR690, miR709, and miR720 were clearly detected at both mature and precursor levels by the array analysis, indicating a limited cross-reaction between pre-miRNAs and their mature miRNAs. The reliability of this array technology was validated by comparing the results with independent Northern blot analyses and published data. A new approach of data normalization based on Northern blot analysis of one ubiquitously expressed miRNA is introduced and compared with traditional approaches. We expect this miRNA array platform to be useful for a wide variety of biological studies.

TBX22 missense mutations found in patients with X-linked cleft palate affect DNA binding, sumoylation, and transcriptional repression

The T-box transcription factor TBX22 is essential for normal craniofacial development, as demonstrated by the finding of nonsense, frameshift, splice-site, or missense mutations in patients with X-linked cleft palate (CPX) and ankyloglossia. To better understand the function of TBX22, we studied 10 different naturally occurring missense mutations that are phenotypically equivalent to loss-of-function alleles. Since all missense mutations are located in the DNA-binding T-box domain, we first investigated the preferred recognition sequence for TBX22. Typical of T-box proteins, the resulting sequence is a palindrome based around near-perfect copies of AGGTGTGA. DNA-binding assays indicate that missense mutations at or near predicted contact points with the DNA backbone compromise stable DNA-protein interactions. We show that TBX22 functions as a transcriptional repressor and that TBX22 missense mutations result in impaired repression activity. No effect on nuclear localization of TBX22 was observed. We find that TBX22 is a target for the small ubiquitin-like modifier SUMO-1 and that this modification is required for TBX22 repressor activity. Although the site of SUMO attachment at the lysine at position 63 is upstream of the T-box domain, loss of SUMO-1 modification is consistently found in all pathogenic CPX missense mutations. This implies a general mechanism linking the loss of SUMO conjugation to the loss of TBX22 function. Orofacial clefts are well known for their complex etiology and variable penetrance, involving both genetic and environmental risk factors. The sumoylation process is also subject to and profoundly affected by similar environmental stresses. Thus, we suggest that SUMO modification may represent a common pathway that regulates normal craniofacial development and is involved in the pathogenesis of both Mendelian and idiopathic forms of orofacial clefting.

Differential requirements for RAD51 in Physcomitrella patens and Arabidopsis thaliana development and DNA damage repair

RAD51, the eukaryotic homolog of the bacterial RecA recombinase, plays a central role in homologous recombination (HR) in yeast and animals. Loss of RAD51 function causes lethality in vertebrates but not in other animals or in the flowering plant Arabidopsis thaliana, suggesting that RAD51 is vital for highly developed organisms but not for others. Here, we found that loss of RAD51 function in the moss Physcomitrella patens, a plant of less complexity, caused a significant vegetative phenotype, indicating an important function for RAD51 in this organism. Moreover, loss of RAD51 caused marked hypersensitivity to the double-strand break-inducing agent bleomycin in P. patens but not in Arabidopsis. Therefore, HR is used for somatic DNA damage repair in P. patens but not in Arabidopsis. These data imply fundamental differences in the use of recombination pathways between plants. Moreover, these data demonstrate that the importance of RAD51 for viability is independent of taxonomic position or complexity of an organism. The involvement of HR in DNA damage repair in the slowly evolving species P. patens but not in fast-evolving Arabidopsis suggests that the choice of the recombination pathway is related to the speed of evolution in plants.

Chlorophyll Biosynthesis in Bacteria: The Origins of Structural and Functional Diversity

The use of photochemical reaction centers to convert light energy into chemical energy, chlorophototrophy, occurs in organisms belonging to only five eubacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, and Firmicutes. All chlorophototrophs synthesize two types of pigments: (a) chlorophylls and bacteriochlorophylls, which function in both light harvesting and uniquely in photochemistry; and (b) carotenoids, which function primarily as photoprotective pigments but can also participate in light harvesting. Although hundreds of carotenoids have been identified, only 12 types of chlorophylls (Chl a, b, d; divinyl-Chl a and b; and 8(1)-hydroxy-Chl a) and bacteriochlorophylls (BChl a, b, c, d, e, and g) are currently known to occur in bacteria. This review summarizes recent progress in the identification of genes and enzymes in the biosynthetic pathways leading to Chls and BChls, the essential tetrapyrrole cofactors of photosynthesis, and addresses the mechanisms for generating functional diversity for solar energy capture and conversion in chlorophototrophs.

Functional significance of channels and transporters expressed in the inner ear and kidney

A number of ion channels and transporters are expressed in both the inner ear and kidney. In the inner ear, K+cycling and endolymphatic K+, Na+, Ca2+, and pH homeostasis are critical for normal organ function. Ion channels and transporters involved in K+cycling include K+channels, Na+-2Cl−-K+cotransporter, Na+/K+-ATPase, Cl−channels, connexins, and K+/Cl−cotransporters. Furthermore, endolymphatic Na+and Ca2+homeostasis depends on Ca2+-ATPase, Ca2+channels, Na+channels, and a purinergic receptor channel. Endolymphatic pH homeostasis involves H+-ATPase and Cl−/HCO3−exchangers including pendrin. Defective connexins (GJB2 and GJB6), pendrin (SLC26A4), K+channels (KCNJ10, KCNQ1, KCNE1, and KCNMA1), Na+-2Cl−-K+cotransporter (SLC12A2), K+/Cl−cotransporters (KCC3 and KCC4), Cl−channels (BSND and CLCNKA + CLCNKB), and H+-ATPase (ATP6V1B1 and ATPV0A4) cause hearing loss. All these channels and transporters are also expressed in the kidney and support renal tubular transport or signaling. The hearing loss may thus be paralleled by various renal phenotypes including a subtle decrease of proximal Na+-coupled transport (KCNE1/KCNQ1), impaired K+secretion (KCNMA1), limited HCO3−elimination (SLC26A4), NaCl wasting (BSND and CLCNKB), renal tubular acidosis (ATP6V1B1, ATPV0A4, and KCC4), or impaired urinary concentration (CLCNKA). Thus, defects of channels and transporters expressed in the kidney and inner ear result in simultaneous dysfunctions of these seemingly unrelated organs.

Automated segmentation and classification of high throughput yeast assay spots

Several technologies for characterizing genes and proteins from humans and other organisms use yeast growth or color development as read outs. The yeast two-hybrid assay, for example, detects protein-protein interactions by measuring the growth of yeast on a specific solid medium, or the ability of the yeast to change color when grown on a medium containing a chromogenic substrate. Current systems for analyzing the results of these types of assays rely on subjective and inefficient scoring of growth or color by human experts. Here, an image analysis system is described for scoring yeast growth and color development in high throughput biological assays. The goal is to locate the spots and score them in color images of two types of plates named "X-Gal" and "growth assay" plates, with uniformly placed spots (cell areas) on each plate (both plates in one image). The scoring system relies on color for the X-Gal spots, and texture properties for the growth assay spots. A maximum likelihood projection-based segmentation is developed to automatically locate spots of yeast on each plate. Then color histogram and wavelet texture features are extracted for scoring using an optimal linear transformation. Finally, an artificial neural network is used to score the X-Gal and growth assay spots using the extracted features. The performance of the system is evaluated using spots of 60 images. After training the networks using training and validation sets, the system was assessed on the test set. The overall accuracies of 95.4% and 88.2% are achieved, respectively, for scoring the X-Gal and growth assay spots.

Overview of genetic diagnosis in cancer

Both cytogenetic and molecular genetic studies can contribute to the management of patients with cancer. In some cases genetic markers are specific to particular tumor types and are useful in diagnosis. This can be helpful in distinguishing histologically similar tumors that may respond differently to treatment and can sometimes be of prognostic value. Genetic markers can also be tools for following the response of a tumor to therapy, providing a sensitive means of detection of relapse. This introductory unit considers some of the types of genetic changes that occur in association with malignancies and major approaches used in their detection.

Inhibition of IS2transposition by factor for inversion stimulation

The effect of factor for inversion stimulation (Fis) protein on IS2 transposition was investigated. A full-length IS2 was found to transpose at a frequency 64 times lower in a normal Escherichia coli than in a fis- mutant. To investigate whether Fis affects IS2 transposition by DNA binding, gel retardation and DNase I footprinting experiments were performed. Analysis of Fis binding to the left terminus of IS2 revealed that Fis binds to nucleotide number 44-60 located between the -35 and -10 regions of the major IS2 promoter. To further determine whether Fis binding affects IS2 transcription, the major IS2 promoter was fused to a luciferase gene and assayed for its transcription efficiency in the presence or absence of Fis. The results showed that Fis reduced transcription from the major IS2 promoter by approximately sixfold. Analysis of Fis binding to the right terminal repeat of IS2 revealed that Fis binds to the inner end of the repeat, which is the same region as the place where the IS2 transposase binds. These results suggest that Fis inhibits IS2 transposition by blocking the binding sites of IS2 transposase and by repressing the transcription of IS2 genes.

Aging skeletal muscle shows a drastic increase in the small heat shock proteins αB-crystallin/HspB5 and cvHsp/HspB7

Most heat shock proteins operate as molecular chaperones and play a central role in the maintenance of normal cellular function. In skeletal muscle, members of the alpha-crystallin domain-containing family of small heat shock proteins are believed to form a cohort of essential stress proteins. Since alphaB-crystallin (alphaBC/HspB5) and the cardiovascular heat shock protein (cvHsp/HspB7) are both implicated in the molecular response to fibre transformation and muscle wasting, it was of interest to investigate the fate of these stress proteins in young adult versus aged muscle. The age-related loss of skeletal muscle mass and strength, now generally referred to as sarcopenia, is one of the most striking features of the senescent organism. In order to better understand the molecular pathogenesis of age-related muscle wasting, we have performed a two-dimensional gel electrophoretic analysis, immunoblotting and confocal microscopy study of aged rat gastrocnemius muscle. Fluorescent labelling of the electrophoretically separated soluble muscle proteome revealed an overall relatively comparable protein expression pattern of young adult versus aged fibres, but clearly an up-regulation of alphaBC and cvHsp. This was confirmed by immunofluorescence microscopy and immunoblot analysis, which showed a dramatic age-induced increase in these small heat shock proteins. Immunodecoration of other major stress proteins showed that they were not affected or less drastically changed in their expression in aged muscle. These findings indicate that the increase in muscle-specific small heat shock proteins constitutes an essential cellular response to fibre aging and might therefore be a novel therapeutic option to treat sarcopenia of old age.

Absence of Y chromosome in human placental site trophoblastic tumor

Placental site trophoblastic tumor is a neoplasm of extravillous intermediate trophoblast at the implantation site, preceded in the majority of cases by a female gestational event. Our pilot investigation suggested that the development of this tumor might require a paternally derived X chromosome and the absence of a Y chromosome. Twenty cases of placental site trophoblastic tumor were included in this study. Genotyping at 15 polymorphic loci and one sex determination locus was performed by multiplex PCR followed by capillary electrophoresis. X chromosome polymorphisms were determined by PCR amplification of exon 1 of the human androgen receptor gene using primers flanking the polymorphic CAG repeats within this region. Genotyping at 15 polymorphic loci was informative and paternal alleles were present in all tumors, confirming the trophoblastic origin of the tumors. The presence of an X chromosome and the absence of a Y chromosome were observed in all tumors. Among 13 cases in which analysis of the X chromosome polymorphism was informative, all but one demonstrated at least two X alleles and seven cases showed one identifiable paternal X allele. These results confirm a unique pathogenetic mechanism in placental site trophoblastic tumor, involving an exclusion of the Y chromosome from the genome and, therefore, a tumor arising from the trophectoderm of a female conceptus. As epigenetic regulations of imprinting during X chromosome inactivation are of significant biological implications, placental site trophoblastic tumor may provide an important model for studying the sex chromosome biology and the proliferative advantage conferred by the paternal X chromosome.