Regulation of recombination at yeast nuclear pores controls repair and triplet repeat stability.

Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, we found that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery. This positioning is transient, occurs in late S phase, requires replication, and is associated with decreased subnuclear mobility of the locus. In contrast to persistent double-stranded breaks, expanded CAG repeats at the nuclear envelope associate with pores but not with the inner nuclear membrane protein Mps3. Relocation requires Nup84 and the Slx5/8 SUMO-dependent ubiquitin ligase but not Rad51, Mec1, or Tel1. Importantly, the presence of the Nup84 pore subcomplex and Slx5/8 suppresses CAG repeat fragility and instability. Repeat instability in nup84, slx5, or slx8 mutant cells arises through aberrant homologous recombination and is distinct from instability arising from the loss of ligase 4-dependent end-joining. Genetic and physical analysis of Rad52 sumoylation and binding at the CAG tract suggests that Slx5/8 targets sumoylated Rad52 for degradation at the pore to facilitate recovery from acute replication stress by promoting replication fork restart. We thereby confirmed that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process.

Recombination dynamics in ZnO nanowires: Surfaces states versus mode quality factor

In this work, we investigate the influence of finite size on the recombinations dynamics of ZnO nanowires. We demonstrate that diameter as well as lenght of nanowires determine the lifetime of the neutral donor bound excitons. Our findings suggest that while the length is mainly responsible for different mode quality factors of the cavity-like nanowires, the diameter determines the influence of surface states as alternative recombinations channels for the optical modes trapped in the nanocavity. In addition, comparing nanowires grown using different catalyst we show that the surfaces states strongly depend on each precursor characteristics.

Sex-Chromosome Homomorphy in Palearctic Tree Frogs Results from Both Turnovers and X-Y Recombination.

Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X-Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (∼5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X-Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.

The role of MAR elements in DNA recombination

The untargeted integration of foreign DNA into the mammalian cell genome, extensively used in gene therapy and biotechnology, remains an incompletely understood process. It is believed to be based on cellular DNA double strand break (DSB) repair machinery and to involve two major steps: i) the formation of long gene arrays (concatemers), and ii) recombination of the resulting concatemer with the genome. The main DSB repair pathways in eukaryotes include non-homologous end-joining (NHEJ), homologous recombination (HR), and microhomology-mediated end-joining (MMEJ). However, it is still not clear, which of these pathways are responsible for transgene integration. Here, we show that NHEJ is not the primary pathway used by mammalian cells in the transgene integration process, while the components of the HR pathway seem to be important for genomic integration but not concatemerization. Instead, concatemer formation appears to be mediated by a subset of the MMEJ pathway, termed synthesis-dependent MMEJ (SD-MMEJ). This mechanism also seems to be preferentially used for plasmid integration into the genome, as confirmed by the analysis of plasmid-to-genome junction sequences, which were found to display an SD-MMEJ pattern. Therefore, we propose the existence of two distinct SD-MMEJ subpathways, relying on different subsets of enzymes. One of these mechanisms appears to be responsible for concatemerization, while the other mechanism, partially dependent in HR enzymes, seems to mediate recombination with the genome. Previous studies performed by our group suggested that matrix attachment regions (MARs), which are epigenetic regulatory DNA elements that participate in the formation of chromatin boundaries and augment transcription, may mediate increased plasmid integration into the genome of CHO cells by stimulating DNA recombination. In the present work, we demonstrate that MAR-mediated plasmid integration results from the enhanced SD-MMEJ pathway. Analysis of transgene integration loci and junction DNA sequences validated the prevalent use of this pathway by the MAR elements to target plasmid DNA into gene-rich areas of the CHO genome. We propose that this finding should in the future help to engineer cells for improved recombinant protein production. In addition to investigating the process of transgene integration, we designed recombination assays to better characterize the components of the MMEJ and SD-MMEJ pathways. We also used CHO cells expressing cycle-sensitive reporter genes to demonstrate a potential role of HR proteins in the cell cycle regulation.

p21 as a Transcriptional Co-Repressor of S-Phase and Mitotic Control Genes

It has been previously described that p21 functions not only as a CDK inhibitor but also as a transcriptional co-repressor in some systems. To investigate the roles of p21 in transcriptional control, we studied the gene expression changes in two human cell systems. Using a human leukemia cell line (K562) with inducible p21 expression and human primary keratinocytes with adenoviral-mediated p21 expression, we carried out microarray-based gene expression profiling. We found that p21 rapidly and strongly repressed the mRNA levels of a number of genes involved in cell cycle and mitosis. One of the most strongly down-regulated genes was CCNE2 (cyclin E2 gene). Mutational analysis in K562 cells showed that the N-terminal region of p21 is required for repression of gene expression of CCNE2 and other genes. Chromatin immunoprecipitation assays indicated that p21 was bound to human CCNE2 and other p21-repressed genes gene in the vicinity of the transcription start site. Moreover, p21 repressed human CCNE2 promoter-luciferase constructs in K562 cells. Bioinformatic analysis revealed that the CDE motif is present in most of the promoters of the p21-regulated genes. Altogether, the results suggest that p21 exerts a repressive effect on a relevant number of genes controlling S phase and mitosis. Thus, p21 activity as inhibitor of cell cycle progression would be mediated not only by the inhibition of CDKs but also by the transcriptional down-regulation of key genes.

A role for homologous recombination proteins in cell cycle regulation.

Eukaryotic cells respond to DNA breaks, especially double-stranded breaks (DSBs), by activating the DNA damage response (DDR), which encompasses DNA repair and cell cycle checkpoint signaling. The DNA damage signal is transmitted to the checkpoint machinery by a network of specialized DNA damage-recognizing and signal-transducing molecules. However, recent evidence suggests that DNA repair proteins themselves may also directly contribute to the checkpoint control. Here, we investigated the role of homologous recombination (HR) proteins in normal cell cycle regulation in the absence of exogenous DNA damage. For this purpose, we used Chinese Hamster Ovary (CHO) cells expressing the Fluorescent ubiquitination-based cell cycle indicators (Fucci). Systematic siRNA-mediated knockdown of HR genes in these cells demonstrated that the lack of several of these factors alters cell cycle distribution, albeit differentially. The knock-down of MDC1, Rad51 and Brca1 caused the cells to arrest in the G2 phase, suggesting that they may be required for the G2/M transition. In contrast, inhibition of the other HR factors, including several Rad51 paralogs and Rad50, led to the arrest in the G1/G0 phase. Moreover, reduced expression of Rad51B, Rad51C, CtIP and Rad50 induced entry into a quiescent G0-like phase. In conclusion, the lack of many HR factors may lead to cell cycle checkpoint activation, even in the absence of exogenous DNA damage, indicating that these proteins may play an essential role both in DNA repair and checkpoint signaling.

Microscopy of Fission Yeast Sexual Lifecycle.

The fission yeast Schizosaccharomyces pombe has been an invaluable model system in studying the regulation of the mitotic cell cycle progression, the mechanics of cell division and cell polarity. Furthermore, classical experiments on its sexual reproduction have yielded results pivotal to current understanding of DNA recombination and meiosis. More recent analysis of fission yeast mating has raised interesting questions on extrinsic stimuli response mechanisms, polarized cell growth and cell-cell fusion. To study these topics in detail we have developed a simple protocol for microscopy of the entire sexual lifecycle. The method described here is easily adjusted to study specific mating stages. Briefly, after being grown to exponential phase in a nitrogen-rich medium, cell cultures are shifted to a nitrogen-deprived medium for periods of time suited to the stage of the sexual lifecycle that will be explored. Cells are then mounted on custom, easily built agarose pad chambers for imaging. This approach allows cells to be monitored from the onset of mating to the final formation of spores.

Mitotic regulation by Polo-like kinase 1 and the Chromosomal Passenger Complex

During mitosis, the duplicated genome must be accurately divided between two daughter cells. Polo-like kinase 1 (Plk1) and Aurora B kinase, together with its binding partners Incenp, Survivin and Borealin (chromosomal passenger complex, CPC), have key roles in coordinating mitotic events. The accuracy of cell division is safeguarded by a signaling cascade termed the mitotic spindle checkpoint (SC), which ensures that chromosomes are not physically separated before correct bipolar attachments have been formed between kinetochores and spindle microtubules (MT). An inhibitory “wait anaphase” signal, which delays chromosome separation (anaphase onset), is created at individual kinetochores and broadcasted throughout the cell in response to lack of kinetochore-microtubule (kMT) attachment or proper interkinetochore tension. It is believed that the fast turnover of SC molecules at kinetochores contributes to the cell’s ability to produce this signal and enables rapid responses to changing cellular conditions. Kinetochores that lack MT attachment and tension express a certain phosphoepitope called the 3F3/2 phosphoepitope, which has been linked to SC signaling. In the experimental part, we investigated the regulation of the 3F3/2 phosphoepitope, analyzed whether CPC molecules turn over at centromeres, and dissected the mitotic roles of the CPC using a microinjection technique that allowed precise temporal control over its function. We found that the kinetochore 3F3/2 phosphoepitope is created by Plk1, and that CPC proteins exhibit constant exchange at centromeres. Moreover, we found that CPC function is necessary in the regulation of chromatid movements and spindle morphology in anaphase. In summary, we identified new functions of key mitotic regulators Plk1 and CPC, and provided insighs into the coordination of mitotic events.

Functional characterization of proteins required for mitotic progression and the spindle assembly checkpoint

During mitotic cell division, the genetic material packed into chromosomes is divided equally between two daughter cells. Before the separation of the two copies of a chromosome (sister chromatids), each chromosome has to be properly connected with microtubules of the mitotic spindle apparatus and aligned to the centre of the cell. The spindle assembly checkpoint (SAC) monitors connections between microtubules and chromosomes as well as tension applied across the centromere. Microtubules connect to a chromosome via kinetochores, which are proteinaceous organelles assembled onto the centromeric region of the sister chromatids. Improper kinetochore-microtubule attachments activate the SAC and block chromosome segregation until errors are corrected and all chromosomes are connected to the mitotic spindle in a bipolar manner. The purpose of this surveillance mechanism is to prevent loss or gain of chromosomes in daughter cells that according to current understanding contributes to cancer formation. Numerous proteins participate in the regulation of mitotic progression. In this thesis, the mitotic tasks of three kinetochore proteins, Shugoshin 1 (Sgo1), INCENP, and p38 MAP kinase (p38 MAPK), were investigated. Sgo1 is a protector of centromeric cohesion. It is also described in the tension-sensing mechanism of the SAC and in the regulation of kinetochore-microtubule connections. Our results revealed a central role for Sgo1 in a novel branch of kinetochore assembly. INCENP constitutes part of the chromosomal passenger complex (CPC). The other members of the core complex are the Aurora B kinase, Survivin and Borealin. CPC is an important regulatory element of cell division having several roles at various stages of mitosis. Our results indicated that INCENP and Aurora B are highly dynamic proteins at the mitotic centromeres and suggested a new role for CPC in regulation of chromosome movements and spindle structure during late mitosis. The p38 MAPK has been implicated in G1 and G2 checkpoints during the cell cycle. However, its role in mitotic progression and control of SAC signaling has been controversial. In this thesis, we discovered a novel function for p38γ MAPK in chromosome orientation and spindle structure as well as in promotion of viability of mitotic cells.

Nuclear Matrix in Apoptotic Cell Death and Cell Proliferation. The role of Nuclear Mitotic Apparatus (NuMA) Protein

The nucleus is a membrane enclosed organelle containing most of the genetic information of the cell in the form of chromatin. The nucleus, which can be divided into many sub-organelles such as the nucleoli, the Cajal bodies and the nuclear lamina, is the site for several essential cellular functions such as the DNA replication and its regulation and most of the RNA synthesis and processing. The nucleus is often affected in disease: the size and the shape of the nucleus, the chromatin distribution and the size of the nucleoli have remained the basis for the grading of several cancers. The maintenance of the vertebrate body shape depends on the skeleton. Similarly, in a smaller context, the shape of the cell and the nucleus are mainly regulated by the cytoskeletal and nucleoskeletal elements. The nuclear matrix, which by definition is a detergent, DNase and salt resistant proteinaceous nuclear structure, has been suggested to form the nucleoskeleton responsible for the nuclear integrity. Nuclear mitotic apparatus protein, NuMA, a component of the nuclear matrix, is better known for its mitotic spindle organizing function. NuMA is one of the nuclear matrix proteins suggested to participate in the maintenance of the nuclear integrity during interphase but its interphase function has not been solved to date. This thesis study concentrated on the role of NuMA and the nuclear matrix as structural and functional components of the interphase nucleus. The first two studies clarified the essential role of caspase-3 in the disintegration of the nuclear structures during apoptosis. The second study also showed NuMA and chromatin to co-elute from cells in significant amounts and the apoptotic cleavage of NuMA was clarified to have an important role in the dissociation of NuMA from the chromatin. The third study concentrated on the interphase function of NuMA showing NuMA depletion to result in cell cycle arrest and the cytoplasmic relocalization of NuMA interaction partner GAS41. We suggest that the relocalization of the transcription factor GAS41 may mediate the cell cycle arrest. Thus, this study has given new aspects in the interactions of NuMA, chromatin and the nuclear matrix.

Charge transport in disordered materials : simulations, theory, and numerical modeling of hopping transport and electron-hole recombination

Min avhandling behandlar hur oordnade material leder elektrisk ström. Bland materialen som studeras finns ledande polymerer, d.v.s. plaster som leder ström, och mer allmänt organiska halvledare. Av de här materialen har man kunnat bygga elektroniska komponenter, och man hoppas på att kunna trycka hela kretsar av organiska material. För de här tillämpningarna är det viktigt att förstå hur materialen själva leder elektrisk ström. Termen oordnade material syftar på material som saknar kristallstruktur. Oordningen gör att elektronernas tillstånd blir lokaliserade i rummet, så att en elektron i ett visst tillstånd är begränsad t.ex. till en molekyl eller ett segment av en polymer. Det här kan jämföras med kristallina material, där ett elektrontillstånd är utspritt över hela kristallen (men i stället har en väldefinierad rörelsemängd). Elektronerna (eller hålen) i det oordnade materialet kan röra sig genom att tunnelera mellan de lokaliserade tillstånden. Utgående från egenskaperna för den här tunneleringsprocessen, kan man bestämma transportegenskaperna för hela materialet. Det här är utgångspunkten för den så kallade hopptransportmodellen, som jag har använt mig av. Hopptransportmodellen innehåller flera drastiska förenklingar. Till exempel betraktas elektrontillstånden som punktformiga, så att tunneleringssannolikheten mellan två tillstånd endast beror på avståndet mellan dem, och inte på deras relativa orientation. En annan förenkling är att behandla det kvantmekaniska tunneleringsproblemet som en klassisk process, en slumpvandring. Trots de här grova approximationerna visar hopptransportmodellen ändå många av de fenomen som uppträder i de verkliga materialen som man vill modellera. Man kan kanske säga att hopptransportmodellen är den enklaste modell för oordnade material som fortfarande är intressant att studera. Man har inte hittat exakta analytiska lösningar för hopptransportmodellen, därför använder man approximationer och numeriska metoder, ofta i form av datorberäkningar. Vi har använt både analytiska metoder och numeriska beräkningar för att studera olika aspekter av hopptransportmodellen. En viktig del av artiklarna som min avhandling baserar sig på är att jämföra analytiska och numeriska resultat. Min andel av arbetet har främst varit att utveckla de numeriska metoderna och applicera dem på hopptransportmodellen. Därför fokuserar jag på den här delen av arbetet i avhandlingens introduktionsdel. Ett sätt att studera hopptransportmodellen numeriskt är att direkt utföra en slumpvandringsprocess med ett datorprogram. Genom att föra statisik över slumpvandringen kan man beräkna olika transportegenskaper i modellen. Det här är en så kallad Monte Carlo-metod, eftersom själva beräkningen är en slumpmässig process. I stället för att följa rörelsebanan för enskilda elektroner, kan man beräkna sannolikheten vid jämvikt för att hitta en elektron i olika tillstånd. Man ställer upp ett system av ekvationer, som relaterar sannolikheterna för att hitta elektronen i olika tillstånd i systemet med flödet, strömmen, mellan de olika tillstånden. Genom att lösa ekvationssystemet fås sannolikhetsfördelningen för elektronerna. Från sannolikhetsfördelningen kan sedan strömmen och materialets transportegenskaper beräknas. En aspekt av hopptransportmodellen som vi studerat är elektronernas diffusion, d.v.s. deras slumpmässiga rörelse. Om man betraktar en samling elektroner, så sprider den med tiden ut sig över ett större område. Det är känt att diffusionshastigheten beror av elfältet, så att elektronerna sprider sig fortare om de påverkas av ett elektriskt fält. Vi har undersökt den här processen, och visat att beteendet är väldigt olika i endimensionella system, jämfört med två- och tredimensionella. I två och tre dimensioner beror diffusionskoefficienten kvadratiskt av elfältet, medan beroendet i en dimension är linjärt. En annan aspekt vi studerat är negativ differentiell konduktivitet, d.v.s. att strömmen i ett material minskar då man ökar spänningen över det. Eftersom det här fenomenet har uppmätts i organiska minnesceller, ville vi undersöka om fenomenet också kan uppstå i hopptransportmodellen. Det visade sig att det i modellen finns två olika mekanismer som kan ge upphov till negativ differentiell konduktivitet. Dels kan elektronerna fastna i fällor, återvändsgränder i systemet, som är sådana att det är svårare att ta sig ur dem då elfältet är stort. Då kan elektronernas medelhastighet och därmed strömmen i materialet minska med ökande elfält. Elektrisk växelverkan mellan elektronerna kan också leda till samma beteende, genom en så kallad coulombblockad. En coulombblockad kan uppstå om antalet ledningselektroner i materialet ökar med ökande spänning. Elektronerna repellerar varandra och ett större antal elektroner kan leda till att transporten blir långsammare, d.v.s. att strömmen minskar.

Nuclear morphometry, apoptotic and mitotic indices, and tubular differentiation in Libyan breast cancer

Aims of this study were to evaluate the relations of nuclear morphometry, mitotic and apoptotic indices, and tubular differentiation with clinicopathological features and survival rate in Libyan women. The data were compared with corresponding results on Finnish, and Nigerian female breast cancer patients. Histological samples of breast cancer (BC) from 131 patients were retrospectively studied. Mitotic activity indices (MAI and SMI), apoptotic index (AI), and fraction of fields with tubular differentiation (FTD) were estimated. Samples were also studied by computerized nuclear morphometry, such as mean nuclear area (MNA). Demographic and clinicopathological features were analyzed from 234 patients. The Libyan BC was dominantly premenopausal, and aggressive in behavior. There were statistically significant correlations between the mean nuclear area, fraction of fields with tubular differentiation, apoptotic index and proliferative indices, and most clinicopathological features. The highest significances were shown between lymph node status and the proliferative and apoptotic indices (p=0.003 with SMI, and p=0.005 with AI). There were significant associations between clinical stage and SMI and AI (p=0.002 and 0.009, respectively). The most significant associations with grade were observed with MNA and FTD (p<0.0001 and 0.001, respectively). The proliferative differences between Libyan, Nigerian and Finnish populations were prominent. These indices in Libyan were lower than in Nigerian, but higher than in Finnish patients. The Libyan patients’ AI is slightly higher than in Nigeria, but much higher than in Finland. The differences between countries may be associated with the known variation in the distribution of genetic markers in these populations. The results also indicated that morphometric factors can be reliable prognostic indicators in Libyan BC patients.

Preparation of mitotic chromosomes of leaf-cutting ants from the genera Atta and Acromyrmex

Some modifications were made to the methodology of Imai et al. (Jpn. J. Genet. 63: 159-185, 1988) for cytogenetic analysis of the leaf-cutting ants Atta sexdens piriventris and Acromyrmex heyeri (Hymenoptera, Formicidae), shortening preparation time and improving chromosomal preparations. The brain ganglia of prepupae were dissected in a 0.0025% hypotonic solution of colchicine, placed on a glass slide on a cold plate (4 ± 1oC) for 20 min. The material was fixed directly on the cold slide (with cold fixative I), macerated with a histological needle and fixed again with fixative I, followed by fixatives II and III, all of them cold. The slide was flame-dried right after the use of fixative III, and it was allowed to air-dry at room temperature for 2 h. The resulting metaphases presented less contracted chromosomes, with separated and well defined sister chromatids at a high frequency, when the material was processed in the manner described and stained with 3% Giemsa in phosphate buffer (pH 6.8) for 15 min.

Evaluation of techniques for C and ASG banding of the mitotic chromosomes of Anastrepha species (Diptera, Tephritidae)

Methods previously described by Canovai et al. (Caryologia 47: 241-247, 1994) which produced C and ASG bands in mitotic chromosomes of Ceratitis capitata were applied to the chromosomes of several Anastrepha species. Metaphase plate yield was substantially increased by use of imaginal disks together with cerebral ganglia. The C-bands were quite prominent allowing the resolution of tiny blocks of heterochromatin. The ASG method produced G-like banded chromosomes, which permitted recognition of each individual chromosome. These simple techniques do not require special equipment and may be valuable for karyotype variability studies in fruit flies and other Diptera

Effects of caffeine on mitotic index in Drosophila prosaltans (Diptera)

The effect of two concentrations of caffeine (1500 mg/ml and 2500 mg/ml) on mitotic indices of Drosophila prosaltans was analyzed in larval brain cells. Although the differences detected between treated and control cells were not significant, the percentages obtained suggest a possible effect of caffeine in slowing the process of cell division