Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes.

Many types of tumors exhibit characteristic chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletions are also observed. Typically, a region that is aberrant in more tumors, or whose copy number change is stronger, would be considered as a more promising candidate to be biologically relevant to cancer. We sought for an intuitive method to define such aberrations and prioritize them. We define V, the "volume" associated with an aberration, as the product of three factors: (a) fraction of patients with the aberration, (b) the aberration's length and (c) its amplitude. Our algorithm compares the values of V derived from the real data to a null distribution obtained by permutations, and yields the statistical significance (p-value) of the measured value of V. We detected genetic locations that were significantly aberrant, and combine them with chromosomal arm status (gain/loss) to create a succinct fingerprint of the tumor genome. This genomic fingerprint is used to visualize the tumors, highlighting events that are co-occurring or mutually exclusive. We apply the method on three different public array CGH datasets of Medulloblastoma and Neuroblastoma, and demonstrate its ability to detect chromosomal regions that were known to be altered in the tested cancer types, as well as to suggest new genomic locations to be tested. We identified a potential new subtype of Medulloblastoma, which is analogous to Neuroblastoma type 1.

Topological origins of chromosomal territories.

Using freely jointed polymer model we compare equilibrium properties of crowded polymer chains whose segments are either permeable or not permeable for other segments to pass through. In particular, we addressed the question whether non-permeability of long chain molecules, in the absence of excluded volume effect, is sufficient to compartmentalize highly crowded polymer chains, similarly to what happens during formation of chromosomal territories in interphase nuclei. Our results indicate that even polymers without excluded volume compartmentalize and show strongly reduced intermingling when they are mutually non-permeable. Judging from the known fact that chromatin fibres originating from different chromosomes show very limited intermingling in interphase nuclei, we propose that regular chromatin fibres during chromosome decondensation can hardly serve as a substrate of cellular type II DNA topoisomerases.

Agronomic performance, chromosomal stability and resistance to velvetbean caterpillar of transgenic soybean expressing cry1Ac gene

The objective of this work was to analyze the agronomic performance and chromosomal stability of transgenic homozygous progenies of soybean [Glycine max (L.) Merrill.], and to confirm the resistance of these plants against Anticarsia gemmatalis. Eleven progenies expressing cry1Ac, hpt and gusA genes were evaluated for agronomic characteristics in relation to the nontransformed parent IAS 5 cultivar. Cytogenetical analysis was carried out on transgenic and nontransgenic plants. Two out of the 11 transgenic progenies were also evaluated, in vitro and in vivo, for resistance to A. gemmatalis. Two negative controls were used in resistance bioassays: a transgenic homozygous line, containing only the gusA reporter gene, and nontransgenic 'IAS 5' plants. The presence of cry1Ac transgene affected neither the development nor the yield of plants. Cytogenetical analysis showed that transgenic plants presented normal karyotype. In detached-leaf bioassay, cry1Ac plants exhibited complete efficacy against A. gemmatalis, whereas negative controls were significantly damaged. Whole-plant feeding assay confirmed a very high protection of cry1Ac against velvetbean caterpillar, while nontransgenic 'IAS 5' plants and homozygous gusA line exhibited 56.5 and 71.5% defoliation, respectively. The presence of cry1Ac transgene doesn't affect the majority of agronomic traits (including yield) of soybean and grants high protection against A. gemmatalis.

Genetic and karyotypic structure of a hybrid zone between the chromosomal races Cordon and Valais in the common shrew, Sorex araneus

Hybrid zones between genetically differentiated populations provide material to study evolutionary processes. Since the discovery of chromosomal races in Sorex araneus, contact zones have attracted attention of scientists. So far, studies on genetic markers in Sorex hybrid zones are missing. The acrocentric chromosomal race Cordon and the highly metacentric race Valais meet and hybridize at Les Houches in the Western Alps. On a transect through the hybrid zone, 273 shrews were caught at 15 localities over 4 years. Karyotype as well as the nuclear protein loci Alb and Pg were analyzed. F-st and F-is values were calculated by F-statistics. An analysis on pooled samples revealed the genetical differences between the hybridizing races as the only cause of population structuring. Genetical markers show dines with very strong frequency shifts at a mountain torrent, but behave differently through the zone. The performance of the torrent in maintaining the hybrid zone, selection against hybrids, possible assortative mating and linkage of the Valais Pg allele to a diagnostic chromosome arm, are discussed.

Outcome of a Modified Broström-Gould Procedure for Lateral Ankle Instability

Introduction: Ankle sprains affect 200'000 persons/year in Switzerland. Most incidences are successfully treated by conservative measures but 20% require reconstruction for symptomatic chronic lateral ankle instability. This study evaluates the functional outcome after a modified Broström-Gould technique as measured by different clinical scores and compares the functional outcome of this technique with other surgical treatments of ankle instability. Methods: This retrospective cohort study evaluates 47 patients who underwent a modified Broström-Gould procedure using suture anchors to refix the lateral ankle capsuloligamentary structures at our institution from 2005 to 2009 with a minimum follow-up of one year (13-72 Mo). All patients were operated by one single surgeon and evaluated by an independent examiner. The function was assessed using 4 scores including: the AOFAS (American Orthopaedic Foot and Ankle Society's Score) hindfoot score; the FAAM (Foot and Ankle Ability Measurement); the CAIT (Cumberland Ankle Instability Tool); the CAIS (Chronic Ankle Instability Scale). Results: Six patients were excluded leaving 41 patients for examination. 34 patients (83%) thought that their ankle was more stable after the surgery, 7 (17%) did not feel any difference. 27 patients were very satisfied, 11 satisfied and 3 not satisfied. Reasons for non satisfaction included persistent instability and pain. Ankle mobility returned to normal in 93% of patients. Five patients had transcient hypoesthesy in the area of the superficial peroneal nerve. One patient suffered from a superficial infection treated successfully by local measures. 80% had the perception of a normal ankle, 20% thought to be below normal. At follow-up the AOFAS was 89/100 (37-100), the FAAM 85/100% (35-100%), the CAIT 20/30 (5-30), and the CAIS 74/100% (27-100%). Conclusions: The modified Broström-Gould procedure, which belongs to the anatomic ankle stabilizations is relatively simple and offers good outcome that satisfied 93% of the patients in the present study. No active stabilisator is sacrificed. Preservation of the ankle mobility is better and the complication rate is lower than after non-anatomical procedures described in the literature. The CAIT appeared as the most severe score compared to the other scales used in our study.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements.Results: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion: We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.

The fixation of metacentric chromosomes during the chromosomal evolution in the common shrew (Sorex araneus, Insectivora)

Rb fusions between acrocentric chromosomes leading to metacentrics tend to become fixed during the chromosomal evolution in the common shrew. Using microsatellite markers preliminary results show that populations are only slightly subdivided and genetic drift seems not to play an important role for the fixation of metacentrics. A significant segregation distortion in favour of metacentric chromosomes was found during male meiosis. This suggests that cytological factors such as facilitated fusion between acrocentric chromosomes or choice-effects at the level of gametes are more likely to play a role for the chromosomal evolution in the common shrew.

Chromosomal evolution and zoogeographic origin of southeast Asian shrews (genus Crocidura).

To the origins and evolution of Indomalayan shrews, we investigated the chromosomal variations of 14 species of Crocidura from SE Asia. Intraspecific polymorphism was mainly due to variation in the number of short chromosomal arms but C. lepidura and C. hutanis showed a polymorphism due to a centric fusion. The undifferentially stained karyotypes were similar in 9 species, all possessing 2n = 38 and FN = 54-56 (68); C. fuliginosa had 2n = 40 and FN = 54-58. These karyotypes are close to the presumed ancestral state for the genus Crocidura. Four species from Sulawesi had a reduced diploid number (2n = 30-34), a trend not observed among other SE Asian species but present in few Palaearctic taxa. Compared to the apparent stasis of karyotypic evolution observed among other SE Asian species, the high degree of interspecific differences reported among Sulawesian shrews is unusual and needs further investigation. Stasis and reduction in diploid number found in both Indomalayan and Palaeractic species suggest that these two groups share a common ancestry. This is in sharp contrast to most Afrotropical species which evolved towards higher diploid and fundamental numbers. The zoogeographical implications of these results are discussed.

Regulation of chromosomal replication in Caulobacter crescentus.

The alpha-proteobacterium Caulobacter crescentus is characterized by its asymmetric cell division, which gives rise to a replicating stalked cell and a non-replicating swarmer cell. Thus, the initiation of chromosomal replication is tightly regulated, temporally and spatially, to ensure that it is coordinated with cell differentiation and cell cycle progression. Waves of DnaA and CtrA activities control when and where the initiation of DNA replication will take place in C. crescentus cells. The conserved DnaA protein initiates chromosomal replication by directly binding to sites within the chromosomal origin (Cori), ensuring that DNA replication starts once and only once per cell cycle. The CtrA response regulator represses the initiation of DNA replication in swarmer cells and in the swarmer compartment of pre-divisional cells, probably by competing with DnaA for binding to Cori. CtrA and DnaA are controlled by multiple redundant regulatory pathways that include DNA methylation-dependent transcriptional regulation, temporally regulated proteolysis and the targeting of regulators to specific locations within the cell. Besides being critical regulators of chromosomal replication, CtrA and DnaA are also master transcriptional regulators that control the expression of many genes, thus connecting DNA replication with other events of the C. crescentus cell cycle.

Cervical nerve root synovial sarcoma in a child with chromosomal (X;18) translocation. Case report and review of the literature.

We report on an 11-year-old female with a history of cervicobrachialgia and progressive weakness of the right arm. Cervical spine MRI showed an enhancing heterogeneous intradural mass occupying the right C6-C7 foramen. She underwent a right C6-C7 foraminotomy with a complete macroscopic removal of the lesion. Pathological examination revealed a synovial sarcoma. Treatment was completed by chemotherapy and proton radiotherapy, and the girl remained free of symptoms for 3 years. After appearance of new symptoms, a local recurrence was confirmed, and despite aggressive treatment with salvage chemotherapy and radiotherapy, the disease progressed beyond medical control, and the child died, 6 years after diagnosis. Early recognition of this rare entity compared to its more benign differential diagnosis is crucial, as an aggressive management is needed.

Aerodynamical instability of web

Diplomityön tavoitteena oli tutkia miten ilman turbulenttisuus vaikuttaa tasaisesti liikkuvan rainan tilaan. Yhtenä sovelluskohteena teollisuudessa voidaan mainita esimerkiksi leiju-kuivain. Tiedetään, että konenopeuksien kasvu ja siitä johtuva ilmavirran nopeuden kasvu aiheuttaa voimavaikutuksia rainaan ja voi aiheuttaa lepatusta. Lepatus johtaa dynaamiseen epästabiilisuuteen, joka voidaan havaita, kun lineaarinen systeemi tulee epävakaaksi ja joh-taa epälineaariseen, rajoitettuun värähtelyyn. Lepatus huonontaa tuotteiden laatua ja voi johtaa ratakatkoihin. Työssä on esitetty tietoa ilman ja rainan vuorovaikutuksesta, jota hyödyntämällä voidaan kehittää yksinkertaistettu malli, jonka avulla liikkuvaa rainaa voidaan simuloida kuivaimes-sa. Kaasufaasin virtausyhtälöt on ratkaistu eri turbulenttimalleja käyttäen. Myös viskoelas-tisen rainan muodonmuutosta on tarkasteltu. Koska rainalle ei ole kirjallisuudesta saatavilla tarkkoja fysikaalisia ja mekaanisia arvoja, näitä ominaisuuksia testattiin eri arvoilla, jotta rainan käyttäytymistä jännityksen alaisena voidaan tarkastella. Näiden ominaisuuksien tun-teminen on ensiarvoisen tärkeää määritettäessä rainan aeroviskoelastista käyttäytymistä. Virtaussimulointi on kallista ja aikaa vievää. Tämä tarkoittaa uusien tutkimusmenetelmien omaksumista. Tässä työssä vaihtoehtoisena lähestymistapana on esitetty yksinkertaistettu malli, joka sisältää ilman ja rainan vuorovaikutusta kuvaavat ominaisuudet. Mallin avulla saadaan tietoa epälineaarisuuden ja turbulenssin vaikutuksesta sekä monimutkaisesta yh-teydestä stabiilisuuden ja ulkoisesti aikaansaadun värähtelyn sekä itse aiheutetun värähtelyn välillä. Työn lopussa on esitetty havainnollinen esimerkki, jolla voidaan kuvata olosuhteita, jossa rainan tasainen liike muuttuu epävakaaksi. Kun turbulenttisuudesta johtuva painevaih-telu ylittää tietyn rajan, rainan värähtely kasvaa muuttuen satunnaisesta järjestäytyneeksi. Saaduttulokset osoittavat, että turbulenttisuudella on suuri vaikutus eikä sitä voi jättää huomioimatta. Myös rainan viskoelastiset ominaisuudet tulee huomioida, jotta rainan käyt-täytymistä voidaan kuvata tarkasti.

Vanishing chromosomal inversion clines in Drosophila subobscura from Chile: Is behavioral thermoregulation to blame?

Chromosomal inversion clines paralleling the long-standing ones in native Palearctic populations of Drosophila subobscura evolved swiftly after this species invaded the Americas in the late 1970s and early 1980s. However, the new clines did not consistently continue to converge on the Old World baseline. Our recent survey of Chilean populations of D. subobscura shows that inversion clines have faded or even changed sign with latitude. Here, we investigate the hypothesis that this fading of inversion clines might be due to the Bogert effect, namely, that flies' thermoregulatory behavior has eventually compensated for environmental variation in temperature, thus buffering selection on thermal-related traits. We show that latitudinal divergence in thermal preference (T-p) has evolved in Chile for females, with higher-latitude flies having a lower mean T-p. Plastic responses in T-p also lessen latitudinal thermal variation because flies developed at colder temperatures prefer warmer microclimates. Our results are consistent with the idea that active behavioral thermoregulation might buffer environmental variation and reduce the potential effect of thermal selection on other traits as chromosomal arrangements.