Phylogeographical structure, postglacial recolonization and barriers to gene flow in the distinctive Valais chromosome race of the common shrew (Sorex araneus).

Using one male-inherited and eight biparentally inherited microsatellite markers, we investigate the population genetic structure of the Valais chromosome race of the common shrew (Sorex araneus) in the Central Alps of Europe. Unexpectedly, the Y-chromosome microsatellite suggests nearly complete absence of male gene flow among populations from the St-Bernard and Simplon regions (Switzerland). Autosomal markers also show significant genetic structuring among these two geographical areas. Isolation by distance is significant and possible barriers to gene flow exist in the study area. Two different approaches are used to better understand the geographical patterns and the causes of this structuring. Using a principal component analysis for which testing procedure exists, and partial Mantel tests, we show that the St-Bernard pass does not represent a significant barrier to gene flow although it culminates at 2469 m, close to the highest altitudinal record for this species. Similar results are found for the Simplon pass, indicating that both passes represented potential postglacial recolonization routes into Switzerland from Italian refugia after the last Pleistocene glaciations. In contrast with the weak effect of these mountain passes, the Rhône valley lowlands significantly reduce gene flow in this species. Natural obstacles (the large Rhône river) and unsuitable habitats (dry slopes) are both present in the valley. Moreover, anthropogenic changes to landscape structures are likely to have strongly reduced available habitats for this shrew in the lowlands, thereby promoting genetic differentiation of populations found on opposite sides of the Rhône valley.

Die Hypercholesterinämie in der Allgemeinpraxis: zwei Repräsentativbefragungen in der Schweiz. [Hypercholesterolemia in general practice: 2 representative surveys in Switzerland].

Two representative surveys of general practitioners in 1987 and 1989 showed, that cigarette smoking and high blood pressure are considered the most important risk factors for coronary heart disease. Elevated blood cholesterol level rank third. Between the two surveys no significant changes took place. The blood cholesterol level is usually measured at a check-up visit or in presence of another risk factor. Routine measurement is not common. At what level do Swiss physicians initiate a therapy? The median range in 1989 for a diet therapy was 6.2-6.7 mmol/l (240-260 mg%) for a 30 years old person, and 6.7-7.2 mmol/l for a 60 years old person. Lipid-lowering drugs are used at about 1 mmol/l (40 mg%) higher levels and there is less agreement between the physicians. Within two years the levels of initiating therapy decreased significantly. Differences between the three Swiss language regions (german/french/italian) in initiating therapy can be seen. 90% of the physicians mentioned compliance problems with a diet therapy. In 1989 half of the surveyed doctors experienced insufficient results in both diet and drug treatment. Further, compliance problems and side effects of drug treatment are mentioned. Half of the physicians reported having tested their own cholesterol level in the last 12 months. Older physicians are considerably more conscious of high cholesterol levels than younger.

Independent evolution of hypervariable regions of HIV-1 gp120: V4 as a swarm of N-Linked glycosylation variants

In this study we have characterized intra-patient length polymorphism in V4 by cloning and sequencing a C2-C4 fragment from HIV plasma RNA in patients at different stages of HIV disease. Clonal analysis of clade B, G, and CRF02 isolates during early infection shows extensive intra-patient V4 variability, due to the presence of indel-associated polymorphism. Indels, coupled to amino acid substitution events, affect the number and distribution of potential N-glycosylation sites, resulting in the coexistence, within the same patient, of V4 subsets, each characterized by different sizes, amino acid sequences, and potential N-glycosylation patterns. In contrast, V3 appears to be relatively homogeneous, with similar V3 associated to significantly different V4 within the same clinical specimen. Based on these data, we propose that during early chronic infection V4 is present as a highly divergent quasispecies, enabling the virus to adopt different conformational structures according to immune constrains and other selective pressures

Mutated regions of nucleophosmin 1 elicit both CD4+ and CD8+ T-cell responses in patients with acute myeloid leukemia.

Mutations in the nucleophosmin gene (NPM1(mut)) are one of the most frequent molecular alterations in acute myeloid leukemia (AML), and immune responses may contribute to the favorable prognosis of AML patients with NPM1(mut). In the present study, we were able to demonstrate both CD4(+) and CD8(+) T-cell responses against NPM1(mut). Ten peptides derived from wild-type NPM1 and NPM1(mut) were subjected to ELISPOT analysis in 33 healthy volunteers and 27 AML patients. Tetramer assays against the most interesting epitopes were performed and Cr(51)-release assays were used to show the cytotoxicity of peptide-specific T cells. Moreover, HLA-DR-binding epitopes were used to test the role of CD4(+) T cells in NPM1 immunogenicity. Two epitopes (epitopes #1 and #3) derived from NPM1(mut) induced CD8(+) T-cell responses. A total of 33% of the NPM1(mut) AML patients showed immune responses against epitope #1 and 44% against epitope #3. Specific lysis of leukemic blasts was detected. To obtain robust immune responses against tumor cells, the activation of CD4(+) T cells is crucial. Therefore, overlapping (OL) peptides were analyzed in ELISPOT assays and OL8 was able to activate both CD8(+) and CD4(+) T cells. The results of the present study show that NPM1(mut) induces specific T-cell responses of CD4(+) and CD8(+) T cells and therefore is a promising target for specific immunotherapies in AML.

Staphylococcus aureus clfB and spa alleles of the repeat regions are segregated into major phylogenetic lineages.

To reliably differentiate among Staphylococcus aureus isolates we recently developed the Double Locus Sequence Typing (DLST) based on the analysis of partial sequences of clfB and spa genes. This method is highly discriminatory and gives unambiguous definition of types. The highly clonal population structure of S. aureus suggests that isolates with identical clfB or spa alleles belong to the same clonal complex (CC) defined by Multi-Locus Sequence Typing (MLST). To test this hypothesis as well as to investigate putative intra-CC genetic structure, we analyzed a total of 289 isolates (186 MSSA and 103 MRSA) with DLST-, spa- and MLST-typing. Among the 289 strains, 242 were clustered into 7 major MLST CCs, 40 into minor CCs and 7 were not grouped into CCs. A total of 205 DLST- and 129 spa-types were observed. With one exception, all DLST-clfB, DLST-spa and spa-type alleles were segregated into CCs. DLST-types sharing an identical allele (clfB or spa) were clustered using eBURST. Except for one strain, all isolates from each DLST cluster belonged to the same CC. However, using both DLST- and spa-typing we were not able to disclose a clear intra-CC structure. Nevertheless, the high diversity of these loci confirmed that they are good markers for local epidemiological investigations.

Positive and negative regulation of T cell responses by fibroblastic reticular cells within paracortical regions of lymph nodes.

Fibroblastic reticular cells (FRC) form the structural backbone of the T cell rich zones in secondary lymphoid organs (SLO), but also actively influence the adaptive immune response. They provide a guidance path for immigrating T lymphocytes and dendritic cells (DC) and are the main local source of the cytokines CCL19, CCL21, and IL-7, all of which are thought to positively regulate T cell homeostasis and T cell interactions with DC. Recently, FRC in lymph nodes (LN) were also described to negatively regulate T cell responses in two distinct ways. During homeostasis they express and present a range of peripheral tissue antigens, thereby participating in peripheral tolerance induction of self-reactive CD8(+) T cells. During acute inflammation T cells responding to foreign antigens presented on DC very quickly release pro-inflammatory cytokines such as interferon γ. These cytokines are sensed by FRC which transiently produce nitric oxide (NO) gas dampening the proliferation of neighboring T cells in a non-cognate fashion. In summary, we propose a model in which FRC engage in a bidirectional crosstalk with both DC and T cells to increase the efficiency of the T cell response. However, during an acute response, FRC limit excessive expansion and inflammatory activity of antigen-specific T cells. This negative feedback loop may help to maintain tissue integrity and function during rapid organ growth.

Anorectal malformations and pregnancy-related disorders: a registry-based case-control study in 17 European regions.

OBJECTIVE: To identify pregnancy-related risk factors for different manifestations of congenital anorectal malformations (ARMs). DESIGN: A population-based case-control study. SETTING: Seventeen EUROCAT (European Surveillance of Congenital Anomalies) registries, 1980-2008. POPULATION: The study population consisted of 1417 cases with ARM, including 648 cases of isolated ARM, 601 cases of ARM with additional congenital anomalies, and 168 cases of ARM-VACTERL (vertebral, anal, cardiac, tracheo-esophageal, renal, and limb defects), along with 13 371 controls with recognised syndromes or chromosomal abnormalities. METHODS: Multiple logistic regression analyses were used to calculate adjusted odds ratios (ORs) for potential risk factors for ARM, such as fertility treatment, multiple pregnancy, primiparity, maternal illnesses during pregnancy, and pregnancy-related complications. MAIN OUTCOME MEASURES: Adjusted ORs for pregnancy-related risk factors for ARM. RESULTS: The ARM cases were more likely to be firstborn than the controls (OR 1.6, 95% CI 1.4-1.8). Fertility treatment and being one of twins or triplets seemed to increase the risk of ARM in cases with additional congenital anomalies or VACTERL (ORs ranging from 1.6 to 2.5). Maternal fever during pregnancy and pre-eclampsia were only associated with ARM when additional congenital anomalies were present (OR 3.9, 95% CI 1.3-11.6; OR 3.4, 95% CI 1.6-7.1, respectively), whereas maternal epilepsy during pregnancy resulted in a five-fold elevated risk of all manifestations of ARM (OR 5.1, 95% CI 1.7-15.6). CONCLUSIONS: This large European study identified maternal epilepsy, fertility treatment, multiple pregnancy, primiparity, pre-eclampsia, and maternal fever during pregnancy as potential risk factors primarily for complex manifestations of ARM with additional congenital anomalies and VACTERL.

The central Sesia-Lanzo zone (Western Italian Alps) - New field observations and lithostratigraphic subdivisions

An extensive study of the central part of the Sesia Lanzo Zone has been undertaken to identify pre-Alpine protoliths and to reconstruct the lithologic and tectonic setting of this part of the Western Alps. Three main complexes have been defined: 1) the Polymetamorphic Basement Complex, corresponding to the lower unit of the Sesia Lanzo Zone after COMPAGNONI et al. (1977), is further subdivided into the three following units: a) an Internal Unit characterized by eo-Alpine high pressure (HP) assemblages (DAL PIAZ et al., 1972) (Eclogitic Micaschists); b) an Intermediate Unit where HP parageneses are partially re-equilibrated under greenschist conditions and c) an External Unit where the main foliation is defined by a greenschist paragenesis (Gneiss Minuti auct.). 2) the Monometamorphic Cover Complex, subdivided into the followings: a) the Bonze Unit, composed of sheared metagabbros, eclogitized metabasalts with MORB geochemical affinity and related metasediments (micaschists, quartzites and Mn-cherts) and b) the Scalaro Unit, containing predominantly metasediments of supposed Permo-Triassic age (yellow dolomitic marbles, calcschists and conglomeratic limestones, micaschists and quartzites with thin levels of basic rocks with within plate basalts [WPB] geochimical affinity). Multiple lithostratigraphic sequences for the Monometamorphic Cover Complex are proposed. The contact between the Bonze and Scalaro Units is defined by repetitions of dolomitic marbles and metabasalts; the ages of the metasediments have been assigned solely by analogy with other sediments of the Western Alps, due to the absence of fossils. The Monometamorphic Cover Complex can be considered as the autochthonous cover of the Sesia Lanzo Zone because of the primary contacts with the basement and because of the presence of preAlpine HT basement blocks in the cover sequences. 3) The pre-Alpine high temperature (HT) Basement Complex (or `'Seconda Zona Diorito-Kinzigitica''), comprises HT Hercynian rocks like kinzigites, amphibolites, granulites and calcite marbles; this Complex is always located between the Internal and the External Units and can be followed continuously for several kilometers south of the Gressoney Valley to the Orco Valley. A schematic evolution for the Sesia Lanzo Zone is proposed; based on available data together with new geochronological data, this study shows that the internal and external parts of the polymetamorphic basement of the Sesia Zone experienced different cooling histories .

Toarcian radiolaria from Mt. Mangart (Slovenian-Italian border) and their paleoecological implications

Diverse and well-preserved Toarcian radiolarians have been recovered from a succession of organic-rich shale with intercalations of siliceous limestone. The succession is located at the Slovenian-Italian border in the Julian Alps and was deposited on a subsided block pertaining to the south Tethyan passive continental margin. Twenty spumellarian and 17 nassellarian genera were found in total. Thirty-six taxa were identified to species level and one new species, Bistarkum mangartense n. sp., is described. The assemblages show a high predominance of spumellarians over nassellarians. Spongy spumellarians, especially Orbiculiforma ?, are markedly abundant. Pantanelliidae are generally rare but reach a pronounced peak of 13% in one stratigraphic level. Among nassellarians, Parahsuum is the most abundant but members belonging to Syringocapsidae are scarce to absent. In addition to paleolatitude and water column depth, ecological conditions accompanying the early Toarcian global anoxic event may have to a considerable extent determined the specific taxonomic composition of these radiolarian faunas. (C) 2003 Elsevier B.V. All rights reserved.

Using matrix attachment regions to improve recombinant protein production.

Chinese hamster ovary (CHO) cells are the system of choice for the production of complex molecules, such as monoclonal antibodies. Despite significant progress in improving the yield from these cells, the process to the selection, identification, and maintenance of high-producing cell lines remains cumbersome, time consuming, and often of uncertain outcome. Matrix attachment regions (MARs) are DNA sequences that help generate and maintain an open chromatin domain that is favourable to transcription and may also facilitate the integration of several copies of the transgene. By incorporating MARs into expression vectors, an increase in the proportion of high-producer cells as well as an increase in protein production are seen, thereby reducing the number of clones to be screened and time to production by as much as 9 months. In this chapter, we describe how MARs can be used to increase transgene expression and provide protocols for the transfection of CHO cells in suspension and detection of high-producing antibody cell clones.

Congenital diaphragmatic hernia: evaluation of prenatal diagnosis in 20 European regions.

OBJECTIVE: To evaluate prenatal diagnosis of congenital diaphragmatic hernia by ultrasound in well-defined European populations. DESIGN: Data from 20 registries of congenital malformations in 12 European countries were included. The prenatal ultrasound screening programs in the countries ranged from no routine screening to three ultrasound investigations per patient being routinely performed. RESULTS: There were 187 cases with congenital diaphragmatic hernia, with an overall prenatal detection rate of 59% (110/187). There was considerable variation in prenatal detection rate between regions. There was a significant difference in the detection rate of isolated congenital diaphragmatic hernia (59/116, 51%) compared with congenital diaphragmatic hernia associated with multiple malformations, karyotype anomalies or syndromes (51/71, 72%) (P = 0.01). Termination of pregnancy was performed in 39 cases (21%) of which 14 cases were isolated congenital diaphragmatic hernia. Mean gestational age at discovery was 24.2 weeks (range, 11-38 weeks). CONCLUSIONS: The overall prenatal detection rate of congenital diaphragmatic hernia is high (59%) but varies significantly between European regions. The gestational age at discovery was greater than 24 weeks in half of the prenatally diagnosed cases.