Functional and Genetic characterization of new genomic islands from an E. coli strain associated with neonatal meningitis.

Enterobacteriaceae genomes evolve through mutations, rearrangements and horizontal gene transfer (HGT). The latter evolutionary pathway works through the acquisition DNA (GEI) modules of foreign origin that enhances fitness of the host to a given environment. The genome of E. coli IHE3034, a strain isolated from a case of neonatal meningitis, has recently been sequenced and its subsequent sequence analysis has predicted 18 possible GEIs, of which: 8 have not been previously described, 5 fully meet the pathogenic island definition and at least 10 that seem to be of prophagic origin. In order to study the GEI distribution of our reference strain, we screened for the presence 18 GEIs a panel of 132 strains, representative of E. coli diversity. Also, using an inverse nested PCR approach we identified 9 GEI that can form an extrachromosomal circular intermediate (CI) and their respective attachment sites (att). Further, we set up a qPCR approach that allowed us to determine the excision rates of 5 genomic islands in different growth conditions. Four islands, specific for strains appertaining to the sequence type complex 95 (STC95), have been deleted in order to assess their function in a Dictyostelium discoideum grazing assays. Overall, the distribution data presented here indicate that 16 IHE3034 GEIs are more associated to the STC95 strains. Also the functional and genetic characterization has uncovered that GEI 13, 17 and 19 are involved in the resistance to phagocitation by Dictyostelium d thus suggesting a possible role in the adaptation of the pathogen during certain stages of infection.

Effect of Paramuricea clavata (Risso, 1826) "forest" on the benthic populations of Tremiti Islands Effetto "foresta" di Paramuricea clavata (Risso, 1826) sui popolamenti bentonici delle Isole Tremiti

Mediterranean coralligenous habitats are biogenic reefs characterised by high species diversity and built mainly by encrusting calcareous red algae, growing in dim light conditions. The global climate change and several human activities may threaten species living in these habitats, especially some of those that are considered particularly relevant in structuring and in maintaining the complexity and diversity of the benthic assemblages. Among them, the red gorgonian, Paramuricea clavata (Risso, 1826), which can form dense populations, in the last decades showed worrying mass mortality events. Understand the role of this “animal forests” in the coralligenous assemblages is of fundamental importance in order to design appropriate monitoring programs and conservation policies, especially in the marine protected areas. For this purpose, benthic assemblages were studied in presence and absence of red gorgonians at two sites at the Tremiti islands. Overall, the benthic assemblages significantly differed among sites, nevertheless in both places, clear differences between assemblages associated and not associated to the gorgonian forests were found. In particular, encrusting corallinered algae were significantly more abundant in the gorgonian understories at both sites. This result indicates that the gorgonians may promote the development of calcareous algae, which are the main builders of the coralligenous habitats. Moreover species diversity resulted higher in the assemblages associated to the gorgonians. The present study highlights the role of Paramuricea clavata as a relevant ecosystem engineer in the coralligenous habitats.

Transform Tectonics and Non-Volcanic Oceanic Islands

Oceanic islands can be divided, according to their origin, in volcanic and tectonic. Volcanic islands are due to excess volcanism. Tectonic islands are mainly formed due to vertical tectonic motions of blocks of oceanic lithosphere along transverse ridges flanking transform faults at slow and ultraslow mid-ocean ridges. Vertical tectonic motions are due to a reorganization of the geometry of the transform plate boundary, with the transition from a transcurrent tectonics to a transtensive and/or transpressive tectonics, with the formation of the transverse ridges. Tectonic islands can be located also at the ridge–transform intersection: in this case the uplift is due by the movement of the long-lived detachment faults located along the flanks of the mid-ocean ridges. The "Vema" paleoisland (equatorial Atlantic) is at the summit of the southern transverse ridge of the Vema transform. It is now 450 m bsl and it is capped by a carbonate platform 500 m-thick, dated by 87Sr/86Sr at 10 Ma. Three tectonic paleoislands are on the summit of the transverse ridge flanking the Romanche megatrasform (equatorial Atlantic). They are now about 1,000 m bsl and they are formed by 300 m-thick carbonate platforms dated by 87Sr/86Sr, between 11 and 6 Ma. The tectonic paleoisland “Atlantis Bank" is located in the South-Western Indian Ridge, along the Atlantis II transform, and it is today 700 m bsl. The only modern example of oceanic tectonics island is the St. Paul Rocks (equatorial Atlantic), located along the St. Paul transform. This archipelago is the top of a peridotitic massif that it is now a left overstep undergoing transpression. Oceanic volcanic islands are characterized by rapid growth and subsequent thermal subsidence and drowning; in contrast, oceanic tectonic islands may have one or more stages of emersion related to vertical tectonic events along the large oceanic fracture zones.

Evolutionary forces shaping genomic islands of population differentiation in humans

Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP) showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM). A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i) as much as 20% of islands are in non-genic regions ii) these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii) most loci are strongly differentiated between Africans and non-Africans, a result consistent with known human demographic history.

Isolated Islands? Memory of the Holocaust in Formal and Non-Formal Education. The Case Study of Post-Communist Poland

Existing studies revealed several conflicts around the memory of the Holocaust in Poland: between understanding the need to teach about the Holocaust and indifference toward anti-Jewish graffiti; a conflict around the perception of Polish help to Jews; and the competing images of Polish and Jewish suffering during World War II. Those conflicts will be addressed in the paper as reflecting educational gaps in the Polish education system (lack of bad memory). This paper will look at the consciousness of young Poles, in terms of attitudes toward Jews, the Holocaust and memory of the Holocaust. The data presented are the preliminary results of the author’s longitudinal study „Attitudes of Young Poles toward the Jews and the Holocaust”. Quantitative and qualitative studies include field studies and participant observation of educational projects in Tykocin, Treblinka, Warsaw, Lublin, Bodzentyn and Kielce. The paper will present some components of the development of education about the Holocaust in Poland. There is a need to evaluate the attempt to bring back the memory of Jewish neighbours in some of the states of Central and Eastern Europe, a process with an ongoing effort to renovate monuments, destroyed cemeteries and synagogues. The number and scope of such initiatives in Poland indicate that civic institutions and individuals are intensifying their efforts to teach their fellow citizens about the Holocaust, however their impact should be assessed in detail.

Attempting to improve standardized test results using Study Islands' web-based mastery program

State standardized testing has always been a tool to measure a school’s performance and to help evaluate school curriculum. However, with the school of choice legislation in 1992, the MEAP test became a measuring stick to grade schools by and a major tool in attracting school of choice students. Now, declining enrollment and a state budget struggling to stay out of the red have made school of choice students more important than ever before. MEAP scores have become the deciding factor in some cases. For the past five years, the Hancock Middle School staff has been working hard to improve their students’ MEAP scores in accordance with President Bush's “No Child Left Behind” legislation. In 2005, the school was awarded a grant that enabled staff to work for two years on writing and working towards school goals that were based on the improvement of MEAP scores in writing and math. As part of this effort, the school purchased an internet-based program geared at giving students practice on state content standards. This study examined the results of efforts by Hancock Middle School to help improve student scores in mathematics on the MEAP test through the use of an online program called “Study Island.” In the past, the program was used to remediate students, and as a review with an incentive at the end of the year for students completing a certain number of objectives. It had also been used as a review before upcoming MEAP testing in the fall. All of these methods may have helped a few students perform at an increased level on their standardized test, but the question remained of whether a sustained use of the program in a classroom setting would increase an understanding of concepts and performance on the MEAP for the masses. This study addressed this question. Student MEAP scores and Study Island data from experimental and comparison groups of students were compared to understand how a sustained use of Study Island in the classroom would impact student test scores on the MEAP. In addition, these data were analyzed to determine whether Study Island results provide a good indicator of students’ MEAP performance. The results of the study suggest that there were limited benefits related to sustained use of Study Island and gave some indications about the effectiveness of the mathematics curriculum at Hancock Middle School. These results and implications for instruction are discussed.

The ecological consequences of megafaunal loss: giant tortoises and wetland biodiversity

The giant tortoises of the Galapagos have become greatly depleted since European discovery of the islands in the 16th Century, with populations declining from an estimated 250000 to between 8000 and 14000 in the 1970s. Successful tortoise conservation efforts have focused on species recovery, but ecosystem conservation and restoration requires a better understanding of the wider ecological consequences of this drastic reduction in the archipelago's only large native herbivore. We report the first evidence from palaeoecological records of coprophilous fungal spores of the formerly more extensive geographical range of giant tortoises in the highlands of Santa Cruz Island. Upland tortoise populations on Santa Cruz declined 500-700years ago, likely the result of human impact or possible climatic change. Former freshwater wetlands, a now limited habitat-type, were found to have converted to Sphagnum bogs concomitant with tortoise loss, subsequently leading to the decline of several now-rare or extinct plant species.