Showing papers by "University of Bologna published in 2007"

Synthetic molecular motors and mechanical machines.

Abstract: The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Multiwavelength study of massive galaxies at z~2. I. Star formation and galaxy growth

Abstract: Examining a sample of massive galaxies at 1.4 10 11 L⊙, show a mid-IR excess which is likely due to the presence of obscured active nuclei, as shown in a companion paper. There is a tight and roughly linear correlation between stellar mass and SFR for 24µm-detected galaxies. For a given mass, the SFR at z = 2 was larger by a factor of ∼ 4 and ∼ 30 relative to that in star forming galaxies at z = 1 and z = 0, respectively. Typical ultraluminous infrared galaxies (ULIRGs) at z = 2 are relatively ’transparent’ to ultraviolet light, and their activity is long lived ( > ∼ 400 Myr), unlike that in local ULIRGs and high redshift submillimeter-selected galaxies. ULIRGs are the common mode of star formation in massive galaxies at z = 2, and the high duty cycle suggests that major mergers are not the dominant trigger for this activity. Current galaxy formation models underpredict the normalization of the mass-SFR correlation by about a factor of 4, and the space density of ULIRGs by an order of magnitude, but give better agreement for z > 1.4 quiescent galaxies. Subject headings: galaxies: evolution — galaxies: formation — cosmology: observations — galaxies: starbursts — galaxies: high-redshift

The Future of Energy Supply: Challenges and Opportunities

Abstract: Each generation is confronted with new challenges and new opportunities. In a restricted system like the Earth, however, opportunities discovered and exploited by a generation can cause challenges to the subsequent ones. Fossil fuels have offered astounding opportunities during the 20th century in the rich countries of the western world, but now mankind has to face the challenges arising from fossil-fuel exploitation. The proven reserves of fossil fuels are progressively decreasing, and their continued use produces harmful effects, such as pollution that threatens human health and greenhouse gases associated with global warming. Currently the world&s growing thirst for oil amounts to almost 1000 barrels a second, which means about 2 liters a day per each person living on the Earth (Figure 1). The current global energy consumption is equivalent to 13 terawatts (TW), that is, a steady 13 trillion watts of power demand. How long can we keep running this road?

Mapping autism risk loci using genetic linkage and chromosomal rearrangements

Abstract: Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,181 [corrected] families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.

zCOSMOS: A Large VLT/VIMOS Redshift Survey Covering 0 < z < 3 in the COSMOS Field*

Abstract: zCOSMOS is a large-redshift survey that is being undertaken in the COSMOS field using 600 hr of observation with the VIMOS spectrograph on the 8 m VLT. The survey is designed to characterize the environments of COSMOS galaxies from the 100 kpc scales of galaxy groups up to the 100 Mpc scale of the cosmic web and to produce diagnostic information on galaxies and active galactic nuclei. The zCOSMOS survey consists of two parts: (1) zCOSMOSbright, a magnitude-limited I-band I_(AB) < 22.5 sample of about 20,000 galaxies with 0.1 < z < 1.2 covering the whole 1.7 deg^2 COSMOS ACS field, for which the survey parameters at z ~ 0.7 are designed to be directly comparable to those of the 2dFGRS at z ~ 0.1; and (2) zCOSMOS-deep, a survey of approximately 10,000 galaxies selected through color-selection criteria to have 1.4 < z < 3.0, within the central 1 deg^2. This paper describes the survey design and the construction of the target catalogs and briefly outlines the observational program and the data pipeline. In the first observing season, spectra of 1303 zCOSMOS-bright targets and 977 zCOSMOS-deep targets have been obtained. These are briefly analyzed to demonstrate the characteristics that may be expected from zCOSMOS, and particularly zCOSMOS-bright, when it is finally completed between 2008 and 2009. The power of combining spectroscopic and photometric redshifts is demonstrated, especially in correctly identifying the emission line in single-line spectra and in determining which of the less reliable spectroscopic redshifts are correct and which are incorrect. These techniques bring the overall success rate in the zCOSMOS-bright so far to almost 90% and to above 97% in the 0.5 < z < 0.8 redshift range. Our zCOSMOS-deep spectra demonstrate the power of our selection techniques to isolate high-redshift galaxies at 1.4 < z < 3.0 and of VIMOS to measure their redshifts using ultraviolet absorption lines.

CMS physics technical design report, volume II: Physics performance

Abstract: CMS is a general purpose experiment, designed to study the physics of pp collisions at 14 TeV at the Large Hadron Collider (LHC). It currently involves more than 2000 physicists from more than 150 institutes and 37 countries. The LHC will provide extraordinary opportunities for particle physics based on its unprecedented collision energy and luminosity when it begins operation in 2007. The principal aim of this report is to present the strategy of CMS to explore the rich physics programme offered by the LHC. This volume demonstrates the physics capability of the CMS experiment. The prime goals of CMS are to explore physics at the TeV scale and to study the mechanism of electroweak symmetry breaking--through the discovery of the Higgs particle or otherwise. To carry out this task, CMS must be prepared to search for new particles, such as the Higgs boson or supersymmetric partners of the Standard Model particles, from the start-up of the LHC since new physics at the TeV scale may manifest itself with modest data samples of the order of a few fb−1 or less. The analysis tools that have been developed are applied to study in great detail and with all the methodology of performing an analysis on CMS data specific benchmark processes upon which to gauge the performance of CMS. These processes cover several Higgs boson decay channels, the production and decay of new particles such as Z' and supersymmetric particles, Bs production and processes in heavy ion collisions. The simulation of these benchmark processes includes subtle effects such as possible detector miscalibration and misalignment. Besides these benchmark processes, the physics reach of CMS is studied for a large number of signatures arising in the Standard Model and also in theories beyond the Standard Model for integrated luminosities ranging from 1 fb−1 to 30 fb−1. The Standard Model processes include QCD, B-physics, diffraction, detailed studies of the top quark properties, and electroweak physics topics such as the W and Z0 boson properties. The production and decay of the Higgs particle is studied for many observable decays, and the precision with which the Higgs boson properties can be derived is determined. About ten different supersymmetry benchmark points are analysed using full simulation. The CMS discovery reach is evaluated in the SUSY parameter space covering a large variety of decay signatures. Furthermore, the discovery reach for a plethora of alternative models for new physics is explored, notably extra dimensions, new vector boson high mass states, little Higgs models, technicolour and others. Methods to discriminate between models have been investigated. This report is organized as follows. Chapter 1, the Introduction, describes the context of this document. Chapters 2-6 describe examples of full analyses, with photons, electrons, muons, jets, missing ET, B-mesons and τ's, and for quarkonia in heavy ion collisions. Chapters 7-15 describe the physics reach for Standard Model processes, Higgs discovery and searches for new physics beyond the Standard Model

The human footprint in the carbon cycle of temperate and boreal forests

Abstract: A study of forest ecosystems from across western Europe and the United States has settled a long-running controversy — and raised many new questions. At issue is the influence of nitrogen deposition on the global carbon cycle, particularly the part played by human activity. The new study demonstrates that via the direct effects of forest management and indirectly via the use of nitrogen fertilizers and nitrogen oxide production by cars and industry, human activities have had a profound and largely positive effect on the carbon balance or net ecosystem production. (That's the balance between ecosystem carbon fixation through photosynthesis and its subsequent release through plant and soil respiration.) The implications of these findings for practical questions such as the merits of fertilizing forests with nitrogen, are considered in the accompanying News and Views by Peter Hogberg. The profound, overwhelming effects of human activities on the carbon balance of temperate and boreal forests are demonstrated. Apart from the direct effects of forest management, they show that carbon sequestration by this important component of the biosphere is driven by the imbalance in the global nitrogen cycle determined by human activities. Temperate and boreal forests in the Northern Hemisphere cover an area of about 2 × 107 square kilometres and act as a substantial carbon sink (0.6–0.7 petagrams of carbon per year)1. Although forest expansion following agricultural abandonment is certainly responsible for an important fraction of this carbon sink activity, the additional effects on the carbon balance of established forests of increased atmospheric carbon dioxide, increasing temperatures, changes in management practices and nitrogen deposition are difficult to disentangle, despite an extensive network of measurement stations2,3. The relevance of this measurement effort has also been questioned4, because spot measurements fail to take into account the role of disturbances, either natural (fire, pests, windstorms) or anthropogenic (forest harvesting). Here we show that the temporal dynamics following stand-replacing disturbances do indeed account for a very large fraction of the overall variability in forest carbon sequestration. After the confounding effects of disturbance have been factored out, however, forest net carbon sequestration is found to be overwhelmingly driven by nitrogen deposition, largely the result of anthropogenic activities5. The effect is always positive over the range of nitrogen deposition covered by currently available data sets, casting doubts on the risk of widespread ecosystem nitrogen saturation6 under natural conditions. The results demonstrate that mankind is ultimately controlling the carbon balance of temperate and boreal forests, either directly (through forest management) or indirectly (through nitrogen deposition).

Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery

Abstract: Achieving the full potential of zinc-finger nucleases (ZFNs) for genome engineering in human cells requires their efficient delivery to the relevant cell types. Here we exploited the infectivity of integrase-defective lentiviral vectors (IDLV) to express ZFNs and provide the template DNA for gene correction in different cell types. IDLV-mediated delivery supported high rates (13-39%) of editing at the IL-2 receptor common gamma-chain gene (IL2RG) across different cell types. IDLVs also mediated site-specific gene addition by a process that required ZFN cleavage and homologous template DNA, thus establishing a platform that can target the insertion of transgenes into a predetermined genomic site. Using IDLV delivery and ZFNs targeting distinct loci, we observed high levels of gene addition (up to 50%) in a panel of human cell lines, as well as human embryonic stem cells (5%), allowing rapid, selection-free isolation of clonogenic cells with the desired genetic modification.

Cyclin G1 Is a Target of miR-122a, a MicroRNA Frequently Down-regulated in Human Hepatocellular Carcinoma

Abstract: We investigated the role of microRNAs (miRNAs) in the pathogenesis of human hepatocellular carcinoma (HCC). A genome-wide miRNA microarray was used to identify differentially expressed miRNAs in HCCs arisen on cirrhotic livers. Thirty-five miRNAs were identified. Several of these miRNAs were previously found deregulated in other human cancers, such as members of the let-7 family, mir-221, and mir-145. In addition, the hepato-specific miR-122a was found down-regulated in approximately 70% of HCCs and in all HCC-derived cell lines. Microarray data for let-7a, mir-221, and mir-122a were validated by Northern blot and real-time PCR analysis. Understanding the contribution of deregulated miRNAs to cancer requires the identification of gene targets. Here, we show that miR-122a can modulate cyclin G1 expression in HCC-derived cell lines and an inverse correlation between miR-122a and cyclin G1 expression exists in primary liver carcinomas. These results indicate that cyclin G1 is a target of miR-122a and expand our knowledge of the molecular alterations involved in HCC pathogenesis and of the role of miRNAs in human cancer.

IL-6 triggers malignant features in mammospheres from human ductal breast carcinoma and normal mammary gland

Abstract: High serum levels of IL-6 correlate with poor outcome in breast cancer patients. However, no data are available on the relationship between IL-6 and mammary stem/progenitor cells, which may fuel the genesis of breast cancer in vivo. Herein, we address this issue in the MCF-7 breast cancer cell line and in primary human mammospheres (MS), multicellular structures enriched in stem/progenitor cells of the mammary gland. MS from node invasive breast carcinoma tissues expressed IL-6 mRNA at higher levels than did MS from matched non-neoplastic mammary glands. In addition, IL-6 mRNA was detected only in basal-like breast carcinoma tissues, an aggressive breast carcinoma variant showing stem cell features. IL-6 treatment triggered Notch-3-dependent upregulation of the Notch ligand Jagged-1 and promotion of MS and MCF-7-derived spheroid growth. Moreover, IL-6 induced Notch-3-dependent upregulation of the carbonic anhydrase IX gene and promoted a hypoxia-resistant/invasive phenotype in MCF-7 cells and MS. Finally, autocrine IL-6 signaling relied upon Notch-3 activity to sustain the aggressive features of MCF-7-derived hypoxia-selected cells. In conclusion, these data support the hypothesis that IL-6 induces malignant features in Notch-3-expressing stem/progenitor cells from human ductal breast carcinoma and normal mammary gland.

Photochemistry and Photophysics of Coordination Compounds: Ruthenium

Abstract: Ruthenium compounds, particularly Ru(II) polypyridine complexes, are the class of transition metal complexes which has been most deeply investigated from a photochemical viewpoint. The reason for such great interest stems from a unique combination of chemical stability, redox properties, excited-state reactivity, luminescence emission, and excited-state lifetime. Ruthenium polypyridine complexes are indeed good visible light absorbers, feature relatively intense and long-lived luminescence, and can undergo reversible redox processes in both the ground and excited states. This chapter presents some general concepts on the photochemical properties of Ru(II) polypyridine complexes and gives an overview of various research topics involving ruthenium photochemistry which have emerged in the last 15 years. In particular, aspects connected to supramolecular photochemistry and photophysics are discussed, such as multicomponent systems for light harvesting and photoinduced charge separation, systems for photoinduced multielectron/hole storage, and photocatalytic processes based on supramolecular Ru(II) polypyridine species. Interaction with biological systems and dye-sensitized photoelectrochemical cells are also briefly discussed.

Phenolic molecules in virgin olive oils: a survey of their sensory properties, health effects, antioxidant activity and analytical methods. An overview of the last decade.

Abstract: Among vegetable oils, virgin olive oil (VOO) has nutritional and sensory characteristics that to make it unique and a basic component of the Mediterranean diet. The importance of VOO is mainly attributed both to its high content of oleic acid a balanced contribution quantity of polyunsaturated fatty acids and its richness in phenolic compounds, which act as natural antioxidants and may contribute to the prevention of several human diseases. The polar phenolic compounds of VOO belong to different classes: phenolic acids, phenyl ethyl alcohols, hydroxy-isochromans, flavonoids, lignans and secoiridoids. This latter family of compounds is characteristic of Oleaceae plants and secoiridoids are the main compounds of the phenolic fraction. Many agronomical and technological factors can affect the presence of phenols in VOO. Its shelf life is higher than other vegetable oils, mainly due to the presence of phenolic molecules having a catechol group, such as hydroxytyrosol and its secoiridoid derivatives. Several assays have been used to establish the antioxidant activity of these isolated phenolic compounds. Typical sensory gustative properties of VOO, such as bitterness and pungency, have been attributed to secoiridoid molecules. Considering the importance of the phenolic fraction of VOO, high performance analytical methods have been developed to characterize its complex phenolic pattern. The aim of this review is to realize a survey on phenolic compounds of virgin olive oils bearing in mind their chemical-analytical, healthy and sensory aspects. In particular, starting from the basic studies, the results of researches developed in the last ten years will be focused.

Implantable cardioverter-defibrillators and prevention of sudden cardiac death in hypertrophic cardiomyopathy

Abstract: ContextRecently, the implantable cardioverter-defibrillator (ICD) has been promoted for prevention of sudden death in hypertrophic cardiomyopathy (HCM). However, the effectiveness and appropriate selection of patients for this therapy is incompletely resolved.ObjectiveTo study the relationship between clinical risk profile and incidence and efficacy of ICD intervention in HCM.Design, Setting, and PatientsMulticenter registry study of ICDs implanted between 1986 and 2003 in 506 unrelated patients with HCM. Patients were judged to be at high risk for sudden death; had received ICDs; underwent evaluation at 42 referral and nonreferral institutions in the United States, Europe, and Australia; and had a mean follow-up of 3.7 (SD, 2.8) years. Measured risk factors for sudden death included family history of sudden death, massive left ventricular hypertrophy, nonsustained ventricular tachycardia on Holter monitoring, and unexplained prior syncope.Main Outcome MeasureAppropriate ICD intervention terminating ventricular tachycardia or fibrillation.ResultsThe 506 patients were predominately young (mean age, 42 [SD, 17] years) at implantation, and most (439 [87%]) had no or only mildly limiting symptoms. ICD interventions appropriately terminated ventricular tachycardia/fibrillation in 103 patients (20%). Intervention rates were 10.6% per year for secondary prevention after cardiac arrest (5-year cumulative probability, 39% [SD, 5%]), and 3.6% per year for primary prevention (5-year probability, 17% [SD, 2%]). Time to first appropriate discharge was up to 10 years, with a 27% (SD, 7%) probability 5 years or more after implantation. For primary prevention, 18 of the 51 patients with appropriate ICD interventions (35%) had undergone implantation for only a single risk factor; likelihood of appropriate discharge was similar in patients with 1, 2, or 3 or more risk markers (3.83, 2.65, and 4.82 per 100 person-years, respectively; P = .77). The single sudden death due to an arrhythmia (in the absence of advanced heart failure) resulted from ICD malfunction. ICD complications included inappropriate shocks in 136 patients (27%).ConclusionsIn a high-risk HCM cohort, ICD interventions for life-threatening ventricular tachyarrhythmias were frequent and highly effective in restoring normal rhythm. An important proportion of ICD discharges occurred in primary prevention patients who had undergone implantation for a single risk factor. Therefore, a single marker of high risk for sudden death may be sufficient to justify consideration for prophylactic defibrillator implantation in selected patients with HCM.

The Happy Few: The Internationalisation of European Firms

Abstract: Policymakers tend to view the internationalisation of firms from the perspective of export, import and FDI statistics. A lack of statistical information at the firm level has so far prevented the systematic inclusion of firm-level analysis in the policymaker's standard toolbox. Some firm-level datasets are now available, however, and their analysis reveals some new facts that are simply unobservable at the aggregate level.

Aortic Diameter ≥5.5 cm Is Not a Good Predictor of Type A Aortic Dissection Observations From the International Registry of Acute Aortic Dissection (IRAD)

Abstract: Background— Studies of aortic aneurysm patients have shown that the risk of rupture increases with aortic size. However, few studies of acute aortic dissection patients and aortic size exist. We used data from our registry of acute aortic dissection patients to better understand the relationship between aortic diameter and type A dissection. Methods and Results— We examined 591 type A dissection patients enrolled in the International Registry of Acute Aortic Dissection between 1996 and 2005 (mean age, 60.8 years). Maximum aortic diameters averaged 5.3 cm; 349 (59%) patients had aortic diameters <5.5 cm and 229 (40%) patients had aortic diameters <5.0 cm. Independent predictors of dissection at smaller diameters (<5.5 cm) included a history of hypertension (odds ratio, 2.17; 95% confidence interval, 1.03 to 4.57; P=0.04), radiating pain (odds ratio, 2.08; 95% confidence interval, 1.08 to 4.0; P=0.03), and increasing age (odds ratio, 1.03; 95% confidence interval, 1.00 to 1.05; P=0.03). Marfan syndrome pati...

The use of biomarkers in biomonitoring: a 2-tier approach assessing the level of pollutant-induced stress syndrome in sentinel organisms.

Abstract: The paper outlines a 2-tier approach for wide-scale biomonitoring programmes. To obtain a high level of standardization, we suggest the use of caged organisms (mussels or fish). An "early warning", highly sensitive, low-cost biomarker is employed in tier 1 (i.e. lysosomal membrane stability (LMS) and survival rate, a marker for highly polluted sites). Tier 2 is used only for animals sampled at sites in which LMS changes are evident and there is no mortality, with a complete battery of biomarkers assessing the levels of pollutant-induced stress syndrome. Possible approaches for integrating biomarker data in a synthetic index are discussed, along with our proposal to use a recently developed Expert System. The latter system allows a correct selection of biomarkers at different levels of biological organisation (molecular/cellular/tissue/organism) taking into account trends in pollutant-induced biomarker changes (increasing, decreasing, bell-shape). A selection of biomarkers of stress, genotoxicity and exposure usually employed in biomonitoring programmes is presented, together with a brief overview of new biomolecular approaches.

Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy

Abstract: Noonan and LEOPARD syndromes are developmental disorders with overlapping features, including cardiac abnormalities, short stature and facial dysmorphia. Increased RAS signaling owing to PTPN11, SOS1 and KRAS mutations causes approximately 60% of Noonan syndrome cases, and PTPN11 mutations cause 90% of LEOPARD syndrome cases. Here, we report that 18 of 231 individuals with Noonan syndrome without known mutations (corresponding to 3% of all affected individuals) and two of six individuals with LEOPARD syndrome without PTPN11 mutations have missense mutations in RAF1, which encodes a serine-threonine kinase that activates MEK1 and MEK2. Most mutations altered a motif flanking Ser259, a residue critical for autoinhibition of RAF1 through 14-3-3 binding. Of 19 subjects with a RAF1 mutation in two hotspots, 18 (or 95%) showed hypertrophic cardiomyopathy (HCM), compared with the 18% prevalence of HCM among individuals with Noonan syndrome in general. Ectopically expressed RAF1 mutants from the two HCM hotspots had increased kinase activity and enhanced ERK activation, whereas non-HCM-associated mutants were kinase impaired. Our findings further implicate increased RAS signaling in pathological cardiomyocyte hypertrophy.

Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state

Abstract: We have shown previously that transgene expression can be suppressed in hematopoietic cells using vectors that are responsive to microRNA (miRNA) regulation. Here we investigate the potential of this approach for more sophisticated control of transgene expression. Analysis of the relationship between miRNA expression levels and target mRNA suppression suggested that suppression depends on a threshold miRNA concentration. Using this information, we generated vectors that rapidly adjust transgene expression in response to changes in miRNA expression. These vectors sharply segregated transgene expression between closely related states of therapeutically relevant cells, including dendritic cells, hematopoietic and embryonic stem cells, and their progeny, allowing positive/negative selection according to the cells' differentiation state. Moreover, two miRNA target sites were combined to restrict transgene expression to a specific cell type in the liver. Notably, the vectors did not detectably perturb endogenous miRNA expression or regulation of natural targets. The properties of miRNA-regulated vectors should allow for safer and more effective therapeutic applications.