Dualities in population genetics: a fresh look with new dualities

We apply our general method of duality, introduced in [Giardina', Kurchan, Redig, J. Math. Phys. 48, 033301 (2007)], to models of population dynamics. The classical dualities between forward and ancestral processes can be viewed as a change of representation in the classical creation and annihilation operators, both for diffusions dual to coalescents of Kingman's type, as well as for models with finite population size. Next, using SU(1,1) raising and lowering operators, we find new dualities between the Wright-Fisher diffusion with $d$ types and the Moran model, both in presence and absence of mutations. These new dualities relates two forward evolutions. From our general scheme we also identify self-duality of the Moran model.Comment: 36 pages, to appear on Stochastic Processes and their Application

Changing distribution patterns of canine vector borne diseases in Italy: leishmaniosis vs. dirofilariosis

Ecological and climatic changes, human and animal population dynamics are among the several factors that have favoured the spread or the (re)introduction and establishment of "novel" vector species and pathogens they transmit in previously disease-free geographical areas. As key examples of the changing pattern of distribution of canine vector borne diseases (CVBDs), the current distribution of canine leishmaniosis (CanL) by Leishmania infantum and dirofilariosis by Dirofilaria immitis causing heart worm disease (HW) in Italy is discussed on the basis of retrospective historical reports until the 90's and later on until 2009. For long time, D. immitis has been considered mainly present along the Po River Valley and northward areas, while L. infantum in south-central Italy and Sicily and Sardinia. Comparison of current available and historical data (up to 1989) confirms that HW and CanL, although with different prevalence rates, have been changing their distribution patterns in Italy as a result of many biological and ecological factors, including those related to vector distribution and introduction of new species (e.g. the Asian tiger mosquito Aedes albopictus, a competent vector of D. immitis). New autochthonous foci of HW in southern Italy (i.e. Apulia and Calabria regions) have recently been reported

A systematic study of harnessing low-temperature geothermal energy from oil and gas reservoirs

Mature hydrocarbon fields co-produce significant volumes of water. As the produced water increases over the life of the field, the project's operating costs increase (due to greater water management expenditure), while the oil revenues decrease. Typically, these waste streams of water have temperatures of 65–150 °C. The combination of moderate temperatures and large water volumes may be suitable for electricity generation and/or district heating. Being able to capture the geothermal energy from existing hydrocarbon fields could extend their lifespan by delaying their economic cut-off point. In this paper, mature oil and gas reservoirs worldwide are critically reviewed, where waste heat recovery has already been tested, or its potential identified. A roadmap of screening criteria based on geological, reservoir, production and economic parameters is then proposed, to assess how, where and when low-temperature waste heat recovery is feasible. The roadmap is tested against the Villafortuna–Trecate oil field in Italy, where the aquifer not only provides pressure support to the reservoir, but also represents a natural, in-situ hydrothermal resource. The results suggest that a single-well could recover approximately 25 GWh of electric power over a 10-year period, with an installed capacity of 500 kW

-In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1

BACKGROUND: Histones are short proteins involved in chromatin packaging; in eukaryotes, two H2a-H2b and H3-H4 histone dimers form the nucleosomal core, which acts as the fundamental DNA-packaging element. The double histone fold is a rare globular protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus originating a histone pseudodimer. This fold is included in a few prokaryotic histones and in the regulatory region of guanine nucleotide exchange factors of the Sos family. For the prokaryotic histones, there is no direct structural counterpart in the nucleosomal core particle, while the pseudodimer from Sos proteins is very similar to the dimer formed by histones H2a and H2b RESULTS: The absence of a H3-H4-like histone pseudodimer in the available structural databases prompted us to search for proteins that could assume such fold. The application of several secondary structure prediction and fold recognition methods allowed to show that the viral protein gi|22788712 is compatible with the structure of a H3-H4-like histone pseudodimer. Further in silico analyses revealed that this protein module could retain the ability of mediating protein-DNA interactions, and could consequently act as a DNA-binding domain. CONCLUSION: Our results suggest a possible functional role in viral pathogenicity for this novel double histone fold domain; thus, the computational analyses here reported will be helpful in directing future biochemical studies on gi|22788712 protein

Dualities in population genetics: A fresh look with new dualities

We apply our general method of duality, introduced in [15], to models of population dynamics. The classical dualities between forward and ancestral processes can be viewed as a change of representation in the classical creation and annihilation operators, both for diffusions dual to coalescents of Kingman’s type, as well as for models with finite population size. Next, using SU(1, 1) raising and lowering operators, we find new dualities between the Wright-Fisher diffusion with d types and the Moran model, both in presence and absence of mutations. These new dualities relates two forward evolutions. From our general scheme we also identify self-duality of the Moran model

Fast Generation of Broken-Symmetry States in a Large System Including Multiple Iron-Sulfur Assemblies: Investigation of QM/MM Energies, Clusters Charges, and Spin Populations

A density functional theory study is presented regarding the energetics and the Mulliken population analyses of a quantum mechanical/molecular mechanical (QM/MM) system including multiple iron-sulfur clusters in the QM region. The [FeFe]-hydrogenase from Desulfovibrio desulfuricans was studied, and both the active site (an Fe6S6 assembly generally referred to as the H-cluster) and an ancillary Fe4S4 site were treated at the BP86-RI/TZVP level. The antiferromagnetic coupling that characterizes both sites was modeled using the broken-symmetry (BS) approach. For such a QM system, 36 different BS couplings can be defined, depending on the localization of spin excess on the various spin centers. All the BS states were obtained by means of an effective and simple method for spin localization, that is here described and compared with more sophisticated approaches already available in literature. The variation of the QM/MM energy among the various geometry-optimized protein models was found to be less than 25 kJ mol(-1). This energy variation almost doubles if no geometry optimization is performed. A detailed analysis of the additive nature of these variations in QM/MM energy is reported. The Mulliken charges show very small variations among the 36 BS states, whereas the Mulliken spin populations were found to be somewhat more variable. The relevance of such variations is discussed in light of the available Mossbauer and Electron Paramagnetic Resonance (EPR) spectroscopic data for the enzyme. Finally, the influence of the basis set on the spin populations, charges, and structural parameters of the models was investigated, by means of QM/MM computations on the same system at the BP86-RI/SVP level. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 3949-3960, 201

Mechanistic and Physiological Implications of the Interplay among Iron-Sulfur Clusters in [FeFe]-Hydrogenases. A QM/MM Perspective

Key stereoelectronic properties of Desulfovibrio desulfuricans [FeFe]-hydrogenase (DdH) were investigated by quantum mechanical description of its complete inorganic core, which includes a Fe6S6 active site (the H-cluster), as well as two ancillary Fe4S4 assemblies (the F and F' clusters). The partially oxidized, active-ready form of DdH is able to efficiently bind dihydrogen, thus starting H-2 oxidation catalysis. The calculations allow us to unambiguously assign a mixed Fe(H)Fe(I) state to the catalytic core of the active-ready enzyme and show that H-2 uptake exerts subtle, yet crucial influences on the redox properties of DdH. In fact, H-2 binding can promote electron transfer from the H-cluster to the solvent-exposed F'-cluster, thanks to a 50% decrease of the energy gap between the HOMO (that is localized on the H-cluster) and the LUMO (which is centered on the F'-cluster). Our results also indicate that the binding of the redox partners of DdH in proximity of its F'-cluster can trigger one-electron oxidation of the H-2-bound enzyme, a process that is expected to have an important role in H-2 activation. Our findings are analyzed not only from a mechanistic perspective, but also in consideration of the physiological role of DdH. In fact, this enzyme is known to be able to catalyze both the oxidation and the evolution of H-2, depending on the cellular metabolic requirements. Hints for the design of targeted mutations that could lead to the enhancement of the oxidizing properties of DdH are proposed and discussed

long to short term denudation rates in the southern apennines geomorphological markers and chronological constraints

Long- to short-term denudation rates in the southern Apennines: geomorphological markers and chronological constraints Age constraints of geomorphological markers and consequent estimates of long- to short-term denudation rates from southern Italy are given here. Geomorphic analysis of the valley of the Tanagro River combined with apatite fission track data and radiometric dating provided useful information on the ages and evolution of some significant morphotectonic markers such as regional planated landscapes, erosional land surfaces and fluvial terraces. Reconstruction of paleotopography and estimation of the eroded volumes were perfomed starting from the plano-altimetric distribution of several orders of erosional land surfaces surveyed in the study area. Additional data about denudation rates related to the recent and/or active geomorphological system have been obtained by estimating the amount of suspended sediment yield at the outlet of some catchments using empirical relationships based on the hierarchical arrangement of the drainage network. Denudation rates obtained through these methods have been compared with the sedimentation rates calculated for two adjacent basins (the Pantano di San Gregorio and the Vallo di Diano), on the basis of published tephrochronological constraints. These rates have also been compared with those calculated for the historical sediment accumulation in a small catchment located to the north of the study area, with long-term exhumation data from thermochronometry, and with uplift rates from the study area. Long- and short-term denudation rates are included between 0.1 and 0.2 mm/yr, in good agreement with regional data and long-term sedimentation rates from the Vallo di Diano and the Pantano di San Gregorio Magno basins. On the other hand, higher values of exhumation rates from thermochronometry suggest the existence of past erosional processes faster than the recent and present-day exogenic dismantling. Finally, the comparison between uplift and denudation rates indicates that the fluvial erosion did not match the tectonic uplift during the Quaternary in this sector of the chain. The axial zone of the southern Apennines should therefore be regarded as a landscape in conditions of geomorphological disequilibrium

Investigation of the Phenomenological and Psychopathological Features of Trichotillomania in an Italian Sample

Trichotillomania (TTM) is still a scarcely known and often inadequately treated disorder in Italian clinical settings, despite growing evidence about its severe and disabling consequences. The current study investigated the phenomenology of TTM in Italian individuals; in addition, we sought to examine patterns of self-esteem, anxiety, depression, and OCD-related symptoms in individuals with TTM compared to healthy participants. The current study represents the first attempt to investigate the phenomenological and psychopathological features of TTM in Italian hair pullers. One hundred and twenty-two individuals with TTM were enrolled: 24 were assessed face-to-face (face-to-face group) and 98 were recruited online (online group). An additional group of 22 face-to-face assessed healthy controls (HC group) was included in the study. The overall female to male ratio was 14:1, which is slightly higher favoring female than findings reported in literature. Main results revealed that a higher percentage of individuals in the online group reported pulling from the pubic region than did face-to-face participants; furthermore, the former engaged in examining the bulb and running the hair across the lips and reported pulling while lying in bed at higher frequencies than the latter. Interestingly, the online TTM group showed greater functional and psychological impairment, as well as more severe psychopathological characteristics (self-esteem, physiological and social anxiety, perfectionism, overestimation of threat, and control of thoughts), than the face-to-face one. Differences between the two TTM groups may be explained by the anonymity nature of the online group, which may have led to successful recruitment of more serious TTM cases, or fostered more open answers to questions. Overall, results revealed that many of the phenomenological features of Italian TTM participants matched those found in U.S. clinical settings, even though some notable differences were observed; therefore, cross-cultural invariance might represent a characteristic of OCD-related disorders

Mechanistic Analysis of Nucleophilic Substrates Oxidation by Functional Models of Vanadium-Dependent Haloperoxidases: A Density Functional Theory Study

Density functional theory has been used to investigate the structural, electronic, and reactivity properties of an established functional model for vanadium-dependent haloperoxidases, K[VO(O 2 )Hheida] (Hheida 2– = 2,2′-[(2-hydroxyethyl)imino]diacetate). Possible solution species were determined on the basis of potential exogenous donors present under the conditions necessary for reactivity. The energetically favored solution-state species is a 1:1 complex of Hheida and vanadium with a coordinated hydroxyethyl donor trans to the vanadium–oxido bond which is in agreement with the reported solid-state structure for K[VO(O 2 )Hheida]. Transition states of the oxidation reaction were located for four substrates: chloride, bromide, iodide, and dimethyl sulfide. The role of protonation and its effects on reactivity were examined for each substrate. Protonation of the peroxido moiety leads to a significant drop in the activation barrier for oxidation. In contrast no transition states could be located for an oxido-transfer process involving the oxido ligand. Barriers of activation calculated for halide oxidation were similar, providing support to the hypothesis that the p K a of the halide in acetonitrile is responsible for the decrease in reactivity between I – , Br – , and Cl – . The results presented herein provide a mechanistic correlation between a functional model and the enzyme, making K[VO(O 2 )Hheida] a “complete” functional model for vanadium-dependent haloperoxidase.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55972/1/515_ftp.pd