The earliest known Italian case of bilateral non-osseous calcaneonavicular coalition from the mediaeval cemetery of Troina (Enna, Sicily)

In this article, we detail a case of tarsal coalition in the osteological remains of an adult female individual from the mediaeval cemetery of the Catena district of Troina (Enna, Sicily). The burial that contains the skeleton described in this work (Burial 2) was subjected to a multidisciplinary analysis starting from the excavation on the field and ending with a full palaeopathological study including palaeoradiology and 3D virtual reconstructions. The obtained results contribute to our understanding of this congenital condition in the past and represent, to the best of our knowledge, the first case ever reported from Sicily and the Italian peninsula of bilateral non-osseous calcaneonavicular tarsal coalition

Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We present a new technique for characterizing the kinetics of loop formation in vitro, as observed using the tethered particle method, and apply it to experimental data on looping induced by lambda repressor. Our method uses a modified (diffusive) hidden Markov analysis that directly incorporates the Brownian motion of the observed tethered bead. We compare looping lifetimes found with our method (which we find are consistent over a range of sampling frequencies) to those obtained via the traditional threshold-crossing analysis (which can vary depending on how the raw data are filtered in the time domain). Our method does not involve any time filtering and can detect sudden changes in looping behavior. For example, we show how our method can identify transitions between long-lived, kinetically distinct states that would otherwise be difficult to discern

Calibration of Tethered Particle Motion Experiments

The Tethered Particle Motion (TPM) method has been used to observe and characterize a variety of protein-DNA interactions including DNA loping and transcription. TPM experiments exploit the Brownian motion of a DNA-tethered bead to probe biologically relevant conformational changes of the tether. In these experiments, a change in the extent of the bead’s random motion is used as a reporter of the underlying macromolecular dynamics and is often deemed sufficient for TPM analysis. However, a complete understanding of how the motion depends on the physical properties of the tethered particle complex would permit more quantitative and accurate evaluation of TPM data. For instance, such understanding can help extract details about a looped complex geometry (or multiple coexisting geometries) from TPM data. To better characterize the measurement capabilities of TPM experiments involving DNA tethers, we have carried out a detailed calibration of TPM magnitude as a function of DNA length and particle size. We also explore how experimental parameters such as acquisition time and exposure time affect the apparent motion of the tethered particle. We vary the DNA length from 200 bp to 2.6 kbp and consider particle diameters of 200, 490 and 970 nm. We also present a systematic comparison between measured particle excursions and theoretical expectations, which helps clarify both the experiments and models of DNA conformation

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067

Effect of promoter architecture on the cell-to-cell variability in gene expression

According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effort that addresses the question of how changes in promoter architecture affect noise in gene expression in a systematic rather than case-by-case fashion. In this article, we make such a systematic investigation, based on a simple microscopic model of gene regulation that incorporates stochastic effects. In particular, we show how operator strength and operator multiplicity affect this variability. We examine different modes of transcription factor binding to complex promoters (cooperative, independent, simultaneous) and how each of these affects the level of variability in transcription product from cell-to-cell. We propose that direct comparison between in vivo single-cell experiments and theoretical predictions for the moments of the probability distribution of mRNA number per cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte

Lac repressor mediated DNA looping: Monte Carlo simulation of constrained DNA molecules complemented with current experimental results

Tethered particle motion (TPM) experiments can be used to detect time-resolved loop formation in a single DNA molecule by measuring changes in the length of a DNA tether. Interpretation of such experiments is greatly aided by computer simulations of DNA looping which allow one to analyze the structure of the looped DNA and estimate DNA-protein binding constants specific for the loop formation process. We here present a new Monte Carlo scheme for accurate simulation of DNA configurations subject to geometric constraints and apply this method to Lac repressor mediated DNA looping, comparing the simulation results with new experimental data obtained by the TPM technique. Our simulations, taking into account the details of attachment of DNA ends and fluctuations of the looped subsegment of the DNA, reveal the origin of the double-peaked distribution of RMS values observed by TPM experiments by showing that the average RMS value for anti-parallel loop types is smaller than that of parallel loop types. The simulations also reveal that the looping probabilities for the anti-parallel loop types are significantly higher than those of the parallel loop types, even for loops of length 600 and 900 base pairs, and that the correct proportion between the heights of the peaks in the distribution can only be attained when loops with flexible Lac repressor conformation are taken into account. Comparison of the in silico and in vitro results yields estimates for the dissociation constants characterizing the binding affinity between O1 and Oid DNA operators and the dimeric arms of the Lac repressor. © 2014 Biton et al

Il commercio ambulante degli immigrati in spiaggia a Rimini: una ricerca su "economie etniche" e processi migratori

L'articolo, esito di una procedura di peer review della rivista Mondi migranti (rivista di fascia A nei settori scientifici 14/C1-C2-D1) \ue8 il prodotto di una ricerca commissionata dal Comune di Rimini. L'impostazione del saggio ruota attorno al problema di quali approcci, quali modelli euristici ed esplicativi, siano pi\uf9 idenei a cogliere la complessit\ue0 di un fenomeno locale/globale di irregolarit\ue0 - nel lavoro e nel soggiorno - quale il commercio ambulante. Ci si concentra sull'asse formalit\ue0/informalit\ue0 delle attivit\ue0 economiche introducendo come categoria centrale la nozione di "economia etnica", confrontando le sue caratteristiche con quelle relative ad attivit\ue0 economiche che non sono definite etniche. In secondo luogo, \ue8 stata anteposta alle consuete ripartizioni per nazionalit\ue0 o gruppi di nazionalit\ue0, o per propensione socio-culturale o religiosa, la considerazione dei molteplici percorsi migratori interni nei paesi di origine, e poi da tali paesi a quelli di immigrazione, fino alle singole destinazioni di approdo, pi\uf9 o meno temporanee o definitive. L'ipotesi che ha sostenuto questo lavoro \ue8 che l'interazione con la domanda di lavoro o con attivit\ue0 economiche pi\uf9 o meno formalizzate nei contesti di destinazione, e la molteplicit\ue0 delle dinamiche che si innestano nei paesi di approdo, contino nel co-determinare gli esiti dei processi migratori almeno quanto contino le caratteristiche dei contesti di partenza. Sulla base di questi presupposti \ue8 stata svolta un'indagine empirica sull'importante e massiccio fenomeno del commercio ambulante degli immigrati in spiaggia a Rimini, che pur rappresentando un fenomeno locale, ha al suo interno caratteristiche che lo inquadrano nelle dinamiche dei processi migratori che stanno attraversando le societ\ue0 contemporanee

Enhanced Compensation for Voltage Regulators Based on Three-Stage CMOS Operational Amplifiers for Large Capacitive Loads

This work presents a compensation technique for a three-stage operational amplifier that is derived from nested Miller compensation and comprises a voltage gain stage in the inner compensation path. The voltage gain k of this stage is able to both increase the Miller effect across the inner compensation capacitor and reduce the high-frequency impedance of the output node when compared to the case of standard nested Miller compensation. As a consequence, the gain-bandwidth product is k times higher, while the inner and the outer compensation capacitors are reduced by a factor k 2 and k, respectively. The proposed compensation technique was applied to a three-stage operational amplifier used to implement a voltage regulator: simulations of the regulator showed a significant improvement of slew rate, settling time, and transient output voltage drop when a load current is suddenly requested