Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay

The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation. Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to environmental conditions. We developed a computational technique based on stochastic modeling, to infer condition-specific individual mRNA half-lives directly from gene expression time-courses. Predictions from our method were validated by experimentally measured mRNA decay rates during the intraerythrocytic developmental cycle of Plasmodium falciparum. We then applied our methodology to publicly available data on the reproductive and metabolic cycle of budding yeast. Strikingly, our analysis revealed, in all cases, the presence of periodic changes in decay rates of sequentially induced genes and co-ordination strategies between transcription and degradation, thus suggesting a general principle for the proper coordination of transcription and degradation machinery in response to internal and/or external stimuli. Citation: Cacace F, Paci P, Cusimano V, Germani A, Farina L (2012) Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay. PLoS Comput Biol 8(11): e1002772. doi:10.1371/journal.pcbi.100277

Weak Corrections are Relevant for Dark Matter Indirect Detection

The computation of the energy spectra of Standard Model particles originated from the annihilation/decay of dark matter particles is of primary importance in indirect searches of dark matter. We compute how the inclusion of electroweak corrections significantly alter such spectra when the mass M of dark matter particles is larger than the electroweak scale: soft electroweak gauge bosons are copiously radiated opening new channels in the final states which otherwise would be forbidden if such corrections are neglected. All stable particles are therefore present in the final spectrum, independently of the primary channel of dark matter annihilation/decay. Such corrections are model independent.Comment: 38 pages (half are technical appendices), 7 figure

The state observer as a tool for the estimation of gene expression

n/

Maximal rank of space curves in the range A

We prove the following statement, which has been conjecturedsince 1985:There exists a constant K such that for all natural numbers d, g with g≤Kd^(3/2) there exists an irreducible component of the Hilbert schemeof P3 whose general element is a smooth, connected curve of degree d and genus g, of maximal rank

Distributed kalman filtering over sensor networks with unknown random link failures

In this letter we consider the distributed consensus-based filtering problem for linear time-invariant systems over sensor networks subject to random link failures when the failure sequence is not known at the receiving side. We assume that the information exchanged, traveling along the channel, is corrupted by a noise and hence, it is no more possible to discriminate with certainty if a link failure has occurred. Therefore, in order to process the only significant information, we endow each sensor with detectors which decide on the presence of link failures. At each sensor the proposed approach consists of three steps: 1) failure detection; 2) local data aggregation; and 3) Kalman consensus filtering. Numerical examples show the effectiveness of this method

A dendrochronological analysis of Pinus pinea L. on the Italian mid-Tyrrhenian coast

In order to assess the response of the radial growth of Pinus pinea L. to climatic variability in Central Italy, dendrochronological and dendroclimatological analyses were carried out on five different populations scattered along the Tyrrhenian coasts of the peninsula. The aim of this study is to contribute to the understanding of the ecological demands of this species, particularly in the study area. For each site total ring, early-, and late-wood width chronologies were developed. Multidimensional analyses were performed for the three tree-ring datasets in order to analyze the relations between sites chronologies. Both Principal Component Analyses and hierarchical classifications highlighted an important difference of one site in respect to the other, probably due to site characteristics. Correlation functions were performed to infer the main climatic factors controlling the radial growth of the species. For a comparative study, we limited our attention to the common interval 1926-2003 (78 years) in which the response of the tree-ring chronologies to climate at both local and regional scale was investigated. Positive moisture balance in the late spring-summer period of the year of growth is the climatic driver of P. pinea radial growth in the study area. Moreover, this study shows how low summer temperatures strongly favor the radial growth of the species.Fil: Piraino, Sergio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza. Instituto Argentino de Investigaciones de Zonas Aridas; ArgentinaFil: Camiz, Sergio. Universita degli studi di Roma "Sapienza". Dipartimento di Matematica; ItaliaFil: Di Filippo, Alfredo. Universita Degli Studi Della Tuscia. DendrologyLab; ItaliaFil: Piovesan, Gianluca. Universita Degli Studi Della Tuscia. DendrologyLab; ItaliaFil: Spada, Francesco. Universita degli studi di Roma "Sapienza". Dipartimento de biología ambientale; Itali

Tapias Score for Predicting Recurrences in Resected Solitary Fibrous Tumor of the Pleura

n/

State-of-the-art on steel exoskeletons for seismic retrofit of existing RC buildings

Since ‘80s the use of external additive structures, commonly called exoskeletons, is considered one of the possible alternatives for seismic retrofit of existing r.c. structures with low dissipative capacity. The first Japanese and American codes dealing with structural rehabilitation issues, as well as many applications on the use of steel devices at the international level, are testimony of this trend, especially in high seismic hazard areas. Nowadays, the use of this intervention strategy has become of great actuality, not only because it can be implemented in a safe way without interrupting the building use, but also because it can be effectively adopted, in cases of restructuring operations with lateral addition, for the integrated (formal, energetic and functional) retrofit of the entire construction. In the present work, after a thorough state-of-the art of the main researches and applications on steel exoskeletons, their typological classification into families and the definition of the key project parameters, indispensable to both properly conceive and design such systems, have been performed