Search results for "Reference"

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

2013

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this …

Optimised lyophilisation-based method for different biomolecule single-extractions from the same rat brain sample: Suitability for RNA and protein ex…

2019

Abstract Background Optimisation of tissue processing procedures in preclinical studies reduces the number of animals used and allows integrated multilevel study in the same sample. Multiple extraction of different biomolecules from the same sample has several limitations. New method Using brain samples from rats subjected to ischemic stroke, we combined lyophilisation of flash-frozen tissue, mechanical pulverisation and cryopreservation in a method to optimise tissue handling and preservation for independent RNA or protein single-extract methods, and subsequent RT-qPCR or Western blot analyses. Results Lyophilisation resulted in 70% tissue weight loss. RNA (OD260/280∼1.8) and protein yield…

Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative

2017

The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the iden…

Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina.

2010

A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially and constitutively expressed protein isoforms, which were associated to 203 ORFs in the A. balhimycina genome. These data, providing insights on the major metabolic pathways/molecular processes operating in this organism, were used to compile 2-DE reference maps covering 3-10, 4-7 and 4.5-5.5 pH gradients available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-prot…

Expanding the protein catalogue in the proteome reference map of human breast cancer cells

2006

In this report we present a catalogue of 162 proteins (including isoforms and variants) identified in a prototype of proteomic map of breast cancer cells. This work represents the prosecution of previous studies describing the protein complement of breast cancer cells of the line 8701-BC, which has been well characterized for several parameters, providing to be a useful model for the study of breast cancer-associated candidate biomarkers. In particular, 110 spots were identified ex novo by PMF, or validated following previous gel matching identification method; 30 were identified by N-terminal microsequencing and the remaining by gel matching with maps available from our former work. As a c…

Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

2022

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Spatial Frames of Reference in Old Latin

This paper investigates the spatial Frames of Reference (FoRs) in Old Latin within the framework of Cognitive Linguistics (cf. Talmy 1983; Levinson 2003; Levinson & Wilkins 2006). Differently from modern Indo-European languages, which are heavily based on the so-called relative or egocentric FoR, ancient Indo-European languages such as Vedic and Homeric Greek did not make use of such an egocentric orientation system at their earliest stage, since the relation between FIGURE and GROUND was not specified by imposing an external deictic observer’s viewpoint (cf. Bartolotta 2018; 2021). The historical-comparative analysis of the most ancient literary texts in the Indo-European tradition giv…

From vertical to horizontal architecture

2006

Some of the main challenges related to wireless sensor networks implementation are low-quality communication, energy conservation, resource-constrained computation, distributed network management, data processing and the scalability of the protocols. This combination makes the implementation of software a demanding task and encourages to new approaches when thinking of software architecture.In this paper an architecture combining a low protocol stack with a cross-layer management entity is presented. One of the main ideas behind the architecture presented is to make application programming easier and to simplify the protocol stack in such a way that it would suit better for the limited reso…

A Constructive Arboricity Approximation Scheme

2020

The arboricity \(\varGamma \) of a graph is the minimum number of forests its edge set can be partitioned into. Previous approximation schemes were nonconstructive, i.e., they approximate the arboricity as a value without computing a corresponding forest partition. This is because they operate on pseudoforest partitions or the dual problem of finding dense subgraphs.

Treatment of flying phobia using virtual reality exposure with or without cognitive restructuring: Participant's preferences

2015

This study analyses participants’ preferences regarding two exposure treatment modali- ties for Fear of Flying (FF): virtual reality exposure treatment (VRET) by itself or VRET plus cognitive restructuring (VRET+CR). An alternating treatment conditions design was established and a non-concurrent multiple baseline design across individuals (four participants) was used. Both conditions were equally effective and after the treatment all the participants took a flight. At the end of each session the participants were asked for their opinion on the condition they received. High mean scores were obtained in both conditions; non-significant differences between the two condi- tions were found. When…