THERMODYNAMICS OF A BROWNIAN BRIDGE POLYMER MODEL IN A RANDOM ENVIRONMENT

We consider a directed random walk making either 0 or $+1$ moves and a Brownian bridge, independent of the walk, conditioned to arrive at point $b$ on time $T$. The Hamiltonian is defined as the sum of the square of increments of the bridge between the moments of jump of the random walk and interpreted as an energy function over the bridge connfiguration; the random walk acts as the random environment. This model provides a continuum version of a model with some relevance to protein conformation. The thermodynamic limit of the specific free energy is shown to exist and to be self-averaging, i.e. it is equal to a trivial --- explicitly computed --- random variable. An estimate of the asymptotic behaviour of the ground state energy is also obtained.Comment: 20 pages, uuencoded postscrip

Cerebellum in timing control: Evidence from contingent negative variation after cerebellar tDCS

Background and aims Timing control is defined as the ability to quantify time. The temporal estimation of supra-seconds range is generally seen as a conscious cognitive process, while the sub-seconds range is a more automatic cognitive process. It is accepted that cerebellum contributes to temporal processing, but its function is still debated. The aim of this research was to better explore the role of cerebellum in timing control. We transitorily inhibited cerebellar activity and studied the effects on CNV components in healthy subjects. Methods Sixteen healthy subjects underwent a S1-S2 duration discrimination motor task, prior and after cathodal and sham cerebellar tDCS, in two separate sessions. In S1-S2 task they had to judge whether the duration of a probe interval trial was shorter (Short-ISI-trial:800 ms), longer (long-ISI-trail:1600 ms), or equal to the Target interval of 1200 ms. For each interval trial for both tDCS sessions, we measured: total and W2-CNV areas, the RTs of correct responses and the absolute number of errors prior and after tDCS. Results After cathodal tDCS a significant reduction in total-CNV and W2-CNV amplitudes selectively emerged for Short (p < 0.001; p = 0.003 respectively) and Target-ISI-trial (total-CNV: p < 0.001; W2-CNV:p = 0.003); similarly, a significant higher number of errors emerged for Short (p = 0.004) and Target-ISI-trial (p = 0.07) alone. No differences were detected for Longer-ISI-trials and after sham stimulation. Conclusions These data indicate that cerebellar inhibition selectively altered the ability to make time estimations for second and sub-second intervals. We speculate that cerebellum regulates the attentional mechanisms of automatic timing control by making predictions of interval timing

Mental flexibility in Parkinson's disease with central fatigue: Data from the frontal assessment battery

Background and aims Central fatigue is defined as a reduced energy level or an increased perception of effort, often associated to a failure in initiating and maintaining tasks that require self-motivation. It is common in Parkinson's disease population and it has been hypothesized to be related to a dysfunction in the striato-talamo- prefrontal loop. The aim of the present study was to explore the association between fatigue and executive functions as index of integrity of the striato-thalamo-prefrontal loop. Methods Twenty-nine non-demented PD patients without fatigue - PDnF, 28 non-demented PD patients with fatigue - PDF and 26 age and sex- matched controls underwent an evaluation with the Frontal Assessment Battery (FAB), MMSE, PSQI, BDI, STAI Y1-2, PDQ-39. Differences between groups in FAB scores (total and subitems) were analyzed by means of Kruskal-Wallis test. Moreover, a correlation between fatigue and FAB was also analyzed. Results Overall parkinsonian population displayed worse performance than controls in frontal scores especially inhibitory control (p = 0.008) and sensitivity to interference (p = 0.014). PDF displayed significantly worse than PDnF in verbal fluency (p = 0.05). Fatigue severity inversely correlated with executive performance (p b 0.001). Conclusions Phonemic fluency tasks are thought to reflect the simultaneous engagement of several executive functions such as attention, working memory, retrieval, information processing. The association of central fatigue with a deficit in mental flexibility, could support the hypothesis that central fatigue is a reliable index of the impairment of higher executive functions needed in order to effectively assess costs and benefits related to adaptive decision- making behavior

Peptide Orientation Affects Selectivity in Ion-Exchange Chromatography

Here we demonstrate that separation of proteolytic peptides, having the same net charge and one basic residue, is affected by their specific orientation toward the stationary phase in ion-exchange chromatography. In electrostatic repulsion−hydrophilic interaction chromatography (ERLIC) with an anion-exchange material, the C-terminus of the peptides is, on average, oriented toward the stationary phase. In cation exchange, the average peptide orientation is the opposite. Data with synthetic peptides, serving as orientation probes, indicate that in tryptic/Lys-C peptides the C-terminal carboxyl group appears to be in a zwitterionic bond with the side chain of the C-terminal Lys/Arg residue. In effect, the side chain is then less basic than the N-terminus, accounting for the specific orientation of tryptic and Lys-C peptides. Analyses of larger sets of peptides, generated from lysates by either Lys-N, Lys-C, or trypsin, reveal that specific peptide orientation affects the ability of charged side chains, such as phosphate residues, to influence retention. Phosphorylated residues that are remote in the sequence from the binding site affect retention less than those that are closer. When a peptide contains multiple charged sites, then orientation is observed to be less rigid and retention tends to be governed by the peptide’s net charge rather than its sequence. These general observations could be of value in confirming a peptide’s identification and, in particular, phosphosite assignments in proteomics analyses. More generally, orientation accounts for the ability of chromatography to separate peptides of the same composition but different sequence

A systems approach to prion disease

Prions cause transmissible neurodegenerative diseases and replicate by conformational conversion of normal benign forms of prion protein (PrPC) to disease-causing PrPSc isoforms. A systems approach to disease postulates that disease arises from perturbation of biological networks in the relevant organ. We tracked global gene expression in the brains of eight distinct mouse strain–prion strain combinations throughout the progression of the disease to capture the effects of prion strain, host genetics, and PrP concentration on disease incubation time. Subtractive analyses exploiting various aspects of prion biology and infection identified a core of 333 differentially expressed genes (DEGs) that appeared central to prion disease. DEGs were mapped into functional pathways and networks reflecting defined neuropathological events and PrPSc replication and accumulation, enabling the identification of novel modules and modules that may be involved in genetic effects on incubation time and in prion strain specificity. Our systems analysis provides a comprehensive basis for developing models for prion replication and disease, and suggests some possible therapeutic approaches

Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation

Using sample-matched transcriptomics and proteomics measurements it is now possible to begin to understand the impact of post-transcriptional regulatory programs in Enterobacteria. In bacteria post-transcriptional regulation is mediated by relatively few identified RNA-binding protein factors including CsrA, Hfq and SmpB. A mutation in any one of these three genes, csrA, hfq, and smpB, in Salmonella is attenuated for mouse virulence and unable to survive in macrophages. CsrA has a clearly defined specificity based on binding to a specific mRNA sequence to inhibit translation. However, the proteins regulated by Hfq and SmpB are not as clearly defined. Previous work identified proteins regulated by hfq using purification of the RNA-protein complex with direct sequencing of the bound RNAs and found binding to a surprisingly large number of transcripts. In this report we have used global proteomics to directly identify proteins regulated by Hfq or SmpB by comparing protein abundance in the parent and isogenic hfq or smpB mutant. From these same samples we also prepared RNA for microarray analysis to determine if alteration of protein expression was mediated post-transcriptionally. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression. These proteins represent a broad spectrum of Salmonella proteins required for many biological processes including host cell invasion, motility, central metabolism, LPS biosynthesis, two-component regulatory systems, and fatty acid metabolism. Our results represent one of the first global analyses of post-transcriptional regulons in any organism and suggest that regulation at the translational level is widespread and plays an important role in virulence regulation and environmental adaptation for Salmonella

d- and l-amino acids in Antarctic lakes: assessment of a very sensitive HPLC-MS method

Amino acids represent a fraction of organic matter in marine and freshwater ecosystems, and a source of carbon, nitrogen and energy. l-Amino acids are the most common enantiomers in nature because these chiral forms are used during the biosynthesis of proteins and peptide. To the contrary, the occurrence of d-amino acids is usually linked to the presence of bacteria. We investigated the distribution of l- and d-amino acids in the lacustrine environment of Terra Nova Bay, Antarctica, in order to define their natural composition in this area and to individuate a possible relationship with primary production. A simultaneous chromatographic separation of 40 l- and d-amino acids was performed using a chiral stationary phase based on teicoplainin aglycone (chirobiotic tag). The chromatographic separation was coupled to two different mass spectrometers-an LTQ-Orbitrap XL (Thermo Fisher Scientific) and an API 4000 (ABSciex)-in order to investigate their quantitative performance. High-performance liquid chromatography coupled with mass spectrometry methods were evaluated through the estimation of their linear ranges, repeatability, accuracy and detection and quantification limits. The high-resolution mass spectrometer LTQ-Orbitrap XL presented detection limits between 0.4 and 7 mu g l (-1), while the triple quadrupole mass spectrometer API 4000 achieved the best detection limits reported in the literature for the quantification of amino acids (between 4 and 200 ng l (-1)). The most sensitive method, HPLC-API 4000, was applied to lake water samples

Phonon distributions of a single bath mode coupled to a quantum dot

The properties of an unconventional, single mode phonon bath coupled to a quantum dot, are investigated within the rotating wave approximation. The electron current through the dot induces an out of equilibrium bath, with a phonon distribution qualitatively different from the thermal one. In selected transport regimes, such a distribution is characterized by a peculiar selective population of few phonon modes and can exhibit a sub-Poissonian behavior. It is shown that such a sub-Poissonian behavior is favored by a double occupancy of the dot. The crossover from a unequilibrated to a conventional thermal bath is explored, and the limitations of the rotating wave approximation are discussed.Comment: 21 Pages, 7 figures, to appear in New Journal of Physics - Focus on Quantum Dissipation in Unconventional Environment

LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

<p>Abstract</p> <p>Background</p> <p>Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, highly complex and noisy. Accordingly, it has sparked new developments in Bioinformatics, especially in the fields of algorithm development, statistics and software engineering. In a quantitative label-free mass spectrometry experiment, crucial steps are the detection of peptide features in the mass spectra and the alignment of samples by correcting for shifts in retention time. At the moment, it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists only for peptide identification algorithms but no data that represents a ground truth for the evaluation of feature detection, alignment and filtering algorithms.</p> <p>Results</p> <p>We present <it>LC-MSsim</it>, a simulation software for LC-ESI-MS experiments. It simulates ESI spectra on the MS level. It reads a list of proteins from a FASTA file and digests the protein mixture using a user-defined enzyme. The software creates an LC-MS data set using a predictor for the retention time of the peptides and a model for peak shapes and elution profiles of the mass spectral peaks. Our software also offers the possibility to add contaminants, to change the background noise level and includes a model for the detectability of peptides in mass spectra. After the simulation, <it>LC-MSsim </it>writes the simulated data to mzData, a public XML format. The software also stores the positions (monoisotopic m/z and retention time) and ion counts of the simulated ions in separate files.</p> <p>Conclusion</p> <p><it>LC-MSsim </it>generates simulated LC-MS data sets and incorporates models for peak shapes and contaminations. Algorithm developers can match the results of feature detection and alignment algorithms against the simulated ion lists and meaningful error rates can be computed. We anticipate that <it>LC-MSsim </it>will be useful to the wider community to perform benchmark studies and comparisons between computational tools.</p