Effect of uniaxial strain on plasmon excitations in graphene

Uniaxial strain is known to modify significantly the electronic properties of graphene, a carbon single layer of atomic width. Here, we study the effect of applied strain on the composite excitations arising from the coupling of charge carriers and plasmons in graphene, i.e. the plasmarons. Specifically, we predict that the plasmaron energy dispersion, which has been recently observed experimentally in unstrained graphene, is shifted and broadened by applied uniaxial strain. Thus, strain constitutes an additional parameter which may be useful to tune graphene properties in plasmaronic devices.Comment: Invited oral lecture at the 23rd AIRAPT International Conference on "High Pressure Science and Technology", Mumbai (India), September 25-30, 2011. To be published in J. Phys.: Conf. Series (2012

The regions of the sequence most exposed to the solvent within the amyloidogenic state of a protein initiate the aggregation process.

Formation of misfolded aggregates is an essential part of what proteins can do. The process of protein aggregation is central to many human diseases and any aggregating event needs to be prevented within a cell and in protein design. In order to aggregate, a protein needs to unfold its native state, at least partially. The conformational state that is prone to aggregate is difficult to study, due to its aggregating potential and heterogeneous nature. Here, we use a systematic approach of limited proteolysis, in combination with electrospray ionisation mass spectrometry, to investigate the regions that are most flexible and solvent-exposed within the native, ligand-bound and amyloidogenic states of muscle acylphosphatase (AcP), a protein previously shown to form amyloid fibrils in the presence of trifluoroethanol. Seven proteases with different degrees of specificity have been used for this purpose. Following exposure to the aggregating conditions, a number of sites along the sequence of AcP become susceptible to proteolytic digestion. The pattern of proteolytic cleavages obtained under these conditions is considerably different from that of the native and ligand-bound conformations and includes a portion within the N-terminal tail of the protein (residues 6-7), the region of the sequence 18-23 and the position 94 near the C terminus. There is a significant overlap between the regions of the sequence found to be solvent-exposed from the present study and those previously identified to be critical in the rate-determining steps of aggregation from protein engineering approaches. This indicates that a considerable degree of solvent exposure is a feature of the portions of a protein that initiate the process of aggregation

CoCoNet—boosting RNA contact prediction by convolutional neural networks

Co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict accurate protein contact or distance maps. Such information can be used as constraints in structure prediction and massively increase prediction accuracy. Unfortunately, the same ML methods cannot readily be applied to RNA as they rely on large structural datasets only available for proteins. Here, we demonstrate how the available smaller data for RNA can be used to improve prediction of RNA contact maps. We introduce an algorithm called CoCoNet that is based on a combination of a Coevolutionary model and a shallow Convolutional Neural Network. Despite its simplicity and the small number of trained parameters, the method boosts the positive predictive value (PPV) of predicted contacts by about 70% with respect to DCA as tested by cross-validation of about eighty RNA structures. However, the direct inclusion of the CoCoNet contacts in 3D modeling tools does not result in a proportional increase of the 3D RNA structure prediction accuracy. Therefore, we suggest that the field develops, in addition to contact PPV, metrics which estimate the expected impact for 3D structure modeling tools better. CoCoNet is freely available and can be found at https://github.com/KIT-MBS/coconet

Analyses chimiques des eaux du fleuve Niger à Niamey : premiers résultats d'une campagne annuelle de mesures

Nous avons déterminé, d'août 1984 à février 1986, les concentrations des silicates, chlorures, nitrites, phosphates, potassium, sodium, calcium, magnésium, ammonium et fer ferrique ainsi que le pH, la conductivité, la turbidité, l'oxygène dissous, l'alcalinité et la D.B.O. dans l'eau du fleuve Niger à hauteur de la ville de Niamey. L'exploitation statistique de ces résultats fait apparaître l'existence de deux périodes stables et d'une période instable au cours de l'année. (Résumé d'auteur

Indole-3-acetic acid regulates the central metabolic pathways in Escherichia coli.

The physiological changes induced by indoleacetic acid (IAA) treatment were investigated in the totally sequenced Escherichia coli K-12 MG1655. DNA macroarrays were used to measure the mRNA levels for all the 4290 E. coli protein-coding genes; 50 genes (1-1 %) exhibited significantly different expression profiles. In particular, genes involved in the tricarboxylic acid cycle, the glyoxylate shunt and amino acid biosynthesis (leucine, isoleucine, valine and proline) were up-regulated, whereas the fermentative adhE gene was down-regulated. To confirm the indications obtained from the macroarray analysis the activity of 34 enzymes involved in central metabolism was measured; this showed an activation of the tricarboxylic acid cycle and the glyoxylate shunt. The malic enzyme, involved in the production of pyruvate, and pyruvate dehydrogenase, required for the channelling of pyruvate into acetyl-CoA, were also induced in IAA-treated cells. Moreover, it was shown that the enhanced production of acetyl-CoA and the decrease of NADH/NAD+ ratio are connected with the molecular process of the IAA response. The results demonstrate that IAA treatment is a stimulus capable of inducing changes in gene expression, enzyme activity and metabolite level involved in central metabolic pathways in E. col

Four conjectures in Nonlinear Analysis

In this chapter, I formulate four challenging conjectures in Nonlinear Analysis. More precisely: a conjecture on the Monge-Amp\`ere equation; a conjecture on an eigenvalue problem; a conjecture on a non-local problem; a conjecture on disconnectedness versus infinitely many solutions.Comment: arXiv admin note: text overlap with arXiv:1504.01010, arXiv:1409.5919, arXiv:1612.0819

A Novel Approach for an Integrated Straw tube-Microstrip Detector

We report on a novel concept of silicon microstrips and straw tubes detector, where integration is accomplished by a straw module with straws not subjected to mechanical tension in a Rohacell $^{\circledR}$ lattice and carbon fiber reinforced plastic shell. Results on mechanical and test beam performances are reported on as well.Comment: Accepted by Transactions on Nuclear Science (2005). 11 pages, 9 figures, uses lnfprep.st

The modulation of sirtuins and apoptotic proteins in rats after exhaustive exercise

A large body of evidence shows that a single bout of strenuous exercise induces oxidative stress in circu- lating human lymphocytes leading to lipid peroxide- tion, DNA damage, mitochondrial perturbations, and protein oxidation. In a training experiment, Wistar rats were divided into control group (CG) and exer- cise group (EG). After a running level exercise until exhaustion, we observed an increase in the mRNA content and protein expression of SIRT1 and SIRT7 in the EG compared to the CG. Moreover, such train- ing exercise did not change mRNA transcripts and protein expression of FOXO3A and GADD45. We also observed an increase of pro-apoptotic protein bax and a decrease of the anti-apoptotic protein bcl-2 in the EG. Accordingly, we observed a caspase-3 activation and poly (ADP-ribose) polymerase (PARP) cleavage only in EG rats. Statistical analysis of the data showed a significant correlation between SIRT1 and SIRT7 expression and apoptotic proteins such as bax, bcl-2 in both tissues. We conclude that, in both muscle, such exercise activates both a damaging apoptotic mecha- nism with bax increase and bcl-2 decrease and a counterbalancing protective mechanism with SIRT1 and SIRT7 increase