Prediction of peptide and protein propensity for amyloid formation

Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔGº values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation

The population genomics of begomoviruses: global scale population structure and gene flow

<p>Abstract</p> <p>Background</p> <p>The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, <it>Begomovirus</it>, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people.</p> <p>Results</p> <p>We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations.</p> <p>Conclusions</p> <p>Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global <it>Begomovirus </it>population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity.</p

Bedside Sublingual Video Imaging of Microcirculation in Assessing Bacterial Infection in Cirrhosis

Bacterial infections are common in cirrhosis and can lead to life-threatening complications. Sidestream dark-field (SDF) imaging has recently emerged as a noninvasive tool for capturing real-time video images of sublingual microcirculation in critically ill patients with sepsis. The objective of this study was to assess the utility of SDF in determining underlying infection in patients with cirrhosis. Sublingual microcirculation was compared among patients with compensated cirrhosis (Group A, n = 13), cirrhosis without sepsis (Group B, n = 18), cirrhosis with sepsis (Group C, n = 14), and sepsis only (Group D, n = 10). The blood flow was semi-quantitatively evaluated in four equal quadrants in small (10–25 mm); medium (26–50 mm); and large (51–100 mm) sublingual capillaries. The blood flow was described as no flow (0), intermittent flow (1), sluggish flow (2), and continuous flow (3). The overall flow score or microvascular flow index (MFI) was measured for quantitative assessment of microcirculation and predicting power for concurrent infection in cirrhosis. Marked impairment was observed at all levels of microvasculature in Groups B and C when compared with Group A. This effect was restricted to small vessels only when Group B was compared with Group C. MFI < 1.5 was found to have highest sensitivity (100%) and specificity (100%) for infection in decompensated cirrhosis. SDF imaging of sublingual microcirculation can be a useful bedside diagnostic tool to assess bacterial infection in cirrhosis

The preparation of N-acetyl-Co(III)-microperoxidase-8 (NAcCoMP8) and its ligand substitution reactions: A comparison with aquacobalamin (vitamin B12a).

International audienceThe synthesis of the Co(III) porphyrin octapeptide N-acetyl-Co(III) microperoxidase-8 (NAcCoMP8) is described. NAcCoMP8 provides a means of comparing and contrasting the chemistry of Co(III) porphyrins and corrins to assess the influence of the macrocycle. Log K values, and ΔH and ΔS, for the coordination of anionic (CN(-), N3(-), NO2(-), HSO3(-)) and neutral (pyridine, N-methylimidazole, methoxylamine and hydroxylamine) ligands by aquacobalamin (H2OCbl(+)) and NAcCoMP8 are reported. Anions bind more strongly to H2OCbl(+) than to NAcCoMP8 while the converse is true for the neutral ligands. Density Functional Theory (DFT) calculations and QTAIM analyses suggest the bonding between Co(III) and these ligands is predominantly ionic although anionic ligands induce a significant covalency, the extent of which is important for the stability of the complex. The CoL bond length (L=an anion) in a Co(III) corrin, while longer than in a Co(III) porphyrin, is shorter than might be expected as assessed from CoL bond lengths when L=neutral ligand. It is likely that this stems from coulombic interaction between L and the residual charge at the metal center (2+ in corrin; 1+ in porphyrin). Co(III) in H2OCbl(+) is more labile towards substitution by CN(-) than NAcCoMP8 but the converse is true when the entering ligand is neutral N-methylimidazole. The extent of participation of the incoming ligand in the transition state of the reaction is controlled by the log K value so the nature of the incoming ligand determines in which of these two macrocyclic systems Co(III) is the more labile

Effect of smoking on the gingival capillary density: assessment of gingival capillary density with orthogonal polarization spectral imaging

Microvascular changes because of smoking are frequently presumed in models because of the negative effect of smoking portrayed on the microcirculation. We hypothesized that cigarette smoke might lead to a decrease in gingival capillary density. Capillary density was assessed with orthogonal polarization spectral (OPS) imaging, a technique using special optics by which a virtual light source is created at a depth of 1 mm within the mucosa. The light is absorbed by haemoglobin, resulting in an image of the capillaries in negative contrast. The gingival capillary density was measured in 20 healthy male dental students with a mean age of 25. Ten of the students were smokers and 10 were non-smokers. In each subject six images of the right maxillary pre-molar region were obtained, and the mean gingival capillary density was determined through the use of K&K software technology. The mean capillary density in smokers was 69.3 +/- 8.9 capillaries per visual field compared with a mean capillary density in non-smokers of 60.6 +/- 5.4 (p=0.33). No significant differences were found between the gingival capillary density of smokers and non-smoker

Direct in vivo assessment of microcirculatory dysfunction in severe falciparum malaria.

BACKGROUND: This study sought to describe and quantify microcirculatory changes in the mucosal surfaces of patients with severe malaria, by direct in vivo observation using orthogonal polarization spectral (OPS) imaging. METHODS: The microcirculation in the rectal mucosa of adult patients with severe malaria was assessed by use of OPS imaging, at admission and then daily. Comparison groups comprised patients with uncomplicated falciparum malaria, patients with bacterial sepsis, and healthy individuals. RESULTS: Erythrocyte velocities were measured directly in 43 adult patients with severe falciparum malaria, of whom 20 died. Microcirculatory blood flow was markedly disturbed, with heterogeneous obstruction that was proportional to severity of disease. Blocked capillaries were found in 29 patients (67%) and were associated with concurrent hyperdynamic blood flow (erythrocyte velocity, &gt;750 mm/s) in adjacent vessels in 27 patients (93%). The proportion of blocked capillaries correlated with the base deficit in plasma and with the concentration of lactate. Abnormalities disappeared when the patients recovered. In healthy individuals and in patients with uncomplicated malaria or sepsis, no stagnant erythrocytes were detected, and, in patients with sepsis, hyperdynamic blood flow was prominent. CONCLUSION: Patients with severe falciparum malaria show extensive microvascular obstruction that is proportional to the severity of the disease. This finding underscores the prominent role that microvascular obstruction plays in the pathophysiology of severe malaria and illustrates the fundamental difference between the microvascular pathophysiology of malaria and that of bacterial sepsis