Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation

The synaptic vesicle protein synaptobrevin engages with syntaxin and SNAP-25 to form the SNARE complex, which drives membrane fusion in neuronal exocytosis. In the SNARE complex, the SNARE motif of synaptobrevin forms a 55-residue helix, but it has been assumed to be mostly unstructured in its prefusion form. NMR data for full-length synaptobrevin in dodecylphosphocholine micelles reveals two transient helical segments flanked by natively disordered regions and a third more stable helix. Transient helix I comprises the most N-terminal part of the SNARE motif, transient helix II extends the SNARE motif into the juxtamembrane region, and the more stable helix III is the transmembrane domain. These helices may have important consequences for SNARE complex folding and fusion: helix I likely forms a nucleation site, the C-terminal disordered SNARE motif may act as a folding arrest signal, and helix II likely couples SNARE complex folding and fusion.     

Treatment of pyoderma gangrenosum with granulocyte and monocyte adsorption apheresis

Pyoderma gangrenosum is an intractable skin disorder characterized by the development of erythematous pustules or nodules that rapidly progress to destructive, necrotizing, non-infective ulcers. We assessed the efficacy of granulocyte and monocyte adsorption apheresis (GCAP) therapy in two new patients, a 67-year-old man with ulcerations on his lower leg, and a 44-year-old man with turgid erythematous lesions with burrowing abscesses and sinus formation on his hip, groin, and thighs. Both patients received 10 GCAP treatments at 5-day intervals. Their skin lesions responded well. The 9 cmx6 cm ulcer on the lower right leg of the 67-year-old patient was completely covered by regenerated skin at the completion of therapy. The turgid skin lesions containing pustules and ulcers of the other patient showed amelioration and a marked decrease in the volume of exudate. Our results suggest that GCAP is a useful treatment modality for pyoderma gangrenosum.     

Deformation strain is the main physical driver for skeletal precursors to undergo osteogenesis in earlier stages of osteogenic cell maturation

Mesenchymal stem cells play a major role during bone remodelling and are thus of high interest for tissue engineering and regenerative medicine applications. Mechanical stimuli, that is, deformation strain and interstitial fluid‐flow‐induced shear stress, promote osteogenic lineage commitment. However, the predominant physical stimulus that drives early osteogenic cell maturation is not clearly identified. The evaluation of each stimulus is challenging, as deformation and fluid‐flow‐induced shear stress interdepend. In this study, we developed a bioreactor that was used to culture mesenchymal stem cells harbouring a strain‐responsive AP‐1 luciferase reporter construct, on porous scaffolds. In addition to the reporter, mineralization and vitality of the cells was investigated by alizarin red staining and 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide. Quantification of the expression of genes associated to bone regeneration and bone remodelling was used to confirm alizarin red measurements. Controlled perfusion and deformation of the 3‐dimensional scaffold facilitated the alteration of the expression of osteogenic markers, luciferase activity, and calcification. To isolate the specific impact of scaffold deformation, a computational model was developed to derive a perfusion flow profile that results in dynamic shear stress conditions present in periodically loaded scaffolds. In comparison to actually deformed scaffolds, a lower expression of all measured readout parameters indicated that deformation strain is the predominant stimulus for skeletal precursors to undergo osteogenesis in earlier stages of osteogenic cell maturation.     

Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design

Simulations of virus-like particles needed for computer-aided vaccine design highlight the need for new algorithms that accelerate molecular dynamics. Such simulations via conventional molecular dynamics present a practical challenge due to the millions of atoms involved and the long timescales of the phenomena of interest. These phenomena include structural transitions, self-assembly, and interaction with a cell surface. A promising approach for addressing this challenge is multiscale factorization. The approach is distinct from coarse-graining techniques in that it (1) avoids the need for conjecturing phenomenological governing equations for coarse-grained variables, (2) provides simulations with atomic resolution, (3) captures the cross-talk between disturbances at the atomic and the whole virus-like particle scale, and (4) achieves significant speedup over molecular dynamics. A brief review of multiscale factorization method is provided, as is a prospective on its development.     

Toward understanding early Earth evolution: Prescription for approach from terrestrial noble gas and light element records in lunar soils

Because of the almost total lack of geological record on the Earth''s surface before 4 billion years ago, the history of the Earth during this period is still enigmatic. Here we describe a practical approach to tackle the formidable problems caused by this lack. We propose that examinations of lunar soils for light elements such as He, N, O, Ne, and Ar would shed a new light on this dark age in the Earth''s history and resolve three of the most fundamental questions in earth science: the onset time of the geomagnetic field, the appearance of an oxygen atmosphere, and the secular variation of an Earth–Moon dynamical system.     

Sequential Treatment of Guillain-Barré Syndrome with Extracorporeal Elimination and Intravenous Immunoglobulin

Abstract: Plasma exchange and administration of intravenous immunoglobulin (IgG) are established treatments for Guillain-Barré syndrome (GBS). Elimination of postulated pathogenetic factors by plasma exchange or selective adsorption treatment using affinity-type adsorption columns and subsequent immunomodulation by intravenous IgG may provide a more effective treatment. Forty-five patients with acute GBS were prospectively examined using a clinical score. We treated 11 patients by plasma exchange, 13 patients by selective adsorption using a tryptophan-linked polyvinyl alcohol gel adsorbent, and 21 patients by selective adsorption followed by intravenous IgG. The patients treated sequentially by selective adsorption and intravenous IgG improved significantly better than the patients who received plasma treatment only. The results suggest that sequential treatment of GBS may be superior to plasma treatment alone. The higher cost of combined treatment may be offset by lower overall expenditure.     

Influence of E. coli Strain Nissle 1917 (EcN) on Intestinal Gas Dynamics and Abdominal Sensation

E. coli strain Nissle 1917 (EcN) is a probiotic clinically used with various indications. However, especially at the beginning of treatment, some patients report abdominal bloating. In a prospective, randomized, double-blind study in 30 healthy individuals we assessed the influences of EcN on intestinal gas dynamics and abdominal sensation. After one week without medication volunteers orally received 2.5–25 × 10⁹ colony-forming units of EcN or placebo per day for 21 days. EcN was well tolerated and did not significantly affect abdominal symptoms, stool frequency or stool consistency. During gas challenge at different days no difference in the perception scores (range from 0 = no perception to 6 = pain) was observed between the two groups: the mean perception score was 1.2 (SD 0.2) in the EcN group and 1.4 (SD 0.2) in the placebo group. EcN had no relevant influence on intestinal gas dynamics.     

Molecular dynamics simulations provide molecular insights into the role of HLA‐B51 in Behçet's disease pathogenesis

Behçet's disease is an inflammatory disorder of unknown etiology. Genetic tendency has an important role in its pathogenesis, and HLA‐B51, a class I MHC antigen, has been recognized as the strongest susceptibility factor for Behçet's disease. Despite the confirmation of the association of HLA‐B51 with Behçet's disease in different populations, its pathogenic mechanisms remain elusive. HLA‐B51 differs in only two amino acids from HLA‐B52, other split antigen of HLA‐B5, which is not associated with Behçet's disease. These two amino acids are located in the B pocket of the antigen‐binding groove, which occupies the second amino acids of the bound peptides. To understand the nature of the HLA–peptide interactions, differences in structure and dynamics of two HLA alleles were investigated by molecular dynamics simulations using YAYDGKDYI, LPRSTVINI, and IPYQDLPHL peptides. For HLA‐B51, all bound peptides fluctuated to larger extent than HLA‐B52. Free energy profiles of unbinding process for YAYDGKDYI by steered molecular dynamics simulations showed that unbinding from HLA‐B52 results in greater free energy differences than HLA‐B51. These results suggest the possibility of an instability of HLA‐B51 associated with the repertoire of peptides, and this finding may provide significant insight to its pathogenic role in Behçet's disease.     

The emergent dynamics of isotype switch

The supplanting of the 1° IgM response by the 2° isotype-switched response is one of the best known phenomena of immune system dynamics. Given that the conditions determining which B cells will switch isotype and which ones will not are intrinsic to the entities of the immune system, it should be possible to predict the effects that the small-scale (e.g. molecular) properties have on the large scale dynamics of isotype switch. However, in practice, it is notoriously difficult to predict large scale, emergent effects from small scale conditions. Thus, it is unclear what effects (if any), mutation, IgM avidity and chronic immunization exert on isotype switch. To explore these effects, we have constructed a model of isotype switch. With this model, a modified version of the IMMSIM cellular automaton, we are able to alter small scale parameters at will and thus determine the conditions that lead to the observed large scale dynamics of isotype switch. We show that isotype switch is stabilized by high-IgM avidity, affinity/isotype-dependent cell division, and, surprisingly, mutation. We also demonstrate that chronic immunization leads, in our model, to a severe depletion of the IgM response even while the IgG response remains normal.