A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.

The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.

Particle-based modeling of heterogeneous chemical kinetics including mass transfer.

Connecting the macroscopic world of continuous fields to the microscopic world of discrete molecular events is important for understanding several phenomena occurring at physical boundaries of systems. An important example is heterogeneous catalysis, where reactions take place at active surfaces, but the effective reaction rates are determined by transport limitations in the bulk fluid and reaction limitations on the catalyst surface. In this work we study the macro-micro connection in a model heterogeneous catalytic reactor by means of stochastic rotation dynamics. The model is able to resolve the convective and diffusive interplay between participating species, while including adsorption, desorption, and reaction processes on the catalytic surface. Here we apply the simulation methodology to a simple straight microchannel with a catalytic strip. Dimensionless Damkohler numbers are used to comment on the spatial concentration profiles of reactants and products near the catalyst strip and in the bulk. We end the discussion with an outlook on more complicated geometries and increasingly complex reactions.

Adherence to antiretroviral therapy & its determinants amongst HIV patients in India.

BACKGROUND & OBJECTIVE: Very high levels of adherence are required for ART to be effective. There is limited information available from India on adherence to ART and its predictors. We carried out this study to examine adherence levels and to explore the factors associated with adherence among PLHA receiving ART in India. METHODS: Using a cross-sectional study design 310 HIV+ patients receiving ART (252 paying out-of-pocket; 58 free via employee-insurance programme) were interviewed from Pune and Delhi health facilities, using a semi-structural questionnaire. RESULTS: The median age for patients was 36 yr. The median time from diagnosis of HIV-infection was 34.5 months, median time on ART was 16 months and median CD4 cell count at start of ART was 110 cells/microl. 98 per cent of the respondents were using a non protease inhibitor (PI) treatment regimen. Mean 4-day adherence was 93 per cent. Adherence was lower over longer periods of recall: 20 per cent reported missed does over the past 7 days; 33 per cent reported ever missing a full day's medications and 16 per cent had a treatment interruption of more than 7-days at least once. On univariate analysis less than university education, being unemployed, obtaining free treatment, severe depression, baseline CD4 count>200/microl, hospitalization >2 times, having moderate to severe side-effects and taking 4 or more medicines were associated with lower adherence (<90%). However, only obtaining free treatment (adjusted OR, 4.05, 95% CI 1.42-11.54, P=0.009) and severe depression (adjusted OR 4.48, 95% CI 1.64-12.27, P=0.003) were associated with lower adherence in multivariate analysis. INTERPRETATION & CONCLUSION: Although the overall adherence was high, lower levels of adherence were documented among patients receiving free ART. Provision of free treatment without adequate patient preparation and adherence support may compromise the success of ART scale up programmes. Early diagnosis and management of depression need special focus.

The EH and SH3 domain Ese proteins regulate endocytosis by linking to dynamin and Eps15.

Clathrin-mediated endocytosis is a multistep process which requires interaction between a number of conserved proteins. We have cloned two mammalian genes which code for a number of endocytic adaptor proteins. Two of these proteins, termed Ese1 and Ese2, contain two N-terminal EH domains, a central coiled-coil domain and five C-terminal SH3 domains. Ese1 is constitutively associated with Eps15 proteins to form a complex with at least 14 protein-protein interaction surfaces. Yeast two-hybrid assays have revealed that Ese1 EH and SH3 domains bind epsin family proteins and dynamin, respectively. Overexpression of Ese1 is sufficient to block clathrin-mediated endocytosis in cultured cells, presumably through disruption of higher order protein complexes, which are assembled on the endogenous Ese1-Eps15 scaffold. The Ese1-Eps15 scaffold therefore links dynamin, epsin and other endocytic pathway components.

EH domain-dependent interactions between Eps15 and clathrin-coated vesicle protein p95.

The endocytic protein Eps15 contains three copies of the EH domain, a protein module thought to function in protein-protein interactions. Using overlay assays with an Eps15 EH domain fusion protein, we have now identified a protein of 95 kDa (p95) as a major EH domain-binding partner in a wide variety of tissues. The amino acids asparagine-proline-phenylalanine (NPF) form the core of an EH domain-binding motif and three NPF repeats are found in the endocytic protein synaptojanin-170. We have confirmed previous studies indicating that synaptojanin-170 is an EH domain-binding protein, and have used peptide blocking experiments to demonstrate that the interaction is mediated through the NPF repeats. Interestingly, the same peptide also blocks EH domain-binding to p95. Finally, we have shown that p95 is enriched on clathrin-coated vesicles, suggesting an endocytic role for the protein. These data support an important role for EH domain-NPF motif interactions in endocytosis.

MR imaging, MR angiography, and MR spectroscopy of the brain in eclampsia.

PURPOSE: To compare the MR imaging and MR angiographic changes with in vivo proton MR spectroscopic findings and to determine the spectral differences between edema and ischemia in patients with eclampsia. METHODS: Spin-echo MR imaging, MR angiography, and single-voxel proton MR spectroscopy were performed in 10 patients with eclampsia. MR studies were obtained within 3 to 5 days of diagnosis and repeated after 2 weeks with identical parameters. RESULTS: Multifocal subcortical/cortical hyperintensities were noted in all 10 patients on T2-weighted images; in two patients, hyperintensities were seen in both cerebral hemispheres. In nine patients, MR angiograms showed narrowing of the major vessels constituting the circle of Willis that resolved after 2 weeks. In one patient with subtle imaging changes, MR angiography showed mild bilateral narrowing of the proximal middle and posterior cerebral arteries that did not change after 2 weeks, whereas imaging abnormalities worsened. Findings at single-voxel MR spectroscopy of the reversible T2 hyperintense lesions were significantly different from findings in the control group for N-acetylaspartate (NAA)/creatine ratios. One patient with mild abnormalities at MR imaging and MR angiography had lactate and decreased creatine and NAA, and on a follow-up study had a further decrease of NAA and creatine as well as a decrease in lactate. CONCLUSION: In vivo proton MR spectroscopy may help to differentiate cerebral edema from ischemia in patients with eclampsia and thus may help to determine the prognosis for these patients.

Mkh1, a MEK kinase required for cell wall integrity and proper response to osmotic and temperature stress in Schizosaccharomyces pombe.

We have identified a Schizosaccharomyces pombe gene, mkh1, that encodes a MEK kinase (MEKK) homolog. The coding region of mkh1 is contained within a single exon encoding a 1,116-amino-acid protein. The putative catalytic domain of Mkh1 is 54% identical to the catalytic domain of S. cerevisiae Bck1, the most closely related protein. Deletion of mkh1 did not significantly affect cell growth or division under standard conditions. However, mkh1delta cell growth was inhibited by high KCl or NaCl concentrations. mkh1delta cells required a longer time to reenter the cell cycle after prolonged stationary-phase arrest. Also, mkh1delta cells exhibited a round cell shape, while overexpression of Mkh1 resulted in an elongated cell shape. mkh1delta cells exhibited a more dramatic phenotype when grown in nutrient-limiting conditions at high temperature or in hyperosmotic medium. In such conditions, completion of cytokinesis was inhibited, resulting in the growth of pseudohyphal filaments with multiple septa and nuclei. Also, mkh1delta cells were hypersensitive to beta-glucanase treatment. Together these results suggest that Mkh1 regulates cell morphology, cell wall integrity, salt resistance, cell cycle reentry from stationary-phase arrest, and filamentous growth in response to stress. These phenotypes are essentially identical to those exhibited by cells lacking Pmk1/Spm1, a recently identified mitogen-activated protein kinase. Our evidence suggests that Pmk1/Spm1 acts downstream from Mkh1 in a common pathway. Our results also suggest that Mkh1 and Pck2 act independently to maintain cell wall integrity, cell morphology, and salt resistance but act in opposition to regulate filamentous growth.

Comprehensive typing of HLA-DPB1 alleles by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).

Comprehensive typing of 53 HLA-DPB1 alleles was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method using 78 polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) defined DNA specimens (14 retrospective, 64 prospective). A single primer pair was used to amplify the second exon to obtain DPB1-specific amplified product of 294 bp. A combination of RFLPs and cleaved/uncleaved patterns of various endonucleases was employed to resolve DPB1 alleles. A panel of 13 endonucleases (RsaI, Sau96I, BsrBI, DdeI, BsaJI, BssHII, ScaI, ScaI, BbvI, BsgI, FokI, Bsp1286I and BstUI) yielded unique RFLP patterns for all but 2 pairs of DPB1 alleles. However, these remaining 2 pairs of rare alleles could be resolved by an additional digestion with AciI (DPB1*3901 from 4001 and DPB1*4901 from 5301). The unique RFLP patterns of 21 DPB1 alleles using PCR-SSOP typed DNA specimens had been verified. Of the 1,378 possible heterozygotic patterns, 69 pairs and a triplet had been identified that would yield identical RFLP patterns. However, all but one pair, DPB1*3901/5301 from 4001/4901, of these heterozygotes could be resolved by double digestions with appropriately selected endonucleases from the panel used here. Thus, PCR-RFLP remains a simple and effective method for high resolution DPB1 typing.