Structural and functional basis for inhibition of erythrocyte invasion by antibodies that target Plasmodium falciparum EBA-175

Disrupting erythrocyte invasion by Plasmodium falciparum is an attractive approach to combat malaria. P. falciparum EBA-175 (PfEBA-175) engages the host receptor Glycophorin A (GpA) during invasion and is a leading vaccine candidate. Antibodies that recognize PfEBA-175 can prevent parasite growth, although not all antibodies are inhibitory. Here, using x-ray crystallography, small-angle x-ray scattering and functional studies, we report the structural basis and mechanism for inhibition by two PfEBA-175 antibodies. Structures of each antibody in complex with the PfEBA-175 receptor binding domain reveal that the most potent inhibitory antibody, R217, engages critical GpA binding residues and the proposed dimer interface of PfEBA-175. A second weakly inhibitory antibody, R218, binds to an asparagine-rich surface loop. We show that the epitopes identified by structural studies are critical for antibody binding. Together, the structural and mapping studies reveal distinct mechanisms of action, with R217 directly preventing receptor binding while R218 allows for receptor binding. Using a direct receptor binding assay we show R217 directly blocks GpA engagement while R218 does not. Our studies elaborate on the complex interaction between PfEBA-175 and GpA and highlight new approaches to targeting the molecular mechanism of P. falciparum invasion of erythrocytes. The results suggest studies aiming to improve the efficacy of blood-stage vaccines, either by selecting single or combining multiple parasite antigens, should assess the antibody response to defined inhibitory epitopes as well as the response to the whole protein antigen. Finally, this work demonstrates the importance of identifying inhibitory-epitopes and avoiding decoy-epitopes in antibody-based therapies, vaccines and diagnostics

Molecular Cloud Formation Behind Shock Waves

We examine the formation of molecular gas behind shocks in atomic gas using a chemical/dynamical model, particular emphasis is given to constraints the chemistry places on the dynamical evolution. The most important result of this study is to stress the importance of shielding the molecular gas from the destructive effects of UV radiation. For shock ram pressures comparable to or exceeding typical local ISM pressures, self-shielding controls the formation time of H2 but CO formation requires shielding of the interstellar radiation field by dust grains. We find that the molecular hydrogen fractional abundance can become significant well before CO forms. The timescale for (CO) molecular cloud formation is not set by H2 formation, but rather by the timescale for accumulating a sufficient column density or extinction, A_V > 0.7. The local ratio of atomic to molecular gas (4:1), coupled with short estimates for cloud lifetimes (3-5 Myr), suggests that the timescales for accumulating molecular clouds from atomic material typically must be no longer than about 12-20 Myr. Based on the shielding requirement, this implies that the typical product of pre-shock density and velocity must be n*v > 20 cm^-3 km s^-1. Based on these results we find that flow-driven formation of molecular clouds in the local interstellar medium can occur sufficiently rapidly to account for observations. We also provide detailed predictions of atomic and molecular emission and absorption that track molecular cloud formation, with a view toward helping to verify cloud formation by shock waves. Finally, we provide an analytic solution for time-dependent H2 formation which may be of use in numerical hydrodynamic calculations.Comment: 43 pages, 13 figures, accepted by ApJ main journa

Phase diagrams of the 2D t-t'-U Hubbard model from an extended mean field method

It is well-known from unrestricted Hartree-Fock computations that the 2D Hubbard model does not have homogeneous mean field states in significant regions of parameter space away from half filling. This is incompatible with standard mean field theory. We present a simple extension of the mean field method that avoids this problem. As in standard mean field theory, we restrict Hartree-Fock theory to simple translation invariant states describing antiferromagnetism (AF), ferromagnetism (F) and paramagnetism (P), but we use an improved method to implement the doping constraint allowing us to detect when a phase separated state is energetically preferred, e.g. AF and F coexisting at the same time. We find that such mixed phases occur in significant parts of the phase diagrams, making them much richer than the ones from standard mean field theory. Our results for the 2D t-t'-U Hubbard model demonstrate the importance of band structure effects.Comment: 6 pages, 5 figure

Breast milk and in utero transmission of HIV-1 select for envelope variants with unique molecular signatures

Additional file 5: Figure S5. Representative CD4 infectivity curves using Affinofile cells for IUT (top) and BMT (bottom) maternal–infant pairs. Affinofile cells were induced to generate a 100-fold range of CD4 surface density (ABS/cell) and infected with 2000 IU pseudotyped virus. Percent infection was measured as the percent luciferase relative to infected and maximally induced Affinofile cells. Data shown are representative curves among 3–4 experimental replicates

Mucositis after Allogeneic Hematopoietic Stem Cell Transplantation: A Cohort Study of Methotrexate- and Non-Methotrexate-Containing Graft-versus-Host Disease Prophylaxis Regimens

AbstractOral mucositis occurs in up to 75% of recipients of high-dose chemoradiotherapy conditioning regimens used for allogeneic hematopoietic stem cell transplantation (HSCT). As a result of mucositis, narcotic analgesia and total parenteral nutrition (TPN) are commonly required after HSCT. Methotrexate, an antiproliferative graft-versus-host disease (GVHD) prophylaxis agent, impairs mucosal regeneration and worsens and prolongs mucositis. We assessed the effect of substituting sirolimus for methotrexate as GVHD prophylaxis on outcomes associated with mucositis. Two patient cohorts undergoing allogeneic HLA-matched related donor peripheral blood stem cell transplantation with cyclophosphamide/total body irradiation conditioning were prospectively analyzed for mucositis severity and retrospectively reviewed for correlative outcomes. GVHD prophylaxis consisted of sirolimus/tacrolimus (ST) in the study group and tacrolimus/methotrexate (TM) in the control group. Thirty patients received ST and 24 patients received TM as GVHD prophylaxis between October 2000 and May 2003. Mild, moderate, and severe mucositis was noted in 37%, 57%, and 7% of the ST group and 8%, 42%, and 50% of the TM group (P = .0002). Less TPN was used in the ST group than the TM group (17% versus 43% of posttransplantation hospital days; P = .02). The total number of narcotic days was lower in the ST group in comparison with the TM group (median, 13.5 versus 17 days; P = .08). The time to first hospital discharge was shorter in the ST group compared with the TM group (median, 18 versus 22 days; P = .07). The substitution of sirolimus for methotrexate as GVHD prophylaxis is associated with a reduction in mucositis severity. As a result, TPN and narcotic use are reduced, and hospitalization duration is shortened. Less toxic GVHD prophylaxis regimens without methotrexate may have a significant effect on patient quality of life, patient outcomes, and economic outcomes associated with allogeneic stem cell transplantation

Evolution of Chemistry and Molecular Line Profile during Protostellar Collapse

Understanding the chemical evolution in star-forming cores is a necessary pre-condition to correctly assess physical conditions when using molecular emission. We follow the evolution of chemistry and molecular line profiles through the entire star formation process, including a self-consistent treatment of dynamics, dust continuum radiative transfer, gas energetics, chemistry, molecular excitation, and line radiative transfer. In particular, the chemical code follows a gas parcel as it falls toward the center, passing through regimes of density, dust temperature, and gas temperature that are changing both because of the motion of the parcel and the evolving luminosity of the central source. We combine a sequence of Bonnor-Ebert spheres and the inside-out collapse model to describe dynamics from the pre-protostellar stage to later stages. The overall structures of abundance profiles show complex behavior that can be understood as interactions between freeze-out and evaporation of molecules. We find that the presence or absence of gas-phase CO has a tremendous effect on the less abundant species. In addition, the ambient radiation field and the grain properties have important effects on the chemical evolution, and the variations in abundance have strong effects on the predicted emission line profiles. Multi-transition and multi-position ob servations are necessary to constrain the parameters and interpret observations correctly in terms of physical conditions. Good spatial and spectral resolution is also important in distinguishing evolutionary stages.Comment: 41 pages, 26 figures, accepted for publication in Ap

Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

Functional properties of measles virus proteins derived from a subacute sclerosing panencephalitis patient who received repeated remdesivir treatments

Subacute sclerosing panencephalitis (SSPE) is a rare but fatal late neurological complication of measles, caused by persistent measles virus (MeV) infection of the central nervous system. There are no drugs approved for the treatment of SSPE. Here, we followed the clinical progression of a 5-year-old SSPE patient after treatment with the nucleoside analog remdesivir, conducted a post-mortem evaluation of the patient’s brain, and characterized the MeV detected in the brain. The quality of life of the patient transiently improved after the first two courses of remdesivir, but a third course had no further clinical effect, and the patient eventually succumbed to his condition. Post-mortem evaluation of the brain displayed histopathological changes including loss of neurons and demyelination paired with abundant presence of MeV RNA-positive cells throughout the brain. Next-generation sequencing of RNA isolated from the brain revealed a complete MeV genome with mutations that are typically detected in SSPE, characterized by a hypermutated M gene. Additional mutations were detected in the polymerase (L) gene, which were not associated with resistance to remdesivir. Functional characterization showed that mutations in the F gene led to a hyperfusogenic phenotype predominantly mediated by N465I. Additionally, recombinant wild-type-based MeV with the SSPE-F gene or the F gene with the N465I mutation was no longer lymphotropic but instead efficiently disseminated in neural cultures. Altogether, this case encourages further investigation of remdesivir as a potential treatment of SSPE and highlights the necessity to functionally understand SSPE-causing MeV.</p