Modelling, Cloning, and Expression of the J domain of C. elegans Rme-8 Protein

Rme-8 is a J domain containing plasma membrane protein that is required for endocytosis in various cells The J domain is a characteristic structural motif found mainly in heat shock protein 40 (Hsp 40 or DnaJ) and other proteins such as Rme-8 Within the J domain is a tripeptide, the HPD motif, that is required by the J domain protein to interact with and stimulate the ATPase activity of Hsp70 a major cellular chaperone Rme-8 protein in C elegans CeRme-8 has not been identified with a particular Hsp70 partner CeHsp70 1 is the only cytosolic Hsp70 in C elegans therefore, we hypothesize that it is the binding partner for the J domain of CeRme-8 To test this hypothesis, we first need to express and purify the J domain of CeRme-8 We report herein the successful cloning and expression of the J domain of CeRme-8 Computer modelling revealed that the amino acid sequence of the J domain of CeRme-8 folds into the canonical J domain conformation, containing the HPD tripeptide Complementary DNA of the J domain of CeRme-8 was cloned into the pGEX-Tev-KG plasmid, in frame with the gene for glutathione S transferase ( to yield a GST CeRme-8 fusion protein IPTG induced expression of the expected 37 kilodalton fusion protein was confirmed by both SDS-PAGE and western blotting using antibody against GST Work is ongoing to develop a protocol for purification of both GST tagged and untagged J domains of CeRme-8 Future work will involve testing the effect of the J domain protein on the ATPase activity of CeHsp70-

Experimental observation of chiral phonons in monolayer WSe2

Chirality characterizes an object that is not identical to its mirror image. In condensed matter physics, Fermions have been demonstrated to obtain chirality through structural and time-reversal symmetry breaking. These systems display unconventional electronic transport phenomena such as the quantum Hall effect and Weyl semimetals. However, for bosonic collective excitations in atomic lattices, chirality was only theoretically predicted and has never been observed. We experimentally show that phonons can exhibit intrinsic chirality in monolayer tungsten diselenide, whose lattice breaks the inversion symmetry and enables inequivalent electronic K and -K valley states. The time-reversal symmetry is also broken when we selectively excite the valley polarized holes by circularly polarized light. Brillouin-zone-boundary phonons are then optically created by the indirect infrared absorption through the hole-phonon interactions. The unidirectional intervalley transfer of holes ensures that only the phonon modes in one valley are excited. We found that such photons are chiral through the transient infrared circular dichroism, which proves the valley phonons responsible to the indirect absorption has non-zero pseudo-angular momentum. From the spectrum we further deduce the energy transferred to the phonons that agrees with both the first principle calculation and the double-resonance Raman spectroscopy. The chiral phonons have significant implications for electron-phonon coupling in solids, lattice-driven topological states, and energy efficient information processing

Germline-like predecessors of broadly neutralizing antibodies lack measurable binding to HIV-1 envelope glycoproteins: Implications for evasion of immune responses and design of vaccine immunogens

Several human monoclonal antibodies (hmAbs) including b12, 2G12, and 2F5 exhibit relatively potent and broad HIV-1-neutralizing activity. However, their elicitation in vivo by vaccine immunogens based on the HIV-1 envelope glycoprotein (Env) has not been successful. We have hypothesized that HIV-1 has evolved a strategy to reduce or eliminate the immunogenicity of the highly conserved epitopes of such antibodies by using "holes" (absence or very weak binding to these epitopes of germline antibodies that is not sufficient to initiate and/or maintain an efficient immune response) in the human germline B cell receptor (BCR) repertoire. To begin to test this hypothesis we have designed germline-like antibodies corresponding most closely to b12, 2G12, and 2F5 as well as to X5, m44, and m46 which are cross-reactive but with relatively modest neutralizing activity as natively occurring antibodies due to size and/or other effects. The germline-like X5, m44, and m46 bound with relatively high affinity to all tested Envs. In contrast, germline-like b12, 2G12, and 2F5 lacked measurable binding to Envs in an ELISA assay although the corresponding mature antibodies did. These results provide initial evidence that Env structures containing conserved vulnerable epitopes may not initiate humoral responses by binding to germline antibodies. Even if such responses are initiated by very weak binding undetectable in our assay it is likely that they will be outcompeted by responses to structures containing the epitopes of X5, m44, m46, and other antibodies that bind germline BCRs with much higher affinity/avidity. This hypothesis, if further supported by data, could contribute to our understanding of how HIV-1 evades immune responses and offer new concepts for design of effective vaccine immunogens.postprin

CHD1L protein is overexpressed in human ovarian carcinomas and is a novel predictive biomarker for patients survival

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Iron force constants of bridgmanite at high pressure: Implications for iron isotope fractionation in the deep mantle

The isotopic compositions of iron in major mantle minerals may record chemical exchange between deep-Earth reservoirs as a result of early differentiation and ongoing plate tectonics processes. Bridgmanite (Bdg), the most abundant mineral in the Earth’s lower mantle, can incorporate not only Al but also Fe with different oxidation states and spin states, which in turn can influence the distribution of Fe isotopes between Bdg and ferropericlase (Fp) and between the lower mantle and the core. In this study, we combined first-principles calculations with high-pressure nuclear resonant inelastic X-ray scattering measurements to evaluate the effects of Fe site occupancy, valence, and spin states at lower-mantle conditions on the reduced Fe partition function ratio (β-factor) of Bdg. Our results show that the spin transition of octahedral-site (B-site) Fe3+ in Bdg under mid-lower-mantle conditions generates a +0.09‰ increase in its β-factor, which is the most significant effect compared to Fe site occupancy and valence. Fe2+-bearing Bdg varieties have smaller β-factors relative to Fe3+-bearing varieties, especially those containing B-site Fe3+. Our models suggest that Fe isotopic fractionation between Bdg and Fp is only significant in the lowermost mantle due to the occurrence of low-spin Fe2+ in Fp. Assuming early segregation of an iron core from a deep magma ocean, we find that neither core formation nor magma ocean crystallization would have resulted in resolvable Fe isotope fractionation. In contrast, Fe isotopic fractionation between low-spin Fe3+-bearing Bdg/Fe2+-bearing Fp and metallic iron at the core-mantle boundary may have enriched the lowermost mantle in heavy Fe isotopes by up to +0.20‰

PDLIM2 restricts Th1 and Th17 differentiation and prevents autoimmune disease

Background: PDLIM2 is essential for the termination of the inflammatory transcription factors NF-κB and STAT but is dispensable for the development of immune cells and immune tissues/organs. Currently, it remains unknown whether and how PDLIM2 is involved in physiologic and pathogenic processes. Results: Here we report that naive PDLIM2 deficient CD4+ T cells were prone to differentiate into Th1 and Th17 cells. PDLIM2 deficiency, however, had no obvious effect on lineage commitment towards Th2 or Treg cells. Notably, PDLIM2 deficient mice exhibited increased susceptibility to experimental autoimmune encephalitis (EAE), a Th1 and/or Th17 cell-mediated inflammatory disease model of multiple sclerosis (MS). Mechanistic studies further indicate that PDLIM2 was required for restricting expression of Th1 and Th17 cytokines, which was in accordance with the role of PDLIM2 in the termination of NF-κB and STAT activation.Conclusion: These findings suggest that PDLIM2 is a key modulator of T-cell-mediated immune responses that may be targeted for the therapy of human autoimmune diseases. © 2012 Qu et al.; licensee BioMed Central Ltd

Haplotypes versus genotypes on pedigrees

Abstract. Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysis with haplotype data have not yet been developed, and the computational complexity of such problems has been an open question. Furthermore, it is not clear in which scenarios haplotype data would provide better estimates than genotype data for quantities such as recombination rates. To answer these questions, a reduction is given from genotype problem instances to haplotype problem instances, and it is shown that solving the haplotype problem yields the solution to the genotype problem, up to constant factors or coefficients. The pedigree analysis problems we will consider are the likelihood, maximum probability haplotype, and minimum recombination haplotype problems. Two algorithms are introduced: an exponential-time hidden Markov model (HMM) for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data. Pedigree analysis, both linkage and association studies, has a long history of important contributions to genetics, including disease-gene finding and some of the first genetic maps for humans. Recent contributions include fine-scale recombination maps in humans [4], regions linked to Schizophrenia that might be missed by genome-wide association studies [11], and insights into the relationship between cystic fibrosis and fertility [13]. Algorithms for pedigree problems are of great interest to the computer science community, in part because of connections to machine learning algorithms, optimization methods, and combinatorics [7, 16

Effect of temperature anisotropy on various modes and instabilities for a magnetized non-relativistic bi-Maxwellian plasma

Using kinetic theory for homogeneous collisionless magnetized plasmas, we present an extended review of the plasma waves and instabilities and discuss the anisotropic response of generalized relativistic dielectric tensor and Onsager symmetry properties for arbitrary distribution functions. In general, we observe that for such plasmas only those electromagnetic modes whose magnetic field perturbations are perpendicular to the ambient magneticeld, i.e.,B1 \perp B0, are effected by the anisotropy. However, in oblique propagation all modes do show such anisotropic effects. Considering the non-relativistic bi-Maxwellian distribution and studying the relevant components of the general dielectric tensor under appropriate conditions, we derive the dispersion relations for various modes and instabilities. We show that only the electromagnetic R- and L- waves, those derived from them and the O-mode are affected by thermal anisotropies, since they satisfy the required condition B1\perpB0. By contrast, the perpendicularly propagating X-mode and the modes derived from it (the pure transverse X-mode and Bernstein mode) show no such effect. In general, we note that the thermal anisotropy modifies the parallel propagating modes via the parallel acoustic effect, while it modifies the perpendicular propagating modes via the Larmor-radius effect. In oblique propagation for kinetic Alfven waves, the thermal anisotropy affects the kinetic regime more than it affects the inertial regime. The generalized fast mode exhibits two distinct acoustic effects, one in the direction parallel to the ambient magnetic field and the other in the direction perpendicular to it. In the fast-mode instability, the magneto-sonic wave causes suppression of the firehose instability. We discuss all these propagation characteristics and present graphic illustrations

Characterization of Human DNA Polymerase Delta and Its Subassemblies Reconstituted by Expression in the Multibac System

Mammalian DNA polymerase δ (Pol δ), a four-subunit enzyme, plays a crucial and versatile role in DNA replication and DNA repair processes. We have reconstituted human Pol δ complexes in insect cells infected with a single baculovirus into which one or more subunits were assembled. This system allowed for the efficient expression of the tetrameric Pol δ holoenzyme, the p125/p50 core dimer, the core+p68 trimer and the core+p12 trimer, as well as the p125 catalytic subunit. These were isolated in milligram amounts with reproducible purity and specific activities by a highly standardized protocol. We have systematically compared their activities in order to gain insights into the roles of the p12 and p68 subunits, as well as their responses to PCNA. The relative specific activities (apparent kcat) of the Pol δ holoenzyme, core+p68, core+p12 and p125/p50 core were 100, 109, 40, and 29. The corresponding apparent Kd's for PCNA were 7.1, 8.7, 9.3 and 73 nM. Our results support the hypothesis that Pol δ interacts with PCNA through multiple interactions, and that there may be a redundancy in binding interactions that may permit Pol δ to adopt flexible configurations with PCNA. The abilities of the Pol δ complexes to fully extend singly primed M13 DNA were examined. All the subassemblies except the core+p68 were defective in their abilities to completely extend the primer, showing that the p68 subunit has an important function in synthesis of long stretches of DNA in this assay. The core+p68 trimer could be reconstituted by addition of p12