The HSP40 family chaperone isoform DNAJB6b prevents neuronal cells from tau aggregation

BACKGROUND

Alzheimer's disease (AD) is the most common neurodegenerative disorder with clinical presentations of progressive cognitive and memory deterioration. The pathologic hallmarks of AD include tau neurofibrillary tangles and amyloid plaque depositions in the hippocampus and associated neocortex. The neuronal aggregated tau observed in AD cells suggests that the protein folding problem is a major cause of AD. J-domain-containing proteins (JDPs) are the largest family of cochaperones, which play a vital role in specifying and directing HSP70 chaperone functions. JDPs bind substrates and deliver them to HSP70. The association of JDP and HSP70 opens the substrate-binding domain of HSP70 to help the loading of the clients. However, in the initial HSP70 cycle, which JDP delivers tau to the HSP70 system in neuronal cells remains unclear.

RESULTS

We screened the requirement of a diverse panel of JDPs for preventing tau aggregation in the human neuroblastoma cell line SH-SY5Y by a filter retardation method. Interestingly, knockdown of DNAJB6, one of the JDPs, displayed tau aggregation and overexpression of DNAJB6b, one of the isoforms generated from the DNAJB6 gene by alternative splicing, reduced tau aggregation. Further, the tau bimolecular fluorescence complementation assay confirmed the DNAJB6b-dependent tau clearance. The co-immunoprecipitation and the proximity ligation assay demonstrated the protein-protein interaction between tau and the chaperone-cochaperone complex. The J-domain of DNAJB6b was critical for preventing tau aggregation. Moreover, reduced DNAJB6 expression and increased tau aggregation were detected in an age-dependent manner in immunohistochemical analysis of the hippocampus tissues of a mouse model of tau pathology.

CONCLUSIONS

In summary, downregulation of DNAJB6b increases the insoluble form of tau, while overexpression of DNAJB6b reduces tau aggregation. Moreover, DNAJB6b associates with tau. Therefore, this study reveals that DNAJB6b is a direct sensor for its client tau in the HSP70 folding system in neuronal cells, thus helping to prevent AD.

Fructobacillus apis sp. nov., isolated from the gut of honeybee (Apis mellifera)

A Gram-positive, facultatively anaerobic, catalase-negative, fructose-dependent strain (W13^T) was isolated from the gut of honeybee (Apis mellifera). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain W13^T represents a distinct line of descent within the genus Fructobacillus, with the closest neighbours being Fructobacillus broussonetiae BCRC 81240^T (98.9 % sequence similarity) and Fructobacillus durionis DSM 19113^T (96.8 % sequence similarity). Comparative sequencing of the additional phylogenetic markers rpoC and recA confirmed the 16S rRNA gene tree topology. The complete genome of strain W13^T consisted of 1 292 712 bp with a G+C content of 48.3 mol%. Pairwise comparisons of the average nucleotide identity values and digital DNA-DNA hybridization values between the genomes of W13^T and its close phylogenetic neighbours, F. broussonetiae BCRC 81240^T and F. durionis DSM 19113^T, resulted in 76.2-84.1 % and 20.2-27.6 %, respectively. The main cellular fatty acids of strain W13^T were C_16 : 0, C_18 : 1  ω9c and C_18 : 1  ω7c. Thus, we propose a novel species within the genus Fructobacillus, with the name Fructobacillus apis sp. nov. and the type strain is W13^T (= NBRC 115637^T=BCRC 81365^T).

Functional Relationship of ATP Hydrolysis, Presynaptic Filament Stability, and Homologous DNA Pairing Activity of the Human Meiotic Recombinase DMC1

DMC1 and RAD51 are conserved recombinases that catalyze homologous recombination. DMC1 and RAD51 share similar properties in DNA binding, DNA-stimulated ATP hydrolysis, and catalysis of homologous DNA strand exchange. A large body of evidence indicates that attenuation of ATP hydrolysis leads to stabilization of the RAD51-ssDNA presynaptic filament and enhancement of DNA strand exchange. However, the functional relationship of ATPase activity, presynaptic filament stability, and DMC1-mediated homologous DNA strand exchange has remained largely unexplored. To address this important question, we have constructed several mutant variants of human DMC1 and characterized them biochemically to gain mechanistic insights. Two mutations, K132R and D223N, that change key residues in the Walker A and B nucleotide-binding motifs ablate ATP binding and render DMC1 inactive. On the other hand, the nucleotide-binding cap D317K mutant binds ATP normally but shows significantly attenuated ATPase activity and, accordingly, forms a highly stable presynaptic filament. Surprisingly, unlike RAD51, presynaptic filament stabilization achieved via ATP hydrolysis attenuation does not lead to any enhancement of DMC1-catalyzed homologous DNA pairing and strand exchange. This conclusion is further supported by examining wild-type DMC1 with non-hydrolyzable ATP analogues. Thus, our results reveal an important mechanistic difference between RAD51 and DMC1.

Deep sequencing of small RNA libraries reveals dynamic expression patterns of microRNAs in multiple developmental stages of Bactrocera dorsalis

In eukaryotes, microRNAs (miRNAs) are small, conserved, noncoding RNAs that have emerged as critical regulators of gene expression. The oriental fruit fly Bactrocera dorsalis is one of the most economically important fruit fly pests in East Asia and the Pacific. Although transcriptome analyses have greatly enriched our knowledge of its structural genes, little is known about post-transcriptional regulation by miRNAs in this dipteran species. In this study, small RNA libraries corresponding to four B. dorsalis developmental stages (eggs, larvae, pupae and adults) were constructed and sequenced. Approximately 30.7 million reads of 18-30 nucleotides were obtained, with 123 known miRNAs and 60 novel miRNAs identified amongst these libraries. More than half of the miRNAs were stage-specific during the four developmental stages. A set of miRNAs was found to be up- or down-regulated during development by comparison of their reads at different developmental stages. Moreover, a small part of miRNAs owned both miR-#-3p and miR-#-5p types, with enormously variable miR-#-3p/miR-#-5p ratios in the same library and amongst different developmental stages for each miRNA. Taking these findings together, the current study has uncovered a number of miRNAs and provided insights into their possible involvement in developmental regulation by expression profiling of miRNAs. Further analyses of the expression and function of these miRNAs could increase our understanding of regulatory networks in this insect and lead to novel approaches for its control.

Enhancement of ADP release from the RAD51 presynaptic filament by the SWI5-SFR1 complex

Homologous recombination catalyzed by the RAD51 recombinase eliminates deleterious DNA lesions from the genome. In the presence of ATP, RAD51 forms a nucleoprotein filament on single-stranded DNA, termed the presynaptic filament, to initiate homologous recombination-mediated DNA double-strand break repair. The SWI5-SFR1 complex stabilizes the presynaptic filament and enhances its ability to mediate the homologous DNA pairing reaction. Here we characterize the RAD51 presynaptic filament stabilization function of the SWI5-SFR1 complex using optical tweezers. Biochemical experiments reveal that SWI5-SFR1 enhances ATP hydrolysis by single-stranded DNA-bound RAD51. Importantly, we show that SWI5-SFR1 acts by facilitating the release of ADP from the presynaptic filament. Our results thus provide mechanistic understanding of the function of SWI5-SFR1 in RAD51-mediated DNA recombination.

Interstitial-mediated diffusion in germanium under proton irradiation

We report experiments on the impact of 2.5 MeV proton irradiation on self-diffusion and dopant diffusion in germanium (Ge). Self-diffusion under irradiation reveals an unusual depth independent broadening of the Ge isotope multilayer structure. This behavior and the observed enhanced diffusion of B and retarded diffusion of P demonstrates that an interstitial-mediated diffusion process dominates in Ge under irradiation. This fundamental finding opens up unique ways to suppress vacancy-mediated diffusion in Ge and to solve the donor deactivation problem that hinders the fabrication of Ge-based nanoelectronic devices.

Theory of nanocluster size distributions from ion beam synthesis

Ion beam synthesis of nanoclusters is studied via both kinetic Monte Carlo simulations and the self-consistent mean-field solution to a set of coupled rate equations. Both approaches predict the existence of a steady-state shape for the cluster-size distribution that depends only on a characteristic length determined by the effective diffusion coefficient, the ion solubility, and the volumetric ion flux. The average cluster size in the steady-state regime is determined by the implanted species or matrix interface energy.

Expression of sex-determining genes in human sebaceous glands and their possible role in the pathogenesis of acne

BACKGROUND

The human skin, especially the sebaceous gland, is a steroidogenic organ similar to the gonads and adrenal cortex, possessing all the enzymes required for steroid sex-hormone synthesis and metabolism. Factors regulating cutaneous steroidogenesis associated with disease status remain largely unknown.

OBJECTIVE

We hypothesized that transcription factors involved in sex formation and regulation of steroidogenesis in the classical steroidogenic organs are also expressed in the sebaceous glands. Their possible role in the pathogenesis of acne were investigated.

METHODS

We used reverse transcription polymerase chain reaction (RT-PCR), in situ hybridization and Western blotting to analyse the expression of SF-1, WT-1, SRY, SOX-9 and DAX-1 mRNAs and their proteins in cultured human sebocytes and the facial skin of acne patients.

RESULTS

The in situ hybridization study showed SOX-9 mRNA mainly localized in basal keratinocytes, the basal layer of the sebaceous glands and eccrine glands. Immortalized human sebaceous gland cells (SZ95) expressed mRNA for SOX-9, WT-1 and DAX-1 but not for SF-1 or SRY. The expression of DAX-1 protein was slightly inhibited by 10(-6) m oestradiol (E2) at 6 h but enhanced by 10(-6) m dihydrotestosterone (DHT) at 48 h. The facial expression of SOX-9 seemed to be higher in the acne-prone male patients, while DAX-1 was stronger in subjects without acne, although both were statistically insignificant.

CONCLUSION

Our findings confirm the expression of some sex-determining genes in human sebaceous glands. Further studies on a larger patient population including the normal controls are needed to elucidate the functional significance of these transcription factors in the pathogenesis of acne.

Large melting-point hysteresis of Ge nanocrystals embedded in SiO2

The melting behavior of Ge nanocrystals embedded within SiO2 is evaluated using in situ transmission electron microscopy. The observed melting-point hysteresis is large (+/-17%) and nearly symmetric about the bulk melting point. This hysteresis is modeled successfully using classical nucleation theory without the need to invoke epitaxy.

Dynamics of inherent structure in supercooled liquids near kinetic glass transition

We present a description of the dynamics of a supercooled binary Lennard-Jones liquid in term of the potential landscape of the system. The slowing down of the dynamics in supercooled liquids near the kinetic glass transition is related to the existence of basins in the potential landscape. The inherent structures that are the local potential minima in the configuration space obtained by a quench process are employed to represent the configurations of the basins. We present time correlation functions of the inherent structure, both the self and the coherent part, as a function of wave vector. We also calculated the mean-square displacement, and the non-Gaussian parameter of the van Hove self-correlation function. Compared with the dynamics of original configurations, the short-time relaxation has almost been eliminated by the quench process. However, the long-time alpha relaxations remain essentially the same. We conclude that the long-time alpha relaxation is the result of cross-basin transition in the potential landscape in the configuration space.

Prothymosin alpha enhances protective immune responses induced by oral DNA vaccination against pseudorabies delivered by Salmonella choleraesuis

Previously, we showed that vaccination with the glycoprotein D (gD) gene of pseudorabies virus (PrV) delivered by Escherichia coli induced protective immune responses. In this study, we report that oral DNA vaccination with attenuated Salmonella choleraesuis carrying the PrV gD gene conferred protective immunity in mice against PrV. Moreover, co-delivery of the prothymosin alpha gene carried by S. choleraesuis enhanced the vaccine efficacy. Our results thus demonstrate for the first time, to our knowledge, the effectiveness of oral DNA vaccination using S. choleraesuis as a delivery vehicle and the potential usefulness of prothymosin alpha as a DNA vaccine adjuvant.

[QTLs and epistasis underlying rice (Oryza sativa L.) panicle length in different genetic background and environments]

A double haploid (DH) population and a recombinant inbred (RI) population derived from a cross between a japonica male parent Azucena and indica female parents, IR64 and IR1552 respectively, were used in both field and pot experiments for detecting QTLs and epistasis for rice panicle length in different genetic background and different environments. Panicle length (PL) was measured at maturity. QTLs for PL were detected using single marker analysis and interval mapping. Epistasis effects on the trait were also analyzed. Nine QTLs were detected in DH population, including 5 QTLs detected from field experiment and 4 from pot experiment, among them 3 QTLs mapped on chromosomes 1 and 4 were identified in both field and pot experiments. No significant epistasis effect was detected for PL. Four QTLs were detected in RI population, among them 2 from field condition and 2 from pot experiment. 6 pairs of epistasis loci were detected in RI population. One QTL mapped on chromosome 4 and two pairs of epistatic loci were detected in both field and pot experiments. One QTL on chromosome four was identified in both populations, and one marker locus RG323 on chromosome one was involved in additive effect in DH population, but epistasis effects in RI population.

Collective dynamics in fully hydrated phospholipid bilayers studied by inelastic x-ray scattering

The short wavelength density fluctuation of DLPC (dilaurylphosphatidylcholine) bilayers close to full hydration has been studied by the inelastic x-ray scattering technique below and above the main transition temperature. The analysis based on a generalized three effective eigenmode theory allows us to construct the dispersion relation of the high frequency sound mode for the first time. The marked softening of the excitation near k = 14 nm(-1), corresponding to the lipid chain-chain correlation peak in the structure factor, in the L(alpha) phase implies prevalent occurrences of short-wavelength in-plane motions of lipid chains that might be of importance for transportation of small molecules across membranes.

Analysis of inelastic x-ray scattering spectra of low-temperature water

We analyze a set of high-resolution inelastic x-ray scattering (IXS) spectra from H2O measured at T=259, 273, and 294 K using two different phenomenological models. Model I, called the "dynamic cage model," combines the short time in-cage dynamics described by a generalized Enskog kinetic theory with a long-time cage relaxation dynamics described by an alpha relaxation. This model is appropriate for supercooled water where the cage effect is dominant and the existence of an alpha relaxation is evident from molecular-dynamics (MD) simulation data of extended simple point charge (SPC/E) model water. Model II is essentially a generalized hydrodynamic theory called the "three effective eigenmode theory" by de Schepper et al. 11. This model is appropriate for normal liquid water where the cage effect is less prominent and there is no evidence of the alpha relaxation from the MD data. We use the model I to analyze IXS data at T=259 K (supercooled water). We successfully extract the Debye-Waller factor, the cage relaxation time from the long-time dynamics, and the dispersion relation of high-frequency sound from the short time dynamics. We then use the model II to analyze IXS data at all three temperatures, from which we are able to extract the relaxation rate of the central mode and the damping of the sound mode as well as the dispersion relation for the high-frequency sound. It turns out that the dispersion relations extracted from the two models at their respective temperatures agree with each other giving the high-frequency sound speed of 2900+/-300 m/s. This is to be compared with a slightly higher value reported previously, 3200+/-320 m/s, by analyzing similar IXS data with a phenomenological-damped harmonic oscillator model 22. This latter model has traditionally been used exclusively for the analysis of inelastic scattering spectra of water. The k-dependent sound damping and central mode relaxation rate extracted from our model analyses are compared with the known values in the hydrodynamic limit.

Model for dynamics in supercooled water

We propose a phenomenological model for the intermediate scattering function (ISF) associated with density fluctuation in low temperature water. The motivation is twofold: to extract various physical parameters associated with the ISF computed from extended simple-point-charge model water at supercooled temperatures, and to apply this model to analyze high resolution inelastic x-ray scattering data of water in the future. The ISF of the center of mass of low temperature water computed from 10 M-step molecular dynamics (MD) data shows clearly time-separated two-step relaxation with a well-defined plateau in-between. We interpret this result as due to the formation of a stable hydrogen-bonded, tetrahedrally coordinated cage around a typical molecule in low temperature water. We thus model the long-time cage relaxation by the well-known Kohlrausch form exp[-(t/tau)(beta)] with an amplitude factor which is a k-dependent Debye-Waller factor A(k), and treat the short-time relaxation as due to molecular collisional motions within the cage. The latter motions can be described by the generalized Enskog equation, taking into account the confinement effect of the cage. We shall show that the effect of the confinement changes the collisional dynamics by modifying certain input parameters in the kinetic theory by a factor [1-A(k)](1/2). We solve the generalized Enskog equation approximately but analytically by a Q-dependent triple relaxation time kinetic model. This kinetic model was previously shown to account for the large k behavior of Rayleigh-Brillouin scattering from moderately dense, simple fluids. We find that our model fits well with the MD generated collective as well as single-particle ISFs. For the short-time collisional dynamics, we fix values of the hard sphere diameter sigma and pair correlation function at contact g(sigma), without introducing any adjustable parameters. The calculated ISFs reproduce the correct Brillouin peak frequencies at low k values. From the long-time dynamics, we deduce values of the Debye-Waller factor A(k), the Kohlrausch exponent beta(k), and the cage relaxation time tau(k).

SH3 domain of Bruton's tyrosine kinase can bind to proline-rich peptides of TH domain of the kinase and p120cbl

X-linked agammaglobulinemia (XLA), an inherited disease, is caused by mutations in the Bruton's tyrosine kinase (BTK). The absence of functional BTK leads to failure of B-cell differentiation; this incapacitates antibody production in XLA patients, who suffer from recurrent, sometimes lethal, bacterial infections. BTK plays an important role in B-cell development; it interacts with several proteins in the context of signal transduction. Point mutation in the BTK gene that leads to deletion of C-terminal 14 aa residues of BTK SH3 domain was found in a patient family. To understand the role of BTK, we studied binding of BTK SH3 domain (aa 216-273, 58 residues) and truncated SH3 domain (216-259, 44 residues) with proline-rich peptides; the first peptide constitutes the SH3 domain of BTK, while the latter peptide lacks 14 amino acid residues of the C terminal. Proline-rich peptides selected from TH domain of BTK and p120cbl were studied. It is known that BTK TH domain binds to SH3 domains of various proteins. We found that BTK SH3 domain binds to peptides of BTK TH domain. This suggests that BTK SH3 and TH domains may associate in inter- or intramolecular fashion, which raises the possibility that the kinase may be regulating its own activity by restricting the availability of both its ligand-binding modules. We also found that truncated SH3 domain binds to BTK TH domain peptide less avidly than does normal SH3 domain. Also, we show that the SH3 and truncated SH3 domains bind to peptide of p120cbl, but the latter domain binds weakly. It is likely that the truncated SH3 domain fails to present to the ligand the crucial residues in the correct context, hence the weaker binding. These results delineate the importance of C-terminal in binding of SH3 domains and indicate also that improper folding and the altered binding behavior of mutant BTK SH3 domain likely leads to XLA.