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Cytosine methylation at CG sites ((m)CG) plays critical roles in development, epigenetic inheritance, and genome stability in mammals and plants. In the dicot model plant Arabidopsis thaliana, methyltransferase 1 (MET1), a principal CG methylase, functions to maintain (m)CG during DNA replication, with its null mutation resulting in global hypomethylation and pleiotropic developmental defects. Null mutation of a critical CG methylase has not been characterized at a whole-genome level in other higher eukaryotes, leaving the generality of the Arabidopsis findings largely speculative. Rice is a model plant of monocots, to which many of our important crops belong. Here we have characterized a null mutant of OsMet1-2, the major CG methylase in rice. We found that seeds homozygous for OsMet1-2 gene mutation (OsMET1-2(-/-)), which directly segregated from normal heterozygote plants (OsMET1-2(+/-)), were seriously maldeveloped, and all germinated seedlings underwent swift necrotic death. Compared with wild type, genome-wide loss of (m)CG occurred in the mutant methylome, which was accompanied by a plethora of quantitative molecular phenotypes including dysregulated expression of diverse protein-coding genes, activation and repression of transposable elements, and altered small RNA profiles. Our results have revealed conservation but also distinct functional differences in CG methylases between rice and Arabidopsis.

Fibrillar amyloid-β (Aβ) is the major constituent of senile plaques in the brain of patients with Alzheimer's disease (AD). Aβ is a short peptide generated from amyloid precursor protein with two main isoforms, Aβ40 and Aβ42, with the latter having two additional hydrophobic residues at the C-terminus. The two isoforms have distinct characteristics, in which Aβ42 plays a more pathogenic role. Some early-onset familial AD cases possess an elevated Aβ42/Aβ40 level, and biochemical studies show the two species interact with each other. Therefore, understanding structural conversion in the aggregation of mixed Aβ isoforms is essential for elucidating AD pathogenesis. Here, we systematically examined the differences between Aβ42, Aβ40 and various Aβ42/Aβ40 mixtures by monitoring the fibrillization kinetics, epitope changes, assembly, morphology and induced cytotoxicity. We found that the minor Aβ species in different mixing ratios modulated the major aggregation pathway. Size exclusion chromatography, circular dichroism spectroscopy and photo-crosslinking assay showed that soluble Aβ42 oligomers were stabilized after Aβ40 addition, and the equimolar Aβ42/Aβ40 mixture rapidly formed spherical oligomers. These oligomers were the most toxic among those examined as evidenced by neurite degeneration and neuronal toxicity. However, the oligomers were not responsible for intracellular calcium elevation. Overall, our results demonstrated that differently mixed Aβ species repartitioned oligomer intermediates on the major aggregation pathway. Furthermore, the equimolar mixture rapidly formed structurally stable and the most toxic oligomers. These results provided information on the potential pathological mechanisms underlying the elevated Aβ42/Aβ40 ratio in familial AD patients and in the local environment of sporadic AD brains., (© 2014 FEBS.)

Sex chromosome dosage compensation balances homogametic sex chromosome expression with autosomal expression in the heterogametic sex, leading to sex chromosome expression parity between the sexes. If compensation is incomplete, this can lead to expression imbalance and sex-biased gene expression. Recent work has uncovered an intriguing and variable pattern of dosage compensation across species that includes a lack of complete dosage compensation in ZW species compared with XY species. This has led to the hypothesis that ZW species do not require complete compensation or that complete compensation would negatively affect their fitness. To date, only one study, a study of the moth Bombyx mori, has discovered evidence for complete dosage compensation in a ZW species. We examined another moth species, Manduca sexta, using high-throughput sequencing to survey gene expression in the head tissue of males and females. We found dosage compensation to be complete in M. sexta with average expression between the Z chromosome in males and females being equal. When genes expressed at very low levels are removed by filtering, we found that average autosome expression was highly similar to average Z expression, suggesting that the majority of genes in M. sexta are completely dosage compensated. Further, this compensation was accompanied by sex-specific gene expression associated with important sexually dimorphic traits. We suggest that complete dosage compensation in ZW species might be more common than previously appreciated and linked to additional selective processes, such as sexual selection. More ZW and lepidopteran species should now be examined in a phylogenetic framework, to understand the evolution of dosage compensation.

The membrane roughness of Neuro-2a neroblastoma cells is measured by using noninterferometric wide-field optical profilometry. The cells are treated with the fibril and oligomer conformers of amyloid-beta (Aβ) 42, which is a peptide of 42 amino acids related to the development of Alzheimer's disease. We find that both the Aβ42 fibrils and Aβ42 oligomers reduced the cell membrane roughness, but the effect of Aβ42 oligomers was faster and stronger than that of the fibrils. We also apply direct-current electric field (dcEF) stimulations on the cells. A dcEF of 300 mV/mm can increase the membrane roughness under the treatment of Aβ42. These results suggest that Aβ42 can decrease the membrane compliance of live neuroblastoma cells, and dcEFs may counteract this effect.

Dendritic cells (DCs) are professional antigen presenting cells that activate and modulate immune responses, but the mechanisms underlying DC activation have not been fully understood. In this study, we investigated the role of Notch signaling in DC activation by using murine bone marrow-derived DCs. Triggering of Toll-like receptors (TLRs) of DCs led to upregulated expression of Notch ligands. Disruption of Notch signaling by the deletion of RBP-J, the critical transcription factor mediating the canonical signaling from all Notch receptors, resulted in a reduced capacity of DCs in activating T cells. Moreover, RBP-J deficiency altered the polarization of T cell activation, as manifested by downregulated interferon-γ and upregulated interleukin-4 and -10 expressions after LPS or Poly(I:C) stimulation. Furthermore, we found that RBP-J(-/-) DCs had reduced intracellular calcium after TLR-triggering. Immunofluorescent staining showed that RBP-J deficient DCs exhibited attenuated cytoskeleton reorganization when contacting T cells. In summary, our results suggested that the canonical Notch signaling promotes the cytoskeleton reorganization and the TLR-mediated DC activation.

Autophagy is a catabolic process that functions in recycling and degrading cellular proteins, and is also induced as an adaptive response to the increased metabolic demand upon nutrient starvation. However, the prosurvival role of autophagy in response to metabolic stress due to deprivation of glutamine, the most abundant nutrient for mammalian cells, is not well understood. Here, we demonstrated that when extracellular glutamine was withdrawn, autophagy provided cells with sub-mM concentrations of glutamine, which played a critical role in fostering cell metabolism. Moreover, we uncovered a previously unknown connection between metabolic responses to ATG5 deficiency and glutamine deprivation, and revealed that WT and atg5 (-/-) MEFs utilized both common and distinct metabolic pathways over time during glutamine deprivation. Although the early response of WT MEFs to glutamine deficiency was similar in many respects to the baseline metabolism of atg5 (-/-) MEFs, there was a concomitant decrease in the levels of essential amino acids and branched chain amino acid catabolites in WT MEFs after 6 h of glutamine withdrawal that distinguished them from the atg5 (-/-) MEFs. Metabolomic profiling, oxygen consumption and pathway focused quantitative RT-PCR analyses revealed that autophagy and glutamine utilization were reciprocally regulated to couple metabolic and transcriptional reprogramming. These findings provide key insights into the critical prosurvival role of autophagy in maintaining mitochondrial oxidative phosphorylation and cell growth during metabolic stress caused by glutamine deprivation.

Background: Deep sequencing is a powerful tool for novel small RNA discovery. Illumina small RNA sequencing library preparation requires a pre-adenylated 3' end adapter containing a 5',5'-adenyl pyrophosphoryl moiety. In the absence of ATP, this adapter can be ligated to the 3' hydroxyl group of small RNA, while RNA self-ligation and concatenation are repressed. Pre-adenylated adapters are one of the most essential and costly components required for library preparation, and few are commercially available., Results: We demonstrate that DNA oligo with 5' phosphate and 3' amine groups can be enzymatically adenylated by T4 RNA ligase 1 to generate customized pre-adenylated adapters. We have constructed and sequenced a small RNA library for tomato (Solanum lycopersicum) using the T4 RNA ligase 1 adenylated adapter., Conclusion: We provide an efficient and low-cost method for small RNA sequencing library preparation, which takes two days to complete and costs around $20 per library. This protocol has been tested in several plant species for small RNA sequencing including sweet potato, pepper, watermelon, and cowpea, and could be readily applied to any RNA samples.

Amyloid formation is initiated by protein misfolding, followed by self-association to ultimately form amyloid fibrils. The discovery of toxic prefibrillar oligomers in many amyloidosis underscores the importance of understanding the folding mechanism prior to such aggregation. Here, we investigated the folding properties of the natively unfolded amyloid-β (Aβ) peptide and the familial variants (A21G, E22Q, E22G, E22K, and D23N) in Alzheimer's disease (AD). In combinations of native electrophoresis, analytical ultracentrifugation, fluorescence emission, and far-UV circular dichroism, we showed that all Aβ40 variants are predominantly monomeric with similar residual secondary structures, but distinct hydrophobic-exposed protein surfaces. Guanidine hydrochloride (GdnHCl) denaturation in the absence and presence of trifluoroethanol (TFE) showed that Aβ variants adopt an apparent 2-state equilibrium model with different stabilities, in which wild type is less stable than A21G but more stable than D23N and E22 mutants. By correlating the folding stability with the nucleation phase in fibrillization, we found the more stable the variant, the slower the nucleation, except for D23N. Besides, the unfolding of Aβ conformation leads to reduced formation of mature fibrils, but an increase in nonfibrillar, amorphous type of aggregates. Overall, we demonstrated that folding stability of Aβ is an important determinant of the nucleation kinetics.

Abnormally high concentrations of Zn(2+), Cu(2+), and Fe(3+) are present along with amyloid-β (Aβ) in the senile plaques in Alzheimer disease, where Al(3+) is also detected. Aβ aggregation is the key pathogenic event in Alzheimer disease, where Aβ oligomers are the major culprits. The fundamental mechanism of these metal ions on Aβ remains elusive. Here, we employ 4,4'-Bis(1-anilinonaphthalene 8-sulfonate) and tyrosine fluorescence, CD, stopped flow fluorescence, guanidine hydrochloride denaturation, and photo-induced cross-linking to elucidate the effect of Zn(2+), Cu(2+), Fe(3+), and Al(3+) on Aβ at the early stage of the aggregation. Furthermore, thioflavin T assay, dot blotting, and transmission electron microscopy are utilized to examine Aβ aggregation. Our results show that Al(3+) and Zn(2+), but not Cu(2+) and Fe(3+), induce larger hydrophobic exposures of Aβ conformation, resulting in its significant destabilization at the early stage. The metal ion binding induces Aβ conformational changes with micromolar binding affinities and millisecond binding kinetics. Cu(2+) and Zn(2+) induce similar assembly of transiently appearing Aβ oligomers at the early state. During the aggregation, we found that Zn(2+) exclusively promotes the annular protofibril formation without undergoing a nucleation process, whereas Cu(2+) and Fe(3+) inhibit fibril formation by prolonging the nucleation phases. Al(3+) also inhibits fibril formation; however, the annular oligomers co-exist in the aggregation pathway. In conclusion, Zn(2+), Cu(2+), Fe(3+), and Al(3+) adopt distinct folding and aggregation mechanisms to affect Aβ, where Aβ destabilization promotes annular protofibril formation. Our study facilitates the understanding of annular Aβ oligomer formation upon metal ion binding.

Quercetin, a naturally occurring flavonoid abundant in fruits and vegetables, has been demonstrated as a multipotent bioflavonoid with great potential for the prevention and treatment of cancer. Apoptosis is thought to be an important response to most chemotherapeutic agents in leukemia cells. However, the underlying mechanism of induction of apoptosis by quercetin involving epigenetic regulation is poorly understood. In the present study, by evaluation of fragmentation of DNA, poly (ADP-ribose) polymerase (PARP) and procaspases, we found that quercetin was able to induce apoptosis of human leukemia HL-60 cells in a dose-dependent manner. Quercetin triggered the extrinsic apoptosis pathway through activation of caspase-8 and induction of Bid cleavage, Bax conformation change and cytochrome c release. Furthermore, quercetin induced Fas ligand (FasL) expression involving activation of the extracellular signal-regulated kinase (ERK) and Jun N-terminus kinase (JNK) signaling pathways. In addition to activation of c-Jun, quercetin increased histone H3 acetylation which resulted in the promotion of the expression of FasL. Quercetin exhibited potential for the activation of histone acetyltransferase (HAT) and the inhibition of histone deacetyltransferase (HADC), both of which contributed to histone acetylation. However, only the activation effect on HAT was associated with the ERK and JNK pathway. These results demonstrated that quercetin induced FasL-related apoptosis by transactivation through activation of c-jun/AP-1 and promotion of histone H3 acetylation in HL-60 cells.

The aim of this study was to investigate the role of Delta-like 1 (Dll1) in differentiation and antigen pre-sensation of mouse bone marrow-derived dendritic cells (DCs). In the presence of granulocyte macrophage colony stimulating factor (GM-CSF) and interleukin 4 (IL-4), mouse bone marrow cells were co-cultured with OP9-Dll1 and OP9-GFP cell lines respectively. After 8 days, the immature DCs were stimulated with tumor antigen. The surface molecules of the activated DCs including MHC II, CD80 and CD86 were analyzed by flow cytometry. Levels of IL-12 and IL-10 in the culture supernatant were detected by ELISA. In addition, the proliferation of T-cells co-cultured with DCs was analyzed by FACS through mixed T-lymphocyte reaction. The results showed that compared with OP9-GFP, the bone marrow cells co-cultured with OP9-Dll1 produced significantly more CD11c(+) DCs (p < 0.05), and possessed higher levels of surface molecule expression including MHC II, CD80 and CD86 after tumor antigen stimulation. The DCs secreted higher level of IL-12 (p < 0.05) and less IL-10 (p < 0.01). They also resulted in significantly stronger T-cell proliferation response. It is concluded that Dll1 can promote the differentiation of DCs from mouse bone marrow cells and enhance their antigen presentation capacity.

Amyloid fibrils are filamentous and insoluble forms of peptides or proteins. Proline has long been considered to be incompatible with the cross-beta structural motif of amyloid fibrils. On the basis of solid-state NMR spectroscopy data, we present a structural model of an in-register parallel beta sheet for the amyloid fibrils formed from a human prion protein fragment, huPrP(127-47). We have developed a simple solid-state NMR spectroscopy technique to identify solvent-protected backbone amide protons in a H/D exchange experiment without disaggregating the amyloid fibrils, from which we find that proline residue P(137) does not disrupt the beta-sheet structure from G(127) to G(142). We suggest that the resultant kink at P(137) generates a twist between adjacent peptide strands to maintain hydrogen bonding in the beta-sheet regions flanking the P(137) residue. Although proline can be well integrated into the cross-beta structure of amyloid fibrils, the kink formed at the position of the proline residue will considerably weaken the hydrogen bonding between the neighboring strands, especially when the mutation site is near the central region of a beta sheet.

Background: Hepatitis C virus (HCV) core protein is a multi-functional viral protein that interacts with several target proteins of both viral and cellular origin., Aim and Methods: To gain insight into the mechanism of action of HCV core protein, we used a yeast two-hybrid system to identify the core protein-interacting cellular targets., Results: A cDNA clone encoding an aspartoacylase was obtained, termed aspartoacylase 3 (ACY3). Interaction between ACY3 and HCV core protein was verified using a co-immunoprecipitation assay in vitro, and a mammalian two-hybrid system in vivo. Fluorescence microscopy showed green fluorescence protein-fused ACY3 localized in the cytoplasm., Conclusion: Our data suggest that ACY3 is an HCV core binding protein, which may play a role in the development of HCV-associated diseases.

Objective: To analyze the interaction of hepatitis C virus (HCV) core protein with HCBP1 and observe the expression and cellular localization of HCBP1., Methods: The cDNA fragments encoding HCV core protein and HCBP1 were amplified by PCR and subsequently cloned into pGEM T vector, respectively. After sequence verification, the two recombined vectors were respectively subcloned into two hybrid plasmids, pM and pVP16. pM-core, pVP16- HCBP1 and the reporter vector pG5CAT were co-transfected into COS-7 cells, and the interaction between HCV core protein and HCBP1 was assayed by detecting CAT gene expression after 48 h. The expression and subcellular localization of the fusion protein in the transfected COS-7 cells were analyzed by Western blotting and fluorescence microscopy, respectively., Results: CAT-ELISA showed that the absorbance of the co-transfection group was significantly higher than that o f the negative control groups but lower than that of the positive control group. Western blotting confirmed the expression of fusion protein in the transfected COS-7 cells. Fluorescence microscopy showed that the fusion protein was distributed mainly in the cytoplasm, and in contrast, diffuse EGFP expression was detected in COS-7 cells transfected with the empty vector., Conclusion: Mammalian two-hybrid assay confirms the capacity of HCBP1 to bind HCV core protein, and the expression vector for HCBP1-EGFP fusion gene has been constructed successfully and expressed in COS-7 cells.

The amyloid beta peptide (Abeta), composed of 40 or 42 amino acids, is a critical component in the etiology of the neurodegenerative Alzheimer disease. Abeta is prone to aggregate and forms amyloid fibrils progressively both in vitro and in vivo. To understand the process of amyloidogenesis, it is pivotal to examine the initial stages of the folding process. We examined the equilibrium folding properties, assembly states, and stabilities of the early folding stages of Abeta40 and Abeta42 prior to fibril formation. We found that Abeta40 and Abeta42 have different conformations and assembly states upon refolding from their unfolded ensembles. Abeta40 is predominantly an unstable and collapsed monomeric species, whereas Abeta42 populates a stable structured trimeric or tetrameric species at concentrations above approximately 12.5 microm. Thermodynamic analysis showed that the free energies of Abeta40 monomer and Abeta42 trimer/tetramer are approximately 1.1 and approximately 15/ approximately 22 kcal/mol, respectively. The early aggregation stages of Abeta40 and Abeta42 contain different solvent-exposed hydrophobic surfaces that are located at the sequences flanking its protease-resistant segment. The amyloidogenic folded structure of Abeta is important for the formation of spherical beta oligomeric species. However, beta oligomers are not an obligatory intermediate in the process of fibril formation because oligomerization is inhibited at concentrations of urea that have no effect on fibril formation. The distinct initial folding properties of Abeta40 and Abeta42 may play an important role in the higher aggregation potential and pathological significance of Abeta42.

Caspase recruitment domains (CARDs) are small helical protein domains that adopt the Greek key fold. For the two CARDs studied to date, RICK-CARD and caspase-1-CARD (CP1-CARD), the proteins unfold by an apparent two-state process at equilibrium. However, the folding kinetics are complex for both proteins and may contain kinetically trapped species on the folding pathway. In the case of RICK-CARD, the time constants of the slow refolding phases are consistent with proline isomerism. RICK-CARD contains three prolines, P47 in turn 3, and P85 and P87. The latter two prolines constitute a nonconserved PxP motif in helix 6. To examine the role of the prolines in the complex folding kinetics of RICK-CARD, we generated seven proline-to-alanine mutants, including three single mutants, three double mutants, and one triple mutant. We examined the spectroscopic properties, equilibrium folding, binding to CP1-CARD, and folding kinetics. The results show that P85 is critical for maintaining the function of the protein and that all mutations decrease the stability. Results from single mixing and sequential mixing stopped-flow studies strongly suggest the presence of parallel folding pathways consisting of at least two unfolded populations. The mutations affect the distribution of the two unfolded species, thereby affecting the population that folds through each channel. The two conformations also are present in the triple mutant, demonstrating that interconversion between them is not due to prolyl isomerism. Overall, the data show that the complex folding pathway, especially formation of kinetically trapped species, is not due to prolyl isomerism.

Aim: To assess the inhibitory effect of Huangqi Zhechong decoction on hepatic fibrosis in rats induced by CCl(4) plus alcohol and high fat low protein diet., Methods: Male SD rats were randomly divided into hepatic fibrosis model group, control group and 3 treatment groups consisting of 12 rats in each group. Except for the normal control group, all the rats were subcutaneously injected with CCl(4) at a dosage of 3 mL/kg. In 3 treated groups, either high-dose group (9 mL/kg), or medium-dose group (6 mL/kg), or low-dose group (3 mL/kg) was daily gavaged with Huangqi Zhechong decoction, and saline vehicle was given to model and normal control rats. Enzyme-linked immunosorbent assay (ELISA) and biochemical examinations were used to determine the changes of alanine aminotransferase (ALT), aspartate aminotransferase (AST), hyaluronic acid (HA), laminin (LN), type-III-procollagen-N-peptide (PIIIP), and type IV collagen content in serum, and hydroxyproline (Hyp) content in liver after sacrificing the rats. Pathologic changes, particularly fibrosis were examined by hematoxylin and eosin (HE) and Van Gieson staining., Results: Compared with the model control group, serum ALT, AST, HA, LN, PIIIP and type IV collagen levels dropped markedly in Huangqi Zhechong decoction groups, especially in the medium-dose Huangqi Zhechong decoction group (1 954+/-576 U/L vs 759+/-380 U/L, 2 735+/-786 U/L vs 1 259+/-829 U/L, 42.74+/-7.04 ng/mL vs 20.68+/-5.85 ng/mL, 31.62+/-5.84 ng/mL vs 14.87+/-1.45 ng/mL, 3.26+/-0.69 ng/mL vs 1.47+/-0.46 ng/mL, 77.68+/-20.23 ng/mL vs 25.64+/-4.68 ng/mL, respectively) (P<0.05). The Hyp content in liver tissue was also markedly decreased (26.47+/-11.24 mg/mgprot vs 9.89+/-3.74 mg/mgprot) (P<0.01). Moreover, the stage of the rat liver fibrosis in Huangqi Zhechong decoction groups was lower than that in model group, and more dramatic drop was observed in medium-dose Huangqi Zhechong decoction group (P<0.01)., Conclusion: Huangqi Zhechong decoction can inhibit hepatic fibrosis resulted from chronic liver injure, retard the development of cirrhosis, and notably ameliorate the liver function. It may be a safe and effective therapeutic drug for patients with fibrosis.