Genome-wide patterns of histone modifications in fission yeast

We have used oligonucleotide tiling arrays to construct genome-wide high-resolution histone acetylation maps for fission yeast. The maps are corrected for nucleosome density and reveal surprisingly uniform patterns of modifications for five different histone acetylation sites. We found that histone acetylation and methylation patterns are generally polar, i.e. they change as a function of distance from the ATG codon. A typical fission yeast gene shows a distinct peak of histone acetylation around the ATG and gradually decreased acetylation levels in the coding region. The patterns are independent of gene length but dependent on the gene expression levels. H3K9Ac shows a stronger peak near the ATG and is more reduced in the coding regions of genes with high expression compared with genes with low expression levels. H4K16Ac is strongly reduced in coding regions of highly expressed genes. A second microarray platform was used to confirm the 5′ to 3′ polarity effects observed with tiling microarrays. By comparing coding region histone acetylation data in HDAC mutants and wild type, we found that hos2 affects primarily the 5′ regions, sir2 and clr6 affect middle regions, and clr6 affects 3′ regions. Thus, mechanisms involving different HDACs modulate histone acetylation levels to maintain a 5′ to 3′ polarity within the coding regions. Electronic Supplementary Material Supplementary material is available for this article at and accessible for authorised users.     

Post-translational modifications of self antigens: implications for autoimmunity

Alterations in amino acid sequence can generate neo-epitopes from self proteins, causing autoaggressive immune attack. There is a range of possible post-translational modifications (PTMs) of mammalian proteins that can allow immune recognition of neo-self epitopes. These effects can vary from overt increase in affinity of MHC or T-cell receptor binding, to more subtle effects on the activity of proteolytic enzymes involved in antigen processing. Furthermore, intriguing insights into how the complex interactions between inflammation, enzyme activity and protein modification can direct self recognition are beginning to be unearthed.     

Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications

Genome integrity is constantly monitored by sophisticated cellular networks, collectively termed the DNA damage response (DDR). A common feature of DDR proteins is their mobilization in response to genotoxic stress. Here, we outline how the development of various complementary methodologies has provided valuable insights into the spatiotemporal dynamics of DDR protein assembly/disassembly at sites of DNA strand breaks in eukaryotic cells. Considerable advances have also been made in understanding the underlying molecular mechanisms for these events, with post-translational modifications of DDR factors being shown to play prominent roles in controlling the formation of foci in response to DNA-damaging agents. We review these regulatory mechanisms and discuss their biological significance to the DDR.     

腺样体扁桃体肥大相关B细胞免疫活化调控机制的研究进展

B细胞通过其表面分布的 B细胞受体 （BCR） 识别外界抗原,是机体产生保护性抗体与免疫记忆的关键步骤。 B细胞免疫活化调控与诸多上呼吸道疾病是密切相关的。儿童常见疾病腺样体扁桃体肥大 （ATH）,其特征性病理本质为淋巴滤泡的增生,但其确切机制尚未明确。本文综述静息态下维持B细胞存活的BCR滋养信号研究,阐述了B细胞免疫活化及产生快速高效免疫记忆的调控机制,尤其是活化早期分子事件,强调mIgG-tail对记忆性抗体应答的相关作用。B细胞活化调控过程出现异常可破坏免疫稳态平衡,导致疾病的发生。本文总结了B细胞免疫活化调控与ATH的机制关联,尝试探讨信号转导通路失调或突变对ATH的可能影响。旨在深入理解ATH的致病机理,以期挖掘潜在研究突破口,寻找ATH新的诊疗靶点。     

Active release of surface proteins: a mechanism associated with the immune escape of Acanthocheilonema viteae microfilariae

Living Acanthocheilonema viteae microfilariae obtained from peripheral blood of parasitised Meriones unguiculatus were surface-labelled with 125I. Four major surface exposed proteins of approximately 14.50, 14.55, 17.5, 19 kDa and one less abundant protein of 40 kDa were identified. Under non-reducing conditions the low-molecular-weight (LMW) proteins were isolated as multimers suggesting the presence of intermolecular disulphide linkages. In gels containing Triton X-100 the labelled epicuticular proteins behaved lipophilically. By cultivation of surface-labelled and metabolically labelled microfilaria in vitro, a continuous shedding of two LMW proteins was demonstrated. These proteins were produced in large amounts and released into the culture supernatant as monomeric and pentameric molecules. Concomitant with this release, one of the proteins appeared to lose its lipophilic character, giving rise to a hydrophilic 14.50-kDa entity. Although most of the extracted surface proteins reacted with sera from patent jirds, these sera failed to recognise the surface of living microfilariae. However, microfilariae pretreated with glutaraldehyde or attenuated with Na-azide could be labelled with surface specific antibodies.     

Localization of proteins associated with the outer hair cell plasma membrane in the gerbil cochlea

There is substantial evidence that the motility of mammalian outer hair cells is generated close to or within the plasma membrane. Several analogies between the outer hair cell cortical lattice and the membrane-related cytoskeleton of erythrocytes have been noted. In erythrocytes a member of the anion exchanger protein family, AE1, also known as Band 3, is involved in membrane-cytoskeleton linkage via Protein 4.1. In the following paper, the presence of these two proteins in gerbilline outer hair cells is confirmed by western blot. Furthermore, co-localization of these two proteins was detected in the lateral wall of outer hair cells by immunofluorescence and postembedding electron immunohistochemistry. Band 3 is restricted to this region, whereas Protein 4.1 has a somewhat more dispersed distribution.

Thus, the structure of these sensory receptor cells may result from an adaptation of a strategy used by other motile cells. The proteins investigated likely have a support function and may comprise “pillars” seen between the lateral plasma membrane and the cytoskeleton in micrographs of outer hair cells. The possibility that Band 3 comprises “protein particles” seen in the lateral plasma membrane, or maybe directly involved in the voltage-dependent force generation in outer hair cells, is also discussed.     

Alkylated cellulosic membranes with enhanced albumin affinity: Influence of competing proteins

4-Vinyl pyridine was grafted to the surface of the cellulosic membrane Cuprophan, and subsequently alkylated with both non-fatty acid-like C10 (GVP-C10) and fatty acid-like C16 (GVP-C16) aliphatic chains. In vitro albumin adsorption studies from single and binary protein solutions, as well as from dilute plasma demonstrated a significant enhancement (1.4-3.89 times) of albumin binding to both the GVP-C10 and GVP-C 16 surfaces, relative to unmodified Cuprophan. It is speculated that enhanced albumin adsorption to a surface may improve surface thromboresistance. Further, these results suggest that there is no difference between the enhanced albumin adsorption of the fatty acid and nonfatty like alkyl chains, C10 and C16.     

Complement regulatory proteins in kidneys of patients with anti‐neutrophil cytoplasmic antibody (ANCA)‐associated vasculitis

The complement system activation is involved in the development of anti‐neutrophil cytoplasmic antibody‐associated vasculitis (AAV). The study aimed to investigate the expression of complement regulatory proteins (CRPs) CD46, CD55 and CD59 in kidneys of 51 AVV patients. The expression of CD46, CD55 and CD59 in kidneys was detected by immunohistochemistry and double immunofluorescence staining. The immunohistochemical examination revealed that expression of the three CRPs could be detected in the glomeruli and tubules of both AAV patients and normal controls. The expression levels of the three CRPs in glomeruli of patients with AAV were significantly lower than those of normal controls. The scores of CD46 and CD55 expression in the tubules of AAV patients were significantly lower than those of normal controls, while there was no significant difference between the scores of CD59 expression in tubules of AAV patients and those of normal controls. Among AAV patients, the expression level of CD46 in glomeruli correlated inversely with the proportion of normal glomeruli, while it correlated with tubular atrophy in renal interstitium (r = –0·305, P = 0·026; r = 0·330, P = 0·023, respectively). The expression levels of CD55 and CD59 in glomeruli correlated with the proportion of total crescents (r = 0·384, P = 0·006; r = 0·351, P = 0·011, respectively). Double immunofluorescence staining indicated that all three CRPs were expressed on endothelial cells, podocytes and mesangial cells in glomeruli. The expression levels of the three CRPs were dysregulated in kidneys of patients with AAV. The expression levels of CD46, CD55 and CD59 were associated with the severity of renal injury of AAV patients.     

Exploring the antibacterial mechanism of essential oils by membrane permeability,apoptosis and biofilm formation combination with proteomics analysis against methicillin-resistant staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the important causes of food poisoning and infectious diseases worldwide, it can produce a large number of virulence factors, enhance the colonization ability of the host so that it can quickly colonize and spread on the surface of the objects. Essential oil (EO) is one of the natural products with antimicrobial properties, can be used as an important source of antibacterial agent discovery, and has a broad development prospect. However, the unclear mechanisms of antibacterial action have become an obstacle to its further development and use. Hence, the objective of the present study was to reveal the antibacterial mechanism of EO from Amomum villosum Lour (A villosum Lour) against MRSA using label-free quantitative proteomics, investigate the effect of EO on the bacterial proteome, enzymatic activities and leakage of bacterial intracellular biomacromolecule. Proteomic analysis of MRSA in the presence of EO found that a total of 144 differential expressed proteins (DEPs) between the control and treatment group, in which 42 proteins were distinctly up-regulated and 102 proteins were down-regulated. Besides, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, determination of cell membrane permeability and apoptosis, scanning electron microscopy (SEM) observations, bacterial surface hydrophobicity, and biofilm formation measurement were performed. Collectively, the above results indicated that the cell membrane damage by EO leads to the loss of membrane integrity and causes leakage of intracellular macromolecular substances, inhibition of protein, and biofilm synthesis. These findings manifested that EO exerts antibacterial effect by multiple avenues and expands our understanding of the antibacterial mechanism, it has potential application value in food preservative and pharmaceutical industries.     

Altered expression of cell cycle regulatory proteins in gastrointestinal stromal tumors: markers with potential prognostic implications

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of the digestive tract. The prediction of the malignant potential of GISTs is still difficult. Altered cell cycle regulation may underlie the tumorigenesis and/or the progression of human malignancies. Although p53 and Bcl-2 have been extensively investigated in GISTs, little is known about the frequency of expression and possible clinical implications of alterations of other cell cycle regulatory proteins in these neoplasms. We have previously investigated the role of loss of p16(INK4A) by loss of heterozygosity and immunohistochemistry in the progression of GISTs and found that loss of heterozygosity of 9p and loss of p16 expression are confined to malignant GISTs. This has led us to investigate the role of other cell cycle regulatory proteins in these tumors. Twenty-three cases of GIST (9 low malignant potential [LMP], 10 primary malignant, and 4 intra-abdominal recurrences) were examined. All cases were strongly positive for KIT (CD117). Immunohistochemical stains were carried out on tissue microarrays to evaluate the expression of proteins involved in the G(1)-S transition and proteins that regulate apoptosis including Rb, E2F1, cyclin D1, CDK4, CDK6, p27(KIP1), p21(WAF1/CIP1), p53, Mdm2, Bcl-2, and Bax. The positive phenotypes identified were as follows: Rb, 39.1%; E2F1, 69.6%; cyclin D1, 30.4%; CDK4, 100%; CDK6, 30.4%; 39.1%; p27(KIP1), 47.8%; p21(WAF1/CIP1), 39.1%; p53, 43.5%; Mdm2, 17.4%; Bcl-2, 91.3%; and Bax, 100%. Malignant GISTs are more likely to be associated with a positive E2F1 and p53 phenotype and a negative p16 and p27(KIP1) phenotype. It was concluded that aberration of the cell cycle regulators is a frequent finding and may be a contributing factor to the pathogenesis of GISTs. While some alterations are seen in LMP and malignant GISTs and therefore may represent an early event in molecular tumorigenesis of GISTs, other alterations are more common in malignant GISTs than LMP and therefore have potential utility as complementary tools for the prognostication of GISTs.     

Thin filament proteins mutations associated with skeletal myopathies: Defective regulation of muscle contraction

In humans, more than 140 different mutations within seven genes (ACTA1, TPM2, TPM3, TNNI2, TNNT1, TNNT3, and NEB) that encode thin filament proteins (skeletal α-actin, β-tropomyosin, γ-tropomyosin, fast skeletal muscle troponin I, slow skeletal muscle troponin T, fast skeletal muscle troponin T, and nebulin, respectively) have been identified. These mutations have been linked to muscle weakness and various congenital skeletal myopathies including nemaline myopathy, distal arthrogryposis, cap disease, actin myopathy, congenital fiber type disproportion, rod-core myopathy, intranuclear rod myopathy, and distal myopathy, with a dramatic negative impact on the quality of life. In this review, we discuss studies that use various approaches such as patient biopsy specimen samples, tissue culture systems or transgenic animal models, and that demonstrate how thin filament proteins mutations alter muscle structure and contractile function. With an enhanced understanding of the cellular and molecular mechanisms underlying muscle weakness in patients carrying such mutations, better therapy strategies can be developed to improve the quality of life.     

The behavioral treatment of essential hypertension: An update and comparison with pharmacological treatment

This review summarizes findings from controlled studies on the treatment of essential hypertension by relaxation and/or biofeedback and examines the efficacy of behavioral versus pharmacological approaches. It is concluded that behavioral treatment is superior to (a) no-treatment, (b) blood pressure-self-monitoring, and (c) attention-control conditions, but exceptions are noted. Although behavioral treatments compared with each other usually show no significant differences in effectiveness, behavioral treatment is clearly less effective than pharmacotherapy in the control of essential hypertension. Despite this last conclusion, a behavioral approach may be of real clinical value in the treatment of some patients, based upon findings of 24-hour reductions in blood pressure and the generalization and long-term maintenance of treatment effects. Predictors of response to behavioral treatment are examined, and the conclusions of this review are discussed in terms of their similarity to findings from comparative studies of psychotherapies. Recommendations for research and a stepped-care treatment approach are presented.     

Profile of autoantibody to basement membrane zone proteins in patients with mucous membrane pemphigoid: long-term follow up and influence of therapy

Mucous membrane pemphigoid (MMP) is an autoimmune mucocutaneous blistering disease characterized by autoantibodies to components within the basement membrane zone. In this study, we report the titers of autoantibodies to antigens in the BMZ, in the sera of 13 patients, treated with intravenous immunoglobulin as monotherapy over a consecutive 18-month period. Using bovine gingiva lysate as substrate in an immunoblot assay, autoantibodies to human bullous pemphigoid antigens (BPAg1 and BPAg2), human beta4 integrin, and laminin 5 were measured. A statistically significant (P < 0.05) decline in the autoantibody titers to beta4-integrin was observed after 3.42 months of initiating the IVIg therapy. These titers were undetectable after 13 months of therapy. The titers of antibodies to BPAg1 and BPAg2 did not correlate with disease activity or response to therapy. Antibodies to laminins were not detected. In patients with MMP, autoantibody titers to beta4-integrin correlate with disease activity and response to therapy.     

Comprehensive proteomic analysis and pathogenic role of membrane vesicles of Listeria monocytogenes serotype 4b reveals proteins associated with virulence and their possible interaction with host

Membrane vesicles (MVs) are produced by various Gram positive and Gram negative pathogenic bacteria and play an important role in virulence. In this study, the membrane vesicles (MVs) of L. monocytogenes were isolated from the culture supernatant. High-resolution electron microscopy and dynamic light scattering analysis revealed that L. monocytogenes MVs are spherical with a diameter of 200 to 300 nm in size. Further, comprehensive proteomic analyses of MVs and whole cells of L. monocytogenes were performed using LC/MS/MS. A total of 1355 and 312 proteins were identified in the L. monocytogenes cells and MVs, respectively. We identified that 296 proteins are found in both whole cells, and MV proteome and 16 proteins were identified only in the MVs. Also, we have identified the virulence factors such as listeriolysin O (LLO), internalin B (InlB), autolysin, p60, NLP/P60 family protein, UPF0356 protein, and PLC-A in MVs. Computational prediction of host-MV interactions revealed a total of 1841 possible interactions with the host involving 99 MV proteins and 1513 host proteins. We elucidated the possible pathway that mediates internalization of L. monocytogenes MV to host cells and the subsequent pathogenesis mechanisms. The in vitro infection assays showed that the purified MVs could induce cytotoxicity in Caco-2 cells. Using endocytosis inhibitors, we demonstrated that MVs are internalized via actin-mediated endocytosis. These results suggest that L. monocytogenes MVs can interact with host cell and contribute to the pathogenesis of L. monocytogenes during infection.     

Centrosome abnormalities in non-small cell lung cancer: correlations with DNA aneuploidy and expression of cell cycle regulatory proteins

The aims of this study were to investigate centrosome abnormalities in non-small cell lung cancer (NSCLC), and to assess their relationship with DNA aneuploidy, the expression of the cell cycle-associated proteins, and clinicopathological profiles. Tissue microarrays were constructed from 175 NSCLCs. We analyzed centrosome abnormalities and the expression of p16^INK4a, p53, and pRb using immunohistochemistry. Centrosome abnormalities were noted in 29% of the tumors and were even observed in the normal cells adjacent to the tumor. The frequency of DNA aneuploidy was significantly higher in the tumors containing centrosome abnormalities than in the tumors with a normal centrosome. p16^INK4a expression and loss of pRb expression, but not p53 expression, were significantly associated with centrosome abnormalities. Clinically, centrosome abnormalities were not found to have any prognostic value for NSCLCs. These results suggest that centrosome abnormalities may be associated with inactive pRb-pathway and contribute to pulmonary carcinogenesis by the level of increasing chromosome instability.     

Autosomal dominant inheritance with sex-limited manifestation: An unusual mode of transmission in humans and animals

Autosomal dominant, sex-limited inheritance is a distinct mode of transmission that should not be conflated with X-linked inheritance. From animal studies, we know that sex-limited inheritance implies the chance to “turn off” some genes in either males or females, in order to meliorate the phenotype, for example, by improving the fecundity. In this way, sex-limited genes play an important role in the evolution of diverse species of animals. In human genetics, however, the biological significance of sex-limited genes is unknown until today. When screening the literature, we found, thus far, three human examples of sex-limited transmission. Autosomal dominant, male-limited inheritance has meticulously been studied in a particular form of precocious puberty. Limitation to females was described in autosomal dominant lymphedema of the CESLR1 type, being underpinned by convincing molecular findings. Another example is white lentiginosis of Grosshans that shows clinical evidence of such mode of transmission although molecular findings are lacking as yet. In the animal kingdom, autosomal dominant sex-limited inheritance is a well-established phenomenon that has extensively been studied in various species such as butterflies, damselflies, fish (cichlids), and birds. Hence, at this point in time, it seems likely that other human examples of this mode of inheritance have previously been reported or will be published in the future.     

Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study

Essential hypertension is a major cardiovascular risk factor and a large proportion of this risk is genetic. Identification of genomic regions consistently associated with hypertension has been difficult in association studies to date as this requires large sample sizes.We previously published a large genome-wide linkage scan in Americans of African (AA) and European (EA) descent in the GenNet Network of the Family Blood Pressure Program (FBPP). A highly significant linkage peak was identified on chr1q spanning a region of 100 cM. In this study, we genotyped 1569 SNPs under this linkage peak in 2379 individuals to identify whether common genetic variants were associated with blood pressure (BP) at this locus.Our analysis, using two different family-based association tests, provides suggestive evidence (P≤2 × 10⁻⁵) for a collection of single nucleotide polymorphisms (SNPs) associated with BP. In EAs, using diastolic BP as a quantitative phenotype, three variants located in or near the GPA33, CD247, and F5 genes, emerge as our top hits; for systolic BP, variants in GPA33, CD247, and REN are our best findings. No variant in AAs came close to suggestive evidence after multiple-test corrections (P≥8 × 10⁻⁵).In summary, we show that systematic follow-up of a linkage signal can help discover candidate variants for essential hypertension that require a follow-up in yet larger samples. The failure to identify common variants is either because of low statistical power or the existence of rare coding variants in specific families or both, which require additional studies to clarify.     

Receptor-evoked Ca2+ mobilization in pancreatic acinar cells: Evidence for a regulatory role of protein kinase C by a mechanism involving the transition of high-affinity receptors to a low-affinity state

In order to establish a regulatory role for phosphoproteins in the process of receptor-stimulated Ca²⁺ mobilization, isolated pancreatic acinar cells, loaded with fura-2, were stimulated with cholecystokin-in-octapeptide (CCK₈) in the presence of either staurosporine, a general inhibitor of protein kinase activity, or 12-O-tetradecanoylphorbol 13-acetate (TPA), an activator of protein kinase C. Staurosporine alone did not affect the average free cytosolic Ca²⁺ concentration ([Ca²⁺]_i,av) in a suspension of acinar cells. However, in the presence of 1.0 M Staurosporine the stimulatory effect of submaximal concentrations of CCK₈ was significantly enhanced. The potentiating effect of the inhibitor was paralleled by the increased production of inositol 1,4,5-trisphosphate. In addition, staurosporine evoked a transient increase in [Ca²⁺]_i,av in cells prestimulated with a submaximal concentration of CCK₈. The data obtained with staurosporine indicate that CCK₈-stimulated phosphorylations exert a negative feedback role in the process of receptor-mediated Ca²⁺ mobilization. The involvement of protein kinase C was investigated by studying the effects of TPA on CCK₈-induced Ca²⁺ mobilization. The phorbol ester induced a rightward shift of the dose/response curve for the CCK₈-evoked increase in [Ca²⁺]_i,av, which, in contrast to the unlimited shift obtained with the receptor antagonist D-lorglumide, reached a maximum of approximately one order of a magnitude at 10 nM TPA. The inhibitory effect of TPA was completely overcome by CCK₈ at concentrations at or beyond 10 nM. This observation has led to the hypothesis that protein kinase C, directly or indirectly, converts the CCK receptor from a high-affinity state to a low-affinity state. Substantial evidence in favour of this hypothesis was provided by the observation that the increase in [Ca²⁺]_i,av evoked by the CCK₈ analogue JMV-180, which acts as an agonist at the high-affinity receptor, was completely blocked by TPA pretreatment. TPA also evoked a rightward shift of the dose/response curve for the carbachol-induced increase in [Ca²⁺]_i,av, indicating that the protein-kinase-C-mediated transition of the affinity state of receptors is a more general phenomenon. In the presence of submaximal CCK₈ concentrations, TPA dose-dependently decreased the poststimulatory elevated [Ca²⁺]_i,av to the prestimulatory level, indicating that protein kinase C also inhibits the process of sustained Ca²⁺ mobilization. The effects of TPA were counteracted by staurosporine, suggesting that the effects of the inhibitor itself were indeed due to inhibition of the receptor-mediated activation of protein kinase C. The data presented are in support of a negative-feedback role for protein kinase C in the process of receptor-mediated Ca²⁺ mobilization by a process that involves phosphorylation of the CCK receptor, thereby transforming it from a high-affinity state into a low-affinity state.