Cdk5 targets active Src for ubiquitin-dependent degradation by phosphorylating Src(S75)

The non-receptor tyrosine kinase Src is a critical regulator of cytoskeletal contraction, cell adhesion, and migration. In normal cells, Src activity is stringently controlled by Csk-dependent phosphorylation of Src(Y530), and by Cullin-5-dependent ubiquitinylation, which affects active Src(pY419) exclusively, leading to its degradation by the proteosome. Previous work has shown that Src activity is also limited by Cdk5, a proline-directed kinase, which has been shown to phosphorylate Src(S75). Here we show that this phosphorylation promotes the ubiquitin-dependent degradation of Src, thus restricting the availability of active Src. We demonstrate that Src(S75) phosphorylation occurs in vivo in epithelial cells, and like ubiquitinylation, is associated only with active Src. Preventing Cdk5-dependent phosphorylation of Src(S75), by site-specific mutation of S75 or by Cdk5 inhibition or suppression, increases Src(Y419) phosphorylation and kinase activity, resulting in Src-dependent cytoskeletal changes. In transfected cells, ubiquitinylation of Src(S75A) is about 35% that of wild-type Src-V5, and its half-life is approximately 2.5-fold greater. Cdk5 suppression leads to a comparable decrease in the ubiquitinylation of endogenous Src and a similar increase in Src stability. Together, these findings demonstrate that Cdk5-dependent phosphorylation of Src(S75) is a physiologically significant mechanism of regulating intracellular Src activity.

Hepatitis B virus X protein induces hypermethylation of p16(INK4A) promoter via DNA methyltransferases in the early stage of HBV-associated hepatocarcinogenesis

The aim of the present study was to authenticate the involvement of DNA methyltransferases (DNMTs) and methyl-CpG binding domain protein 2 (MBD2) in the process of HBx induced p16(INK4A) promoter hypermethylation in HBV-related hepatocellular carcinoma (HCC) and their corresponding noncancerous liver tissues. Eighty-eight fresh tissue specimens of surgically resected HBV-associated HCC and their corresponding noncancerous liver tissues were studied. The methylation status of the p16(INK4A) promoter was determined by methylation-specific polymerase chain reaction (MSP). Reverse transcription and real-time polymerase chain reaction (RT-PCR) showed the expression of DNMTs, MBD2 and HBx. Western blot and immunohistochemistry were used for the protein analysis of HBx, DNMT1, DNMT3A and P16. Tissue HBV-DNA levels were determined by RT-PCR. HBV genotype was examined by nested PCR and restriction fragment length polymorphism (RFLP). In the corresponding noncancerous liver tissues, higher HBx expression was associated with the hypermethylation of the p16(INK4A) promoter. HBx was positively correlated with the DNMT1 and DNMT3A at both the mRNA and protein level. Furthermore, HBx, DNMT1 and DNMT3A protein expression were negatively correlated with p16 protein expression. In HCC tissues, HBx was positively correlated with DNMT1 and DNMT3A at both mRNA and protein level, but HBx expression did not correlate with hypermethylation of the p16(INK4A) promoter or p16 protein expression. The methylation status of the p16(INK4A) promoter did not correlate with clinicopathological characteristics. DNMT1 and DNMT3A may play important roles in the process of HBx inducing hypermethylation of the p16(INK4A) promoter in the early stages of HBV-associated HCC. HBx-DNMTs-p16(INK4A) promoter hypermethylation may constitute a mechanism for tumorigenesis during HBV-associated hepatocarcinogenesis.

Kinetic studies on the degradation of crystal violet by the Fenton oxidation process

The degradation of dye crystal violet (CV) by Fenton oxidation process was investigated. The UV-Vis spectrogram has shown that CV can be degraded effectively by Fenton oxidation process. Different system variables namely initial H(2)O(2) concentration, initial Fe(2 + ) concentration and reaction temperature, which have effect on the degradation of CV by Fenton oxidation process, have been studied systematically. The degradation kinetics of CV was also elucidated based on the experimental data. The degradation of CV obeys the first-order reaction kinetics. The kinetic model can be described as k=1.5 exp(-(7.5)/(RT))[H(2)O(2)](0)(0.8718)[Fe(2+)](0)(0.5062). According to the IR spectrogram, it is concluded that the benzene ring of crystal violet has been destroyed by Fenton oxidation. The result will be useful in treating dyeing wastewater containing CV by Fenton oxidation process.

Unique histological features of the left atrial posterior wall

The left atrial posterior wall (LAPW) plays a critical role in atrial fibrillation, but the underlying mechanism remains unclear. In the present study, we sought to characterize the histological features of the LAPW. Different atrial regions were dissected from hearts of normal Sprague-Dawley rats and humans. Haematoxylin/eosin and van Gieson staining were used to analyse atrial cardiomyocyte arrangement and collagen distribution, respectively. Intercellular junctions were evaluated by transmission electron microscopy. In contrast with other atrial regions, the LAPW exhibited more disorganized cardiomyocytes, larger intercellular spaces and variable myocardial fibre arrangement. The proportion of collagen was significantly higher in the LAPW than in other atrial regions. Interestingly, desmosomes were sparse along with intercellular gaps in the LAPW. In summary, distinct disarrangement of cardiomyocytes and an abundance of collagen exist in the LAPW. The sparsity of desmosomes in the LAPW may be related to the heterogeneous distribution and separation of atrial myocytes.

Mutation L437P in the 2B domain of keratin 1 causes diffuse palmoplantar keratoderma in a Chinese pedigree

Diffuse palmoplantar keratoderma (DPPK) is an autosomal dominant genodermatosis characterized by uniform hyperkeratosis of the palm and sole epidermis. This disorder can be caused by mutations in the genes keratin 1, keratin 9, keratin 16, desmoglein 1 and plakoglobin. Here we present a DPPK Chinese pedigree and identify the aetiology as a novel missense mutation, L437P, located in a highly conserved helix motif in domain 2B of KRT1. Functional analysis shows that overexpression of the L437P mutant in cultured cells leads to abnormal intermediate filament networks and filament aggregation. This gain-of-function mutation highlights the role of domain 2B in mediating filament assembly.

Cloning, mapping and mutation analysis of human geneGJB5 encoding gap junction protein beta-5

By homologous EST searching and nested PCR a new human geneGJB5 encoding gap junction protein beta-5 was identified.GJB5 was genetically mapped to human chromosome 1p33-p35 by FISH. RT-PCR revealed that it was expressed in skin, placenta and fetal skin. DNA sequencing ofGJB5 was carried out in 142 patients with sensorineural hearing impairment and probands of 36 families with genetic diseases, including erythrokeratodermia (5 families), Charcot-Marie-Tooth disease (13), ptosis (4), and retinitis pigmentosa and deafness (14). Two missense mutations (686A-->G, H229R; 25C-->T, L9F) were detected in two sensorineural hearing impairment families. A heterologous deletion of 18 bp within intron was found in 3 families with heredity hearing impairment, and in one of the 3 families, a missense mutation (R265P) was identified also. But the deletion and missense mutation seemed not segregating with hearing impairment in the family. No abnormal mRNA or mRNA expression was detected in deletion carriers by RT-PCR analysis in skin tissue. Mutation analysis in 199 unaffected individuals revealed that two of them were carriers with the same 18 bp deletion.

Negative words on surgical wards result in therapeutic failure of patient-controlled analgesia and further release of cortisol after abdominal surgeries

BACKGROUND

The perception of pain is germane to the environmental stimuli. Nurses on surgical wards are the main contributor in influencing patients' psychophysiological fettle. The aim of the study was to investigate the effect of different words, negative or positive, from nurses on postoperative pain therapy with patient-controlled analgesia (PCA).

METHODS

1500 ASA I-II patients, who underwent abdominal hysterectomy, were screened and 771 were randomized into one of four groups. In the no words group (NW, N.=35), no words was delivered. The positive (PW, N.=248), partially negative (NW1, N.=241) and totally negative (NW2, N.=247) groups received corresponding words when treating with morphine PCA, the words were given singly at the 3(rd), 6(th), 12(th), 18(th) h and repeatedly at the 3(rd) and 6(th) h, and each group was redivided into six subgroups according to varying time points. Pain intensity, morphine consumption, side effects, overall sedation and satisfaction scores were recorded and plasma cortisol was tested.

RESULTS

A total of 614 patients completed the study. Negative words expressed significant influence on pain therapy at the 3(rd) and 6(th) h after surgeries (P<0.01), and this effect was more convenient in repeatedly treated patients (P<0.001). Positive and the 12(th) and 18(th) h negative words displayed little role in pain management. Morphine consumption, side effects, satisfaction and cortisol level converted with the change of the pain intensity. No intergroup differences were observed in patients' overall conditions.

CONCLUSION

Negative words on surgical wards influenced postoperative pain management at the earlier period of time after abdominal surgeries associated with the HPA axis activation.

Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution

In the Post Genome Age, there is an urgent need to develop the reliable and effective computational methods to predict the subcellular localization for the explosion of newly found proteins. Here, a novel method of pseudo amino acid (PseAA) composition, the so-called "amino acid composition distribution" (AACD), is introduced. First, a protein sequence is divided equally into multiple segments. Then, amino acid composition of each segment is calculated in series. After that, each protein sequence can be represented by a feature vector. Finally, the feature vectors of all sequences thus obtained are further input into the multi-class support vector machines to predict the subcellular localization. The results show that AACD is quite effective in representing protein sequences for the purpose of predicting protein subcellular localization.

Estimating residue evolutionary conservation by introducing von Neumann entropy and a novel gap-treating approach

Evolutionary conservation derived from a multiple sequence alignment is a powerful indicator of the functional significance of a residue, and it can help to predict active sites, ligand-binding sites, and protein interaction interfaces. The results of the existing algorithms in identifying the residue’s conservation strongly depend on the sequence alignment, making the results highly variable. Here, by introducing the amino acid similarity matrix, we propose a novel gap-treating approach by combining the evolutionary information and von Neumann entropies to compute the residue conservation scores. It is indicated through a series of tested results that the new approach is quite encouraging and promising and may become a useful tool in complementing the existing methods.

Identification of Bacteroides fragilisby a modified immuno polymerase chain reaction (mIPCR), using a specific monoclonal antibody

Bacteroides fragilis is the anaerobic species most commonly isolated from human clinical specimens, and is resistant to many antimicrobial agents. A monoclonal antibody, mAb4H8 (IgG3), reacting with a specific epitope in the lipopolysaccharide (LPS) isolated from most of the B. fragilis strains, was produced and employed with modified Immuno Polymerase Chain Reaction (mIPCR) for identification of B. fragilis with a detection limit of 10(4) cfu/mL bacterial suspension. A number of bacterial strains were examined, including B. fragilis, Bacteroides spp. other than B. fragilis and other genera. All the B. fragilis strains with the immunodominant (beta1,6-linked D-galactosyl chain) epitope were positive. None of the other strains showed the positive reaction. The results indicate that mIPCR assay with mAb4H8 has a high specificity and high sensitivity.

Two eudesmane sesquiterpenes from Laggera pterodonta

Two new eudesmane sesquiterpenes, 2alpha-hydroxy pterodontic acid (1) and pterodolide [3alpha-(2-methyl-2,3-epoxy)-butyric-4alpha-acetoxy-8beta-ethoxy eudesma-7(11)-en-8alpha,12-olide (2), along with five known compounds (3-7) were isolated from the aerial parts of Laggera pterodonta. Their structures were elucidated on the basis of spectroscopic methods. The immunosuppressive activity of the isolated compounds was investigated.

Non-viral ex vivo transduction of human hepatocyte cells to express factor VIII using a human ribosomal DNA-targeting vector

BACKGROUND

In gene therapy, one of the most important issues is the choice of the vectors. pHrneo is a human-derived vector previously constructed by our group, which can target a foreign gene into a human ribosomal DNA (hrDNA) locus.

METHODS AND RESULTS

In this study, we inserted an expression cassette of reconstructive hFVIII (hFVIII-BDDAK39) to pHrneo to construct a targeting vector: pHrneo-BDDAK39. Through electroporation of pHrneo-BDDAK39 into HL7702 cells (human hepatocyte), we identified the homologous recombinants using polymerase chain reaction, and tested the expression of hFVIII-BDDAK39 located at the hrDNA locus. The hFVIII-BDDAK39 was successfully targeted into the hrDNA locus of HL7702 by pHrneo-BDDAK39, and the efficiency of site-specific integration was 1.1 x 10(-5). The hFVIII-BDDAK39 at the hrDNA locus of HL7702 was found to be able to express efficiently (4.3 +/- 0.9 ng 10(-6) cells 24 h(-1)).

CONCLUSION

It has been indicated that the targeting vector pHrneo-BDDAK39 can be used in gene therapy for hemophilia A.

Prediction of protein subcellular localization by support vector machines using multi-scale energy and pseudo amino acid composition

As more and more genomes have been discovered in recent years, there is an urgent need to develop a reliable method to predict the subcellular localization for the explosion of newly found proteins. However, many well-known prediction methods based on amino acid composition have problems utilizing the sequence-order information. Here, based on the concept of Chou's pseudo amino acid composition (PseAA), a new feature extraction method, the multi-scale energy (MSE) approach, is introduced to incorporate the sequence-order information. First, a protein sequence was mapped to a digital signal using the amino acid index. Then, by wavelet transform, the mapped signal was broken down into several scales in which the energy factors were calculated and further formed into an MSE feature vector. Following this, combining this MSE feature vector with amino acid composition (AA), we constructed a series of MSEPseAA feature vectors to represent the protein subcellular localization sequences. Finally, according to a new kind of normalization approach, the MSEPseAA feature vectors were normalized to form the improved MSEPseAA vectors, named as IEPseAA. Using the technique of IEPseAA, C-support vector machine (C-SVM) and three multi-class SVMs strategies, quite promising results were obtained, indicating that MSE is quite effective in reflecting the sequence-order effects and might become a useful tool for predicting the other attributes of proteins as well.

Endometrial expression of epithelial neutrophil-activating peptide-78 during the menstrual cycle or in progestin-only contraceptive users with breakthrough bleeding and the influence of doxycycline therapy

BACKGROUND

Endometrial breakthrough bleeding is characterized by an inflammatory reaction and increased production of proinflammatory mediators, one of which may be epithelial neutrophil-activating peptide-78 (ENA-78), a chemokine with neutrophil-activating properties.

METHODS AND RESULTS

We therefore investigated the endometrial expression of ENA-78 in Norplant users as progestin-only contraceptive with various bleeding patterns (n=35) as compared with non-users with a normal menstrual cycle (n=55). The endometrial stromal cells (ESCs) were the major site of ENA-78 expression with the highest levels found during the secretory phase. The expression of ENA-78 was increased in Norplant users with irregular bleeding as compared with those with regular cycles and amenorrhoea. The levels of ENA-78 detected in uterine washes and sera after the use of Norplant for 3-6 months (n=25) increased compared with baseline (P < 0.05). These levels did not significantly change in Norplant users who received doxycycline (Dox) therapy (25 mg/twice daily for 6 months) when measured midway through or at the conclusion of study when compared with the baseline (n=25). Treatments with medroxyprogesterone acetate (MPA) and tumour necrosis factor-alpha (TNF-alpha) (25 ng/ml), but not 17beta-estradiol (E2) or E2 + MPA (10(-8) M), representing endometrium exposed to contraceptive and inflammatory conditions, respectively, increased the levels of ENA-78 production by ESCs, and this was reduced by co-treatments with Dox (25 microg/ml) (P < 0.05).

CONCLUSIONS

The endometrial production of ENA-78 is altered in progestin-only contraceptive users experiencing breakthrough bleeding and is regulated by MPA and TNF-alpha in ESCs. Although Dox therapy did not alter uterine ENA-78 secretion, its suppression in ESCs suggests that Dox, acting site-specifically and through an anti-inflammatory mechanism, may influence the outcome of breakthrough bleeding in contraceptive users.

Prediction of protein homo-oligomer types by pseudo amino acid composition: Approached with an improved feature extraction and Naive Bayes Feature Fusion

The interaction of non-covalently bound monomeric protein subunits forms oligomers. The oligomeric proteins are superior to the monomers within the scope of functional evolution of biomacromolecules. Such complexes are involved in various biological processes, and play an important role. It is highly desirable to predict oligomer types automatically from their sequence. Here, based on the concept of pseudo amino acid composition, an improved feature extraction method of weighted auto-correlation function of amino acid residue index and Naive Bayes multi-feature fusion algorithm is proposed and applied to predict protein homo-oligomer types. We used the support vector machine (SVM) as base classifiers, in order to obtain better results. For example, the total accuracies of A, B, C, D and E sets based on this improved feature extraction method are 77.63, 77.16, 76.46, 76.70 and 75.06% respectively in the jackknife test, which are 6.39, 5.92, 5.22, 5.46 and 3.82% higher than that of G set based on conventional amino acid composition method with the same SVM. Comparing with Chou's feature extraction method of incorporating quasi-sequence-order effect, our method can increase the total accuracy at a level of 3.51 to 1.01%. The total accuracy improves from 79.66 to 80.83% by using the Naive Bayes Feature Fusion algorithm. These results show: 1) The improved feature extraction method is effective and feasible, and the feature vectors based on this method may contain more protein quaternary structure information and appear to capture essential information about the composition and hydrophobicity of residues in the surface patches that buried in the interfaces of associated subunits; 2) Naive Bayes Feature Fusion algorithm and SVM can be referred as a powerful computational tool for predicting protein homo-oligomer types.