Tag/hybridization-based sensitive detection of polymerase chain reaction products

The polymerase chain reaction (PCR) is an important technology to amplify a single copy or a few copies of DNA segment in genomic DNAs, visualizing the segment as DNA fragment. Thus, PCR is frequently used in various examinations such as detection of bacteria and fungi in the food industry. Here, we report a simple and sensitive method for detection of PCR products using single-strand tag sequence and hybridization of the tag sequence to the complementary tag sequence immobilized on solid material (STH). The detection sensitivity was found to be at least 50 times higher than electrophoresis/ethidium bromide (EtBr) visualization for approximately a 500-bp fragment and higher than the ordinary hybridization, that is, hybridization of denatured PCR product to probe sequence immobilized on solid material.     

Inhibition of interleukin-12 production by Trypanosoma brucei in rat macrophages

The immune response of a host infected with Trypanosoma brucei is modulated by trypomastigotes. We examined the changes in cytokine production in T. brucei gambiense (Wellcome strain; WS) infected rats and the influence on production of interleukin (IL)-12 by macrophages. The blood concentration of interferon-gamma, tumor necrosis factor-alpha, and IL-10 increased beginning the second day after infection. However, an increase in IL-12p40 was not observed until 4 days after infection. When spleen macrophages and Kupffer cells harvested from uninfected rats and HS-P cells (a rat macrophagelike cell line) were cocultured with WS, IL-12p40 production did not change. When HS-P cells were cultured with WS, transport of nuclear factor-kappaB into the nucleus increased. Levels of macrophage colony-stimulating factor (M-CSF) and granulocyte macrophage colony-stimulating factor mRNA in the spleens and livers of WS-infected rats were high in comparison with uninfected rats, suggesting that the WS promotes macrophage proliferation. The level of IL-12p40 mRNA in HS-P cells cocultured with WS increased in response to transfection with a small interfering RNA against M-CSF or addition of anti-M-CSF antibody. These results suggest that the WS inhibits IL-12p40 mRNA production by promoting production of macrophage colony-stimulating factor by macrophages.     

TNF-alpha and insulin, alone and synergistically, induce plasminogen activator inhibitor-1 expression in adipocytes

Obesity is associated with hyperinsulinemia and elevatedconcentrations of tumor necrosis factor- (TNF-) inadipose tissue. TNF- has been implicated as an inducer of thesynthesis of plasminogen activator inhibitor-1 (PAI-1), the primaryphysiological inhibitor of fibrinolysis, mediated by plasminogenactivators in cultured adipocytes. To identify mechanism(s) throughwhich TNF- induces PAI-1, 3T3-L1 preadipocytes were differentiatedinto adipocytes and exposed to TNF- for 24 h. TNF- selectivelyincreased the synthesis of PAI-1 without increasing activity ofplasminogen activators. Both superoxide (generated by xanthine oxidaseplus hypoxanthine) and hydrogen peroxide were potent inducers of PAI-1, and hydroxyl radical scavengers completely abolished the TNF- induction of PAI-1. Exposure of adipocytes to TNF- or insulin aloneover 5 days increased PAI-1 production. These agonists exert synergistic effects. Results obtained suggest that TNF- stimulates PAI-1 production by adipocytes, an effect potentiated by insulin, andthat adipocyte generation of reactive oxygen centered radicals mediatesthe induction of PAI-1 production by TNF-. Because induction ofPAI-1 by TNF- is potentiated synergistically by insulin, both agonists appear likely to contribute to the impairment of fibrinolytic system capacity typical in obese, hyperinsulinemic patients.

     

Inhibitory Mechanism of FAT4 Gene Expression in Response to Actin Dynamics during Src-Induced Carcinogenesis

Oncogenic transformation is characterized by morphological changes resulting from alterations in actin dynamics and adhesive activities. Emerging evidence suggests that the protocadherin FAT4 acts as a tumor suppressor in humans, and reduced FAT4 gene expression has been reported in breast and lung cancers and melanoma. However, the mechanism controlling FAT4 gene expression is poorly understood. In this study, we show that transient activation of the Src oncoprotein represses FAT4 mRNA expression through actin depolymerization in the immortalized normal human mammary epithelial cell line MCF-10A. Src activation causes actin depolymerization via the MEK/Erk/Cofilin cascade. The MEK inhibitor U0126 blocks the inhibitory effect of Src on FAT4 mRNA expression and Src-induced actin depolymerization. To determine whether actin dynamics act on the regulation of FAT4 mRNA expression, we treated MCF-10A cells with the ROCK inhibitor Y-27632. Y-27632 treatment decreased FAT4 mRNA expression. This suppressive effect was blocked by siRNA-mediated knockdown of Cofilin1. Furthermore, simultaneous administration of Latrunculin A (an actin depolymerizing agent), Y-27632, and Cofilin1 siRNA to the cells resulted in a marked reduction of FAT4 mRNA expression. Intriguingly, we also found that FAT4 mRNA expression was reduced under both low cell density and low stiffness conditions, which suggests that mechanotransduction affects FAT4 mRNA expression. Additionally, we show that siRNA-mediated FAT4 knockdown induced the activity of the Hippo effector YAP/TAZ in MCF-10A cells. Taken together, our results reveal a novel inhibitory mechanism of FAT4 gene expression through actin depolymerization during Src-induced carcinogenesis in human breast cells.     

Genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in Nepal

Background and Aims

This study was conducted to reveal the genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in various agroecological regions in Nepal.

Method

A total of 63 strains were isolated from common bean grown in the soils collected from seven bean fields in Nepal and characterized based on the partial sequences of 16S–23S internal transcribed spacer (ITS) regions, 16S rDNA, nodC, and nifH. Symbiotic properties of some representative strains with host plants were examined to elucidate their characteristics in relation to genotype and their origin.

Results

The isolated strains belonged to Rhizobium leguminosarum, Rhizobium etli, Rhizobium phaseoli, and one unknown Rhizobium lineage, all belonging to a common symbiovar (sv.) phaseoli. Nine ITS genotypes were detected mainly corresponding to a single site, including a dominant group at three sites harboring highly diverse multiple ITS sequences. Three symbiotic genotypes corresponded to a geographical region, not to the ribosomal DNA group, suggesting horizontal transfer of symbiotic genes separately in each region. Great differences in nitrogenase activity and nodule forming ability among the strains irrespective of their species and origin were observed.

Conclusions

Nepalese Himalaya harbor phylogenetically highly diverse and site-specific strains of common bean rhizobia, some of which could have high potential of symbiotic nitrogen fixation.     

Antibody expression in protease-deficient strains of the methylotrophic yeast Ogataea minuta

When human antibody genes were expressed in the methylotrophic yeast Ogataea minuta, the secreted antibody became partially degraded. To suppress the degradation, a vacuolar protease-deficient strain was constructed and its antibody production was evaluated. Although antibody productivity was improved in the vacuolar protease-deficient strain, the secreted antibody still became partially degraded. Peptide sequencing revealed that the cleavage occurred in the CH1 region of the heavy chain, implying that the cleavage was caused by an aspartic protease, Yps1p. To inhibit this cleavage, Yps1p-deficient strains were constructed and their antibody production was evaluated. As a result, the partial degradation of the antibody was suppressed in the O. minuta multiple-protease-deficient strains.     

Sex-specific HDL cholesterol changes with weight loss and their association with anthropometric variables: the LIFE study

Decrease in the level of high-density lipoprotein cholesterol (HDLC) has been observed in women who start dieting, but not in men. Patterns of HDLC change during intentional weight loss through 30-months of follow-up, and their association with changes in anthropometric measurements were examined in obese women (N = 112) and men (N = 100). Missing HDLC values at 6-, 12-, 18-, and 30-month follow-up (N = 16, 34, 55, and 50, respectively) due to dropout were imputed by multiple imputation. Mean ages and BMIs of subjects at baseline were 47.2 years and 34.8 kg/m(2) for women, and 50.4 years and 35.0 kg/m(2) for men. On average, participants lost weight steadily for 12 months, followed by slow regain. During the first 6 months, HDLC decreased significantly in women (-4.1 mg/dl, P = 0.0007), but not in men. Significant HDLC increases were observed in both men and women from 6- to 12-month follow-up. HDLC changes in women were positively associated with changes in hip circumference from baseline to 12-month independent of changes in triglycerides (TG), glucose, and insulin. Rapid decrease of predominantly subcutaneous fat in the femoral and gluteal area might be associated with HDLC decrease in women during initial weight loss.     

Mathematical modelling and experiments for the proliferation and differentiation of Drosophila intestinal stem cells I

We study the proliferation and differentiation of stem cells in the Drosophila posterior midgut epithelium, which mainly consists of intestinal stem cells (ISCs); semi-differentiated cells, i.e. enteroblasts (EBs); and two types of fully differentiated cells, i.e. enteroendocrine cells (EEs) and enterocytes (ECs). The cellular system of ISCs is controlled by Wnt and Notch signalling pathways. In this article, we experimentally show that EBs are not capable of efficiently differentiating into ECs in the absence of Wnt signalling. On the basis of the experimental results and known facts, we propose a scheme and a simple ordinary differential equation (ODE) model for the proliferation and differentiation of ISCs. This is a first step towards understanding the universal mechanism for the maintenance of the cellular system of tissue stem cells controlled by signalling pathways.     

Chlorophenol hydroxylase activity encoded by TfdB from 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading Bradyrhizobium sp. strain RD5-C2

The tfdB gene encoding chlorophenol hydroxylase and its homolog were found in 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading strain RD5-C2, which belongs to Bradyrhizobium sp. of alpha-Proteobacteria. The nucleotide and deduced amino acid sequence identities of the two genes, designated tfdBa and tfdBb, were 60% and 57% respectively. Their nucleotide sequences most closely matched those of previously reported tfdB, which consisted of those from 2,4-D-degrading beta- and gamma-Proteobacteria and Sphingomonas sp. in alpha-Proteobacteria, with 61-67% identity. The TfdBa expressed in Escherichia coli showed the highest activity for 2,4-dichlorophenol but a narrower range of activity for the other chlorophenols than previously reported TfdBs. In the case of TfdBb, however, no observable activity for any chlorophenols or phenol was detected, although production of a protein with an appropriate molecular size was observed. Based on codon usage patterns and the GC content of the genes, it probable that the tfdBa genes in the 2,4-D-degrading Bradyrhizobium sp. were obtained through horizontal gene transfer.     

Changes in the components of biliary and plasma lipids in selenium-deficient rats

We constructed a chronic oxidative stress model in which Se-deficient diet was fed to male Wister rats for 8 weeks. As expected, effects of oxidative damage, including Fe accumulation and increase in peroxidized lipids, were identified in the liver owing to the lack of glutathione peroxidase. Although the oxidative stress caused Fe accumulation in the liver, the Fe concentration in bile of the SeD rat was almost the same as that in the control rats. The constant excretion of Fe into bile supported the Fe accumulation in the liver. No differences were observed in the principal components of biliary lipids, i.e., bile acids, phospholipids, and cholesterol, between the two groups; moreover, these trends were also reflected in the plasma. Due to the trapping of reactive oxygen species, only bilirubin concentrations in the bile and plasma were decreased in the SeD group, when compared with those in the control group. Measurement of bilirubin concentration may be used as a supplemental oxidative stress marker.