Gold Nanoparticle and Polymerase Chain Reaction (PCR)-Based Colorimetric Assay for the Identification of Campylobacter spp. in Chicken Carcass.

Campylobacteriosis is a common cause of gastrointestinal disease. In this study, we suggest a general strategy of applying gold nanoparticles (AuNPs) in colorimetric biosensors to detect Campylobacter in chicken carcass. Polymerase chain reaction (PCR) was utilized for the amplification of the target genes, and the thiolated PCR products were collected. Following the blending of colloid AuNPs with PCR products, the thiol bound to the surface of AuNPs, forming AuNP-PCR products. The PCR products had a sufficient negative charge, which enabled AuNPs to maintain a dispersed formation under electrostatic repulsion. This platform presented a color change as AuNPs aggregate. It did not need additional time and optimization of pH for PCR amplicons to adhere to the AuNPs. The specificity of AuNPs of modified primer pairs for mapA from Campylobacter jejuni and ceuE from Campylobacter coli was activated perfectly (C. jejuni, p-value: 0.0085; C. coli, p-value: 0.0239) when compared to Salmonella Enteritidis and Escherichia coli as non-Campylobacter species. Likewise, C. jejuni was successfully detected from artificially contaminated chicken carcass samples. According to the sensitivity test, at least 15 ng/µL of Campylobacter PCR products or 1×103 CFU/mL of cells in the broth was needed for the detection using the optical method.

Molecular Generative Model Based on an Adversarially Regularized Autoencoder.

Deep generative models are attracting great attention as a new promising approach for molecular design. A variety of models reported so far are based on either a variational autoencoder (VAE) or a generative adversarial network (GAN), but they have limitations such as low validity and uniqueness. Here, we propose a new type of model based on an adversarially regularized autoencoder (ARAE). It basically uses latent variables like VAE, but the distribution of the latent variables is estimated by adversarial training like in GAN. The latter is intended to avoid both the insufficiently flexible approximation of posterior distribution in VAE and the difficulty in handling discrete variables in GAN. Our benchmark study showed that ARAE indeed outperformed conventional models in terms of validity, uniqueness, and novelty per generated molecule. We also demonstrated a successful conditional generation of drug-like molecules with ARAE for the control of both cases of single and multiple properties. As a potential real-world application, we could generate epidermal growth factor receptor inhibitors sharing the scaffolds of known active molecules while satisfying drug-like conditions simultaneously.

ConDo: protein domain boundary prediction using coevolutionary information.

MOTIVATION: Domain boundary prediction is one of the most important problems in the study of protein structure and function. Many sequence-based domain boundary prediction methods are either template-based or machine learning (ML) based. ML-based methods often perform poorly due to their use of only local (i.e. short-range) features. These conventional features such as sequence profiles, secondary structures and solvent accessibilities are typically restricted to be within 20 residues of the domain boundary candidate. RESULTS: To address the performance of ML-based methods, we developed a new protein domain boundary prediction method (ConDo) that utilizes novel long-range features such as coevolutionary information in addition to the aforementioned local window features as inputs for ML. Toward this purpose, two types of coevolutionary information were extracted from multiple sequence alignment using direct coupling analysis: (i) partially aligned sequences, and (ii) correlated mutation information. Both the partially aligned sequence information and the modularity of residue-residue couplings possess long-range correlation information. AVAILABILITY AND IMPLEMENTATION: https://github.com/gicsaw/ConDo.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Data-assisted protein structure modeling by global optimization in CASP12.

In CASP12, 2 types of data-assisted protein structure modeling were experimented. Either SAXS experimental data or cross-linking experimental data was provided for a selected number of CASP12 targets that the CASP12 predictor could utilize for better protein structure modeling. We devised 2 separate energy terms for SAXS data and cross-linking data to drive the model structures into more native-like structures that satisfied the given experimental data as much as possible. In CASP11, we successfully performed protein structure modeling using simulated sparse and ambiguously assigned NOE data and/or correct residue-residue contact information, where the only energy term that folded the protein into its native structure was the term which was originated from the given experimental data. However, the 2 types of experimental data provided in CASP12 were far from being sufficient enough to fold the target protein into its native structure because SAXS data provides only the overall shape of the molecule and the cross-linking contact information provides only very low-resolution distance information. For this reason, we combined the SAXS or cross-linking energy term with our regular modeling energy function that includes both the template energy term and the de novo energy terms. By optimizing the newly formulated energy function, we obtained protein models that fit better with provided SAXS data than the X-ray structure of the target. However, the improvement of the model relative to the 1 modeled without the SAXS data, was not significant. Consistent structural improvement was achieved by incorporating cross-linking data into the protein structure modeling.

Protein structure modeling and refinement by global optimization in CASP12.

For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain re-modeling. For better template selection and model selection, we updated our model quality assessment (QA) method with the newly developed SVMQA (support vector machine for quality assessment). For 3D chain building, we updated our energy function by including restraints generated from predicted residue-residue contacts. New energy terms for the predicted secondary structure and predicted solvent accessible surface area were also introduced. For difficult targets, we proposed a new method, LEEab, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term. For TBM (template-based modeling) targets, LEE performed better than LEEab, but for FM targets, LEEab was better. For model refinement, we modified our CASP11 molecular dynamics (MD) based protocol by using explicit solvents and tuning down restraint weights. Refinement results from MD simulations that used a new augmented statistical energy term in the force field were quite promising. Finally, when using inaccurate information (such as the predicted contacts), it was important to use the Lorentzian function for which the maximal penalty arising from wrong information is always bounded.

DEMETER plant DNA demethylase induces antiviral response by interferon signalling in animal cells.

DNA methylation is a prominent epigenetic modification in plants and animals regulated by similar mechanisms but the process of DNA demethylation is profoundly different. Unlike vertebrates that require a series of enzymatic conversions of 5-methylcytosine (5mC) into other bases for DNA demethylation, plants utilize the DEMETER (DME) family of 5mC DNA glycosylases to catalyze a direct removal of 5mC from DNA. Here we introduced Arabidopsis DME into human HEK-293T cells to allow direct 5mC excision, and observed that direct DNA demethylation activity was successfully implemented by DME expression. In addition, DME induced diverse cellular responses such as cell proliferation inhibition, cell cycle dysregulation and S phase arrest. Microarray and methylome analyses revealed that DME upregulated a number of genes including cell cycle components, heat shock proteins, and notably, various interferon-stimulated genes. Moreover, DME-mediated DNA demethylation activated endogenous repeat elements, which are likely to form dsRNAs as viral mimics and eventually trigger interferon cascades to establish the antiviral state. This work demonstrates that plant DNA demethylase catalyzes DNA demethylation with a bypass of initial base conversion steps, and the interferon signaling plays a pivotal role to alleviate genotoxic stresses associated with DME-induced DNA demethylation in mammalian cells.

SHC1 sensitizes cancer cells to the 8-Cl-cAMP treatment.

8-Chloro-cyclic AMP (8-Cl-cAMP) is a cyclic AMP analog that induces growth inhibition and apoptosis in a broad spectrum of cancer cells. Previously, we found that 8-Cl-cAMP-induced growth inhibition is mediated by AMP-activated protein kinase (AMPK) as well as p38 mitogen-activated protein kinase (p38 MAPK). To identify downstream mediators of the 8-Cl-cAMP signaling, we performed co-immunoprecipitation combined with mass spectrometry using the anti-AMPK or p38 MAPK antibodies. Through this approach, SHC1 was identified as one of the binding partners of p38 MAPK. SHC1 phosphorylation was suppressed by 8-Cl-cAMP in HeLa and MCF7 cancer cells, which was mediated by its metabolites, 8-Cl-adenosine and 8-Cl-ATP; however, 8-Cl-cAMP showed no effect on SHC1 phosphorylation in normal human fibroblasts. SHC1 siRNA induced AMPK and p38 MAPK phosphorylation and growth inhibition in cancer cells, and SHC1 overexpression re-sensitized human foreskin fibroblasts to the 8-Cl-cAMP treatment. SHC1 phosphorylation was unaffected by Compound C (an AMPK inhibitor) and SB203580 (a p38 MAPK inhibitor), which suggests that SHC1 is upstream of AMPK and p38 MAPK in the 8-Cl-cAMP-stimulated signaling cascade. On the basis of these findings, we conclude that SHC1 functions as a sensor during the 8-Cl-cAMP-induced growth inhibition in SHC1-overexpressing cancer cells.

Sharp low-energy feature in single-particle spectra due to forward scattering in d-wave cuprate superconductors.

There is an enormous interest in the renormalization of the quasiparticle (qp) dispersion relation of cuprate superconductors both below and above the critical temperature T_{c} because it enables the determination of the fluctuation spectrum to which the qp's are coupled. A remarkable discovery by angle-resolved photoemission spectroscopy (ARPES) is a sharp low-energy feature (LEF) in qp spectra well below the superconducting energy gap but with its energy increasing in proportion to T_{c} and its intensity increasing sharply below T_{c}. This unexpected feature needs to be reconciled with d-wave superconductivity. Here, we present a quantitative analysis of ARPES data from Bi_{2}Sr_{2}CaCu_{2}O_{8+δ} (Bi2212) using Eliashberg equations to show that the qp scattering rate due to the forward scattering impurities far from the Cu-O planes is modified by the energy gap below T_{c} and shows up as the LEF. This is also a necessary step to analyze ARPES data to reveal the spectrum of fluctuations promoting superconductivity.

Chabazite and zeolite 13X for CO2 capture under high pressure and moderate temperature conditions.

Mesoporous chabazite ion-exchanged with Ca(2+) was effective for CO2 capture at 20 bar and 473 K, whereas 13X as a support material enabled recyclable carbonation of ca. 8 wt% Mg(OH)2 approaching the theoretical maximum for CO2 capture with 10% H2O.

p104 binds to Rac1 and reduces its activity during myotube differentiation of C2C12 cell.

The p104 protein inhibits cellular proliferation when overexpressed in NIH3T3 cells and has been shown to associate with p85α, Grb2, and PLCγ1. In order to isolate other proteins that interact with p104, yeast two-hybrid screening was performed. Rac1 was identified as a binding partner of p104 and the interaction between p104 and Rac1 was confirmed by immunoprecipitation. Using a glutathione S-transferase (GST) pull-down assay with various p104 fragments, the 814-848 amino acid residue at the carboxyl-terminal region of p104 was identified as the key component to interact with Rac1. The CrkII which is involved in the Rac1-mediated cellular response was also found to interact with p104 protein. NIH3T3 cells which overexpressed p104 showed a decrease of Rac1 activity. However, neither the proline-rich domain mutant, which is unable to interact with CrkII, nor the carboxy-terminal deletion mutant could attenuate Rac1 activity. During the differentiation of myoblasts, the amount of p104 protein as well as transcript level was increased. The overexpression of p104 enhanced myotube differentiation, whereas siRNA of p104 reversed this process. In this process, more Rac1 and CrkII were bound to increased p104. Based on these results, we conclude that p104 is involved in muscle cell differentiation by modulating the Rac1 activity.

Angle and frequency dependence of self-energy from spin fluctuation mediated d-wave pairing for high temperature superconductors.

We investigated the characteristics of spin fluctuation mediated superconductivity employing the Eliashberg formalism. The effective interaction between electrons was modeled in terms of the spin susceptibility measured by inelastic neutron scattering experiments on single crystal La(2-x)Sr(x)CuO4 superconductors. The diagonal self-energy and off-diagonal self-energy were calculated by solving the coupled Eliashberg equation self-consistently for the chosen spin susceptibility and tight-binding dispersion of electrons. The full momentum and frequency dependence of the self-energy is presented for optimally doped, overdoped, and underdoped LSCO cuprates in a superconductive state. These results may be compared with the experimentally deduced self-energy from ARPES experiments.

Treatment of osteonecrosis in the knee joint of a rabbit using autologous cultured osteoblasts.

BACKGROUND: [corrected] To develop a successful treatment modality for osteonecrosis, an appropriate animal model is essential. We have proposed a new osteonecrosis model that shows the total amount of necrosis and in which we observed new bone formation after transplanting autologous cultured osteoblasts. MATERIALS AND METHODS: The femoral condyles of the right knees of New Zealand white rabbits were exposed after dissecting the ligaments surrounding the distal femur. After which, the metaphyseal-diaphyseal junction was cut using a saw, and the entire femoral condyle was isolated. After three liquid nitrogen treatments, the isolated femoral condyle was internally fixated to the femoral shaft using two or three Kirschner wires. Bone marrow isolated from the iliac crest was cultivated to differentiate it into osteoblasts, and the cultured cells were then injected into the necrotic bone. RESULTS: Viable osteocytes with well-stained nuclei were not present in the necrotic areas at any stage of the development of the osteonecrosis model within 24 wk after osteonecrosis induction. However, new bone formation with osteocytes and blood vessels was observed in the necrotic bone 12 wk after transplanting the autologous cultured osteoblasts. CONCLUSIONS: The distal femoral condyle of the rabbit is an appropriate model for demonstrating osteonecrosis and treatment evaluation owing to its easy reproducibility and treatment interpretation. Therefore, autologous cultured osteoblast treatment would seem to be a potentially successful treatment modality for osteonecrosis.

Involvement of Akt2/protein kinase B ß (PKBß) in the 8-Cl-cAMP-induced cancer cell growth inhibition.

8-chloro-cyclic AMP (8-Cl-cAMP), which induces differentiation, growth inhibition, and apoptosis in various cancer cells, has been investigated as a putative anti-cancer drug. However, the exact mechanism of 8-Cl-cAMP functioning in cancer cells is not fully understood. Akt/protein kinase B (PKB) genes (Akt1, Akt2, and Akt3) encode enzymes belonging to the serine/threonine-specific protein kinase family. It has been suggested that Akt/PKB enhances cell survival by inhibiting apoptosis. Recently, we showed that 8-Cl-cAMP and 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) inhibited cancer cell growth through the activation of AMPK and p38 MAPK. Therefore, we anticipated that the phosphorylation of Akt/PKB would be decreased upon treatment with 8-Cl-cAMP. However, treatment with 8-Cl-cAMP and AICAR induced the phosphorylation of Akt/PKB, which was inhibited by ABT702 (an adenosine kinase inhibitor) and NBTI (an adenosine transporter inhibitor). Furthermore, whereas Compound C (an AMPK inhibitor), AMPK-DN (AMPK-dominant negative) mutant, and SB203580 (a p38 MAPK inhibitor) did not block the 8-Cl-cAMP-induced phosphorylation of Akt/PKB, TCN (an Akt1/2/3 specific inhibitor) and an Akt2/PKBß-targeted siRNA inhibited the 8-Cl-cAMP- and AICAR-mediated phosphorylation of AMPK and p38 MAPK. TCN also reversed the growth inhibition mediated by 8-Cl-cAMP and AICAR. Moreover, an Akt1/PKBα-targeted siRNA did not reduce the phosphorylation of AMPK and p38 MAPK after treatment with 8-Cl-cAMP. These results suggest that Akt2/PKBß activation promotes the phosphorylation of AMPK and p38 MAPK during the 8-Cl-cAMP- and AICAR-induced growth inhibition.

Novel p104 protein regulates cell proliferation through PI3K inhibition and p27(Kip1) expression.

The protein p104 was first isolated as a binding partner of the Src homology domain of phospholipase Cgamma1, and has been shown to associate with p85alpha, Grb2. The ectopic expression of p104 reduced cellular growth rate, which was also achieved with the overexpression of only the proline-rich region of p104. The proline-rich region of p104 has been found to inhibit the colony formation of platelet-derived growth factor BB-stimulated NIH3T3 cells and MCF7 cancer cells on soft agar. Mutagenesis analysis showed that the second and third proline-rich regions are essential for growth control, as well as for interaction with p85alpha. Overexpression of p104 increased the level of the cyclin-dependent kinase inhibitor, p27(Kip1), and inhibited the activity of phosphoinositide 3-kinase (PI3K). In summary, p104 interacts with p85alpha and is involved in the regulation of p27(Kip1) expression for the reduction of cellular proliferation.

Involvement of AMP-activated protein kinase and p38 mitogen-activated protein kinase in 8-Cl-cAMP-induced growth inhibition.

8-Cl-cAMP (8-chloro-cyclic AMP), which induces differentiation, growth inhibition and apoptosis in various cancer cells, has been investigated as a putative anti-cancer drug. Although we reported that 8-Cl-cAMP induces growth inhibition via p38 mitogen-activated protein kinase (MAPK) and a metabolite of 8-Cl-cAMP, 8-Cl-adenosine mediates this process, the action mechanism of 8-Cl-cAMP is still uncertain. In this study, it was found that 8-Cl-cAMP-induced growth inhibition is mediated by AMP-activated protein kinase (AMPK). 8-Cl-cAMP was shown to activate AMPK, which was also dependent on the metabolic degradation of 8-Cl-cAMP. A potent agonist of AMPK, 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) could also induce growth inhibition and apoptosis. To further delineate the role of AMPK in 8-Cl-cAMP-induced growth inhibition and apoptosis, we used two approaches: pharmacological inhibition of the enzyme with compound C and expression of a dominant negative mutant (a kinase-dead form of AMPKalpha2, KD-AMPK). AICAR was able to activate p38 MAPK and pre-treatment with AMPK inhibitor or expression of KD-AMPK blocked this p38 MAPK activation. Cell growth inhibition was also attenuated. Furthermore, p38 MAPK inhibitor attenuated 8-Cl-cAMP- or AICAR-induced growth inhibition but had no effect on AMPK activation. These results demonstrate that 8-Cl-cAMP induced growth inhibition through AMPK activation and p38 MAPK acts downstream of AMPK in this signaling pathway.

Jak2 and Tyk2 are necessary for lineage-specific differentiation, but not for the maintenance of self-renewal of mouse embryonic stem cells.

As the LIF-induced Jak1/STAT3 pathway has been reported to play a crucial role in self-renewal of mESCs, we sought to determine if Jak2, which is also expressed in mESCs, might also be involved in the pathway. By employing an RNAi strategy, we established both Jak2 and Jak2/Tyk2 knockdown mESC clones. Both Jak2 and Jak2/Tyk2 knockdown clones maintained the undifferentiated state as wild-type controls, even in a very low concentration of LIF. However, we observed not only faster onset of differentiation but also differential expression of tissue-specific lineage genes for ectodermal and mesodermal, but not endodermal origins from embryoid bodies generated from both types of knockdown clones compared to the wild-type. Furthermore, the reduced level of Jak2 caused differentiation of mESCs in the presence of LIF when the Wnt pathway was activated by LiCl treatment. Taken together, we demonstrated that Jak2 and Tyk2 are not involved in LIF-induced STAT3 pathway for self-renewal of mESCs, but play a role in early lineage decision of mESCs to various differentiated cell types.

Identification of Jmjd1a as a STAT3 downstream gene in mES cells.

Mouse embryonic stem (mES) cells can be maintained in undifferentiated state in the presence of a cytokine, leukemia inhibitory factor (LIF). Many investigators found that STAT3 activation is important for the maintenance of pluripotency by LIF. However, the downstream pathways of STAT3 activation are still unknown. To look for STAT3-downstream target genes, we performed DD-RT PCR in the presence or absence of LIF. Through further confirmation, we finally selected 8 genes whose expressions were significantly dependent upon the presence of LIF. Among them, Jmjd1a was down-regulated after LIF withdrawal, and it was selected for further investigation. Its expression started to decrease 1 day after the removal of LIF, and disappeared on day 3. It was also shown that STAT3 could bind to the promoter region of Jmjd1a gene. These data demonstrate that Jmjd1a might be a critical signaling molecule underlying the maintenance of pluripotency in mES cells.

Rap1 and p38 MAPK mediate 8-chloro-cAMP-induced growth inhibition in mouse fibroblast DT cells.

8-Cl-cAMP, which is known to induce differentiation, growth inhibition, and apoptosis in various cancer cells, has been investigated as a putative anti-cancer drug. Previously, we reported that 8-Cl-cAMP and its metabolite 8-Cl-adenosine induce growth inhibition and apoptosis through p38 mitogen-activated protein kinase (MAPK) activation. To further investigate the signal mechanisms that regulate the cellular effects of 8-Cl-cAMP, we focused on a small GTPase Rap1 that is known to be involved in growth inhibition and reverse-transformation. 8-Cl-cAMP and 8-Cl-adenosine could increase Rap1 activity, which was blocked by ABT702-an adenosine kinase inhibitor. This suggests that 8-Cl-cAMP-induced Rap1 activation is also dependent on the metabolic degradation of 8-Cl-cAMP. Overexpression of a constitutively active mutant form of Rap1 (Rap1V12) attenuated cellular growth and soft-agar colony formation, which was basically the same effect as that observed with the 8-Cl-cAMP treatment. Furthermore, the Rap1V12 transfectant showed a high level of p38 MAPK activation. However, 8-Cl-cAMP-induced Rap1 activation was not diminished by SB203580, a p38 MAPK inhibitor, suggesting that Rap1 activation might act upstream of p38 MAPK activation during 8-Cl-cAMP-induced growth inhibition.

Adiponectin increases fatty acid oxidation in skeletal muscle cells by sequential activation of AMP-activated protein kinase, p38 mitogen-activated protein kinase, and peroxisome proliferator-activated receptor alpha.

Adiponectin has recently received a great deal of attention due to its beneficial effects on insulin resistance and metabolic disorders. One of the mechanisms through which adiponectin exerts such effects involves an increase in fatty acid oxidation in muscle and liver. In the present study, we demonstrate that 5'-AMP-activated protein kinase (AMPK) and p38 mitogen-activated protein kinase (MAPK) are involved in the activation of peroxisome proliferator-activated receptor (PPAR)alpha by adiponectin in muscle cells. Adiponectin increases the transcriptional activity of PPARalpha and the expression of its target genes, including ACO, CPT1, and FABP3 in C2C12 myotubes. These effects were suppressed by the overexpression of a dominant-negative form of AMPK. Moreover, chemical inhibitors of AMPK and p38 MAPK potently repressed fatty acid oxidation and the induction of PPARalpha target gene expression by adiponectin. Interestingly, araA, an AMPK inhibitor, prevented the activation of p38 MAPK, whereas SB203580, a p38 MAPK inhibitor, did not affect AMPK activation, suggesting that p38 MAPK is a downstream signaling factor of AMPK. Taken together, these results suggest that adiponectin stimulates fatty acid oxidation in muscle cells by the sequential activation of AMPK, p38 MAPK, and PPARalpha.