Summary

Histone H3K4 methylation is associated with active genes and, along with H3K27 methylation, is part of a bivalent chromatin mark that typifies poised developmental genes in embryonic stem cells (ESCs). However, its functional roles in ESC maintenance and differentiation are not established. Here we show that mammalian Dpy-30, a core subunit of the SET1/MLL histone methyltransferase complexes, modulates H3K4 methylation in vitro, and directly regulates chromosomal H3K4 trimethylation (H3K4me3) throughout the mammalian genome. Depletion of Dpy-30 does not affect ESC self-renewal, but significantly alters the differentiation potential of ESCs, particularly along the neural lineage. The differentiation defect is accompanied by defects in gene induction and in H3K4 methylation at key developmental loci. Our results strongly indicate an essential functional role for Dpy-30 and SET1/MLL complex-mediated H3K4 methylation, as a component of the bivalent mark, at developmental genes during the ESC fate transitions.

The copper(I)-catalyzed azide-alkyne cycloaddition, the most widely recognized reaction of click chemistry, is accelerated by tris(triazolylmethyl)amine-based ligands. Here, we compared two new ligands in this family, BTTP and the corresponding sulfated ligand BTTPS, for three bioconjugation applications: (1) labeling of alkyne-tagged glycoproteins in crude cell lysates, (2) labeling of alkyne/azide-tagged glycoproteins on the surface of live mammalian cells, and (3) labeling of azides in surface proteins of live Escherichia coli. Though BTTPS exhibits faster kinetics than BTTP in accelerating the CuAAC in in vitro kinetic measurements, its labeling efficiency is slightly lower than BTTP in conjugating biomolecules bearing a significant amount of negative charges due to electrostatic repulsion. Nevertheless, the negative charge conferred by the sulfate at physiological conditions significantly reduced the cellular internalization of the coordinated Cu(I), thus making BTTPS-Cu(I) a better choice for live cell labeling.

Non-destructive estimation using digital cameras is a common approach for estimating leaf area index (LAI) of terrestrial vegetation. However, no attempt has been made so far to develop non-destructive approaches to LAI estimation for aquatic vegetation. Using the submerged plant species Potamogeton malainus, the objective of this study was to determine whether the gap fraction derived from vertical photographs could be used to estimate LAI of aquatic vegetation. Our results suggested that upward-oriented photographs taken from beneath the water surface were more suitable for distinguishing vegetation from other objects than were downward-oriented photographs taken from above the water surface. Exposure settings had a substantial influence on the identification of vegetation in upward-oriented photographs. Automatic exposure performed nearly as well as the optimal trial exposure, making it a good choice for operational convenience. Similar to terrestrial vegetation, our results suggested that photographs taken for the purpose of distinguishing gap fraction in aquatic vegetation should be taken under diffuse light conditions. Significant logarithmic relationships were observed between the vertical gap fraction derived from upward-oriented photographs and plant area index (PAI) and LAI derived from destructive harvesting. The model we developed to depict the relationship between PAI and gap fraction was similar to the modified theoretical Poisson model, with coefficients of 1.82 and 1.90 for our model and the theoretical model, respectively. This suggests that vertical upward-oriented photographs taken from below the water surface are a feasible alternative to destructive harvesting for estimating PAI and LAI for the submerged aquatic plant Potamogeton malainus.

Management of water levels for flood control, water quality, and water safety purposes has become a priority for many lakes worldwide. However, the effects of water level management on the distribution and composition of aquatic vegetation has received little attention. Relevant studies have used either limited short-term or discrete long-term data and thus are either narrowly applicable or easily confounded by the effects of other environmental factors. We developed classification tree models using ground surveys combined with 52 remotely sensed images (15–30 m resolution) to map the distributions of two groups of aquatic vegetation in Taihu Lake, China from 1989–2010. Type 1 vegetation included emergent, floating, and floating-leaf plants, whereas Type 2 consisted of submerged vegetation. We sought to identify both inter- and intra-annual dynamics of water level and corresponding dynamics in the aquatic vegetation. Water levels in the ten-year period from 2000–2010 were 0.06–0.21 m lower from July to September (wet season) and 0.22–0.27 m higher from December to March (dry season) than in the 1989–1999 period. Average intra-annual variation (CVa) decreased from 10.21% in 1989–1999 to 5.41% in 2000–2010. The areas of both Type 1 and Type 2 vegetation increased substantially in 2000–2010 relative to 1989–1999. Neither annual average water level nor CVa influenced aquatic vegetation area, but water level from January to March had significant positive and negative correlations, respectively, with areas of Type 1 and Type 2 vegetation. Our findings revealed problems with the current management of water levels in Taihu Lake. To restore Taihu Lake to its original state of submerged vegetation dominance, water levels in the dry season should be lowered to better approximate natural conditions and reinstate the high variability (i.e., greater extremes) that was present historically.

Members of the Bacteroidales order are among the most abundant gram-negative bacteria of the human colonic microbiota. These species decorate their cell surface glycoproteins with fucosylated glycans, which are believed to play important roles in host intestinal colonization. Currently, there is no method for the enrichment of these glycoproteins for their identification. Here, we describe a chemical approach directed toward labeling and detecting fucosylated glycoproteins from cultured Bacteroidales species, namely Bacteroides fragilis and Parabacteroides distasonis. We treated these bacteria with an alkyne-bearing fucose analog, which is metabolically integrated into the bacterial surface fucosylated glycoproteins. The alkyne-tagged glycoproteins can then react with azide-bearing biophysical probes via bioorthogonal click chemistry for detection or glycoproteomic analysis.

High dimensional bioinformatics data sets provide an excellent and challenging research problem in machine learning area. In particular, DNA microarrays generated gene expression data are of high dimension with significant level of noise. Supervised kernel learning with an SVM classifier was successfully applied in biomedical diagnosis such as discriminating different kinds of tumor tissues. Correlation Kernel has been recently applied to classification problems with Support Vector Machines (SVMs). In this paper, we develop a novel and parsimonious positive semidefinite kernel. The proposed kernel is shown experimentally to have better performance when compared to the usual correlation kernel. In addition, we propose a new kernel based on the correlation matrix incorporating techniques dealing with indefinite kernel. The resulting kernel is shown to be positive semidefinite and it exhibits superior performance to the two kernels mentioned above. We then apply the proposed method to some cancer data in discriminating different tumor tissues, providing information for diagnosis of diseases. Numerical experiments indicate that our method outperforms the existing methods such as the decision tree method and KNN method.

Background

EPCs were isolated primarily in 1997 by Asahara et al. and recent studies indicated that bone-marrow-derived EPCs contributed little to the endothelium of tumor vessels. Tumors of the CNS system demonstrate various features of angiogenesis.

Methods

EPCs derived from rat bone marrow were isolated and cultured in M199 medium without any induced factors. EPCs were studied using immunohistochemical staining, Flow cytometry and culture under three-dimensional condition to determine EPCs’ characteristics in vitro. We also established an animal model by injecting EPCs marked with Hoechst 33342 into the back of BALB/c nude mice and performed hematoxylin-eosin (HE) and immunofluorescent staining to study EPCs’ features in vivo. To research effect of EPCs on glioma, animals bearing tumors model with C6 glioma were established. About 27 day after injection, we performed immunohistochemical staining and Immunofluorescence staining.

Results

Our results showed that EPCs derived from rat bone marrow appeared typical morphological characteristics and were positive of CD34, CD133, KDR and CD31 antigens at different time in vitro under the special M199 medium without any induced factors. The percentage of cells that expressed CD133 decreased gradually. In brief, the present study showed that EPCs derived from rat bone marrow differentiated into ECs in medium the without any induced factors and formed tubular structures in three-dimensional circumstances. Animal experiments suggested that EPCs differentiated into ECs and other else non-endothelial cells, and that EPCs contributed M199 of glioma.

Discussion

These findings provides some novel results about biological characteristics of EPCs in vivo and ex vivo, and an update on the effect of EPCs on glioma and which would be helpful for the overall understanding of EPCs and make EPCs to be implied on the clinical therapy.

Background

Fragile X syndrome (FXS) is caused by the absence of the mRNA-binding protein Fragile X mental retardation protein (FMRP), encoded by the Fmr1 gene. Overactive signaling by group 1 metabotropic glutamate receptor (Grp1 mGluR) could contribute to slowed synaptic development and other symptoms of FXS. Our previous study has identified that facilitation of synaptic long-term potentiation (LTP) by D1 receptor is impaired in Fmr1 knockout (KO) mice. However, the contribution of Grp1 mGluR to the facilitation of synaptic plasticity by D1 receptor stimulation in the prefrontal cortex has been less extensively studied.

Results

Here we demonstrated that DL-AP3, a Grp1 mGluR antagonist, rescued LTP facilitation by D1 receptor agonist SKF81297 in Fmr1KO mice. Grp1 mGluR inhibition restored the GluR1-subtype AMPA receptors surface insertion by D1 activation in the cultured Fmr1KO neurons. Simultaneous treatment of Grp1 mGluR antagonist with D1 agonist recovered the D1 receptor signaling by reversing the subcellular redistribution of G protein-coupled receptor kinase 2 (GRK2) in the Fmr1KO neurons. Treatment of SKF81297 alone failed to increase the phosphorylation of NR2B-containing N-methyl D-aspartate receptors (NMDARs) at Tyr-1472 (p-NR2B-Tyr1472) in the cultures from KO mice. However, simultaneous treatment of DL-AP3 could rescue the level of p-NR2B-Tyr1472 by SKF81297 in the cultures from KO mice. Furthermore, behavioral tests indicated that simultaneous treatment of Grp1 mGluR antagonist with D1 agonist inhibited hyperactivity and improved the learning ability in the Fmr1KO mice.

Conclusion

The findings demonstrate that mGluR1 inhibition is a useful strategy to recover D1 receptor signaling in the Fmr1KO mice, and combination of Grp1 mGluR antagonist and D1 agonist is a potential drug therapy for the FXS.

A strategy for analyzing flavone C-glucosides in the leaves of different species of bamboo was developed. Firstly, the flavone C-glycosides were extracted from the bamboo leaves (51 species in 17 genera) with methanol and chromatographed on silica gel 60 plates in automatic developing chamber (ADC2), and a qualitative survey using simple derivatization steps with the NP reagent was carried out. The flavone C-glycosides were found in 40 of 51 species of bamboo examined. Secondly, an HPLC method with photodiode array and multiple wavelength detector was optimized and validated for the simultaneous determination of flavone C-glycosides, including isoorientin, isovitexin, orientin, and vitexin in the leaves of three species of bamboo and the flavone C-glycosides were confirmed by LC/MS. The optimized HPLC method proved to be linear in the concentration range tested (0.2–100 μg/mL, r2 ≥ 0.9997), precise (RSD ≤ 1.56%), and accurate (88–106%). The concentration ranges of isoorientin, isovitexin, orientin, and vitexin in three bamboo leaves samples were 1.00–2.78, 0–0.31, 0–0.07, and 0.20–0.68 mg/g, respectively. The proposed method was validated to be simple and reliable and can be a tool for quality control of bamboo leaf extract or its commercial products.

Background

Our previous studies demonstrated that simvastatin reduced neuronal death, increased neurogenesis, and promoted functional recovery after TBI. Objective: To investigate the effect of simvastatin on angiogenesis after TBI, and the related signaling pathways.

Methods

Saline or simvastatin (1 mg/kg) was administered orally to rats starting at day 1 after TBI or sham surgery and then daily for 14 days. Rats were sacrificed at 3 and 14 days after treatment. Brain sections and tissues were prepared for immunohistochemical staining, ELISA, and Western blot analysis, respectively. Cultured rat brain microvascular endothelial cells (RBMVECs) were subjected to oxygen-glucose deprivation (OGD) followed by immunocytochemical staining with phallotoxins and vascular endothelial growth factor receptor-2 (VEGFR-2). Western blot analysis was carried out to examine the simvastatin-induced activation of the v-akt murine thymoma viral oncogene homolog (Akt) signaling pathway. The expression of VEGFR-2 was detected by ELISA.

Results

Simvastatin significantly increased the length of vascular perimeter, promoted the proliferation of endothelial cells, and improved the sensorimotor function after TBI. Simvastatin stimulated endothelial cell tube formation after OGD in vitro. VEGFR-2 expression in both brain tissues and cultured RBMVECs was enhanced after simvastatin treatment, which may be modulated by activation of Akt. Akt-dependent endothelial nitric oxide synthase (eNOS) phosphorylation was also induced by simvastatin in vivo and in vitro.

Conclusion

Simvastatin augments TBI-induced angiogenesis in the lesion boundary zone and hippocampus and improves functional recovery. Simvastatin also promotes angiogenesis in vitro. These beneficial effects on angiogenesis may be related to simvastatin-induced activation of the VEGFR-2/Akt/eNOS signaling pathway.

Megavoltage, cone-beam computed tomography (MV CBCT) employing an electronic portal imaging device (EPID) is a highly promising technique for providing soft-tissue visualization in image-guided radiotherapy. However, current EPIDs based on active matrix flat-panel imagers (AMFPIs), which are regarded as the gold standard for portal imaging and referred to as conventional MV AMFPIs, require high radiation doses to achieve this goal due to poor x-ray detection efficiency (~2% at 6 MV). To overcome this limitation, the incorporation of thick, segmented, crystalline scintillators, as a replacement for the phosphor screens used in these AMFPIs, has been shown to significantly improve the DQE performance, leading to improved image quality for projection imaging at low dose. Toward the realization of practical AMFPIs capable of low dose, soft-tissue visualization using MV CBCT imaging, two prototype AMFPIs incorporating segmented scintillators with ~11 mm thick CsI:Tl and BGO crystals were evaluated. Each scintillator consists of 120 × 60 crystalline elements separated by reflective septal walls, with an element-to-element pitch of 1.016 mm. The prototypes were evaluated using a bench-top CBCT system, allowing the acquisition of 180 projection, 360° tomographic scans with a 6 MV radiotherapy photon beam. Reconstructed images of a spatial resolution phantom, as well as of a water-equivalent phantom, embedded with tissue equivalent objects having electron densities (relative to water) varying from ~0.28 to ~1.70, were obtained down to one beam pulse per projection image, corresponding to a scan dose of ~4 cGy – a dose similar to that required for a single portal image obtained from a conventional MV AMFPI. By virtue of their significantly improved DQE, the prototypes provided low contrast visualization, allowing clear delineation of an object with an electron density difference of ~2.76%. Results of contrast, noise and contrast-to-noise ratio are presented as a function of dose and compared to those from a conventional MV AMFPI.

Physiological responses to abiotic stress in plants exhibit sexual differences. Females usually experience greater negative effects than males; however, little is known about the molecular mechanisms of sexual differences in abiotic stress responses. In the present study, transcriptional responses to salinity treatments were compared between male and female individuals of the poplar Populus yunnanensis. It was found that several functional groups of genes involved in important pathways were differentially expressed, including photosynthesis-related genes, which were mainly up-regulated in males but down-regulated in females. This gene expression pattern is consistent with physiological observations showing that salinity inhibited photosynthetic capacity more in females than in males. Furthermore, genes located in autosomes rather than in the female-specific region of the W chromosome are the major contributors to the sexual differences in the salinity tolerance of poplars. In conclusion, this study provided molecular evidence of sexual differences in the salinity tolerance of poplars. The identified sex-related genes in salinity tolerance and their functional groups will enhance our understanding of sexual differences in salinity stress at the transcription level.

The catalytic and regulatory subunits of class I phosphoinositide 3-kinase (PI3K) have oncogenic potential. The catalytic subunit p110α and the regulatory subunit p85 undergo cancer-specific gain-of-function mutations that lead to enhanced enzymatic activity, ability to signal constitutively and oncogenicity. The β, γ and δ isoforms of p110 are cell-transforming as overexpressed wild-type proteins. Class I PI3Ks have the unique ability to generate phosphoinositide 3,4,5 trisphosphate (PIP3). Class II and class III PI3Ks lack this ability. Genetic and cell biological evidence suggests that PIP3 is essential for PI3K-mediated oncogenicity, explaining why class II and class III enzymes have not been linked to cancer. Mutational analysis reveals the existence of at least two distinct molecular mechanisms for the gain of function seen with cancer-specific mutations in p110α, one causing independence from upstream receptor tyrosine kinases, the other inducing independence from Ras. An essential component of the oncogenic signal that is initiated by PI3K is the TOR (target of rapamycin) kinase. TOR is an integrator of growth and of metabolic inputs. In complex with the raptor protein (TORC1), it controls cap-dependent translation, and this function is essential for PI3K-initiated oncogenesis.

In previous attempts to identify aquatic vegetation from remotely-sensed images using classification trees (CT), the images used to apply CT models to different times or locations necessarily originated from the same satellite sensor as that from which the original images used in model development came, greatly limiting the application of CT. We have developed an effective normalization method to improve the robustness of CT models when applied to images originating from different sensors and dates. A total of 965 ground-truth samples of aquatic vegetation types were obtained in 2009 and 2010 in Taihu Lake, China. Using relevant spectral indices (SI) as classifiers, we manually developed a stable CT model structure and then applied a standard CT algorithm to obtain quantitative (optimal) thresholds from 2009 ground-truth data and images from Landsat7-ETM+, HJ-1B-CCD, Landsat5-TM and ALOS-AVNIR-2 sensors. Optimal CT thresholds produced average classification accuracies of 78.1%, 84.7% and 74.0% for emergent vegetation, floating-leaf vegetation and submerged vegetation, respectively. However, the optimal CT thresholds for different sensor images differed from each other, with an average relative variation (RV) of 6.40%. We developed and evaluated three new approaches to normalizing the images. The best-performing method (Method of 0.1% index scaling) normalized the SI images using tailored percentages of extreme pixel values. Using the images normalized by Method of 0.1% index scaling, CT models for a particular sensor in which thresholds were replaced by those from the models developed for images originating from other sensors provided average classification accuracies of 76.0%, 82.8% and 68.9% for emergent vegetation, floating-leaf vegetation and submerged vegetation, respectively. Applying the CT models developed for normalized 2009 images to 2010 images resulted in high classification (78.0%–93.3%) and overall (92.0%–93.1%) accuracies. Our results suggest that Method of 0.1% index scaling provides a feasible way to apply CT models directly to images from sensors or time periods that differ from those of the images used to develop the original models.

The Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is the standard method for bioorthogonal conjugation. However, current Cu(I) catalyst formulations are toxic, hindering their use in living systems. Here we report that BTTES, a tris(triazolylmethyl)amine-based ligand for Cu(I), promotes the cycloaddition reaction rapidly in living systems without apparent toxicity. This catalyst allows, for the first time, noninvasive imaging of fucosylated glycans during zebrafish early embryogenesis. We microinjected embryos with alkyne-bearing GDP-fucose at the one-cell stage and detected the metabolically incorporated unnatural sugars using the biocompatible click chemistry. Labeled glycans could be imaged in the enveloping layer of zebrafish embryos between blastula and early larval stages. This new method paves the way for rapid, noninvasive imaging of biomolecules in living organisms.

Abstract

Traumatic brain injury (TBI) elicits a strong inflammatory response that contributes to the acute pathological processes seen following TBI, including cerebral edema and disruption of the blood–brain barrier (BBB), in addition to longer-term neurological damage and cognitive impairment. Proteasome inhibitors reduce vascular thrombotic and inflammatory events and consequently protect vascular function. In the present study we evaluated the neuroprotective effect of Velcade® (bortezomib), a potent and selective inhibitor of proteasomes, which is in clinical use for the treatment of multiple myeloma. When administered within 2 h after TBI onset, Velcade reduced inflammatory responses, lesion volume, and neurological functional deficits, and enhanced neuronal survival. Western blot and ELISA showed that Velcade decreased the expression of NF-κB. These results suggest that in the experimental setting, Velcade is an effective neuroprotective agent for the treatment of TBI.

Objective

Our previous studies demonstrated that simvastatin treatment promotes neuronal survival and reduces inflammatory cytokine release from astrocytes after traumatic brain injury (TBI) in rats. Since reactive astrocytes produce inflammation mediators, in the current study we investigated the effect of simvastatin on astrocyte activation after TBI and its underlying signaling mechanisms.

Methods

Saline or simvastatin (1 mg/kg) was orally administered to rats starting at Day 1 after TBI and then daily for 14 days. Rats were sacrificed at 1, 3, 7, 14 days after treatment. Brain sections and tissues were prepared for immunohistochemical staining and Western blot analysis, respectively. Cultured astrocytes were subjected to oxygen-glucose deprivation (OGD) and followed by immunocytochemical staining with GFAP/caveolin-1 and Western blot analysis. Lipid rafts were isolated from the cell lysate and Western blot was carried out to detect the changes in epidermal growth factor receptor (EGFR) expression and phosphorylation in the lipid rafts.

Results

Simvastatin significantly promoted neuronal survival after TBI and attenuated activation of astrocytes. Simvastatin modified the caveolin-1 expression in lipid rafts in astrocyte cell membrane, suppressed the phosphorylation of EGFR in lipid rafts of astrocytes after OGD, and inhibited the OGD-induced interleukin-1 (IL-1) production.

Conclusions

These data suggest that simvastatin reduces reactive astrogliosis and rescues neuronal cells after TBI. These beneficial effects of simvastatin may be mediated by inhibiting astrocyte activation after TBI through modifying the caveolin-1 expression in lipid rafts and the subsequent modulation of EGFR phosphorylation in lipid rafts.

Populus yunnanensis was employed as a model species to detect sexual differences in growth, physiological, biochemical, and ultrastructural responses to cadmium (Cd) stress, nitrogen (N) deposition, and their combination. Compared with the control conditions, Cd decreased plant biomass, damaged the photosynthetic apparatus, visible as a decreased maximum efficiency of photosystem II (PSII; Fv/Fm) and effective quantum yield of PSII (Yield), depressed gas exchange capacity, and induced oxidative stress, visible as the disruption of antioxidative enzymes and accumulation of reactive oxygen species (ROS), in both sexes. On the other hand, Cd toxicity was mitigated by the recovery of gas exchange capacity, a decrease in ROS, and improvement of the redox imbalance in both sexes when N deposition was applied. However, males showed a higher gas exchange capacity, lower enzyme inhibition and ROS accumulation, stronger abilities to maintain cellular redox homeostasis, and a better maintenance of chloroplast ultrastructure than did females when exposed to Cd stress alone. Although males exhibited a higher Cd content in leaves than did females, males also accumulated higher levels of non-protein thiols (NP-SHs) and free amino acids (FAAs) for detoxification than did females. Sexual differences induced by Cd, visible, for example, in Fv/Fm, Yield, net photosynthesis rate (A), and stomatal conductance (gs), decreased under N deposition, as no significant differences between the sexes existed in these parameters under the combined treatment. The results indicated that females are more sensitive to Cd stress and suffer more injuries than do males. Moreover, N deposition can mitigate Cd toxicity and decrease sexual differences in Cd sensitivity.

CDDO-Me, a synthetic triterpenoid derived from oleanolic acid, is a promising anticancer agent that has shown strong activity against a wide variety cancer types in vitro and in vivo. We have previously shown that CDDO-Me induces apoptosis in prostate cancer cells irrespective of their hormonal status. To further understand the proapoptotic mechanism of CDDO-Me, we investigated the role of reactive oxygen species (ROS) in mediating the apoptosis inducing activity of CDDO-Me in LNCaP and PC-3 prostate cancer cell lines. Here, we show that CDDO-Me induces ROS generation from both nonmitochondrial and mitochondrial sources, which is associated with induction of apoptosis as characterized by increased annexin V-binding, cleavage of PARP-1 and procaspases -3,-8, -9, loss of mitochondrial membrane potential and release of cytochrome c. In addition, CDDO-Me inhibited cell survival Akt, NF-κB and mTOR signaling proteins. The inhibition of ROS generation by N-acetylcysteine (NAC) or by overexpression of antioxidant enzymes glutathione peroxidase (GPx) and superoxide dismutase1 (SOD1) prevented CDDO-Me-induced apoptosis. Pretreatment with NAC blocked annexin V-binding, cleavage of PARP-1 and procaspases -3,-8, -9, loss of mitochondrial membrane potential and release of cytochrome c by CDDO-Me. NAC also prevented the inhibition of constitutively active Akt, NF-κB and mTOR by CDDO-Me. Together, these data indicate that ROS plays an essential role in induction of apoptosis by CDDO-Me in prostate cancer cells.

In this study, we tested the hypothesis that TO901317 promotes synapse plasticity and axonal regeneration after stroke. Adult male C57BL/6J mice were subjected to middle cerebral artery occlusion (MCAo) and treated with or without TO901317 starting 24 h after MCAo daily for 14 days. Axonal damage and regeneration were evaluated by immunostaining. TO901317 significantly increased synaptophysin expression and axonal regeneration, as well as decreased the expressions of amyloid betaA4 precursor protein and Nogo receptor (NgR) in the ischemic brain. To test whether TO901317 regulates the phosphorylation of phosphatidylinositol 3-kinase (p-PI3K) and Akt (p-Akt) activity in the ischemic brain, MCAo mice were treated with or without TO901317 starting 24 h after MCAo daily for 4 days and were then killed at 5 days after MCAo. TO901317 treatment significantly increased p-PI3K and p-Akt activity, but did not increase total PI3K expression in the ischemic brain. Using primary cortical neuron (PCN) culture, TO901317 significantly increased synaptophysin expression, p-PI3K activity, and decreased NgR expression compared with nontreated controls. TO901317 also significantly increased neurite outgrowth, and inhibition of the PI3K/Akt pathway by LY294002 decreased neurite outgrowth in both controls and TO901317-treated groups in cultured hypoxic PCN. These data indicate that TO901317 promotes synaptic plasticity and axonal regeneration, and that PI3K/Akt signaling activity contributes to neurite outgrowth.

Human longevity is a complex phenotype that has a significant genetic predisposition. Like other biological processes, ageing process is governed through the regulation of signaling pathways and transcription factors. The DNA damage theory of ageing suggests that ageing is a consequence of un-repaired DNA damage accumulation. Intensive research has been carried out to elucidate the role of DNA repair systems in the ageing process. Decision Trees and Naive Bayesian Algorithm are two data-mining based classification methods for systematically analyzing data about human DNA repair genes. In this paper we develop a linearly combined kernel with Support Vector Machine (SVM) to analyze the ageing related data. The popular supervised learning algorithm enables better discrimination between ageing-related and non-ageing-related DNA repair genes. The linear combination of linear kernel and polynomial kernel of degree 3 in conjunction with SVM allows better classification accuracy in DNA repair gene data set. Compared to Decision Trees and Naive Bayesian Algorithm, SVM with the proposed kernel can achieve 65% AUC (Area Under ROC Curve) values, in contrast to 51.1% and 52.1% respectively. More importantly, we obtain 5 significant ageingrelated genes selected through the training on the whole data set and they are PCNA, PARP, APEX1, MLH1 and XRCC6. Different from the two methods, we can identify another important gene PCNA in the pathways the two methods targeted, while they failed to. And two novel genes PARP, MLH1 are selected as well. The two genes might provide potential insights for biologists in ageing research. SVM is a powerful and robust classification algorithm that can yield higher predictive accuracies. The selection of proper kernel plays a more important role in fulfilling the classification task. The important genes identified not only can target critical pathways related to ageing but also detected genes that may reveal possible related ageing biomarkers.

Carbohydrates, or glycans, are one of the most abundant and structurally diverse biopolymers constitute the third major class of biomolecules, following DNA and proteins. However, the study of carbohydrate sugar chains has lagged behind compared to that of DNA and proteins, mainly due to their inherent structural complexity. However, their analysis is important because they serve various important roles in biological processes, including signaling transduction and cellular recognition. In order to glean some light into glycan function based on carbohydrate structure, kernel methods have been developed in the past, in particular to extract potential glycan biomarkers by classifying glycan structures found in different tissue samples. The recently developed weighted qgram method (LK-method) exhibits good performance on glycan structure classification while having limitations in feature selection. That is, it was unable to extract biologically meaningful features from the data. Therefore, we propose a biochemicallyweighted tree kernel (BioLK-method) which is based on a glycan similarity matrix and also incorporates biochemical information of individual q-grams in constructing the kernel matrix. We further applied our new method for the classification and recognition of motifs on publicly available glycan data. Our novel tree kernel (BioLK-method) using a Support Vector Machine (SVM) is capable of detecting biologically important motifs accurately while LK-method failed to do so. It was tested on three glycan data sets from the Consortium for Functional Glycomics (CFG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) GLYCAN and showed that the results are consistent with the literature. The newly developed BioLK-method also maintains comparable classification performance with the LK-method. Our results obtained here indicate that the incorporation of biochemical information of q-grams further shows the flexibility and capability of the novel kernel in feature extraction, which may aid in the prediction of glycan biomarkers.

Gallic acid, an organic acid, also known as 3,4,5-trihydroxybenzoic acid, is cytotoxic against certain cancer cells, without harming normal cells. The objective of this study is to evaluate whether gallic acid can inhibit glioma cell viability, proliferation, invasion and reduce glioma cell mediated angiogenesis. Treatment of U87 and U251n glioma cells with gallic acid inhibited cell viability in a dose- and time-dependent manner. BrdU and tube formation assays indicated that gallic acid significantly decreased glioma cell proliferation and tube formation in mouse brain endothelial cells, respectively. In addition, gallic acid decreased U87 cell invasion in vitro. Western blot analysis showed that expression of ADAM17, p-Akt and p-Erk was suppressed by gallic acid in both U87 and U251n cell lines. These data suggest that suppression of ADAM17 and downregulation of PI3K/Akt and Ras/MAPK signaling pathways may contribute to gallic acid-induced decrease of invasiveness. Gallic acid may be a valuable candidate for treatment of brain tumor.