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1.  Molecular Characterization of PauR and Its Role in Control of Putrescine and Cadaverine Catabolism through the γ-Glutamylation Pathway in Pseudomonas aeruginosa PAO1 
Journal of Bacteriology  2013;195(17):3906-3913.
Pseudomonas aeruginosa PAO1 grows on a variety of polyamines as the sole source of carbon and nitrogen. Catabolism of polyamines is mediated by the γ-glutamylation pathway, which is complicated by the existence of multiple homologous enzymes with redundant specificities toward different polyamines for a more diverse metabolic capacity in this organism. Through a series of markerless gene knockout mutants and complementation tests, specific combinations of pauABCD (polyamine utilization) genes were deciphered for catabolism of different polyamines. Among six pauA genes, expression of pauA1, pauA2, pauA4, and pauA5 was found to be inducible by diamines putrescine (PUT) and cadaverine (CAD) but not by diaminopropane. Activation of these promoters was regulated by the PauR repressor, as evidenced by constitutively active promoters in the pauR mutant. The activities of these promoters were further enhanced by exogenous PUT or CAD in the mutant devoid of all six pauA genes. The recombinant PauR protein with a hexahistidine tag at its N terminus was purified, and specific bindings of PauR to the promoter regions of most pau operons were demonstrated by electromobility shift assays. Potential interactions of PUT and CAD with PauR were also suggested by chemical cross-linkage analysis with glutaraldehyde. In comparison, growth on PUT was more proficient than that on CAD, and this observed growth phenotype was reflected in a strong catabolite repression of pauA promoter activation by CAD but was completely absent as reflected by activation by PUT. In summary, this study clearly establishes the function of PauR in control of pau promoters in response to PUT and CAD for their catabolism through the γ-glutamylation pathway.
doi:10.1128/JB.00275-13
PMCID: PMC3754595  PMID: 23794626
2.  Effect of Xiaoyaosan Decoction on Learning and Memory Deficit in Rats Induced by Chronic Immobilization Stress 
Xiaoyaosan (XYS) decoction is a famous prescription which can protect nervous system from stress and treat liver stagnation and spleen deficiency syndrome (LSSDS). In this experiment, we observed the effect of XYS decoction on chronic immobilization stress (CIS) induced learning and memory deficit in rats from behaviors and changes of proteins in hippocampus. We used XYS decoction to treat CIS induced learning and memory deficit in rats with rolipram as positive control, used change of body weight and behavioral tests to determine whether the rats have LSSDS and have learning and memory deficit or not. We used Western blotting to determine the content of postsynaptic density protein 95 (PSD-95) and synaptophysin (SYP) in hippocampus. Results showed that XYS could improve the situation of slow weight gain induced by CIS, improve the ability of learning and memory, reverse the symptom of liver stagnation and spleen deficiency syndrome (LSSDS) in rats, and increase the levels of PSD-95 and SYP on the hippocampal nerve synapses. These findings suggested that XYS decoction may be helpful in reversing CIS induced learning and memory deficit by increasing the levels of PSD-95 and SYP on the hippocampal nerve synapses and improving synaptic plasticity.
doi:10.1155/2013/297154
PMCID: PMC3891437  PMID: 24459529
3.  Effect of whey protein on plasma amino acids in diabetic mice 
The aim of this study was to investigate the effect of whey protein on plasma amino acid levels in a mouse model of type II diabetes, using high-performance liquid chromatography (HPLC). The composition and content of amino acids in the whey proteins were analyzed using HPLC. Type I and type II diabetic mouse models were prepared using streptozotocin (STZ) and normal mice were used as a control. The ICR mice in each group were then randomly divided into four subgroups, to which 0, 10, 20 and 40% whey protein, respectively, was administered for four weeks. Changes in the plasma amino acid levels were observed in each group. The proportions of leucine, isoleucine and valine in the whey proteins were 14.40, 5.93 and 5.32% of the total amino acids, respectively, that is, the branched-chain amino acid content was 25.65%. The levels of branched-chain amino acids increased in the plasma of the normal and model mice following the administration of whey proteins by gavage and the amino acid levels increased as the concentration of the administered protein increased. In addition, the branched-chain amino acid levels in the blood of the model mice were higher than those in the normal mice. The levels of plasma amino acids in diabetic mice increased following gavage with whey protein, which is rich in branched-chain amino acids.
doi:10.3892/etm.2013.1329
PMCID: PMC3829761  PMID: 24255674
HPLC; diabetic mice; branched-chain amino acids; whey protein
4.  Enhancing Cell Nucleus Accumulation and DNA Cleavage Activity of Anti-Cancer Drug via Graphene Quantum Dots 
Scientific Reports  2013;3:2852.
Graphene quantum dots (GQDs) maintain the intrinsic layered structural motif of graphene but with smaller lateral size and abundant periphery carboxylic groups, and are more compatible with biological system, thus are promising nanomaterials for therapeutic applications. Here we show that GQDs have a superb ability in drug delivery and anti-cancer activity boost without any pre-modification due to their unique structural properties. They could efficiently deliver doxorubicin (DOX) to the nucleus through DOX/GQD conjugates, because the conjugates assume different cellular and nuclear internalization pathways comparing to free DOX. Also, the conjugates could enhance DNA cleavage activity of DOX markedly. This enhancement combining with efficient nuclear delivery improved cytotoxicity of DOX dramatically. Furthermore, the DOX/GQD conjugates could also increase the nuclear uptake and cytotoxicity of DOX to drug-resistant cancer cells indicating that the conjugates may be capable to increase chemotherapy efficacy of anti-cancer drugs that are suboptimal due to the drug resistance.
doi:10.1038/srep02852
PMCID: PMC3790198  PMID: 24092333
5.  Correction: Metabolic Response of Candida albicans to Phenylethyl Alcohol under Hyphae-Inducing Conditions 
PLoS ONE  2013;8(8):10.1371/annotation/d395f7a5-ac0a-41e2-abd8-fa947717f6a3.
doi:10.1371/annotation/d395f7a5-ac0a-41e2-abd8-fa947717f6a3
PMCID: PMC3782339  PMID: 24098613
6.  Metabolic Response of Candida albicans to Phenylethyl Alcohol under Hyphae-Inducing Conditions 
PLoS ONE  2013;8(8):e71364.
Phenylethyl alcohol was one of the first quorum sensing molecules (QSMs) identified in C. albicans. This extracellular signalling molecule inhibits the hyphal formation of C. albicans at high cell density. Little is known, however, about the underlying mechanisms by which this QSM regulates the morphological switches of C. albicans. Therefore, we have applied metabolomics and isotope labelling experiments to investigate the metabolic changes that occur in C. albicans in response to phenylethyl alcohol under defined hyphae-inducing conditions. Our results showed a global upregulation of central carbon metabolism when hyphal development was suppressed by phenylethyl alcohol. By comparing the metabolic changes in response to phenylethyl alcohol to our previous metabolomic studies, we were able to short-list 7 metabolic pathways from central carbon metabolism that appear to be associated with C. albicans morphogenesis. Furthermore, isotope-labelling data showed that phenylethyl alcohol is indeed taken up and catabolised by yeast cells. Isotope-labelled carbon atoms were found in the majority of amino acids as well as in lactate and glyoxylate. However, isotope-labelled carbon atoms from phenylethyl alcohol accumulated mainly in the pyridine ring of NAD+/NADH and NADP−/NADPH molecules, showing that these nucleotides were the main products of phenylethyl alcohol catabolism. Interestingly, two metabolic pathways where these nucleotides play an important role, nitrogen metabolism and nicotinate/nicotinamide metabolism, were also short-listed through our previous metabolomics works as metabolic pathways likely to be closely associated with C. albicans morphogenesis.
doi:10.1371/journal.pone.0071364
PMCID: PMC3741116  PMID: 23951145
7.  Effects of rocuronium and vecuronium on initial rundown of endplate potentials in the isolated phrenic nerve diaphragm preparation of rats 
SpringerPlus  2013;2:155.
Rocuronium and vecuronium, two non-depolarizing neuromuscular blockers, have been widely used in surgery procedures. However, their electrophysiological properties need to be more widely explored. We examined the effects of rocuronium and vecuronium on initial rundown of endplate potential amplitudes in the non-uniform stretched muscle preparation of the rat isolated phrenic nerve diaphragm. More specifically, the endplate potentials were recorded with one microelectrode from a single endplate. The effects of rocuronium or vecuronium each at 4 concentrations (0.5 ×, l ×, 2 ×, 4 × EC95; EC95 = concentration of the drug required to produce the inhibitory effect by 95%) on the amplitude of endplate potentials and its rundown were observed. Treatment of the isolated rat phrenic nerve-diaphragm preparation with rocuronium (2.5–20 μg/ml) or vecuronium (0.5–4 μg/ml) decreased the amplitude of endplate potentials and inhibited its rundown in a concentration-dependent manner. At the concentration (2.5 μg/ml for rocuronium and 0.5 μg/ml for vecuronium) that did not alter the endplate potential amplitude, the onset of reduced endplate potential rundown was 3 and 5 min after administration of rocuronium or vecuronium, respectively. The results suggest that rocuronium and vecuronium block the neuromuscular junction presynaptically and that rocuronium does it faster than vecuronium.
doi:10.1186/2193-1801-2-155
PMCID: PMC3639353  PMID: 23641322
Rocuronium; Vecuronium; Motor endplate; Neuromuscular junction; Diaphragm
8.  Genome-Wide Microarrray Analysis Reveals Roles for the REF-1 Family Member HLH-29 in Ferritin Synthesis and Peroxide Stress Response 
PLoS ONE  2013;8(3):e59719.
In Caenorhabditis elegans, the six proteins that make up the REF-1 family have been identified as functional homologs of the Hairy/Enhancer of Split (HES) proteins. These transcription factors act in both Notch dependent and Notch-independent pathways to regulate embryonic events during development; however, their post-embryonic functions are not well defined. As a first step toward understanding how the REF-1 family works together to coordinate post-embryonic events, we used gene expression microarray analysis to identify transcriptional targets of HLH-29 in L4/young adult stage animals. Here we show that HLH-29 targets are genes needed for the regulation of growth and lifespan, including genes required for oxidative stress response and fatty acid metabolism, and the ferritin genes, ftn-1 and ftn-2. We show that HLH-29 regulates ftn-1 expression via promoter sequences upstream of the iron-dependent element that is recognized by the hypoxia inducible factor, HIF-1. Additionally, hlh-29 mutants are more resistant to peroxide stress than wild-type animals and ftn-1(RNAi) animals, even in the presence of excess iron. Finally we show that HLH-29 acts parallel to DAF-16 but upstream of the microphthalmia transcription factor ortholog, HLH-30, to regulate ftn-1 expression under normal growth conditions.
doi:10.1371/journal.pone.0059719
PMCID: PMC3606163  PMID: 23533643
9.  Effect of glutamine on apoptosis of intestinal epithelial cells of severe acute pancreatitis rats receiving nutritional support in different ways 
Objective: To investigate the effect of glutamine (Gln) on pro-inflammatory cytokines (TNF-α, IL-2 and IL-10) and the balance between pro-inflammatory cytokines and anti-inflammatory cytokines in severe acute pancreatitis (SAP) rats receiving nutritional support in different ways. Methods: Male SD rats (n=80) were randomly assigned into 5 groups: sham group, SAP+ parenteral nutrition (PN) group, SAP+ enteral nutrition (EN) group, SAP+EN+Gln group and SAP+PN+Gln group. At the same time, rats in 5 groups were sacrificed at 4 and 7 days after nutritional support. ELISA was employed to detect the pro-inflammatory cytokines including TNF-α, IL-2 and IL-10. Results: The serum TNF-α in the EN+Gln group after 7-day treatment was significantly lower than that in the EN, PN and PN+Gln groups at corresponding time point (P<0.05). The serum IL-2 in the EN+Gln group after 7-day treatment was markedly higher than that in the EN, PN and PN+Gln groups at corresponding time point (P<0.01). After 7-day treatment, the serum IL-2 in the EN+Gln and EN groups were markedly higher than that after 4-day treatment (P<0.01), but the serum IL-2 in the PN group was significantly lower than that after 4-day treatment (P<0.01). The serum IL-10 after 7-day treatment was markedly lower than that after 4-day treatment in all groups (P<0.01), and PN group had the lowest serum IL-10. Serum IL-10 in the EN+Gln group was significantly higher than that in the PN and PN+Gln groups at both time points (P<0.01). The serum IL-10 in the EN group was significantly higher than that in the PN group after 4-day treatment (P<0.01), but the serum IL-10 in the EN group was comparable to that in the PN group after 7-day treatment. The serum IL-10/TNF-α in the EN+Gln group was only slightly higher than that in the control group at both time points. The serum IL-10/TNF-α in the EN group was significantly lower than that in the EN+Gln group at both time points (P<0.05). The serum IL-10/TNF-α in the PN group was markedly lower than that in the EN group and EN+Gln group (P<0.05 and P<0.01, respectively).Conclusion: EN in combination with Gln are superior to EN alone, PN alone and PN in combination with Gln in regulating inflammation in SAP rats, and the EN has more potent capability to regulate the balance between pro-inflammation and anti-inflammation than PN.
PMCID: PMC3563192  PMID: 23412711
Pancreatitis; glutamine; inflammatory cytokines; rat
10.  Akt1 Mediates Neuronal Differentiation in Zebrafish via a Reciprocal Interaction with Notch Signaling 
PLoS ONE  2013;8(1):e54262.
Akt1 is well known for its role in regulating cell proliferation, differentiation, and apoptosis and is implicated in tumors and several neurological disorders. However, the role of Akt1 in neural development has not been well defined. We have isolated zebrafish akt1 and shown that this gene is primarily transcribed in the developing nervous system, and its spatiotemporal expression pattern suggests a role in neural differentiation. Injection of akt1 morpholinos resulted in loss of neuronal precursors with a concomitant increase in post-mitotic neurons, indicating that knockdown of Akt1 is sufficient to cause premature differentiation of neurons. A similar phenotype was observed in embryos deficient for Notch signaling. Both the ligand (deltaA) and the downstream target of Notch (her8a) were downregulated in akt1 morphants, indicating that Akt1 is required for Delta-Notch signaling. Furthermore, akt1 expression was downregulated in Delta-Notch signaling-deficient embryos and could be induced by constitutive activation of Notch signaling. In addition, knockdown of Akt1 was able to nullify the inhibition of neuronal differentiation caused by constitutive activation of Notch signaling. Taken together, these results provide in vivo evidence that Akt1 interacts with Notch signaling reciprocally and provide an explanation of why Akt1 is essential for the inhibition of neuronal differentiation.
doi:10.1371/journal.pone.0054262
PMCID: PMC3544797  PMID: 23342113
11.  Comparative Effects of Er-Xian Decoction, Epimedium Herbs, and Icariin with Estrogen on Bone and Reproductive Tissue in Ovariectomized Rats 
Er-Xian Decoction (EXD), Epimedium herbs (herbs of Epimedium brevicornum Maxim, EBH), and icariin (ICA) have been proven to have estrogen-like and antiosteoporotic activity and are used for the treatment of osteoporosis, menopausal syndrome, and age-associated diseases. The present study found that EXD, EBH, and ICA treatments, emulating estrogen, significantly contributed to bone density and architecture in OVX rats and that EXD is similar to estrogen and exerts a concomitant effect on bone formation and bone resorption at the tissue level, while EBH and ICA produced bone-protective effects mainly by inhibiting bone resorption. Nevertheless, EXD, EBH, and ICA treatments manifested a fewer adverse effects on the uterus, mammary gland, and vagina compared to estrogen administrations. Among the EXD, EBH, and ICA, EXD was found to have superior efficacy and safety profile.
doi:10.1155/2012/241416
PMCID: PMC3511842  PMID: 23227099
12.  Effects and Interaction of Icariin, Curculigoside, and Berberine in Er-Xian Decoction, a Traditional Chinese Medicinal Formula, on Osteoclastic Bone Resorption 
Er-Xian decoction (EXD), a traditional Chinese medicine, has been reported to have a protective effect against bone loss in ovariectomized osteoporotic rats, and the inclusion of icariin (I), curculigoside (C), and berberine (B) in EXD displays inhibitory effects on osteoclastic bone resorption. In the present paper, we investigated the interaction and effects of I, C, B, and their combination on bone resorption activity in vitro on osteoclasts derived from rat bone marrow cells. ICB synergistically decreased the formation of bone resorption pits, the number of multinucleated osteoclasts, and the activity of tartrate-resistant acid phosphatase (TRAP) and showed antagonistic or additive effects on cathepsin K activity in the coculture system of osteoblasts and bone marrow cells in the presence of 1, 25-dihydroxyvitamin D3 and dexamethasone. The combination of ICB also enhanced the inhibitory effects on the formation of F-actin ring, a cytoskeleton structure of osteoclasts induced from bone marrow cells with macrophage colony stimulation factor (M-CSF) and receptor activator of NF-κB ligand (RANKL). In addition, ICB synergistically improved the ratio of protein expression of osteoprotegerin (OPG) and RANKL in osteoblasts and interfered with the mitogen-activated protein kinases (MAPKs) pathway in osteoclast. These results clearly show that I, C, B, and their combination in EXD exert effects of mutual reinforcement. However, IBC does not show an intensified adverse effect in the ovariectomized murine model, as revealed by change in body and uterine weight, confirming the safety of EXD. These observations are in agreement with the rationality of the formula used in this paper.
doi:10.1155/2012/490843
PMCID: PMC3519276  PMID: 23243450
13.  Dopamine D2 receptor-mediated Akt/PKB signalling: initiation by the D2S receptor and role in quinpirole-induced behavioural activation 
ASN NEURO  2012;4(6):e00098.
The short and long isoforms of the dopamine D2 receptor (D2S and D2L respectively) are highly expressed in the striatum. Functional D2 receptors activate an intracellular signalling pathway that includes a cAMP-independent route involving Akt/GSK3 (glycogen synthase kinase 3). To investigate the Akt/GSK3 response to the seldom-studied D2S receptor, we established a rat D2S receptor-expressing cell line [HEK (human embryonic kidney)-293/rD2S]. We found that in HEK-293/rD2S cells, the D2/D3 agonists bromocriptine and quinpirole significantly induced Akt and GSK3 phosphorylation, as well as ERK1/2 (extracellular-signal-regulated kinase 1/2) activation. The D2S receptor-induced Akt signals were profoundly inhibited by the internalization blockers monodansyl cadaverine and concanavalin A. Activation of the D2S receptor in HEK-293/rD2S cells appeared to trigger Akt/phospho-Akt translocation to the cell membrane. In addition to our cell culture experiments, we studied D2 receptor-dependent Akt in vivo by systemic administration of the D2/D3 agonist quinpirole. The results show that quinpirole evoked Akt-Ser473 phosphorylation in the ventral striatum. Furthermore, intra-accumbens administration of wortmannin, a PI3K (phosphoinositide 3-kinase) inhibitor, significantly suppressed the quinpirole-evoked behavioural activation. Overall, we demonstrate that activation of the dopamine D2S receptor stimulates Akt/GSK3 signalling. In addition, in vivo Akt activity in the ventral striatum appears to play an important role in systemic D2/D3 agonist-induced behavioural activation.
doi:10.1042/AN20120013
PMCID: PMC3449306  PMID: 22909302
Akt (protein kinase B); dopamine D2S receptor; glycogen synthase kinase 3; nucleus accumbens; receptor internalization; CNS, central nervous system; ConA, concanavalin A; CREB, cAMP-response-element-binding protein; Cy3, indocarbocyanine; DA, dopamine; DAPI, 4′,6-diamidino-2-phenylindole; EGF, epidermal growth factor; ERK, extracellular-signal-regulated kinase; GSK, glycogen synthase kinase; HEK, human embryonic kidney; HRP, horseradish peroxidase; MAPK, mitogen-activated protein kinase; MDC, monodansylcadaverine; MEK, MAPK/ERK kinase; MEM, minimum essential medium; METH, methamphetamine; Nrf2, nuclear factor-erythroid 2-related factor 2; PDGF, platelet-derived growth factor; PI3K, phosphoinositide 3-kinase
14.  The association between online gaming, social phobia, and depression: an internet survey 
BMC Psychiatry  2012;12:92.
Background
Online gaming technology has developed rapidly within the past decade, and its related problems have received increasing attention. However, there are few studies on the psychiatric symptoms associated with excessive use of online games. The aim of this study is to investigate the characteristics of online gamers, and the association between online gaming hours, social phobia, and depression using an internet survey.
Methods
An online questionnaire was designed and posted on a popular online game websites, inviting the online gamers to participate the survey. The content of the questionnaire included demographic data, profiles of internet usage and online gaming, and self-rating scales of Depression and Somatic Symptoms Scale (DSSS), Social Phobia Inventory (SPIN), and Chen Internet Addiction Scale (CIAS).
Results
A total of 722 online gamers with a mean age of 21.8 ± 4.9 years completed the online survey within one month. 601 (83.2%) participants were male, and 121 (16.8%) were female. The mean weekly online gaming time was 28.2 ± 19.7 hours, which positively associated with history of online gaming (r = 0.245, p < 0.001), total DSSS (r = 0.210, p < 0.001), SPIN (r = 0.150, p < 0.001), and CIAS (r = 0.290, p < 0.001) scores. The female players had a shorter history of online gaming (6.0 ± 3.1 vs. 7.2 ± 3.6 years, p = 0.001) and shorter weekly online gaming hours (23.2 ± 17.0 vs. 29.2 ± 20.2 hours, p = 0.002), but had higher DSSS (13.0 ± 9.3 vs. 10.9 ± 9.7, p = 0.032) and SPIN (22.8 ± 14.3 vs. 19.6 ± 13.5, p = 0.019) scores than the male players. The linear regression model showed that higher DSSS scores were associated with female gender, higher SPIN scores, higher CIAS scores, and longer weekly online gaming hours, with controlling for age and years of education.
Conclusion
The online gamers with longer weekly gaming hours tended to have a longer history of online gaming, and more severe depressive, social phobic, and internet addiction symptoms. Female online gamers had fewer weekly online gaming hours and a shorter previous online gaming history, but tended to have more severe somatic, pain, and social phobic symptoms. The predictors for depression were higher social phobic symptom, higher internet addiction symptoms, longer online gaming hours, and female gender.
doi:10.1186/1471-244X-12-92
PMCID: PMC3545926  PMID: 22839747
15.  The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs 
PLoS Genetics  2012;8(4):e1002617.
Small RNAs regulate diverse biological processes by directing effector proteins called Argonautes to silence complementary mRNAs. Maturation of some classes of small RNAs involves terminal 2′-O-methylation to prevent degradation. This modification is catalyzed by members of the conserved HEN1 RNA methyltransferase family. In animals, Piwi-interacting RNAs (piRNAs) and some endogenous and exogenous small interfering RNAs (siRNAs) are methylated, whereas microRNAs are not. However, the mechanisms that determine animal HEN1 substrate specificity have yet to be fully resolved. In Caenorhabditis elegans, a HEN1 ortholog has not been studied, but there is evidence for methylation of piRNAs and some endogenous siRNAs. Here, we report that the worm HEN1 ortholog, HENN-1 (HEN of Nematode), is required for methylation of C. elegans small RNAs. Our results indicate that piRNAs are universally methylated by HENN-1. In contrast, 26G RNAs, a class of primary endogenous siRNAs, are methylated in female germline and embryo, but not in male germline. Intriguingly, the methylation pattern of 26G RNAs correlates with the expression of distinct male and female germline Argonautes. Moreover, loss of the female germline Argonaute results in loss of 26G RNA methylation altogether. These findings support a model wherein methylation status of a metazoan small RNA is dictated by the Argonaute to which it binds. Loss of henn-1 results in phenotypes that reflect destabilization of substrate small RNAs: dysregulation of target mRNAs, impaired fertility, and enhanced somatic RNAi. Additionally, the henn-1 mutant shows a weakened response to RNAi knockdown of germline genes, suggesting that HENN-1 may also function in canonical RNAi. Together, our results indicate a broad role for HENN-1 in both endogenous and exogenous gene silencing pathways and provide further insight into the mechanisms of HEN1 substrate discrimination and the diversity within the Argonaute family.
Author Summary
Small RNAs serve as sentinels of the genome, policing activity of selfish genetic elements, modulating chromatin dynamics, and fine-tuning gene expression. Nowhere is this more important than in the germline, where endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) promote formation of functional gametes and ensure viable, fertile progeny. Small RNAs act primarily by associating with effector proteins called Argonautes to direct repression of complementary mRNAs. HEN1 methyltransferases, which methylate small RNAs, play a critical role in accumulation of these silencing signals. In this study, we report that the 26G RNAs, a class of C. elegans endo-siRNAs, are differentially methylated in male and female germlines. 26G RNAs derived from the two germlines are virtually indistinguishable, except that they associate with evolutionarily divergent Argonautes. Our data support a model wherein the methylation status and, consequently, stability of a small RNA are determined by the associated Argonaute. Therefore, selective expression of Argonautes that permit or prohibit methylation may represent a new mechanism for regulating small RNA turnover. As we observe this phenomenon in the germline, it may be particularly pertinent for directing inheritance of small RNAs, which can carry information not encoded in progeny DNA that is essential for continued transgenerational genome surveillance.
doi:10.1371/journal.pgen.1002617
PMCID: PMC3330095  PMID: 22548001
16.  Mechanical pain sensitivity of deep tissues in children - possible development of myofascial trigger points in children 
Background
It is still unclear when latent myofascial trigger points (MTrPs) develop during early life. This study is designed to investigate the mechanical pain sensitivity of deep tissues in children in order to see the possible timing of the development of latent MTrPs and attachment trigger points (A-TrPs) in school children.
Methods
Five hundreds and five healthy school children (age 4- 11 years) were investigated. A pressure algometer was used to measure the pressure pain threshold (PPT) at three different sites in the brachioradialis muscle: the lateral epicondyle at elbow (site A, assumed to be the A-TrP site), the mid-point of the muscle belly (site B, assumed to be the MTrP site), and the muscle-tendon junction as a control site (site C).
Results
The results showed that, for all children in this study, the mean PPT values was significantly lower (p < 0.05) at the assumed A-TrP site (site A) than at the other two sites, and was significantly lower (p < 0.05) at the assumed MTrP site (site B) than at the control site (site C). These findings are consistent if the data is analyzed for different genders, different dominant sides, and different activity levels.
Conclusions
It is concluded that a child had increased sensitivity at the tendon attachment site and the muscle belly (endplate zone) after age of 4 years. Therefore, it is likely that a child may develop an A-Trp and a latent MTrP at the brachioradialis muscle after the age of 4 years. The changes in sensitivity, or the development for these trigger points, may not be related to the activity level of children aged 7-11 years. Further investigation is still required to indentify the exact timing of the initial occurrence of a-Trps and latent MTrPs.
doi:10.1186/1471-2474-13-13
PMCID: PMC3298468  PMID: 22316064
myofascial trigger points; children; pressure pain threshold; algometry
17.  Promoter Recognition and Activation by the Global Response Regulator CbrB in Pseudomonas aeruginosa▿† 
Journal of Bacteriology  2011;193(11):2784-2792.
In Pseudomonas aeruginosa, the CbrA/CbrB two-component system is instrumental in the maintenance of the carbon-nitrogen balance and for growth on carbon sources that are energetically less favorable than the preferred dicarboxylate substrates. The CbrA/CbrB system drives the expression of the small RNA CrcZ, which antagonizes the repressing effects of the catabolite repression control protein Crc, an RNA-binding protein. Dicarboxylates appear to cause carbon catabolite repression by inhibiting the activity of the CbrA/CbrB system, resulting in reduced crcZ expression. Here we have identified a conserved palindromic nucleotide sequence that is present in upstream activating sequences (UASs) of promoters under positive control by CbrB and σ54 RNA polymerase, especially in the UAS of the crcZ promoter. Evidence for recognition of this palindromic sequence by CbrB was obtained in vivo from mutational analysis of the crcZ promoter and in vitro from electrophoretic mobility shift assays using crcZ promoter fragments and purified CbrB protein truncated at the N terminus. Integration host factor (IHF) was required for crcZ expression. CbrB also activated the lipA (lipase) promoter, albeit less effectively, apparently by interacting with a similar but less conserved palindromic sequence in the UAS of lipA. As expected, succinate caused CbrB-dependent catabolite repression of the lipA promoter. Based on these results and previously published data, a consensus CbrB recognition sequence is proposed. This sequence has similarity to the consensus NtrC recognition sequence, which is relevant for nitrogen control.
doi:10.1128/JB.00164-11
PMCID: PMC3133114  PMID: 21478360
18.  p-Cu2O-shell/n-TiO2-nanowire-core heterostucture photodiodes 
Nanoscale Research Letters  2011;6(1):575.
This study reports the deposition of cuprous oxide [Cu2O] onto titanium dioxide [TiO2] nanowires [NWs] prepared on TiO2/glass templates. The average length and average diameter of these thermally oxidized and evaporated TiO2 NWs are 0.1 to 0.4 μm and 30 to 100 nm, respectively. The deposited Cu2O fills gaps between the TiO2 NWs with good step coverage to form nanoshells surrounding the TiO2 cores. The p-Cu2O/n-TiO2 NW heterostructure exhibits a rectifying behavior with a sharp turn-on at approximately 0.9 V. Furthermore, the fabricated p-Cu2O-shell/n-TiO2-nanowire-core photodiodes exhibit reasonably large photocurrent-to-dark-current contrast ratios and fast responses.
doi:10.1186/1556-276X-6-575
PMCID: PMC3218093  PMID: 22040099
19.  The Landscape of C. elegans 3′UTRs 
Science (New York, N.Y.)  2010;329(5990):432-435.
Three-prime untranslated regions (3′UTRs) of metazoan messenger RNAs (mRNAs) contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3′ rapid amplification of complementary DNA (cDNA) ends, full-length cDNAs, and RNA-seq, we defined ∼26,000 distinct 3′UTRs in Caenorhabditis elegans for ∼85% of the 18,328 experimentally supported protein-coding genes and revised ∼40% of gene models. Alternative 3′UTR isoforms are frequent, often differentially expressed during development. Average 3′UTR length decreases with animal age. Surprisingly, no polyadenylation signal (PAS) was detected for 13% of polyadenylation sites, predominantly among shorter alternative isoforms. Trans-spliced (versus non–trans-spliced) mRNAs possess longer 3′UTRs and frequently contain no PAS or variant PAS. We identified conserved 3′UTR motifs, isoform-specific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3′UTRs, both genome-wide and throughout development.
doi:10.1126/science.1191244
PMCID: PMC3142571  PMID: 20522740
20.  Phosphodiesterase-4D knockout and RNAi-mediated knockdown enhance memory and increase hippocampal neurogenesis via increased cAMP signaling 
Phosphodiesterase-4 (PDE4) plays an important role in mediating memory via the control of intracellular cyclic AMP (cAMP) signaling; inhibition of PDE4 enhances memory. However, development of PDE4 inhibitors as memory enhancers has been hampered by their major side effect of emesis. PDE4 has four subtypes (PDE4A-D), consisting of 25 splice variants. Mice deficient in PDE4D displayed memory enhancement in radial-arm maze, water-maze, and object recognition tests. These effects were mimicked by repeated treatment with rolipram in wild-type mice. In addition, similar to rolipram-treated wild-type mice, PDE4D-deficient mice also displayed increased hippocampal neurogenesis and phosphorylated cAMP-response element binding protein (pCREB). Further, microinfusion of lentiviral vectors, which contained microRNAs (miRNAs) targeting long-form PDE4D isoforms, into bilateral dentate gyri of the mouse hippocampus down-regulated PDE4D4 and PDE4D5, enhanced memory, and increased hippocampal neurogenesis and pCREB. Finally, while rolipram and PDE4D-deficiency shortened alpha2 adrenergic receptor-mediated anesthesia, a surrogate measure of emesis, miRNA-mediated PDE4D knockdown in the hippocampus did not. The present results suggest that PDE4D, in particular long-form PDE4Ds, plays a critical role in the mediation of memory and hippocampal neurogenesis, which are mediated by cAMP/CREB signaling; reduced expression of PDE4D, at least PDE4D4 and PDE4D5, in the hippocampus enhances memory but appears not to cause emesis. These novel findings will aid in the development of PDE4 subtype- or variant-selective inhibitors for treatment of disorders involving impaired cognition, including Alzheimer’s disease.
doi:10.1523/JNEUROSCI.5236-10.2011
PMCID: PMC3079568  PMID: 21209202
phosphodiesterase-4 (PDE4); microRNA; memory; neurogenesis; CREB; knockout
21.  l-Lysine Catabolism Is Controlled by l-Arginine and ArgR in Pseudomonas aeruginosa PAO1▿  
Journal of Bacteriology  2010;192(22):5874-5880.
In comparison to other pseudomonads, Pseudomonas aeruginosa grows poorly in l-lysine as a sole source of nutrient. In this study, the ldcA gene (lysine decarboxylase A; PA1818), previously identified as a member of the ArgR regulon of l-arginine metabolism, was found essential for l-lysine catabolism in this organism. LdcA was purified to homogeneity from a recombinant strain of Escherichia coli, and the results of enzyme characterization revealed that this pyridoxal-5-phosphate-dependent decarboxylase takes l-lysine, but not l-arginine, as a substrate. At an optimal pH of 8.5, cooperative substrate activation by l-lysine was depicted from kinetics studies, with calculated Km and Vmax values of 0.73 mM and 2.2 μmole/mg/min, respectively. Contrarily, the ldcA promoter was induced by exogenous l-arginine but not by l-lysine in the wild-type strain PAO1, and the binding of ArgR to this promoter region was demonstrated by electromobility shift assays. This peculiar arginine control on lysine utilization was also noted from uptake experiments in which incorporation of radioactively labeled l-lysine was enhanced in cells grown in the presence of l-arginine but not l-lysine. Rapid growth on l-lysine was detected in a mutant devoid of the main arginine catabolic pathway and with a higher basal level of the intracellular l-arginine pool and hence elevated ArgR-responsive regulons, including ldcA. Growth on l-lysine as a nitrogen source can also be enhanced when the aruH gene encoding an arginine/lysine:pyruvate transaminase was expressed constitutively from plasmids; however, no growth of the ldcA mutant on l-lysine suggests a minor role of this transaminase in l-lysine catabolism. In summary, this study reveals a tight connection of lysine catabolism to the arginine regulatory network, and the lack of lysine-responsive control on lysine uptake and decarboxylation provides an explanation of l-lysine as a poor nutrient for P. aeruginosa.
doi:10.1128/JB.00673-10
PMCID: PMC2976436  PMID: 20833801
22.  A 1HNMR-Based Metabonomics Study of Postmenopausal Osteoporosis and Intervention Effects of Er-Xian Decoction in Ovariectomized Rats 
A metabonomics method using 1H nuclear magnetic resonance spectroscopy (1HNMR) was applied to obtain a systematic view of the development and progression of postmenopausal osteoporosis. Using partial least squares discriminant analysis (PLS-DA), 26 and 34 characteristic resonances were found respectively in urine and plasma of ovariectomized rats (Variable importance, VIP value ≥1.0), and the significant altered metabolites identified in the plasma and urine were 10 and 9, respectively. Changes in these metabolites were related to the pathways of lipid, energy and amino acid metabolism, some of which involved the oxidative system. The described method was also used to analyze the therapeutic effects of Er-Xian Decoction (EXD), a traditional Chinese medicine widely used in the clinical treatment of osteoporosis in China. The results showed that EXD administration could provide satisfactory effects on osteoporosis through partially regulating the perturbed pathways of lipid, energy and amino acid metabolism and improving the anti-oxidative ability.
doi:10.3390/ijms12117635
PMCID: PMC3233428  PMID: 22174622
1HNMR; metabonomics; ovariectomized rats; postmenopausal osteoporosis; Er-Xian Decoction
23.  Antidepressant- and anxiolytic-like effects of the phosphodiesterase-4 (PDE4) inhibitor rolipram on behavior depend on cyclic AMP-response element binding protein (CREB)-mediated neurogenesis in the hippocampus 
Inhibition of phosphodiesterase-4 (PDE4), an enzyme that catalyzes the hydrolysis of cyclic AMP (cAMP), increases phosphorylation of cAMP-response element binding protein (pCREB) and hippocampal neurogenesis, and produces antidepressant-like effects on behavior; however, causal links among these have not been established. In the present study, chronic administration of rolipram produced antidepressant- and anxiolytic-like effects on behavior in mice. It also increased cAMP and pCREB levels in the hippocampus and prefrontal cortex, but increased Sox2, a marker for mitotic progenitor cells, only in the hippocampus. Chronic rolipram treatment also increased hippocampal neurogenesis, as evidenced by increased bromodeoxyuridine (BrdU)-positive cells in the hippocampal dentate gyrus. Methylazoxymethanol (MAM), which is toxic to proliferating cells, reversed rolipram-induced increases in BrdU-positive cells and pCREB in the hippocampus and partially blocked its behavioral effects. Approximately 84% of BrdU-positive cells became newborn neurons, 93% of which co-expressed pCREB; these proportions were not altered by rolipram or MAM, either alone or in combination. Finally, three weeks following the end of MAM treatment, when neurogenesis was no longer inhibited, rolipram again increased hippocampal pCREB, with its antidepressant- and anxiolytic-like effects resumed. Overall, the present results suggest that rolipram produces its effects on behavior in a manner that at least partially depends on its neurogenic action in the hippocampus, targeting mitotic progenitor cells rather than newborn or mature neurons; cAMP/CREB signaling in hippocampal newborn neurons is critical for neurogenesis and contributes to the behavioral effects of rolipram.
doi:10.1038/npp.2009.66
PMCID: PMC2743762  PMID: 19516250
phosphodiesterase-4 (PDE4); neurogenesis; CREB; hippocampus; behavior; mice
24.  Dual Inhibitors of Phosphodiesterase-4 and Serotonin Reuptake 
Journal of medicinal chemistry  2009;52(6):1530-1539.
A new class of multi-target compounds was synthesized by linking a novel selective serotonin reuptake inhibitor (SSRI)a to a PDE4 inhibitor. The new dual PDE4 inhibitor/SSRI showed antidepressant-like activity in the forced swim test in mice The SSRIs 14, 2-{5-[3-(5-fluoro-2-methoxy-phenyl)-ethyl]-tetrahydro-furan-2-yl}-ethylamine and 15, 2-{5-[3-(5-fluoro-2-methoxy-phenyl)-propyl]-tetrahydro-furan-2-yl}-ethylamine were both individually linked to the PDE4 inhibitor 19, (4-(3,4-dimethoxy-phenyl)-4a,5,8,8a-tetrahydro-2H-phthalazin-1-one) via a five carbon chain. The dual PDE4 inhibitor/SSRI 21, 2-{5-[3-(5-fluoro-2-methoxy-phenyl)-ethyl]-tetrahydro-furan-2-yl}-ethylamine)-pentyl]-4,5,8,8a-tetrahydro-2H-phthalazin-1-one showed potent and selective serotonin reuptake inhibition (IC50 value of 127 nM). The dual PDE4 inhibitor/SSRI 21 also inhibited PDE4D3 with a Ki value of 2.0 nM. The dual PDE4 inhibitor/SSRI was significantly more effective than the individual SSRI alone or fluoxetine in the forced swim test at standard doses. On a molar basis, the antidepressant-like effect of the dual PDE4 inhibitor/SSRI 21 showed a 129-fold increase in in vivo efficacy compared to fluoxetine.
doi:10.1021/jm8010993
PMCID: PMC2762440  PMID: 19256502
25.  Association of Changes in Norepinephrine and Serotonin Transporter Expression with the Long-Term Behavioral Effects of Antidepressant Drugs 
Previous work has shown that repeated desipramine treatment causes downregulation of the norepinephrine transporter (NET) and persistent antidepressant-like effects on behavior, ie effects observed 2 days after discontinuation of drug treatment when acute effects are minimized. The present study examined whether this mechanism generalizes to other antidepressants and also is evident for the serotonin transporter (SERT). Treatment of rats for 14 days with 20 mg/kg per day protriptyline or 7.5 mg/kg per day sertraline reduced NET and SERT expression, respectively, in cerebral cortex and hippocampus; these treatments also induced a persistent antidepressant-like effect on forced-swim behavior. Increased serotonergic neurotransmission likely mediated the behavioral effect of sertraline, as it was blocked by inhibition of serotonin synthesis with p-chlorophenylalanine; a parallel effect was observed previously for desipramine and noradrenergic neurotransmission. Treatment with 20 mg/kg per day reboxetine for 42, but not 14, days reduced NET expression; antidepressant-like effects on behavior were observed for both treatment durations. Treatment for 14 days with 70 mg/kg per day venlafaxine, which inhibits both the NET and SERT, or 10 mg/kg per day phenelzine, a monoamine oxidase inhibitor, produced antidepressant-like effects on behavior without altering NET or SERT expression. For all drugs tested, reductions of NET and SERT protein were not accompanied by reduced NET or SERT mRNA in locus coeruleus or dorsal raphe nucleus, respectively. Overall, the present results suggest an important, though not universal, role for NET and SERT regulation in the long-term behavioral effects of antidepressants. Understanding the mechanisms underlying transporter regulation in vivo may suggest novel targets for the development of antidepressant drugs.
doi:10.1038/npp.2008.183
PMCID: PMC2727703  PMID: 18923402
antidepressant drugs; norepinephrine transporter; serotonin transporter; p-chlorophenylalanine

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