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1.  Sumoylation in Aspergillus nidulans: sumO inactivation, overexpression and live-cell imaging 
Sumoylation, the reversible covalent attachment of small ubiquitin-like modifier (SUMO) peptides has emerged as an important regulator of target protein function. In Saccharomyces cerevisiae, but not in Schizosaccharyomes pombe, deletion of the gene encoding SUMO peptides is lethal. We have characterized the SUMO-encoding gene, sumO, in the filamentous fungus Aspergillus nidulans. The sumO gene was deleted in a diploid and sumO• haploids were recovered. The mutant was viable but exhibited impaired growth, reduced conidiation and self-sterility. Overexpression of epitope-tagged SumO peptides revealed multiple sumoylation targets in A. nidulans and SumO overexpression resulted in greatly increased levels of protein sumoylation without obvious phenotypic consequences. Using five-piece fusion PCR, we generated a gfp-sumO fusion gene expressed from the sumO promoter for live cell imaging of GFP-SumO and GFP-SumO-conjugated proteins. Localisation of GFP-SumO is dynamic, accumulating in punctate spots within the nucleus during interphase, lost at the onset of mitosis and re-accumulating during telophase.
doi:10.1016/j.fgb.2007.12.009
PMCID: PMC4220683  PMID: 18262811
SUMO; conidiation; sexual development; fusion PCR; cell cycle
2.  An Efficient System for Heterologous Expression of Secondary Metabolite Genes in Aspergillus nidulans 
Fungal secondary metabolites (SMs) are an important source of medically valuable compounds. Genome projects have revealed that fungi have many SM biosynthetic gene clusters that are not normally expressed. To access these potentially valuable, cryptic clusters, we have developed a heterologous expression system in Aspergillus nidulans. We have developed an efficient system for amplifying genes from a target fungus, placing them under control of a regulatable promoter, transferring them into A. nidulans and expressing them. We have validated this system by expressing non-reducing polyketide synthases of Aspergillus terreus and additional genes required for compound production and release. We have obtained compound production and release from six of these NR-PKSs and have identified the products. To demonstrate that the procedure allows transfer and expression of entire secondary metabolite biosynthetic pathways, we have expressed all the genes of a silent A. terreus cluster and demonstrate that it produces asperfuranone. Further, by expressing the genes of this pathway in various combinations, we have clarified the asperfuranone biosynthetic pathway. We have also developed procedures for deleting entire A. nidulans SM clusters. This allows us to remove clusters that might interfere with analyses of heterologously expressed genes and to eliminate unwanted toxins.
doi:10.1021/ja401945a
PMCID: PMC3697937  PMID: 23621425
3.  Molecular genetic analysis of the orsellinic acid/F9775 gene cluster of Aspergillus nidulans†‡ 
Molecular bioSystems  2009;6(3):587-593.
F-9775A and F-9775B are cathepsin K inhibitors that arise from a chromatin remodelling deletant strain of Aspergillus nidulans. A polyketide synthase gene has been determined to be responsible for their formation and for the simpler, archetypical polyketide orsellinic acid. We have discovered simple culture conditions that result in the production of the three compounds, and this facilitates analysis of the genes responsible for their synthesis. We have now analysed the F9775/orsellinic acid gene cluster using a set of targeted deletions. We find that the polyketide synthase alone is required for orsellinic acid biosynthesis and only two additional genes in the cluster are required for F9775 A and B synthesis. Our deletions also yielded the bioactive metabolites gerfelin and diorcinol.
doi:10.1039/b904541d
PMCID: PMC2903553  PMID: 20174687
4.  Identification and Characterization of the Asperthecin Gene Cluster of Aspergillus nidulans▿ † 
Applied and Environmental Microbiology  2008;74(24):7607-7612.
The sequencing of Aspergillus genomes has revealed that the products of a large number of secondary metabolism pathways have not yet been identified. This is probably because many secondary metabolite gene clusters are not expressed under normal laboratory culture conditions. It is, therefore, important to discover conditions or regulatory factors that can induce the expression of these genes. We report that the deletion of sumO, the gene that encodes the small ubiquitin-like protein SUMO in A. nidulans, caused a dramatic increase in the production of the secondary metabolite asperthecin and a decrease in the synthesis of austinol/dehydroaustinol and sterigmatocystin. The overproduction of asperthecin in the sumO deletion mutant has allowed us, through a series of targeted deletions, to identify the genes required for asperthecin synthesis. The asperthecin biosynthesis genes are clustered and include genes encoding an iterative type I polyketide synthase, a hydrolase, and a monooxygenase. The identification of these genes allows us to propose a biosynthetic pathway for asperthecin.
doi:10.1128/AEM.01743-08
PMCID: PMC2607171  PMID: 18978088
5.  Cytoplasmic Dynein's Mitotic Spindle Pole Localization Requires a Functional Anaphase-promoting Complex, γ-Tubulin, and NUDF/LIS1 in Aspergillus nidulans 
Molecular Biology of the Cell  2005;16(8):3591-3605.
In Aspergillus nidulans, cytoplasmic dynein and NUDF/LIS1 are found at the spindle poles during mitosis, but they seem to be targeted to this location via different mechanisms. The spindle pole localization of cytoplasmic dynein requires the function of the anaphase-promoting complex (APC), whereas that of NUDF does not. Moreover, although NUDF's localization to the spindle poles does not require a fully functional dynein motor, the function of NUDF is important for cytoplasmic dynein's targeting to the spindle poles. Interestingly, a γ-tubulin mutation, mipAR63, nearly eliminates the localization of cytoplasmic dynein to the spindle poles, but it has no apparent effect on NUDF's spindle pole localization. Live cell analysis of the mipAR63 mutant revealed a defect in chromosome separation accompanied by unscheduled spindle elongation before the completion of anaphase A, suggesting that γ-tubulin may recruit regulatory proteins to the spindle poles for mitotic progression. In A. nidulans, dynein is not apparently required for mitotic progression. In the presence of a low amount of benomyl, a microtubule-depolymerizing agent, however, a dynein mutant diploid strain exhibits a more pronounced chromosome loss phenotype than the control, indicating that cytoplasmic dynein plays a role in chromosome segregation.
doi:10.1091/mbc.E04-12-1071
PMCID: PMC1182300  PMID: 15930134
6.  γ-Tubulin Plays an Essential Role in the Coordination of Mitotic EventsV⃞ 
Molecular Biology of the Cell  2004;15(3):1374-1386.
Recent data from multiple organisms indicate that γ-tubulin has essential, but incompletely defined, functions in addition to nucleating microtubule assembly. To investigate these functions, we examined the phenotype of mipAD159, a cold-sensitive allele of the γ-tubulin gene of Aspergillus nidulans. Immunofluorescence microscopy of synchronized material revealed that at a restrictive temperature mipAD159 does not inhibit mitotic spindle formation. Anaphase A was inhibited in many nuclei, however, and after a slight delay in mitosis (∼6% of the cell cycle period), most nuclei reentered interphase without dividing. In vivo observations of chromosomes at a restrictive temperature revealed that mipAD159 caused a failure of the coordination of late mitotic events (anaphase A, anaphase B, and chromosomal disjunction) and nuclei reentered interphase quickly even though mitosis was not completed successfully. Time-lapse microscopy also revealed that transient mitotic spindle abnormalities, in particular bent spindles, were more prevalent in mipAD159 strains than in controls. In experiments in which microtubules were depolymerized with benomyl, mipAD159 nuclei exited mitosis significantly more quickly (as judged by chromosomal condensation) than nuclei in a control strain. These data reveal that γ-tubulin has an essential role in the coordination of late mitotic events, and a microtubule-independent function in mitotic checkpoint control.
doi:10.1091/mbc.E03-06-0405
PMCID: PMC363147  PMID: 14668489
7.  TINA Interacts with the NIMA Kinase in Aspergillus nidulans and Negatively Regulates Astral Microtubules during Metaphase ArrestV⃞ 
Molecular Biology of the Cell  2003;14(8):3169-3179.
The tinA gene of Aspergillus nidulans encodes a protein that interacts with the NIMA mitotic protein kinase in a cell cycle-specific manner. Highly similar proteins are encoded in Neurospora crassa and Aspergillus fumigatus. TINA and NIMA preferentially interact in interphase and larger forms of TINA are generated during mitosis. Localization studies indicate that TINA is specifically localized to the spindle pole bodies only during mitosis in a microtubule-dependent manner. Deletion of tinA alone is not lethal but displays synthetic lethality in combination with the anaphase-promoting complex/cyclosome mutation bimE7. At the bimE7 metaphase arrest point, lack of TINA enhanced the nucleation of bundles of cytoplasmic microtubules from the spindle pole bodies. These microtubules interacted to form spindles joined in series via astral microtubules as revealed by live cell imaging. Because TINA is modified and localizes to the spindle pole bodies at mitosis, and lack of TINA causes enhanced production of cytoplasmic microtubules at metaphase arrest, we suggest TINA is involved in negative regulation of the astral microtubule organizing capacity of the spindle pole bodies during metaphase.
doi:10.1091/mbc.E02-11-0715
PMCID: PMC181558  PMID: 12925754
8.  Spindle Formation in Aspergillus Is Coupled to Tubulin Movement into the NucleusV⃞ 
Molecular Biology of the Cell  2003;14(5):2192-2200.
In many important organisms, including many algae and most fungi, the nuclear envelope does not disassemble during mitosis. This fact raises the possibility that mitotic onset and/or exit might be regulated, in part, by movement of important mitotic proteins into and out of the nucleoplasm. We have used two methods to determine whether tubulin levels in the nucleoplasm are regulated in the fungus Aspergillus nidulans. First, we have used benomyl to disassemble microtubules and create a pool of free tubulin that can be readily observed by immunofluorescence. We find that tubulin is substantially excluded from interphase nuclei, but is present in mitotic nuclei. Second, we have observed a green fluorescent protein/α-tubulin fusion in living cells by time-lapse spinning-disk confocal microscopy. We find that tubulin is excluded from interphase nuclei, enters the nucleus seconds before the mitotic spindle begins to form, and is removed from the nucleoplasm during the M-to-G1 transition. Our data indicate that regulation of intranuclear tubulin levels plays an important, perhaps essential, role in the control of mitotic spindle formation in A. nidulans. They suggest that regulation of protein movement into the nucleoplasm may be important for regulating mitotic onset in organisms with intranuclear mitosis.
doi:10.1091/mbc.E02-10-0641
PMCID: PMC165107  PMID: 12802085
9.  Isolation of mip (microtubule-interacting protein) mutations of Aspergillus nidulans. 
Molecular and Cellular Biology  1986;6(8):2963-2968.
We identified four mutations in two previously undescribed loci involved in microtubule function in Aspergillus nidulans as extragenic suppressors of benA33, a heat-sensitive beta-tubulin mutation. Three of the four mutations map to a locus closely linked to riboB on linkage group VIII; we designated this locus mipA (for microtubule-interacting protein). We were not able to map the remaining suppressor because of chromosomal rearrangements. However, since it recombines with riboB at a significantly higher frequency than the mipA alleles, it is unlikely to be in mipA; thus, we designated it mipB1. The mip mutations are not allelic to the previously identified loci that encode alpha- and beta-tubulin, and it is likely that mipA and mipB encode previously unidentified nontubulin proteins involved in microtubule function. Each of the mip mutations suppresses the heat sensitivity conferred by benA33 and suppresses the blockage of nuclear division and movement conferred by this mutation at high temperatures. Interactions between mipA and benA are allele specific. All of the mipA mutations are cryptic in a wild-type benA background but cause cold sensitivity in combination with benA33. These mutations also confer cold sensitivity in combination with benA31 and benA32 and reduce the resistance conferred by these mutations to the antimicrotubule agent benomyl but do not suppress the heat sensitivity conferred by these alleles. Finally, the mipA alleles suppress the heat sensitivity conferred by benA11, benA17, and benA21 but do not confer cold sensitivity in combination with these alleles.
Images
PMCID: PMC367866  PMID: 3537728
10.  Management of pregnancy in patients with hypertrophic cardiomyopathy. 
British Medical Journal  1979;1(6180):1749-1750.
The outcome of 54 pregnancies in 23 patients with hypertrophic cardiomyopathy was analysed. No mother or infant died in the perinatal period. Six patients developed dyspnoea requiring treatment with diuretics. Beta-adrenergic blocking drugs were given in 18 pregnancies and three of the infants in this were small for dates and in two fetal bradycardia occurred. The results comfirmed that pregnancy is safe in patients with hypertrophic cardiomyopathy. A flexible approach should be adopted towards administering beta-adrenergic blocking drugs to pregnant women with hypertrophic cardiomyopathy. Many such patients do well without these drugs and can thus avoid the potential hazards--namely, small-for-dates babies and fetal bradycardia--that are associated with them.
PMCID: PMC1599373  PMID: 572730
11.  γ-Tubulin and the C-Terminal Motor Domain Kinesin-like Protein, KLPA, Function in the Establishment of Spindle Bipolarity in Aspergillus nidulans 
Molecular Biology of the Cell  2001;12(10):3161-3174.
Previous research has found that a γ-tubulin mutation in Schizosaccharomyces pombe is synthetically lethal with a deletion of the C-terminal motor domain kinesin-like protein gene pkl1, but the lethality of the double mutant prevents a phenotypic analysis of the synthetic interaction. We have investigated interactions between klpA1, a deletion of an Aspergillus nidulans homolog of pkl1, and mutations in the mipA, γ-tubulin gene. We find that klpA1 dramatically increases the cold sensitivity and slightly reduces the growth rate at all temperatures, of three mipA alleles. In synchronized cells we find that klpA1 causes a substantial but transient inhibition of the establishment of spindle bipolarity. At a restrictive temperature, mipAD123 causes a slight, transient inhibition of spindle bipolarity and a more significant inhibition of anaphase A. In the mipAD123/klpA1 strain, formation of bipolar spindles is more strongly inhibited than in the klpA1 single mutant and many spindles apparently never become bipolar. These results indicate, surprisingly, that γ-tubulin and the klpA kinesin have overlapping roles in the establishment of spindle bipolarity. We propose a model to account for these data.
PMCID: PMC60164  PMID: 11598200
12.  Alanine-scanning Mutagenesis of Aspergillus γ-Tubulin Yields Diverse and Novel PhenotypesV⃞ 
Molecular Biology of the Cell  2001;12(7):2119-2136.
We have created 41 clustered charged-to-alanine scanning mutations of the mipA, γ-tubulin, gene of Aspergillus nidulans and have created strains carrying these mutations by two-step gene replacement and by a new procedure, heterokaryon gene replacement. Most mutant alleles confer a wild-type phenotype, but others are lethal or conditionally lethal. The conditionally lethal alleles exhibit a variety of phenotypes under restrictive conditions. Most have robust but highly abnormal mitotic spindles and some have abnormal cytoplasmic microtubule arrays. Two alleles appear to have reduced amounts of γ-tubulin at the spindle pole bodies and nucleation of spindle microtubule assembly may be partially inhibited. One allele inhibits germ tube formation. The cold sensitivity of two alleles is strongly suppressed by the antimicrotubule agents benomyl and nocodazole and a third allele is essentially dependent on these compounds for growth. Together our data indicate that γ-tubulin probably carries out functions essential to mitosis and organization of cytoplasmic microtubules in addition to its well-documented role in microtubule nucleation. We have also placed our mutations on a model of the structure of γ-tubulin and these data give a good initial indication of the functionally important regions of the molecule.
PMCID: PMC55667  PMID: 11452008
13.  ABHD6 blockade exerts antiepileptic activity in PTZ-induced seizures and in spontaneous seizures in R6/2 mice 
Neuron  2014;83(2):361-371.
The serine hydrolase α/β-hydrolase domain 6 (ABHD6) hydrolyzes the most abundant endocannabinoid (eCB) in the brain, 2-arachidonoylglycerol (2-AG), and controls its availability at cannabinoid receptors. We show that ABHD6 inhibition decreases pentylenetetrazole (PTZ)-induced generalized tonic-clonic and myoclonic seizure incidence, and severity. This effect is retained in cnr1−/− or cnr2−/− mice, but blocked by addition of a subconvulsive dose of picrotoxin, suggesting the involvement of GABAA receptors. ABHD6 inhibition also blocked spontaneous seizures in R6/2 mice, a genetic model of Juvenile Huntington’s disease known to exhibit dysregulated eCB signaling. ABHD6 blockade retained its antiepileptic activity over chronic dosing and was not associated with psychomotor or cognitive effects. While the etiology of seizures in R6/2 mice remains unsolved, involvement of the hippocampus is suggested by interictal epileptic discharges, increased expression of vGLUT1 but not vGAT, and reduced Neuropeptide Y (NPY) expression. We conclude that ABHD6 inhibition may represent a novel antiepileptic strategy.
doi:10.1016/j.neuron.2014.06.030
PMCID: PMC4136499  PMID: 25033180
14.  Follow-Up Care Experiences and Perceived Quality of Care Among Long-Term Survivors of Breast, Prostate, Colorectal, and Gynecologic Cancers 
Journal of Oncology Practice  2014;10(4):e231-e239.
Long-term survivors commonly report follow-up care years after their diagnosis; however, many patients' follow-up lacks important components. Care is more likely to be rated as high quality when one main provider is identified and an oncology specialist is involved.
Introduction:
Post-treatment follow-up represents a crucial aspect of quality cancer care; however, data are lacking regarding follow-up care experiences, perception of provider involvement in care, and perceived quality of care from diverse samples of long-term survivors diagnosed as adults.
Methods:
Questionnaires were mailed in 2005 to 2006 to breast, prostate, colorectal, endometrial, and ovarian cancer survivors (4 to 14 years after diagnosis), sampled from California SEER cancer registries.
Results:
Most survivors (n = 1,490) reported recent follow-up care (68.7%), generally from oncology specialists only (47.4%) or shared between oncology and primary care providers (PCPs; 27.6%). Most survivors reported follow-up care advice (79.9%); fewer reported late-effects advice or receipt of a treatment summary (41.7% and 19.9%, respectively). Survivors who identified a PCP as their main follow-up care physician were as likely as those identifying an oncology specialist to rate their care as high quality (odds ratio [OR], 2.56; 95% CI, 0.98 to 6.74); however, survivors who could not identify a main follow-up care provider were less likely to report high-quality care (OR, 0.20; 95% CI, 0.08 to 0.50). Compared with follow-up care by an oncology specialist only, care by a PCP only was associated with a lower quality-of-care rating (OR, 0.34; 95% CI, 0.13 to 0.91), but there was no significant difference in quality rating by survivors when care was shared by an oncology specialist and PCP compared with an oncology specialist only.
Conclusion:
Long-term survivors commonly report follow-up care years after their diagnosis; however, many patients' follow-up lacks important components. Care is more likely to be rated as high quality when one main provider is identified and an oncology specialist is involved.
doi:10.1200/JOP.2013.001175
PMCID: PMC4094647  PMID: 24695901
15.  Estimating the Expected Value of Sample Information Using the Probabilistic Sensitivity Analysis Sample 
Medical Decision Making  2015;35(5):570-583.
Health economic decision-analytic models are used to estimate the expected net benefits of competing decision options. The true values of the input parameters of such models are rarely known with certainty, and it is often useful to quantify the value to the decision maker of reducing uncertainty through collecting new data. In the context of a particular decision problem, the value of a proposed research design can be quantified by its expected value of sample information (EVSI). EVSI is commonly estimated via a 2-level Monte Carlo procedure in which plausible data sets are generated in an outer loop, and then, conditional on these, the parameters of the decision model are updated via Bayes rule and sampled in an inner loop. At each iteration of the inner loop, the decision model is evaluated. This is computationally demanding and may be difficult if the posterior distribution of the model parameters conditional on sampled data is hard to sample from. We describe a fast nonparametric regression-based method for estimating per-patient EVSI that requires only the probabilistic sensitivity analysis sample (i.e., the set of samples drawn from the joint distribution of the parameters and the corresponding net benefits). The method avoids the need to sample from the posterior distributions of the parameters and avoids the need to rerun the model. The only requirement is that sample data sets can be generated. The method is applicable with a model of any complexity and with any specification of model parameter distribution. We demonstrate in a case study the superior efficiency of the regression method over the 2-level Monte Carlo method.
doi:10.1177/0272989X15575286
PMCID: PMC4471064  PMID: 25810269
expected value of sample information; economic evaluation model; Monte Carlo methods; Bayesian decision theory; computational methods; nonparametric regression; generalized additive model.
16.  Continued rapid increase in thyroid cancer incidence in California: trends by patient, tumor, and neighborhood characteristics 
Background
Thyroid cancer incidence is increasing worldwide. Incorporating 22 years of incidence data through 2009, we extend examination of these trends among a wide array of subgroups defined by patient (age, sex, race/ethnicity, and nativity), tumor (tumor size and stage), and neighborhood (socioeconomic status and residence in ethnic enclaves) characteristics, to identify possible reasons for this increase.
Methods
Thyroid cancer incidence data on 10,940 men and 35,147 women were obtained from the California Cancer Registry for 1988–2009. Population data were obtained from the 1990 and 2000 US Census. Incidence rates and 95% confidence intervals (CI) were calculated and incidence trends evaluated using Joinpoint regression to evaluate the timing and magnitude of change (annual percent change (APC) and rate ratios).
Results
The incidence of papillary thyroid cancer continues to increase in both men (APC=5.4, 95% CI: 4.5–6.3 for 1998–2009) and women (APC=3.8, 95% CI: 3.4–4.2 for 1998–2001 and APC=6.3, 95% CI: 5.7–6.9 for 2001–2009). Increasing incidence was observed in all subgroups examined.
Conclusions
While some variation in the magnitude or temporality of the increase in thyroid cancer incidence exists across subgroups, the patterns (1) suggest that changes in diagnostic technology alone do not account for the observed trends and (2) point to the importance of modifiable behavioral, lifestyle, or environmental factors in understanding this epidemic.
Impact
Given the dramatic and continued increase in thyroid cancer incidence rates, studies addressing the causes of these trends are critical.
doi:10.1158/1055-9965.EPI-13-1089
PMCID: PMC4071298  PMID: 24842625
thyroid cancer; incidence rates; temporal trends; surveillance; California
17.  Non-invasive in vivo magnetic resonance measures of glutathione synthesis in human and rat liver as an oxidative stress biomarker 
Hepatology (Baltimore, Md.)  2014;59(6):2321-2330.
Oxidative stress plays a central role in the progression of liver disease and in damage to liver via toxic xenobiotics. We have developed methods for non-invasive assessment of hepatic oxidative stress defences by measuring flux through the glutathione synthesis pathway. 13C-labelled glutathione is endogenously produced and detected by in vivo magnetic resonance following administration of [2-13C]-glycine. We report successful first-in-man demonstration of this approach, and preclinical studies demonstrating perturbed glutathione metabolism in models of acute and chronic oxidative stress. Human studies employed oral administration of [2-13C]-glycine and 13C spectroscopy on a 3T clinical MRI scanner, and demonstrated detection and quantification of endogenously produced 13C-glutathione following labelled glycine ingestion. Plasma analysis demonstrated that glycine 13C fractional enrichment achieved steady state during the 6h ingestion period. Mean rate of synthesis of hepatic 13C-labelled glutathione was 0.32 ± 0.18 mmole/kg/h. Preclinical models of acute oxidative stress and non-alcoholic steatohepatitis (NASH) comprised CCl4-treated and high fat, high carbohydrate diet-fed Sprague Dawley rats respectively, using intravenous administration of [2-13C]-glycine and observation of 13C-label metabolism on a 7T preclinical MR system. Preclinical studies demonstrated a 54% elevation of glutathione content and a 31% increase in flux through the glutathione synthesis pathway at 12h after acute insult caused by CCl4 administration, and 23% decrease in glutathione content and evidence of early steatohepatitis in the model of NASH.
Conclusion
Our data demonstrate in vivo 13C-labelling and detection of glutathione as a biomarker of tissue oxidative stress defences, detecting chronic and acute oxidative stress insults. The methods are applicable to clinical research studies of hepatic oxidative stress in disease states over time as well as to monitoring the effects of therapeutic interventions.
doi:10.1002/hep.26925
PMCID: PMC4160151  PMID: 24242936
13C spectroscopy; dynamic magnetic resonance; metabolism; glutathione synthetase; serine hydroxymethyltransferase
18.  A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens-Specific Cell Wall Binding Domain Creates an Anti-Clostridium Antimicrobial with Improved Thermostability 
Viruses  2015;7(6):3019-3034.
Clostridium perfringens is the third leading cause of human foodborne bacterial disease and is the presumptive etiologic agent of necrotic enteritis among chickens. Treatment of poultry with antibiotics is becoming less acceptable. Endolysin enzymes are potential replacements for antibiotics. Many enzymes are added to animal feed during production and are subjected to high-heat stress during feed processing. To produce a thermostabile endolysin for treating poultry, an E. coli codon-optimized gene was synthesized that fused the N-acetylmuramoyl-l-alanine amidase domain from the endolysin of the thermophilic bacteriophage ΦGVE2 to the cell-wall binding domain (CWB) from the endolysin of the C. perfringens-specific bacteriophage ΦCP26F. The resulting protein, PlyGVE2CpCWB, lysed C. perfringens in liquid and solid cultures. PlyGVE2CpCWB was most active at pH 8, had peak activity at 10 mM NaCl, 40% activity at 150 mM NaCl and was still 16% active at 600 mM NaCl. The protein was able to withstand temperatures up to 50 °C and still lyse C. perfringens. Herein, we report the construction and characterization of a thermostable chimeric endolysin that could potentially be utilized as a feed additive to control the bacterium during poultry production.
doi:10.3390/v7062758
PMCID: PMC4488725  PMID: 26075507
alternative antimicrobial; bacteriophage; endolysin; food safety; feed additive; peptidoglycan hydrolase; thermostabile; thermostable
19.  Vascular endothelial growth factor and tryptase changes after chemoembolization in hepatocarcinoma patients 
AIM: To evaluate vascular endothelial growth factor (VEGF) and tryptase in hepatocellular cancer (HCC) before and after trans-arterial chemoembolization (TACE).
METHODS: VEGF and tryptase serum concentrations were assessed from 71 unresectable HCC patients before and after hepatic TACE performed by binding DC-Beads® to doxorubicin. VEGF levels were examined for each serum sample using the Quantikine Human VEGF-enzyme-linked immuno-absorbent assay (ELISA), whereas tryptase serum concentrations were assessed for each serum sample by means of fluoro-enzyme immunoassay (FEIA) using the Uni-CAP100 tool. Differences between serum VEGF and tryptase values before and after TACE were evaluated using Student t test. Person's correlation was used to assess the degree of association between the two variables.
RESULTS: VEGF levels and serum tryptase in HCC patients before TACE had a mean value and standard deviation (SD) of 114.31 ± 79.58 pg/mL and 8.13 ± 3.61 μg/L, respectively. The mean levels and SD of VEGF levels and serum tryptase in HCC patients after TACE were 238.14 ± 109.41 pg/mL and 4.02 ± 3.03 μg/L. The changes between the mean values of concentration of VEGF and tryptase before treatment and after treatment was statistically significant (P < 0.000231 and P < 0.00124, by Wilcoxon-Mann-Whitney respectively). A significant correlation between VEGF levels before and after TACE and between tryptase levels before and after TACE was demonstrated (r = 0.68, P = 0.003; r = 0.84, P = 0.000 respectively).
CONCLUSION: Our pilot results suggest that the higher serum VEGF levels and the lower tryptase levels following TACE may be potential biomarkers changing in response to therapy.
doi:10.3748/wjg.v21.i19.6018
PMCID: PMC4438038  PMID: 26019468
Serum levels; Tryptase; Vascular endothelial growth factor; Hepatocellular cancer; Chemoembolization
20.  Structure and function of a spectrin-like regulator of bacterial cytokinesis 
Nature communications  2014;5:5421.
Bacterial cell division is facilitated by a molecular machine — the divisome — that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by the tubulin homologue FtsZ is regulated by several factors, including the divisome component EzrA. Here we describe the structure of the 60 kDa cytoplasmic domain of EzrA, which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. We also identify at least two binding sites for FtsZ on EzrA and map regions of EzrA that are responsible for regulating FtsZ assembly. The individual repeats, and their linear organisation, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and we thus propose that EzrA is the founding member of the bacterial spectrin family.
doi:10.1038/ncomms6421
PMCID: PMC4243239  PMID: 25403286
21.  Lysosomal Signaling Molecules Regulate Longevity in Caenorhabditis elegans 
Science (New York, N.Y.)  2015;347(6217):83-86.
Lysosomes are crucial cellular organelles for human health that function in digestion and recycling of extracellular and intracellular macromolecules. We describe a signaling role for lysosomes that affects aging. In the worm, Caenorhabditis elegans, the lysosomal acid lipase LIPL-4 triggered nuclear translocalization of a lysosomal lipid chaperone LBP-8, consequently promoting longevity by activating the nuclear hormone receptors NHR-49 and NHR-80. We used high-throughput metabolomic analysis to identify several lipids whose abundance was increased in worms constitutively over-expressing LIPL-4. Among them, oleoylethanolamide directly bound to LBP-8 and NHR-80 proteins, activated transcription of target genes of NHR-49 and NHR-80, and promoted longevity in C. elegans. These findings reveal a lysosome-to-nucleus signaling pathway that promotes longevity and suggest a function of lysosomes as signaling organelles in metazoans.
doi:10.1126/science.1258857
PMCID: PMC4425353  PMID: 25554789
22.  NFκB1 is a suppressor of neutrophil-driven hepatocellular carcinoma 
Nature Communications  2015;6:6818.
Hepatocellular carcinoma (HCC) develops on the background of chronic hepatitis. Leukocytes found within the HCC microenvironment are implicated as regulators of tumour growth. We show that diethylnitrosamine (DEN)-induced murine HCC is attenuated by antibody-mediated depletion of hepatic neutrophils, the latter stimulating hepatocellular ROS and telomere DNA damage. We additionally report a previously unappreciated tumour suppressor function for hepatocellular nfkb1 operating via p50:p50 dimers and the co-repressor HDAC1. These anti-inflammatory proteins combine to transcriptionally repress hepatic expression of a S100A8/9, CXCL1 and CXCL2 neutrophil chemokine network. Loss of nfkb1 promotes ageing-associated chronic liver disease (CLD), characterized by steatosis, neutrophillia, fibrosis, hepatocyte telomere damage and HCC. Nfkb1S340A/S340Amice carrying a mutation designed to selectively disrupt p50:p50:HDAC1 complexes are more susceptible to HCC; by contrast, mice lacking S100A9 express reduced neutrophil chemokines and are protected from HCC. Inhibiting neutrophil accumulation in CLD or targeting their tumour-promoting activities may offer therapeutic opportunities in HCC.
The role of neutrophils in cancer development is not widely appreciated. Here, the authors show that NF-κB-deficient hepatocytes overproduce chemokines, leading to hepatocellular carcinoma due to excessive neutrophil recruitment, and that neutrophil depletion prevents liver cancer in these mice.
doi:10.1038/ncomms7818
PMCID: PMC4410629  PMID: 25879839
23.  Glycogen synthase kinase-3 controls IL-10 expression in CD4+ effector T-cell subsets through epigenetic modification of the IL-10 promoter 
European Journal of Immunology  2015;45(4):1103-1115.
The serine/threonine kinase glycogen synthase kinase-3 (GSK3) plays an important role in balancing pro- and anti-inflammatory cytokines. We have examined the role of GSK3 in production of IL-10 by subsets of CD4+ T helper cells. Treatment of naive murine CD4+ T cells with GSK3 inhibitors did not affect their production of IL-10. However, treatment of Th1 and Th2 cells with GSK3 inhibitors dramatically increased production of IL-10. GSK3 inhibition also led to upregulation of IL-10 among Th1, Th2, and Th17 subsets isolated from human blood. The encephalitogenic potential of GSK3 inhibitor treated murine Th1 cells was significantly reduced in adoptive transfer experiments by an IL-10-dependent mechanism. Analysis of the murine IL-10 promoter in response to inhibition of GSK3 in Th1 cells showed modification to a transcriptionally active state indicated by changes in histone H3 acetylation and methylation. Additionally, GSK3 inhibition increased expression of the transcription factors c-Maf, Nfil3, and GATA3, correlating with the increase in IL-10. These findings are important in the context of autoimmune disease since they show that it is possible to reprogram disease-causing cells through GSK3 inhibition.
doi:10.1002/eji.201444661
PMCID: PMC4405077  PMID: 25627813
CD4+ T cells; Epigenetic; Glycogen synthase kinase-3; IL-10
24.  Functional microRNAs and target sites are created by lineage-specific transposition 
Human Molecular Genetics  2013;23(7):1783-1793.
Transposable elements (TEs) account for nearly one-half of the sequence content in the human genome, and de novo germline transposition into regulatory or coding sequences of protein-coding genes can cause heritable disorders. TEs are prevalent in and around protein-coding genes, providing an opportunity to impart regulation. Computational studies reveal that microRNA (miRNA) genes and miRNA target sites reside within TE sequences, but there is little experimental evidence supporting a role for TEs in the birth of miRNAs, or as platform for gene regulation by miRNAs. In this work, we validate miRNAs and target sites derived from TE families prevalent in the human genome, including the ancient long interspersed nuclear element 2 (LINE2/L2), mammalian-wide interspersed repeat (MIR) retrotransposons and the primate-specific Alu family. We show that genes with 3′ untranslated region (3′ UTR) MIR elements are enriched for let-7 targets and that these sites are conserved and responsive to let-7 expression. We also demonstrate that 3′ UTR-embedded Alus are a source of miR-24 and miR-122 target sites and that a subset of active genomic Alus provide for de novo target site creation. Finally, we report that although the creation of miRNA genes by Alu elements is relatively uncommon relative to their overall genomic abundance, Alu-derived miR-1285-1 is efficiently processed from its genomic locus and regulates genes with target sites contained within homologous elements. Taken together, our data provide additional evidence for TEs as a source for miRNAs and miRNA target sites, with instances of conservation through the course of mammalian evolution.
doi:10.1093/hmg/ddt569
PMCID: PMC3943519  PMID: 24234653
25.  A TLR2/S100A9/CXCL-2 Signaling Network is Necessary for Neutrophil Recruitment in Acute and Chronic Liver Injury in the Mouse 
Journal of hepatology  2013;60(4):782-791.
Background and aims
Neutrophils are important immune effectors required for sterile and non-sterile inflammatory responses. However, neutrophils are associated with pathology in drug-induced liver injury, acute alcoholic liver disease and ischemia-reperfusion injury. An understanding of the complex mechanisms that control neutrophil recruitment to the injured liver is desirable for developing strategies aimed at limiting neutrophil-mediated cellular damage.
Methods
Wt, tlr2−/−, tlr4−/− and s100a9−/− mice were administered CCl4 either acutely (8, 24, 48 or 72 hrs) or chronically (8 weeks) and livers investigated by histological (IHC for neutrophils, fibrogenesis, proliferation and chemotactic proteins) or molecular approaches (qRT-PCR for neutrophil chemoattractant chemokines and cytokines as well as pro-fibrogenic genes).
Results
Mice lacking TLR2 or S100A9 failed to recruit neutrophils to the injured liver and had a defective hepatic induction of the neutrophil chemokine CXCL-2. Hierarchy between TLR2 and S100A9 proved to be complex. While induction of S100A9 was dependent on TLR2 in isolated neutrophils, there was a more complicated two-way signalling cross-talk between TLR2 and S100A9 in whole liver. However, wound-healing and regenerative responses of the liver were unaffected in these genetic backgrounds as well as in wild type mice in which neutrophils were depleted by infusion of Ly-6G antibody.
Conclusion
We have identified TLR2 and S100A8/S100A9 as key regulators of hepatic CXCL-2 expression and neutrophil recruitment. This novel TLR2-S100A9-CXCL-2 pathway may be of use in development of new strategies for selectively manipulating neutrophils in liver disease without impairing normal wound healing and regenerative responses.
doi:10.1016/j.jhep.2013.12.005
PMCID: PMC3960359  PMID: 24333183
Liver fibrosis; Neutrophil; Toll like receptor; Inflammation; S100A9

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