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1.  Gene structure and expression of the MboI restriction--modification system. 
Nucleic Acids Research  1993;21(10):2309-2313.
The genes from Moraxella bovis encoding the MboI restriction--modification system were cloned and expressed in Escherichia coli. Three open reading frames were found in the sequence containing the genes. These genes, which we named mboA, mboB, and mboC, had the same orientation in the genome. Genes mboA and mboC encoded MboI methyltransferases (named M.MboA and M.MboC) with 294 and 273 amino acid residues, respectively. The mboB gene coded for MboI restriction endonuclease (R.MboI) with 280 amino acid residues. Recombinant E.coli-MBOI, which contained the whole MboI system, overproduced R.MboI. R.MboI activity from E.coli-MBOI was 480-fold that of M.bovis. The amino acid sequences deduced from these genes were compared with those of other restriction--modification systems. The protein sequences of the MboI system had 38-49% homology with those of the DpnII system.
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PMCID: PMC309525  PMID: 8506128
2.  Glucosylceramide synthase upregulates MDR1 expression in the regulation of cancer drug resistance through cSrc and β-catenin signaling 
Molecular Cancer  2010;9:145.
Background
Drug resistance is the outcome of multiple-gene interactions in cancer cells under stress of anticancer agents. MDR1 overexpression is most commonly detected in drug-resistant cancers and accompanied with other gene alterations including enhanced glucosylceramide synthase (GCS). MDR1 encodes for P-glycoprotein that extrudes anticancer drugs. Polymorphisms of MDR1 disrupt the effects of P-glycoprotein antagonists and limit the success of drug resistance reversal in clinical trials. GCS converts ceramide to glucosylceramide, reducing the impact of ceramide-induced apoptosis and increasing glycosphingolipid (GSL) synthesis. Understanding the molecular mechanisms underlying MDR1 overexpression and how it interacts with GCS may find effective approaches to reverse drug resistance.
Results
MDR1 and GCS were coincidently overexpressed in drug-resistant breast, ovary, cervical and colon cancer cells; silencing GCS using a novel mixed-backbone oligonucleotide (MBO-asGCS) sensitized these four drug-resistant cell lines to doxorubicin. This sensitization was correlated with the decreased MDR1 expression and the increased doxorubicin accumulation. Doxorubicin treatment induced GCS and MDR1 expression in tumors, but MBO-asGCS treatment eliminated "in-vivo" growth of drug-resistant tumor (NCI/ADR-RES). MBO-asGCS suppressed the expression of MDR1 with GCS and sensitized NCI/ADR-RES tumor to doxorubicin. The expression of P-glycoprotein and the function of its drug efflux of tumors were decreased by 4 and 8 times after MBO-asGCS treatment, even though this treatment did not have a significant effect on P-glycoprotein in normal small intestine. GCS transient transfection induced MDR1 overexpression and increased P-glycoprotein efflux in dose-dependent fashion in OVCAR-8 cancer cells. GSL profiling, silencing of globotriaosylceramide synthase and assessment of signaling pathway indicated that GCS transfection significantly increased globo series GSLs (globotriaosylceramide Gb3, globotetraosylceramide Gb4) on GSL-enriched microdomain (GEM), activated cSrc kinase, decreased β-catenin phosphorylation, and increased nuclear β-catenin. These consequently increased MDR1 promoter activation and its expression. Conversely, MBO-asGCS treatments decreased globo series GSLs (Gb3, Gb4), cSrc kinase and nuclear β-catenin, and suppressed MDR-1 expression in dose-dependent pattern.
Conclusion
This study demonstrates, for the first time, that GCS upregulates MDR1 expression modulating drug resistance of cancer. GSLs, in particular globo series GSLs mediate gene expression of MDR1 through cSrc and β-catenin signaling pathway.
doi:10.1186/1476-4598-9-145
PMCID: PMC2903501  PMID: 20540746
3.  Mutant strains of Chlamydomonas reinhardtii that move backwards only 
The Journal of Cell Biology  1984;98(6):2026-2034.
Mutations at three independent loci in Chlamydomonas reinhardtii result in a striking alteration of cell motility. Mutant cells representing the three mbo loci move backwards only, propelled by a symmetrical "flagellar" type of bending pattern. The characteristic asymmetric "ciliary" type of flagellar bend pattern responsible for forward movement that predominates in wild-type cells is seldom seen in the mutants. This defect in motility was found to be a property of the mutant axonemes themselves: the isolated axonemes, reactivated by addition of ATP, showed exclusively the symmetrical wave form, and the protein composition of these axonemes differed from the wild-type composition. Axonemes obtained from mbo1 , mbo2 , and mbo3 cells were found to be deficient in six polypeptides regularly present in wild type. The mbo2 axonemes were deficient in two additional polypeptides. The polypeptides were identified in autoradiograms of two-dimensional SDS polyacrylamide gel electrophoretograms of 35S- or 32P-labeled axonemes. One of the six polypeptides has previously been identified; it is a component missing in a mutant deficient for inner dynein arms. Of the five axonemal polypeptides newly identified by the mbo mutants, four were shown to be present as phosphoproteins in wild-type axonemes. One of the additional polypeptides deficient in mbo2 axonemes was also shown to be phosphorylated in wild-type axonemes. Detailed ultrastructural analysis of the mbo1 flagella and the mbo1 , mbo2A , and mbo3 axonemes revealed that the mutants specifically lack the beak- like projections found within the B-tubules of outer doublets 5 and 6.
PMCID: PMC2113042  PMID: 6725408
4.  Organosulfates as Tracers for Secondary Organic Aerosol (SOA) Formation from 2-Methyl-3-Buten-2-ol (MBO) in the Atmosphere 
Environmental Science & Technology  2012;46(17):9437-9446.
2-Methyl-3-buten-2-ol (MBO) is an important biogenic volatile organic compound (BVOC) emitted by pine trees and a potential precursor of atmospheric secondary organic aerosol (SOA) in forested regions. In the present study, hydroxyl radical (OH)-initiated oxidation of MBO was examined in smog chambers under varied initial nitric oxide (NO) and aerosol acidity levels. Results indicate measurable SOA from MBO under low-NO conditions. Moreover, increasing aerosol acidity was found to enhance MBO SOA. Chemical characterization of laboratory-generated MBO SOA reveals that an organosulfate species (C5H12O6S, MW 200) formed and was substantially enhanced with elevated aerosol acidity. Ambient fine aerosol (PM2.5) samples collected from the BEARPEX campaign during 2007 and 2009, as well as from the BEACHON-RoMBAS campaign during 2011, were also analyzed. The MBO-derived organosulfate characterized from laboratory-generated aerosol was observed in PM2.5 collected from these campaigns, demonstrating that it is a molecular tracer for MBO-initiated SOA in the atmosphere. Furthermore, mass concentrations of the MBO-derived organosulfate are well correlated with MBO mixing ratio, temperature, and acidity in the field campaigns. Importantly, this compound accounted for an average of 0.25% and as high as 1% of the total organic aerosol mass during BEARPEX 2009. An epoxide intermediate generated under low-NO conditions is tentatively proposed to produce MBO SOA.
doi:10.1021/es301648z
PMCID: PMC3557936  PMID: 22849588
5.  Palliative Venting Gastrostomy in Patients with Malignant Bowel Obstruction and Ascites 
Annals of surgical oncology  2012;20(2):497-505.
Background
Fluoroscopic-guided placement of a percutaneous decompression gastrostomy tube (PDGT) is used to palliate patients with malignant bowel obstruction (MBO). We report our clinical experience in cases of MBO and ascites that were known to be technically difficult and at increased risk for complications after PDGT placement.
Methods
Between October 2005 and April 2010, a total of 89 consecutive oncology patients with MBO and ascites underwent at least one attempt at PDGT placement. We retrospectively reviewed the electronic medical record to collect demographic details, procedure information, and morbidity and mortality data. Kaplan–Meier curves were used to calculate median survival after PDGT.
Results
Ninety-three new gastrostomy encounters occurred in 89 patients. The primary and secondary technical success rates were 72 % (67 of 93) and 77.4 % (72 of 93), respectively. Inadequate gastric distention was the reason for failure in 84.6 % (22 of 26) of the cases in which the initial PDGT attempt was unsuccessful. For ascites management, 13 patients underwent paracentesis and 78 patients underwent placement of an intraperitoneal catheter. The overall complication rate in successful placements was 13.9 %, with a major complication rate of 9.7 %. After PDGT, the median overall survival rate was 28.5 days (95 % confidence interval 20–42).
Conclusions
PDGT is feasible in the majority of patients with MBO and ascites, although there is an inherent risk of major complications. An intraperitoneal catheter can be used to manage ascites to facilitate PDGT.
doi:10.1245/s10434-012-2643-5
PMCID: PMC4262403  PMID: 22965572
6.  Cloning and characterization of the MboII restriction-modification system. 
Nucleic Acids Research  1991;19(5):1007-1013.
The two genes encoding the class IIS restriction-modification system MboII from Moraxella bovis were cloned separately in two compatible plasmids and expressed in E. coli RR1 delta M15. The nucleotide sequences of the MboII endonuclease (R.MboII) and methylase (M.MboII) genes were determined and the putative start codon of R.MboII was confirmed by amino acid sequence analysis. The mboIIR gene specifies a protein of 416 amino acids (MW: 48,617) while the mboIIM gene codes for a putative 260-residue polypeptide (MW: 30,077). Both genes are aligned in the same orientation. The coding region of the methylase gene ends 11 bp upstream of the start codon of the restrictase gene. Comparing the amino acid sequence of M.MboII with sequences of other N6-adenine methyltransferases reveals a significant homology to M.RsrI, M.HinfI and M.DpnA. Furthermore, M.MboII shows homology to the N4-cytosine methyltransferase BamHI.
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PMCID: PMC333773  PMID: 2020540
7.  The International Conference on Malignant Bowel Obstruction: A Meeting of the Minds to Advance Palliative Care Research 
Journal of pain and symptom management  2007;34(1 Suppl):S1-S6.
There is a dearth of well-designed clinical research focusing on palliative care in cancer patients, especially those who are near the end of life. Reasons for this include ethical dilemmas in conducting such trials, communication barriers between specialties, and unclear standards for best care practices. To ensure that patients with incurable illnesses are offered the best available care, it is essential to develop and disseminate research methodologies well suited to this population. Given the multidimensional and culture-dependent nature of the end-of-life experience, it is necessary to adopt an interdisciplinary approach to developing research methods. As a means of initiating the process of palliative clinical research methodology development, malignant bowel obstruction (MBO) was used as a model to develop a research protocol. Although many treatment options for MBO have been proposed, existing literature offers little guidance with regard to algorithms for optimal management. To this end, an interdisciplinary summit of international leaders in quality-of-life research, ethno-cultural variability, palliative medicine, surgical oncology, gastroenterology, major consortium research, medical ethics, and patient advocacy/cancer survivors was convened in Pasadena, California, on November 12-13, 2004. Participants also represented the broad ethnic and racial perspectives required to develop culturally sensitive research methods. Consensus on methodological approaches was attained through vigorous debate. Using the conference-developed MBO model to implement trials will advance palliative care research.
doi:10.1016/j.jpainsymman.2007.04.005
PMCID: PMC2834265  PMID: 17544251
Palliative care research; malignant bowel obstruction; quality of life; end of life care
8.  Mixed backbone antisense oligonucleotides: design, biochemical and biological properties of oligonucleotides containing 2'-5'-ribo- and 3'-5'-deoxyribonucleotide segments. 
Nucleic Acids Research  1997;25(2):370-378.
We have designed and synthesized mixed backbone oligonucleotides (MBOs) containing 2'-5'-ribo- and 3'-5'-deoxyribonucleotide segments. Thermal melting studies of the phosphodiester MBOs (three 2'-5'linkages at each end) with the complementary 3'-5'-DNA and -RNA target strands suggest that 2'-5'-ribonucleoside incorporation into 3'-5'-oligodeoxyribonucleotides reduces binding to the target strands compared with an all 3'-5'-oligodeoxyribonucleotide of the same sequence and length. Increasing the number of 2'-5'linkages (from six to nine) further reduces binding to the DNA target strand more than the RNA target strand [Kandimalla,E.R. and Agrawal,S. (1996)Nucleic Acids Symp. Ser., 35, 125-126]. Phosphorothioate (PS) analogs of MBOs destabilize the duplex with the DNA target strand more than the duplex with the RNA target strand. Circular dichroism studies indicate that the duplexes of MBOs with the DNA and RNA target strands have spectral characteristics of both A- and B-type conformations. Compared with the control oligonucleotide, MBOs exhibit moderately higher stability against snake venom phosphodiesterase, S1 nuclease and in fetal calf serum. Although 2'-5'modification does not evoke RNase H activity, this modification does not effect the RNase H activation property of the 3'-5'-deoxyribonucleotide segment adjacent to the modification. In vitro studies with MBOs suggest that they have lesser effects on cell proliferation, clotting prolongation and hemolytic complement lysis than do control PS oligodeoxyribonucleotides. PS analogs of MBOs show HIV-1 inhibition comparable with that of a control PS oligodeoxyribonucleotide with all 3'-5'linkages. The current results suggest that a limited number of 2'-5'linkages could be used in conjunction with PS oligonucleotides to further modulate the properties of antisense oligonucleotides as therapeutic agents.
PMCID: PMC146429  PMID: 9016567
9.  Malignant bowel obstruction in advanced cancer patients: epidemiology, management, and factors influencing spontaneous resolution 
Malignant bowel obstruction (MBO) is a frequent complication in advanced cancer patients, especially in those with abdominal tumors. Clinical management of MBO requires a specific and individualized approach that is based on disease prognosis and the objectives of care. The global prevalence of MBO is estimated to be 3% to 15% of cancer patients. Surgery should always be considered for patients in the initial stages of the disease with a preserved general status and a single level of occlusion. Less invasive approaches such as duodenal or colonic stenting should be considered when surgery is contraindicated in obstructions at the single level. The priority of care for inoperable and consolidated MBO is to control symptoms and promote the maximum level of comfort possible. The spontaneous resolution of an inoperable obstructive process is observed in more than one third of patients. The mean survival is of no longer than 4–5 weeks in patients with consolidated MBO. Polymodal medical treatment based on a combination of glucocorticoids, strong opioids, antiemetics, and antisecretory drugs achieves very high symptomatic control. This review focuses on the epidemiological aspects, diagnosis, surgical criteria, medical management, and factors influencing the spontaneous resolution of MBO in advanced cancer patients.
doi:10.2147/CMAR.S29297
PMCID: PMC3421464  PMID: 22904637
malignant bowel obstruction; cancer; intestinal obstruction; bowel occlusion
10.  Malignant bowel obstruction: A retrospective clinical analysis 
Malignant bowel obstruction (MBO) is a disease with a poor prognosis, particularly in patients with advanced bowel or gynecological cancers. Multimodality teatments may be used to relieve the symptoms in patients with MBO; however, there is currently no consensus regarding the optimal treatment and no strong evidence supporting the efficacy of any treatment in improving the quality of life (QOL) and prolonging survival. We conducted a search through our medical center database of cancer registries for MBO cases between January, 1995 and December, 2008 and analyzed the clinicopathological characteristics and association between treatments and prognosis or QOL. The primary type of cancer causing MBO was found to be adenocarcinoma of colon. The overall survival time was found to be significantly higher among patients presenting with MBO as the initial symptom and improved QOL was achieved in patients who received surgical treatment. The mean survival time and the functional status of colorectal cancer patients receiving targeted therapy and chemotherapy were more satisfactory compared with those receiving surgery alone or conservative treatment. Furthermore, for end-stage cancer patients with MBO, hospice care was effective in reducing pain scores and relieving the symptoms of the disease.
doi:10.3892/mco.2013.216
PMCID: PMC3915666  PMID: 24649301
bowel obstruction; cancer
11.  Mangotoxin production of Pseudomonas syringae pv. syringae is regulated by MgoA 
BMC Microbiology  2014;14:46.
Background
The antimetabolite mangotoxin is a key factor in virulence of Pseudomonas syringae pv. syringae strains which cause apical necrosis of mango trees. Previous studies showed that mangotoxin biosynthesis is governed by the mbo operon. Random mutagenesis led to the identification of two other gene clusters that affect mangotoxin biosynthesis. These are the gacS/gacA genes and mgo operon which harbors the four genes mgoBCAD.
Results
The current study shows that disruption of the nonribosomal peptide synthetase (NRPS) gene mgoA resulted in loss of mangotoxin production and reduced virulence on tomato leaves. Transcriptional analyses by qPCR and promoter reporter fusions revealed that mbo expression is regulated by both gacS/gacA and mgo genes. Also, expression of the mgo operon was shown to be regulated by gacS/gacA. Heterologous expression under the native promoter of the mbo operon resulted in mangotoxin production in non-producing P. syringae strains, but not in other Pseudomonas species. Also introduction of the mbo and mgo operons in nonproducing P. protegens Pf-5 did not confer mangotoxin production but did enhance transcription of the mbo promoter.
Conclusions
From the data obtained in this study, we conclude that both mbo and mgo operons are under the control of the gacS/gacA two-component system and that the MgoA product acts as a positive regulator of mangotoxin biosynthesis.
doi:10.1186/1471-2180-14-46
PMCID: PMC3945005  PMID: 24555804
Antimetabolite toxin; mgo operon; GacS/GacA; Plant-microbe interaction
12.  Results-oriented management though MBO. 
Management by Objectives (MBO) as it has been implemented in the Houston Academy of Medicine--Texas Medical Center Library is described. That MBO must be a total management system and not just another library program is emphasized throughout the discussion and definitions of the MBO system parts: (1) mission statement; (2) role functions; (3) role relationships; (4) effectiveness areas; (5) objective; (6) action plans; and (7) performance review and evaluation. Examples from the library's implementation are given within the discussion of each part to give the reader a clearer picture of the library's actual experiences with the MBO process. Tables are included for further clarification. In conclusion some points are made which the author feels are particularly crucial to any library MBO implementation.
PMCID: PMC226932  PMID: 476316
13.  Outcomes following percutaneous upper gastrointestinal decompressive tube placement for malignant bowel obstruction in ovarian cancer 
Gynecologic oncology  2013;129(1):103-106.
Objective
The objective of this study was to evaluate peri-operative and survival outcomes of ovarian cancer patients undergoing percutaneous upper gastrointestinal decompression for malignant bowel obstruction (MBO).
Methods
Retrospective chart review was used to identify patients with ovarian, peritoneal, or fallopian tube cancer who underwent palliative decompressive treatment for MBO from 1/2002–12/2010. Kaplan-Meier methods were used to estimate the median survival (MS) and multivariate analysis used to determine if any variables were associated with the hazard of death.
Results
Fifty-three patients met inclusion criteria. Median length of diagnosis prior to intervention was 21 months. Fifteen (28.3%) patients experienced complications and 9 required revision. Forty-nine (92.5%) experienced relief of symptoms after placement, and 91% tolerated some form of oral intake. Following placement, 19 (36%) patients received additional chemotherapy and 21(41%) patients received total parental nutrition (TPN). Thirty-five patients were discharged home/outpatient facility, 16 to hospice care, and 2 died prior to discharge. MS for all patients was 46 days. Patients who received chemotherapy had a MS of 169 days compared to 33 days (p<0.001). We failed to find an association between survival and TPN or performance status.
Conclusions
Malignant bowel obstruction is a common complication of ovarian cancer. Management is palliative; risks and benefits of any therapy must be considered. Percutaneous decompressive therapy provides relief from associated symptoms, and allows patients to be discharged home. Median survival in this group is limited, and decisions regarding aggressive therapy should be individualized.
doi:10.1016/j.ygyno.2013.01.021
PMCID: PMC4098040  PMID: 23369942
14.  Mixed Backbone Antisense Glucosylceramide Synthase Oligonucleotide (MBO-asGCS) loaded Solid Lipid Nanoparticles: In Vitro Characterization and Reversal of Multidrug Resistance in NCI/ADR-RES Cells 
International journal of pharmaceutics  2010;400(1-2):251-259.
In this study, Solid Lipid Nanoparticles (SLN) loaded with MBO-asGCS oligonucleotide were prepared, characterized and evaluated for cytotoxicity against NCI/ADR-RES human ovary cancer cells. Two types of cetyl trimethy ammonium bromide (CTAB) stabilized SLN, with or without ceramideVI, were prepared by mixed homogenization/ultrasonication technique. Complexes were characterized for size, zeta-potential, and stability in biorelevant media and against DNaseI activity. Binding and release studies were further confirmed by gel electrophoresis. Cytotoxicity of the SLN against NCI/ADR-RES cells was evaluated by quantizing ATP. SLN with CeramideVI had lower particle size (74.6nm) with improved stability in RPMI media when compared to reference SLN without ceramideVI (167.16nm). Both SLN however had similar cytotoxicity profile with an optimum binding at CTAB to MBO-asGCS ratio of 6:1. Blank SLN, and free MBO-asGCS in the presence and absence of free doxorubicin had insignificant effect on the viability of NCI/ADR-RES cells. However, when cells were concurrently treated with MBO-asGCS loaded SLN and free doxorubicin, cell viability significantly decreased to approximately 12%. These results suggested that SLN enhanced internalization and uptake of MBO-asGCS oligonucleotide, which led to the downregulation of GCS and subsequently reversing the resistance of the cells to doxorubicin.
doi:10.1016/j.ijpharm.2010.08.044
PMCID: PMC2952652  PMID: 20816930
solid lipid nanoparticle; antisense oligonucleotide; stability; cancer therapy; drug delivery
15.  A novel strategy for the identification of protein–DNA contacts by photocrosslinking and mass spectrometry 
Nucleic Acids Research  2004;32(16):e132.
Photochemical crosslinking is a method for studying the molecular details of protein–nucleic acid interactions. In this study, we describe a novel strategy to localize crosslinked amino acid residues that combines laser-induced photocrosslinking, proteolytic digestion, Fe3+-IMAC (immobilized metal affinity chromatography) purification of peptide–oligodeoxynucleotide heteroconjugates and hydrolysis of oligodeoxynucleotides by hydrogen fluoride (HF), with efficient matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The new method is illustrated by the identification of the DNA-binding site of the restriction endonuclease MboI. Photoactivatable 5-iododeoxyuridine was incorporated into a single site within the DNA recognition sequence (GATC) of MboI. Ultraviolet irradiation of the protein–DNA complex with a helium/cadmium laser at 325 nm resulted in 15% crosslinking yield. Proteolytic digestion with different proteases produced various peptide–oligodeoxynucleotide adducts that were purified together with free oligodeoxynucleotide by Fe3+-IMAC. A combination of MS analysis of the peptide–nucleosides obtained after hydrolysis by HF and their fragmentation by MS/MS revealed that Lys209 of MboI was crosslinked to the MboI recognition site at the position of the adenine, demonstrating that the region around Lys209 is involved in specific binding of MboI to its DNA substrate. This method is suitable for the fast identification of the site of contact between proteins and nucleic acids starting from picomole quantities of crosslinked complexes.
doi:10.1093/nar/gnh131
PMCID: PMC519130  PMID: 15383647
16.  Mechanism and Kinetics of Inducible Nitric Oxide Synthase Auto-S-Nitrosation and Inactivation† 
Biochemistry  2012;51(5):1028-1040.
Nitric oxide (NO), the product of the nitric oxide synthase (NOS) reaction, was previously shown to result in S-nitrosation of the NOS Zn2+-tetrathiolate and inactivation of the enzyme. To probe the potential physiological significance of NOS S-nitrosation, the inactivation timescale of the inducible NOS isoform (iNOS) was determined and found to directly correlate with an increase in iNOS S-nitrosation. A kinetic model of NOS inactivation in which arginine is treated as a suicide substrate was developed. In this model, NO synthesized at the heme cofactor is partitioned between release into solution (NO release pathway) and NOS S-nitrosation followed by NOS inactivation (inactivation pathway). Experimentally determined progress curves of NO formation were fit to the model. The NO release pathway was perturbed through addition of the NO traps oxymyoglobin (MbO2) and β2 H-NOX, which yielded partition ratios between NO release and inactivation of ~100 at 4 μM MbO2 and ~22,000 at saturating trap concentrations. The results suggest that a portion of the NO synthesized at the heme cofactor reacts with the Zn2+-tetrathiolate without being released into solution. Perturbation of the inactivation pathway through addition of the reducing agents GSH or TCEP resulted in a concentration-dependent decrease in iNOS S-nitrosation that directly correlated with protection from iNOS inactivation. iNOS inactivation was most responsive to physiological concentrations of GSH with an apparent Km value of 13 mM. NOS turnover that leads to NOS S-nitrosation might be a mechanism to control NOS activity, and NOS S-nitrosation could play a role in the physiological generation of nitrosothiols.
doi:10.1021/bi201818c
PMCID: PMC3277664  PMID: 22242685
17.  Novel F141L Pre-S2 Mutation in Hepatitis B Virus Increases the Risk of Hepatocellular Carcinoma in Patients with Chronic Genotype C Infections ▿  
Journal of Virology  2010;85(1):123-132.
Several lines of evidence have suggested that some naturally occurring mutations of hepatitis B virus (HBV) play a critical role in hepatocellular carcinoma (HCC). Here, we describe a novel HCC-related pre-S2 mutation, F141L. To prove the relationship between the F141L mutation and HCC, molecular epidemiology studies using MboII PCR restriction analysis (PRA) were performed, and the molecular mechanism was investigated through construction of a stable hepatocyte cell line expressing the large surface HB protein (LHB) with the F141L mutation (F141L-LHB). Application of MboII PRA to samples from 241 Korean patients with chronic liver diseases of different clinical stages confirmed that F141L mutants were significantly related to HCC, even in comparison to liver cirrhosis (HCC, 26.3% of patients, or 26/99; liver cirrhosis, 3.8% of patients, or 2/52; P = 0.001). By studying stable cell lines, we found that F141L-LHBs could induce cell cycle progression by downregulating the p53 and p21 pathways and upregulating CDK4 and cyclin A. Furthermore, we found that in a colony-forming assay, the colony-forming rates in cell lines expressing F141L-LHBs were about twice as high as those of the wild type. In conclusion, our results suggest that F141L-LHBs may contribute importantly to the pathogenesis of HCC by inducing cell proliferation and transformation. So, the F141L mutation examined in this study could serve as a diagnostic marker for the prognosis of HCC.
doi:10.1128/JVI.01524-10
PMCID: PMC3014212  PMID: 20962085
18.  Genetic signatures of a demographic collapse in a large-bodied forest dwelling primate (Mandrillus leucophaeus) 
Ecology and Evolution  2012;2(3):550-561.
It is difficult to predict how current climate change will affect wildlife species adapted to a tropical rainforest environment. Understanding how population dynamics fluctuated in such species throughout periods of past climatic change can provide insight into this issue. The drill (Mandrillus leucophaeus) is a large-bodied rainforest adapted mammal found in West Central Africa. In the middle of this endangered monkey's geographic range is Lake Barombi Mbo, which has a well-documented palynological record of environmental change that dates to the Late Pleistocene. We used a Bayesian coalescent-based framework to analyze 2,076 base pairs of mitochondrial DNA across wild drill populations to infer past changes in female effective population size since the Late Pleistocene. Our results suggest that the drill underwent a nearly 15-fold demographic collapse in female effective population size that was most prominent during the Mid Holocene (approximately 3-5 Ka). This time period coincides with a period of increased dryness and seasonality across Africa and a dramatic reduction in forest coverage at Lake Barombi Mbo. We believe that these changes in climate and forest coverage were the driving forces behind the drill population decline. Furthermore, the warm temperatures and increased aridity of the Mid Holocene are potentially analogous to current and future conditions faced by many tropical rainforest communities. In order to prevent future declines in population size in rainforest-adapted species such as the drill, large tracts of forest should be protected to both preserve habitat and prevent forest loss through aridification.
doi:10.1002/ece3.98
PMCID: PMC3399144  PMID: 22822434
Bayesian Skyline Plot; bottleneck; climate change; Cross-Sanaga-Bioko forests; drill; Mandrillus
19.  Identification and Characterization of Two Novel Proteins Affecting Fission Yeast γ-tubulin Complex FunctionV⃞ 
Molecular Biology of the Cell  2004;15(5):2287-2301.
The γ-tubulin complex, via its ability to organize microtubules, is critical for accurate chromosome segregation and cytokinesis in the fission yeast, Schizosaccharomyces pombe. To better understand its roles, we have purified the S. pombe γ-tubulin complex. Mass spectrometric analyses of the purified complex revealed known components and identified two novel proteins (i.e., Mbo1p and Gfh1p) with homology to γ-tubulin–associated proteins from other organisms. We show that both Mbo1p and Gfh1p localize to microtubule organizing centers. Although cells deleted for either mbo1+ or gfh1+ are viable, they exhibit a number of defects associated with altered microtubule function such as defects in cell polarity, nuclear positioning, spindle orientation, and cleavage site specification. In addition, mbo1Δ and gfh1Δ cells exhibit defects in astral microtubule formation and anchoring, suggesting that these proteins have specific roles in astral microtubule function. This study expands the known roles of γ-tubulin complex components in organizing different types of microtubule structures in S. pombe.
doi:10.1091/mbc.E03-10-0728
PMCID: PMC404023  PMID: 15004232
20.  Renin Gene Polymorphisms in Bangladeshi Hypertensive Population 
Journal of Genomics  2014;2:45-53.
Objective: Linkages of renin gene polymorphisms with hypertension have been implicated in several populations with contrasting results. Present study aims to assess the pattern of renin gene polymorphisms in Bangladeshi hypertensive individuals.
Methodology: Introns 1, 9 of renin gene and 4063 bases upstream of promoter sequence of renin gene were amplified from the genomic DNA of the total 124 (hypertensive and normotensive) subjects using respective primers. Polymerase chain reaction-based restriction fragment length polymorphisms were performed using BglI, MboI and TaqI restriction enzymes.
Results: Homozygosity was common in renin gene regarding BglI (bb=48.4%, Bb=37.9%, BB=13.7%, χ2 =1.91, P>0.05), TaqI (TT=81.5%, Tt=14.5%, tt=4.0%, χ2 =7.50, P<0.01) and MboI (mm=63.7%, Mm=32.3%, MM=4.0%, χ2=0.00, P>0.05) polymorphisms among total study population. For BglI and TaqI genotype distribution, hypertensive subjects (BglI: χ2 =6.66, P<0.05; TaqI: χ2 = 10.28, P<0.005) significantly deviate from Hardy-Weinberg Equilibrium law compared to normotensive subjects (BglI: χ2=0.51, P>0.05; TaqI: χ2=0.20, P>0.05). On the other hand, with respect to MboI polymorphisms of renin gene, only normotensive subjects deviate from the law (patients: χ2=1.28, P>0.05; vs controls: χ2=6.81, P<0.01). In the context of allelic frequency, common T allele was clearly prevalent (T frequency=0.86, t frequency = 0.14) for TaqI, but rare alleles b and m were more frequent for both BglI (b frequency=0.69, B frequency=0.31) and MboI (m frequency=0.80 M frequency=0.20) polymorphisms, respectively.
Conclusion: Thus, we report that Bangladeshi hypertensive subjects did not show any distinct pattern of renin gene polymorphisms compared to their healthy control subjects with regard to their genotypic and allelic frequencies.
doi:10.7150/jgen.5193
PMCID: PMC4105428  PMID: 25057323
Renin gene polymorphism; genetic variation; hypertension; renin; BglI polymorphism; TaqI polymorphism; MboI polymorphism; association analysis; Hardy-Weinberg equilibrium.
21.  Comparing Techniques for the Identification of the MTHFR A1298C Polymorphism 
The restriction fragment length polymorphism (RFLP) technique with the MboII enzyme is used by a number of researchers as a methodology for the identification of the genetic polymorphism MTHFR A1298C. However, the reliability of this enzyme for genotyping this polymorphism has been questioned, since the silent polymorphism T1317C, located close to the polymorphic region A1298C on gene MTHFR, also has a recognition site for MboII. Thus, the fragments formed by the digestion of MboII present similar sizes, making it difficult to differentiate the allele MTHFR 1298A in the presence of the allele MTHFR 1317C. Hence, we investigated the A1298C polymorphism in a Brazilian population of renal transplant patients, using the RFLP technique with digestion by Mbo II and using sequencing, in order to examine the concordance between the two techniques. Our results showed an 8.6% difference in genotyping between RFLP and sequencing, but the statistical concordance test presented a kappa coefficient equal to 0.81 (CI 95% 0.74–88), which indicates a virtually perfect concordance, according to the criterion of Landis and Koch. Therefore, we concluded that the RFLP technique is concordant with automated sequencing in the detection of polymorphism A1298C under our laboratory conditions.
PMCID: PMC2361162  PMID: 19137091
restriction fragment length polymorphism; DNA sequence; methylenetetrahydrofolate reductase
22.  Influence of Asian and Western United States Agricultural Areas and Fires on the Atmospheric Transport of Pesticides in the Western United States 
Environmental science & technology  2008;42(17):6519-6525.
Historic and current use pesticides (HUPs and CUPs), with respect to use in the United States and Canada, were identified in trans-Pacific and regional air masses at Mt. Bachelor Observatory (MBO), a remote high elevation mountain in Oregon’s Cascade Range located in the United States, during the sampling period of April 2004 to May 2006 (n=69), including NASA’s INTEX-B campaign (spring 2006). Elevated hexachlorobenzene (HCB) and α-hexachlorocyclohexane (α-HCH) concentrations were measured during trans-Pacific atmospheric transport events at MBO, suggesting that Asia is an important source region for these HUPs. Regional atmospheric transport events at MBO resulted in elevated dacthal, endosulfan, metribuzin, triallate, trifluralin, and chlorpyrifos concentrations, with episodic increases in concentration during some spring application periods, suggesting that the Western U.S. is a significant source region for these CUPs. Endosulfan I, γ-HCH, and dacthal concentrations were significantly positively correlated (p-value < 0.05) with increased air mass time in Western U.S. agricultural areas. Elevated γ-HCH concentrations were measured at MBO during both trans-Pacific and regional atmospheric transport events, including regional fire events. In addition to γ-HCH, elevated Σchlordane, α-HCH, HCB, and trifluralin concentrations were associated with fires in Western North America due to revolatilization of these pesticides from soils and vegetation. Trans-chlordane/cis-chlordane and α-HCH/γ-HCH ratios were calculated and may be used to distinguish between free tropospheric and regional and/or Asian air masses.
PMCID: PMC4145850  PMID: 18800524
23.  Errors and pitfalls: Briefing and accusation of medical malpractice – the second victim 
In June 2012, the German Medical Association (Bundesärztekammer) published the statistics of medical malpractice for 2011 (published at http://www.bundesaerztekammer.de). Still ENT-specific accusations of medical malpractice are by far the fewest in the field of hospitals and actually even in the outpatient context. Clearly most of the unforeseen incidents still occur in the disciplines of trauma surgery and orthopedics. In total, however, an increasing number of errors in treatment can be noticed on the multidisciplinary level: in 25.5% of the registered cases, an error in treatment was found to be the origin of damage to health justifying a claim for compensation of the patient. In the year before, it was only 24.7%. The reasons may be manifold, but the medical system itself certainly plays a major role in this context: the recent developments related to health policy lead to a continuous economisation of medical care. Rationing and limited remuneration more and more result in the fact that therapeutic decision are not exclusively made for the benefit of the patient but that they are oriented at economic or bureaucratic aspects. Thus, in the long term, practising medicine undergoes a change. According to the §§ 1, 3 of the professional code of conduct for doctors (Musterberufsordnung für Ärzte; MBO-Ä) medical practice as liberal profession is principally incompatible with the pursuit of profit, however, even doctors have to earn money which more and more makes him play the role of a businessman. Lack of personnel and staff savings lead to excessive workloads of physicians, caregivers, and nurses, which also favour errors. The quality and even the confidential relationship between doctor and patient, which is important for the treatment success, are necessarily affected by the cost pressure. The victims in this context are not only the patients but also the physicians find themselves in the continuous conflict between ethical requirements of their profession and the actual requirements of the realities in the healthcare field. But also the technical and scientific progress bear new risks beside the therapeutic successes, further especially bigger hospitals require high efforts regarding organisation favouring errors in cases of deficiencies. Even the increasing juridification of the medicine that is expected to achieve a provisional highlight with the planned law of patients’ rights leads to an important focus on the quality of medical care (see also [1]). The explicit legal regulation of patients’ rights, which have never been out of question up to now, confirms the impression of patients who have to be protected from their doctors. This development favours a natural mistrust in the quality of the treatment and the desire of legal verification in cases of treatment failures. A totally perfect and error-free treatment, however, will never occur. Already this fact leads to the obligation to do everything possible to reduce the risk to an absolute minimum. The risks that might arise from a relation of treatment are manifold. Not only may the patient undergo risks that arise in particular from lacking or insufficient briefing, complications, or medical malpractice.
Also the doctor has to fear legal consequences if he does not stick clearly to the increasing requirements that jurisdiction and legislation impose – not least by the planned law of patients’ rights. In the following, the basic principles and particularities will be described that apply for the patients’ briefing. Further the different types of medical malpractice will be explained in relation to the resulting procedural consequences. Finally some current problematic fields will be described with regard to other possible liabilities or responsibilities of physicians in hospitals or doctor’s offices.
doi:10.3205/cto000102
PMCID: PMC3884545  PMID: 24403978
error in treatment; error in briefing; documentation; organization default; liability for medical malpractice
24.  Postpyloric decompression tube placement through a gastrostomy for malignant bowel obstruction 
BMC Research Notes  2013;6:217.
Background
Malignant bowel obstruction affect a patient’s quality of life, but, management of MBO is controversial.
Case presentation
A 51-year-old woman who had been diagnosed as uterine cervix cancer 2 years ago and had undergone surgery, chemotherapy and radiotherapy, was admitted to our hospital. She was diagnosed as having a recurrence of peritoneal metastasis and bowel obstruction. For her nasal pain, we considered insertion of a postpyloric decompression tube through the gastrostomy instead of via the nasal cavity. After insertion of a percutaneous gastrostomy tube was performed endoscopically, we introduced a postpyloric decompression tube through her gastrostomy. She could be discharged home, and 91 days later, she died in her home under hospice care, as she had wished.
Conclusions
Insertion of a postpyloric decompression tube through a gastrostomy might be useful in the management of advanced cancer patients with bowel obstruction.
doi:10.1186/1756-0500-6-217
PMCID: PMC3680198  PMID: 23731859
Malignant bowel obstruction; Gastrostomy; Palliative care; Quality of life
25.  Differentiation of Helicobacter pylori strains directly from gastric biopsy specimens by PCR-based restriction fragment length polymorphism analysis without culture. 
Journal of Clinical Microbiology  1997;35(12):3021-3025.
Recent studies have shown the usefulness of PCR-based restriction fragment length polymorphism (RFLP) analysis for differentiating Helicobacter pylori strains isolated by culture. For this study, a PCR-based RFLP assay was developed for directly typing H. pylori strains from gastric biopsy specimens. Nineteen gastric biopsy specimens obtained from patients undergoing endoscopy for gastrointestinal complaints were cultured for isolation of H. pylori. Genomic DNA preparations from these gastric biopsy specimens and the corresponding H. pylori isolates were tested by our PCR-based RFLP assay. The 1,179-bp H. pylori DNA fragments amplified by the PCR assay were digested with the restriction enzymes HhaI, MboI, and AluI and analyzed by agarose gel electrophoresis. HhaI, MboI, and AluI digestion produced 11, 10, and 6 distinguishable digestion patterns, respectively, from the 19 H. pylori isolates tested and generated 13, 11, and 6 different patterns, respectively, from the 19 gastric biopsy specimens. The patterns from 13 of the 19 gastric biopsy specimens matched those of the H. pylori isolates from the corresponding patients. The patterns from the remaining six biopsy specimens appeared to represent infection by two strains of H. pylori; the pattern of one strain was identical to that of the isolate from the corresponding patient. By combining all the restriction enzyme digestion patterns obtained by using HhaI, MboI, and AluI, we observed 19 distinct RFLP patterns from the 19 specimens. The results suggest that the PCR-based RFLP analysis method may be useful as a primary technique to identify and distinguish H. pylori strains directly from gastric biopsy specimens without culture of the organisms.
PMCID: PMC230115  PMID: 9399487

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