bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development
Authors: Tse William KF , Eisenhaber Birgit , Ho Steven HK , Ng Qimei , Eisenhaber Frank , Jiang Yun-Jin 
Published: December 2009

Abstract

Background
Deconjugation of ubiquitin and/or ubiquitin-like modified protein substrates is essential to modulate protein-protein interactions and, thus, signaling processes in cells. Although deubiquitylating (deubiquitinating) enzymes (DUBs) play a key role in this process, however, their function and regulation remain insufficiently understood. The "loss-of-function" phenotype studies can provide important information to elucidate the gene function, and zebrafish is an excellent model for this goal.

Results
From an in silico genome-wide search, we found more than 90 putative DUBs encoded in the zebrafish genome belonging to six different subclasses. Out of them, 85 from five classical subclasses have been tested with morpholino (MO) knockdown experiments and 57 of them were found to be important in early development of zebrafish. These DUB morphants resulted in a complex and pleiotropic phenotype that, regardless of gene target, always affected the notochord. Based on the huC neuronal marker expression, we grouped them into five sets (groups I to V). Group I DUBs (otud7b, uchl3 and bap1) appear to be involved in the Notch signaling pathway based on the neuronal hyperplasia, while group IV DUBs (otud4, usp5, usp15 and usp25) play a critical role in dorsoventral patterning through the BMP pathway.

Conclusion
We have identified an exhaustive list of genes in the zebrafish genome belonging to the five established classes of DUBs. Additionally, we performed the corresponding MO knockdown experiments in zebrafish as well as functional studies for a subset of the predicted DUB genes. The screen results in this work will stimulate functional follow-up studies of potential DUB genes using the zebrafish model system.
Polymorphism in the flanking regions of the PbGP43 gene from the human pathogen Paracoccidioides brasiliensis: search for protein binding sequences and poly(A) cleavage sites
Authors: Rocha Antonio A , Morais Flávia V , Puccia Rosana 
Published: December 2009

Abstract

Background

Paracoccidioides brasiliensis is a thermo-dimorphic fungus that causes paracoccidiodomycosis (PCM). Glycoprotein gp43 is the fungal main diagnostic antigen, which can also protect against murine PCM and interact with extracellular matrix proteins. It is structurally related to glucanases, however not active, and whose expression varies considerably. We have presently studied polymorphisms in the PbGP43 flanking regions to help understand such variations.

Results
we tested the protein-binding capacity of oligonucleotides covering the PbGP43 proximal 5' flanking region, including overlap and mutated probes. We used electrophoretic mobility shift assays and found DNA binding regions between positions -134 to -103 and -255 to -215. Only mutation at -230, characteristic of P. brasiliensis phylogenetic species PS2, altered binding affinity. Next, we cloned and sequenced the 5' intergenic region up to position -2,047 from P. brasiliensis Pb339 and observed that it is composed of three tandem repetitive regions of about 500 bp preceded upstream by 442 bp. Correspondent PCR fragments of about 2,000 bp were found in eight out of fourteen isolates; in PS2 samples they were 1,500-bp long due to the absence of one repetitive region, as detected in Pb3. We also compared fifty-six PbGP43 3' UTR sequences from ten isolates and have not observed polymorphisms; however we detected two main poly(A) clusters (1,420 to 1,441 and 1,451 to 1,457) of multiple cleavage sites. In a single isolate we found one to seven sites.

Conclusions
We observed that the amount of PbGP43 transcripts accumulated in P. brasiliensis Pb339 grown in defined medium was about 1,000-fold higher than in Pb18 and 120-fold higher than in Pb3. We have described a series of features in the gene flanking regions and differences among isolates, including DNA-binding sequences, which might impact gene regulation. Little is known about regulatory sequences in thermo-dimorphic fungi. The peculiar structure of tandem repetitive fragments in the 5' intergenic region of PbGP43, their characteristic sequences, besides the presence of multiple poly(A) cleavage sites in the 3' UTR will certainly guide future studies.
Glycosylation-mediated phenylpropanoid partitioning in Populus tremuloides cell cultures
Authors: Payyavula Raja S , Babst Benjamin A , Nelsen Matthew P , Harding Scott A , Tsai Chung-Jui 
Published: December 2009

Abstract

Background
Phenylpropanoid-derived phenolic glycosides (PGs) and condensed tannins (CTs) comprise large, multi-purpose non-structural carbon sinks in Populus. A negative correlation between PG and CT concentrations has been observed in several studies. However, the molecular mechanism underlying the relationship is not known.

Results

Populus cell cultures produce CTs but not PGs under normal conditions. Feeding salicyl alcohol resulted in accumulation of salicins, the simplest PG, in the cells, but not higher-order PGs. Salicin accrual reflected the stimulation of a glycosylation response which altered a number of metabolic activities. We utilized this suspension cell feeding system as a model for analyzing the possible role of glycosylation in regulating the metabolic competition between PG formation, CT synthesis and growth. Cells accumulated salicins in a dose-dependent manner following salicyl alcohol feeding. Higher feeding levels led to a decrease in cellular CT concentrations (at 5 or 10 mM), and a negative effect on cell growth (at 10 mM). The competition between salicin and CT formation was reciprocal, and depended on the metabolic status of the cells. We analyzed gene expression changes between controls and cells fed with 5 mM salicyl alcohol for 48 hr, a time point when salicin accumulation was near maximum and CT synthesis was reduced, with no effect on growth. Several stress-responsive genes were up-regulated, suggestive of a general stress response in the fed cells. Salicyl alcohol feeding also induced expression of genes associated with sucrose catabolism, glycolysis and the Krebs cycle. Transcript levels of phenylalanine ammonia lyase and most of the flavonoid pathway genes were reduced, consistent with down-regulated CT synthesis.

Conclusions
Exogenous salicyl alcohol was readily glycosylated in Populus cell cultures, a process that altered sugar utilization and phenolic partitioning in the cells. Using this system, we identified candidate genes for glycosyltransferases that may mediate the glycosylation, and for transporters that mediate the subcellular compartmentalization of sugars and phenolic glycosides. The suspension cells appear to represent a facile system for dissecting the regulation of phenolic carbon partitioning, and in turn, its effects on growth in Populus.
Effects of phone versus mail survey methods on the measurement of health-related quality of life and emotional and behavioural problems in adolescents
Authors: Erhart Michael , Wetzel Ralf M , Krügel André , Ravens-Sieberer Ulrike 
Published: December 2009

AbstractBackgroundTelephone interviews have become established as an alternative to traditional mail surveys for collecting epidemiological data in public health research. However, the use of telephone and mail surveys raises the question of to what extent the results of different data collection methods deviate from one another. We therefore set out to study possible differences in using telephone and mail survey methods to measure health-related quality of life and emotional and behavioural problems in children and adolescents.MethodsA total of 1700 German children aged 8-18 years and their parents were interviewed randomly either by telephone or by mail. Health-related Quality of Life (HRQoL) and mental health problems (MHP) were assessed using the KINDL-R Quality of Life instrument and the Strengths and Difficulties Questionnaire (SDQ) children's self-report and parent proxy report versions. Mean Differences ("d" effect size) and differences in Cronbach alpha were examined across modes of administration. Pearson correlation between children's and parents' scores was calculated within a multi-trait-multi-method (MTMM) analysis and compared across survey modes using Fisher-Z transformation.ResultsTelephone and mail survey methods resulted in similar completion rates and similar socio-demographic and socio-economic makeups of the samples. Telephone methods resulted in more positive self- and parent proxy reports of children's HRQoL (SMD ≤ 0.27) and MHP (SMD ≤ 0.32) on many scales. For the phone administered KINDL, lower Cronbach alpha values (self/proxy Total: 0.79/0.84) were observed (mail survey self/proxy Total: 0.84/0.87). KINDL MTMM results were weaker for the phone surveys: mono-trait-multi-method mean r = 0.31 (mail: r = 0.45); multi-trait-mono-method mean (self/parents) r = 0.29/0.36 (mail: r = 0.34/0.40); multi-trait-multi-method mean r = 0.14 (mail: r = 0.21). Weaker MTMM results were also observed for the phone administered SDQ: mono-trait-multi-method mean r = 0.32 (mail: r = 0.40); multi-trait-mono-method mean (self/parents) r = 0.24/0.30 (mail: r = 0.20/0.32); multi-trait-multi-method mean r = 0.14 (mail = 0.14). The SDQ classification into borderline and abnormal for some scales was affected by the method (OR = 0.36-1.55).ConclusionsThe observed differences between phone and mail surveys are small but should be regarded as relevant in certain settings. Therefore, while both methods are valid, some changes are necessary. The weaker reliability and MTMM validity associated with phone methods necessitates improved phone adaptations of paper and pencil questionnaires. The effects of phone versus mail survey modes are partly different across constructs/measures.
Design and pre-clinical profiling of a Plasmodium falciparum MSP-3 derived component for a multi-valent virosomal malaria vaccine
Authors: Tamborrini Marco , Mueller Markus S , Stoffel Sabine A , Westerfeld Nicole , Vogel Denise , Boato Francesca , Zurbriggen Rinaldo , Robinson John A , Pluschke Gerd 
Published: December 2009

AbstractBackgroundClinical profiling of two components for a synthetic peptide-based virosomal malaria vaccine has yielded promising results, encouraging the search for additional components for inclusion in a final multi-valent vaccine formulation. This report describes the immunological characterization of linear and cyclized synthetic peptides comprising amino acids 211-237 ofPlasmodium falciparummerozoite surface protein (MSP-3).MethodsThese peptides were coupled to phosphatidylethanolamine (PE); the conjugates were intercalated into immunopotentiating reconstituted influenza virosomes (IRIVs) and then used for immunizations in mice to evaluate their capacity to elicitP. falciparumcross-reactive antibodies.ResultsWhile all MSP-3-derived peptides were able to elicit parasite-binding antibodies, stabilization of turn structures by cyclization had no immune-enhancing effect. Therefore, further pre-clinical profiling was focused on FB-12, a PE conjugate of the linear peptide. Consistent with the immunological results obtained in mice, all FB-12 immunized rabbits tested seroconverted and consistently elicited antibodies that interacted with blood stage parasites. It was observed that a dose of 50 μg was superior to a dose of 10 μg and that influenza pre-existing immunity improved the immunogenicity of FB-12 in rabbits. FB-12 production was successfully up-scaled and the immunogenicity of a vaccine formulation, produced according to the rules of Good Manufacturing Practice (GMP), was tested in mice and rabbits. All animals tested developed parasite-binding antibodies. Comparison of ELISA and IFA titers as well as the characterization of a panel of anti-FB-12 monoclonal antibodies indicated that at least the majority of antibodies specific for the virosomally formulated synthetic peptide were parasite cross-reactive.ConclusionThese results reconfirm the suitability of IRIVs as a carrier/adjuvant system for the induction of strong humoral immune responses against a wide range of synthetic peptide antigens. The virosomal formulation of the FB-12 peptidomimetic is suitable for use in humans and represents a candidate component for a virosomal multi-valent malaria subunit vaccine.
Effect of hyperlipidemia on the expression of circadian genes in apolipoprotein E knock-out atherosclerotic mice
Authors: Hou Likun , Lu Chao , Huang Yang , Chen Sifeng , Hua Luchun , Qian Ruizhe 
Published: December 2009

Abstract

Background
Circadian patterns of cardiovascular vulnerability were well characterized, with a peak incidence of acute myocardial infarction and stroke secondary to atherosclerosis in the morning, which showed the circadian clock may take part in the pathological process of atherosclerosis induced by hyperlipidemia. Hence, the effect of hyperlipidemia on the expression of circadian genes was investigated in atherosclerotic mouse model.

Results
In apoE-/-mice on regular chow or high-fat diet, an atherosclerotic mouse model induced by heperlipidemia, we found that the peak concentration of serum lipids was showed four or eight hours later in apoE-/- mice, compared to C57BL/6J mice. During the artificial light period, a reduce in circulating level of serum lipids corresponded with the observed increase of the expression levels of some the transcription factors involved in lipid metabolism, such as PPARα and RXRα. Meanwhile, the expression of circadian genes was changed following with amplitude reduced or the peak mRNA level delayed.

Conclusions
Our studies indicated that heperlipidemia altered both the rhythmicity and expression of circadian genes. Diet-induced circadian disruption may affect the process of atherosclerosis and some acute cardiovascular disease.
Methylation associated inactivation of RASSF1A and its synergistic effect with activated K-Ras in nasopharyngeal carcinoma
Authors: Wang Tao , Liu Hongli , Chen Yeshan , Liu Wei , Yu Jing , Wu Gang 
Published: December 2009

Abstract

Background
Epigenetic silencing of tumor suppressor genes associated with promoter methylation is considered to be a hallmark of oncogenesis. RASSF1A is a candidate tumor suppressor gene which was found to be inactivated in many human cancers. Although we have had a prelimilary cognition about the function of RASSF1A, the exact mechanisms about how RASSF1A functions in human cancers were largely unknown. Moreover, the effect of mutated K-Ras gene on the function of RASSF1A is lacking. The aim of this study was to investigate the expression profile and methylation status of RASSF1A gene, and to explore its concrete mechanisms as a tumor suppressor gene in Nasopharyngeal Carcinoma.

Methods
We examined the expression profile and methylation status of RASSF1A in two NPC cell lines, 38 primary nasopharyngeal carcinoma and 14 normal nasopharyngeal epithelia using RT-PCR and methylated specific PCR(MSP) respectively. 5-aza-dC was then added to confirm the correlation between hypermethylation status and inactivation of RASSF1A. The NPC cell line CNE-2 was transfected with exogenous pcDNA3.1(+)/RASSF1A plasmid in the presence or absence of mutated K-Ras by liposome-mediated gene transfer method. Flow cytometry was used to examine the effect of RASSF1A on cell cycle modulation and apoptosis. Meanwhile, trypan blue dye exclusion assays was used to detect the effect of RASSF1A transfection alone and the co-transfection of RASSF1A and K-Ras on cell proliferation.

Results
Promoter methylation of RASSF1A could be detected in 71.05% (27/38) of NPC samples, but not in normal nasopharyngeal epithelia. RASSF1A expression in NPC primary tumors was lower than that in normal nasopharyngeal epithelial (p < 0.01). Expression of RASSF1A was down-regulated in two NPC cell lines. Loss of RASSF1A expression was greatly restored by the methyltransferase inhibitor 5-aza-dC in CNE-2. Ectopic expression of RASSF1A in CNE-2 could increase the percentage of G0/G1 phase cells (p < 0.01), inhibit cell proliferation and induce apoptosis (p < 0.001). Moreover, activated K-Ras could enhance the growth inhibition effect induced by RASSF1A in CNE-2 cells (p < 0.01).

Conclusion
Expression of RASSF1A is down-regulated in NPC due to the hypermethylation of promoter. Exogenous expression of RASSF1A is able to induce growth inhibition effect and apoptosis in tumor cell lines, and this effect could be enhanced by activated K-Ras.
The classification of mental disorder: a simpler system for DSM–V and ICD–11
Authors: Goldberg David 
Published: January 2010

SummaryThis article proposes a simplification to the chapter structure of current classifications of mental disorder, which cause unnecessary estimates of ‘comorbidity’ and pay major attention to symptom similarity as a criterion for deciding on groupings. A simpler system, taking account of recent developments in aetiology, is proposed. There is at present no simple solution to the problems posed by the structure of our classification, but the advantages as well as the shortcomings of changing our approach to diagnosis are discussed.
Impact of a Pharmaceutical Care Intervention on Blood Pressure Control in a Chain Pharmacy Practice
Authors: Robinson J Daniel , Segal Richard , Lopez Larry M , Doty Randell E 
Published: December 2009

BACKGROUND Hypertension affects over 50 million Americans, with only 50% of patients being adequately controlled. Several pharmacist counseling and pharmacist-physician comanagement studies have documented that community pharmacist interventions improve blood pressure (BP) management. OBJECTIVE To determine whether community pharmacists can improve clinical endpoints including hypertension control, drug therapy dosing, adherence to prescribed regimens, adverse drug reaction incidence, patient understanding, response to therapy, and quality-of-life. METHODS The program included the education and training of a group of 18 chain community pharmacists in hypertension therapies, monitoring, and management. Protocols and documentation tools were based on nationally accepted clinical practice guidelines for hypertension in place at the time of the study. Pharmaceutical care (PC) was then compared with usual care (UC) over a 12-month period. RESULTS The study initially enrolled 180 PC and 196 UC patients, with 44% (PC) and 32% (UC) of the patients reporting a final BP measurement. A larger proportion (50%) of PC patients who had poorly controlled hypertension at baseline (>140/90 mm Hg) were controlled compared with UC patients (22%). The average reduction in systolic BP was 9.9 mm Hg in PC patients compared with 2.8 mm Hg in UC patients (p < 0.05). Changes in diastolic BP were similar in the PC and UC groups. Based on patient self-report, PC patients were more likely to say that they take their medicines as prescribed compared with UC patients (p < 0.05). The 1- to 6-month antihypertensive adherence rate was higher in PC patients (0.91 ± 0.15) compared to UC patients (0.78 ± 0.30) (p = 0.02); there was no significant difference in adherence rate during the 7- to 12-month period. CONCLUSIONS Community pharmacists can positively affect patient medication adherence during the 6-month period following counseling by a pharmacist along with an improvement in patient BP. However, there is much room for improvement in PC programs and in the number of patients who properly adhere to their medications.
Lofexidine, an α2-Receptor Agonist for Opioid Detoxification
Authors: Gish Emily C , Miller Jamie L , Honey Brooke L , Johnson Peter N 
Published: December 2009

Objective: To review the pharmacology, toxicology, pharmacokinetics, efficacy, adverse effects, drug interactions, and dosage guidelines for lofexidine, an α2-agonist, for opioid detoxification. Data Sources: Primary literature was identified through a MEDLINE search (1950–September 2009), EMBASE (1988–Juty 2009), International Pharmaceutical Abstracts (1970–September 2009), and the Cochrane Library (1996–September 2009) using the key words lofexidine and opioid withdrawal. Abstracts were included in the absence of published results of studies. Study Selection and Data Extraction: Studies published in English-language literature reporting on animal and human pharmacology, toxicology, and pharmacokinetics were included in addition to clinical trials using lofexidine for opioid detoxification in comparison to placebo or active controls. Data Synthesis: Lofexidine is an α2-agonist structurally related to clonidine. It is not an effective antihypertensive agent; however, it decreases the sympathetic outflow responsible for many opioid withdrawal symptoms. Nine clinical studies were reviewed representing 354 patients receiving lofexidine including a recent Phase 3 clinical trial. Eight studies involved comparisons of lofexidine to an opioid receptor agonist or clonidine for opioid detoxification. In these trials, lofexidine dosing was titrated to a maximum of 1.6–3.2 mg/day in divided doses for a total of 5–18 days. The data suggest that lofexidine has positive efficacy in reducing opioid withdrawal symptoms and is at least as effective as the opioid receptor agonists utilized for detoxification. Not all withdrawal symptoms are alleviated by α2-agonists, with many patients complaining of insomnia and aching. The most common adverse event with lofexidine in the Phase 3 trial was insomnia. Hypotension was also reported; however, the studies comparing clonidine with lofexidine suggest decreased incidence and severity of adverse events with lofexidine. Conclusions: Lofexidine appears to be a promising agent for opioid detoxification. If approved, it would be the first nonopioid agent approved for this indication. Further large-scale controlled studies are needed to identify the safest, most effective dosage regimen required to achieve opioid detoxification.