bluuebunny/crossref_metadata_2025 huggingface dataset:
GBParsy: A GenBank flatfile parser library with high speed
Authors: Lee Tae-Ho , Kim Yeon-Ki , Nahm Baek Hie
Published: July 2008

Background

GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and the description in a GBF. Currently, several parser libraries for the GBF have been developed. However, with the accumulation of DNA sequence information from eukaryotic chromosomes, parsing a eukaryotic genome sequence with these libraries inevitably takes a long time, due to the large GBF file and its correspondingly large genomic nucleotide sequence and related feature information. Thus, there is significant need to develop a parsing program with high speed and efficient use of system memory.

Results

We developed a library, GBParsy, which was C language-based and parses GBF files. The parsing speed was maximized by using content-specified functions in place of regular expressions that are flexible but slow. In addition, we optimized an algorithm related to memory usage so that it also increased parsing performance and efficiency of memory usage. GBParsy is at least 5 - 100× faster than current parsers in benchmark tests.

Conclusion

GBParsy is estimated to extract annotated information from almost 100 Mb of a GenBank flatfile for chromosomal sequence information within a second. Thus, it should be used for a variety of applications such as on-time visualization of a genome at a web site.
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)
Authors: Keller Alexander , Schleicher Tina , Förster Frank , Ruderisch Benjamin , Dandekar Thomas , Müller Tobias , Wolf Matthias
Published: July 2008

Background

Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment.

Results

The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae.

Conclusion

In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics.
An amphioxus orthologue of the estrogen receptor that does not bind estradiol: Insights into estrogen receptor evolution
Authors: Paris Mathilde , Pettersson Katarina , Schubert Michael , Bertrand Stephanie , Pongratz Ingemar , Escriva Hector , Laudet Vincent
Published: July 2008

Background

The origin of nuclear receptors (NRs) and the question whether the ancestral NR was a liganded or an unliganded transcription factor has been recently debated. To obtain insight into the evolution of the ligand binding ability of estrogen receptors (ER), we comparatively characterized the ER from the protochordate amphioxus (Branchiostoma floridae), and the ER from lamprey (Petromyzon marinus), a basal vertebrate.

Results

Extensive phylogenetic studies as well as signature analysis allowed us to confirm that the amphioxus ER (amphiER) and the lamprey ER (lampER) belong to the ER group. LampER behaves as a "classical" vertebrate ER, as it binds to specific DNA Estrogen Responsive Elements (EREs), and is activated by estradiol (E2), the classical ER natural ligand. In contrast, we found that although amphiER binds EREs, it is unable to bind E2 and to activate transcription in response to E2. Among the 7 natural and synthetic ER ligands tested as well as a large repertoire of 14 cholesterol derivatives, only Bisphenol A (an endocrine disruptor with estrogenic activity) bound to amphiER, suggesting that a ligand binding pocket exists within the receptor. Parsimony analysis considering all available ER sequences suggest that the ancestral ER was not able to bind E2 and that this ability evolved specifically in the vertebrate lineage. This result does not support a previous analysis based on ancestral sequence reconstruction that proposed the ancestral steroid receptor to bind estradiol. We show that biased taxonomic sampling can alter the calculation of ancestral sequence and that the previous result might stem from a high proportion of vertebrate ERs in the dataset used to compute the ancestral sequence.

Conclusion

Taken together, our results highlight the importance of comparative experimental approaches vs ancestral reconstructions for the evolutionary study of endocrine systems: comparative analysis of extant ERs suggests that the ancestral ER did not bind estradiol and that it gained the ability to be regulated by estradiol specifically in the vertebrate lineage, before lamprey split.
A genome-wide 20 K citrus microarray for gene expression analysis
Authors: Martinez-Godoy M Angeles , Mauri Nuria , Juarez Jose , Marques M Carmen , Santiago Julia , Forment Javier , Gadea Jose
Published: July 2008

Background

Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant.

Results

We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database [1] was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability.

Conclusion

This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global studies in citrus by using it to catalogue genes expressed in citrus globular embryos.
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
Authors: Singer Gregory AC , Wu Jiejun , Yan Pearlly , Plass Christoph , Huang Tim HM , Davuluri Ramana V
Published: July 2008

Background

Independent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell.

Results

We have developed a custom microarray platform that tiles roughly 35,000 alternative putative promoters from nearly 7,000 genes in the human genome. To demonstrate the utility of this array platform, we have analyzed the patterns of promoter usage in 17β-estradiol (E2)-treated and untreated MCF7 cells and show widespread usage of alternative promoters. Most intriguingly, we show that the downstream promoter in E2-sensitive multiple promoter genes tends to be very close to the 3'-terminus of the gene, suggesting exotic mechanisms of expression regulation in these genes.

Conclusion

The usage of alternative promoters greatly multiplies the transcriptional complexity available within the human genome. The fact that many of these promoters are incapable of driving the synthesis of a meaningful protein-encoding transcript further complicates the story.
Identification of the genetic determinants of Salmonella enterica serotype Typhimurium that may regulate the expression of the type 1 fimbriae in response to solid agar and static broth culture conditions
Authors: Chuang Yin-Ching , Wang Ke-Chuan , Chen Yi-Tseng , Yang Chia-Huei , Men Shang-Chin , Fan Chia-Chun , Chang Li-Huan , Yeh Kuang-Sheng
Published: July 2008

Background

Type 1 fimbriae are the most commonly found fimbrial appendages on the outer membrane of Salmonella enterica serotype Typhimurium. Previous investigations indicate that static broth culture favours S. Typhimurium to produce type 1 fimbriae, while non-fimbriate bacteria are obtained by growth on solid agar media. The phenotypic expression of type 1 fimbriae in S. Typhimurium is the result of the interaction and cooperation of several genes in the fim gene cluster. Other gene products that may also participate in the regulation of type 1 fimbrial expression remain uncharacterized.

Results

In the present study, transposon insertion mutagenesis was performed on S. Typhimurium to generate a library to screen for those mutants that would exhibit different type 1 fimbrial phenotypes than the parental strain. Eight-two mutants were obtained from 7,239 clones screened using the yeast agglutination test. Forty-four mutants produced type 1 fimbriae on both solid agar and static broth media, while none of the other 38 mutants formed type 1 fimbriae in either culture condition. The flanking sequences of the transposons from 54 mutants were cloned and sequenced. These mutants can be classified according to the functions or putative functions of the open reading frames disrupted by the transposon. Our current results indicate that the genetic determinants such as those involved in the fimbrial biogenesis and regulation, global regulators, transporter proteins, prophage-derived proteins, and enzymes of different functions, to name a few, may play a role in the regulation of type 1 fimbrial expression in response to solid agar and static broth culture conditions. A complementation test revealed that transforming a recombinant plasmid possessing the coding sequence of a NAD(P)H-flavin reductase gene ubiB restored an ubiB mutant to exhibit the type 1 fimbrial phenotype as its parental strain.

Conclusion

Genetic determinants other than the fim genes may involve in the regulation of type 1 fimbrial expression in S. Typhimurium. How each gene product may influence type 1 fimbrial expression is an interesting research topic which warrants further investigation.
Testing for differences in distribution tails to test for differences in 'maximum' lifespan
Authors: Gao Guimin , Wan Wen , Zhang Sijian , Redden David T , Allison David B
Published: July 2008

Background

Investigators are actively testing interventions intended to increase lifespan and wish to test whether the interventions increase maximum lifespan. Based on the fact that one cannot be assured of observing population maximum lifespans in finite samples, in previous work, we constructed and validated several tests of difference in the upper parts of lifespan distributions between a treatment group and a control group by testing whether the probabilities that observations are above some threshold defining 'old' or being in the tail of the survival distribution are equal in the two groups. However, a limitation of these tests is that they do not consider how much above the threshold any particular observation is.

Methods

In this article we propose new methods which improve upon our previous tests by considering not only whether an observation is above some threshold, but also the magnitudes by which observations exceed the threshold.

Results

Simulations show that the new methods control type I error rates quite well and that the power of the new methods is usually higher than that of the tests we previously proposed. In illustrative analyses of two real datasets involving rodents, when setting the threshold equal to 110 (100) weeks for the first (second) datasets, the new methods detected differences in 'maximum lifespan' between groups at nominal alpha levels of 0.01 (0.05) for the first (second) datasets and provided more significant results than competitor tests.

Conclusion

The new methods not only have good performance in controlling the type I error rates but also improve the power compared with the tests we previously proposed.
Physicians' communication skills with patients and legal liability in decided medical malpractice litigation cases in Japan
Authors: Hamasaki Tomoko , Takehara Tadamichi , Hagihara Akihito
Published: July 2008

Background

In medical malpractice litigations in recent years in Japan, it is notable that the growing number of medical litigation cases includes the issue of a doctor's explanation to the patient as a pivotal point. The objective of this study was to identify factors of physicians' communication skills with patients, as related to their legal liability, and differences in doctors' communication skills with patients by the type of medical facility.

Methods

Decisions of medical malpractice litigation cases between 1988 and 2005 in Japan, the pivotal issue of which was a physician's explanation, were analyzed in the study. The content of each decision was summarized using the study variables (information about the patient, doctor, manner of the doctor's explanation, and subsequent litigation), and a database comprising the content of each decision (N = 100) was constructed. In order to evaluate an association between doctors' communication skills with patients and the outcome of the litigation, the analysis was performed based on the outcome of litigation or the type of medical facility.

Results

The ratio of acknowledged physician liability by court decision was lower in cases in which the doctor's explanation occurred before treatment or surgery (p = 0.013). The ratio of acknowledged physician liability by court decision was higher in cases of elective or non-urgent treatment (p = 0.046). The ratio of acknowledged physician liability by court decision was higher in clinics than in hospital groups (p = 0.036).

Conclusion

These findings are beneficial for the prevention of medical disputes and improvement of patient-physician communication.
Caustic ingestion in adults: The role of endoscopic classification in predicting outcome
Authors: Cheng Hao-Tsai , Cheng Chi-Liang , Lin Cheng-Hui , Tang Jui-Hsiang , Chu Yin-Yi , Liu Nai-Jen , Chen Pang-Chi
Published: July 2008

Background

The ingestion of caustic substances induces an extensive spectrum of injuries to the aerodigestive tract which include extensive necrosis and perforation of the esophagus and stomach. The gold standard of safely assessing depth, extent of injury, and appropriate therapeutic regimen is esophagogastroduodenoscopy (EGD). The objective of this study was to report our clinical experience and to evaluate the role of a 6-point EGD classification system of injury in predicting outcomes in adult patients diagnosed with caustic agent ingestion.

Methods

The study was a retrospective medical chart review from 273 patients admitted to the Chang Gung Memorial Hospital in Tao-Yuan, Taiwan between June 1999 and July 2006 for treatment of caustic ingestion. The patients underwent EGD within 24 hours of admission and mucosal damage was graded using Zagar's modified endoscopic classification scheme. After treatment, patients were followed in the outpatient clinic for a minimum of 6 months.

Results

A total of 273 patients were included for analysis. Grade 3b injury was the most common caustic injury (n = 82, 30.03%), followed by grade 2b injuries (n = 62, 22.71%). Stricture was the most common complication (n = 66, 24.18%), followed by aspiration pneumonia (n = 31, 11.36%), and respiratory failure (n = 21, 7.69%). Compared to grade 3a mucosal injury, grade 3b mucosal injuries were at greater risk of prolonged hospital stay (odds ratio [OR]: 2.44; 95% confidence interval [CI]: 1.25–4.80), ICU admission (OR: 10.82; 95% CI: 2.05–200.39), and gastrointestinal (OR: 4.15; 95% CI: 1.55–13.29) and systemic complications (OR: 4.07; 95% CI: 1.81–14.07).

Conclusion

In patients with caustic ingestion, EGD should be performed within 12 to 24 hours and categorized according to a 6-point scale. Patients with grade 3b burns identified on endoscopy have high rates of morbidity. The 6-point scale is useful for predicting immediate and long-term complications, and guiding appropriate therapy.
Efficacy of laser capture microdissection plus RT-PCR technique in analyzing gene expression levels in human gastric cancer and colon cancer
Authors: Makino Hiroshi , Uetake Hiroyuki , Danenberg Kathleen , Danenberg Peter V , Sugihara Kenichi
Published: July 2008

Background

Thymidylate synthase, dihydropyrimidine dehydrogenase, thymidine phosphorylase, and orotate phosphoribosyltransferase gene expressions are reported to be valid predictive markers for 5-fluorouracil sensitivity to gastrointestinal cancer. For more reliable predictability, their expressions in cancer cells and stromal cells in the cancerous tissue (cancerous stroma) have been separately investigated using laser capture microdissection.

Methods

Thymidylate synthase, dihydropyrimidine dehydrogenase, thymidine phosphorylase, and orotate phosphoribosyltransferase mRNA in cancer cells and cancerous stroma from samples of 47 gastric and 43 colon cancers were separately quantified by reverse transcription polymerase chain reaction after laser capture microdissection.

Results

In both gastric and colon cancers, thymidylate synthase and orotate phosphoribosyltransferase mRNA expressions were higher (p < 0.0001, p <0.0001 respectively in gastric cancer and P = 0.0002, p < 0.0001 respectively in colon cancer) and dihydropyrimidine dehydrogenase mRNA expressions were lower in cancer cells than in cancerous stroma (P = 0.0136 in gastric cancer and p < 0.0001 in colon cancer). In contrast, thymidine phosphorylase mRNA was higher in cancer cells than in cancerous stroma in gastric cancer (p < 0.0001) and lower in cancer cells than in cancerous stroma in colon cancer (P = 0.0055).

Conclusion

By using this method, we could estimate gene expressions separately in cancer cells and stromal cells from colon and gastric cancers, in spite of the amount of stromal tissue. Our method is thought to be useful for accurately evaluating intratumoral gene expressions.
Implication of TRIMalpha and TRIMCyp in interferon-induced anti-retroviral restriction activities
Authors: Carthagena Laetitia , Parise Mélanie C , Ringeard Mathieu , Chelbi-Alix Mounira K , Hazan Uriel , Nisole Sébastien
Published: July 2008

Background

TRIM5α is a restriction factor that interferes with retroviral infections in a species-specific manner in primate cells. Although TRIM5α is constitutively expressed, its expression has been shown to be up-regulated by type I interferon (IFN). Among primates, a particular case exists in owl monkey cells, which express a fusion protein between TRIM5 and cyclophilin A, TRIMCyp, specifically interfering with HIV-1 infection. No studies have been conducted so far concerning the possible induction of TRIMCyp by IFN. We investigated the consequences of IFN treatment on retroviral restriction in diverse primate cells and evaluated the implication of TRIM5α or TRIMCyp in IFN-induced anti-retroviral activities.

Results

First, we show that human type I IFN can enhance TRIM5α expression in human, African green monkey and macaque cells, as well as TRIMCyp expression in owl monkey cells. In TRIM5α-expressing primate cell lines, type I IFN has little or no effect on HIV-1 infection, whereas it potentates restriction activity against N-MLV in human and African green monkey cells. In contrast, type I IFN treatment of owl monkey cells induces a great enhancement of HIV-1 restriction, as well as a strain-tropism independent restriction of MLV. We were able to demonstrate that TRIM5α is the main mediator of the IFN-induced activity against N-MLV in human and African green monkey cells, whereas TRIMCyp mediates the IFN-induced HIV-1 restriction enhancement in owl monkey cells. In contrast, the type I IFN-induced anti-MLV restriction in owl monkey cells is independent of TRIMCyp expression.

Conclusion

Together, our observations indicate that both TRIM5α and TRIMCyp are implicated in IFN-induced anti-retroviral response in primate cells. Furthermore, we found that type I IFN also induces a TRIMCyp-independent restriction activity specific to MLV in owl monkey cells.
Inhibition of foot-and-mouth disease virus replication in vitro and in vivo by small interfering RNA
Authors: Pengyan Wang , Yan Ren , Zhiru Guo , Chuangfu Chen
Published: July 2008

By using bioinformatics computer programs, all foot-and-mouth disease virus (FMDV) genome sequences in public-domain databases were analyzed. Based on the results of homology analysis, 2 specific small interfering RNA (siRNA) targeting homogenous 3D and 2B1 regions of 7 serotypes of FMDV were prepared and 2 siRNA-expression vectors, pSi-FMD2 and pSi-FMD3, were constructed. The siRNA-expressing vectors were used to test the ability of siRNAs to inhibit virus replication in baby hamster kidney (BHK-21) cells and suckling mice, a commonly used small animal model. The results demonstrated that transfection of BHK-21 cells with siRNA-expressing plasmids significantly weakened the cytopathic effect (CPE). Moreover, BHK-21 cells transiently transfected with short hairpin RNA (shRNA)-expressing plasmids were specifically resistant to the infection of the FMDV serotypes A, O, and Asia I and this the antiviral effects persisted for almost 48 hours. We measured the viral titers, the 50% tissue culture infective dose (TCID50) in cells transfected with anti-FMDV siRNAs was found to be lower than that of the control cells. Furthermore, subcutaneous injection of siRNA-expressing plasmids in the neck of the suckling mice made them less susceptible to infection with O, and Asia I serotypes of FMDV.
Skin protection creams in medical settings: successful or evil?
Authors: Xhauflaire-Uhoda Emmanuelle , Macarenko Elena , Denooz Raphaël , Charlier Corinne , Piérard Gérald E
Published: July 2008

Background

Chronic exposure to mild irritants including cleansing and antiseptic products used for hand hygiene generates insults to the skin. To avoid unpleasant reactions, skin protection creams are commonly employed, but some fail to afford protection against a variety of xenobiotics. In this study, two skin protection creams were assayed comparatively looking for a protective effect if any against a liquid soap and an alcohol-based gel designed for hand hygiene in medical settings.

Methods

Corneosurfametry and corneoxenometry are two in vitro bioessays which were selected for their good reproducibility, sensitivity and ease of use. A Kruskal-Wallis ANOVA test followed by the Dunn test was realized to compare series of data obtained.

Results

Significant differences in efficacy were obtained between the two assayed skin protection creams. One of the two tested creams showed a real protective effect against mild irritants, but the other tested cream presented an irritant potential in its application with mild irritants.

Conclusion

The differences observed for the two tested skin protection creams were probably due to their galenic composition and their possible interactions with the offending products. As a result, the present in vitro bioassays showed contrasted effects of the creams corresponding to either a protective or an irritant effect on human stratum corneum.
Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures
Authors: Dias João ML , Oehmen Adrian , Serafim Luísa S , Lemos Paulo C , Reis Maria AM , Oliveira Rui
Published: July 2008

Background

This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA) copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients.

Results

The model was validated with experimental data collected in a sequencing batch reactor (SBR) operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments), and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i) either with acetate or (ii) with propionate as carbon source material. Metabolic flux analysis (MFA) was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA) was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to ~0.17 C-mol/(C-mol.h). The results were compared with published pure culture metabolic studies.

Conclusion

Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of acetate and propionate are fed to the cultures, the catabolic activity is primarily guaranteed through acetate uptake, and the characteristic P/O ratio of acetate prevails over that of propionate. This study suggests that the PHA production process by mixed microbial cultures has the potential to be comparable or even more favourable than pure cultures.
Flexion reminder device to discourage recurrent posterior dislocation of a total hip replacement: a case report
Authors: Wong King , Sivan Manoj , Matthews Gordon
Published: July 2008

Introduction

Recurrent dislocation of a total hip replacement prosthesis is a frustrating complication for both the surgeon and the patient. For positional dislocations with no indications for revision surgery, the current best treatment is physiotherapy, the use of abduction braces and avoidance of unsafe hip positions. Abduction braces can be cumbersome and have poor compliance. We report the successful use of a new lightweight flexion reminder device that can be used to treat people with this condition.

Case presentation

A 64-year-old British woman experienced recurrent positional posterior dislocation after primary hip replacement, particularly when involved in activities involving unsafe flexion of the operated hip. She disliked using an abduction brace and hence was given a simple 'flexion reminder device' that could be strapped to the thigh. Beyond the safe flexion limit, the padded top end of the device hitched against the groin crease and reminded her not to flex further, to avoid dislocation. She experienced no discomfort in wearing the device continuously throughout the day and was very satisfied. She has had no further dislocations in the 2 years since she began using it.

Conclusion

In cases of arthroplasty dislocation caused mainly by an unsafe hip position, and with no indication for revision surgery, this new lightweight and easily worn flexion reminder device may be a good option for avoiding such positional dislocations, particularly those caused by unsafe flexion.
Mosaicism for r(X) and der(X)del(X)(p11.23)dup(X)(p11.21p11.22) provides insight into the possible mechanism of rearrangement
Authors: Shchelochkov Oleg A , Cooper M Lance , Ou Zhishuo , Peacock Sandra , Yatsenko Svetlana A , Brown Chester W , Fang Ping , Stankiewicz Pawel , Cheung Sau Wai
Published: July 2008

We report a patient with a unique and complex cytogenetic abnormality involving mosaicism for a small ring X and deleted Xp derivative chromosome with tandem duplication at the break point. The patient presented with failure to thrive, muscular hypotonia, and minor facial anatomic anomalies, all concerning for Turner syndrome. Brain MRI revealed mild thinning of the corpus callosum, an apparent decrease in ventricular white matter volume, and an asymmetric myelination pattern. Array comparative genome hybridization analysis revealed mosaicism for the X chromosome, deletion of the short arm of an X chromosome, and a duplication of chromosome region Xp11.21-p11.22. G-banded chromosome and FISH analyses revealed three abnormal cell lines: 46,X,der(X)del(X)(p11.23)dup(X)(p11.21p11.22)/46,X,r(X)(q11.1q13.1)/45,X. The small ring X chromosome was estimated to be 5.2 Mb in size and encompassed the centromere and Xq pericentromeric region. X chromosome inactivation (XCI) studies demonstrated a skewed pattern suggesting that the ring X remained active, likely contributing to the observed clinical features of brain dysmyelination. We hypothesize that a prezygotic asymmetric crossing over within a loop formed during meiosis in an X chromosome with a paracentric inversion resulted in an intermediate dicentric chromosome. An uneven breakage of the dicentric chromosome in the early postzygotic period might have resulted in the formation of one cell line with the X chromosome carrying a terminal deletion and pericentromeric duplication of the short arm and the second cell line with the X chromosome carrying a complete deletion of Xp. The cell line carrying the deletion of Xp could have then stabilized through self-circularization and formation of the ring X chromosome.
Circuit life span in critically ill children on continuous renal replacement treatment: a prospective observational evaluation study
Authors: del Castillo Jimena , López-Herce Jesús , Cidoncha Elena , Urbano Javier , Mencía Santiago , Santiago Maria J , Bellón Jose M
Published: July 2008

Introduction

One of the greatest problems with continuous renal replacement therapy (CRRT) is early coagulation of the filters. Few studies have monitored circuit function prospectively. The purpose of this study was to determine the variables associated with circuit life in critically ill children with CRRT.

Methods

A prospective observational study was performed in 122 children treated with CRRT in a pediatric intensive care unit from 1996 to 2006. Patient and filter characteristics were analyzed to determine their influence on circuit life. Data were collected on 540 filters in 122 patients and an analysis was performed of the 365 filters (67.6%) that were changed due to circuit coagulation.

Results

The median circuit life was 31 hours (range 1 to 293 hours). A univariate and multivariate logistic regression study was performed to assess the influence of each one of the factors on circuit life span. No significant differences in filter life were found according to age, weight, diagnoses, pump, site of venous access, blood flow rate, ultrafiltration rate, inotropic drug support, or patient outcome. The mean circuit life span was longer when the heparin dose was greater than 20 U/kg per hour (39 versus 29.1 hours; P = 0.008), with hemodiafiltration compared with hemofiltration (34 versus 22.7 hours; P = 0.001), with filters with surface areas of 0.4 to 0.9 m2 (38.2 versus 26.1 hours; P = 0.01), and with a catheter size of 6.5 French or greater (33.0 versus 25.0 hours; P = 0.04). In the multivariate analysis, hemodiafiltration, heparin dose of greater than 20 U/kg per hour, filter surface area of 0.4 m2 or greater, and initial creatinine of less than 2 mg/dL were associated with a filter life of more than 24 and 48 hours. Total effluent rate of greater than 35 mL/kg per hour was associated only with a filter life of more than 24 hours.

Conclusion

Circuit life span in CRRT in children is short but may be increased by the use of hemodiafiltration, higher heparin doses, and filters with a high surface area.
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
Authors: Chu Vu T , Gottardo Raphael , Raftery Adrian E , Bumgarner Roger E , Yeung Ka Yee
Published: July 2008

We present MeV+R, an integration of the JAVA MultiExperiment Viewer program with Bioconductor packages. This integration of MultiExperiment Viewer and R is easily extensible to other R packages and provides users with point and click access to traditionally command line driven tools written in R. We demonstrate the ability to use MultiExperiment Viewer as a graphical user interface for Bioconductor applications in microarray data analysis by incorporating three Bioconductor packages, RAMA, BRIDGE and iterativeBMA.
The selective nonpeptide CXCR2 antagonist SB225002 ameliorates acute experimental colitis in mice
Authors: Bento Allisson Freire , Leite Daniela Ferraz Pereira , Claudino Rafaela Franco , Hara Daniela Balz , Leal Paulo César , Calixto João B
Published: July 2008

Although neutrophils are strongly implicated in eliminating pathogens, excessive recruitment may cause tissue damage. Therefore, reducing cell influx during an inflammatory process may be a potential target for treating inflammatory bowel diseases (IBD). As CXCR2 is involved in neutrophil migration, this study aimed to evaluate whether the systemic therapeutic treatment with selective CXCR2 antagonist SB225002 ameliorates experimental colitis, which was induced in mice by 2,4,6-trinitrobenzene sulfonic acid (TNBS). After colitis establishment (24 h), mice were treated with SB225002. At later time-points, up to 72 h, mice were monitored for body weight loss and overall mortality. At the time of sacrifice, colonic tissues were scored for macro- and microscopic damage, and cytokine levels, myeloperoxidase (MPO) activity, and protein expression were analyzed. TNBS administration induced macro- and microscopic damage in colon tissue, leading in most cases to animal death. Curative treatment with SB225002 significantly reduced all of the parameters analyzed, leading to an improvement of inflammatory signs. SB225002 reduced neutrophil influx, MPO activity, IL-1β, MIP-2, and keratinocyte-derived chemokine (KC) levels and the expression of vascular endothelial growth factor, inducible NO synthase, and cyclooxygenase-2 proteins into the colon tissue. Levels of IL-4 and IL-10 were increased significantly in the colons of animals treated with SB225002. Additionally, curative treatment with mouse anti-KC significantly reduced MPO activity and colonic damage. These results taken together demonstrate that a selective blockade of CXCR2 consistently reduced TNBS-induced colitis, suggesting that the use of SB225002 is a potential therapeutic approach for the treatment of IBD and other related inflammatory disorders.
Novel Treatment for Lithium-Induced Nephrogenic Diabetes Insipidus Rat Model Using the Sendai-Virus Vector Carrying Aquaporin 2 Gene
Authors: Suga Hidetaka , Nagasaki Hiroshi , Kondo Taka-aki , Okajima Yoshiki , Suzuki Chizuko , Ozaki Nobuaki , Arima Hiroshi , Yamamoto Tokunori , Ozaki Noriyuki , Akai Masaro , Sato Aiko , Uozumi Nobuyuki , Inoue Makoto , Hasegawa Mamoru , Oiso Yutaka
Published: July 2008

Congenital nephrogenic diabetes insipidus (NDI) is a chronic disorder involving polyuria and polydipsia that results from unresponsiveness of the renal collecting ducts to the antidiuretic hormone vasopressin. Either of the genetic defects in vasopressin V2 receptor or the water channel aquaporin 2 (AQP2) cause the disease, which interfere the water reabsorption at the epithelium of the collecting duct. An unconscious state including a perioperative situation can be life threatening because of the difficulty to regulate their water balance. The Sendai virus (SeV) vector system deleting fusion protein (F) gene (SeV/ΔF) is considered most suitable because of the short replication cycle and nontransmissible character. An animal model for NDI with reduced AQP2 by lithium chloride was used to develop the therapy. When the SeV/ΔF vector carrying a human AQP2 gene (AQP2-SeV/ΔF) was administered retrogradely via ureter to renal pelvis, AQP2 was expressed in the renal collecting duct to reduce urine output and water intake by up to 40%. In combination with the retorograde administration to pelvis, this system could be the cornerstone for the applicable therapies on not only NDI patients but also other diseases associate with the medullary collecting duct.
Identification and Analysis of Prophet of Pit-1-Binding Sites in Human Pit-1 Gene
Authors: Ikeshita Nobuko , Kawagishi Mayuko , Shibahara Hiromi , Toda Keizo , Yamashita Tomoe , Yamamoto Daisuke , Sugiyama Yuka , Iguchi Genzo , Iida Keiji , Takahashi Yutaka , Kaji Hidesuke , Chihara Kazuo , Okimura Yasuhiko
Published: July 2008

Prophet of Pit-1 (Prop1) is a transcription factor that regulates Pit-1 gene expression. Because Pit-1 regulates the differentiation of pituitary cells and the expressions of GH, prolactin and TSHβ genes, Prop1 mutation results in combined pituitary hormone deficiency in humans. However, Prop1-binding sites in human Pit-1 gene and the mechanism leading to combined pituitary hormone deficiency have remained unclear. In this study, we identified and analyzed Prop1-binding elements of the human Pit-1 gene. Prop1 stimulated the expression of the reporter plasmid containing Pit-1 gene from translation start site to −1340 dose dependently in GH3 cells. The activation by Prop1 was observed in GH3 and TtT/GF cells but not COS7, HeLa, JEG3, and HuH7 cells. Deletion analysis of Pit-1 gene showed that the Prop1-responsive elements were present within the −257-bp region. Within the −257-bp region, there are four elements similar to consensus sequence of paired-like transcription factors. Because Prop1 is a member of paired-like transcription factors, we assessed the elements. EMSA and transient transfection assay using the mutation of the elements revealed that the element from −63 to −53 (the proximal Prop1 binding element) was essential to Prop1-binding and Prop1-induced activation of Pit-1 reporter plasmid. A region at −8kb of human Pit-1 gene is similar to the distal region containing Prop1-binding elements in mouse Pit-1 gene. We showed the region functioned as an enhancer. Furthermore, chromatin immunoprecipitation assay showed that the proximal element could bind Prop1 in vivo cultured cells. Taken together, these findings indicated the novel functioning binding elements of Prop1 in human Pit-1 gene.
Endogenous Peroxisome Proliferator-Activated Receptor-γ Augments Fatty Acid Uptake in Oxidative Muscle
Authors: Norris Andrew W. , Hirshman Michael F. , Yao Jianrong , Jessen Niels , Musi Nicolas , Chen Lihong , Sivitz William I. , Goodyear Laurie J. , Kahn C. Ronald
Published: July 2008

In the setting of insulin resistance, agonists of peroxisome proliferator-activated receptor (PPAR)-γ restore insulin action in muscle and promote lipid redistribution. Mice with muscle-specific knockout of PPARγ (MuPPARγKO) develop excess adiposity, despite reduced food intake and normal glucose disposal in muscle. To understand the relation between muscle PPARγ and lipid accumulation, we studied the fuel energetics of MuPPARγKO mice. Compared with controls, MuPPARγKO mice exhibited significantly increased ambulatory activity, muscle mitochondrial uncoupling, and respiratory quotient. Fitting with this latter finding, MuPPARγKO animals compared with control siblings exhibited a 25% reduction in the uptake of the fatty acid tracer 2-bromo-palmitate (P < 0.05) and a 13% increase in serum nonesterified fatty acids (P = 0.05). These abnormalities were associated with no change in AMP kinase (AMPK) phosphorylation, AMPK activity, or phosphorylation of acetyl-CoA carboxylase in muscle and occurred despite increased expression of fatty acid transport protein 1. Palmitate oxidation was not significantly altered in MuPPARγKO mice despite the increased expression of several genes promoting lipid oxidation. These data demonstrate that PPARγ, even in the absence of exogenous activators, is required for normal rates of fatty acid uptake in oxidative skeletal muscle via mechanisms independent of AMPK and fatty acid transport protein 1. Thus, when PPARγ activity in muscle is absent or reduced, there will be decreased fatty acid disposal leading to diminished energy utilization and ultimately adiposity.
Deoxyribonucleic Acid Methylation Controls Cell Type-Specific Expression of Steroidogenic Factor 1
Authors: Hoivik Erling A. , Aumo Linda , Aesoy Reidun , Lillefosse Haldis , Lewis Aurélia E. , Perrett Rebecca M. , Stallings Nancy R. , Hanley Neil A. , Bakke Marit
Published: July 2008

Steroidogenic factor 1 (SF1) is expressed in a time- and cell-specific manner in the endocrine system. In this study we present evidence to support that methylation of CpG sites located in the proximal promoter of the gene encoding SF1 contributes to the restricted expression pattern of this nuclear receptor. DNA methylation analyses revealed a nearly perfect correlation between the methylation status of the proximal promoter and protein expression, such that it was hypomethylated in cells that express SF1 but hypermethylated in nonexpressing cells. Moreover, in vitro methylation of this region completely repressed reporter gene activity in transfected steroidogenic cells. Bisulfite sequencing of DNA from embryonic tissue demonstrated that the proximal promoter was unmethylated in the developing testis and ovary, whereas it was hypermethylated in tissues that do not express SF1. Together these results indicate that the DNA methylation pattern is established early in the embryo and stably inherited thereafter throughout development to confine SF1 expression to the appropriate tissues. Chromatin immunoprecipitation analyses revealed that the transcriptional activator upstream stimulatory factor 2 and RNA polymerase II were specifically recruited to this DNA region in cells in which the proximal promoter is hypomethylated, providing functional support for the fact that lack of methylation corresponds to a transcriptionally active gene. In conclusion, we identified a region within the SF1/Sf1 gene that epigenetically directs cell-specific expression of SF1.
GATA-4 Regulates Bcl-2 Expression in Ovarian Granulosa Cell Tumors
Authors: Kyrönlahti Antti , Rämö Maarit , Tamminen Maija , Unkila-Kallio Leila , Butzow Ralf , Leminen Arto , Nemer Mona , Rahman Nafis , Huhtaniemi Ilpo , Heikinheimo Markku , Anttonen Mikko
Published: July 2008

Excessive cell proliferation and decreased apoptosis have been implicated in the pathogenesis of ovarian granulosa cell tumors (GCTs). We hypothesized that transcription factor GATA-4 controls expression of the antiapoptotic factor Bcl-2 and the cell cycle regulator cyclin D2 in normal and neoplastic granulosa cells. To test this hypothesis, a tissue microarray based on 80 GCTs was subjected to immunohistochemistry for GATA-4, Bcl-2, and cyclin D2, and the data were correlated to clinical and histopathological parameters. In addition, quantitative RT-PCR for GATA-4, Bcl-2, and cyclin D2 was performed on 21 human GCTs. A mouse GCT model was used to complement these studies. The role of GATA-4 in the regulation of Bcl2 and ccdn2 (coding for cyclin D2) was studied by transactivation assays, and by disrupting GATA-4 function with dominant negative approaches in mouse and human GCT cell lines. We found that GATA-4 expression correlated with Bcl-2 and cyclin D2 expression in human and murine GCTs. Moreover, GATA-4 enhanced Bcl-2 and cyclin D2 promoter activity in murine GCT cells. Whereas GATA-4 overexpression up-regulated and dominant negative GATA-4 suppressed Bcl-2 expression in human GCT cells, the effects on cyclin D2 were negligible. Our results reveal a previously unknown relationship between GATA-4 and Bcl-2 in mammalian granulosa cells and GCTs, and suggest that GATA-4 influences granulosa cell fate by transactivating Bcl-2.
Mammalian Hyaluronidase Induces Ovarian Granulosa Cell Apoptosis and Is Involved in Follicular Atresia
Authors: Orimoto Adriana M. , Dumaresq-Doiron Karine , Jiang Jin-Yi , Tanphaichitr Nongnuj , Tsang Benjamin K. , Carmona Euridice
Published: July 2008

During ovarian folliculogenesis, the vast majority of follicles will undergo atresia by apoptosis, allowing a few dominant follicles to mature. Mammalian hyaluronidases comprise a family of six to seven enzymes sharing the same catalytic domain responsible for hyaluronan hydrolysis. Interestingly, some of these enzymes have been shown to induce apoptosis. In the ovary, expression of three hyaluronidases (Hyal-1, Hyal-2, and Hyal-3) has been documented. However, their precise cellular localization and role in ovarian regulation have not yet been defined. We herein investigated the possible involvement of these enzymes in ovarian atresia. First, we established a mouse model for ovarian atresia (gonadotropin withdrawal by anti-equine chorionic gonadotropin treatment) and showed that the mRNA levels of Hyal-1, Hyal-2, and Hyal-3 were significantly increased in apoptotic granulosa cells as well as in atretic follicles. Second, using ovaries of normally cycling mice, we demonstrated the correlation of Hyal-1 mRNA and protein expression with cleavage of caspase-3. In addition, we showed that expression of all three hyaluronidases induced apoptosis in transfected granulosa cells. Significantly, the induction of apoptosis by hyaluronidases was independent of catalytic activity, because enzymatically inactive Hyal-1 mutant (D157A/E159A) was as efficient as the wild-type enzyme in apoptosis induction. The activation of the extrinsic apoptotic signaling pathway was involved in this induction, because increased levels of cleaved caspase-8, caspase-3, and poly-ADP-ribose polymerase (PARP) were observed upon hyaluronidase ectopic expression. Our present findings provide a better understanding of the role of hyaluronidases in ovarian functions, showing for the first time their involvement in follicular atresia.