bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity
Authors: Smits Theo HM , Jaenicke Sebastian , Rezzonico Fabio , Kamber Tim , Goesmann Alexander , Frey Jürg E , Duffy Brion
Published: January 2010

Background

Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora.

Results

The genome of the type strain of E. pyrifoliae strain DSM 12163T, was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Comparative genomics with the pome fruit epiphyte Erwinia tasmaniensis Et1/99 showed that both species are overall highly similar, although specific differences were identified, for example the presence of some phage gene-containing regions and a high number of putative genomic islands containing transposases in the E. pyrifoliae DSM 12163T genome.

Conclusions

The E. pyrifoliae genome is an important addition to the published genome of E. tasmaniensis and the unfinished genome of E. amylovora providing a foundation for re-sequencing additional strains that may shed light on the evolution of the host-range and virulence/pathogenicity of this important group of plant-associated bacteria.
Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish
Authors: Borchardt Thilo , Looso Mario , Bruckskotten Marc , Weis Patrick , Kruse Julia , Braun Thomas
Published: January 2010

Background

The newtNotophthalmus viridescenspossesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration.

Results

A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish.

Conclusion

We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.
Identification of genes differentially expressed during interaction of resistant and susceptible apple cultivars (Malus × domestica) with Erwinia amylovora
Authors: Baldo Angela , Norelli Jay L , Farrell Robert E , Bassett Carole L , Aldwinckle Herb S , Malnoy Mickael
Published: January 2010

Background

The necrogenic enterobacterium, Erwinia amylovora is the causal agent of the fire blight (FB) disease in many Rosaceaespecies, including apple and pear. During the infection process, the bacteria induce an oxidative stress response with kinetics similar to those induced in an incompatible bacteria-plant interaction. No resistance mechanism to E. amylovora in host plants has yet been characterized, recent work has identified some molecular events which occur in resistant and/or susceptible host interaction with E. amylovora: In order to understand the mechanisms that characterize responses to FB, differentially expressed genes were identified by cDNA-AFLP analysis in resistant and susceptible apple genotypes after inoculation with E. amylovora.

Results

cDNA were isolated from M.26 (susceptible) and G.41 (resistant) apple tissues collected 2 h and 48 h after challenge with a virulent E. amylovora strain or mock (buffer) inoculated. To identify differentially expressed transcripts, electrophoretic banding patterns were obtained from cDNAs. In the AFLP experiments, M.26 and G.41 showed different patterns of expression, including genes specifically induced, not induced, or repressed by E. amylovora. In total, 190 ESTs differentially expressed between M.26 and G.41 were identified using 42 pairs of AFLP primers. cDNA-AFLP analysis of global EST expression in a resistant and a susceptible apple genotype identified different major classes of genes. EST sequencing data showed that genes linked to resistance, encoding proteins involved in recognition, signaling, defense and apoptosis, were modulated by E. amylovora in its host plant. The expression time course of some of these ESTs selected via a bioinformatic analysis has been characterized.

Conclusion

These data are being used to develop hypotheses of resistance or susceptibility mechanisms in Malus to E. amylovora and provide an initial categorization of genes possibly involved in recognition events, early signaling responses the subsequent development of resistance or susceptibility. These data also provided potential candidates for improving apple resistance to fire blight either by marker-assisted selection or genetic engineering.
QTLs and candidate genes for desiccation and abscisic acid content in maize kernels
Authors: Capelle Valérie , Remoué Carine , Moreau Laurence , Reyss Agnès , Mahé Aline , Massonneau Agnès , Falque Matthieu , Charcosset Alain , Thévenot Claudine , Rogowsky Peter , Coursol Sylvie , Prioul Jean-Louis
Published: January 2010

Background

Kernel moisture at harvest is an important trait since a low value is required to prevent unexpected early germination and ensure seed preservation. It is also well known that early germination occurs in viviparous mutants, which are impaired in abscisic acid (ABA) biosynthesis. To provide some insight into the genetic determinism of kernel desiccation in maize, quantitative trait loci (QTLs) were detected for traits related to kernel moisture and ABA content in both embryo and endosperm during kernel desiccation. In parallel, the expression and mapping of genes involved in kernel desiccation and ABA biosynthesis, were examined to detect candidate genes.

Results

The use of an intermated recombinant inbred line population allowed for precise QTL mapping. For 29 traits examined in an unreplicated time course trial of days after pollination, a total of 78 QTLs were detected, 43 being related to kernel desiccation, 15 to kernel weight and 20 to ABA content. Multi QTL models explained 35 to 50% of the phenotypic variation for traits related to water status, indicating a large genetic control amenable to breeding. Ten of the 20 loci controlling ABA content colocated with previously detected QTLs controlling water status and ABA content in water stressed leaves. Mapping of candidate genes associated with kernel desiccation and ABA biosynthesis revealed several colocations between genes with putative functions and QTLs. Parallel investigation via RT-PCR experiments showed that the expression patterns of the ABA-responsive Rab17 and Rab28 genes as well as the late embryogenesis abundant Emb5 and aquaporin genes were related to desiccation rate and parental allele effect. Database searches led to the identification and mapping of two zeaxanthin epoxidase (ZEP) and five novel 9-cis-epoxycarotenoid dioxygenase (NCED) related genes, both gene families being involved in ABA biosynthesis. The expression of these genes appeared independent in the embryo and endosperm and not correlated with ABA content in either tissue.

Conclusions

A high resolution QTL map for kernel desiccation and ABA content in embryo and endosperm showed several precise colocations between desiccation and ABA traits. Five new members of the maize NCED gene family and another maize ZEP gene were identified and mapped. Among all the identified candidates, aquaporins and members of the Responsive to ABA gene family appeared better candidates than NCEDs and ZEPs.
A novel mutation in the glycogen synthase 2 gene in a child with glycogen storage disease type 0
Authors: Soggia Ana Priscila , Correa-Giannella Maria Lúcia , Fortes Maria Angela Henriques , Luna Ana Mercedes Cavaleiro , Pereira Maria Adelaide Albergaria
Published: January 2010

Background

Glycogen storage disease type 0 is an autosomal recessive disease presenting in infancy or early childhood and characterized by ketotic hypoglycemia after prolonged fasting and postprandial hyperglycemia and hyperlactatemia. Sixteen different mutations have been identified to date in the gene which encodes hepatic glycogen synthase, resulting in reduction of glycogen storage in the liver.

Case Presentation

Biochemical evaluation as well as direct sequencing of exons and exon-intron boundary regions of the GYS2 gene were performed in a patient presenting fasting hypoglycemia and postprandial hyperglycemia and her parents. The patient was found to be compound heterozygous for one previously reported nonsense mutation (c.736 C>T; R243X) and a novel frameshift mutation (966_967delGA/insC) which introduces a stop codon 21 aminoacids downstream from the site of the mutation that presumably leads to loss of 51% of the COOH-terminal part of the protein. The glycemia and lactatemia of the parents after an oral glucose tolerance test were evaluated to investigate a possible impact of the carrier status on the metabolic profile. The mother, who presented a positive family history of type 2 diabetes, was classified as glucose intolerant and the father, who did not exhibit metabolic changes after the glucose overload, had an antecedent history of hypoglycemia after moderate alcohol ingestion.

Conclusion

The current results expand the spectrum of known mutations in GYS2 and suggest that haploinsufficiency could explain metabolic abnormalities in heterozygous carriers in presence of predisposing conditions.
Long-term follow-up of beryllium sensitized workers from a single employer
Authors: Duggal Mona , Deubner David C , Curtis Anne M , Cullen Mark R
Published: January 2010

Background

Up to 12% of beryllium-exposed American workers would test positive on beryllium lymphocyte proliferation test (BeLPT) screening, but the implications of sensitization remain uncertain.

Methods

Seventy two current and former employees of a beryllium manufacturer, including 22 with pathologic changes of chronic beryllium disease (CBD), and 50 without, with a confirmed positive test were followed-up for 7.4 +/-3.1 years.

Results

Beyond predicted effects of aging, flow rates and lung volumes changed little from baseline, while DLCO dropped 17.4% of predicted on average. Despite this group decline, only 8 subjects (11.1%) demonstrated physiologic or radiologic abnormalities typical of CBD. Other than baseline status, no clinical or laboratory feature distinguished those who clinically manifested CBD at follow-up from those who did not.

Conclusions

The clinical outlook remains favorable for beryllium-sensitized individuals over the first 5-12 years. However, declines in DLCO may presage further and more serious clinical manifestations in the future. These conclusions are tempered by the possibility of selection bias and other study limitations.
Long-term prognosis of diabetic patients with acute myocardial infarction in the era of acute revascularization
Authors: Takara Ayako , Ogawa Hiroshi , Endoh Yasuhiro , Mori Fumiaki , Yamaguchi Jun-ichi , Takagi Atsushi , Koyanagi Ryo , Shiga Tsuyoshi , Kasanuki Hiroshi , Hagiwara Nobuhisa
Published: January 2010

Background

The long-term prognosis of diabetic patients with acute myocardial infarction (AMI) treated by acute revascularization is uncertain, and the optimal pharmacotherapy for such cases has not been fully evaluated.

Methods

To elucidate the long-term prognosis and prognostic factors in diabetic patients with AMI, a prospective, cohort study involving 3021 consecutive AMI patients was conducted. All patients discharged alive from hospital were followed to monitor their prognosis every year. The primary endpoint of the study was all-cause mortality, and the secondary endpoint was the occurrence of major cardiovascular events. To elucidate the effect of various factors on the long-term prognosis of AMI patients with diabetes, the patients were divided into two groups matched by propensity scores and analyzed retrospectively.

Results

Diabetes was diagnosed in 1102 patients (36.5%). During the index hospitalization, coronary angioplasty and coronary thrombolysis were performed in 58.1% and 16.3% of patients, respectively. In-hospital mortality of diabetic patients with AMI was comparable to that of non-diabetic AMI patients (9.2% and 9.3%, respectively). In total, 2736 patients (90.6%) were discharged alive and followed for a median of 4.2 years (follow-up rate, 96.0%). The long-term survival rate was worse in the diabetic group than in the non-diabetic group, but not significantly different (hazard ratio, 1.20 [0.97-1.49], p = 0.09). On the other hand, AMI patients with diabetes showed a significantly higher incidence of cardiovascular events than the non-diabetic group (1.40 [1.20-1.64], p < 0.0001). Multivariate analysis revealed that three factors were significantly associated with favorable late outcomes in diabetic AMI patients: acute revascularization (HR, 0.62); prescribing aspirin (HR, 0.27); and prescribing renin-angiotensin system (RAS) inhibitors (HR, 0.53). There was no significant correlation between late outcome and prescription of beta-blockers (HR, 0.97) or calcium channel blockers (HR, 1.27). Although standard Japanese-approved doses of statins were associated with favorable outcome in AMI patients with diabetes, this was not statistically significant (0.67 [0.39-1.06], p = 0.11).

Conclusions

Although diabetic patients with AMI have more frequent adverse events than non-diabetic patients with AMI, the present results suggest that acute revascularization and standard therapy with aspirin and RAS inhibitors may improve their prognosis.
Geocoding police collision report data from California: a comprehensive approach
Authors: Bigham John M , Rice Thomas M , Pande Swati , Lee Junhak , Park Shin Hyoung , Gutierrez Nicolas , Ragland David R
Published: January 2010

Background

Collision geocoding is the process of assigning geographic descriptors, usually latitude and longitude coordinates, to a traffic collision record. On California police reports, relative collision location is recorded using a highway postmile marker or a street intersection. The objective of this study was to create a geocoded database of all police-reported, fatal and severe injury collisions in the California Statewide Integrated Traffic Records System (SWITRS) for years 1997-2006 for use by public agencies.

Results

Geocoding was completed with a multi-step process. First, pre-processing was performed using a scripting language to clean and standardize street name information. A state highway network with postmile values was then created using a custom tool written in Visual Basic for Applications (VBA) in ArcGIS software. Custom VBA functionality was also used to incorporate the offset direction and distance. Intersection and address geocoding was performed using ArcGIS, StreetMap Pro 2003 digital street network, and Google Earth Pro. A total of 142,007 fatal and severe injury collisions were identified in SWITRS. The geocoding match rate was 99.8% for postmile-coded collisions and 86% for intersection-coded collisions. The overall match rate was 91%.

Conclusions

The availability of geocoded collision data will be beneficial to clinicians, researchers, policymakers, and practitioners in the fields of traffic safety and public health. Potential uses of the data include studies of collision clustering on the highway system, examinations of the associations between collision occurrence and a variety of variables on environmental and social characteristics, including housing and personal demographics, alcohol outlets, schools, and parks. The ability to build maps may be useful in research planning and conduct and in the delivery of information to both technical and non-technical audiences.
THOC5/FMIP, an mRNA export TREX complex protein, is essential for hematopoietic primitive cell survival in vivo
Authors: Mancini Annalisa , Niemann-Seyde Susanne C , Pankow Rüdiger , El Bounkari Omar , Klebba-Färber Sabine , Koch Alexandra , Jaworska Ewa , Spooncer Elaine , Gruber Achim D , Whetton Anthony D , Tamura Teruko
Published: January 2010

Background

The transcription/export complex is evolutionarily conserved from yeast to man and is required for coupled transcription elongation and nuclear export of mRNAs. FMIP(Fms interacting protein) is a member of the THO (suppressors of the transcriptional defects of hpr1delta by overexpression) complex which is a subcomplex of the transcription/export complex. THO complex (THOC) components are not essential for bulk poly (A)+ RNA export in higher eukaryotes, but for the nuclear export of subset of mRNAs, however, their exact role is still unclear.

Results

To study the role of THOC5/Fms interacting protein in vivo, we generated THOC5/Fms interacting protein knockout mice. Since these mice are embryonic lethal, we then generated interferon inducible conditional THOC5/Fms interacting protein knockout mice. After three poly injections all of the mice died within 14 days. No pathological alterations, however, were observed in liver, kidney or heart. Thus we considered the hematopoietic system and found that seven days after poly injection, the number of blood cells in peripheral blood decreased drastically. Investigation of bone marrow cells showed that these became apoptotic within seven days after poly injection. Committed myeloid progenitor cells and cells with long term reconstituting potential were lost from bone marrow within four days after poly injection. Furthermore, infusion of normal bone marrow cells rescued mice from death induced by loss of THOC5/Fms interacting protein.

Conclusion

THOC5/Fms interacting protein is an essential element in the maintenance of hematopoiesis. Furthermore, mechanistically depletion of THOC5/Fms interacting protein causes the down-regulation of its direct interacting partner, THOC1 which may contribute to altered THO complex function and cell death.
Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
Authors: Hansen Matthew , Everett Logan , Singh Larry , Hannenhalli Sridhar
Published: January 2010

Background

Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation.

Results

Here we present a novel mixture modeling approach where a TF-Gene pair is presumed to be significantly correlated (with unknown coefficient) in an (unknown) subset of expression samples. The parameters of the model are estimated using a Maximum Likelihood approach. The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction. We have validated our approach using synthetic data and on four biological cases in cow, yeast, and humans.

Conclusions

While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.
Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells
Authors: Bowen Nathan J , Walker L DeEtte , Matyunina Lilya V , Logani Sanjay , Totten Kimberly A , Benigno Benedict B , McDonald John F
Published: January 2010

Background

Accumulating evidence suggests that somatic stem cells undergo mutagenic transformation into cancer initiating cells. The serous subtype of ovarian adenocarcinoma in humans has been hypothesized to arise from at least two possible classes of progenitor cells: the ovarian surface epithelia (OSE) and/or an as yet undefined class of progenitor cells residing in the distal end of the fallopian tube.

Methods

Comparative gene expression profiling analyses were carried out on OSE removed from the surface of normal human ovaries and ovarian cancer epithelial cells (CEPI) isolated by laser capture micro-dissection (LCM) from human serous papillary ovarian adenocarcinomas. The results of the gene expression analyses were randomly confirmed in paraffin embedded tissues from ovarian adenocarcinoma of serous subtype and non-neoplastic ovarian tissues using immunohistochemistry. Differentially expressed genes were analyzed using gene ontology, molecular pathway, and gene set enrichment analysis algorithms.

Results

Consistent with multipotent capacity, genes in pathways previously associated with adult stem cell maintenance are highly expressed in ovarian surface epithelia and are not expressed or expressed at very low levels in serous ovarian adenocarcinoma. Among the over 2000 genes that are significantly differentially expressed, a number of pathways and novel pathway interactions are identified that may contribute to ovarian adenocarcinoma development.

Conclusions

Our results are consistent with the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as the origin of ovarian adenocarcinoma. While our findings do not rule out the possibility that ovarian cancers may also arise from other sources, they areinconsistentwith claims that ovarian surface epithelia cannot serve as the origin of ovarian cancer initiating cells.
Expression of semaphorin 3A and its receptors in the human intervertebral disc: potential role in regulating neural ingrowth in the degenerate intervertebral disc
Authors: Tolofari Sotonye K , Richardson Stephen M , Freemont Anthony J , Hoyland Judith A
Published: January 2010

Introduction

Intervertebral disc (IVD) degeneration is considered a major underlying factor in the pathogenesis of chronic low back pain. Although the healthy IVD is both avascular and aneural, during degeneration there is ingrowth of nociceptive nerve fibres and blood vessels into proximal regions of the IVD, which may contribute to the pain. The mechanisms underlying neural ingrowth are, however, not fully understood. Semaphorin 3A (sema3A) is an axonal guidance molecule with the ability to repel nerves seeking their synaptic target. This study aimed to identify whether members of the Class 3 semaphorins were expressed by chondrocyte-like cells of the IVD addressing the hypothesis that they may play a role in repelling axons surrounding the healthy disc, thus maintaining its aneural condition.

Methods

Human IVD samples were investigated using reverse transcription polymerase chain reaction (RT-PCR) to identify gene expression of sema3A, 3F and their receptors: neuropilins (1 and 2) and plexins (A1-4). Sema3A protein was also localised within sections of normal and degenerate human IVD and immunopositivity quantified. Serial sections were stained using PGP9.5 and CD31 to correlate semaphorin 3A expression with nerve and blood vessel ingrowth, respectively.

Results

Sema3A protein was expressed highly in the healthy disc, primarily localised to the outer annulus fibrosus. In degenerate samples, sema3A expression decreased significantly in this region, although cell clusters within the degenerate nucleus pulposus exhibited strong immunopositivity. mRNA for sema3A receptors was also identified in healthy and degenerate tissues. CD31 and PGP9.5 were expressed most highly in degenerate tissues correlating with low expression of sema3A.

Conclusions

This study is the first to establish the expression of semaphorins and their receptors in the human IVD with a decrease seen in the degenerate painful IVD. Sema3A may therefore, amongst other roles, act as a barrier to neuronal ingrowth within the healthy disc.
Intensivists' base specialty of training is associated with variations in mortality and practice patterns
Authors: Billington Emma O , Zygun David A , Stelfox H Tom , Peets Adam D
Published: January 2010

Introduction

Current evidence regarding whether the staffing of intensive care units (ICUs) with a trained Intensivist benefits patient outcomes is discordant. We sought to determine whether, among certified Intensivists, base specialty of training could contribute to variation in practice patterns and patient outcomes in ICUs.

Methods

The records of all patients who were admitted to one of three closed multi-system ICUs within tertiary care centers in the Calgary Health Region, Alberta, Canada, during a five year period were retrospectively reviewed. Outcomes for patients admitted by Intensivists with base training in General Internal Medicine, Pulmonary Medicine, or other eligible base specialties (Anesthesia, General Surgery, and Emergency Medicine combined) were compared.

Results

ICU mortality in the entire cohort (n = 9,808) was 17.2% and in-hospital mortality was 32.0%. After controlling for potential confounders, ICU mortality (odds ratio (OR): 0.69; 95% confidence interval (CI): 0.52 to 0.94) was significantly lower for patients admitted by Intensivists with Pulmonary Medicine as a base specialty of training, but not ICU length of stay (LOS) (coefficient: 0.11; -0.20 to 0.42) or hospital mortality (OR: 0.88; 0.68 to 1.13). There was no difference in ICU or hospital mortality or length of stay between the three base specialty groups for patients who were admitted and managed by a single Intensivist for their entire ICU admission (n = 4,612). However, we identified significant variation in practice patterns between the three specialty groups for the number of invasive procedures performed and decisions to limit life-sustaining therapies.

Conclusions

Intensivists' base specialty of training is associated with practice pattern variations. This may contribute to differences in processes and outcomes of patient care.
Olive Tree community treatment centre for individuals with personality disorder: naturalistic service evaluation
Authors: Pretorius Johannes L. , Albeniz Alberto , Broome Matthew
Published: January 2010

Aims and method

Community treatment for individuals with personality disorder is a fast developing field. We report here on the effectiveness of one such approach. We examine the referral pathway of all clients between January 2005 and April 2008, including the mean days spent in our unit, the days spent in a psychiatric hospital before and after admission to our unit, and the results of changes in the rating scales we routinely use.

Results

Drop-out rates and the mean duration of therapy were acceptable. There has been a clear reduction of in-patient bed use and a small but significant improvement of most psychometric test results.

Clinical implications

This study provides further evidence for the effectiveness of community treatment for individuals with personality disorder.
Current role of service increment for teaching funding in psychiatry
Authors: Dave Subodh , Dogra Nisha , Leask Stuart J.
Published: January 2010

Universities are the main provider of medical student education in the UK; however, its delivery, especially the clinical years but increasingly also the pre-clinical years, often takes place in National Health Service hospitals. Trusts are paid for this privilege through service increment for teaching (SIFT). Developments in clinical governance structures have meant that there is now increased scrutiny and transparency in the funding of clinical services. Lack of similarly robust educational governance structures has led to the risk of educational funds being used to deliver clinical services. This paper examines the current role of SIFT funding and the possible ways forward, using a case study.
Hypoxia-Inducible Factor-1 α Expression Predicts Superior Survival in Patients With Diffuse Large B-Cell Lymphoma Treated With R-CHOP
Authors: Evens Andrew M. , Sehn Laurie H. , Farinha Pedro , Nelson Beverly P. , Raji Adekunle , Lu Yi , Brakman Adam , Parimi Vamsi , Winter Jane N. , Schumacker Paul T. , Gascoyne Randy D. , Gordon Leo I.
Published: January 2010

Purpose

Hypoxia-inducible factor (HIF) controls the expression of genes in response to hypoxia, as well as a wide range of other cellular processes. We previously showed constitutive stabilization of HIF-1α in the majority of patients with diffuse large B-cell lymphoma (DLBCL). To our knowledge, the prognostic significance of HIF in lymphoma has never been investigated.

Patients and Methods

We studied the immunohistochemical protein expression of HIF-1α on tissue microarrays from 153 patients with DLBCL treated in sequential cohorts with cyclophosphamide, doxorubicin, oncovin, and prednisone (CHOP) or rituximab-CHOP (R-CHOP) from 1999 to 2002. Results were correlated with patient outcome.

Results

Median follow-up for all patients was 80 months. Among all patients, HIF-1α was expressed in 62% of germinal center and 59% of non–germinal center patients. With HIF-1α analyzed as a dependent variable, there were no survival differences in CHOP-treated patients. In the R-CHOP group, however, HIF-1α protein expression correlated with significantly improved progression-free survival (PFS) and overall survival (OS). Five-year PFS for HIF-1α–positive patients was 71% v 43% for HIF-1α–negative patients (P = .0187), whereas 5-year OS was 75% and 54%, respectively (P = .025). In multivariate analysis with International Prognostic Index criteria, HIF-1α remained a significant predictor for PFS (P = .026) and OS (P = .043). Compared with other biomarkers, HIF-1α correlated only with BCL6 (P = .004). In terms of gene expression, we found several common gene associations of HIF-1α and the stromal-1 signature with genes predominantly involved in regulation of the extracellular matrix (eg, BGN, COL1A2, COL5A1, and PLOD2).

Conclusion

The expression of HIF-1α protein is an important independent favorable prognostic factor for survival in patients with DLBCL treated with R-CHOP.
Understanding large multiprotein complexes: applying a multiple allosteric networks model to explain the function of the Mediator transcription complex
Authors: Lewis Brian A.
Published: January 2010

The regulation of transcription and of many other cellular processes involves large multi-subunit protein complexes. In the context of transcription, it is known that these complexes serve as regulatory platforms that connect activator DNA-binding proteins to a target promoter. However, there is still a lack of understanding regarding the function of these complexes. Why do multi-subunit complexes exist? What is the molecular basis of the function of their constituent subunits, and how are these subunits organized within a complex? What is the reason for physical connections between certain subunits and not others? In this article, I address these issues through a model of network allostery and its application to the eukaryotic RNA polymerase II Mediator transcription complex. The multiple allosteric networks model (MANM) suggests that protein complexes such as Mediator exist not only as physical but also as functional networks of interconnected proteins through which information is transferred from subunit to subunit by the propagation of an allosteric state known as conformational spread. Additionally, there are multiple distinct sub-networks within the Mediator complex that can be defined by their connections to different subunits; these sub-networks have discrete functions that are activated when specific subunits interact with other activator proteins.
CDC6 interaction with ATR regulates activation of a replication checkpoint in higher eukaryotic cells
Authors: Yoshida Kazumasa , Sugimoto Nozomi , Iwahori Satoko , Yugawa Takashi , Narisawa-Saito Mako , Kiyono Tohru , Fujita Masatoshi
Published: January 2010

CDC6, a replication licensing protein, is partially exported to the cytoplasm in human cells through phosphorylation by Cdk during S phase, but a significant proportion remains in the nucleus. We report here that human CDC6 physically interacts with ATR, a crucial checkpoint kinase, in a manner that is stimulated by phosphorylation by Cdk. CDC6 silencing by siRNAs affected ATR-dependent inhibition of mitotic entry elicited by modest replication stress. Whereas a Cdk-phosphorylation-mimicking CDC6 mutant could rescue the checkpoint defect by CDC6 silencing, a phosphorylation-deficient mutant could not. Furthermore, we found that the CDC6-ATR interaction is conserved in Xenopus. We show that the presence of Xenopus CDC6 during S phase is essential for Xenopus ATR to bind to chromatin in response to replication inhibition. In addition, when human CDC6 amino acid fragment 180-220, which can bind to both human and Xenopus ATR, was added to Xenopus egg extracts after assembly of the pre-replication complex, Xenopus Chk1 phosphorylation was significantly reduced without lowering replication, probably through a sequestration of CDC6-mediated ATR-chromatin interaction. Thus, CDC6 might regulate replication-checkpoint activation through the interaction with ATR in higher eukaryotic cells.
Thermodynamic characterization of naturally occurring RNA tetraloops
Authors: Sheehy Justin P. , Davis Amber R. , Znosko Brent M.
Published: January 2010

Although tetraloops are one of the most frequently occurring secondary structure motifs in RNA, less than one-third of the 30 most frequently occurring RNA tetraloops have been thermodynamically characterized. Therefore, 24 stem–loop sequences containing common tetraloops were optically melted, and the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each stem–loop were determined. These new experimental values, on average, are 0.7 kcal/mol different from the values predicted for these tetraloops using the model proposed by Vecenie CJ, Morrow CV, Zyra A, Serra MJ. 2006. Biochemistry 45: 1400–1407. The data for the 24 tetraloops reported here were then combined with the data for 28 tetraloops that were published previously. A new model, independent of terminal mismatch data, was derived to predict the free energy contribution of previously unmeasured tetraloops. The average absolute difference between the measured values and the values predicted using this proposed model is 0.4 kcal/mol. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA stem–loops containing tetraloops and, furthermore, should allow for improved prediction of secondary structure from sequence. It was also shown that tetraloops within the sequence 5′-GCCNNNNGGC-3′ are, on average, 0.6 kcal/mol more stable than the same tetraloop within the sequence 5′-GGCNNNNGCC-3′. More systemic studies are required to determine the full extent of non-nearest-neighbor effects on tetraloop stability.
Proteome analysis of castor bean seeds
Authors: Campos Francisco A. P. , Nogueira Fabio C. S. , Cardoso Kiara C. , Costa Gustavo C. L. , Del Bem Luiz E. V. , Domont Gilberto B. , Da Silva Marcio J. , Moreira Raquel C. , Soares Arlete A. , Jucá Tiago L.
Published: January 2010

Castor bean (Ricinus communis L.) seeds serve as raw material for the production of nonedible oil used in medicine and industry, whereas the presence of allergenic and toxic proteins in the residue left after oil extraction precludes the use of this protein-rich by-product in animal feeding. To better understand the enzymes involved in the biosynthesis and degradation of fatty acids and to identify proteins with toxic/anti-nutritional properties, extracts of developing and germinating seeds were prepared and prefractionated according to solubility properties of the proteins. An enriched plastid organelle fraction embracing mostly plastids and mitochondria was also prepared. Two-dimensional electrophoresis (2DE) reference maps of these fractions were obtained from which nearly 400 proteins were identified by matrix-assisted laser desorption ionization-time of flight-time of flight (MALDI-TOF-TOF) mass spectrometry after a search in a National Center for Biotechnology Information (NCBI) database and in an expressed sequence tag (EST) primary bank prepared from a cDNA library of developing seeds. These proteomics techniques resulted in the identification of several classes of seed reserve proteins such as 2S albumins, legumin-like and seed storage proteins, as well as other proteins of plastidial or mitochondrial functions and proteins involved in plant defense against biotic and abiotic stresses. It is expected that the collected data will facilitate the application of genetic techniques to improve the quality/profile of castor seed fatty acids, and pave the way for a rational approach to inactivate allergenic and toxic proteins, allowing the use of castor bean meal in animal feeding.
Enhanced production of podophyllotoxins by co-culture of transformed Linum album cells with plant growth-promoting fungi
Authors: Baldi Ashish , Farkya Sunita , Jain Abhishek , Gupta Nishant , Mehra Rahul , Datta Vatsala , Srivastava Ashok Kumar , Bisaria Virendra Swarup
Published: January 2010

To investigate the plant growth-promoting effect and stimulation of lignan biosynthesis, the effect of culture filtrates/live co-culture of two arbuscular mycorrhizae-like fungi, Piriformospora indica and Sebacina vermifera, on growth of Linum album cells and on production of podophyllotoxin (PT) and 6-methoxypodophyllotoxin (6-MPT) was studied. For elicitation studies, different volumes of culture filtrates (autoclaved and membrane-filtered) of P. indica/S. vermifera were added to suspension cultures of L. album. The culture filtrates of both the fungi exhibited a positive effect on product formation. For co-culture experiments, both fungi were individually co-cultivated at different concentrations with L. album in suspension cultures for different time periods. This resulted in significant enhancement of PT and 6-MPT content in the plant cells. The activity of phenylalanine ammonia lyase (PAL) was observed to be related to the lignan accumulation, indicating its role as the key enzyme of the phenylpropanoid pathway. The study resulted in total lignan (PT and 6-MPT) production of 745.6 mg/l with a very high PT productivity of 52.4 mg/(l.d).
Evaluation of errors in a clinical laboratory: a one-year experience
Authors: Goswami Binita , Singh Bhawna , Chawla Ranjna , Mallika Venkatesan
Published: January 2010

Background: Efficient laboratory service is the cornerstone of modern health care systems. Scientific innovations have contributed to substantial improvements in the field of laboratory science, but errors still prevail. These errors are classified as preanalytical, analytical and postanalytical, depending upon the time of presentation.

Methods: The data for 67,438 routine venous blood specimens were scrutinized, and errors were documented over the period of 1 year in the clinical biochemistry laboratory of Govind Ballabh Pant Hospital in Delhi, India.

Results: Preanalytical errors were most common, with a frequency of 77.1% followed by postanalytical 15% and analytical 7.9%, respectively.

Conclusions: Our study illustrates the importance of proper venipuncture procedures, analytical expertise and correct transcription of numerical data for precise and accurate reporting of results to clinicians. There is an urgent need for close inter-departmental cooperation to meet the goal of ensuring patient well being.

Clin Chem Lab Med 2010;48:63–6.
Constraints on clade ages from fossil outgroups
Authors: Hedman Matthew M.
Published: January 2010

This paper presents a method for constraining the age of a clade with the ages of the earliest fossil specimens in that clade's outgroups. Given a sufficiently deep, robust, well-resolved, and stratigraphically consistent cladogram, this method can yield useful age constraints even in the absence of specific information about the fossil preservation and recovery rates of individual taxa. The algorithm is applied to simulated data sets to demonstrate that this method can yield robust constraints of clade ages if there are sufficient fossil outgroups available and if there is a finite chance that additional outgroups may be discovered in the future. Finally, the technique is applied to actual fossil data to explore the origin of modern placental mammals. Using data from recently published cladograms, this method indicates that if all Mesozoic eutherians are regarded as outgroups of Placentalia, then the last common ancestor of modern placental mammals and their Cenozoic allies lived between 65 and 88–98 million years ago, depending on the assumed cladogram and the number of outgroups included in the analysis.
Phyllocarid crustaceans from the Silurian Eramosa Lagerstätte (Ontario, Canada): taxonomy and functional morphology
Authors: Collette Joseph H. , Rudkin David M.
Published: January 2010

Two species of well-preserved phyllocarid crustaceans,Ceratiocaris macrouran. sp. andCeratiocaris papilioSalter, occur in the Eramosa Formation Lagerstätte of Ontario, Canada, represented by several dozen articulated fossils preserving limbs and thoracic segmentation.Ceratiocaris macrouran. sp. is distinguished by possession of an exceptionally elongate telson in relation to its body length.Ceratiocaris papiliopreserves fine detail of the abdominal scale-like ornamentation, allowing reinterpretation and enhanced characterization of this key feature.Ceratiocaris papiliohas a wide paleogeographic distribution across Laurentia but is restricted to shallow marine depositional settings within the middle Silurian.
Ptiloncodus Harris, 1962; a Laurentian enigma
Authors: Ethington R. L. , Ross L. M.
Published: January 2010

Ptiloncodus Harris, 1962, a hook-shaped microfossil, is present in late Floian through Hirnantian [=late Ibexian through Gamachian] rocks in regions marginal to Laurentia. Specimens from the Great Basin provide additional information about this enigmatic microfossil. Two fused clusters of Ptiloncodus elements from western Utah do not duplicate clusters reported previously from coeval strata in central Nevada. EDS spectra confirm the long-standing assumption that these fossils are composed of calcium phosphate. SEM images show that short crystallites are aligned to provide fibrous surficial ultrastructure in the hooked part of these fossils, but more open arrangement is displayed at the top of the shank where paired lobate structures are attached. The join between the lobes and the shank is weak; these two parts of the fossil separate easily so that most specimens did not retain lobes. The shanks end in rounded terminations or in paired knobs that range from low protuberances to near hornlike features. The new data do not support any of several suggestions that compare Ptiloncodus to extant organisms, and uncertainty continues about its affinity and the function of its skeletal elements.
New crustacean microcoprolites of the Upper Triassic limestones of the Sambosan Accretionary Complex, Japan
Authors: Senowbari-Daryan Baba , Chablais Jerome , Martini Rossana
Published: January 2010

We report here the first crustacean microcoprolites from the Sambosan Accretionary Complex (AC) in Japan. Three species of crustacean (order Decapoda) microcoprolites - Payandea japanica n. sp., Favreina tosaensis n. sp., and a species belonging to the genus Parafavreina? sp. are described from the Late Carnian to Rhaetian shallow-water limestones of the Sambosan AC, which were originated on extinct and subsiding volcanoes forming a mid-oceanic atoll-type buildup in the Panthalassan Ocean. Coprolites, which occur within a lagoonal to back-reef facies, provide new insight into the micropaleontology and sedimentology of the Sambosan limestones. Their presence in this tropical shallow-water depositional setting heightens their status of sedimentary facies indicators of such environments. Furthermore the occurrence of these Tethyan coprolites genera in Japan improves our knowledge of the distribution of Triassic crustacean decapods across the Panthalassan Ocean.
Rediscovery of figured Paleogene echinoid specimens from Clark and Martin (1901)
Authors: Zachos Louis G. , Levin Daniel
Published: January 2010

Clark and Martin (1901), in their study of the Paleogene deposits of Maryland, figured drawings of a fragment of a spatangoid echinoid from the Lower Eocene Nanjemoy Formation and a broken echinoid spine from the Upper Paleocene Aquia Formation. Echinoids are an important element of Paleogene faunas in the eastern United States, but these are the only reported occurrences of this age from either Maryland or Virginia and are therefore significant to the understanding of the evolution and paleogeography of echinoids in this region. The figured specimens were attributed to collections at Johns Hopkins University, but without catalog numbers. During study of the paleobiology collections of the National Museum of Natural History (NMNH), Smithsonian Institution, two vials were discovered with small, handwritten labels referencing the figure numbers in Clark and Martin (1901). The contained specimens were recognized as those figured in the report. They have been cataloged in the NMNH collections as follows:
Sagenograptoides, a new name for the retiolitid graptolite Sagenograptus Lenz and Kozłowska-Dawidziuk, 2001
Authors: Lenz Alfred C. , Kozłowska Anna
Published: January 2010

In 2001, Lenz and Kozłowska-Dawidziuk assigned the name Sagenograptus (species name S. arctos) to a late Wenlock retiolitid graptolite from Arctic Canada. We thank Rimma Sobolevskaya for subsequently informing us that the name Sagenograptus (species S. gagarini) had, already in 1962, been applied by Obut and Sobolevskaya to a Tremadoc dendroid graptolite from Taimyr. The generic name for the Arctic Wenlock retiolitid is here changed to Sagenograptoides.