bluuebunny/crossref_metadata_2025 huggingface dataset:
The Serine/threonine kinase Stk33 exhibits autophosphorylation and phosphorylates the intermediate filament protein Vimentin
Authors: Brauksiepe Bastienne , Mujica Alejandro O , Herrmann Harald , Schmidt Erwin R
Published: September 2008

Background

Colocalization of Stk33 with vimentin by double immunofluorescence in certain cells indicated that vimentin might be a target for phosphorylation by the novel kinase Stk33. We therefore tested in vitro the ability of Stk33 to phosphorylate recombinant full length vimentin and amino-terminal truncated versions thereof. In order to prove that Stk33 and vimentin are also in vivo associated proteins co-immunoprecipitation experiments were carried out. For testing the enzymatic activity of immunoprecipitated Stk33 we incubated precipitated Stk33 with recombinant vimentin proteins. To investigate whether Stk33 binds directly to vimentin, an in vitro co-sedimentation assay was performed.

Results

The results of the kinase assays demonstrate that Stk33 is able to specifically phosphorylate the non-α-helical amino-terminal domain of vimentin in vitro. Furthermore, co-immunoprecipitation experiments employing cultured cell extracts indicate that Stk33 and vimentin are associated in vivo. Immunoprecipitated Stk33 has enzymatic activity as shown by successful phosphorylation of recombinant vimentin proteins. The results of the co-sedimentation assay suggest that vimentin binds directly to Stk33 and that no additional protein mediates the association.

Conclusion

We hypothesize that Stk33 is involved in the in vivo dynamics of the intermediate filament cytoskeleton by phosphorylating vimentin.
FERN – a Java framework for stochastic simulation and evaluation of reaction networks
Authors: Erhard Florian , Friedel Caroline C , Zimmer Ralf
Published: September 2008

Background

Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary.

Results

In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment.

Conclusion

FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alone program and within new systems biology applications. Finally, complex scenarios requiring intervention during the simulation progress can be modelled easily with FERN.
PredGPI: a GPI-anchor predictor
Authors: Pierleoni Andrea , Martelli Pier Luigi , Casadio Rita
Published: September 2008

Background

Several eukaryotic proteins associated to the extracellular leaflet of the plasma membrane carry a Glycosylphosphatidylinositol (GPI) anchor, which is linked to the C-terminal residue after a proteolytic cleavage occurring at the so called ω-site. Computational methods were developed to discriminate proteins that undergo this post-translational modification starting from their aminoacidic sequences. However more accurate methods are needed for a reliable annotation of whole proteomes.

Results

Here we present PredGPI, a prediction method that, by coupling a Hidden Markov Model (HMM) and a Support Vector Machine (SVM), is able to efficiently predict both the presence of the GPI-anchor and the position of the ω-site. PredGPI is trained on a non-redundant dataset of experimentally characterized GPI-anchored proteins whose annotation was carefully checked in the literature.

Conclusion

PredGPI outperforms all the other previously described methods and is able to correctly replicate the results of previously published high-throughput experiments. PredGPI reaches a lower rate of false positive predictions with respect to other available methods and it is therefore a costless, rapid and accurate method for screening whole proteomes.
HECTAR: A method to predict subcellular targeting in heterokonts
Authors: Gschloessl Bernhard , Guermeur Yann , Cock J Mark
Published: September 2008

Background

The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic heterokonts which possess a complex chloroplast, acquired as the result of a secondary endosymbiosis. This is because the bipartite target peptides that deliver proteins to these chloroplasts can be easily confused with the signal peptides of secreted proteins, causing currently available algorithms to make erroneous predictions. HECTAR, a subcellular targeting prediction method which takes into account the specific properties of heterokont proteins, has been developed to address this problem.

Results

HECTAR is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide. The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95. The method is based on a hierarchical architecture which implements the divide and conquer approach to identify the different possible target peptides one at a time. At each node of the hierarchy, the most relevant outputs of various existing subcellular prediction methods are combined by a Support Vector Machine.

Conclusion

The HECTAR method is able to predict the subcellular localisation of heterokont proteins with high accuracy. It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts. A variant of HECTAR, called HECTAR
SEC
, can be used to identify signal peptide and type II signal anchor sequences in proteins from any eukaryotic organism. Both HECTAR and HECTAR
SEC
are available as a web application at the following address: http://www.sb-roscoff.fr/hectar/.
Distinct roles of Shh and Fgf signaling in regulating cell proliferation during zebrafish pectoral fin development
Authors: Prykhozhij Sergey V , Neumann Carl J
Published: September 2008

Background

Cell proliferation in multicellular organisms must be coordinated with pattern formation. The major signaling pathways directing pattern formation in the vertebrate limb are well characterized, and we have therefore chosen this organ to examine the interaction between proliferation and patterning. Two important signals for limb development are members of the Hedgehog (Hh) and Fibroblast Growth Factor (Fgf) families of secreted signaling proteins. Sonic hedgehog (Shh) directs pattern formation along the anterior/posterior axis of the limb, whereas several Fgfs in combination direct pattern formation along the proximal/distal axis of the limb.

Results

We used the genetic and pharmacological amenability of the zebrafish model system to dissect the relative importance of Shh and Fgf signaling in regulating proliferation during development of the pectoral fin buds. In zebrafish mutants disrupting the shh gene, proliferation in the pectoral fin buds is initially normal, but later is strongly reduced. Correlating with this reduction, Fgf signaling is normal at early stages, but is later lost in shh mutants. Furthermore, pharmacological inhibition of Hh signaling for short periods has little effect on either Fgf signaling, or on expression of G1- and S-phase cell-cycle genes, whereas long periods of inhibition lead to the downregulation of both. In contrast, even short periods of pharmacological inhibition of Fgf signaling lead to strong disruption of proliferation in the fin buds, without affecting Shh signaling. To directly test the ability of Fgf signaling to regulate proliferation in the absence of Shh signaling, we implanted beads soaked with Fgf protein into shh mutant fin buds. We find that Fgf-soaked beads rescue proliferation in the pectoral find buds of shh mutants, indicating that Fgf signaling is sufficient to direct proliferation in zebrafish fin buds in the absence of Shh.

Conclusion

Previous studies have shown that both Shh and Fgf signaling are crucial for outgrowth of the vertebrate limb. The results presented here show that the role of Shh in this process is indirect, and is mediated by its effect on Fgf signaling. By contrast, the activity of the Fgf pathway affects proliferation directly and independently of its effect on Shh. These results show that Fgf signaling is of primary importance in directing outgrowth of the limb bud, and clarify the role of the Shh-Fgf feedback loop in regulating proliferation.
Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication
Authors: Tingaud-Sequeira Angèle , Chauvigné François , Fabra Mercedes , Lozano Juanjo , Raldúa Demetrio , Cerdà Joan
Published: September 2008

Background

Teleost radiation in the oceans required specific physiological adaptations in eggs and early embryos to survive in the hyper-osmotic seawater. Investigating the evolution of aquaporins (AQPs) in these vertebrates should help to elucidate how mechanisms for water homeostasis evolved. The marine teleost gilthead sea bream (Sparus aurata) has a mammalian aquaporin-1 (AQP1)-related channel, termed AQP1o, with a specialized physiological role in mediating egg hydration. However, teleosts have an additional AQP isoform structurally more similar to AQP1, though its relationship with AQP1o is unclear.

Results

By using phylogenetic and genomic analyses we show here that teleosts, unlike tetrapods, have two closely linked AQP1 paralogous genes, termed aqp1a and aqp1b (formerly AQP1o). In marine teleosts that produce hydrated eggs, aqp1b is highly expressed in the ovary, whereas in freshwater species that produce non-hydrated eggs, aqp1b has a completely different expression pattern or is not found in the genome. Both Aqp1a and Aqp1b are functional water-selective channels when expressed in Xenopus laevis oocytes. However, expression of chimeric and mutated proteins in oocytes revealed that the sea bream Aqp1b C-terminus, unlike that of Aqp1a, contains specific residues involved in the control of Aqp1b intracellular trafficking through phosphorylation-independent and -dependent mechanisms.

Conclusion

We propose that 1) Aqp1a and Aqp1b are encoded by distinct genes that probably originated specifically in the teleost lineage by duplication of a common ancestor soon after divergence from tetrapods, 2) Aqp1b possibly represents a neofunctionalized AQP adapted to oocytes of marine and catadromous teleosts, thereby contributing to a water reservoir in eggs and early embryos that increases their survival in the ocean, and 3) Aqp1b independently acquired regulatory domains in the cytoplasmatic C-terminal tail for the specific control of Aqp1b expression in the plasma membrane.
Identification of transcripts involved in meiosis and follicle formation during ovine ovary development
Authors: Baillet Adrienne , Mandon-Pépin Béatrice , Cabau Cédric , Poumerol Elodie , Pailhoux Eric , Cotinot Corinne
Published: September 2008

Background

The key steps in germ cell survival during ovarian development are the entry into meiosis of oogonies and the formation of primordial follicles, which then determine the reproductive lifespan of the ovary. In sheep, these steps occur during fetal life, between 55 and 80 days of gestation, respectively. The aim of this study was to identify differentially expressed ovarian genes during prophase I meiosis and early folliculogenesis in sheep.

Results

In order to elucidate the molecular events associated with early ovarian differentiation, we generated two ovary stage-specific subtracted cDNA libraries using SSH. Large-scale sequencing of these SSH libraries identified 6,080 ESTs representing 2,535 contigs. Clustering and assembly of these ESTs resulted in a total of 2,101 unique sequences depicted in 1,305 singleton (62.11%) and 796 contigs (37.9%) ESTs (clusters). BLASTX evaluation indicated that 99% of the ESTs were homologous to various known genes/proteins in a broad range of organisms, especially ovine, bovine and human species. The remaining 1% which exhibited any homology to known gene sequences was considered as novel. Detailed study of the expression patterns of some of these genes using RT-PCR revealed new promising candidates for ovary differentiation genes in sheep.

Conclusion

We showed that the SSH approach was relevant to determining new mammalian genes which might be involved in oogenesis and early follicle development, and enabled the discovery of new potential oocyte and granulosa cell markers for future studies. These genes may have significant implications regarding our understanding of ovarian function in molecular terms, and for the development of innovative strategies to both promote and control fertility.
Staphylococcus epidermidis: A differential trait of the fecal microbiota of breast-fed infants
Authors: Jiménez Esther , Delgado Susana , Maldonado Antonio , Arroyo Rebeca , Albújar Mar , García Natalia , Jariod Manel , Fernández Leonides , Gómez Adolfo , Rodríguez Juan M
Published: September 2008

Background

Breast milk is an important source of staphylococci and other bacterial groups to the infant gut. The objective of this work was to analyse the bacterial diversity in feces of breast-fed infants and to compare it with that of formula-fed ones. A total of 23 women and their respective infants (16 breast-fed and 7 formula-fed) participated in the study. The 16 women and their infants provided a sample of breast milk and feces, respectively, at days 7, 14, and 35. The samples were plated onto different culture media. Staphylococcal and enterococcal isolates were submitted to genetic profiling and to a characterization scheme, including detection of potential virulence traits and sensitivity to antibiotics.

Results

The feeding practice had a significant effect on bacterial counts. A total of 1,210 isolates (489 from milk, 531 from breast-fed and 190 from formula-fed infants) were identified.Staphylococcus epidermidiswas the predominant species in milk and feces of breast-fed infants while it was less prevalent in those of formula fed-infants.Enterococcus faecaliswas the second predominant bacterial species among the fecal samples provided by the breast-fed infants but it was also present in all the samples from the formula-fed ones. The biofilm-relatedicaDgene and themecAgene were only detected in a low number of theS. epidermidisstrains. Several enterococcal isolates were also characterized and none of them contained thecylAor thevanABDEGantibiotic-resistance genes. All were sensitive to vancomycin.

Conclusion

The presence ofS. epidermidisis a differential trait of the fecal microbiota of breast-fed infants. Globally, the staphyloccal isolates obtained from milk and feces of breast-fed infants contain a low number of virulence determinants and are sensitive to most of the antibiotics tested.
Overlapping functions of the starch synthases SSII and SSIII in amylopectin biosynthesis in Arabidopsis
Authors: Zhang Xiaoli , Szydlowski Nicolas , Delvallé David , D'Hulst Christophe , James Martha G , Myers Alan M
Published: September 2008

Background

The biochemical mechanisms that determine the molecular architecture of amylopectin are central in plant biology because they allow long-term storage of reduced carbon. Amylopectin structure imparts the ability to form semi-crystalline starch granules, which in turn provides its glucose storage function. The enzymatic steps of amylopectin biosynthesis resemble those of the soluble polymer glycogen, however, the reasons for amylopectin's architectural distinctions are not clearly understood. The multiplicity of starch biosynthetic enzymes conserved in plants likely is involved. For example, amylopectin chain elongation in plants involves five conserved classes of starch synthase (SS), whereas glycogen biosynthesis typically requires only one class of glycogen synthase.

Results

Null mutations were characterized inAtSS2, which codes for SSII, and mutant lines were compared to lines lacking SSIII and to anAtss2,Atss3double mutant. Loss of SSII did not affect growth rate or starch quantity, but caused increased amylose/amylopectin ratio, increased total amylose, and deficiency in amylopectin chains with degree of polymerization (DP) 12 to DP28. In contrast, loss of both SSII and SSIII caused slower plant growth and dramatically reduced starch content. Extreme deficiency in DP12 to DP28 chains occurred in the double mutant, far more severe than the summed changes in SSII- or SSIII-deficient plants lacking only one of the two enzymes.

Conclusion

SSII and SSIII have partially redundant functions in determination of amylopectin structure, and these roles cannot be substituted by any other conserved SS, specifically SSI, GBSSI, or SSIV. Even though SSIII is not required for the normal abundance of glucan chains of DP12 to DP18, the enzyme clearly is capable of functioning in production such chains. The role of SSIII in producing these chains cannot be detected simply by analysis of an individual mutation. Competition between different SSs for binding to substrate could in part explain the specific distribution of glucan chains within amylopectin.
A large waterborne outbreak of campylobacteriosis in Norway: The need to focus on distribution system safety
Authors: Jakopanec Irena , Borgen Katrine , Vold Line , Lund Helge , Forseth Tore , Hannula Raisa , Nygård Karin
Published: September 2008

Background

On 7 May 2007 the medical officer in Røros (population 5600) reported 15 patients with gastroenteritis. Three days later he estimated hundreds being ill. Untreated tap water from a groundwater source was suspected as the vehicle and chlorination was started 11 May. Campylobacter was isolated from patients' stool samples. We conducted an investigation to identify the source and describe the extent of the outbreak.

Methods

We undertook a retrospective cohort study among a random sample of customers of Røros and neighbouring Holtålen waterworks. Holtålen, which has a different water source, was used as a control city. We conducted telephone interviews to gather data on illness from all household members. One randomly selected household member was asked about detailed exposure history. The regional hospital laboratory tested patients' stools for enteropathogens. Campylobacter isolates were typed by AFLP for genetic similarity at the Norwegian Institute of Public Health. Local authorities conducted the environmental investigation.

Results

We identified 105 cases among 340 individuals from Røros and Holtålen (Attack Rate = 31%). Tap water consumption was the only exposure associated with illness. Among randomly selected household members from Røros, a dose-response relationship was observed in daily consumed glasses of tap water (χ2 for trend = 8.1, p = 0.004). Campylobacter with identical AFLP was isolated from 25 out of 26 submitted stool samples. No pathogens were detected in water samples. We identified several events that might have caused pressure fall and influx of contaminated water into the water distribution system. On two occasions, pressure fall was noticed and parts of the distribution system were outdated.

Conclusion

The investigation confirmed a waterborne outbreak of campylobacteriosis in Røros. Although no single event was identified as the cause of contamination, this outbreak illustrates the vulnerability of water distribution systems. Good quality source water alone is not enough to ensure water safety. For a better risk management, more focus should be put on the distribution system security. Waterworks personnel should monitor the pressure regularly; reduce the leakage by upgrading the distribution network and use chlorination when conducting maintenance work.
A haplotype variation affecting the mitochondrial transportation of hMYH protein could be a risk factor for colorectal cancer in Chinese
Authors: Chen Huimei , Xu Lizhi , Qi Qiufeng , Yao Yanweng , Zhu Ming , Wang Yaping
Published: September 2008

Background

The human MutY homolog (hMYH), a DNA glycolsylase involved in the excision repair of oxidative DNA damage, is currently studied in colorectal cancer (CRC). We previously demonstrated a haplotype variant c.53C>T/c.74G>A of hMYH (T/A) increasing the risk for gastric cancer in Chinese. However, most investigations on correlation between hMYH and CRC are conducted in Western countries and the underlying mechanism has been poorly understood.

Methods

To determine whether the haplotype T/A variant of hMYH was related to colorectal carcinogenesis, we performed a case-control study in 138 colorectal cancer (CRC) patients and 343 healthy controls in a Chinese population. Furthermore, the C/G for wild-type, C/A or T/G for single base variant and T/A for haplotype variant hMYH cDNAs with a flag epitope tag were cloned into pcDNA3.1+ vector and transfected into cos-7 cell line. Their subcellular localizations were determined by immunofluorescence assay.

Results

It was found that the frequency of haplotype variant allele was statistically higher in CRC patients than that in controls (P = 0.02, odds ratio = 5.06, 95% confidence interval = 1.26 – 20.4). Similarly, significant difference of heterozygote frequency was indicated between the two groups (P = 0.019), while no homozygote was found. In addition, immunofluorescence analysis showed that hMYH protein with haplotype T/A variation presented in both nucleus and mitochondria, in contrast to the wild-type protein only converging in mitochondria. However, neither of the single missense mutations alone changed the protein subcelluar localization.

Conclusion

Although preliminarily, these results suggest that: the haplotype variant allele of hMYH leads to a missense protein, which partly affects the protein mitochondrial transportation and results as nuclear localization. This observation might be responsible for the increased susceptibility to cancers, including CRC, in Chinese.
Longitudinal population-based studies of affective disorders: Where to from here?
Authors: Beard John R , Galea Sandro , Vlahov David
Published: September 2008

Background

Longitudinal, population-based, research is important if we are to better characterize the lifetime patterns and determinants of affective disorders. While studies of this type are becoming increasingly prevalent, there has been little discussion about the limitations of the methods commonly used.

Methods

Discussion paper including a brief review of key prospective population-based studies as the basis for a critical appraisal of current approaches.

Results

We identified a number of common methodological weaknesses that restrict the potential of longitudinal research to characterize the diversity, prognosis, and determinants of affective disorders over time. Most studies using comprehensive diagnostic instruments have either been of relatively brief duration, or have suffered from long periods between waves. Most etiologic research has focused on first onset diagnoses, although these may be relatively uncommon after early adulthood and the burden of mental disorders falls more heavily on individuals with recurring disorders. Analysis has tended to be based on changes in diagnostic status rather than anges in symptom levels, limiting study power. Diagnoses have generally been treated as homogeneous entities and few studies have explored whether diagnostic subtypes such as atypical depression vary in their etiology or prognosis. Little research has considered whether there are distinct trajectories of symptoms over time and most has focused on individual disorders such as depression, rather than considering the relationship over time between symptoms of different affective disorders. There has also been limited longitudinal research on factors in the physical or social environment that may influence the onset, recurrence or chronicity of symptoms.

Conclusion

Many important, and in some respects quite basic, questions remain about the trajectory of depression and anxiety disorders over the life course and the factors that influence their incidence, recurrence and prognosis. Innovative approaches that consider symptoms of all affective disorders, and how these change over time, has the potential to greatly increase our understanding of the heterogeneity of these important conditions and of the individual and environmental characteristics that influence their life course.

Using longitudinal research to define sub classes of affective disorders may also be of great benefit for studies seeking to define the genetic determinants of susceptibility to these conditions.
Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias
Authors: van der Walt Eric , Martin Darren P , Varsani Arvind , Polston Jane E , Rybicki Edward P
Published: September 2008

Background

Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered.

Results

We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year.

Conclusion

These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules.
Tetany caused by chronic diarrhea in a child with celiac disease: A case report
Authors: Hurtado-Valenzuela Jaime Gabriel , Sotelo-Cruz Norberto , López-Cervantes Guillermo , de la Barca Ana María Calderón
Published: September 2008

There is no awareness about celiac disease (CD) in Mexico. A 2.9 year old mestizo boy was admitted to a Mexican hospital with muscle cramps and fine tremors. He suffered chronic diarrhea, abdominal distention, hypotrophic limbs, stunting and wasting, and presented hypocalcemia, anemia and high titers of serological markers. Diagnosis of CD was confirmed by a duodenal biopsy. After replacement of calcium and a gluten-free diet, the symptoms resolved within 6 weeks. After 2-months, serum analyses, anthropometric data as well as antibodies titers were normal after 4 years. CD screening tests are needed in chronic diarrhea for any ethnicity patients.
Cessation of deliberate self harm following eye movement desensitisation and reprocessing: A case report
Authors: McLaughlin Derek F , McGowan Iain W , Paterson Michael C , Miller Paul W
Published: September 2008

We present a case report of an eighteen year old female patient presenting with a psychological trauma related complaint. Part of the manifestation of the complaint included acts of self cutting over a number of years. Following two sessions of Eye Movement Desensitization & Reprocessing with one of the authors (DM) her self cutting ceased. This is maintained at thirteen months follow up. We conclude that Eye Movement Desensitization & Reprocessing may be an effective treatment option in reducing repeat self harm where traumatic events are noted to be the precursor to deliberate self harm.
Myeloid dendritic cells display downregulation of C-type lectin receptors and aberrant lectin uptake in systemic lupus erythematosus
Authors: Monrad Seetha U , Rea Kristine , Thacker Seth , Kaplan Mariana J
Published: September 2008

Introduction

There is a growing body of evidence implicating aberrant dendritic cell function as a crucial component in the immunopathogenesis of systemic lupus erythematosus. The purpose of the present study was to characterize the phagocytic capacity and expression of receptors involved in pathogen recognition and self-nonself discrimination on myeloid dendritic cells from patients with lupus.

Methods

Unstimulated or stimulated monocyte-derived dendritic cells were obtained from lupus patients and healthy control individuals, and expression of C-type lectin receptors (mannose receptor and dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin), complement-receptor 3 and Fcγ receptors was determined by flow cytometry. Dextran uptake by lupus and control dendritic cells was also assessed by flow cytometry. Serum IFNγ was quantified by ELISA, and uptake of microbial products was measured using fluorescently labeled zymosan.

Results

When compared with dendritic cells from healthy control individuals, unstimulated and stimulated lupus dendritic cells displayed significantly decreased dextran uptake and mannose receptor and dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin expression. Decreased expression of the mannose receptor was associated with high serum IFNγ levels, but not with maturation status or medications. Diminished dextran uptake and mannose receptor expression correlated with lupus disease activity. There were no differences between control and lupus dendritic cells in the expression of other pattern recognition receptors or in the capacity to uptake zymosan particles

Conclusions

Lupus dendritic cells have diminished endocytic capacity, which correlates with decreased mannose receptor expression. While this phenomenon appears primarily intrinsic to dendritic cells, modulation by serum factors such as IFNγ could play a role. These abnormalities may be relevant to the aberrant immune homeostasis and the increased susceptibility to infections described in lupus.
Exon creation and establishment in human genes
Authors: Corvelo André , Eyras Eduardo
Published: September 2008

Background

A large proportion of species-specific exons are alternatively spliced. In primates, Alu elements play a crucial role in the process of exon creation but many new exons have appeared through other mechanisms. Despite many recent studies, it is still unclear which are the splicing regulatory requirements for de novo exonization and how splicing regulation changes throughout an exon's lifespan.

Results

Using comparative genomics, we have defined sets of exons with different evolutionary ages. Younger exons have weaker splice-sites and lower absolute values for the relative abundance of putative splicing regulators between exonic and adjacent intronic regions, indicating a less consolidated splicing regulation. This relative abundance is shown to increase with exon age, leading to higher exon inclusion. We show that this local difference in the density of regulators might be of biological significance, as it outperforms other measures in real exon versus pseudo-exon classification. We apply this new measure to the specific case of the exonization of anti-sense Alu elements and show that they are characterized by a general lack of exonic splicing silencers.

Conclusions

Our results suggest that specific sequence environments are required for exonization and that these can change with time. We propose a model of exon creation and establishment in human genes, in which splicing decisions depend on the relative local abundance of regulatory motifs. Using this model, we provide further explanation as to why Alu elements serve as a major substrate for exon creation in primates. Finally, we discuss the benefits of integrating such information in gene prediction.
Dramatic caspase-dependent apoptosis in antibody-enhanced dengue virus infection of human mast cells
Authors: Brown Michael G , Huang Yan Y , Marshall Jean S , King Christine A , Hoskin David W , Anderson Robert
Published: September 2008

Severe forms of dengue virus disease, known as dengue hemorrhagic fever and dengue shock syndrome, result from an aberrant immune response involving antibody-dependent enhancement of infection, thrombocytopenia, and a loss of vascular integrity, culminating in hemorrhage, shock, and in some cases, death. Several studies have indicated that dengue virus infection results in the induction of apoptosis of certain cells believed to be contributory players in dengue pathogenesis. However, none have specifically examined the role of antibody enhancement in the context of induction of apoptosis. Here, we show that antibody-enhanced dengue virus infection of the FcR-bearing mast cell/basophil KU812 cell line results in a massive induction of apoptosis. Confocal microscopy and flow cytometry indicate two distinct subpopulations consisting of productively infected cells and apoptotic-uninfected bystanders. Apoptosis was found to be caspase-dependent, involving global caspase activation and cleavage of poly-ADP-ribose polymerase (PARP) and D4-guanosine diphosphate dissociation inhibitor (D4-GDI). Additional FcR-bearing cells, including K562, U937, and human mast cell 1 (HMC-1), were analyzed for apoptosis induction following infection. Although all cells displayed high susceptibility to antibody-enhanced dengue virus infection, only cells of a mast cell phenotype (KU812 and HMC-1) were found to undergo apoptosis. Dengue-induced apoptosis of KU812 cells was shown to require antibody-enhanced dengue virus infection by blockade of FcγRII. Transfection of KU812 cells with L-SIGN/DC-SIGNR was able to overcome the requirement for antibody enhancement with regard to dengue virus infection and apoptosis.
Lithium and hematology: established and proposed uses
Authors: Focosi Daniele , Azzarà Antonio , Kast Richard Eric , Carulli Giovanni , Petrini Mario
Published: September 2008

Lithium (as lithium carbonate) is an unexpensive drug, widely used in psychiatry for over 50 years in treatment of mood instability (bipolar disorder) and as an adjunct to antidepressants. Hematological effects of neutrophilia and increased circulating CD34+ cells of marrow origin have long been known. Lithium was at the center of hematological investigations in the 1980s, but no definitive use in hematology has yet emerged. We review evidence that lithium increases G-CSF and augments G-CSF effects. We suggest possible therapeutic uses of lithium in neutropenia. In bone marrow transplantation, preharvest lithium-assisted hematopoietic stem cell mobilization may be useful as well.
Quality-of-Life Outcomes for Adjuvant Chemotherapy in Early-Stage Non–Small-Cell Lung Cancer: Results From a Randomized Trial, JBR.10
Authors: Bezjak Andrea , Lee Christopher W. , Ding Keyue , Brundage Michael , Winton Timothy , Graham Barbara , Whitehead Marlo , Johnson David H. , Livingston Robert B. , Seymour Lesley , Shepherd Frances A.
Published: September 2008

Purpose

Adjuvant chemotherapy for early stage non–small-cell lung cancer (NSCLC) is now the standard of care, but there is little information regarding its impact on quality of life (QOL). We report the QOL results of JBR.10, a North American, intergroup, randomized trial of adjuvant cisplatin and vinorelbine compared with observation in patients who have completely resected, stages IB to II NSCLC.

Patients and Methods

QOL was assessed with the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire C30 and a trial-specific checklist at baseline and at weeks 5 and 9 for those who received chemotherapy and at follow-up months 3, 6, 9, 12, 18, 24, 30 and 36. A 10-point change in QOL scores from baseline was considered clinically significant.

Results

Four hundred eighty-two patients were randomly assigned on JBR.10. A total of 173 patients (82% of the expected) in the observation arm and 186 (85% of expected) in the chemotherapy arm completed baseline QOL assessments. The two groups were comparable, with low global QOL scores and significant symptom burden, especially pain and fatigue, after thoracotomy. Changes in QOL during chemotherapy were relatively modest; fatigue, nausea, and vomiting worsened, but there was a reduction in pain and no change in global QOL. Patients in the observation arm showed considerable improvements in QOL by 3 months. QOL, except for symptoms of sensory neuropathy and hearing loss, in those treated with chemotherapy returned to baseline by 9 months.

Conclusion

The findings of this trial indicate that the negative effects of adjuvant chemotherapy on QOL appear to be temporary, and that improvements (with a return to baseline function) are likely in most patients.
Adjuvant Paclitaxel Plus Carboplatin Compared With Observation in Stage IB Non–Small-Cell Lung Cancer: CALGB 9633 With the Cancer and Leukemia Group B, Radiation Therapy Oncology Group, and North Central Cancer Treatment Group Study Groups
Authors: Strauss Gary M. , Herndon James E. , Maddaus Michael A. , Johnstone David W. , Johnson Elizabeth A. , Harpole David H. , Gillenwater Heidi H. , Watson Dorothy M. , Sugarbaker David J. , Schilsky Richard L. , Vokes Everett E. , Green Mark R.
Published: September 2008

Purpose

Adjuvant chemotherapy for resected non–small-cell lung cancer (NSCLC) is now accepted on the basis of several randomized clinical trials (RCTs) that demonstrated improved survival. Although there is strong evidence that adjuvant chemotherapy is effective in stages II and IIIA NSCLC, its utility in stage IB disease is unclear. This report provides a mature analysis of Cancer and Leukemia Group B (CALGB) 9633, the only RCT designed specifically for stage IB NSCLC.

Patients and Methods

Within 4 to 8 weeks of resection, patients were randomly assigned to adjuvant chemotherapy or observation. Eligible patients had pathologically confirmed T2N0 NSCLC and had undergone lobectomy or pneumonectomy. Chemotherapy consisted of paclitaxel 200 mg/m2 intravenously over 3 hours and carboplatin at an area under the curve dose of 6 mg/mL per minute intravenously over 45 to 60 minutes every 3 weeks for four cycles. The primary end point was overall survival.

Results

Three hundred-forty-four patients were randomly assigned. Median follow-up was 74 months. Groups were well-balanced with regard to demographics, histology, and extent of surgery. Grades 3 to 4 neutropenia were the predominant toxicity; there were no treatment-related deaths. Survival was not significantly different (hazard ratio [HR], 0.83; CI, 0.64 to 1.08; P = .12). However, exploratory analysis demonstrated a significant survival difference in favor of adjuvant chemotherapy for patients who had tumors ≥ 4 cm in diameter (HR, 0.69; CI, 0.48 to 0.99; P = .043).

Conclusion

Because a significant survival advantage was not observed across the entire cohort, adjuvant chemotherapy should not be considered standard care in stage IB NSCLC. Given the magnitude of observed survival differences, CALGB 9633 was underpowered to detect small but clinically meaningful improvements. A statistically significant survival advantage for patients who had tumors ≥ 4 cm supports consideration of adjuvant paclitaxel/carboplatin for stage IB patients who have large tumors.
Adoptive Cell Therapy for Patients With Metastatic Melanoma: Evaluation of Intensive Myeloablative Chemoradiation Preparative Regimens
Authors: Dudley Mark E. , Yang James C. , Sherry Richard , Hughes Marybeth S. , Royal Richard , Kammula Udai , Robbins Paul F. , Huang JianPing , Citrin Deborah E. , Leitman Susan F. , Wunderlich John , Restifo Nicholas P. , Thomasian Armen , Downey Stephanie G. , Smith Franz O. , Klapper Jacob , Morton Kathleen , Laurencot Carolyn , White Donald E. , Rosenberg Steven A.
Published: September 2008

Purpose

The two approved treatments for patients with metastatic melanoma, interleukin (IL)-2 and dacarbazine, mediate objective response rates of 12% to 15%. We previously reported that adoptive cell therapy (ACT) with autologous antitumor lymphocytes in lymphodepleted hosts mediated objective responses in 51% of 35 patients. Here, we update that study and evaluate the safety and efficacy of two increased-intensity myeloablative lymphodepleting regimens.

Patients and Methods

We performed two additional sequential trials of ACT with autologous tumor-infiltrating lymphocytes (TIL) in patients with metastatic melanoma. Increasing intensity of host preparative lymphodepletion consisting of cyclophosphamide and fludarabine with either 2 (25 patients) or 12 Gy (25 patients) of total-body irradiation (TBI) was administered before cell transfer. Objective response rates by Response Evaluation Criteria in Solid Tumors (RECIST) and survival were evaluated. Immunologic correlates of effective treatment were studied.

Results

Although nonmyeloablative chemotherapy alone showed an objective response rate of 49%, when 2 or 12 Gy of TBI was added, the response rates were 52% and 72% respectively. Responses were seen in all visceral sites including brain. There was one treatment-related death in the 93 patients. Host lymphodepletion was associated with increased serum levels of the lymphocyte homeostatic cytokines IL-7 and IL-15. Objective responses were correlated with the telomere length of the transferred cells.

Conclusion

Host lymphodepletion followed by autologous TIL transfer and IL-2 results in objective response rates of 50% to 70% in patients with metastatic melanoma refractory to standard therapies.
Randomized Trial of a Hypnosis Intervention for Treatment of Hot Flashes Among Breast Cancer Survivors
Authors: Elkins Gary , Marcus Joel , Stearns Vered , Perfect Michelle , Rajab M. Hasan , Ruud Christopher , Palamara Lynne , Keith Timothy
Published: September 2008

Purpose

Hot flashes are a significant problem for many breast cancer survivors. Hot flashes can cause discomfort, disrupted sleep, anxiety, and decreased quality of life. A well-tolerated and effective mind-body treatment for hot flashes would be of great value. On the basis of previous case studies, this study was developed to evaluate the effect of a hypnosis intervention for hot flashes.

Patients and Methods

Sixty female breast cancer survivors with hot flashes were randomly assigned to receive hypnosis intervention (five weekly sessions) or no treatment. Eligible patients had to have a history of primary breast cancer without evidence of detectable disease and 14 or more weekly hot flashes for at least 1 month. The major outcome measure was a bivariate construct that represented hot flash frequency and hot flash score, which was analyzed by a classic sums and differences comparison. Secondary outcome measures were self-reports of interference of hot flashes on daily activities.

Results

Fifty-one randomly assigned women completed the study. By the end of the treatment period, hot flash scores (frequency × average severity) decreased 68% from baseline to end point in the hypnosis arm (P < .001). Significant improvements in self-reported anxiety, depression, interference of hot flashes on daily activities, and sleep were observed for patients who received the hypnosis intervention (P < .005) in comparison to the no treatment control group.

Conclusion

Hypnosis appears to reduce perceived hot flashes in breast cancer survivors and may have additional benefits such as reduced anxiety and depression, and improved sleep.
Helper T-Cell Responses and Clinical Activity of a Melanoma Vaccine With Multiple Peptides From MAGE and Melanocytic Differentiation Antigens
Authors: Slingluff Craig L. , Petroni Gina R. , Olson Walter , Czarkowski Andrea , Grosh William W. , Smolkin Mark , Chianese-Bullock Kimberly A. , Neese Patrice Y. , Deacon Donna H. , Nail Carmel , Merrill Priscilla , Fink Robyn , Patterson James W. , Rehm Patrice K.
Published: September 2008

Purpose

A phase I/II trial was performed to evaluate the safety and immunogenicity of a novel melanoma vaccine comprising six melanoma-associated peptides defined as antigenic targets for melanoma-reactive helper T cells. Source proteins for these peptides include MAGE proteins, MART-1/MelanA, gp100, and tyrosinase.

Patients and Methods

Thirty-nine patients with stage IIIB to IV melanoma were vaccinated with this six-peptide mixture weekly at three dose levels, with a preceding phase I dose escalation and subsequent random assignment among the dose levels. Helper T-lymphocyte responses were assessed by in vitro proliferation assay and delayed-type hypersensitivity skin testing. Patients with measurable disease were evaluated for objective clinical response by Response Evaluation Criteria in Solid Tumors.

Results

Vaccination with the helper peptide vaccine was well tolerated. Proliferation assays revealed induction of T-cell responses to the melanoma helper peptides in 81% of patients. Among 17 patients with measurable disease, objective clinical responses were observed in two patients (12%), with response durations of 1 and 3.9+ years. Durable stable disease was observed in two additional patients for periods of 1.8 and 4.6+ years.

Conclusion

Results of this study support the safety and immunogenicity of a vaccine comprised of six melanoma helper peptides. There is also early evidence of clinical activity.