bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification of the variation in percentage identity for protein sequence alignments
Authors: Raghava GPS , Barton Geoffrey J
Published: September 2006

Background

Percentage Identity (PID) is frequently quoted in discussion of sequence alignments since it appears simple and easy to understand. However, although there are several different ways to calculate percentage identity and each may yield a different result for the same alignment, the method of calculation is rarely reported. Accordingly, quantification of the variation in PID caused by the different calculations would help in interpreting PID values in the literature. In this study, the variation in PID was quantified systematically on a reference set of 1028 alignments generated by comparison of the protein three-dimensional structures. Since the alignment algorithm may also affect the range of PID, this study also considered the effect of algorithm, and the combination of algorithm and PID method.

Results

The maximum variation in PID due to the calculation method was 11.5% while the effect of alignment algorithm on PID was up to 14.6% across three popular alignment methods. The combined effect of alignment algorithm and PID calculation gave a variation of up to 22% on the test data, with an average of 5.3% ± 2.8% for sequence pairs with < 30% identity. In order to see which PID method was most highly correlated with structural similarity, four different PID calculations were compared to similarity scores (Sc) from the comparison of the corresponding protein three-dimensional structures. The highest correlation coefficient for a PID calculation was 0.80. In contrast, the more sophisticated Z-score calculated by reference to randomized sequences gave a correlation coefficient of 0.84.

Conclusion

Although it is well known amongst expert sequence analysts that PID is a poor score for discriminating between protein sequences, the apparent simplicity of the percentage identity score encourages its widespread use in establishing cutoffs for structural similarity. This paper illustrates that not only is PID a poor measure of sequence similarity when compared to the Z-score, but that there is also a large uncertainty in reported PID values. Since better alternatives to PID exist to quantify sequence similarity, these should be quoted where possible in preference to PID. The findings presented here should prove helpful to those new to sequence analysis, and in warning those who seek to interpret the value of a PID reported in the literature.
EGF-induced activation of Akt results in mTOR-dependent p70S6 kinase phosphorylation and inhibition of HC11 cell lactogenic differentiation
Authors: Galbaugh Traci , Cerrito Maria Grazia , Jose Cynthia C , Cutler Mary Lou
Published: September 2006

Background

HC11 mouse mammary epithelial cells differentiate in response to lactogenic hormone resulting in expression of milk proteins including β-casein. Previous studies have shown that epidermal growth factor (EGF) blocks differentiation not only through activation of the Ras/Mek/Erk pathway but also implicated phosphatidylinositol-3-kinase (PI-3-kinase) signaling. The current study analyzes the mechanism of the PI-3-kinase pathway in an EGF-induced block of HC11 lactogenic differentiation.

Results

HC11 and HC11-luci cells, which contain luciferase gene under the control of a β-casein promotor, were treated with specific chemical inhibitors of signal transduction pathways or transiently infected/transfected with vectors encoding dominant negative-Akt (DN-Akt) or conditionally active-Akt (CA-Akt). The expression of CA-Akt inhibited lactogenic differentiation of HC11 cells, and the infection with DN-Akt adenovirus enhanced β-casein transcription and rescued β-casein promotor-regulated luciferase activity in the presence of EGF. Treatment of cells with Rapamycin, an inhibitor of mTOR, blocked the effects of EGF on β-casein promotor driven luciferase activity as effectively as PI-3-kinase inhibitors. While expression of CA-Akt caused a constitutive activation of p70S6 kinase (p70S6K) in HC11 cells, the inhibition of either PI-3-kinase or mTOR abolished the activation of p70S6K by EGF. The activation of p70S6K by insulin or EGF resulted in the phosphorylation of ribosomal protein S6 (RPS6), elongation initiation factor 4E (elF4E) and 4E binding protein1 (4E-BP1). But lower levels of PI-3-K and mTOR inhibitors were required to block insulin-induced phosphorylation of RPS6 than EGF-induced phosphorylation, and insulin-induced phosphorylation of elF4E and 4E-BP1 was not completely mTOR dependent suggesting some diversity of signaling for EGF and insulin. In HC11 cells undergoing lactogenic differentiation the phosphorylation of p70S6K completely diminished by 12 hours, and this was partly attributable to dexamethasone, a component of lactogenic hormone mix. However, p70S6K phosphorylation persisted in the presence of lactogenic hormone and EGF, but the activation could be blocked by a PI-3-kinase inhibitor.

Conclusion

PI-3-kinase signaling contributes to the EGF block of lactogenic differentiation via Akt and p70S6K. The EGF-induced activation of PI-3-kinase-Akt-mTOR regulates phosphorylation of molecules including ribosomal protein S6, eIF4E and 4E-BP1 that influence translational control in HC11 cells undergoing lactogenic differentiation.
How well do HapMap SNPs capture the untyped SNPs?
Authors: Tantoso Erwin , Yang Yuchen , Li Kuo-Bin
Published: September 2006

Background

The recent advancement in human genome sequencing and genotyping has revealed millions of single nucleotide polymorphisms (SNP) which determine the variation among human beings. One of the particular important projects is The International HapMap Project which provides the catalogue of human genetic variation for disease association studies. In this paper, we analyzed the genotype data in HapMap project by using National Institute of Environmental Health Sciences Environmental Genome Project (NIEHS EGP) SNPs. We first determine whether the HapMap data are transferable to the NIEHS data. Then, we study how well the HapMap SNPs capture the untyped SNPs in the region. Finally, we provide general guidelines for determining whether the SNPs chosen from HapMap may be able to capture most of the untyped SNPs.

Results

Our analysis shows that HapMap data are not robust enough to capture the untyped variants for most of the human genes. The performance of SNPs for European and Asian samples are marginal in capturing the untyped variants, i.e. approximately 55%. Expectedly, the SNPs from HapMap YRI panel can only capture approximately 30% of the variants. Although the overall performance is low, however, the SNPs for some genes perform very well and are able to capture most of the variants along the gene. This is observed in the European and Asian panel, but not in African panel. Through observation, we concluded that in order to have a well covered SNPs reference panel, the SNPs density and the association among reference SNPs are important to estimate the robustness of the chosen SNPs.

Conclusion

We have analyzed the coverage of HapMap SNPs using NIEHS EGP data. The results show that HapMap SNPs are transferable to the NIEHS SNPs. However, HapMap SNPs cannot capture some of the untyped SNPs and therefore resequencing may be needed to uncover more SNPs in the missing region.
Coding limits on the number of transcription factors
Authors: Itzkovitz Shalev , Tlusty Tsvi , Alon Uri
Published: September 2006

Background

Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms.

Results

We find that the number of transcription factors from most super-families appears to be bounded. For example, the number of winged helix factors does not generally exceed 300, even in very large genomes. The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family. Coding theory predicts that such upper bounds on the number of transcription factors should exist, in order to minimize cross-binding errors between transcription factors. This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal. We present evidence that transcription factors with similar binding sequences tend to regulate genes with similar biological functions, supporting this prediction.

Conclusion

The present study suggests limits on the transcription factor repertoire of cells, and suggests coding constraints that might apply more generally to the mapping between binding sites and biological function.
Human inflammatory bowel disease does not associate with Lawsonia intracellularis infection
Authors: Michalski Christoph W , Di Mola Fabio Francesco , Kümmel Klaus , Wendt Michael , Köninger Jörg S , Giese Thomas , Giese Nathalia A , Friess Helmut
Published: September 2006

Background

There is increasing evidence that bacterial infection of the intestinal mucosa may contribute to the pathogenesis of inflammatory bowel diseases (IBD). In pigs, an obligate intracellular bacterium, Lawsonia intracellularis (LI), was shown to cause proliferative enteropathy (PE) of which some forms display histological and clinical similarities to human IBD. Since LI-similar Desulfovibrio spp. may infect human cells, we hypothesized that LI might be associated with the development of human IBD.

Results

In human intestinal tissue samples, PCR using LLG, 50SL27, LSA and strictly LI-specific 16SII primers, yielded either no amplicons or products with weak homology to human genomic sequences. Sequencing of these amplicons revealed no specificity for LI. However, amplification of DNA with less specific 16SI primers resulted in products bearing homology to certain Streptococcus species. These 16SI-amplified products were present in healthy and diseased specimens, without obvious prevalence.

Conclusion

LI is not associated with the pathogenesis of UC or CD. Whether an immunologic response to commensal bacteria such as streptococci may contribute to the chronic inflammatory condition in IBD, remained to be determined.
The transcription factor ATF3 is upregulated during chondrocyte differentiation and represses cyclin D1 and A gene transcription
Authors: James Claudine G , Woods Anita , Underhill T Michael , Beier Frank
Published: September 2006

Background

Coordinated chondrocyte proliferation and differentiation are required for normal endochondral bone growth. Transcription factors binding to the cyclicAMP response element (CRE) are known to regulate these processes. One member of this family, Activating Tanscription Factor 3 (ATF3), is expressed during skeletogenesis and acts as a transcriptional repressor, but the function of this protein in chondrogenesis is unknown.

Results

Here we demonstrate thatAtf3mRNA levels increase during mouse chondrocyte differentiationin vitroandin vivo. In addition,Atf3mRNA levels are increased in response to cytochalasin D treatment, an inducer of chondrocyte maturation. This is accompanied by increasedAtf3promoter activity in cytochalasin D-treated chondrocytes. We had shown earlier that transcription of the cell cycle genes cyclin D1 and cyclin A in chondrocytes is dependent on CREs. Here we demonstrate that overexpression of ATF3 in primary mouse chondrocytes results in reduced transcription of both genes, as well as decreased activity of a CRE reporter plasmid. Repression of cyclin A transcription by ATF3 required the CRE in the cyclin A promoter. In parallel, ATF3 overexpression reduces the activity of a SOX9-dependent promoter and increases the activity of a RUNX2-dependent promoter.

Conclusion

Our data suggest that transcriptional induction of theAtf3gene in maturing chondrocytes results in down-regulation of cyclin D1 and cyclin A expression as well as activation of RUNX2-dependent transcription. Therefore, ATF3 induction appears to facilitate cell cycle exit and terminal differentiation of chondrocytes.
Use of the lambda Red recombinase system to produce recombinant prophages carrying antibiotic resistance genes
Authors: Serra-Moreno Ruth , Acosta Sandra , Hernalsteens Jean Pierre , Jofre Juan , Muniesa Maite
Published: September 2006

Background

The Red recombinase system of bacteriophage lambda has been used to inactivate chromosomal genes in E. coli K-12 through homologous recombination using linear PCR products. The aim of this study was to induce mutations in the genome of some temperate Shiga toxin encoding bacteriophages. When phage genes are in the prophage state, they behave like chromosomal genes. This enables marker genes, such as antibiotic resistance genes, to be incorporated into the stx gene. Once the phages' lytic cycle is activated, recombinant Shiga toxin converting phages are produced. These phages can transfer the marker genes to the bacteria that they infect and convert. As the Red system's effectiveness decreased when used for our purposes, we had to introduce significant variations to the original method. These modifications included: confirming the stability of the target stx gene increasing the number of cells to be transformed and using a three-step PCR method to produce the amplimer containing the antibiotic resistance gene.

Results

Seven phages carrying two different antibiotic resistance genes were derived from phages that are directly involved in the pathogenesis of Shiga toxin-producing strains, using this modified protocol.

Conclusion

This approach facilitates exploration of the transduction processes and is a valuable tool for studying phage-mediated horizontal gene transfer.
Kinetics of progenitor hemopoetic stem cells in sepsis: Correlation with patients survival?
Authors: Tsaganos Thomas , Giamarellos-Bourboulis Evangelos J , Kollias Spyridon , Zervakis Dimitrios , Karagianni Vassiliki , Pelekanou Aimilia , Tampaki Ekaterini-Christina , Kontogiorgi Marina , Koroneos Apostolos , Drakoulis Nikolaos , Armaganidis Apostolos , Roussos Charis , Giamarellou Helen
Published: September 2006

Background

Current theories underline the crucial role of pro-inflammatory mediators produced by monocytes for the pathogenesis of sepsis. Since monocytes derive from progenitor hemopoetic cells, the kinetics of stem cells was studied in peripheral blood of patients with sepsis.

Methods

Blood was sampled from 44 patients with septic syndrome due to ventilator-associated pneumonia on days 1, 3, 5 and 7 upon initiation of symptoms. Concentrations of tumour necrosis factor-alpha (TNFα), interleukin (IL)-6, IL-8 and G-CSF were estimated by ELISA. CD34/CD45 cells were determined after incubation with anti-CD45 FITC and anti-CD34 PE monocloncal antibodies and flow cytometric analysis. Samples from eight healthy volunteers served as controls.

Results

Median of CD34/CD45 absolute count of controls was 1.0/μl. Respective values of the total study population were 123.4, 112.4, 121.5 and 120.9/μl on days 1, 3, 5 and 7 (p < 0.0001 compared to controls). Positive correlations were found between the absolute CD34/CD45 count and the absolute monocyte count on days 1, 5 and 7. Survival was prolonged among patients with less than 310/μl CD34/CD45 cells on day 1 compared to those with more than 310/μl of CD34/CD45 cells (p: 0.022). Hazard ratio for death due to sepsis was 5.47 (p: 0.039) for CD34/CD45 cells more than 310/μl. Median IL-6 on day 1 was 56.78 and 233.85 pg/ml respectively for patients with less than 310/μl and more than 310/μl CD34/CD45 cells (p: 0.021).

Conclusion

Stem cells are increased in peripheral blood over all days of follow-up compared to healthy volunteers. Patients with counts on day 1 less than 310/μl are accompanied by increased survival compared to patients with more than 310/μl.
U.S. and Canadian pharmacists' attitudes, knowledge, and professional practice behaviors toward dietary supplements: a systematic review
Authors: Kwan Della , Hirschkorn Kristine , Boon Heather
Published: September 2006

Background

Although dietary supplements (DS) are widely sold in pharmacies, the legal, ethical, and practice responsibilities of pharmacists with respect to these products have not been well defined. This systematic review of pharmacists' attitudes, knowledge, and professional practice behaviours toward DS is intended to inform pharmacy regulators' and educators' decision making around this topic.

Methods

Eligible studies were identified through a systematic database search for all available years through to March 2006. Articles were analyzed for this review if they included survey data on U.S. or Canadian pharmacists' attitudes, knowledge, or professional practice behaviors toward DS published in 1990 or later.

Results

Due to the heterogeneity of the data, it was not possible to draw a conclusion with respect to pharmacists' general attitudes toward DS. Approximately equal numbers of pharmacists report positive as well as negative attitudes about the safety and efficacy of DS. There is strong agreement among pharmacists for the need to have additional training on DS, increased regulation of DS, and quality information on DS. In addition, survey data indicate that pharmacists do not perceive their knowledge of DS to be adequate and that pharmacists do not routinely document, monitor, or inquire about patients' use of DS. Despite this, a large proportion of pharmacists reported receiving questions about DS from patients and other health care practitioners.

Conclusion

Further research is needed to explore the factors that influence pharmacists' beliefs and attitudes about DS, to accurately evaluate pharmacists' knowledge of DS, and to uncover the reasons why pharmacists do not routinely document, monitor, or inquire about patients' use of DS.
Breaking down the Barriers: fMRI Applications in Pain, Analgesia and Analgesics
Authors: Borsook David , Becerra Lino R
Published: September 2006

This review summarizes functional magnetic resonance imaging (fMRI) findings that have informed our current understanding of pain, analgesia and related phenomena, and discusses the potential role of fMRI in improved therapeutic approaches to pain. It is divided into 3 main sections: (1) fMRI studies of acute and chronic pain. Physiological studies of pain have found numerous regions of the brain to be involved in the interpretation of the ‘pain experience’; studies in chronic pain conditions have identified a significant CNS component; and fMRI studies of surrogate models of chronic pain are also being used to further this understanding. (2) fMRI studies of endogenous pain processing including placebo, empathy, attention or cognitive modulation of pain. (3) The use of fMRI to evaluate the effects of analgesics on brain function in acute and chronic pain. fMRI has already provided novel insights into the neurobiology of pain. These insights should significantly advance therapeutic approaches to chronic pain.
Altered hippocampus synaptic function in selenoprotein P deficient mice
Authors: Peters Melinda M , Hill Kristina E , Burk Raymond F , Weeber Edwin J
Published: September 2006

Selenium is an essential micronutrient that function through selenoproteins. Selenium deficiency results in lower concentrations of selenium and selenoproteins. The brain maintains it's selenium better than other tissues under low-selenium conditions. Recently, the selenium-containing protein selenoprotein P (Sepp) has been identified as a possible transporter of selenium. The targeted disruption of the selenoprotein P gene (Sepp1) results in decreased brain selenium concentration and neurological dysfunction, unless selenium intake is excessive However, the effect of selenoprotein P deficiency on the processes of memory formation and synaptic plasticity is unknown. In the present studies Sepp1(-/-) mice and wild type littermate controls (Sepp1(+/+)) fed a high-selenium diet (1 mg Se/kg) were used to characterize activity, motor coordination, and anxiety as well as hippocampus-dependent learning and memory. Normal associative learning, but disrupted spatial learning was observed in Sepp1(-/-) mice. In addition, severe alterations were observed in synaptic transmission, short-term plasticity and long-term potentiation in hippocampus area CA1 synapses of Sepp1(-/-) mice on a 1 mg Se/kg diet and Sepp1(+/+) mice fed a selenium-deficient (0 mg Se/kg) diet. Taken together, these data suggest that selenoprotein P is required for normal synaptic function, either through presence of the protein or delivery of required selenium to the CNS.
Molecular and phylogenetic analysis of HIV-1 variants circulating among injecting drug users in Mashhad-Iran
Authors: Naderi HR , Tagliamonte M , Tornesello ML , Ciccozzi M , Rezza G , Farid R , Buonaguro FM , Buonaguro L
Published: September 2006

Genetic and phylogenetic information on the HIV-1 epidemic in Middle-East Countries, and in particular in Iran, are extremely limited. By March 2004, the Iranian Ministry of Health officially reported a cumulative number of 6'532 HIV positive individuals and 214 AIDS cases in the Iranian HIV-1 epidemic. The intra-venous drug users (IDUs) represent the group at highest risk for HIV-1 infection in Iran, accounting for almost 63% of all HIV-infected population. In this regards, a molecular phylogenetic study has been performed on a sentinel cohort of HIV-1 seropositive IDUs enrolled at the end of 2005 at the University of Mashhad, the largest city North East of Tehran. The study has been performed on both gag and env subgenomic regions amplified by Polymerase Chain Reaction (PCR) from peripheral blood mononuclear cells (PBMCs) and characterized by direct DNA sequence analysis. The results reported here show that the HIV-1 subtype A is circulating in this IDUs sentinel cohort. Moreover, the single phylogenetic cluster as well as the intra-group low nucleotide divergence is indicative of a recent outbreak. Unexpectedly, the Iranian samples appear to be phylogenetically derived from African Sub-Saharan subtype A viruses, raising stirring speculations on HIV-1 introduction into the IDUs epidemic in Mashhad. This sentinel study could represent the starting point for a wider molecular survey of the HIV-1 epidemics in Iran to evaluate in detail the distribution of genetic subtypes and possible natural drug-resistant variants, which are extremely helpful information to design diagnostic and therapeutic strategies.
Analog peptides of type II collagen can suppress arthritis in HLA-DR4 (DRB1*0401) transgenic mice
Authors: Sakurai Yoshihiko , Brand David D , Tang Bo , Rosloniec Edward F , Stuart John M , Kang Andrew H , Myers Linda K
Published: September 2006

Rheumatoid arthritis (RA) is an autoimmune disease associated with the recognition of self proteins secluded in diarthrodial joints. We have previously established that mice transgenic for the human DR genes associated with RA are susceptible to collagen-induced arthritis (CIA) and we have identified a determinant of type II collagen (CII263–270) that triggers T-cell immune responses in these mice. We have also determined that an analog of CII263–270 would suppress disease in DR1 transgenic mice. Because the immunodominant determinant is the same for both DR1 transgenic and DR4 transgenic mice, we attempted to determine whether the analog peptide that was suppressive in DR1 transgenic mice would also be effective in suppressing CIA in DR4 transgenic mice. We treated DR4 transgenic mice with two analog peptides of CII that contained substitutions in the core of the immunodominant determinant: CII256–276 (F263N, E266D) and CII256–270 (F263N, E266A). Mice were observed for CIA, and T-cell proliferative responses were determined. Either peptide administered at the time of immunization with CII significantly downregulated arthritis. Binding studies demonstrated that replacement of the phenylalanine residue in position 263 of the CII peptide with asparagine significantly decreased the affinity of the peptide for the DR4 molecule. In contrast, replacement of the glutamic acid residue in position 266 with aspartic acid or with alanine had differing results. Aspartic acid reduced the affinity (35-fold) whereas alanine did not. Both peptides were capable of suppressing CIA. With the use of either peptide, CII256–276 (F263N, E266D) or CII256–270 (F263N, E266A), the modulation of CIA was associated with an increase in T-cell secretion of IL-4 together with a decrease in IFN-γ. We have identified two analog peptides that are potent suppressors of CIA in DR4 transgenic mice. These experiments represent the first description of an analog peptide of CII recognized by T cells in the context of HLA-DR4 that can suppress autoimmune arthritis.
The hydrocarbon seep tubeworm Lamellibrachia luymesi primarily eliminates sulfate and hydrogen ions across its roots to conserve energy and ensure sulfide supply
Authors: Dattagupta Sharmishtha , Miles Lara L. , Barnabei Matthew S. , Fisher Charles R.
Published: September 2006

Lamellibrachia luymesi (Polychaeta, Siboglinidae) is a deep-sea vestimentiferan tubeworm that forms large bush-like aggregations at hydrocarbon seeps in the Gulf of Mexico. Like all vestimentiferans, L. luymesi obtains its nutrition from sulfide-oxidizing endosymbiotic bacteria, which it houses in an internal organ called the trophosome. This tubeworm has a lifespan of over 170 years and its survival is contingent upon the availability of sulfide during this long period. In sediments underlying L. luymesi aggregations, microbes produce sulfide by coupling sulfate reduction with hydrocarbon oxidation. L. luymesi acquires sulfide from the sediment using a root-like posterior extension of its body that is buried in the sediment. Its symbionts then oxidize the sulfide to produce energy for carbon fixation, and release sulfate and hydrogen ions as byproducts. It is critical for the tubeworm to eliminate these waste ions, and it could do so either across its vascular plume or across its root. In this study, we measured sulfate and proton elimination rates from live L. luymesi and found that they eliminated approximately 85% of the sulfate produced by sulfide oxidation, and approximately 67% of the protons produced by various metabolic processes, across their roots. On the basis of experiments using membrane transport inhibitors, we suggest that L. luymesi has anion exchangers that mediate sulfate elimination coupled with bicarbonate uptake. Roots could be the ideal exchange surface for eliminating sulfate and hydrogen ions for two reasons. First, these ions might be eliminated across the root epithelium using facilitated diffusion, which is energetically economical. Second, sulfate and hydrogen ions are substrates for bacterial sulfate reduction, and supplying these ions into the sediment might help ensure a sustained sulfide supply for L. luymesi over its entire lifespan.
Identification and developmental expression of mRNAs encoding crustacean cardioactive peptide (CCAP) in decapod crustaceans
Authors: Chung J. S. , Wilcockson D. C. , Zmora N. , Zohar Y. , Dircksen H. , Webster S. G.
Published: September 2006

Full-length cDNAs encoding crustacean cardioactive peptide (CCAP) were isolated from several decapod (brachyuran and astacuran) crustaceans: the blue crab Callinectes sapidus, green shore crab Carcinus maenas,European lobster Homarus gamarus and calico crayfish Orconectes immunis. The cDNAs encode open reading frames of 143 (brachyurans) and 139-140 (astacurans) amino acids. Apart from the predicted signal peptides(30-32 amino acids), the conceptually translated precursor codes for a single copy of CCAP and four other peptides that are extremely similar in terms of amino acid sequence within these species, but which clearly show divergence into brachyuran and astacuran groups. Expression patterns of CCAP mRNA and peptide were determined during embryonic development in Carcinususing quantitative RT-PCR and immunohistochemistry with whole-mount confocal microscopy, and showed that significant mRNA expression (at 50% embryonic development) preceded detectable levels of CCAP in the developing central nervous system (CNS; at 70% development). Subsequent CCAP gene expression dramatically increased during the late stages of embryogenesis (80-100%),coincident with developing immunopositive structures. In adult crabs, CCAP gene expression was detected exclusively in the eyestalk, brain and in particular the thoracic ganglia, in accord with the predominance of CCAP-containing cells in this tissue. Measurement of expression patterns of CCAP mRNA in Carcinus and Callinectes thoracic ganglia throughout the moult cycle revealed only modest changes, indicating that previously observed increases in CCAP peptide levels during premoult were not transcriptionally coupled. Severe hypoxic conditions resulted in rapid downregulation of CCAP transcription in the eyestalk, but not the thoracic ganglia in Callinectes, and thermal challenge did not change CCAP mRNA levels. These results offer the first tantalising glimpses of involvement of CCAP in environmental adaptation to extreme, yet biologically relevant stressors, and perhaps suggest that the CCAP-containing neurones in the eyestalk might be involved in adaptation to environmental stressors.
Receptor expression and sympatric speciation: unique olfactory receptor neuron responses in F1 hybrid Rhagoletis populations
Authors: Olsson Shannon B. , Linn Charles E. , Michel Andrew , Dambroski Hattie R. , Berlocher Stewart H. , Feder Jeffrey L. , Roelofs Wendell L.
Published: September 2006

The Rhagoletis pomonella species complex is one of the foremost examples supporting the occurrence of sympatric speciation. A recent study found that reciprocal F1 hybrid offspring from different host plant-infesting populations in the complex displayed significantly reduced olfactory host preference in flight-tunnel assays. Behavioral and electrophysiological studies indicate that olfactory cues from host fruit are important chemosensory signals for flies to locate fruit for mating and oviposition. The reduced olfactory abilities of hybrids could therefore constitute a significant post-mating barrier to gene flow among fly populations. The present study investigated the source of changes in the hybrid olfactory system by examining peripheral chemoreception in F1 hybrid flies, using behaviorally relevant volatiles from the parent host fruit. Single-sensillum electrophysiological analyses revealed significant changes in olfactory receptor neuron (ORN) response specificities in hybrid flies when compared to parent ORN responses. We report that flies from F1 crosses of apple-, hawthorn- and flowering dogwood-origin populations of R. pomonella exhibited distinct ORN response profiles absent from any parent population. These peripheral alterations in ORN response profiles could result from misexpression of multiple receptors in hybrid neurons as a function of genomic incompatibilities in receptor-gene pathways in parent populations. We conclude that these changes in peripheral chemoreception could impact olfactory host preference and contribute directly to reproductive isolation in the Rhagoletis complex, or could be genetically coupled to other host-associated traits.
Tests of absolute photorefractoriness in four species of cardueline finch that differ in reproductive schedule
Authors: MacDougall-Shackleton Scott A. , Katti Madhusudan , Hahn Thomas P.
Published: September 2006

Species with different reproductive schedules may differ in how they respond to the annual change in photoperiod (the adaptive specialization hypothesis). Seasonally breeding species are predicted to use photorefractoriness to terminate reproduction prior to inclement conditions in autumn and winter, whereas opportunistically breeding species may not exhibit photorefractoriness. We tested for absolute photorefractoriness in four species of cardueline finch that differ in their reproductive schedules:opportunistically breeding red crossbills, flexibly breeding pine siskins, and seasonally breeding Cassin's finches and gray-crowned rosy-finches. Field observations indicated that all four species regress their gonads and begin prebasic feather molt in late summer or autumn. However, exposure to a long day photoperiod in autumn (24 h:0 h L:D) resulted in elevation of gonadotropins and testicular recrudescence in all species except Cassin's finches. Thus, by this criterion, some of the seasonally breeding species tested here did not exhibit absolute photorefractoriness. These results indicate that phylogenetic history needs to be taken into account when considering the adaptive nature of photoperiod response systems.
Membrane lipid physiology and toxin catabolism underlie ethanol and acetic acid tolerance inDrosophila melanogaster
Authors: Montooth Kristi L. , Siebenthall Kyle T. , Clark Andrew G.
Published: September 2006

Drosophila melanogaster has evolved the ability to tolerate and utilize high levels of ethanol and acetic acid encountered in its rotting-fruit niche. Investigation of this phenomenon has focused on ethanol catabolism, particularly by the enzyme alcohol dehydrogenase. Here we report that survival under ethanol and acetic acid stress in D. melanogasterfrom high- and low-latitude populations is an integrated consequence of toxin catabolism and alteration of physical properties of cellular membranes by ethanol. Metabolic detoxification contributed to differences in ethanol tolerance between populations and acclimation temperatures viachanges in both alcohol dehydrogenase and acetyl-CoA synthetase mRNA expression and enzyme activity. Independent of changes in ethanol catabolism,rapid thermal shifts that change membrane fluidity had dramatic effects on ethanol tolerance. Cold temperature treatments upregulated phospholipid metabolism genes and enhanced acetic acid tolerance, consistent with the predicted effects of restoring membrane fluidity. Phospholipase D was expressed at high levels in all treatments that conferred enhanced ethanol tolerance, suggesting that this lipid-mediated signaling enzyme may enhance tolerance by sequestering ethanol in membranes as phophatidylethanol. These results reveal new candidate genes underlying toxin tolerance and membrane adaptation to temperature in Drosophila and provide insight into how interactions between these phenotypes may underlie the maintenance of latitudinal clines in ethanol tolerance.
Expression Studies of Neogenin and Its Ligand Hemojuvelin in Mouse Tissues
Authors: Rodriguez Alejandra , Pan Peiwen , Parkkila Seppo
Published: September 2006

Juvenile hemochromatosis is a severe hereditary iron overload disease caused by mutations in the HJV (hemojuvelin) and HAMP (hepcidin) genes. Hepcidin is an important iron regulatory hormone, and hemojuvelin may regulate hepcidin synthesis via the multifunctional membrane receptor neogenin. We explored the expression of murine hemojuvelin and neogenin mRNAs and protein. Real-time RT-PCR analysis of 18 tissues from male and female mice was performed to examine the mRNA expression profiles. To further study protein expression and localization we used immunohistochemistry on several tissues from three mouse strains. Mouse Neo1 mRNA was detectable in the 18 tissues tested, the highest signals being evident in the ovary, uterus, and testis. Neogenin protein was observed in the brain, skeletal muscle, heart, liver, stomach, duodenum, ileum, colon, renal cortex, lung, testis, ovary, oviduct, and uterus. The spleen, thymus, and pancreas were negative for neogenin. The highest signals for Hjv mRNA were detectable in the skeletal muscle, heart, esophagus, and liver. The results indicate that Neo1 mRNA is widely expressed in both male and female mouse tissues with the highest signals detected in the reproductive system. Moreover, Hjv and Neo1 mRNAs are simultaneously expressed in skeletal muscle, heart, esophagus, and liver.
Measurement and Calculation of WWER-440 Pressure Vessel Templates Activity for Support of Vessel Dosimetry
Authors: Zaritsky SM , Vikhrov VI , Erak DY , Kochkin VN , Brodkin EB , Egorov AL
Published: September 2006

Activity of templates (specimens), which were cut out from the inner surface of Kola-1 and Kola-2 WWER-440 reactor pressure vessels (RPVs), were measured, and the results were used to support the RPV dosimetry. Twelve weld and two base metal templates of Kola-1 RPV were cut out after 25 fuel cycles. Thirteen weld and two base metal templates of Kola-2 RPV were cut out after 24 fuel cycles. Probes were taken from four corners of each template for dosimetry measurements. Activity of 54Mn in each probe was measured and the average activity of template material was determined. Calculations were carried out in P3S8 approximation of discrete ordinates method using the DOORS 3.2 code package and BUGLE-96 nuclear data library. Calculated activities were compared with experimental ones. Neutron fluence (for neutrons with E>0.5 MeV) was calculated and calculation uncertainty evaluated based on the comparison of calculated and measured RPV templates activities and on some results of WWER-440 mock-up experiments carried out earlier on the reactor LR-0.
A Three-Dimensional Computed Tomographic Analysis of the Cervical Spine in Unoperated Infants with Cleft Lip and Palate
Authors: Rajion Zainul A. , Townsend Grant C. , Netherway David J. , Anderson Peter J. , Yusof Asilah , Hughes Toby , Shuaib Ibrahim L. , Halim Ahmad Sukari , Samsudin Abdul Rani , David David J.
Published: September 2006

Objective:

To investigate anatomical variations and abnormalities of cervical spine morphology in unoperated infants with cleft lip and palate.

Design:

Retrospective cross-sectional investigation of infants born with nonsyndromic cleft lip and palate using computed tomography scans acquired for investigation of a spectrum of clinical conditions.

Setting:

Computed tomography scan data were obtained from 29 unoperated cleft lip and palate infants and 12 noncleft infants of Malay origin, ages 0 to 12 months.

Methods:

Observational study of cervical spine computed tomography scans. Heights of cervical vertebral bodies (C2-C7) and intervertebral spaces were measured from landmarks identified from computed tomography reformats and three-dimensional computed tomography reconstructions. Linear modeling of heights and spaces, with age as a covariate, was undertaken to identify differences between the samples.

Results:

Anomalous features observed in the cleft lip and palate sample included short posterior arch of C1 (2/29), abnormal development of the anterior arch of C1 (2/29), and fusions of the posterior arch of C2 and C3 (2/29). No anomalies of the cervical spine were observed in the noncleft sample. Although the heights of three cervical vertebral bodies were significantly smaller and two intervertebral spaces were significantly larger in infants with cleft lip and palate compared with noncleft infants (p < .05), overall length of the cervical spine did not differ significantly between the samples.

Conclusion:

There was evidence for subtle upper spinal anomalies in the infant cleft lip and palate population. Our finding of reduced size of some cervical vertebral bodies may reflect delayed upper spinal development in infants with cleft lip and palate.
Analysis of Dental Arch Relationships in Swedish Unilateral Cleft Lip and Palate Subjects: 20-Year Longitudinal Consecutive Series Treated with Delayed Hard Palate Closure
Authors: Lilja Jan , Mars Michael , Elander Anna , Enocson Lars , Hagberg Catharina , Worrell Emma , Batra Puneet , Friede Hans
Published: September 2006

Objective:

To evaluate the dental arch relationships for a consecutive series from Goteborg, Sweden, who had delayed hard palate closure.

Design:

Retrospective study.

Setting:

Sahlgrenska University Hospital, Goteborg, Sweden.

Patients:

The dental study models of 104 consecutive unilateral cleft lip and palate subjects. The study cohort was born between 1979 and 1994. Longitudinal records were available at ages 5 (n = 94), 10 (n = 97), 16 (n = 59), and 19 years (n = 46). Five assessors rated models according to the GOSLON Yardstick on two separate occasions each.

Interventions:

These patients had been operated upon according to the Goteborg protocol of delayed hard palate closure (at age 8 years).

Results:

85% of subjects were rated in groups 1 and 2 (excellent or very good outcome), 12% were rated in group 3 (satisfactory), and 3% were assigned to group 4 (poor). No patients presented in Group 5 (very poor). Weighted kappa statistics for double determination of Yardstick allocation for five assessors demonstrated values between .65 and .90 for interrater agreement (good/very good) and between .70 and .90 for intrarater agreement (very good).

Conclusions:

Delayed hard palate closure as practiced in Goteborg since 1979 has produced the best GOSLON Yardstick ratings in a consecutive series of patients ever recorded worldwide, since the Yardstick was first used in 1983. However, it is noteworthy that a new protocol has been introduced in Goteborg since 1994, in which hard palate closure is done at 3 years due to concerns regarding speech.
The Effect of Phase Saturation Conditions on Wormhole Propagation in Carbonate Acidizing
Authors: Shukla S. , Zhu D. , Hill A. D.
Published: September 2006

Matrix acidizing is a commonly used well stimulation technique in which acid is injected into the formation in order to dissolve a portion of the rock and therefore recover or enhance the permeability in the near-wellbore region. In carbonates, when acid is injected, selective dissolution of the rock takes place, creating highly permeable flow channels, called wormholes. In general, for a matrix acidizing treatment in carbonates, the deeper the wormholes penetrate into the formation, the better the outcome, as characterized by a lower skin factor. Thus, the deeper the wormhole penetration achieved with a given volume of acid, the more efficient the treatment. In this paper, we present laboratory results that show how wormhole propagation is affected by the presence of immiscible phases (gas or oil) when the acid is injected into the rock.

As wormholes are created, not all of the acid reaches the wormhole tip, with a significant portion of the acid being lost as fluid loss to the surrounding matrix. If this fluid loss can be controlled, then more of the acid can reach the wormhole tip, and therefore the penetration of wormholes can be increased. This paper investigates the effect of having gas or oil saturation in the carbonate rock prior to the injection of acid. By reducing the relative permeability to the acid in the matrix surrounding the wormhole, the presence of an immiscible phase can reduce the fluid loss from the main wormhole, thus allowing for deeper penetration of wormholes with a given acid volume.

It was found that gas injection prior to acid injection does significantly reduce the volume of acid required to propagate wormholes through cores. This effect is observed both at room temperature and at higher temperatures. The presence of gas in the core reduced the acid volume needed for wormhole propagation through the core by a factor of up to 3. The paper presents an extensive set of experimental results for both gas-and liquid-saturated carbonate cores subsequently treated with strong HCl solutions. We show that the acid volumes are generally smaller for the nitrogen-saturated cores, and that the wormholes created are narrower and less branched than in the case of water-saturated rocks. We also show that the presence of oil saturation at residual water saturation in the core has a similar beneficial effect on wormhole propagation to gas injection. On the other hand, oil present at its residual saturation had little effect on the acidizing process. All of these results confirm the strong influence that fluid loss from a propagating wormhole has on the efficiency of the acidizing process in carbonates.
Surface-Roughness Design Values for Modern Pipes
Authors: Farshad F. F. , Rieke H. H.
Published: September 2006

The purpose of this paper is to present practicing engineers and scientists with a new means of estimating the absolute surface roughness values, ε, and relative roughness, ε/d, which are specific to modern pipes with specialized internal finishes. Our research thrust has developed new relative-roughness-design equations, values, and derived charts.

Currently, the friction-pressure losses in pipes are being evaluated by practicing engineers by use of Moody's relative-roughness chart (Szilas 1975; Economides et al. 1994). Moody (1944) prepared a relative-roughness chart for a number of common piping materials. Relative roughness provides a simple means for estimating friction factors to be used in computing the friction-pressure losses in piping systems.

An accurate determination of the frictional fluid-pressure drop in pipes is required for design purposes. Currently, these newly developed pipes are used worldwide for various applications, and their surface-roughness values are needed to properly model the hydrodynamics (Farshad et al. 2001; Brown 1984).

Recently, Farshad and Rieke (2005) published a new relative-roughness chart for the modern manufactured oil-country tubular goods (OCTG). Moody did not provide equations for his relative-roughness chart. Equations are the foundation for establishing such correlation charts. In our research, a new set of nonlinear mathematical models was successfully regressed and developed to accurately describe the log/log relationship between pipe diameter and relative roughness. In this paper we provide a set of new equations for our charts. The new equations developed can be used directly in computer models and simulators for frictional pressure-drop calculations.
Improved Mappings for Streamline-Based Simulation
Authors: Mallison B. T. , Gerritsen M. G. , Matringe S. F.
Published: September 2006

Our interest lies in extending the streamline method to compositional simulation. In this paper, we develop improved mappings to and from streamlines that are necessary to obtain reliable predictions of gas injection processes. Our improved mapping to streamlines uses a piecewise linear representation of saturations on the background grid in order to minimize numerical smearing. Our strategy for mapping saturations from streamlines to the background grid is based on kriging. We test our improvements to the streamline method by use of a simple model for miscible flooding based on incompressible Darcy flow. Results indicate that our mappings offer improved resolution and reduce mass-balance errors relative to the commonly used mappings. Our mappings also require fewer streamlines to achieve a desired level of accuracy. In compositional cases where the computational cost of a streamline solve is high, we anticipate that this will lead to an improvement in the efficiency of streamline-based simulation.