bluuebunny/crossref_metadata_2025_split huggingface dataset:
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays
Authors: van den Berg Bart HJ , Konieczka Jay H , McCarthy Fiona M , Burgess Shane C 
Published: January 2009

Abstract

Background
Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily accept EST clone names, which are abundantly represented on arrays. Manual re-annotation of microarrays is impracticable and so we developed a computational re-annotation tool (ArrayIDer) to retrieve the most recent accession mapping files from public databases based on EST clone names or accessions and rapidly generate database accessions for entire microarrays.

Results
We utilized the Fred Hutchinson Cancer Research Centre 13K chicken cDNA array – a widely-used non-commercial chicken microarray – to demonstrate the principle that ArrayIDer could markedly improve annotation. We structurally re-annotated 55% of the entire array. Moreover, we decreased non-chicken functional annotations by 2 fold. One beneficial consequence of our re-annotation was to identify 290 pseudogenes, of which 66 were previously incorrectly annotated.

Conclusion

ArrayIDer allows rapid automated structural re-annotation of entire arrays and provides multiple accession types for use in subsequent functional analysis. This information is especially valuable for systems biology modeling in the non-traditional biomedical model organisms.
Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway
Authors: Jørgensen Thomas R , Goosen Theo , van den Hondel Cees AMJJ , Ram Arthur FJ , Iversen Jens JL 
Published: January 2009

AbstractBackgroundThe filamentous fungus,Aspergillus niger, responds to nutrient availability by modulating secretion of various substrate degrading hydrolases. This ability has made it an important organism in industrial production of secreted glycoproteins. The recent publication of theA. nigergenome sequence and availability of microarrays allow high resolution studies of transcriptional regulation of basal cellular processes, like those of glycoprotein synthesis and secretion. It is known that the activities of certain secretory pathway enzymes involvedN-glycosylation are elevated in response to carbon source induced secretion of the glycoprotein glucoamylase. We have investigated whether carbon source dependent enhancement of protein secretion can lead to upregulation of secretory pathway elements extending beyond those involved inN-glycosylation.ResultsThis study compares the physiology and transcriptome ofA. nigergrowing at the same specific growth rate (0.16 h-1) on xylose or maltose in carbon-limited chemostat cultures. Transcription profiles were obtained using Affymetrix GeneChip analysis of six replicate cultures for each of the two growth-limiting carbon sources. The production rate of extracellular proteins per gram dry mycelium was about three times higher on maltose compared to xylose. The defined culture conditions resulted in high reproducibility, discriminating even low-fold differences in transcription, which is characteristic of genes encoding basal cellular functions. This included elements in the secretory pathway and central metabolic pathways. Increased protein secretion on maltose was accompanied by induced transcription of > 90 genes related to protein secretion. The upregulated genes encode key elements in protein translocation to the endoplasmic reticulum (ER), folding,N-glycosylation, quality control, and vesicle packaging and transport between ER and Golgi. The induction effect of maltose resembles the unfolded protein response (UPR), which results from ER-stress and has previously been defined by treatment with chemicals interfering with folding of glycoproteins or by expression of heterologous proteins.ConclusionWe show that upregulation of secretory pathway genes also occurs in conditions inducing secretion of endogenous glycoproteins – representing a more normal physiological state. Transcriptional regulation of protein synthesis and secretory pathway genes may thus reflect a general mechanism for modulation of secretion capacity in response to the conditional need for extracellular enzymes.
Brain-derived neurotrophic factor modulation of Kv1.3 channel is disregulated by adaptor proteins Grb10 and nShc
Authors: Colley Beverly S , Cavallin Melissa A , Biju KC , Marks David R , Fadool Debra A 
Published: January 2009

Abstract

Background
Neurotrophins are important regulators of growth and regeneration, and acutely, they can modulate the activity of voltage-gated ion channels. Previously we have shown that acute brain-derived neurotrophic factor (BDNF) activation of neurotrophin receptor tyrosine kinase B (TrkB) suppresses the Shaker voltage-gated potassium channel (Kv1.3) via phosphorylation of multiple tyrosine residues in the N and C terminal aspects of the channel protein. It is not known how adaptor proteins, which lack catalytic activity, but interact with members of the neurotrophic signaling pathway, might scaffold with ion channels or modulate channel activity.

Results
We report the co-localization of two adaptor proteins, neuronal Src homology and collagen (nShc) and growth factor receptor-binding protein 10 (Grb10), with Kv1.3 channel as demonstrated through immunocytochemical approaches in the olfactory bulb (OB) neural lamina. To further explore the specificity and functional ramification of adaptor/channel co-localization, we performed immunoprecipitation and Western analysis of channel, kinase, and adaptor transfected human embryonic kidney 293 cells (HEK 293). nShc formed a direct protein-protein interaction with Kv1.3 that was independent of BDNF-induced phosphorylation of Kv1.3, whereas Grb10 did not complex with Kv1.3 in HEK 293 cells. Both adaptors, however, co-immunoprecipitated with Kv1.3 in native OB. Grb10 was interestingly able to decrease the total expression of Kv1.3, particularly at the membrane surface, and subsequently eliminated the BDNF-induced phosphorylation of Kv1.3. To examine the possibility that the Src homology 2 (SH2) domains of Grb10 were directly binding to basally phosphorylated tyrosines in Kv1.3, we utilized point mutations to substitute multiple tyrosine residues with phenylalanine. Removal of the tyrosines 111–113 and 449 prevented Grb10 from decreasing Kv1.3 expression. In the absence of either adaptor protein, channel co-expression reciprocally down-regulated expression and tyrosine phosphorylation of TrkB kinase and related insulin receptor kinase. Finally, through patch-clamp electrophysiology, we found that the BDNF-induced current suppression of the channel was prevented by both nShc and Grb10.

Conclusion
We report that adaptor protein alteration of kinase-induced Kv1.3 channel modulation is related to the degree of direct protein-protein association and that the channel itself can reciprocally modulate receptor-linked tyrosine kinase expression and activity.
The critical role of ERK in death resistance and invasiveness of hypoxia-selected glioblastoma cells
Authors: Kim Jee-Youn , Kim Yong-Jun , Lee Sun , Park Jae-Hoon 
Published: January 2009

Abstract

Background
The rapid growth of tumor parenchyma leads to chronic hypoxia that can result in the selection of cancer cells with a more aggressive behavior and death-resistant potential to survive and proliferate. Thus, identifying the key molecules and molecular mechanisms responsible for the phenotypic changes associated with chronic hypoxia has valuable implications for the development of a therapeutic modality. The aim of this study was to identify the molecular basis of the phenotypic changes triggered by chronic repeated hypoxia.

Methods
Hypoxia-resistant T98G (HRT98G) cells were selected by repeated exposure to hypoxia and reoxygenation. Cell death rate was determined by the trypan blue exclusion method and protein expression levels were examined by western blot analysis. The invasive phenotype of the tumor cells was determined by the Matrigel invasion assay. Immunohistochemistry was performed to analyze the expression of proteins in the brain tumor samples. The Student T-test and Pearson Chi-Square test was used for statistical analyses.

Results
We demonstrate that chronic repeated hypoxic exposures cause T98G cells to survive low oxygen tension. As compared with parent cells, hypoxia-selected T98G cells not only express higher levels of anti-apoptotic proteins such as Bcl-2, Bcl-XL, and phosphorylated ERK, but they also have a more invasive potential in Matrigel invasion chambers. Activation or suppression of ERK pathways with a specific activator or inhibitor, respectively, indicates that ERK is a key molecule responsible for death resistance under hypoxic conditions and a more invasive phenotype. Finally, we show that the activation of ERK is more prominent in malignant glioblastomas exposed to hypoxia than in low grade astrocytic glial tumors.

Conclusion
Our study suggests that activation of ERK plays a pivotal role in death resistance under chronic hypoxia and phenotypic changes related to the invasive phenotype of HRT98G cells compared to parent cells.
Development of real time PCR for detection and quantitation of Dengue Viruses
Authors: Gurukumar KR , Priyadarshini D , Patil JA , Bhagat A , Singh A , Shah PS , Cecilia D 
Published: January 2009

Abstract

Background
Dengue virus (DENV), a mosquito borne flavivirus is an important pathogen causing more than 50 million infections every year around the world. Dengue diagnosis depends on serology, which is not useful in the early phase of the disease and virus isolation, which is laborious and time consuming. There is need for a rapid, sensitive and high throughput method for detection of DENV in the early stages of the disease. Several real-time PCR assays have been described for dengue viruses, but there is scope for improvement. The new generation TaqMan Minor Groove Binding (MGB) probe approach was used to develop an improved real time RT-PCR (qRT-PCR) for DENV in this study.

Results
The 3'UTR of thirteen Indian strains of DENV was sequenced and aligned with 41 representative sequences from GenBank. A region conserved in all four serotypes was used to target primers and probes for the qRT-PCR. A single MGB probe and a single primer pair for all the four serotypes of DENV were designed. The sensitivity of the two step qRT-PCR assay was10 copies of RNA molecules per reaction. The specificity and sensitivity of the assay was 100% when tested with a panel of 39 known positive and negative samples. Viral RNA could be detected and quantitated in infected mouse brain, cell cultures, mosquitoes and clinical samples. Viral RNA could be detected in patients even after seroconversion till 10 days post onset of infection. There was no signal with Japanese Encephalitis (JE), West Nile (WN), Chikungunya (CHK) viruses or with Leptospira, Plasmodium vivax, Plasmodium falciparum and Rickettsia positive clinical samples.

Conclusion
We have developed a highly sensitive and specific qRT-PCR for detection and quantitation of dengue viruses. The assay will be a useful tool for differential diagnosis of dengue fever in a situation where a number of other clinically indistinguishable infectious diseases like malaria, Chikungunya, rickettsia and leptospira occur. The ability of the assay to detect DENV-2 in inoculated mosquitoes makes it a potential tool for detecting DENV in field-caught mosquitoes.
Fetal microchimerism and maternal health during and after pregnancy
Authors: O'Donoghue Keelin 
Published: January 2009

Trafficking of fetal cells into the maternal circulation begins very early in pregnancy and the effects of this cell traffic are longlasting. All types of fetal cells, including stem cells, cross the placenta during normal pregnancy to enter maternal blood, from where they may be recovered in pregnancy for the purpose of genetic prenatal diagnosis. Fetal cells can also be located in maternal tissues during and after pregnancy, and persist as microchimeric cells for decades in marrow and other organs. Although persistent fetal cells were first implicated in autoimmune disease, subsequent reports routinely found microchimeric cells in healthy tissues and in non-autoimmune disease. Parallel studies in animal and human pregnancy now suggest instead that microchimeric fetal cells play a role in the response to tissue injury. However, it is still not clear whether microchimeric fetal cells persisting in the mother are an incidental finding, are naturally pathogenic or act as reparative stem cells, and the environmental or biological stimuli that determine microchimeric cell fate are as yet undetermined. Future studies must also focus on investigating whether fetal cells create functional improvement in response to maternal injury and whether this response can be manipulated. The pregnancy-acquired low-grade chimeric state of women could have far-reaching implications, influencing recovery after injury or surgery, ageing, graft survival after transplantation, survival after cancer as well as deciding the protective effect of pregnancy against diseases later in life. Lifelong persistence of fetal cells in maternal tissues may even explain why women live longer than men.
Processing of Pro–Brain Natriuretic Peptide Is Suppressed by O-Glycosylation in the Region Close to the Cleavage Site
Authors: Semenov Alexander G , Postnikov Alexander B , Tamm Natalia N , Seferian Karina R , Karpova Natalia S , Bloshchitsyna Marina N , Koshkina Ekaterina V , Krasnoselsky Mihail I , Serebryanaya Daria V , Katrukha Alexey G 
Published: January 2009

Abstract
Background: Processing of the brain natriuretic peptide (BNP) precursor, proBNP, is a convertase-dependent reaction that produces 2 molecules—the active BNP hormone and the N-terminal part of proBNP (NT-proBNP). Although proBNP was first described more than 15 years ago, very little is known about the cellular mechanism of its processing. The study of proBNP processing mechanisms is important, because processing impairments could be associated with the development of heart failure (HF).
Methods: The biochemical properties of recombinant proBNP and NT-proBNP and the same molecules derived from the blood of HF patients were analyzed by gel-filtration chromatography, site-directed mutagenesis, and different immunochemical methods with a panel of monoclonal antibodies (MAbs).
Results: Part of the proBNP molecule (amino acid residues 61–76) located near the cleavage site was inaccessible to specific MAbs because of the presence of O-glycans, whereas the same region in NT-proBNP was completely accessible. We demonstrated that a convertase (furin) could effectively cleave deglycosylated (but not intact) proBNP. Of several mutant proBNP forms produced in a HEK 293 cell line, only the T71A variant was effectively processed in the cell.
Conclusions: Only proBNP that was not glycosylated in the region of the cleavage site could effectively be processed into BNP and NT-proBNP. Site-directed mutagenesis enabled us to ascertain the unique suppressing role of T71-bound O-glycan in proBNP processing.
Analytic and Clinical Utility of a Next-Generation, Highly Sensitive Cardiac Troponin I Assay for Early Detection of Myocardial Injury
Authors: Kavsak Peter A , MacRae Andrew R , Yerna Marie-Jeanne , Jaffe Allan S 
Published: January 2009

Abstract
Background: Improvements in cardiac troponin (cTn) assays have increased the rapidity with which clinicians can identify patients with changing cTn concentrations (rise or fall) indicative of acute myocardial injury. The aim of the present study was to characterize a new, high-sensitivity cTnI (hs-cTnI) assay and examine whether increased sensitivity can result in still earlier detection of evolving injury.
Methods: We determined the limit of detection, precision profiles, and preliminary estimates of the 99th percentile for the Beckman Coulter hs-cTnI assay in 125 healthy individuals (age &lt;55 years, 54% male). We compared AccuTnI® and hs-cTnI to assess whether change criteria for early concentration changes (i.e., ≥3SD for low concentrations and 20% difference for concentrations &gt;0.10 μg/L) were exceeded in the first 2 specimens (median time between specimens, 1 h; 25th–75th percentile, 1–3 h) from subjects with symptoms suggestive of cardiac ischemia (n = 290).
Results: The limit of detection for the hs-cTnI assay was 2.06 ng/L, and the 20% CV and 10% CV concentrations were 2.95 and 8.66 ng/L, respectively. The preliminary 99th percentile estimates in lithium heparin, serum, and EDTA plasma were 9.20, 8.00, and 8.60 ng/L, respectively. In 108 patients with myocardial injury based on the peak AccuTnI concentration, applying the change criteria on the 2 earliest specimens identified 81% (95% CI 73%–88%) of patients using the hs-cTnI assay compared to 62% (53%–71%) using the AccuTnI assay (P &lt; 0.001).
Conclusions: Although more extensive validation studies are required, this Beckman Coulter hs-cTnI assay appears to detect patients with evolving myocardial injury earlier.
Co-expression of 9-O-acetylated sialoglycoproteins and their binding proteins on lymphoblasts of childhood acute lymphoblastic leukemia: an anti-apoptotic role
Authors: Mukherjee Kankana , Chava Anil K. , Bandyopadhyay Suman , Mallick Asish , Chandra Sarmila , Mandal Chitra 
Published: January 2009

Abstract
Enhanced levels of 9-O-acetylated sialoglycoproteins (Neu5,9Ac2GPs) as disease-associated molecules was reported to act as signaling molecules for promoting survival of lymphoblasts in childhood acute lymphoblastic leukemia (ALL). Here, we searched for potential physiological ligands for Neu5,9Ac2GPs that could be involved in modulating the survival of lymphoblasts. Accordingly, we examined the presence of binding proteins for Neu5,9Ac2GPs on cell lines and primary cells of patients with B- and T-ALL, at presentation of the disease. Peripheral blood mononuclear cells from normal healthy donors and cells from myeloid leukemia patients were used for comparison. Neu5,9Ac2GPs-binding proteins (BPs) were specifically detected on the surface of both T- and B-ALL-lymphoblasts and ALL-cell lines along with the consistent presence of Neu5,9Ac2GPs. The Neu5,9Ac2GPs and BPs also co-localized on the cell surface and interacted specifically in vitro. Apoptosis of lymphoblasts, induced by serum starvation, was reversed in the presence of purified Neu5,9Ac2GPs due to possible engagement of BPs, and the anti-apoptotic role of this interaction was established. This is the first report of the presence of potential physiological ligands for disease-associated molecules like Neu5,9Ac2GPs, the interaction of which is able to trigger an anti-apoptotic signal conferring a survival advantage to leukemic cells in childhood ALL.
Development and application of a rapid amphipod reproduction test for sediment-quality assessment
Authors: Mann Reinier M. , Hyne Ross V. , Spadaro David A. , Simpson Stuart L. 
Published: January 2009

AbstractMelita plumulosa is an epibenthic, detritivorous amphipod native to eastern Australia that has been adopted as a test organism for toxicity evaluations of contaminated estuarine sediments. In the present study, a 13-d amphipod reproduction test was developed that encompasses gametogenesis, fertilization, and embryo development before hatching. The primary endpoints for the test are fecundity (measured as the number of embryos per individual surviving female) and a fecundity index (fecundity multiplied by the stage of embryo development). This new test has been employed to scrutinize the sediments from a metal-contaminated coastal lagoon. Lake Macquarie (NSW, Australia) is a large, saltwater lagoon that has received metal pollution over many decades, leading to a concentration gradient of trace metals, including Pb, Zn, Cd, and Cu, in the sediments. Within one of the northern bays (Warners Bay), the concentrations of these metals either border on or exceed sediment quality guideline values prescribed by Australian and New Zealand Guidelines for Fresh and Marine Water Quality. In trials with the 13-d amphipod reproduction test, Warners Bay sediments significantly reduced fecundity in the test species. Subsequent tests with clean sediments spiked singly with Pb, Zn, or Cu indicated that no single metal was responsible for the observed toxicity in the field sediments. However, sediments spiked with various combinations of Pb, Zn, Cd, and Cu indicated that Zn in combination with one or more of the other metals was responsible for the reproductive toxicity observed in Warners Bay sediments. In all these tests, measured metal concentrations in overlying water and pore water were low, thus confirming that the observed effects on reproduction could be attributed to dietary exposure to metals.
Non-Chemical Control of Some Important Pests of Sweet Cherry
Authors: Andreev Radoslav , Kutinkova Hristina , Baltas Konstantinos 
Published: January 2009

Non-Chemical Control of Some Important Pests of Sweet CherrySome non-chemical insecticides were tested for efficacy of control of fall webworm,Hyphantria cunea(Drury), and of cherry weevil,Rhynchites auratus(Scop.) in the laboratory and black cherry aphid,Myzus cerasi(Fabr.) under field conditions. Hendreson & Tilton formula was applied for evaluation of efficacy. NeemAzal T/S (azadirahtin) at the concentration 0.5% and Naturalis (Beauveria bassiana) used at 0.2% or 0.3% have shown the best results against black cherry aphid. Good results were also obtained with Pyrethrum FS (pyrethrin + sesame oil + soft potassium soap) used at 0.05% or 0.1%, with NeemAzal T/S at 0.3%, PreFeRal WG (Paecilomyces fumosoroseus) at 0.2% and with Naturalis at 0.1%. The effect of PreFeRal WG, applied at 0.1% was unsatisfactory. Against the fourth instar larvae of fall webworm, excellent results were noted for Pyrethrum (0.05% and 0.1%) and Naturalis (0.1% and 0.2%). Very good effects were also obtained with the BMP 123WP (Bacillus thuringiensis), used in concentration of 0.1%. NeemAzal T/S - 0.5% had still good, albeit lower, efficacy. Against the cherry weevil only Pyrethrum FS was tested. This insecticide resulted in a very good efficacy, when used at the concentration 0.1% and still satisfactory - at 0.05%.
Combination of Mating Disruption and Granulosis Virus for Control of Codling Moth in Bulgaria
Authors: Kutinkova Hristina , Samietz Jörg , Dzhuvinov Vasiliy 
Published: January 2009

Combination of Mating Disruption and Granulosis Virus for Control of Codling Moth in Bulgaria
An application of mating disruption by use of Ecodian CP dispensers (ISAGRO, Italy) in combination with the granulosis virus product Carpovirusine 2000 (Arysta LifeScience, France) against Codling moth (CM), Cydia pomonella, was tested near Plovdiv, Central South Bulgaria. In 2007, the method was applied in an orchard where in the previous year fruit damage reached 18.7% and the CM population was high, as indicated by 3.83 diapausing larvae per tree. Carpovirusine was applied 11 times in the trial plot in combination with Ecodian CP dispensers installed twice during the season. Before harvest, fruit damage in the trial plot amounted to 0.9% and the overwintering population in autumn 2007 was only 0.46 larvae per tree. At the same time in the reference orchard, where 15 insecticide treatments were applied during the season, fruit damage before harvest reached 12.3% and the hibernating population was 7.97 larvae per tree. So, it has been confirmed that combination of both methods might be an effective tool for control of codling moth in the orchards with high population density and resistance to conventional insecticides. This study is being continued.