bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression and subcellular localization of the AQP8 and AQP1 water channels in the mouse gall‐bladder epithelium
Authors: Calamita Giuseppe , Ferri Domenico , Bazzini Claudia , Mazzone Amelia , Bottà Guido , Liquori Giuseppa E. , Paulmichl Markus , Portincasa Piero , Meyer Giuliano , Svelto M. 
Published: May 2008

Background information. Transepithelial transport of water is one of the most distinctive functions by which the gall‐bladder rearranges its bile content. Water is reabsorbed from the gall‐bladder lumen during fasting, whereas it is secreted into the lumen following meal ingestion. Nevertheless, the molecular mechanism by which water is transported across the gall‐bladder epithelium remains mostly unclear.Results. In the present study, we investigate the presence and subcellular localization of AQP (aquaporin) water channels in the mouse gall‐bladder epithelium. Considerable AQP8 mRNA was detected in the gall‐bladder epithelium of mouse, calf, rabbit, guinea pig and man. Studies of subcellular localization were then addressed to the mouse gall‐bladder where the transcript of a second AQP, AQP1, was also detected. Immunoblotting experiments confirmed the presence of AQP8 and AQP1 at a protein level. Immunohistochemistry showed intense expression of AQP8 and AQP1 in the gall‐bladder epithelial cells where AQP8 was localized in the apical membrane, whereas AQP1 was seen both in the apical and basolateral membranes, and in vesicles located in the subapical cytoplasm.Conclusions. The pattern of subcellular distribution of AQP8 and AQP1 strongly corroborates the hypothesis of a transcellular route for the movement of water across the gall‐bladder epithelium. Osmotic water would cross the apical membrane through AQP8 and AQP1, although AQP1 would be the facilitated pathway for the movement of water across the basolateral membrane. The presence of two distinct AQPs in the apical membrane is an unusual finding and may relate to the membrane's ability both to absorb and secrete fluid. It is tempting to hypothesize that AQP1 is hormonally translocated to the gall‐bladder apical membrane to secrete water as in the bile duct epithelium, a functional homologue of the gall‐bladder epithelium, whereas apical AQP8 may account for the absorption of water from gall‐bladder bile.
In situ localization of sulphur in the thioautotrophic symbiotic model Lucina pectinata (Gmelin, 1791) by cryo‐EFTEM microanalysis
Authors: Lechaire Jean‐Pierre , Frébourg Ghislaine , Gaill Françoise , Gros Olivier 
Published: May 2008

Background information. Lucina pectinata is a large tropical lucinid known to harbour sulphide‐oxidizing bacteria in specialized gill cells. Conventional TEM (transmission electron microscopy) has shown that bacteriocytes also harbour visibly ‘empty’ vesicles whose chemical content remains, to date, only roughly determined.Results. In the present study, L. pectinata gill tissues were cryo‐fixed as fast as possible by performing high‐pressure freezing before a freeze‐substitution process and finally performing a cryo‐embedding in Lowicryl. Ultrathin sections were then used for a cryo‐EFTEM (where EFTEM stands for energy‐filtered TEM) microanalysis. Results show that bacteriocytes within the gill tissues contain elemental sulphur in small vesicles produced by the host itself. In instances of sporadic depletion of sulphur in the environment, such structures may act as energy sources for bacterial endosymbionts.Conclusions. The cryo‐EFTEM techniques represent (i) the only method used to date to locate and preserve sulphur at the cellular level and (ii) a powerful tool for sulphur metabolism analysis in thioautotrophic symbiont relationships.
Identification of novel neuronal isoforms of the Rho‐GEF Trio
Authors: Portales‐Casamar Elodie , Briançon‐Marjollet Anne , Fromont Sylvie , Triboulet Robinson , Debant Anne 
Published: May 2008

Background information. The large family of GEFs (guanine nucleotide‐exchange factors) for Rho GTPases activate the GTPases by accelerating their GDP/GTP exchange. The multidomain protein Trio is the founding member of an intriguing subfamily of Rho‐GEFs exhibiting two Rho‐GEF and numerous additional domains. The members of the Trio family play an important role in neuronal physiology, and their structural organization is very well conserved through evolution. It has previously been shown that all the members, except mammalian Trio, display several isoforms, the functions of which have been well established.Results. In this study, we have identified, by a combination of different approaches, novel Trio isoforms that have been generated by alternative splicing, giving rise to proteins that exhibit one or two Rho‐GEF domains (GEFDs). These isoforms are specifically expressed in the nervous system, at a higher level than the full‐length Trio, which is ubiquitously expressed. In addition, we show that all the GEFD1‐containing isoforms induce neurite outgrowth in neuroblastoma cells.Conclusions. We have identified neuronal specific isoforms of Trio which could be essential for Trio function in neuronal morphology.
Modelling the effect of specific inositol 1,4,5‐trisphosphate receptor isoforms on cellular Ca2+ signals
Authors: Dupont Geneviève , Combettes Laurent 
Published: May 2008

Background information. Oscillations of cytosolic Ca2+ are well‐known to rely on the regulatory properties of the InsP3R (inositol 1,4,5‐trisphosphate receptor). Three isoforms of this channel have been identified. They differ in their regulatory properties by Ca2+ and InsP3. Experiments in different cell types clearly indicate that the relative amounts of each isoform affect the time course of Ca2+ changes after agonist stimulation. In the present study, we investigate whether different steady‐state curves for the open probability of the InsP3Rs as a function of Ca2+ imply different dynamical behaviours when these receptors are present in a cellular environment. We therefore describe by a specific phenomenological model the three main types of curves that have been reported: (i) the classical bell‐shaped curve, (ii) the bell‐shaped curve that is shifted towards higher Ca2+ concentrations when InsP3 is increased, and (iii) a monotonous increasing function of cytosolic Ca2+.Results. We show that, although these types of curves can be ascribed to slight differences in the channel regulation by Ca2+ and InsP3, they can indicate important variations as to the receptor role in cellular Ca2+ control. Thus the receptor associated with the classical bell‐shaped curve appears to be the most robust Ca2+ oscillator. If the steady‐state curve is supposed to be a monotonous increasing function of cytosolic Ca2+, the modelled receptor cannot sustain Ca2+ oscillations in the absence of Ca2+ exchanges with the extracellular medium. When the bell‐shaped curve is shifted towards higher Ca2+ concentrations with increasing InsP3 levels, the model predicts that the receptor is less robust to changes in density; this receptor, however, provides a finer control of the steady‐state level of Ca2+ when varying the InsP3 concentration.Conclusions. Our model allows us to propose an explanation for the experimental observations about the effect of selectively expressing or down‐regulating InsP3R isoforms, as well as to make theoretical predictions.
Initial size and dynamics of viral fusion pores are a function of the fusion protein mediating membrane fusion
Authors: Plonsky Ilya , Kingsley David H. , Rashtian Afshin , Blank Paul S. , Zimmerberg Joshua 
Published: May 2008

Background information. Protein‐mediated merger of biological membranes, membrane fusion, is an important process. To investigate the role of fusogenic proteins in the initial size and dynamics of the fusion pore (a narrow aqueous pathway, which widens to finalize membrane fusion), two different fusion proteins expressed in the same cell line were investigated: the major glycoprotein of baculovirus Autographa californica (GP64) and the HA (haemagglutinin) of influenza X31.Results. The host Sf9 cells expressing these viral proteins, irrespective of protein species, fused to human RBCs (red blood cells) upon acidification of the medium. A high‐time‐resolution electrophysiological study of fusion pore conductance revealed fundamental differences in (i) the initial pore conductance; pores created by HA were smaller than those created by GP64; (ii) the ability of pores to flicker; only HA‐mediated pores flickered; and (iii) the time required for pore formation; HA‐mediated pores took much longer to form after acidification.Conclusion. HA and GP64 have divergent electrophysiological phenotypes even when they fuse identical membranes, and fusion proteins play a crucial role in determining initial fusion pore characteristics. The structure of the initial fusion pore detected by electrical conductance measurements is sensitive to the nature of the fusion protein.
Nuclear localization, DNA binding and restricted expression in neural and germ cells of zebrafish Dmrt3
Authors: Li Qin , Zhou Xiang , Guo Yiqing , Shang Xuan , Chen Hao , Lu Heng , Cheng Hanhua , Zhou Rongjia 
Published: May 2008

Background information. The DM (doublesex and male aberrant‐3) genes implicated in sexual development in diverse metazoan organisms have been proved to be involved in development of non‐gonadal tissues. The aim of the present study was to identify and characterize Dmrt3 (DM‐related transcription factor 3) of zebrafish.Results. Zebrafish Dmrt3 has a conserved DMA domain, besides a common DM domain, which clustered it into the DMRTA subfamily. During embryogenesis, Dmrt3 expression increases gradually to a high level at pharyngula stage, which is restricted to the olfactory placode and the neural tube. In the juvenile zebrafish, the gene expression is first detected in undifferentiated gonad on 17 dpf (day post‐fertilization). In adult, Dmrt3 is expressed only in the developing germ cells of both gonads, mainly in spermatogonia, spermatocytes and developing oocytes. The Dmrt3 has a functional NLS (nuclear localization signal) K41GHKR45 within the DM domain, which ensures that Dmrt3 exerts its role in the nucleus. Moreover, EMSA (electrophoretic mobility‐shift assay) indicates that the Dmrt3‐derived DM polypeptide binds to similar sites of both targets of DSX (doublesex) and MAB‐3 (male aberrant‐3).Conclusion. These results suggest that as a DNA‐binding protein, zebrafish Dmrt3 may function in the nucleus as a potential transcription factor to exert potential roles in the development of the olfactory placode, the neural tube and germ cells.
αvβ3 and αvβ5 integrins and their role in muscle precursor cell adhesion
Authors: Sinanan Andrea C. M. , Machell Jon R. A. , Wynne‐Hughes G. Trevor , Hunt Nigel P. , Lewis Mark P. 
Published: May 2008

Background information. Functional adaptation of skeletal muscle is a requirement for different muscle groups (e.g. craniofacial, ocular and limb) to undergo site‐specific changes. Such tissue remodelling depends on dynamic interactions between muscle cells and their extracellular matrix, via participation of multifunctional molecules such as integrins. In view of data suggesting a role in fundamental muscle biology and muscle development in other systems, the present study has focused on expression and function of αv integrins, in cultured adult human craniofacial muscle (masseter) precursor cells and myotubes, and the predominantly fibroblastic IC (interstitial cells) population.Results and conclusions. Flow‐cytometric phenotyping and immunofluorescence phenotyping show that αv, αvβ3 and αvβ5 are expressed in all mononuclear cells (muscle precursors and IC) seeded on muscle extracellular molecules such as gelatin, VN (vitronectin) and FN (fibronectin). In this system, blockade of αv activity using a function‐perturbing antibody abrogates cell migration on VN and FN. αv integrins act predominantly as VN receptors as cell—substrate attachment is diminished when αv neutralizing agents are introduced into cultures seeded on VN, and this inhibition is reversible; these integrins also appear to be minor FN receptors. These results demonstrate that the αv subset of integrins present on both myogenic precursors and IC is an essential cohort of VN and, to a lesser extent, FN receptors mediating cell adhesion and, either directly or indirectly, arbiters of cell motility.
Design of fluorescence resonance energy transfer (FRET)-based cGMP indicators: a systematic approach
Authors: Russwurm Michael , Mullershausen Florian , Friebe Andreas , Jäger Ronald , Russwurm Corina , Koesling Doris 
Published: May 2008

The intracellular signalling molecule cGMP regulates a variety of physiological processes, and so the ability to monitor cGMP dynamics in living cells is highly desirable. Here, we report a systematic approach to create FRET (fluorescence resonance energy transfer)-based cGMP indicators from two known types of cGMP-binding domains which are found in cGMP-dependent protein kinase and phosphodiesterase 5, cNMP-BD [cyclic nucleotide monophosphate-binding domain and GAF [cGMP-specific and -stimulated phosphodiesterases, Anabaena adenylate cyclases and Escherichia coli FhlA] respectively. Interestingly, only cGMP-binding domains arranged in tandem configuration as in their parent proteins were cGMP-responsive. However, the GAF-derived sensors were unable to be used to study cGMP dynamics because of slow response kinetics to cGMP. Out of 24 cGMP-responsive constructs derived from cNMP-BDs, three were selected to cover a range of cGMP affinities with an EC50 between 500 nM and 6 μM. These indicators possess excellent specifity for cGMP, fast binding kinetics and twice the dynamic range of existing cGMP sensors. The in vivo performance of these new indicators is demonstrated in living cells and validated by comparison with cGMP dynamics as measured by radioimmunoassays.
Reconstitution of carbonic anhydrase activity of the cell-surface-binding protein of vaccinia virus
Authors: Ohradanova Anna , Vullo Daniela , Kopacek Juraj , Temperini Claudia , Betakova Tatiana , Pastorekova Silvia , Pastorek Jaromir , Supuran Claudiu T. 
Published: May 2008

The N-terminal region of a 32 kDa cell-surface-binding protein, encoded by the D8L gene of vaccinia virus, shows sequence homology to CAs (carbonic anhydrases; EC 4.2.1.1). The active CAs catalyse the reversible hydration of CO2 to bicarbonate participating in many physiological processes. The CA-like domain of vaccinia protein [vaccCA (vaccinia virus CA-like protein)] contains one of the three conserved histidine residues required for co-ordination to the catalytic zinc ion and for enzyme activity. In the present study, we report the engineering of catalytically active vaccCA mutants by introduction of the missing histidine residues into the wild-type protein. The wild-type vaccCA was inactive as a catalyst and does not bind sulfonamide CA inhibitors. Its position on a phylogram with other hCAs (human CAs) shows a relationship with the acatalytic isoforms CA X and XI, suggesting that the corresponding viral gene was acquired from the human genome by horizontal gene transfer. The single mutants (vaccCA N92H/Y69H) showed low enzyme activity and low affinity for acetazolamide, a classical sulfonamide CA inhibitor. The activity of the double mutant, vaccCA N92H/Y69H, was much higher, of the same order of magnitude as that of some human isoforms, namely CA VA and CA XII. Moreover, its affinity for acetazolamide was high, comparable with that of the most efficient human isoenzyme, CA II (in the low nanomolar range). Multiplication of vaccinia virus in HeLa cells transfected with the vaccCA N92H/Y69H double mutant was approx. 2-fold more efficient than in wild-type vaccCA transfectants, suggesting that the reconstitution of the enzyme activity improved the virus life cycle.
Identification of OBO nonalignments and its implications for OBO enrichment
Authors: Bada Michael , Hunter Lawrence 
Published: May 2008

Abstract
Motivation: Existing projects that focus on the semiautomatic addition of links between existing terms in the Open Biomedical Ontologies can take advantage of reasoners that can make new inferences between terms that are based on the added formal definitions and that reflect nonalignments between the linked terms. However, these projects require that these definitions be necessary and sufficient, a strong requirement that often does not hold. If such definitions cannot be added, the reasoners cannot point to the nonalignments through the suggestion of new inferences.
Results: We describe a methodology by which we have identified over 1900 instances of nonredundant nonalignments between terms from the Gene Ontology (GO) biological process (BP), cellular component (CC) and molecular function (MF) ontologies, Chemical Entities of Biological Interest (ChEBI) and the Cell Type Ontology (CL). Many of the 39.8% of these nonalignments whose object terms are more atomic than the subject terms are not currently examined in other ontology-enrichment projects due to the fact that the necessary and sufficient conditions required for the inferences are not currently examined. Analysis of the ratios of nonalignments to assertions from which the nonalignments were identified suggests that BP–MF, BP–BP, BP–CL and CC–CC terms are relatively well-aligned, while ChEBI–MF, BP–ChEBI and CC–MF terms are relatively not aligned well. We propose four ways to resolve an identified nonalignment and recommend an analogous implementation of our methodology in ontology-enrichment tools to identify types of nonalignments that are currently not detected.
Availability: The nonalignments discussed in this article may be viewed at http://compbio.uchsc.edu/Hunter_lab/Bada/nonalignments_2008_03_06.html. Code for the generation of these nonalignments is available upon request.
Contact: mike.bada@uchsc.edu
Management of an invasive marine species: defining and testing the effectiveness of ballast-water management options using management strategy evaluation
Authors: Dunstan Piers K. , Bax Nicholas J. 
Published: May 2008

Abstract
Dunstan, P. K., and Bax, N. J. 2008. Management of an invasive marine species: defining and testing the effectiveness of ballast-water management options using management strategy evaluation. – ICES Journal of Marine Science, 65: 841–850. Invasive marine and fresh-water species are being spread around the world in ships' ballast water, damaging industries and natural resources. Management policies are being developed nationally and internationally in response to the threat, but these options are not being rigorously evaluated for their potential to meet management objectives. We used management strategy evaluation (MSE) simulation to compare the performance of different management rules for controlling the spread of an invasive sea star, Asterias amurensis, around the southern coast of Australia. A model incorporating population dynamics, oceanographic patterns, and vessel movement was developed to compare the performance of different ballast-water exchange rules at reducing the likelihood of new populations establishing at locations along the coast over time. Static management rules, where ballast exchange was mandated on all voyages, reduced the median likelihood of new invasions from 0.67 with no ballast control to between 0.36 and 0.42 as distance from the coast was varied. Reducing the volume of high-risk ballast water by 95% did not reduce the likelihood of invasion by 95%, but by an average of 21%. Exchanging ballast farther from the coast did not reduce the likelihood of invasion for any of the static management rules. Feedback management rules using a port monitoring programme to assess the risk of transporting larvae between ports were at least as effective as the static rules, but at a significantly reduced cost for this single-species example. MSE provides a method to compare management options against objectives in this uncertain environment, and can be used to evaluate new and expensive treatment options for their effectiveness and value.
Oxidative stress causes telomere damage in Fanconi anaemia cells – a possible predisposition for malignant transformation
Authors: Uziel Orit , Reshef Hagai , Ravid Amiram , Fabian Ina , Halperin Drora , Ram Ron , Bakhanashvili Mary , Nordenberg Jardena , Lahav Meir 
Published: May 2008

SummaryFanconi anaemia (FA) is an autosomal recessive and X‐linked disease characterized by severe genetic instability and increased incidence of cancer. One explanation for this instability may be the cellular hypersensitivity to oxidative stress leading to chromosomal breaks. This study explored the possible oxidative damage to telomeres of FA lymphocyte cell line, HSC536/N, and its possible effect on telomere function. We postulated that combination of oxidative damage with overexpression of telomerase may provide a possible model for malignant transformation in FA. The cells were grown in the presence of telomerase inhibitor and exposed for 1 month to H2O2 combined with various antioxidants. This exposure caused shortening of telomere length and damage to the telomere single stranded overhang, which was prevented by several oxidants. This shortening was associated with development of severe telomere dysfunction. Control cells did not exhibit this sensitivity to H2O2. Telomere dysfunction did not evoke damage response in FA cells, in contrast to normal P53 upregulation in control cells. Reconstitution of telomerase activity protected FA telomeres from further oxidative damage. These results suggest a scenario in which oxidative stress causes telomere shortening and ensuing telomere dysfunction may form the basis for malignant transformation in FA cells. Upregulation of telomerase activity in sporadic FA cells may perpetuate that process, thus explaining the malignant character of FA cells in vivo.
The combination of cyclophosphamide and human T cells genetically engineered to target CD19 can eradicate established B‐cell lymphoma
Authors: Cheadle Eleanor J , Gilham David E , Hawkins Robert E 
Published: May 2008

SummaryT cells genetically engineered to express tumour‐targeting receptors are attractive anti‐cancer therapeutic agents. Human T cells engrafted with a chimeric receptor specific for the B‐cell lymphoma antigen CD19 fused to the CD3ζ receptor (aCD19z) are functional in vitro. Current successful clinical protocols targeting melanoma use pre‐conditioning chemotherapy in combination with T cells. This study demonstrated that interleukin‐2 expanded aCD19z T cells combined with cyclophosphamide effectively treated five‐day established Raji B‐cell lymphoma in an immunocompromised model system with 50% of mice surviving >100 days. This observation strongly supports the combination of antibody targeted T cells with chemotherapy as a novel approach for the therapy of CD19+ B‐cell malignancies.
Combination of the anti‐CD30‐auristatin‐E antibody‐drug conjugate (SGN‐35) with chemotherapy improves antitumour activity in Hodgkin lymphoma
Authors: Oflazoglu Ezogelin , Kissler Kim M. , Sievers Eric L. , Grewal Iqbal S. , Gerber Hans‐Peter 
Published: May 2008

SummaryThe antibody‐drug conjugate (ADC) cAC10‐vcMMAE consists of the tubulin inhibitor monomethyl auristatin E (MMAE) conjugated to the chimeric anti‐CD30 monoclonal antibody cAC10. This ADC potently interferes with the growth of CD30‐positive haematological tumours, including Hodgkin lymphoma (HL) and anaplastic large‐cell lymphoma. This study found improved antitumour activity in a preclinical model of HL when SGN‐35 was combined with chemotherapeutic regimens such as ABVD (doxorubicin, bleomycin, vinblastine and dacarbazine) or gemcitabine. Improved efficacy was also observed in high tumour burden models, indicating that combining ADCs with chemotherapeutic agents may be advantageous for the treatment of patients with relapsed or refractory HL.