julilili42/papers huggingface dataset:
The emerging role of PDZ adapter proteins for regulation of intestinal ion transport
2006-06-24

In the gastrointestinal tract, CFTR, in conjunction with one or several members of the SLC26 anion exchanger family, mediates electrogenic Cl − and HCO 3 − secretion. Na + /H + exchanger isoform NHE3, on the other hand, coupled to one or several of the SLC26 isoforms, mediates electroneutral NaCl absorption. The agonist-induced activation of anion secretion and inhibition of salt absorption causes secretory diarrhea. Current dogma sees the formation of a multiprotein complex of transport proteins, postsynaptic density-95/discs large/zonula occludens-1 (PDZ) adapter proteins, anchoring proteins, the cytoskeleton, and the involved protein kinases as one crucial step in the regulation of these transport processes. Data obtained in heterologous expression studies suggest an important role of these PDZ adapter proteins in trafficking, endocytic recycling, and membrane retention of the respective transmembrane proteins. This article reviews recent advances in our understanding of the role of the PDZ adapter proteins NHERF, E3KARP, PDZK1, IKEPP (NHERF-1 to NHERF-4), CAL, and Shank-2 that bind to CFTR, NHE3, and the intestinal SLC26 members in the regulation of intestinal fluid transport. Current concepts are mostly derived from heterologous expression studies and studies on their role in organ physiology are still in infancy. Recently, however, PDZ adapter protein-deficient mice and organ-specific cell lines have become available, and the first results suggest a more cell-type and possibly signal-specific role of these adapter proteins. This opens the potential for drug development targeted to PDZ domain interactions, which is, in theory, one of the most efficient antidiarrheal strategies.
Nucleotide Metabolism and Cell-Cell Interactions
2006-06-24

Interactions between the vascular endothelium and polymorphonuclear leukocytes (PMNs) are central to PMN emigration into inflamed tissues, and to neutrophil-endothelial crosstalk pathways that modulate inflammatory responses and vascular barrier function. For example, during episodes of inflammation, the transendothelial migration (TEM) of PMNs potentially disturbs vascular barrier and gives rise to intravascular fluid extravasation and edema. However, because of the close special relationship between PMNs and the vascular endothelium, TEM creates an ideal situation for neutrophil-endothelial crosstalk. While investigating innate mechanisms to dampen intravascular fluid loss and edema occurring during TEM, we observed that PMNs release adenine nucleotides after activation (adenosine triphosphate [ATP] and adenosine monophosphate [AMP]). ATP and AMP are metabolized by endothelial cell-surface enzymes, the ecto-apyrase (CD39, metabolizes ATP to AMP) and the 5'-ecto-nucleotidase (CD73, metabolizes AMP to adenosine). Adenosine generated in this fashion can activate endothelial adenosine receptors, leading to increases in intracellular cyclic AMP and resealing of the endothelial junctions, thereby promoting vascular barrier function. This crosstalk pathway provides an endogenous mechanism to dampen vascular leak syndrome during neutrophil-endothelial interaction. In other words, during TEM, neutrophils close the door behind them.
Phylogenomics reveal a robust fungal tree of life
2006-06-26

Our understanding of the tree of life (TOL) is still fragmentary. Until recently, molecular phylogeneticists have built trees based on ribosomal RNA sequences and selected protein sequences, which, however, usually suffered from lack of support for the deeper branches and inconsistencies probably due to limited subsampling of the entire genome. Now, phylogenetic hypotheses can be based on the analysis of full genomes. We used available complete genome data as well as the eukaryote orthologous group (KOG) proteins to reconstruct with confidence basal branches of the fungal TOL. Phylogenetic analysis of a core of 531 KOGs shared among 21 fungal genomes, three animal genomes and one plant genome showed a single tree with high support resulting from four different methods of phylogenetic reconstruction. The single tree that we inferred from our dataset showed excellent nodal support for each branch, suggesting that it reflects the true phylogenetic relationships of the species involved.
Formation of three‐dimensional fetal myocardial tissue cultures from rat for long‐term cultivation
2006-06-26

Abstract Three‐dimensional cardiomyocyte cultures offer new possibilities for the analysis of cardiac cell differentiation, spatial cellular arrangement, and time‐specific gene expression in a tissue‐like environment. We present a new method for generating homogenous and robust cardiomyocyte tissue cultures with good long‐term viability. Ventricular heart cells prepared from fetal rats at embryonic day 13 were cultured in a scaffold‐free two‐step process. To optimize the cell culture model, several digestion protocols and culture conditions were tested. After digestion of fetal cardiac ventricles, the resultant cell suspension of isolated cardiocytes was shaken to initialize cell aggregate formation. In the second step, these three‐dimensional cell aggregates were transferred onto a microporous membrane to allow further microstructure formation. Autonomously beating cultures possessed more than 25 cell layers and a homogenous distribution of cardiomyocytes without central necrosis after 8 weeks in vitro. The cardiomyocytes showed contractile elements, desmosomes, and gap junctions analyzed by immunohistochemistry and electron microscopy. The beat frequency could be modulated by adrenergic agonist and antagonist. Adenoviral green fluorescent protein transfer into cardiomyocytes was possible and highly effective. This three‐dimensional tissue model proved to be useful for studying cell–cell interactions and cell differentiation processes in a three‐dimensional cell arrangement. Developmental Dynamics 235:2200–2209, 2006. © 2006 Wiley‐Liss, Inc.
Zinc, oxidative stress, genetic background and immunosenescence: implications for healthy ageing
2006-06-26

The relevance of zinc for proper functioning of the entire immune system is already well documented. However, the identification of individuals who really need zinc supplementation is still debated in view of the fact that excessive zinc may also be toxic. The risk of developing zinc deficiency in people from industrialized countries is relatively low, except for elderly subjects where zinc intake may be suboptimal and inflammation is chronic. Thus, the role of zinc on the immune system and on the health of European elderly people is becoming of paramount importance, considering also that the elderly population is rapidly increasing. In particular, the factors contributing to and the biochemical markers of zinc deficiency in the elderly are still remain to be established. Epidemiological, functional, and genetic studies aimed at formulating a rationale for the promotion of healthy ageing through zinc supplementation was the subject of an International Conference held in Madrid from 11–13 February 2006 (3(rd )ZincAge Meeting) at the CNIO Institute (local organizer: Maria Blasco, partner of ZincAge)
Demonstration of PDC‐E1 subunits as major antigens in the complement‐fixing fraction M4 and re‐evaluation of PDC‐E1‐specific antibodies in PBC patients
2006-06-26

Abstract: Background: Primary biliary cirrhosis (PBC) is characterized by the presence of antimitochondrial antibodies (AMA). Autoantibodies specific for the mitochondrial M4 antigen can be detected by a complement fixation test (CFT) but not by immunoblotting. The aim of this study was to elucidate the identity of the M4 antigen. Patients and methods: M4 proteins were purified by affinity chromatography using IgG fractions of PBC marker sera being CFT positive ( n =5) or negative ( n =5) and identified by Western blotting, silver staining and sequence analysis. Further, a cohort of 57 PBC patients was tested for the reactivity to M4 and pyruvate dehydrogenase complex (PDC). Results: Two AMA patterns of the marker sera were visualized: CFT‐positive sera were defined as PDC‐E2 + /E1 + and the CFT‐negative sera as PDC‐E2 + /E1 − . The major proteins in the M4 fraction could be related to the PDC‐E1 subunits. A clear‐cut association between anti‐M4 reactivity in the CFT and the reactivity to both PDC subunits could also be documented in the cohort of 57 PBC patients showing anti‐PDC‐E1α and E1β antibodies at a frequency of 74% and 67%. Conclusions: CFT reactivity against M4 antigens could be preferentially identified as a reaction against PDC‐E1. As PDC‐E1 subunits as compared with PDC‐E2 lack lipoyl‐binding sites, they probably have to be considered as an independent and important target.
Combined Behavioral and c-Fos Studies Elucidate the Vital Role of Sodium for Odor Detection
2006-06-26

Salt, known as taste quality, is generally neglected in olfaction, although the olfactory sensory neurons stretch into the salty nasal mucus covering the olfactory epithelium (OE). Using a psychophysical approach, we directly and functionally demonstrate in the awake rat for a variety of structurally diverse odorants that sodium is a critical factor for olfactory perception and sensitivity, both very important components of mammalian communication and sexual behavior. Bathing the olfactory mucus with an iso-osmotic sodium-free buffer solution results in severe deficits in odorant detection. However, sensitivity returns fully within a few hours, indicating continuous mucus production. In the presence of sodium in the mucus covering the OE, all odorants induce odorant-specific c-Fos expression in the olfactory bulb. Yet, if sodium is absent in the mucus, no c-Fos expression is induced as demonstrated for n-octanal. Our noninvasive approach to induce anosmia in mammals here presented--which is fully reversible within hours--opens new possibilities to study the functions of olfactory communication in awake animals.
Interaction between two murein (peptidoglycan) synthases, PBP3 and PBP1B, in Escherichia coli
2006-06-27

Summary The murein (peptidoglycan) sacculus is an essential polymer embedded in the bacterial envelope. The Escherichia coli class B penicillin‐binding protein (PBP) 3 is a murein transpeptidase and essential for cell division. In an affinity chromatography experiment, the bifunctional transglycosylase‐transpeptidase murein synthase PBP1B was retained by PBP3‐sepharose when a membrane fraction of E. coli was applied. The direct protein–protein interaction between purified PBP3 and PBP1B was characterized in vitro by surface plasmon resonance. The interaction was confirmed in vivo employing two different methods: by a bacterial two‐hybrid system, and by cross‐linking/co‐immunoprecipitation. In the bacterial two‐hybrid system, a truncated PBP3 comprising the N‐terminal 56 amino acids interacted with PBP1B. Both synthases could be cross‐linked in vivo in wild‐type cells and in cells lacking FtsW or FtsN. PBP1B localized diffusely and in foci at the septation site and also at the side wall. Statistical analysis of the immunofluorescence signals revealed that the localization of PBP1B at the septation site depended on the physical presence of PBP3, but not on the activity of PBP3. These studies have demonstrated, for the first time, a direct interaction between a class B PBP (PBP3) and a class A PBP (PBP1B) in vitro and in vivo , indicating that different murein synthases might act in concert to enlarge the murein sacculus during cell division.
Orientational Imaging of Subwavelength Au Particles with Higher Order Laser Modes
2006-06-27

We present a new method for the imaging of single metallic nanoparticles that provides information about their shape and orientation. Using confocal microscopy in combination with higher order laser modes, scattering images of individual particles are recorded. Gold nanospheres and nonorods render characteristic patterns reflecting the different particle geometries. In the case of nanorods, the scattering patterns also reveal the orientation of the particles. This novel technique provides a promising tool for the visualization of nonbleaching labels in the biosciences.
Serum- and Glucocorticoid-Inducible Kinase 1 Mediates Salt Sensitivity of Glucose Tolerance
2006-06-27

Excess salt intake decreases peripheral glucose uptake, thus impairing glucose tolerance. Stimulation of cellular glucose uptake involves phosphatidylinositide-3-kinase (PI-3K)–dependent activation of protein kinase B/Akt. A further kinase downstream of PI-3K is serum- and glucocorticoid-inducible kinase (SGK)1, which is upregulated by mineralocorticoids and, thus, downregulated by salt intake. To explore the role of SGK1 in salt-dependent glucose uptake, SGK1 knockout mice (sgk1−/−) and their wild-type littermates (sgk1+/+) were allowed free access to either tap water (control) or 1% saline (high salt). According to Western blotting, high salt decreased and deoxycorticosterone acetate (DOCA; 35 mg/kg body wt) increased SGK1 protein abundance in skeletal muscle and fat tissue of sgk1+/+ mice. Intraperitoneal injection of glucose (3 g/kg body wt) into sgk1+/+ mice transiently increased plasma glucose concentration approaching significantly higher values ([glucose]p,max) in high salt (281 ± 39 mg/dl) than in control (164 ± 23 mg/dl) animals. DOCA did not significantly modify [glucose]p,max in control sgk1+/+ mice but significantly decreased [glucose]p,max in high-salt sgk1+/+ mice, an effect reversed by spironolactone (50 mg/kg body wt). [Glucose]p,max was in sgk1−/− mice insensitive to high salt and significantly higher than in control sgk1+/+ mice. Uptake of 2-deoxy-d-[1,2-3H]glucose into skeletal muscle and fat tissue was significantly smaller in sgk1−/− mice than in sgk1+/+ mice and decreased by high salt in sgk1+/+ mice. Transfection of HEK-293 cells with active S422DSGK1, but not inactive K127NSGK, stimulated phloretin-sensitive glucose uptake. In conclusion, high salt decreases SGK1-dependent cellular glucose uptake. SGK1 thus participates in the link between salt intake and glucose tolerance.
Total Synthesis of (±)‐Symbioimine
2006-06-27

An inside job: A Lewis acid induced intramolecular Diels–Alder (IMDA) reaction is used as the key step in the formation of symbioimine, an iminium alkaloid. The intermediate octahydronaphthalene is obtained from the IMDA reaction, after which extension of the aldehyde to a nitrile, alkylation of the nitrile, and imine formation allows for an efficient route to the target compound (see scheme; TBS=tert-butyldimethylsilyl).
Still Protected Against Smallpox?
2006-06-27

These findings suggest that successful primary vaccination offered full protection for a few decades, with partial protection from severe smallpox possibly lasting a lifetime, for a substantial fraction of the population.
Thyroid hormone receptors TRα1 and TRβ differentially regulate gene expression ofKcnq4and prestin during final differentiation of outer hair cells
2006-06-28

Thyroid hormone (TH or T3) and TH-receptor β (TRβ) have been reported to be relevant for cochlear development and hearing function. Mutations in the TRβ gene result in deafness associated with resistance to TH syndrome. The effect of TRα1 on neither hearing function nor cochlear T3 target genes has been described to date. It is also uncertain whether TRα1 and TRβ can act simultaneously on different target genes within a single cell. We focused on two concomitantly expressed outer hair cell genes, the potassium channel Kcnq4 and the motor protein prestin Slc26a5. In outer hair cells, TH enhanced the expression of the prestin gene through TRβ. Simultaneously Kcnq4 expression was activated in the same cells by derepression of TRα1 aporeceptors mediated by an identified THresponse element, which modulates KCNQ4 promoter activity. We show that T3 target genes can differ in their sensitivity to TH receptors having the ligand either bound (holoreceptors) or not bound (aporeceptors) within single cells, and suggest a role for TRα1 in final cell differentiation.
The A645D Mutation in the Hinge Region of the Human Androgen Receptor (AR) Gene Modulates AR Activity, Depending on the Context of the Polymorphic Glutamine and Glycine Repeats
2006-06-28

Abstract Background: Sufficient androgen receptor (AR) activity is crucial for normal male sexual differentiation. Here we report on two unrelated 46, XY patients suffering from undervirilization and genital malformations. Both patients had a short polyglycine (polyG) repeat of 10 residues and a relatively long polyglutamine (polyQ) repeat of 28 and 30 residues within the transactivation domain of the AR. In addition, they also harbor a rare A645D substitution. Objective: We made a set of AR expression plasmid constructs with varying polyQ and polyG tract sizes in context with or without the A645D substitution and analyzed their in vitro transactivation capacity in transfected CHO cells. Results: We found that a short polyG repeat downmodulated AR activity to approximately 60–65% of the wild-type receptor. This effect was aggravated by A645D in context of a long polyQ repeat to less than 50% activity. In contrast, in the context of a short polyQ and a short polyG repeat, the A645D mutation rescues AR activity to almost wild-type levels, demonstrating a contradictory effect of this mutation, depending on the size of the polymorphic repeats. Conclusions: A combination of a short polyG repeat with a long polyQ repeat and an A645D substitution might contribute to the development of virilization disorders and explain the observed phenotypes of our patients as a form of androgen insensitivity. The whole recreation of AR sequence variations including individual polymorphic repeat sizes could unravel possible interference of mutations and variations on AR activity by in vitro transfection.
Bimetallic Zwitterionic Complexes with an Ambident Stanna-closo-dodecaborate Ligand:  [1-{M(CO)5}-2,7,8-(μ-H)3-{Fe(triphos)}-SnB11H11] (M = Cr, Mo, W)
2006-06-29

Starting from FeBr2 the zwitterionic stannaborate complex [1-{Fe(MeCN)2(triphos)}-SnB11H11] (1) could be obtained in a straightforward one-pot synthesis. Via a facile η1(Sn) to η3(BH) rearrangement reaction 1 can be converted into [2,7,8-(μ-H)3-{Fe(triphos)}-SnB11H11] (2). The nucleophilicity of the tin atom in compound 2 is strongly reduced compared to the dianionic parent stannaborate cluster [SnB11H11]2-. Methylation at the tin atom using standard methods is not feasible. Transition metal fragments can be coordinated at the tin atom of 2 if reactive species such as M(CO)5(THF) (M = Cr, Mo, W) are employed. Reaction of these fragments with 2 yields the bimetallic zwitterions [1-{M(CO)5}-2,7,8-(μ-H)3-{Fe(triphos)}-SnB11H11] (M = Cr, Mo, W) (3, 4, 5), which contain an ambident stannaborate moiety. All new compounds have been characterized using 1H, 11B, 13C, 31P, and 119Sn NMR spectroscopy as well as 31P and 119Sn MAS NMR experiments. Single-crystal X-ray diffraction analyses have been carried out for all novel compounds.
Molecular mass of macromolecules and subunits and the quaternary structure of hemoglobin from the microcrustaceanDaphnia magna
2006-06-29

The molecular masses of macromolecules and subunits of the extracellular hemoglobin from the fresh‐water crustacean Daphnia magna were determined by analytical ultracentrifugation, multiangle laser light scattering and electrospray ionization mass spectrometry. The hemoglobins from hypoxia‐incubated, hemoglobin‐rich and normoxia‐incubated, hemoglobin‐poor Daphnia magna were analyzed separately. The sedimentation coefficient of the macromolecule was 17.4 ± 0.1 S, and its molecular mass was 583 kDa (hemoglobin‐rich animals) determined by AUC and 590.4 ± 11.1 kDa (hemoglobin‐rich animals) and 597.5 ± 49 kDa (hemoglobin‐poor animals), respectively, determined by multiangle laser light scattering. Measurements of the hemoglobin subunit mass of hemoglobin‐rich animals by electrospray ionization mass spectrometry revealed a significant peak at 36.482 ± 0.0015 kDa, i.e. 37.715 kDa including two heme groups. The hemoglobin subunits are modified by O‐linked glycosylation in the pre‐A segments of domains 1. No evidence for phosphorylation of hemoglobin subunits was found. The subunit migration behavior during SDS/PAGE was shown to be influenced by the buffer system used (Tris versus phosphate). The subunit mass heterogeneity found using Tris buffering can be explained by glycosylation of hemoglobin subunits. Based on molecular mass information, Daphnia magna hemoglobin is demonstrated to consist of 16 subunits. The quaternary structure of the Daphnia magna hemoglobin macromolecule was assessed by three‐dimensional reconstructions via single‐particle analysis based on negatively stained electron microscopic specimens. It turned out to be much more complex than hitherto proposed: it displays D4 symmetry with a diameter of approximately 12 nm and a height of about 8 nm.
MC1R Germline Variants Confer Risk for BRAF -Mutant Melanoma
2006-06-30

Germline variants in MC1R , the gene encoding the melanocortin-1 receptor, and sun exposure increase risk for melanoma in Caucasians. The majority of melanomas that occur on skin with little evidence of chronic sun-induced damage (non-CSD melanoma) have mutations in the BRAF oncogene, whereas in melanomas on skin with marked CSD (CSD melanoma) these mutations are less frequent. In two independent Caucasian populations, we show that MC1R variants are strongly associated with BRAF mutations in non-CSD melanomas. In this tumor subtype, the risk for melanoma associated with MC1R is due to an increase in risk of developing melanomas with BRAF mutations.
Iron metabolism in Parkinsonian syndromes
2006-06-30

Abstract Growing evidence suggests an involvement of iron in the pathophysiology of neurodegenerative diseases. Several of the diseases are associated with parkinsonian syndromes, induced by degeneration of basal ganglia regions that contain the highest amount of iron within the brain. The group of neurodegenerative disorders associated with parkinsonian syndromes with increased brain iron content can be devided into two groups: (1) parkinsonian syndromes associated with brain iron accumulation, including Parkinson's disease, diffuse Lewy body disease, parkinsonian type of multiple system atrophy, progressive supranuclear palsy, corticobasal ganglionic degeneration, and Westphal variant of Huntington's disease; and (2) monogenetically caused disturbances of brain iron metabolism associated with parkinsonian syndromes, including aceruloplasminemia, hereditary ferritinopathies affecting the basal ganglia, and panthotenate kinase associated neurodegeneration type 2. Although it is still a matter of debate whether iron accumulation is a primary cause or secondary event in the first group, there is no doubt that iron‐induced oxidative stress contributes to neurodegeneration. Parallels concerning pathophysiological as well as clinical aspects can be drawn between disorders of both groups. Results from animal models and reduction of iron overload combined with at least partial relief of symptoms by application of iron chelators in patients of the second group give hope that targeting the iron overload might be one possibility to slow down the neurodegenerative cascade also in the first group of inevitably progressive neurodegenerative disorders. © 2006 Movement Disorder Society