Geographical distribution and disease associations of the CD45 exon 6 138G variant

CD45 is crucial for normal lymphocyte signalling, and altered CD45 expression has major effects on immune function. Both mice and humans lacking CD45 expression are severely immunodeficient, and single-nucleotide polymorphisms in the CD45 gene that cause altered splicing have been associated with autoimmune and infectious diseases. Recently, we identified an exon 6 A138G polymorphism resulting in an increased proportion of activated CD45RO T cells and altered immune function. Here we report a significantly reduced frequency of the 138G allele in hepatitis C Japanese patients and a possibly reduced frequency in type I diabetes. The allele is widely distributed in the Far East and India, indicating that it may have a significant effect on disease burden in a large part of the human population.     

Loop prediction for a GPCR homology model: Algorithms and results

We present loop structure prediction results of the intracellular and extracellular loops of four G‐protein‐coupled receptors (GPCRs): bovine rhodopsin (bRh), the turkey β1‐adrenergic (β1Ar), the human β2‐adrenergic (β2Ar) and the human A2a adenosine receptor (A2Ar) in perturbed environments. We used the protein local optimization program, which builds thousands of loop candidates by sampling rotamer states of the loops' constituent amino acids. The candidate loops are discriminated between with our physics‐based, all‐atom energy function, which is based on the OPLS force field with implicit solvent and several correction terms. For relevant cases, explicit membrane molecules are included to simulate the effect of the membrane on loop structure. We also discuss a new sampling algorithm that divides phase space into different regions, allowing more thorough sampling of long loops that greatly improves results. In the first half of the paper, loop prediction is done with the GPCRs' transmembrane domains fixed in their crystallographic positions, while the loops are built one‐by‐one. Side chains near the loops are also in non‐native conformations. The second half describes a full homology model of β2Ar using β1Ar as a template. No information about the crystal structure of β2Ar was used to build this homology model. We are able to capture the architecture of short loops and the very long second extracellular loop, which is key for ligand binding. We believe this the first successful example of an RMSD validated, physics‐based loop prediction in the context of a GPCR homology model. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

One year of pomegranate juice intake decreases oxidative stress, inflammation, and incidence of infections in hemodialysis patients: a randomized placebo-controlled trial

Increased systemic inflammation and oxidative stress are well established as nontraditional key players in the pathogenesis of atherosclerosis and are also involved in the innate immunity dysregulation in hemodialysis (HD) patients. The study aim was to investigate the effect of 1-year intake of pomegranate juice, an antioxidant source, on oxidative stress, inflammation, and long-term clinical outcomes. A randomized placebo controlled double-blind trial was designed, enrolling 101 chronic HD patients to receive during each dialysis 100 cc of pomegranate juice, or matching placebo, three times a week for 1 year. The primary endpoints were levels of oxidative stress and inflammation biomarkers. Secondary endpoints were hospitalization due to infections and the progression of atherosclerotic process based on a composite of variables of the carotid arteries: intima media thickness (IMT), number, and structure of plaques. Pomegranate juice intake yielded a significant time response reduction in polymorphonuclear leukocyte priming, protein oxidation, lipid oxidation, and inflammation biomarkers levels. These beneficial effects were abolished 3 months postintervention. Pomegranate juice intake resulted in a significantly lower incidence rate of the second hospitalization due to infections. Furthermore, 25% of the patients in the pomegranate juice group had improvement and only 5% progression in the atherosclerotic process, while more than 50% of patients in the placebo group showed progression and none showed any improvement. Prolonged pomegranate juice intake improves nontraditional CV risk factors, attenuates the progression of the atherosclerotic process, strengthens the innate immunity, and thus reduces morbidity among HD patients.     

Yeast protein–surfactant complexes uncouple microbial electron transfer and increase transmembrane leak of protons

Aims:  To explore the combined effect of yeast proteins and surfactants on bacterial metabolism.
Methods and Results:  Protein-rich cell-free supernatant from heat-shocked yeast Saccharomyces cerevisiae was combined with certain synthetic surfactants. These blends affected the metabolism of a Polyseed inoculum of aerobic bacteria, accelerating CO₂ production and consumption of nutrients from a sterile nutrient broth solution, without a concomitant accumulation of biomass. It is suggested that in the presence of the yeast protein–surfactant complexes, bacterial electron transport is uncoupled from biomass accumulation. The 'uncoupling hypothesis' is supported by experiments with model membranes, in which the same complexes induced proton leak similar to standard chemical uncouplers, such as dinitrophenol, indicating that uncoupling may occur at the stage of generation of the transmembrane pH gradient as the driving force for ATP production.
Conclusions:  Yeast protein–surfactant complexes behave as uncouplers of oxidative metabolism in bacteria and appear to do so by increasing proton permeability of membranes.
Significance and Impact of the Study:  Yeast proteins may be of interest as nontoxic, environmentally benign and economically sound agents accelerating oxidative bacterial metabolism while uncoupling it from biomass accumulation. There are actual and potential implications in waste water/soil decontamination, degreasing and other environmental technologies.     

Comparison between calcium transport and adenosine triphosphatase activity in membrane vesicles derived from rabbit kidney proximal tubules

Characteristics of Ca2+ uptake were studied in a vesicular preparation of proximal tubule plasma membranes from rabbit kidney and compared with the properties of both membrane-bound and solubilized Ca2+-ATPase activities. Calcium uptake required both ATP and MgCl2 and revealed two kinetic components with respect to Ca2+ concentration requirements, one with a high affinity for Ca2+ (1.8 microM), operative in the range of cytosolic Ca2+ activity, and one with a low affinity for Ca2+ (250 microM) which may become active only at abnormally high cytosolic Ca2+ concentrations. The high- and low-affinity components were stimulated to similar extents by phosphate, and required similar concentrations of ATP (0.6 mM) for half-maximal activity. The amount of membrane-bound phosphoenzyme formed from ATP in the presence of Ca2+ was the same regardless of whether only one or both sites were saturated, suggesting that occupancy of the second Ca2+ binding site accelerates the enzyme turnover. Inhibition of Ca2+ transport by Na+ was reversed by the addition of ouabain or an ATP-regenerating system, indicating that this inhibitory effect of Na+ on Ca2+ uptake may be due to the accumulation of ADP in the medium as a result of Na+ pump activity. Low concentrations of carbonyl cyanide p-trifluoromethoxyphenylhydrazone and valinomycin (2.5 and 1 microM, respectively) were without effect on Ca2+ uptake in the presence of phosphate, whereas higher concentrations of the ionophores (200 and 100 microM, respectively) reduced uptake by 60% or more. The calmodulin antagonist 48/80 also reduced Ca2+ uptake with half-maximal effectiveness at 100 micrograms/ml. None of these drugs affected either ATPase activity or the EGTA-induced Ca2+ efflux from preloaded vesicles. The Ca2+ dependence of ATP hydrolysis by the membrane-bound enzyme preparation was similar to that observed for Ca2+ uptake by the vesicles. However, with solubilized enzyme, concentrations of Ca2+ similar to that found in the plasma reduced Ca2+-stimulated ATP hydrolysis to one-half of its maximal rate. This indicates that peritubular Ca2+ may play a role in the regulation of Ca2+ transport across the tubular epithelium. ATP could not be replaced by ITP as a substrate for Ca2+ uptake, and the (Ca2+ + Mg2+)ITPase activity of soluble enzyme was 25-fold lower than in the presence of ATP. This is an indication that the active Ca2+ pumping mechanism in proximal tubules is critically dependent on the nucleoside moiety of the substrate.     

Long-Term Relationships between Synaptic Tenacity, Synaptic Remodeling, and Network Activity

Synaptic plasticity is widely believed to constitute a key mechanism for modifying functional properties of neuronal networks. This belief implicitly implies, however, that synapses, when not driven to change their characteristics by physiologically relevant stimuli, will maintain these characteristics over time. How tenacious are synapses over behaviorally relevant time scales? To begin to address this question, we developed a system for continuously imaging the structural dynamics of individual synapses over many days, while recording network activity in the same preparations. We found that in spontaneously active networks, distributions of synaptic sizes were generally stable over days. Following individual synapses revealed, however, that the apparently static distributions were actually steady states of synapses exhibiting continual and extensive remodeling. In active networks, large synapses tended to grow smaller, whereas small synapses tended to grow larger, mainly during periods of particularly synchronous activity. Suppression of network activity only mildly affected the magnitude of synaptic remodeling, but dependence on synaptic size was lost, leading to the broadening of synaptic size distributions and increases in mean synaptic size. From the perspective of individual neurons, activity drove changes in the relative sizes of their excitatory inputs, but such changes continued, albeit at lower rates, even when network activity was blocked. Our findings show that activity strongly drives synaptic remodeling, but they also show that significant remodeling occurs spontaneously. Whereas such spontaneous remodeling provides an explanation for “synaptic homeostasis” like processes, it also raises significant questions concerning the reliability of individual synapses as sites for persistently modifying network function.     

T cell-specific expression of the human TNF-alpha gene involves a functional and highly conserved chromatin signature in intron 3

Using a phylogenetic approach, we identified highly conserved sequences within intron 3 of the human TNF-alpha gene. These sequences form cell type-specific DNase I hypersensitivity sites and display cell type-specific DNA-protein contacts in in vivo genomic footprints. Consistent with these results, intron 3 confers specific activity upon a TNF-alpha reporter gene in Jurkat T cells, but not THP-1 monocytic cells. Thus, using a combinatorial approach of phylogenetic analysis, DNase I hypersensitivity analysis, in vivo footprinting, and transfection analysis, we demonstrate that intronic regulatory elements are involved in the cell type-specific regulation of TNF-alpha gene expression.     

Effect of anions and redox state on the activity of manganese containing catalase from Thermus thermophilus

Catalase isolated from thermophilic bacterium Thermus thermophilus (Mn-catalase) is composed of six subunits, each containing binuclear manganese clusters at their active site. The enzyme is active when the metal is in the completely reduced (Mn²⁺---Mn²⁺) state in the pH range 7–10, and loses activity on oxidation. ESR data suggest that the metal turns thereby into the (Mn²⁺---Mn⁴⁺) state. The Mn-catalase activity is inhibited by chloride, nitrate, nitrite, azide, and other singly charged anions, except cyanide. The inhibitory effect of anions increases as the pH value is reduced. The inhibition by hydroxylamine takes place through a lag-phase and is weakly dependent on pH value. The reaction mechanism is discussed in relation with current concepts of catalase reactions of heme-proteins and low-molecular binuclear manganese complexes.