Actin is required for endocytosis at the apical surface of Madin-Darby canine kidney cells where ARF6 and clathrin regulate the actin cytoskeleton

In epithelial cell lines, apical but not basolateral clathrin-mediated endocytosis has been shown to be affected by actin-disrupting drugs. Using electron and fluorescence microscopy, as well as biochemical assays, we show that the amount of actin dedicated to endocytosis is limiting at the apical surface of epithelia. In part, this contributes to the low basal rate of clathrin-dependent endocytosis observed at this epithelial surface. ARF6 in its GTP-bound state triggers the recruitment of actin from the cell cortex to the clathrin-coated pit to enable dynamin-dependent endocytosis. In addition, we show that perturbation of the apical endocytic system by expression of a clathrin heavy-chain mutant results in the collapse of microvilli. This phenotype was completely reversed by the expression of an ARF6-GTP-locked mutant. These observations indicate that concomitant to actin recruitment, the apical clathrin endocytic system is deeply involved in the morphology of the apical plasma membrane.     

Light‐dependent oxygen consumption in nitrogen‐fixing cyanobacteria plays a key role in nitrogenase protection1

All colonial diazotrophic cyanobacteria are capable of simultaneously evolving O₂ through oxygenic photosynthesis and fixing nitrogen via nitrogenase. Since nitrogenase is irreversibly inactivated by O₂, accommodation of the two metabolic pathways has led to biochemical and/or structural adaptations that protect the enzyme from O₂. In some species, differentiated cells (heterocysts) are produced within the filaments. PSII is absent in the heterocysts, while PSI activity is maintained. In other, nonheterocystous species, however, a “division of labor” occurs whereby individual cells within a colony appear to ephemerally fix nitrogen while others evolve oxygen. Using membrane inlet mass spectrometry (MIMS) in conjunction with tracer ¹⁸O₂ and inhibitors of photosynthetic and respiratory electron transport, we examined the light dependence of O₂ consumption in Trichodesmium sp. IMS 101, a nonheterocystous, colonial cyanobacterium, and Anabaena flos‐aquae (Lyngb.) Bréb. ex Bornet et Flahault, a heterocystous species. Our results indicate that in both species, intracellular O₂ concentrations are maintained at low levels by the light‐dependent reduction of oxygen via the Mehler reaction. In N₂‐fixing Trichodesmium colonies, Mehler activity can consume ～75% of gross O₂ production, while in Trichodesmium utilizing nitrate, Mehler activity declines and consumes ～10% of gross O₂ production. Moreover, evidence for the coupling between N₂ fixation and Mehler activity was observed in purified heterocysts of Anabaena, where light accelerated O₂ consumption by 3‐fold. Our results suggest that a major role for PSI in N₂‐fixing cyanobacteria is to effectively act as a photon‐catalyzed oxidase, consuming O₂ through pseudocyclic electron transport while simultaneously supplying ATP in both heterocystous and nonheterocystous taxa.     

Prolonging the action of protein and peptide drugs by a novel approach of reversible polyethylene glycol modification

Polyethylene glycol (PEG)-conjugated therapeutic peptides/proteins have been shown to exhibit clinical properties superior to those of their corresponding unmodified parent molecules. However, the desirable pharmacological features gained by protein PEGylation become irrelevant if conjugates are inactivated or cannot reach their target tissues. Here we describe the design and synthesis of MAL-FMS-OSU. This bifunctional agent enables PEG chains to be linked to peptides and proteins through a slowly hydrolysable chemical bond. PEG-FMS-peptide/protein conjugates thus formed undergo spontaneous hydrolysis at a slow rate upon incubation at pH 8.5, 37 degrees C with a t(1/2) value of 8-14 +/- 2 h, generating the unmodified parent molecule. The validity of this approach was studied with exendin-4 and human growth hormone. A single subcutaneous administration of PEG(40,000)-FMS-exendin-4 facilitated a prolonged and stable reduction in glucose levels in mice (t(1/2) = 30 +/- 2 h) and exceeded the effect obtained by the same dose of the native hormone by 7-8 times.     

The importance of thermodynamic equilibrium for high throughput gene expression arrays

We present an analysis of physical chemical constraints on the accuracy of DNA micro-arrays under equilibrium and nonequilibrium conditions. At the beginning of the article we describe an algorithm for choosing a probe set with high specificity for targeted genes under equilibrium conditions. The algorithm as well as existing methods is used to select probes from the full Saccharomyces cerevisiae genome, and these probe sets, along with a randomly selected set, are used to simulate array experiments and identify sources of error. Inasmuch as specificity and sensitivity are maximum at thermodynamic equilibrium, we are particularly interested in the factors that affect the approach to equilibrium. These are analyzed later in the article, where we develop and apply a rapidly executable method to simulate the kinetics of hybridization on a solid phase support. Although the difference between solution phase and solid phase hybridization is of little consequence for specificity and sensitivity when equilibrium is achieved, the kinetics of hybridization has a pronounced effect on both. We first use the model to estimate the effects of diffusion, crosshybridization, relaxation time, and target concentration on the hybridization kinetics, and then investigate the effects of the most important kinetic parameters on specificity. We find even when using probe sets that have high specificity at equilibrium that substantial crosshybridization is present under nonequilibrium conditions. Although those complexes that differ from perfect complementarity by more than a single base do not contribute to sources of error at equilibrium, they slow the approach to equilibrium dramatically and confound interpretation of the data when they dissociate on a time scale comparable to the time of the experiment. For the best probe set, our simulation shows that steady-state behavior is obtained in a relaxation time of approximately 12-15 h for experimental target concentrations approximately (10(-13) - 10(-14))M, but the time is greater for lower target concentrations in the range (10(-15)-10(-16))M. The result points to an asymmetry in the accuracy with which up- and downregulated genes are identified.     

Root exudate of pmi tomato mutant M161 reduces AM fungal proliferation in vitro

Soluble factors released from roots of the pre-mycorrhizal infection (pmi) myc(-) tomato mutant M161 were analyzed and compared with normal wild-type released factors. Aseptic whole exudates from the M161 mutant retarded the proliferation of Glomus intraradices in vitro. When the whole exudate was further fractionated on a C18 SEPAK cartridge, the 50/70% methanol fraction showed an activity against hyphal tip growth of Gigaspora gigantea and Gl. intraradices. Preliminary characterization of the exudate suggests that the inhibitory moieties are heat labile, bind to PVPP (polyvinyl polypyrrolidone), and are not volatile. This is the first reported instance of the inhibition by a myc(-) plant being ascribed to inhibitory component(s) released in root exudate.     

Dynamical analysis of a degenerate primary and secondary humoral immune response

Lymphocyte receptor response to antigen is degenerate. Each receptor can have a high affinity to more than one antigen. The optimal level of degeneracy was previously modeled using different methods; all showing that the degeneracy level should be inversely proportional to the probability that an antigen belongs to the self repertoire. Here we develop a new formalism, reproducing the results of previous models, which enables us to study the relation between receptor degeneracy and the pathogen-immune cell interaction dynamics, in primary and secondary response. We begin by developing a general formalismand reproducing the results obtained by Nemazee: (1) that an optimal immune system will have a capacity which is inversely proportional to the fraction of self-antigens and (2) that the number of self-reactive cells that the body destroys is tuned by this capacity optimization to be 63%. We then use our extended framework to relate the minimal number of B cell precursor required to mount an immune response to the naive B cell production rate. Finally, we analyze the dynamics of the interaction between the immune system and a pathogen and show that memory cells may be used as the first line of defense, while newly created cells are used later to refine the immune response.     

Quantitative microscopy of human DNA topoisomerase II-alpha expression in transitional cell carcinoma of the bladder

OBJECTIVE: To compare the nuclear size of various grades of transitional cell carcinoma (TCC) stained immunohistochemically with the nuclear enzyme topoisomerase II-alpha (topo II-alpha) in bladder urothelial neoplasms. STUDY DESIGN: Histologic sections from 53 consecutive papillary bladder neoplasms were stained immunohistochemically for topo II-alpha expression. There were 18 (33.9%) urothelial neoplasms of low malignant potential (UNLMP), 18 (33.9%) low grade urothelial carcinoma (LGUCa), and 17 (32%) with high grade urothelial carcinoma (HGUCa). The histologic slides were photographed at 400 x magnification and then projected on a screen, and the area with stained nuclei was measured. RESULTS: The cells and nuclei in HGUCa were significantly larger than in LGUCa (P < .05) and UNLMP (P < .01). CONCLUSION: Calculation of the area fraction of nuclei in TCC of the bladder stained with topo II-alpha is an additional method of establishing the grade of these tumors.     

Diversity of microbial communities correlated to physiochemical parameters in a digestion basin of a zero-discharge mariculture system

Bacterial community structure and physiochemical parameters were examined in a sedimentation basin of a zero-discharge mariculture system. The system consisted of an intensively stocked fish basin from which water was recirculated through two separate treatment loops. Surface water from the basin was pumped over a trickling filter in one loop while bottom-water was recirculated through a sedimentation basin followed by a fluidized bed reactor in the other. Ammonia oxidation to nitrate in the trickling filter and organic matter digestion together with nitrate reduction in the sedimentation basin and fluidized bed reactor, allowed zero-discharge operation of the system. Relatively high concentrations of oxygen, nitrate, sulphate and organic matter detected simultaneously in the digestion basin suggested the potential for a wide range of microbially-mediated transformation processes. In this study, physiochemical parameters were correlated to bacterial diversity and distribution in horizontal and vertical profiles within this basin in an effort to obtain a basic understanding of the chemical and microbial processes in this system. Chemical activity and microbial diversity, the latter measured by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments, were higher in the sludge layer than in the overlying aqueous layer of the basin. Chemical parameters in sludge samples close to the basin inlet suggested enhanced microbial activity relative to other sampling areas with evidence of both nitrate and sulphate reduction. Four of the nine DGGE bands identified in this zone were affiliated with the Bacteroidetes phylum. Detected sequences closely related to sequences of organisms involved in the sulphur cycle included Desulfovibrio, Dethiosulfovibrio and apparent sulphur oxidizers from the gamma-proteobacteria. In addition, a number of sequences from the beta and alpha-proteobacteria were identified.     

TGF-beta1 increases microbial clearance but worsens lung injury during Escherichia coli pneumonia in rats

We investigated the effects of either intravenous (IV) or intrabronchial (IB) treatment with transforming growth factor beta1 (TGF-beta1) during bacterial pneumonia in rats. Immediately following IB Escherichia coli inoculation (T0), animals (n=270) were randomized to receive a single treatment with human recombinant TGF-beta1 either via IV or IB, or via both IV and IB routes, or to receive placebo (human serum albumin, HSA) only. Blood and lung analysis was done at 6 and 168 h after E. coli inoculation. Other animals (n=40) were administered IV TGF-beta1 or HSA at T0 and 6, 12 and 24 h after E. coli inoculation to investigate the effects of multiple treatments also on survival rates alone. All animals received ceftriaxone daily. Route of administration did not influence TGF-beta1 (p=ns for the effect of TGF-beta1 comparing IV vs IB routes) and we averaged over this variable in analysis. The relative risk of death (mean +/- sem) was not altered by either single treatments administered at T0 (-0.18 +/- 0.25, p=0.47) or multiple treatments (0.40 +/- 0.50, p=0.66) of TGF-beta1. Single treatment with TGF-beta1 first decreased and then increased vascular leukocytes at 6 and 168 h, respectively, but increased alveolar leukocytes at both time points (p=0.02 comparing the differing effects of TGF-beta1 on vascular and alveolar leukocytes at 6 and 168 h). Although TGF-beta1 decreased blood and lung bacteria counts at 6 and 168 h, it also increased serum tumor necrosis factor levels and lung injury scores at these time points (p<0.05 for the effects of TGF-beta1 on each parameter at 6 and 168 h together). Thus, while increases in lung leukocyte recruitment with TGF-beta1 were associated with improved microbial clearance in this rat model of pneumonia, worsened lung injury may have negated these beneficial host defense effects, and overall survival was not significantly improved. Despite these harmful effects, additional studies may be warranted to better define the influence of exogenous TGF-beta1 on host defense during acute bacterial infections.