Local neighborhood effects on long-term survival of individual trees in a neotropical forest

The survival of approximately 235 000 individual tropical trees and saplings in the 50 ha permanent plot on Barro Colorado Island (BCI), Panama was analyzed over a 13-year interval (1982–1995) as a function of four biotic neighborhood variables: (i) total stem density; (ii) conspecific density; (iii) relative plant size; and (iv) relative species richness. These neighborhood variables were measured in annular rings of width 2.5 m, extending 30 m from a given focal plant, and in one more distant annulus at 47.5–50 m. Because survival was spatially autocorrelated, a Gibbs sampler and a Monte Carlo Markov chain method were used for fitting an autologistic regression model to obtain unbiased estimates of parameter variances for hypothesis testing. After pooling all species at the community level, results showed that all four variables had significant and often strong effects on focal plant survival. Three of the four variables had negative effects on focal plant survival; relative plant size was the only variable with a positive effect (18% increase in the survival odds ratio). The variables with a negative effect on the survival odds ratio, in order of their effect strength in the nearest annulus, were: stem density (a 70% reduction in the survival odds ratio), conspecific density (50% reduction) and species richness (13% reduction). A guild-level analysis revealed considerable heterogeneity among guilds in their responses to these variables. For example, survival of gap species showed a much larger positive response to relative plant size than did survival of shade-tolerant species. Survival of shrub species was positively affected by conspecific density, but canopy tree survival was negatively affected. Conspecific density negatively affected survival of rare species much more strongly than survival of common species. The neighborhood effects of conspecific density disappear within approximately 12–15 m of the focal plant. Although locally strong, the rapid spatial decay of these effects raises unanswered questions about their quantitative contribution to the maintenance of tree diversity on landscape scales in the BCI forest.     

The crystal structure of the first enzyme in the pantothenate biosynthetic pathway,ketopantoate hydroxymethyltransferase,from M tuberculosis

Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate, which is a precursor to coenzyme A and is required for penicillin biosynthesis. The crystal structure of KPHMT from Mycobacterium tuberculosis was determined by the single anomalous substitution (SAS) method at 2.8 A resolution. KPHMT adopts a structure that is a variation on the (beta/alpha) barrel fold, with a metal binding site proximal to the presumed catalytic site. The protein forms a decameric complex, with subunits in opposing pentameric rings held together by a swapping of their C-terminal alpha helices. The structure reveals KPHMT's membership in a small, recently discovered group of (beta/alpha) barrel enzymes that employ domain swapping to form a variety of oligomeric assemblies. The apparent conservation of certain detailed structural characteristics suggests that KPHMT is distantly related by divergent evolution to enzymes in unrelated pathways, including isocitrate lyase and phosphoenolpyruvate mutase.     

Sealed reticulocyte ghosts. An experimental model for the study of Fe2+ transport.

Sealed right-side-out reticulocyte ghosts transported and accumulated iron offered as 59Fe(2+)-ascorbate (Km = 1.1 microM). The uptake of iron by ghosts presented the characteristics of a transporter-mediated process: it responded to osmotic challenge, the rate of transport increased when iron was present in the opposing side, and the transport rate showed the temperature dependence typical of membrane-mediated processes. The transport of iron was dependent on an associated influx of Cl- in order to keep electroneutrality. Other transition metals, such as Cu2+, Zn2+, and Co2+, inhibited the transport of Fe2+. The overall characteristics of the system make reticulocyte sealed ghosts a very useful model in determining the basic mechanisms of membrane iron transport.     

Relationship between an altered membrane form and a low affinity form of the beta-adrenergic receptor occurring during catecholamine-induced desensitization. Evidence for receptor internalization

We have investigated the relationship between the catecholamine-induced occurrence in 1321N1 human astrocytoma cells of beta-adrenergic receptors that exhibit low apparent affinity for hydrophilic ligands in short-time assays with intact cells and a population of beta-adrenergic receptors that migrate in a light vesicle fraction on sucrose density gradients. Pretreatment of cells with concanavalin A prevents the generation of both of these forms of the receptor during incubation with agonists but does not prevent the agonist-induced decrease in isoproterenol-stimulated cyclic AMP production that also occurs during desensitization. Selective labeling of the low affinity beta-receptors with 125I-pindolol followed by centrifugation on sucrose density gradients revealed that all of the receptors in the light vesicle fraction from desensitized cells were of the low affinity type, but that a portion of the low affinity receptors also migrated in a heavier sucrose fraction together with the plasma membrane. In contrast, in control cells, no low affinity receptors were present in the heavy sucrose fractions. The agonist-induced occurrence of these various forms of the beta-adrenergic receptor can be explained on the basis of current models of desensitization involving agonist-induced internalization of beta-adrenergic receptors.     

Experimental concerns in tracer kinetic investigations of apolipoprotein metabolism

The complexity of the metabolism of the plasma lipoproteins makes it impossible to integrate the details of the reactions of specific apolipoproteins and their associated lipids without the use of computerized modeling methods. Because apolipoproteins impart specificity in the transport and chemical processing of plasma lipids, they have been the focus of many in vivo kinetic tracer investigations. The analysis of such kinetic data by modeling techniques has provided important advances in understanding lipoprotein metabolism. An example is the Delipidation Chain, an hypothesis explaining VLDL metabolism in terms of a sequential delipidation process. As a consequence of the advance in knowledge of apolipoprotein structure and metabolism, coupled with progress in computerized modeling of large systems, it has become important to refine the design of in vivo tracer kinetic investigations of the apolipoproteins. Considerations of particular importance include the selection of apolipoprotein tracers which can be shown to undergo the same reactions as the apolipoproteins whose metabolism they trace. If the physical and chemical processes which convert apolipoproteins from one metabolic pool to another are to be analyzed correctly, it is necessary to describe precisely and to measure accurately these pools. Current methods for delineating metabolic pools of apolipoproteins in vivo need to be refined. When accomplished, this will provide new opportunities to investigate the metabolic pathways of the apolipoproteins and their associated lipids. A very important challenge is to design experiments which will differentiate transfer processes, which result in net transport of a reactant, from exchange processes, whereby a tracer and a tracee are exchanged between pools without a net transport event occuring. Since both types of processes occur readily with apolipoproteins, it is important to develop methods to examine them separately. Computerized kinetic modeling provides a means for describing and understanding the complexities of lipoprotein metabolism. A major challenge is for the experimentalist to acquire data which accurately reflect the physiological processes involved in lipoprotein metabolism.     

Rapid detection of lytic antimicrobial activity against yeast and filamentous fungi.

A rapid method for assessing the lytic activity of antimicrobial agents against yeast and fungi has been developed. The assay is based on the release of the intracellular enzyme, maltase (alpha-glucosidase). The released maltase activity was measured colorimetrically by the production of p-nitrophenol from p-nitrophenyl-alpha-D-glucopyranoside (PNPG). The lytic activity of different antimicrobial compounds was measured against yeast cells or germinating spores of filamentous fungi. Lytic anti-yeast activity could be detected within 20 min incubation at 30 degrees C against Saccharomyces cerevisiae, Candida albicans, and Cryptococcus neoformans. Lytic anti-fungal activity appeared after 2 h of incubation at 30 degrees C against germinating spores of Aspergillus niger and Botrytis cinerea. Whole cells of either yeast or fungi did not hydrolyze sufficient PNPG within 3 h at 30 degrees C to yield a detectable color change. Lytic activity of enzymes (e.g., Lyticase), antibiotics (e.g., Amphotericin B), and an antibiotic-producing strain of bacteria were detected using the assay. The anti-yeast assay has been adapted to a 96-well microtiter format. Both assays provided a rapid, sensitive, and reproducible detection of lytic anti-yeast and anti-fungal activity.     

Syntaxin 4 mediates endosome recycling for lytic granule exocytosis in cytotoxic T‐lymphocytes

Adaptive and innate immunity utilize the perforin‐killing pathway to eliminate virus‐infected or cancer cells. Cytotoxic T‐lymphocytes (CTLs) and natural killer cells mediate this process by releasing toxic proteins at the contact area with target cells known as immunological synapse (IS). Formation of a stable IS and exocytosis of toxic proteins requires persistent fusion of Rab11a recycling endosomes with the plasma membrane (PM) that may assure the delivery of key effector proteins. Despite the importance of the recycling endosomal compartment, the membrane fusion proteins that control this process at the IS remain elusive. Here, by performing knockdown experiments we found that syntaxin 4 (STX4) is necessary for cytotoxic activity and CD107a degranulation against target cells in a similar fashion to syntaxin 11, which is involved in lytic granule (LG) exocytosis and immunodeficiency when it is mutated. Using total internal reflection fluorescent microscopy we identified that STX4 mediates fusion of EGFP‐Rab11a vesicles at the IS. Immunoprecipitation experiments in lysates of activated CTLs indicate that endogenous STX4 may drive this fusion step by interacting with cognate proteins: Munc18‐3/SNAP23/VAMP7 and/or VAMP8. These results reveal the role of STX4 in mediating fusion of Rab11a endosomes upstream of lytic granules (LGs) exocytosis and further demonstrate the importance of this pathway in controlling CTL‐mediated cytotoxicity.      

New molecular reporters for rapid protein folding assays

The GFP folding reporter assay uses a C-terminal GFP fusion to report on the folding success of upstream fused polypeptides. The GFP folding assay is widely-used for screening protein variants with improved folding and solubility, but truncation artifacts may arise during evolution, i.e. from de novo internal ribosome entry sites. One way to reduce such artifacts would be to insert target genes within the scaffolding of GFP circular permuted variants. Circular permutants of fluorescent proteins often misfold and are non-fluorescent, and do not readily tolerate fused polypeptides within the fluorescent protein scaffolding. To overcome these limitations, and to increase the dynamic range for reporting on protein misfolding, we have created eight GFP insertion reporters with different sensitivities to protein misfolding using chimeras of two previously described GFP variants, the GFP folding reporter and the robustly-folding "superfolder" GFP. We applied this technology to engineer soluble variants of Rv0113, a protein from Mycobacterium tuberculosis initially expressed as inclusion bodies in Escherichia coli. Using GFP insertion reporters with increasing stringency for each cycle of mutagenesis and selection led to a variant that produced large amounts of soluble protein at 37 degrees C in Escherichia coli. The new reporter constructs discriminate against truncation artifacts previously isolated during directed evolution of Rv0113 using the original C-terminal GFP folding reporter. Using GFP insertion reporters with variable stringency should prove useful for engineering protein variants with improved folding and solubility, while reducing the number of artifacts arising from internal cryptic ribosome initiation sites.     

Protein production and purification

In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.