Direct detection of calmodulin tuning by ryanodine receptor channel targets using a Ca2+-sensitive acrylodan-labeled calmodulin

Calmodulin (CaM) activates the skeletal muscle ryanodine receptor (RyR1) at nanomolar Ca(2+) concentrations but inhibits it at micromolar Ca(2+) concentrations, indicating that binding of Ca(2+) to CaM may provide a molecular switch for modulating RyR1 channel activity. To directly examine the Ca(2+) sensitivity of RyR1-complexed CaM, we used an environment-sensitive acrylodan adduct of CaM. The resulting (ACR)CaM probe displayed high-affinity binding to, and Ca(2+)-dependent regulation of, RyR1 similar to that of unlabeled wild-type (WT) CaM. Upon addition of Ca(2+), (ACR)CaM exhibited a substantial (>50%) decrease in fluorescence (K(Ca) = 2.7 +/- 0.8 microM). A peptide derived from the RyR1 CaM binding domain (RyR1(3614)(-)(43)) caused an even more pronounced Ca(2+)-dependent fluorescence decrease, and a >or=10-fold leftward shift in its K(Ca) (0.2 +/- 0.1 microM). In the presence of intact RyR1 channels in SR vesicles, (ACR)CaM fluorescence spectra were distinct from those in the presence of RyR1(3614)(-)(43), although a Ca(2+)-dependent decrease in fluorescence was still observed. The K(Ca) for (ACR)CaM fluorescence in the presence of SR (0.8 +/- 0.4 microM) was greater than in the presence of RyR1(3614)(-)(43) but was consistent with functional determinations showing the conversion of (ACR)CaM from channel activator (apoCaM) to inhibitor (Ca(2+)CaM) at Ca(2+) concentrations between 0.3 and 1 microM. These results indicate that binding to RyR1 targets evokes significant changes in the CaM structure and Ca(2+) sensitivity (i.e., CaM tuning). However, changes resulting from binding of CaM to the full-length, tetrameric channels are clearly distinct from changes caused by the RyR1-derived peptide. We suggest that the Ca(2+) sensitivity of CaM when in complex with full-length channels may be tuned to respond to physiologically relevant changes in Ca(2+).     

Thar She Blows! A Novel Method for DNA Collection from Cetacean Blow

Background

Molecular tools are now widely used to address crucial management and conservation questions. To date, dart biopsying has been the most commonly used method for collecting genetic data from cetaceans; however, this method has some drawbacks. Dart biopsying is considered inappropriate for young animals and has recently come under scrutiny from ethical boards, conservationists, and the general public. Thus, identifying alternative genetic collection techniques for cetaceans remains a priority, especially for internationally protected species.

Methodology/Principal Findings

In this study, we investigated whether blow-sampling, which involves collecting exhalations from the blowholes of cetaceans, could be developed as a new less invasive method for DNA collection. Our current methodology was developed using six bottlenose dolphins, Tursiops truncatus, housed at the National Aquarium, Baltimore (USA), from which we were able to collect both blow and blood samples. For all six individuals, we found that their mitochondrial and microsatellite DNA profile taken from blow, matched their corresponding mitochondrial and microsatellite DNA profile collected from blood. This indicates that blow-sampling is a viable alternative method for DNA collection.

Conclusion/Significance

In this study, we show that blow-sampling provides a viable and less invasive method for collection of genetic data, even for small cetaceans. In contrast to dart biopsying, the advantage of this method is that it capitalizes on the natural breathing behaviour of dolphins and can be applied to even very young dolphins. Both biopsy and blow-sampling require close proximity of the boat, but blow-sampling can be achieved when dolphins voluntarily bow-ride and involves no harmful contact.     

Efficient Degradation of Lignocellulosic Plant Biomass,without Pretreatment,by the Thermophilic Anaerobe “Anaerocellum thermophilum” DSM 6725

Very few cultivated microorganisms can degrade lignocellulosic biomass without chemical pretreatment. We show here that “Anaerocellum thermophilum” DSM 6725, an anaerobic bacterium that grows optimally at 75°C, efficiently utilizes various types of untreated plant biomass, as well as crystalline cellulose and xylan. These include hardwoods such as poplar, low-lignin grasses such as napier and Bermuda grasses, and high-lignin grasses such as switchgrass. The organism did not utilize only the soluble fraction of the untreated biomass, since insoluble plant biomass (as well as cellulose and xylan) obtained after washing at 75°C for 18 h also served as a growth substrate. The predominant end products from all growth substrates were hydrogen, acetate, and lactate. Glucose and cellobiose (on crystalline cellulose) and xylose and xylobiose (on xylan) also accumulated in the growth media during growth on the defined substrates but not during growth on the plant biomass. A. thermophilum DSM 6725 grew well on first- and second-spent biomass derived from poplar and switchgrass, where spent biomass is defined as the insoluble growth substrate recovered after the organism has reached late stationary phase. No evidence was found for the direct attachment of A. thermophilum DSM 6725 to the plant biomass. This organism differs from the closely related strain A. thermophilum Z-1320 in its ability to grow on xylose and pectin. Caldicellulosiruptor saccharolyticus DSM 8903 (optimum growth temperature, 70°C), a close relative of A. thermophilum DSM 6725, grew well on switchgrass but not on poplar, indicating a significant difference in the biomass-degrading abilities of these two otherwise very similar organisms.Utilization of lignocellulosic biomass derived from renewable plant material to produce ethanol and other fuels is viewed as a major alternative to petroleum-based energy sources (19). The efficient conversion of plant biomass to fermentable sugars remains a formidable challenge, however, due to the recalcitrance of the insoluble starting materials (13, 21, 36). Thermal and chemical pretreatments must be used to solubilize and release the sugars, but such processes are costly and not very efficient (17, 28). Most pretreatments utilize acids, alkali, or organic solvents (39). Moreover, the plant feedstocks vary considerably in their compositions. The main components of plant biomass and the sources of the fermentable sugars, cellulose and hemicellulose, are combined with lignin, which can occupy 20% (wt/wt) or more of the plant cell wall. The development of technologies to efficiently degrade plant biomass therefore faces considerable obstacles. The discovery or engineering of new microorganisms with the ability to convert the components of lignocellulosic biomass into sugars is therefore of high priority.Not many microorganisms are able to degrade pure crystalline cellulose, and the cellulose in plant biomass has a high order of crystallinity and is even less accessible to microbial or enzymatic attack (1, 12-14). Aerobic cellulolytic microorganisms usually secrete (hemi)cellulolytic enzymes containing carbohydrate-binding modules that serve to bind the catalytic domains to insoluble substrates. On the other hand, some anaerobic bacteria and fungi produce a large extracellular multienzyme complex called the cellulosome. This binds to and efficiently degrades cellulose and other polysaccharides, although it has a limited distribution in nature (3, 7). The rate at which microorganisms degrade cellulose increases dramatically with temperature (20), but the most thermophilic cellulosome-producing bacterium that has been characterized, Clostridium thermocellum, grows optimally near only 60°C (3, 9). A few anaerobic thermophiles are known that are able to grow on crystalline cellulose even though they lack cellulosomes, and in those cases the highest optimum growth temperature is 75°C (4, 32). Biomass conversion by thermophilic anaerobic microorganisms has many potential advantages over fermentation at lower temperatures. In particular, the organisms tend to have high rates of growth and metabolism, and the processes are less prone to contamination (30).The gram-positive bacterium “Anaerocellum thermophilum” strain Z-1320 is among the most thermophilic of the cellulolytic anaerobes (32). It grows optimally at 75°C at neutral pH and utilizes both simple and complex polysaccharides, although it does not grow on xylose or pectin (32). The end products of fermentation are lactate, ethanol, acetate, CO₂, and hydrogen. Although A. thermophilum Z-1320 grows very rapidly on crystalline cellulose (4), surprisingly, it has been studied very little since its discovery (32). We report here on the physiology of a very closely related strain, A. thermophilum DSM 6725, the genome of which was recently sequenced (16). The ability of A. thermophilum DSM 6725 to grow on different types of defined and complex substrates was investigated with a focus on switchgrass and poplar. These high-lignin plants have been selected as models for biomass-to-biofuel conversion by the BioEnergy Science Center (funded by the U.S. Department of Energy; http://bioenergycenter.org/). We show that A. thermophilum DSM 6725 is able to grow efficiently on both types of plant substrate without a chemical pretreatment step.     

Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough

Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate-reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.     

Spermatogenesis in an infertile XYY man

Summary Testicular histology and meiosis has been studied in an XYY male patient identified at an infertility clinic. This man was found to have an XYY sex chromosome complement in 15% of spermatogonial metaphases. There was no clear evidence of 2 Y chromosomes at diakinesis but there appeared to be a slight excess of sperm with a fluorescent Y body.     

A possible role for 5-phosphoribosyl 1-pyrophosphate in the stimulation of uterine purine nucleotide synthesis in response to oestradiol-17β

1. It has been reported that the rate of purine nucleotide synthesis de novo in the immature rat uterus is doubled at 6h after administration of oestradiol-17beta. The present work confirms an increased incorporation of glycine and adenine into uterine nucleotides between 2 and 6h after hormone treatment and investigates the mechanism of this response. 2. Activation of regulatory enzymes is unlikely to promote increased nucleotide synthesis: the activities of 5-phosphoribosyl 1-pyrophosphate amidotransferase (EC 2.4.2.14) and adenine phosphoribosyltransferase (EC 2.4.2.7) are the same in uterine extracts from control and oestrogen-treated rats. 3. Therefore it was proposed that oestradiol might promote an increased supply of a rate-limiting substrate. The low oestrogen-sensitive rate of AMP synthesis from adenine and endogenous 5-phosphoribosyl 1-pyrophosphate in the intact uterus compared with the high, oestrogen-insensitive rate in uterine extracts supplemented with 5-phosphoribosyl 1-pyrophosphate is evidence that the supply of 5-phosphoribosyl 1-pyrophosphate limits purine nucleotide formation and may increase after hormone treatment. This proposal is supported by the decrease in AMP synthesis in the whole tissue in the presence of guanine and 7-amino-3-(beta-d-ribofuranosyl)pyrazolo[3,4-d]pyrimidine (formycin). These compounds do not inhibit adenine uptake or adenine phosphoribosyltransferase activity, but they both decrease the availability of 5-phosphoribosyl 1-pyrophosphate, the former by promoting its utilization by hypoxanthine/guanine phosphoribosyltransferase (EC 2.4.2.8) and the latter by inhibiting its synthesis from ribose 5-phosphate and ATP by ribose 5-phosphate pyrophosphokinase (EC 2.7.6.1). 4. It is unlikely that the increased availability of 5-phosphoribosyl 1-pyrophosphate results from hormonal stimulation of ribose 5-phosphate formation. Methylene Blue and phenazine methosulphate both increase ribose 5-phosphate without altering the supply of 5-phosphoribosyl 1-pyrophosphate. 5. The activity of ribose 5-phosphate pyrophosphokinase is low in uterine extracts and increases rapidly in response to oestradiol. Therefore the hormonal activation of the routes of purine nucleotide synthesis both de novo and from preformed precursors may be due, at least in part, to an increased availability of the common rate-limiting substrate 5-phosphoribosyl 1-pyrophosphate, mediated by activation of ribose 5-phosphate pyrophosphokinase.     

Herpes Simplex Virus and Human Cytomegalovirus Replication in WI-38 Cells II. An Ultrastructural Study of Viral Penetration

An electron microscope study was carried out on the early minutes of herpes simplex virus (HSV) and cytomegalovirus (CMV) penetration into WI-38 cells. Both HSV and CMV entered cells either by fusion of the viral envelope with a limiting cell membrane, or via phagocytosis. Both fusion and phagocytosis occurred within 3 min after the initiation of penetration. After fusion, the naked capsids of CMV free in the cytoplasm became coated with a fine, fibrillar material. CMV capsids thus coated retained a well-defined and easily identifiable morphology until the eclipse of visible viral particles between 1 and 1.5 days postinfection. In contrast, naked HSV capsids free in the cytoplasm were never coated. Rather, within minutes after penetration, they assumed a rounded, less regular outline, and were no longer detectable by 90 to 120 min postinfection. The free naked capsids of both viruses appeared to migrate across the cytoplasm toward the nucleus and to become located near nuclear pores. Both HSV and CMV capsids reached the nucleus as early as 5 min after the initiation of penetration. No further interaction with the nucleus could be documented. Particles were also consistently identified in the Golgi region. Phagocytosed particles generally remained within phagosomes, where they appeared to be degraded. However, stages were identified in what is believed to be the escape of enveloped viruses from phagosomes into the cytoplasm via fusion of their envelope with the phagosomal membrane.