Caveolae and calcium handling, a review and a hypothesis

Caveolae are associated with molecules crucial for calcium handling. This review considers the roles of caveolae in calcium handling for smooth muscle and interstitial cells of Cajal (ICC). Structural studies showed that the plasma membrane calcium pump (PMCA), a sodium-calcium exchanger (NCX1), and a myogenic nNOS appear to be colocalized with caveolin 1, the main constituent of these caveolae. Voltage dependent calcium channels (VDCC) are associated but not co-localized with caveolin 1, as are proteins of the peripheral sarcoplasmic reticulum (SR) such as calreticulin. Only the nNOS is absent from caveolin 1 knockout animals. Functional studies in calcium free media suggest that a source of calcium in tonic smooth muscles exists, partly sequestered from extracellular EGTA. This source supported sustained contractions to carbachol using VDCC and dependent on activity of the SERCA pump. This source is postulated to be caveolae, near peripheral SR. New evidence, presented here, suggests that a similar source exists in phasic smooth muscle of the intestine and its ICC. These results suggest that caveolae and peripheral SR are a functional unit recycling calcium through VDCC and controlling its local concentration. Calcium handling molecules associated with caveolae in smooth muscle and ICC were identified and their possible functions also reviewed.     

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein

Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.     

Ergot—a blessing and a scourge

Ergot, the black mass of a particular fungus on cereal grains, especially rye, was the cause of frightful epidemics in Europe more than a thousand years ago, and the ingested contaminated grain has occasioned disease in Russia as late as 1927 and in the United States a generation earlier. Medicinally administered, however, it provides a very important drug in the science of obstetrics.     

Gastrointestinal stromal tumors in a baboon, a spider monkey, and a chimpanzee and a review of the literature

Background  Gastrointestinal stromal tumors (GISTs) are believed to originate from the intestinal pacemaker cells (interstitial cells of Cajal) or their progenitor cells. Spontaneous tumors have been reported in dogs, horses, rhesus, and a chimpanzee and they have been produced experimentally in mice and rats. GISTs represent a diagnostic challenge because they cannot be differentiated from non-lymphoid mesenchymal tumors without using human c-kit (CD117) immunohistochemistry.
Methods  Three neoplasms were incidental findings at necropsy in the stomachs of a baboon and a spider monkey and in the rectum of a chimpanzee.
Results  The GISTs were initially diagnosed grossly and histologically with hematoxylin and eosin as leiomyomas. Immunohistochemical analysis revealed that all three were c-kit (CD117) positive.
Conclusions  These are the first reports of GISTs in the baboon and spider monkey and the second in a chimpanzee. The occurrence of GISTs in non-human primates may provide a unique opportunity to study these tumors.     

Race-centrism: a critique and a research agenda

This article reviews some of the most prominent books in the field of race studies in the USA and identifies their shared assumptions: that racial inequality is the primary principle of stratification in the USA; that is has transformed but not lessened since the civil rights era; that it can be explained by the racist inclinations of the white majority, which operates as a collective, strategic actor to preserve its dominance; and finally, that racial domination plays a similarly crucial role around the world. I explore what kind of questions would need to be answered in order to put these assumptions on firmer empirical and theoretical ground and outline a corresponding research agenda. Some empirical evidence is provided to question the assumption that race plays a dominant role around the world and is associated with more political inequality than ethnic divisions.     

Testing a Primary and a Secondary Endpoint in a Group Sequential Design

Summary We consider a clinical trial with a primary and a secondary endpoint where the secondary endpoint is tested only if the primary endpoint is significant. The trial uses a group sequential procedure with two stages. The familywise error rate (FWER) of falsely concluding significance on either endpoint is to be controlled at a nominal level α. The type I error rate for the primary endpoint is controlled by choosing any α‐level stopping boundary, e.g., the standard O'Brien–Fleming or the Pocock boundary. Given any particular α‐level boundary for the primary endpoint, we study the problem of determining the boundary for the secondary endpoint to control the FWER. We study this FWER analytically and numerically and find that it is maximized when the correlation coefficient ρ between the two endpoints equals 1. For the four combinations consisting of O'Brien–Fleming and Pocock boundaries for the primary and secondary endpoints, the critical constants required to control the FWER are computed for different values of ρ. An ad hoc boundary is proposed for the secondary endpoint to address a practical concern that may be at issue in some applications. Numerical studies indicate that the O'Brien–Fleming boundary for the primary endpoint and the Pocock boundary for the secondary endpoint generally gives the best primary as well as secondary power performance. The Pocock boundary may be replaced by the ad hoc boundary for the secondary endpoint with a very little loss of secondary power if the practical concern is at issue. A clinical trial example is given to illustrate the methods.     

Production of avermectin A2a and monoglycosides A2a and B2a by a strain ofStreptomyces avermitilis

A strain ofStreptomyces avermitilis producing almost predominantly avermectin A2a and monoglycosides A2a and B2a was described. Methods of analytical and preparative high performance liquid chromatography were used for comparison of chromatographic profiles and product isolation, respectively. Identification of isolated compounds was based on¹³C-NMR spectrometric results.     

Antagonistic coevolution between a bacterium and a bacteriophage

Antagonistic coevolution between hosts and parasites is believed to play a pivotal role in host and parasite population dynamics, the evolutionary maintenance of sex and the evolution of parasite virulence. Furthermore, antagonistic coevolution is believed to be responsible for rapid differentiation of both hosts and parasites between geographically structured populations. Yet empirical evidence for host-parasite antagonistic coevolution, and its impact on between-population genetic divergence, is limited. Here we demonstrate a long-term arms race between the infectivity of a viral parasite (bacteriophage; phage) and the resistance of its bacterial host. Coevolution was largely driven by directional selection, with hosts becoming resistant to a wider range of parasite genotypes and parasites infective to a wider range of host genotypes. Coevolution followed divergent trajectories between replicate communities despite establishment with isogenic bacteria and phage, and resulted in bacteria adapted to their own, compared with other, phage populations.     

Simultaneous force and fluorescence measurements of a protein that forms a bond between a living bacterium and a solid surface

All microbial biofilms are initiated through direct physical contact between a bacterium and a solid surface, a step that is controlled by inter- and intramolecular forces. Atomic force microscopy and confocal laser scanning microscopy were used simultaneously to observe the formation of a bond between a fluorescent chimeric protein on the surface of a living Escherichia coli bacterium and a solid substrate in situ. The chimera was composed of a portion of outer membrane protein A (OmpA) fused to the cyan-fluorescent protein AmCyan. Sucrose gradient centrifugation and fluorescent confocal slices through bacteria demonstrated that the chimeric protein was targeted and anchored to the external cell surface. The wormlike chain theory predicted that this protein should exhibit a nonlinear force-extension "signature" consistent with the sequential unraveling of the AmCyan and OmpA domains. Experimentally measured force-extension curves revealed a unique pair of "sawtooth" features that were present when a bond formed between a silicon nitride surface (atomic force microscopy tip) and E. coli cells expressing the OmpA-AmCyan protein. The observed sawtooth pair closely matched the wormlike chain model prediction for the mechanical unfolding of the AmCyan and OmpA substructures in series. These sawteeth disappeared from the measured force-extension curves when cells were treated with proteinase K. Furthermore, these unique sawteeth were absent for a mutant stain of E. coli incapable of expressing the AmCyan protein on its outer surface. Together, these data show that specific proteins exhibit unique force signatures characteristic of the bond that is formed between a living bacterium and another surface.     

Physico-chemistry and aquatic insects of a glacier-fed and a spring-fed alpine stream

1. Physico-chemical conditions and benthic macroinvertebrates were studied in two adjacent alpine streams in the Tyrolean Alps, Austria, for 2 years, and aquatic insect emergence was recorded for 1 year.
2. In the spring-fed system, maximum discharge and increased concentrations of suspended solids, nitrate and particulate phosphorus occurred during snowmelt in June. In the glacier-fed stream, high discharge and strong diel fluctuations in flow and concentrations of suspended solids created a harsh and unstable environment during summer. Glacial ablation, variation in groundwater inflow, and water inputs from tributaries draining calcareous rocks caused water chemistry to vary both seasonally and longitudinally in glacier-fed Rotmoosache.
3. A total of 126 aquatic or semi-aquatic invertebrate taxa were collected, 94 of which were found in the glacier-fed stream and 120 in the spring-fed stream. Chironomid abundance was 2–8 times and taxa richness 2–3 times lower in the glacier-fed stream than in the spring-fed stream, as was the number of chironomid taxa (72 versus 93 total).
4. These results broadly support the conceptual model by Milner & Petts (1994) concerning glacier-fed stream systems. However, single samples and seasonal means showed relatively high invertebrate abundance and richness, especially during winter, indicating a considerable degree of spatial and temporal variability.
5. We suggest that the seasonal shifts from harsh environmental conditions in summer to less severe conditions in autumn and a rather constant environment in winter are an important factor affecting larval development, life-history patterns and the maintenance of relatively high levels of diversity and productivity in glacier-fed streams.     

Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin.

Molecular dynamics simulations in solution are performed for a rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus (RdPf) and one from the mesophilic organism Desulfovibrio vulgaris (RdDv). The two proteins are simulated at four temperatures: 300 K, 373 K, 473 K (two sets), and 500 K; the various simulations extended from 200 ps to 1,020 ps. At room temperature, the two proteins are stable, remain close to the crystal structure, and exhibit similar dynamic behavior; the RMS residue fluctuations are slightly smaller in the hyperthermophilic protein. An analysis of the average energy contributions in the two proteins is made; the results suggest that the intraprotein energy stabilizes RdPf relative to RdDv. At 373 K, the mesophilic protein unfolds rapidly (it begins to unfold at 300 ps), whereas the hyperthermophilic does not unfold over the simulation of 600 ps. This is in accord with the expected stability of the two proteins. At 473 K, where both proteins are expected to be unstable, unfolding behavior is observed within 200 ps and the mesophilic protein unfolds faster than the hyperthermophilic one. At 500 K, both proteins unfold; the hyperthermophilic protein does so faster than the mesophilic protein. The unfolding behavior for the two proteins is found to be very similar. Although the exact order of events differs from one trajectory to another, both proteins unfold first by opening of the loop region to expose the hydrophobic core. This is followed by unzipping of the beta-sheet. The results obtained in the simulation are discussed in terms of the factors involved in flexibility and thermostability.     

Spatial relationship between cytochrome a and a3

We have studied the spatial relationship between cytochromes a and a3 by the enhancement of the spin relaxation of cytochrome a3-NO EPR signals by the paramagnetic a heme at 15 K. An Fe-Fe distance of 12-19A is estimated from the absence of dipolar broadening and from the observation of spin relaxation enhancement in the a3-NO complex. When this result is combined with resonance x-ray diffraction data reported by Blasie et al. (Blasie, J. K., Pachence, J. M., Tavormina, A., Dutton, P. L., Stamatoff, J., Eisenberger, P., and Brown, G. (1982) Biochim. Biophys. Acta 679, 188-197) and the contribution from the exchange interaction is considered, we can limit the iron-iron distance to 12-16 A and estimate the angle between the Fe-Fe vector and mitochondrial membrane normal as 30-60 degrees. We also consider the possible effects of CuA on cytochrome a3-NO.