Further investigations concerning the applicability of laser analysis in quantitative histochemistry

Summary Further investigations on the applicability of the laser technique for qantitative purposes in histochemistry were conducted. Special attention has been paid to the relationship between the volume of the crater burnt out in the tissue by laser ray treatment and the photometric readings of the spectral bands. A statistical evalution of the measurements of crater volumes for quantitative histochemistry as well as determination of the error of the former method used and previously described (Kozik et al., 1970b) have been performed. Special agar standards containing known amounts of Pb(NO₃)₂ and appropriately prepared photographic plates were used. From the results obtained it appeared that the variances calculated for the differences between density of spectral bands for the Pb present in the investigated sample and the density of the respective band for the Ag present in the photographic plate fall in the range of between 14.1 and 19.7%, whereas the error of the method in which the density of spectral bands was related to the crater volumes covered a range from 3.45–7.7%.Based on the discussion of results the authors conclude that both methods of acP assay in histological slices by means of laser microanalysis may be successfully used.     

The structure and biochemistry of the vacuolar H+ ATPase in proximal and distal urinary acidification

Vacuolar H⁺ ATPases participate in renal hydrogen ion secretion in both the proximal and distal nephron. These plasma membrane forms of the vacuolar H⁺ ATPase are regulated physiologically to maintain the acid-base balance of the organism. Proton transporting renal cells have requirements for constitutive acidification of intracellular compartments for normal endocytic and secretory functions. Recent experiments have begun to reveal how the kidney regulates these proton pumps independently. Vacuolar H⁺ ATPases are a family of structurally similar enzyme which differ in the composition of specific subunits. Cytosolic regulatory enzymes are present in renal cells which may affect vacuolar H⁺ ATPases in certain membrane compartments selectively. The vacuolar H⁺ ATPase in the plasma membrane of intercalated cells resides in a specialized proton-transporting apparatus that translocates the enzyme between an intracellular membrane pool and the plasma membrane in response to physiologic stimuli.This review will focus on the structure, enzymology, and regulation of the vacuolar H⁺ ATPase in the mammalian kidney. Because of space limitations, it will cover predominantly work from our laboratory. However, a number of investigators, including Brown (Brownet al., 1987, 1988a,b, 1989), Burckhardt (Sabolicet al., 1985; Turriniet al., 1989; Simon and Burckhardt, 1990), Madsen and Tisher (Madsen and Tisher, 1985; Verlanderet al., 1987, 1989). Steinmetz (Steinmetz, 1986; Stetson and Steinmetz, 1986), Schwartz (Scwartzet al., 1985, 1988; Satlin and Schwartz, 1989), Sabatini and Kurtzman (Sabatiniet al., 1990a,b), DuBose (Diaz-Diazet al., 1986; Gurich and DuBose, 1989), Al-Awqati (Van Adelsberg and Al-Awqati, 1986), and their coworkers, and many other investigators have made important contributions to this field.     

Production of presumptive humoral haematopoietic regulators in canine cyclic haematopoiesis

Abstract. Conditioned media (CM) were prepared according to previously published techniques from the bone marrow of dogs with cyclic haematopoiesis (CH). CM prepared from day 9 marrows inhibited mouse bone marrow CFU-s proliferation rate while CM from day 10 marrows were stimulatory and also contained an erythroid stimulating factor which appeared to be erythropoietin. In addition a highly significant trend from CM containing CFU-s inhibitory materials to media with CFU-s stimulatory activity was observed through cycles day 1 to 8. These studies further support the concept that CH is due to a defect in factors controlling stem cell proliferation and suggest that a major event occurs in CH dog marrow on days 9 and/or 10 of the cycle. Bone marrow transplantation studies (Dale & Graw, 1974; Weiden et al., 1974; Jones et al., 1975b) have indicated that canine cyclic haematopoiesis (CH) is probably due to a disorder in the multipotential stem cells. Morphological evidence (Scott et al., 1973) and the almost synchronous cycling of CFU-e, CFU-c and diffusion chamber progenitor cells (DCPC) (DUM et al., 1977, 1978a, b) lend support to such a theory. However, efforts to identify the mechanisms controlliig multipotential stem cell proliferation in dogs have been handicapped by the lack of suitable techniques to study these cells in the canine. Recently, Wright and co-workers (Wright & Lord, 1978, 1979; Wright et al., 1979; Lord et al., 1979), on the basis of previous observations (Frindel et al., 1976; Frindel & Guigon, 1977), described the preparation of species non-specific, bone marrow conditioned media (CM) which are capable of influencing the proliferation rate of murine colony forming units-spleen (CFU-s). The studies now reported were designed to determine if CM prepared from canine CH marrow would influence the proliferation rate of murine bone marrow CFU-s. The results indicate that a major event, possibly related to the in vivo control of stem cell proliferation in dogs with CH, occurs on days 9–10 of the cycle; day 1 being the first day when the peripheral blood neutrophil count falls below-1600 mm³.     

A seafloor crater in the German Bight and its effects on the benthos

 In 1963 a deep crater was formed about 65 m below sea level in the western part of the German Bight, due to a gas eruption caused by drilling carried out from the platform ’Mr. Louie’. The study area is situated in a sandy to muddy bottom area inhabited by an Amphiura filiformis association (sensu Salzwedel et al. 1985). The crater, sometimes called ’Figge-Maar’, functions as a sediment trap, concentrating particles and organisms from the water column, thus leading to extreme sedimentation rates of about 50 cm, on average, per year. Crater stations, compared with stations situated in the vicinity, show enrichments of juveniles. Echinoderms, especially the subsurface-dwelling heart urchin Echinocardium cordatum and ophiuroids are responsive to enrichment. Other species that are typical of the Amphiura filiformis association are shown to be unable to cope with the special conditions in the crater. Received: 12 June 1998 / Accepted:16 September 1998     

Neurotensin receptors: Binding properties,transduction pathways,and structure

Summary Neurotensin is a 13-amino acid peptide (pGlu-Leu-Tyr-Glu-Asn-Lys-Pro-Arg-Arg-Pro-Tyr-Ile-Leu) originally isolated from hypothalami (Carraway and Leeman, 1973) and later from intestines (Kitabgiet al., 1976) of bovine. The peptide is present throughout the animal kingdom, suggesting its participation to important processes basic to animal life (Carrawayet al., 1982). Neurotensin and its analogue neuromedin-N (Lys-Ile-Pro-Tyr-Ile-Leu) (Minaminoet al., 1984) are synthesized by a common precursor in mammalian brain (Kislauskiset al., 1988) and intestine (Dobneret al., 1987). The central and peripheral distribution and effects of neurotensin have been extensively studied. In the brain, neurotensin is exclusively found in nerve cells, fibers, and terminals (Uhlet al., 1979), whereas the majority of peripheral neurotensin is found in the endocrine N-cells located in the intestinal mucosa (Orciet al., 1976; Helmstaedteret al., 1977). Central or peripheral injections of neurotensin produce completely different pharmacological effects (Table I) indicating that the peptide does not cross the blood-brain barrier. Many of the effects of centrally administered neurotensin are similar to those of neuroleptics or can be antagonized by simultaneous administration of TRH (Table I). The recently discovered nonpeptide antagonist SR 48692 (Gullyet al., 1993) can inhibit several of the central and peripheral effects of neurotensin (Table I).Like many other neuropeptides, neurotensin is a messenger of intracellular communication working as a neurotransmitter or neuromodulator in the brain (Nemeroffet al., 1982) and as a local hormone in the periphery (Hirsch Fernstromet al., 1980). Thus, several pharmacological, morphological, and neurochemical data suggest that one of the functions of neurotensin in the brain is to regulate dopamine neurotransmission along the nigrostriatal and mesolimbic pathways (Quirion, 1983; Kitabgi, 1989). On the other hand, the likely role of neurotensin as a parahormone in the gastrointestinal tract has been well documented (Rosell and Rökaeus, 1981; Kitabgi, 1982).Both central and peripheral modes of action of neurotensin imply as a first step the recognition of the peptide by a specific receptor located on the plasma membrane of the target cell. Formation of the neurotensin-receptor complex is then translated inside the cell by a change in the activity of an intracellular enzyme. This paper describes the binding and structural properties of neurotensin receptors as well as the signal transduction pathways that are activated by the peptide in various target tissues and cells.     

Evolutionary Stable Strategies and Trade-Offs in Generalized Beverton and Holt Growth Models

A generalized Beverton–Holt model is considered in which a parameterγcharacterizes the onset of density dependence. An evolutionary stable strategy analysis of this parameter, reported in Getz (1996), is developed further here, using invasion exponents and the strategy dynamics of Vincentet al.(1993). The parameterγis also allowed to be density dependent, and it is shown that the most successful strategies of this type are those for whichγis large for low densities and close to its minimum for high densities. A biological interpretation is given in the context of mobile females depositing their relatively sessile young on patches of resource, namely, females should overdisperse their young on resources when adult densities are high and underdisperse them when these densities are low. Finally the per capita growth rate parameter is also allowed to depend onγ. It is shown that this dependence provides a mechanism by which periodic or chaotic attractor dynamics could evolve towards equilibrium attractor dynamics.     

Three-trophic-level interactions in cattail hybrid zones

Plant-herbivore and herbivore-parasitoid wasp interactions were examined in three hybrid zones of the cattails Typha latifolia and T. angustifolia in south-eastern Michigan over a 2-year period. Patterns of resource use by two lepidopteran species of seed-eating herbivores were studied and herbivore densities sustained by the hybrid cattail T. x glauca and its parental species were determined. Densities of the commoner seed-eating lepidopteran, Lymnaecia phragmitella, were found to be highest in seed heads of both parental species and lowest in hybrid seed heads in zones of hybridization, thus supporting the hybrid resistance hypothesis of Fritz et al. (1994). Densities of the second herbivore, Dicymolomia julianalis, on the hybrid were lower than on the parental T. latifolia, but did not differ from the mean of the combined herbivore densities of the two parental species. D. julianalis in cattails appears to fit the additive hypothesis (Fritz et al. 1994). Parasitism of L. phragmitella by four species of parasitoid wasp, Itoplectis conquisitor (Ichneumonidae), Scambus hispae (Ichneumonidae), Macrocentrus delicatus (Braconidae), and Temelucha gracilipes (Ichneumonidae), was studied to determine if rates of parasitization by these natural enemics on the different cattails were similar to the patterns of plant exploitation exhibited by their hosts. Parasitism rates of L. phragmitella were significantly higher in larvae reared on hybrid cattails. This study reveals two different patterns of hybrid utilization by two very similar herbivores. Opposite patterns of plant utilization were found for the parasitoids compared with their host (L. phragmitella) in cattail hybrid zones.     

Activation of PKC-ε counteracts maturation and apoptosis of HL-60 myeloid leukemic cells in response to TNF family members

Protein kinase C (PKC)-ε, a component of the serine/threo-nine PKC family, has been shown to influence the survival and differentiation pathways of normal hematopoietic cells. Here, we have modulated the activity of PKC-ε with specific small molecule activator or inhibitor peptides. PKC-ε inhibitor and activator peptides showed modest effects on HL-60 maturation when added alone, but PKC-ε activator peptide significantly counteracted the pro-maturative activity of tumor necrosis factor (TNF)-α towards the monocytic/macrophagic lineage, as evaluated in terms of CD14 surface expression and morphological analyses. Moreover, while PKC-ε inhibitor peptide showed a reproducible increase of TNF-related apoptosis inducing ligand (TRAIL)-induced apoptosis, PKC-ε activator peptide potently counteracted the pro-apoptotic activity of TRAIL. Taken together, the anti-maturative and anti-apoptotic activities of PKC-ε envision a potentially important proleukemic role of this PKC family member.Key words: acute myeloid leukemia, surface antigens, HL-60 cells, apoptosis, maturation.Activation of all protein kinase C (PKC) family of serine and threonine isoenzymes is associated with binding to the negatively charged phospholipids, phosphatidylserine, while different PKC isozymes have varying sensitivities to Ca²⁺ and lipid-derived second messengers such as diacylglycerol (Gonelli et al., 2009). Upon activation, PKC isozymes translocate from the soluble to the particulate cell fraction, including cell membrane, nucleus and mitochondria (Gonelli et al., 2009). PKC primary sequence can be broadly separated into two domains: the N-terminal regulatory domain and the conserved C-terminal catalytic domain.The regulatory domain of PKC is composed of the C1 and C2 domains that mediate PKC interactions with second messengers, phospholipids, as well as inter and intramolecular protein-protein interactions. Differences in the order and number of copies of signaling domains, as well as sequence differences that affect binding affinities, result in the distinct activity of each PKC isozyme (Gonelli et al., 2009).In recent years, a series of peptides derived from PKC have been shown to modulate its activity by interfering with critical protein-protein interactions within PKC and between PKC and PKC-binding proteins (Brandman et al., 2007, Souroujon and Mochly-Rosen, 1998). Focusing on PKC-ε isozyme and using a rational approach, one C2-derived peptide that acts as an isozyme-selective activator (Dorn et al., 1999) and another that acts as a selective inhibitor (Johnson et al., 1996) of PKC-ε, have been identified.These findings are particularly interesting since besides being involved in the physiology of normal cardiac (Braun and Mochly-Rosen, 2003, Johnson et al., 1996, Li et al., 2006), hematopoietic (Gobbi et al., 2009, Mirandola et al., 2006, Racke et al., 2001), and neuronal (Borgatti et al., 1996) cell models, mounting experimental evidences have linked altered PKC-ε functions to solid tumor development (Okhrimenko et al., 2005, Gillespie et al., 2005, Lu et al., 2006). Therefore, taking advantage of the recent availability of small molecule peptides able to activate or inhibit specifically PKC-ε by disrupting protein/protein interactions (Dorn et al., 1999, Johnson et al., 1996), which open important therapeutic perspectives, we have investigated the effects of both PKC-ε activator and PKC-ε inhibitor peptides on the maturation and survival of leukemic cells, using as a model system the HL-60 myeloblastic leukemia cell line, which can be induced to undergo terminal differentiation or apoptotic cell death by a variety of chemical and biological agents (Breitman et al., 1980, Zauli et al., 1996).     

The Discovery of an Uncoupling Mitochondrial Protein in Plants

This paper describes peculiar properties of plant mitochondria and summarizes the experiments that led to the discovery of an uncoupling protein in these mitochondria. Recent advances in the study of the biochemical and physiological properties as well as on genes encoding plant uncoupling proteins are described in articles by Borecky et al., Jezek et al., and Jarmuszkiewicz et al. in this issue.     

The Role of EDTA in Lead Transport and Accumulation by Indian Mustard

Indian mustard (Brassica juncea) plants exposed to Pb and EDTA in hydroponic solution were able to accumulate up to 55 mmol kg⁻¹ Pb in dry shoot tissue (1.1% [w/w]). This represents a 75-fold concentration of Pb in shoot tissue over that in solution. A threshold concentration of EDTA (0.25 mm) was found to be required to stimulate this dramatic accumulation of both Pb and EDTA in shoots. Below this threshold concentration, EDTA also accumulated in shoots but at a reduced rate. Direct measurement of a complex of Pb and EDTA (Pb-EDTA) in xylem exudate of Indian mustard confirmed that the majority of Pb in these plants is transported in coordination with EDTA. The accumulation of EDTA in shoot tissue was also observed to be directly correlated with the accumulation of Pb. Exposure of Indian mustard to high concentrations of Pb and EDTA caused reductions in both the transpiration rate and the shoot water content. The onset of these symptoms was correlated with the presence of free protonated EDTA (H-EDTA) in the hydroponic solution, suggesting that free H-EDTA is more phytotoxic than Pb-EDTA. These studies clearly demonstrate that coordination of Pb transport by EDTA enhances the mobility within the plants of this otherwise insoluble metal ion, allowing plants to accumulate high concentrations of Pb in shoots. The finding that both H-EDTA and Pb-EDTA are mobile within plants also has important implications for the use of metal chelates in plant nutritional research.The synthetic chelate EDTA forms a soluble complex with many metals, including Pb (Kroschwitz, 1995), and can solubilize Pb from soil particles (Means and Crerar, 1978). Recently, application of EDTA to Pb-contaminated soils has been shown to induce the uptake of Pb by plants (Jøgensen, 1993; Huang and Cunningham, 1996; Blaylock et al., 1997; Huang et al., 1997), causing Pb to accumulate to more than 1% (w/w) of shoot dry biomass (Huang and Cunningham, 1996; Blaylock et al., 1997; Huang et al., 1997). For the in situ remediation of Pb-contaminated soils it appears that this chelate-assisted phytoextraction strategy (Salt et al., 1998) may be more effective than a strategy based on the natural ability of certain wild plant species for metal hyperaccumulation (Chaney, 1983; Baker et al., 1988).For more than 40 years, synthetic chelates have been used to supply plants with micronutrients in both soil and hydroponics. Yet the mechanisms by which chelates enhance metal accumulation are still not well characterized (Wallace and Wallace, 1992), and what is known appears contradictory. For example, some evidence suggests that the Fe-chelate EDTA can be absorbed by plants and translocated to shoots (Weinstein et al., 1954; Hill-Cottingham and Llyod-Jones, 1961, 1965). However, Tiffin et al. (1960) concluded that Fe-chelates are excluded from root tissue, and this was supported by Chaney et al. (1972), who demonstrated that Fe is taken up by plants only after first being split from the Fe-chelate complex by the action of a specific plasma membrane-bound Fe-chelate reductase.To optimize the process of chelate-assisted phytoextraction, it is important to understand the biological mechanisms responsible for this process. Because of the stimulatory role of chelate application in the uptake of Pb and other metals by plants, we have investigated the role of EDTA in Pb accumulation in plants. In this study we have demonstrated that the previously described EDTA-enhanced Pb accumulation in Indian mustard (Brassica juncea) is based on the ability of EDTA to chelate and transport Pb from soil into shoot tissue.     

Intraindividual variability in Sinonamuropteridae forewing venation (Grylloblattida; Late Carboniferous): taxonomic and nomenclatural implications

The family Sinonamuropteridae has been erected for nine fossil insect species from the Late Carboniferous Tupo Formation (Ningxia, China), each represented by a single isolated forewing. The family has been assigned to the order Diaphanopterodea (extinct palaeopteran order). We investigated the forewing venation pattern and its variability in this family based on an abundant collection from the same locality. Based on new data on Chelopterum peregrinum Carpenter, 1950 (Grylloblattida; Lower Permian; Wellington Formation, U.S.A.) and the new material, we demonstrate that the nine sinonamuropteridaean species form a single one: Sinonamuropteris ningxiaensis Peng et al., 2005 . The following genera are considered as synonyms of Sinonamuropteris: Separatonerva Peng et al., 2005 syn.n. , Combonerva Peng et al., 2005 syn.n. and Tectonerva Peng et al., 2005 syn.n. The following species (all with Peng et al., 2005 , as their authority) are considered as synonyms of S. ningxiaensis: Separatonerva longa syn.n. , Separatonerva qilianshanensis syn.n. , Combonerva granulata syn.n. , Combonerva huangheensis syn.n. , Tectonerva longovata syn.n. , Sinonamuropsis zhongweiensis syn.n. , Sinonamuropsis rugoverrucosa syn.n. , Sinonamuropsis xiaheyanensis syn.n. The family must be assigned to the neopteran order Grylloblattida.     

CFTR: Domains, Structure, and Function

Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis (CF) (Collins, 1992). Over 500 naturally occurring mutations have been identified in CF gene which are located in all of the domains of the protein (Kerem et al., 1990; Mercier et al., 1993; Ghanem et al., 1994; Fanen et al., 1992; Ferec et al., 1992; Cutting et al., 1990). Early studies by several investigators characterized CFTR as a chloride channel (Anderson et al.; 1991b,c; Bear et al., 1991). The complex secondary structure of the protein suggested that CFTR might possess other functions in addition to being a chloride channel. Studies have established that the CFTR functions not only as a chloride channel but is indeed a regulator of sodium channels (Stutts et al., 1995), outwardly rectifying chloride channels (ORCC) (Gray et al., 1989; Garber et al., 1992; Egan et al., 1992; Hwang et al., 1989; Schwiebert et al., 1995) and also the transport of ATP (Schwiebert et al., 1995; Reisin et al., 1994). This mini-review deals with the studies which elucidate the functions of the various domains of CFTR, namely the transmembrane domains, TMD1 and TMD2, the two cytoplasmic nucleotide binding domains, NBD1 and NBD2, and the regulatory, R, domain.     

In vivo transfer of genes from Escherichia coli to Bacillus subtilis

Summary Escherichia coli cells, carrying plasmid pRD1 with (a) drug resistance markers from Pseudomonas (km^r, carb^r, tc^r) and (b) the nif-gene group from Klebsiella, were incubated together with Bacillus subtilis cells (str^r), whose cell wall had been disintegrated with lysozyme. Upon plating the cell mixtures onto appropriately supplemented selective medium, multiple drug resistant Bacillus subtilis cells were obtained. Their nature was verified by suitable biochemical tests and checking for the presence of additional genetic markers. The majority of the isolates was unstable. Some however retained multiple drug resistance for longer periods of time, and several produced nitrogenase activity. The data are interpreted as evidence not only for the transfer of the respective genes but also for their expression in the gram-positive recipient cells.Abbreviations pRD1 a hybrid plasmid, renamed by Ray Dixon - pRP4 plasmid from Pseudomonas, originally described by Datta et al., J. Bacteriol 108, 1244 (1971) - km ^r, carb ^r, tc ^r, str ^r resistance against kanamycin, carbenicillin, tetracyclin and streptomycin, respectively - r restriction negative. For other bacterial markers refer to Bachmann, B.J. et al., Bacteriological Reviews 40, 116 (1976)     

Evolutionary tradeoff and equilibrium in an aquatic predator-prey system

Due to the conventional distinction between ecological (rapid) and evolutionary (slow) timescales, ecological and population models have typically ignored the effects of evolution. Yet the potential for rapid evolutionary change has been recently established and may be critical to understanding how populations persist in changing environments. In this paper we examine the relationship between ecological and evolutionary dynamics, focusing on a well-studied experimental aquatic predator-prey system (Fussmann et al., 2000, Science, 290, 1358–1360; Shertzer et al., 2002, J. Anim. Ecol., 71, 802–815; Yoshida et al., 2003, Nature, 424, 303–306). Major properties of predator-prey cycles in this system are determined by ongoing evolutionary dynamics in the prey population. Under some conditions, however, the populations tend to apparently stable steady-state densities. These are the subject of the present paper. We examine a previously developed model for the system, to determine how evolution shapes properties of the equilibria, in particular the number and identity of coexisting prey genotypes. We then apply these results to explore how evolutionary dynamics can shape the responses of the system to ‘management’: externally imposed alterations in conditions. Specifically, we compare the behavior of the system including evolutionary dynamics, with predictions that would be made if the potential for rapid evolutionary change is neglected. Finally, we posit some simple experiments to verify our prediction that evolution can have significant qualitative effects on observed population-level responses to changing conditions.     

Long branch attraction,taxon sampling,and the earliest angiosperms: <Emphasis Type="Italic">Amborella</Emphasis> or monocots?

Background  

Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots.     

Shotgun Crystallization Strategy for Structural Genomics II: Crystallization Conditions that Produce High Resolution Structures for T. maritima Proteins

Currently, 119 high resolution structures of Thermotoga maritima proteins have been determined by the Joint Center for Structural Genomics (JCSG, www.jcsg.org). Sixty-seven of these were solved using the first implementation of the multi-tiered crystallization strategy at the JCSG for the efficient crystallization of large numbers of protein targets. Previously, we reported the analysis of all proteins crystallized using this multi-tiered strategy [Lesley, S.A. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 11664–11669; Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037]. Here, we extend the analysis and describe the crystallization characteristics of those proteins that produced diffraction quality crystals, ultimately resulting in high resolution structures. First, we found that over 77% (52) of the crystals used for structure determination were produced directly from high-throughput coarse screens, indicating that less than one quarter of the crystals (15) required fine screening. In addition, as observed for the proteome screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037], the majority of conditions that produced crystals for natively expressed proteins, whose structures have been determined, were distinct from those of their more extensively purified and selenomethionine-labeled counterparts. Finally, 99% of the proteins whose structures were solved crystallized in conditions contained in the JCSG Minimal Core Screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037; Page, R. and Stevens, R.C. (2004) Methods 34, 373–389], a set of 67 conditions previously identified as those most likely to produce crystals of a diverse set of proteins, confirming its success for rapid identification of proteins with a natural propensity to crystallize.     

Palaeoenvironmental aspects of Late Ordovician Sericoidea shell concentrations in an impact crater,Tvären,Sweden

Frisk, Å.M. & Harper, D.A.T. 2010: Palaeoenvironmental aspects of Late Ordovician Sericoidea shell concentrations in an impact crater, Tvären, Sweden. Lethaia, Vol. 44, pp. 383–396. Numerous studies have reported the presence of the small, thin‐shelled cosmopolitan rhynchonelliformean Sericoidea as being environmentally controlled and, together with its close relatives, characteristic of deep‐water, distal, clastic Ordovician and Silurian settings. Assemblages of Sericoidea have been analysed from post‐impact strata in a newly formed Late Ordovician impact crater. In the crater succession, colonization of benthic faunas can be monitored through the post‐impact limestone, demonstrating a number of environmental preferences. Consequently, the crater, as a result of its restricted area, provides an experimental arena for faunal distributions to be correlated with specific environments. The continuous infilling of the crater following its formation reveals a transition from argillaceous mudstones to carbonates deposited in deeper‐water environments to shallower regimes. Rhynchonelliformean brachiopods inhabited the crater depression very late after the impact and are entirely represented by the genus Sericoidea, occurring abundantly in the upper third of the existing crater infill. The deep‐water regime that existed in the depression during the initial interval of crater formation had been substantially reduced. Clearly Sericoidea‐bearing associations associated with shaly substrates did not merely favour and occupy deep‐water environments as previously suggested. The unfavourable conditions triggered by the impact and the inhospitable aftermath allowed Sericoidea to exploit a less‐crowded ecospace. This reorganization, following the catastrophe, from a deep‐water related ecological niche to considerable shallower settings suggests that Sericoidea was a pioneer colonist displaying an opportunist r‐strategy. The shell beds analysed are related to shallower water and this may, moreover, help unravel the dilemma of the general absence of Sericoidea in the deeper‐water Foliomena fauna. □Dalby Limestone, impact crater, Late Ordovician, opportunists, Sericoidea, Tvären.     

Scanner calibration revisited

Background  

Calibration of a microarray scanner is critical for accurate interpretation of microarray results. Shi et al. (BMC Bioinformatics, 2005, 6, Art. No. S11 Suppl. 2.) reported usage of a Full Moon BioSystems slide for calibration. Inspired by the Shi et al. work, we have calibrated microarray scanners in our previous research. We were puzzled however, that most of the signal intensities from a biological sample fell below the sensitivity threshold level determined by the calibration slide. This conundrum led us to re-investigate the quality of calibration provided by the Full Moon BioSystems slide as well as the accuracy of the analysis performed by Shi et al.     

The activities of mycotoxins derived from Fusarium and related substances in a short-term transformation assay using v-Ha-ras-transfected BALB/3T3 cells (Bhas 42 cells)

Cell transformation assays using BALB/3T3 cells can mimic the two-stage process of chemical carcinogenesis in experimental animals. A short-term transformation assay using v-Ha-ras-transfected BALB/3T3 cells (Bhas 42 cells), which was developed by Ohmori et al. and modified by Asada et al., has been reported to detect both tumor initiators and promoters as transformation initiators and promoters, respectively, with their differences based on their protocols. In this new short-term assay, we examined mycotoxins derived from Fusarium and related substances for the initiation and promotion activities of the transformation. The tested substances included deoxynivalenol, nivalenol, fusarenon-X, T-2 toxin, fumonisin B₁, fumonisin B₂, zearalenone, α-zearalanol, β-zearalanol, α-zearalenol and β-zearalenol. Fumonisin B₁ and T-2 toxin were positive for promoting activity in the assay. Especially, T-2 toxin was active at concentrations as low as 0.001–0.002 μg/mL in the culture medium. From a comparison between the results of this study and published carcinogenicity assay data, it was expected that the Bhas 42 cell transformation assay had a good correlation with the two-stage carcinogenicity tests using experimental animals for estimation of the tumor-promoting activity.     

Kinetic models of photosystem II should accommodate the effect of donor side quenching on variable chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence in the microseconds time range

Quantitative data on laser flash-induced variable fluorescence in the 100 ns to 1 ms time range (Belyaeva et al. in Photosynth Res 98:105–119, 2008) confirming those of others (Steffen et al. in Biochemistry 40:173–180, 2001, Biochemistry 44:3123–3132, 2005; Belyaeva et al. in Biophysics 51(6):976–990, 2006), need a substantial correction with respect to magnitude of the normalized variable fluorescence associated with single turnover-induced charge separation in RCs of PS II. Their data are conclusive with the involvement of donor side quenching, the release of which occurs with a rate constant in the range of tens of ms⁻¹, and presumed to be associated with reduction of Y_\textz ⁺ Y_{\text{z}}^{ + } by the OEC.