Iron–sulfur protein folds,iron–sulfur chemistry,and evolution

An inventory of unique local protein folds around Fe–S clusters has been derived from the analysis of protein structure databases. Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe–2S]^2+,+ or [4Fe–4S]^2+,+ clusters. In contrast, high-potential Fe–S clusters, notwithstanding their structural diversity, occur in only three different protein folds. These observations suggest that the extant population of Fe–S protein folds has to a large extent been shaped in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing biosphere, in conditions where iron and sulfide had become poorly available, Fe–S clusters were less stable, and in addition faced competition from heme iron and copper active sites. Among the low-potential Fe–S active sites, protein folds hosting [4Fe–4S]^2+,+ clusters outnumber those with [2Fe–2S]^2+,+ ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe–S sites are evolving within proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the polypeptide chain. The discovery rate of novel Fe–S-containing protein folds underwent a sharp increase around 1995, and has remained stable to this day. The current trend suggests that the mapping of the Fe–S fold space is not near completion, in agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that the extant structural landscape of Fe–S proteins has been shaped to a large extent by primeval geochemical conditions on one hand, and iron–sulfur chemistry on the other.     

Sex, Death, and Evolution in Proto- and Metazoa, 1876–1913

In the period 1875–1920, a debate about the generality and applicability of evolutionary theory to all organisms was motivated by work on unicellular ciliates like Paramecium because of their peculiar nuclear dualism and life cycles. The French cytologist Emile Maupas and the German zoologist August Weismann argued in the 1880s about the evolutionary origins and functions of sex (which in the ciliates is not linked to reproduction), and death (which appeared to be the inevitable fate of lineages denied sexual conjugation), an argument rooted in the question of whether the ciliates and their processes where homologous to other cellular organisms. In the beginning of the twentieth century, this question of homology came to be less important as the ciliates were used by the British protozoologist Clifford Dobell and the American zoologist Herbert Spencer Jennings to study evolutionary processes in general rather than problems of development and cytology. For them, homology mattered less than analogy. This story illustrates two partially distinct problems in evolutionary biology: first, the question of whether all living things have common features and origins; and second, whether their history and current nature can be described by identical mechanisms. Where Maupas (contra Weismann) made the ciliates qualitatively the same as all other organisms in order to create a cohesive evolutionary theory for biology, Jennings and Dobell made them qualitatively different in order to achieve the same end. This revised version was published online in July 2006 with corrections to the Cover Date.     

Reactions between dimanganese,dirhenium, and manganese–rhenium decacarbonyl and oxidants

The dimetal decacarbonyls M₂(CO)₁₀, where M₂ = Mn₂, MnRe, and Re₂, do not react with anionic strong oxidants such as Fe(CN)₆³⁻ or IrCl₆²⁻ in CH₃CN solvent nor with neutral or cationic weak oxidants. Strong cationic oxidants such as NO⁺, Fe(phen)₃³⁺, and Cu²⁺ rapidly oxidize M₂(CO)₁₀ to 2M(CO)₅(NCCH₃)⁺ in acetonitrile solvent. The kinetics for the reaction suggest it proceeds according to a bimolecular outer sphere mechanism.     

The Cell and Protoplasm as Container,Object, and Substance, 1835–1861

This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term “protoplasm” transformed from a botanical term of art in the 1840s to the so-called “living substance” and “the physical basis of life” two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal status with cell theory in the nineteenth century. First, I argue that biologists had to accept that life could inhere in matter alone, regardless of form. Second, I argue that in the 1840s, ideas of what formless, biological matter was capable of dramatically changed: going from a “coagulation paradigm” (Pickstone, 1973) that had existed since Theophrastus, to a more robust conception of matter that was itself capable of movement and self-maintenance. In addition to revisiting Schleiden and Schwann’s original writings on cell theory, this article looks especially closely at Hugo von Mohl’s definition of the protoplasm concept in 1846, how it differed from his primordial utricle theory of cell structure two years earlier. This article draws on Lakoff and Johnson’s theory of “ontological metaphors” to show that the cell, primordial utricle, and protoplasm can be understood as material container, object, and substance, and that these overlapping distinctions help explain the chaotic and confusing early history of cell theory.     

Phase Behavior, Stability, and Mesomorphism of Monostearin–oil–water Gels

This paper is the characterization of a new material comprised of oil, water, monostearin and stearic acid, which can be used as a heart-friendly, low-saturate, trans fatty acid-free spreadable fat and shortening. Oil–water–monstearin mixtures formed a gel above 2% monostearin and 30% water and were stable over a month’s time. An increase in the storage modulus (G′), and peak melting temperature (T _m) was observed over time, which suggests a slow change in structure to a more solid form. Powder x-ray diffraction measurements at temperatures above the Krafft temperature of the monglyceride (57°C) indicated the existence of a lamellar liquid crystalline phase $ {\left( {L_{\alpha } } \right)} This paper is the characterization of a new material comprised of oil, water, monostearin and stearic acid, which can be used as a heart-friendly, low-saturate, trans fatty acid-free spreadable fat and shortening. Oil–water–monstearin mixtures formed a gel above 2% monostearin and 30% water and were stable over a month’s time. An increase in the storage modulus (G′), and peak melting temperature (T _m) was observed over time, which suggests a slow change in structure to a more solid form. Powder x-ray diffraction measurements at temperatures above the Krafft temperature of the monglyceride (57°C) indicated the existence of a lamellar liquid crystalline phase with a (001) reflection occurring at 50 ?. In addition to the 50 ? reflection at small angles, a wide angle reflection at 4.2 ? was observed upon cooling below 60°C, indicating a transition from the to the phase, which upon storage at 22°C for one day converted to the coagel, or β-gel phase.     

Protein–Protein Docking: Past,Present, and Future

The Protein Journal - The biological significance of proteins attracted the scientific community in exploring their characteristics. The studies shed light on the interaction patterns and functions...     

Environment–richness relationships for mammals,birds, reptiles,and amphibians at global and regional scales

Climate has been routinely indicated as a major determinant of broad-scale species richness patterns for a variety of taxa, but studies vary widely in attributing richness variation to the broad-scale distribution of energy, water, ecosystem productivity, habitat heterogeneity, or some combination thereof. Here, I report global and regional environment–richness relationships for the four classes of terrestrial vertebrates (mammals, birds, reptiles, amphibians) using identical sample units and the same set of climate (temperature, precipitation, annual actual evapotranspiration), productivity (normalized difference vegetation index), and topographic (elevation range) variables. My results strongly support concomitant availability of energy and water as the principal constraint on global richness for all vertebrate groups except reptiles, which are largely constrained by temperature. However, environment–richness models for all taxonomic groups varied widely when applied to single (continental-scale) biogeographic realms. In particular, I found strong support for the ‘water–energy dynamics hypothesis’ that models richness as a function of ambient energy (temperature) in high latitudes and water availability (precipitation) at low latitudes, partially independent of productivity. Ectotherm groups were more constrained by temperature than endotherms, and amphibians were more constrained by water availability than other groups. Although habitat heterogeneity, measured as elevation range, was a consistent contributor to global and regional richness models for all groups, its contribution was always minor compared to other variables. I conclude that temperature and water availability are key variables for modeling broad-scale vertebrate richness, but there remains significant room for taxon-specific modeling approaches and for the inclusion of non-climate factors related to evolutionary history and faunal assembly in different regions.     

CXCR4–SDF-1 Signalling, Locomotion, Chemotaxis and Adhesion

Chemokines, small pro-inflammatory chemoattractant cytokines, that bind to specific G-protein-coupled seven-span transmembrane receptors present on plasma membranes of target cells are the major regulators of cell trafficking. In addition some chemokines have been reported to modulate cell survival and growth. Moreover, compelling evidence is accumulating that cancer cells may employ several mechanisms involving chemokine-chemokine receptor axes during their metastasis that also regulate the trafficking of normal cells. Of all the chemokines, stromal-derived factor-1 (SDF-1), an alpha-chemokine that binds to G-protein-coupled CXCR4, plays an important and unique role in the regulation of stem/progenitor cell trafficking. First, SDF-1 regulates the trafficking of CXCR4+ haemato/lymphopoietic cells, their homing/retention in major haemato/lymphopoietic organs and accumulation of CXCR4+ immune cells in tissues affected by inflammation. Second, CXCR4 plays an essential role in the trafficking of other tissue/organ specific stem/progenitor cells expressing CXCR4 on their surface, e.g., during embryo/organogenesis and tissue/organ regeneration. Third, since CXCR4 is expressed on several tumour cells, these CXCR4 positive tumour cells may metastasize to the organs that secrete/express SDF-1 (e.g., bones, lymph nodes, lung and liver). SDF-1 exerts pleiotropic effects regulating processes essential to tumour metastasis such as locomotion of malignant cells, their chemoattraction and adhesion, as well as plays an important role in tumour vascularization. This implies that new therapeutic strategies aimed at blocking the SDF-1-CXCR4 axis could have important applications in the clinic by modulating the trafficking of haemato/lymphopoietic cells and inhibiting the metastatic behaviour of tumour cells as well. In this review, we focus on a role of the SDF-1-CXCR4 axis in regulating the metastatic behaviour of tumour cells and discuss the molecular mechanisms that are essential to this process.     

Achieving disbelief: thought styles,microbial variation,and American and British epidemiology, 1900–1940

The role of bacterial variation in the waxing and waning of epidemics was a subject of lively debate in late nineteenth and early twentieth-century bacteriology and epidemiology. The notion that changes in bacterial virulence were responsible for the rise and fall of epidemic diseases was an often-voiced, but little investigated hypothesis made by late nineteenth-century epidemiologists. It was one of the first hypotheses to be tested by scientists who attempted to study epidemiological questions using laboratory methods. This paper examines how two groups of experimental epidemiologists, the British group led by W. W. C. Topley and Major Greenwood, and an American group directed by Leslie T. Webster at the Rockefeller Institute, studied the role of variations in bacterial virulence in the course of laboratory epidemics of mouse typhoid. Relying on Ludwik Fleck’s concept of thought styles and thought collectives, the paper analyzes the fundamental conceptual differences between these two groups of researchers and analyzes the kinds of innovations they introduced as they attempted to integrate bacteriological and epidemiological approaches. The paper shows that the stylistic differences between the two groups can be understood better in the context of the institutional histories and disciplinary relations of epidemiology and bacteriology in the two countries.     

IGF-I Receptor, Cell–Cell Adhesion, Tumour Development and Progression

The insulin-like growth factor I receptor (IGF-IR) has been implicated in the development and progression of many common cancers and other neoplastic diseases. The tumorigenic potential of IGF-IR relies on its antiapoptotic and transforming activities. The molecular mechanisms by which IGF-IR controls the proliferation and survival of tumour cells have been extensively studied and many pathways have been delineated. However, the role of IGF-IR in the regulation of non-mitogenic cell functions is less well understood. Here we focus on IGF-IR-dependent cell-cell adhesion. Limited studies suggested that IGF-IR can regulate cell aggregation and intercellular adhesion mediated by cadherins and cadherin-associated proteins. We review the mechanisms of this process and discuss the impact of IGF-IR-dependent cell-cell adhesion on the phenotype of tumour cells.     

A direct,ratiometric, and quantitative MALDI–MS assay for protein methyltransferases and acetyltransferases

Protein methylation and acetylation play important roles in biological processes, and misregulation of these modifications is involved in various diseases. Therefore, it is critical to understand the activities of the enzymes responsible for these modifications. Herein we describe a sensitive method for ratiometric quantification of methylated and acetylated peptides via MALDI–MS by direct spotting of enzymatic methylation and acetylation reaction mixtures without tedious purification procedures. The quantifiable detection limit for peptides with our method is approximately 10 fmol. This is achieved by increasing the signal-to-noise ratio through the addition of NH₄H₂PO₄ to the matrix solution and reduction of the matrix α-cyanohydroxycinnamic acid concentration to 2 mg/ml. We have demonstrated the application of this method in enzyme kinetic analysis and inhibition studies. The unique feature of this method is the simultaneous quantification of multiple peptide species for investigation of processivity mechanisms. Its wide buffer compatibility makes it possible to be adapted to investigate the activity of any protein methyltransferase or acetyltransferase.     

α-catenin,vinculin, and F-actin in strengthening E-cadherin cell–cell adhesions and mechanosensing

Classical cadherins play a crucial role in establishing intercellular adhesion, regulating cortical tension, and maintaining mechanical coupling between cells. The mechanosensitive regulation of intercellular adhesion strengthening depends on the recruitment of adhesion complexes at adhesion sites and their anchoring to the actin cytoskeleton. Thus, the molecular mechanisms coupling cadherin-associated complexes to the actin cytoskeleton are actively being studied, with a particular focus on α-catenin and vinculin. We have recently addressed the role of these proteins by analyzing the consequences of their depletion and the expression of α-catenin mutants in the formation and strengthening of cadherin-mediated adhesions. We have used the dual pipette assay to measure the forces required to separate cell doublets formed in suspension. In this commentary, we briefly summarize the current knowledge on the role of α-catenin and vinculin in cadherin-actin cytoskeletal interactions. These data shed light on the tension-dependent contribution of α-catenin and vinculin in a mechanoresponsive complex that promotes the connection between cadherin and the actin cytoskeleton and their requirement in the development of adhesion strengthening.     

Temperature,hydrochemistry and plankton in Wicken Brickpits, 1930–1931

Temperature, selected chemical constituents and plankton were analysed from three depths, fortnightly, by day and occasionally by night, in two flooded brickpits, between May 1930 and August 1931.Br was 3.3 m deep, with clear water and little weed; III was only 1.8 m deep, with thick submerged weed, more sheltered than Br and becoming eutrophic. Neither had direct inflow nor outlet. Both conformed to the second order for dimictic lakes, with summer and winter stratification, leading, for varying periods, to stagnation marked by pH between 6.6 and 7.2 and O₂ much depleted or absent at the bottom.During stagnation, release of SiO₂, soluble inorganic phosphate-P, ammonium ions and bases from the bottom was shown by sampling water close to the mud. This finding preceded the definition of redox potential by others.Thermistor temperature measurements, used for the first time, showed comparable summer gradients in both ponds: on windy days these were usually sigmoid, with discontinuity at various depths, or else nearly isothermal; on calm days, they were exponential, when transmission of heat, from surface to bottom, was apparently due to radiation alone, without water circulation. Stability was then high.Diatoms were abundant in both ponds; but planktonic Rotifera and Crustacea differed in the two, apart fromDiaptomus gracilis, which was dominant in both.     

Microbiological,Epidemiological, and Clinical Characteristics and Outcomes of Patients with Cryptococcosis in Taiwan, 1997–2010

Background

Among members of Cryptococcus neoformans- Cryptococcus gattii species complex, C. neoformans is distributed worldwide whereas C. gattii is considered to be more prevalent in the subtropics and tropics including Taiwan. This nationwide study was undertaken to determine the distribution of genotypes, clinical characteristics and outcomes of 219 patients with proven cryptococcosis at 20 hospitals representative of all geographic areas in Taiwan during 1997–2010.

Methods and Findings

Of 219 isolates analyzed, C. neoformans accounted for 210 isolates (95.9%); nine isolates were C. gattii (4.1%). The predominant genotype was VNI (206 isolates). The other genotypes included VNII (4 isolates), VGI (3 isolates) and VGII (6 isolates). Antifungal minimal inhibition concentrations higher than epidemiologic cutoff values (ECVs) were found in nine VNI isolates (7 for amphotericin B). HIV infection was the most common underlying condition (54/219, 24.6%). Among HIV-negative patients, liver diseases (HBV carrier or cirrhosis) were common (30.2%) and 15.4% did not have any underlying condition. Meningoencephalitis was the most common presentation (58.9%), followed by pulmonary infection (19.6%) and “others” (predominantly cryptococcemia) (18.7%). The independent risk factors for 10-week mortality, by multivariate analysis, were cirrhosis of liver (P = 0.014) and CSF cryptococcal antigen titer ≥512 (P = 0.020). All except one of 54 HIV-infected patients were infected by VNI genotype (98.1%). Of the 13 isolates of genotypes other than VNI, 12 (92.3%) were isolated from HIV-negative patients. HIV-infected patients compared to HIV-negative patients were more likely to have meningoencephalitis and serum cryptococcal antigen ≥1∶512. Patients infected with C. gattii compared to C. neoformans were younger, more likely to have meningoencephalitis (100% vs. 57%), reside in Central Taiwan (56% vs. 31%), and higher 10-week crude mortality (44.4% vs. 22.2%).

Conclusions

Cryptococcus neoformans in Taiwan, more prevalent than C. gatii, has a predominant VNI genotype. Isolates with antifungal MIC higher than ECVs were rare.     

Design,synthesis, and anti-tumor activities of novel triphenylethylene–coumarin hybrids,and their interactions with Ct-DNA

Novel triphenylethylene–coumarin hybrid derivatives containing different amounts of amino side chains were designed and synthesized in good yields under microwave radiation. The derivatives 5b–d which possessed two amino side chains (except morpholinyl) showed a broad-spectrum and good anti-proliferative activity against five tumor cells and low cytotoxicity in osteoblast. UV–vis, fluorescence, and circular dichroism (CD) spectroscopies and thermal denaturation exhibited that compounds 10c, 5c, and 13c bearing amino side chain (except morpholinyl) on 4-phenyl had significant interactions with Ct-DNA by the intercalative mode of binding. Structure–activity relationships (SARs) analysis suggested that the amino alkyl chain would play an important role both in the compounds against tumor cells proliferation and their interactions with DNA.     

Aerobiology in Russia and Neighbouring Countries, 1980–1993

Aerobiological investigations of the last ten years in the former USSR emphasised, preferentially the following problems: content of pollen in the air, pollen transport, and impact of pollen on the health of the human. Pollen grains which cause various allergic diseases have been the main object of extensive aerobiological studies. Ado and his collaborators have made valuable contributions to Aerobiology in the former USSR (Ado 1978, 1980, 1989, 1990; Ado & Gubankova, 1979 a, b). Their investigations confirmed the existence of a correlation between the number of allergic patients and the concentration of pollen grains in the atmosphere, and some peculiarities of the allergic diseases prevalent in towns.

Later, aerobiology was elaborated by the investigations of Kobzar (1987), Kobzar & Kharitonova (1990), Kobzar et al. (1990, 1991), etc. The possibility of airborne pollen grains as indicators of environmental contamination and pollution levels was demonstrated. Various data show the periods during which pollen grains are present in atmosphere, their peaks and the levels of concentration which are able to cause allergies in the territory of the former USSR.     

Analysis of lignin–carbohydrate and lignin–lignin linkages after hydrolase treatment of xylan–lignin,glucomannan–lignin and glucan–lignin complexes from spruce wood

Xylan–lignin (XL), glucomannan–lignin (GML) and glucan–lignin (GL) complexes were isolated from spruce wood, hydrolyzed with xylanase or endoglucanase/β-glucosidase, and analyzed by analytical pyrolysis and 2D-NMR. The enzymatic hydrolysis removed most of the polysaccharide moieties in the complexes, and the lignin content and relative abundance of lignin–carbohydrate linkages increased. Analytical pyrolysis confirmed the action of the enzymatic hydrolysis, with strong decreases of levoglucosane and other carbohydrate-derived products. Unexpectedly it also revealed that the hydrolase treatment alters the pattern of lignin breakdown products, resulting in higher amounts of coniferyl alcohol. From the anomeric carbohydrate signals in the 2D-NMR spectra, phenyl glycoside linkages (undetectable in the original complexes) could be identified in the hydrolyzed GML complex. Lower amounts of glucuronosyl and benzyl ether linkages were also observed after the hydrolysis. From the 2D-NMR spectra of the hydrolyzed complexes, it was concluded that the lignin in GML is less condensed than in XL due to its higher content in β-O-4′ ether substructures (62 % of side chains in GML vs 53 % in XL) accompanied by more coniferyl alcohol end units (16 vs 13 %). In contrast, the XL lignin has more pinoresinols (11 vs 6 %) and dibenzodioxocins (9 vs 2 %) than the GML (and both have ~13 % phenylcoumarans and 1 % spirodienones). Direct 2D-NMR analysis of the hydrolyzed GL complex was not possible due to its low solubility. However, after sample acetylation, an even less condensed lignin than in the GML complex was found (with up to 72 % β-O-4′ substructures and only 1 % pinoresinols). The study provides evidence for the existence of structurally different lignins associated to hemicelluloses (xylan and glucomannan) and cellulose in spruce wood and, at the same time, offers information on some of the chemical linkages between the above polymers.