Nationalism,nation and territory: Jacint Verdaguer and the Catalan Renaixença

This paper seeks to explain the historic importance to Catalan nationalism of the nineteenth-century poet and priest, Jacint Verdaguer. In order to do so, rather than focus on his contribution – and that of the wider cultural revival, the Renaixença – to the development of the Catalan language as the basis for national political mobilization, this paper argues that we cannot fully understand Verdaguer's importance without reference to his role in constructing a geographical narrative linking nation and territory. At the same time, given that national meanings are always contested, the paper proposes a dialectical approach to nationalism that situates the work of writers within the context of power struggles between social groups. Consequently, Veradguer's centrality to Catalan nationalism is ultimately explained by his role in producing a geographical narrative capable of attracting important sectors of rural Catalonia to the hegemonic project of the industrial bourgeoisie.     

Analyzing the Interaction of RseA and RseB, the Two Negative Regulators of the ��E Envelope Stress Response, Using a Combined Bioinformatic and Experimental Strategy

The Escherichia coli envelope stress response is controlled by the alternative sigma factor, σ^E, and is induced when unfolded outer membrane proteins accumulate in the periplasm. The response is initiated by sequential cleavage of the membrane-spanning antisigma factor, RseA. RseB is an important negative regulator of envelope stress response that exerts its negative effects onσ^E activity through its binding to RseA. In this study, we analyze the interaction between RseA and RseB. We found that tight binding of RseB to RseA required intact RseB. Using programs that performed global and local sequence alignment of RseB and RseA, we found regions of high similarity and performed alanine substitution mutagenesis to test the hypothesis that these regions were functionally important. This protocol is based on the hypothesis that functionally dependent regions of two proteins co-evolve and therefore are likely to be sequentially conserved. This procedure allowed us to identify both an N-terminal and C-terminal region in RseB important for binding to RseA. We extensively analyzed the C-terminal region, which aligns with a region of RseA coincident with the major RseB binding determinant in RseA. Both allele-specific suppression analysis and cysteine-mediated disulfide bond formation indicated that this C-terminal region of similarity of RseA and RseB identifies a contact site between the two proteins. We suggest a similar protocol can be successfully applied to pairs of non-homologous but functionally linked proteins to find specific regions of the protein sequences that are important for establishing functional linkage.The Escherichia coli σ^E-mediated envelope stress response is the major pathway to ensure homeostasis in the envelope compartment of the cell (1-3). σ^E regulon members encode periplasmic chaperones and proteases, the machinery for inserting β-barrel proteins into the outer membrane and components controlling the synthesis and assembly of LPS (4-6). This pathway is highly conserved among γ-proteobacteria (6).The σ^E response is initiated when periplasmic protein folding and assembly is compromised (7-9). During steady state growth, σ^E is inhibited by its antisigma factor, RseA, a membrane-spanning protein whose cytoplasmic domain binds to σ^E with picomolar affinity (10-13). Accumulation of unassembled porin monomers serves as a signal to activate the DegS protease to cleave RseA in its periplasmic domain (14, 15). This initiates a proteolytic cascade in which RseP cleaves periplasmically truncated RseA near or within the cytoplasmic membrane to release the RseA_cytoplasmic-σ^E complex, and cytoplasmic ATP-dependent proteases complete the degradation of RseA thereby releasing active σ^E (16-19).RseB, a second negative regulator of the envelope stress response (11, 20, 21), binds to the periplasmic domain of RseA with nanomolar affinity. RseB is an important regulator of the response (2, 22, 23). It prevents RseP from degrading intact RseA, thereby ensuring that proteolysis is initiated only when the DegS protease is activated by a stress signal (21). Additionally, RseB prevents activated DegS from cleaving RseA, suggesting that interaction of RseB with RseA must be altered before the signal transduction cascade is activated (23).The goal of the present studies was to explore how RseB binds to RseA. The interaction partner of RseB is the unstructured periplasmic domain of RseA (RseA-peri). Within RseA-peri, amino acids ∼169-186 constitute a major binding determinant to RseB (23, 24). This peptide alone binds RseB with 6 μm affinity, and deleting this region abrogates binding to RseB (23). Additional regions of RseA-peri also contribute to RseB binding, as intact RseA-peri binds with 20 nm affinity to RseB (23). Much less is known about the regions of RseB required for interaction with RseA. RseB is homodimeric two-domain protein, whose large N-terminal domain shares structural homology with LolA, a protein that transports lipoproteins to outer membrane (24, 25). The smaller C-terminal domain is connected to the N-terminal domain by a linker, and the two domains share a large interface, which may facilitate interdomain signaling. Glutaraldehyde cross-linking studies indicate that the C-terminal domain interacts with RseA, but the regions of interaction were not identified (25).In the present report, we study the interaction of RseB and RseA. We establish that both domains of RseB interact with RseA-peri. Using a global sequence alignment, we discovered several regions in RseA and RseB that had high sequence similarity, despite the low overall sequence similarity between these two proteins, a finding that was independently confirmed by a local sequence similarity algorithm. This suggested that these regions were functionally dependent, and we performed a set of mutagenesis experiments designed to test this idea. Our studies of the binding properties of these mutants revealed that regions in both the N terminus and C terminus of RseB modulate interaction with RseA. Moreover, genetic suppression analysis and cysteine-mediated disulfide bond formation suggest that the region of RseA/B with highest similarity (RseA residues 165-191 (major binding determinant in RseA) and RseB residues 233-258) are interacting partners.     

HIV-1 Tat, apoptosis and the mitochondria: a tubulin link?

A recent in silico search for coding sequences of retroviral origin present in the human genome has unraveled two new envelope genes that add to the 16 genes previously identified. A systematic search among the latter for a fusogenic activity had led to the identification of two bona fide genes, named syncytin-1 and syncytin-2, most probably co-opted by primate genomes for a placental function related to the formation of the syncytiotrophoblast by cell-cell fusion. Here, we show that one of the newly identified envelope gene, named env P(b), is fusogenic in an ex vivo assay, but that its expression – as quantified by real-time RT-PCR on a large panel of human tissues – is ubiquitous, albeit with a rather low value in most tissues. Conversely, the second envelope gene, named env V, discloses a placenta-specific expression, but is not fusogenic in any of the cells tested. Altogether, these results suggest that at least one of these env genes may play a role in placentation, but most probably through a process different from that of the two previously identified syncytins.     

IQ, visuospatial ability and the gender divide: a reply to Bilalić and Mcleod

Bilalic and McLeod's arguments fall short on several grounds.There are excellent logical reasons to expect strong ability/chess expertise links and specific research evidence to date is sparse, with mixed findings. Data are presented from Georgia, which has a high female participation rate in chess, which suggest that differing gender motivation levels and participation rates impact relatively little on chess performance differences at the extreme.     

Phytochemicals: the good, the bad and the ugly?

Phytochemicals are constitutive metabolites that enable plants to overcome temporary or continuous threats integral to their environment, while also controlling essential functions of growth and reproduction. All of these roles are generally advantageous to the producing organisms but the inherent biological activity of such constituents often causes dramatic adverse consequences in other organisms that may be exposed to them. Nevertheless, such effects may be the essential indicator of desirable properties, such as therapeutic potential, especially when the mechanism of bioactivity can be delineated. Careful observation of cause and effect, followed by a coordinated approach to identify the responsible entities, has proved extremely fruitful in discovering roles for phytochemical constituents. The process is illustrated by selected examples of plants poisonous to animals and include the steroidal alkaloid toxin of Veratrum californicum (Western false hellebore), piperidine alkaloids of Lupinus species (lupines), and polyhydroxy indolizidine, pyrrolizidine and nortropane alkaloids of Astragalus and Oxytropis species (locoweeds), Castanospermum australe (Moreton Bay chestnut) and Ipomoea species (morning glories).     

‘Black and white,a significant contrast’: Race,humanism and missionary photography in the Pacific

Taking the example of ‘Studies in black and white’, a genre of photographs taken around the end of the nineteenth century by Methodist missionaries in the Pacific, this article seeks to go beyond conventional analyses that scrutinize colonial photography for forms of domination. I argue that these photographs, and the context in which some of them were published, reveal a complex interplay between two contradictory principles: on the one hand, a Christian humanism, articulating a vision of commonality and equality, and on the other, paternalism, articulating a vision of superiority and inequality .      

Wiskott–Aldrich syndrome: a gene,a multifunctional protein and the beginnings of an explanation

Patients with Wiskott–Aldrich syndrome show various defects in the normal function of platelets and lymphocytes. The recent identification of the gene responsible for this syndrome has led to a surge of studies aimed at solving the puzzle posed by the varied phenotype observed in this disease. It is now known that WASP, the protein product of this gene, can interact with a large number of other proteins known to be involved in the regulation of signal transduction and cytoskeletal organization. Thus, WASP appears to integrate these two basic and fundamental cellular mechanisms. Several groups are now focusing on understanding the function of WASP in detail, and translating this new knowledge into improved therapies.     

Breeding performance,mate fidelity,and nest site fidelity in a long‐lived seabird: behaving against the current?

There is evidence that breeding failure is associated with divorce and dispersal in many bird species. However, deviations from the general pattern “success‐stay/failure‐leave” seem to be common, suggesting that factors other than breeding performance may importantly influence mate and habitat selection. Moreover, variability in response to performance suggests coexistence of different evolutionary strategies of mate and site selection within a population. In this study, we assessed how individuals conform to the success‐stay/failure‐leave pattern in kittiwakes (Rissa tridactyla), and aimed to identify categories of individuals presenting different behavioural patterns. We considered individual attributes (experience, prior residence at the nest site, performance in multiple breeding attempts), pair attributes (arrival asynchrony, timing of failure, pair duration), and productivity in habitat patches. Timing of failure was an important factor. Pair reunion probability was close to 0.5 in failed pairs, but it was consistently higher in early failed than in late failed pairs. Prior residence better explained variability in probability of reunion in failed pairs than pair duration. However, the positive influence of prior residence on the probability of reunion was perceptible only in early failed pairs. Divorce probability in successful pairs increased with arrival asynchrony, and was higher in first‐time than in experienced breeders. Local productivity positively influenced site fidelity probability in early failed birds, but not in late failed ones. Using memory models, we found that dispersal decisions integrate information on individual breeding performance in a temporal scale longer than one year. This study contributed to the identification of relevant states to be considered when addressing mate and nest site choice. Natural selection may operate on slight fitness differences that cannot be detected without high levels of stratification according to the appropriate individual and habitat attributes.     

Extinction and time help drive the marine‐terrestrial biodiversity gradient: is the ocean a deathtrap?

The marine‐terrestrial richness gradient is among Earth's most dramatic biodiversity patterns, but its causes remain poorly understood. Here, we analyse detailed phylogenies of amniote clades, paleontological data and simulations to reveal the mechanisms underlying low marine richness, emphasising speciation, extinction and colonisation. We show that differences in diversification rates (speciation minus extinction) between habitats are often weak and inconsistent with observed richness patterns. Instead, the richness gradient is explained by limited time for speciation in marine habitats, since all extant marine clades are relatively young. Paleontological data show that older marine invasions have consistently ended in extinction. Simulations show that marine extinctions help drive the pattern of young, depauperate marine clades. This role for extinction is not discernible from molecular phylogenies alone, and not predicted by most previously hypothesised explanations for this gradient. Our results have important implications for the marine‐terrestrial biodiversity gradient, and studies of biodiversity gradients in general.     

Hairpin and duplex forms of a self-complementary dodecamer, d-AGATCTAGATCT, and interaction of the duplex form with the peptide KGWGK: can a pentapeptide destabilize DNA?

Ordered forms of a synthetic dodecamer, d-AGATCTAGATCT, a direct repeat of the BglII recognition sequence, have been investigated using UV, CD, and fluorescence spectroscopy. Complex hairpin-duplex equilibria are manifest in UV thermal transitions, which are monophasic in the presence of very low or high NaCl concentrations but distinctly biphasic at intermediate ionic strengths. In 100 mM NaCl, the 1/Tm vs 1n C curve has a reasonable positive slope, which yields delta H and delta S for duplex formation as -66.2 kcal/mol and -190 cal/mol, respectively. Interaction of the dodecamer in duplex form with a tryptophan-containing peptide, KGWGK, has also been investigated to test the "bookmark" hypothesis (Gabbay et al., 1976) under the uniform structural constraint of the oligonucleotide of defined sequence. CD spectra of the peptide (P), the oligonucleotide (N), and their mixtures at different P/N ratios show a dramatic change in peptide spectrum but little change in nucleic acid dichroism with peptide binding. The Tm of P-N complexes decreases with an increase in peptide binding and levels off at saturation binding of P/N = 2.0. The data are interpreted in terms of a groove-cum-intercalation mode of binding, where intercalation to the tryptophan side chain destabilizes the double helix. A Scatchard plot of the binding data is nonlinear, with best-fit values for an overall association constant K = 4.33 x 10(5) M-1, and the number of binding sites n = 3.23 when fitted to the site-exclusion model of binding.     

Dke1—structure, dynamics, and function: a theoretical and experimental study elucidating the role of the binding site shape and the hydrogen-bonding network in catalysis

This study elucidates the role of the protein structure in the catalysis of β-diketone cleavage at the three-histidine metal center of diketone cleaving enzyme (Dke1) by computational methods in correlation with kinetic and mutational analyses. Molecular dynamics simulations, using quantum mechanically deduced parameters for the nonheme Fe(II) cofactor, were performed and showed a distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. It is shown that in the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination. The substrate binding modes and channels for the traffic of water and ligands (2,4-pentandionyl anion, methylglyoxal, and acetate) were identified. To characterize the impact of the hydrophobic protein environment around the metal center on catalysis, a set of hydrophobic residues close to the active site were targeted. The variations resulted in an up to tenfold decrease of the O(2) reduction rates for the mutants. Molecular dynamics studies revealed an impact of the hydrophobic residues on the substrate stabilization in the active site as well as on the orientations of Glu98 and Arg80, which have previously been shown to be crucial for catalysis. Consequently, the Glu98-His104 interaction in the variants is weaker than in the wild-type complex. The role of protein structure in stabilizing the primary O(2) reduction step in Dke1 is discussed on the basis of our results.     

Association between the MMP-9−1562 C>T polymorphism and the risk of stroke: a meta-analysis

Matrix metalloproteinase (MMP)-9 so far is identified as extremely large and complicated MMP family member. Recently, dozens of studies have explored the association between a promoter polymorphism (?1562 C>T) in MMP-9 and stroke susceptibility. However, the conclusions of these studies still remain equivocal. Therefore, our current meta-analysis was conducted to investigate whether or not the MMP-9 promoter polymorphism is related to the risk of stroke. Electronic databases (PubMed, EMBASE, Web of Science, Cochrane Library and the Chinese Biomedical Literature Database) were searched to obtain all the available studies investigating this polymorphism and stroke from inception to October 2013. Overall and subgroup analyses were rigorously conducted after data extraction. Pooled odds ratio (OR) corresponding to 95 % confidence interval (CI) were estimated. The statistical analysis was performed using Review Manager 5.2. Totally, seven studies involving 1,624 cases and 1,525 controls were identified. The overall results suggested that there was no association of the C?1562T variant on stroke risk under the T allele versus C allele [OR _{T vs. C} 0.98, 95 % CI (0.84, 1.15), P = 0.84], the dominant model [OR _{TT+TC vs. CC} 0.95, 95 % CI (0.81, 1.13), P = 0.59], the recessive model [OR _{TT vs. TC+CC} 1.55, 95 % CI (0.86, 2.81), P = 0.15], the homozygote comparison [OR _{TT vs. CC} 1.48, 95 % CI (0.82, 2.68), P = 0.20] and the heterozygote comparison [OR _{TC vs. CC} 0.93, 95 % CI (0.78, 1.10), P = 0.38]. In the subgroup analyses by ethnicity, age, stroke type and source of controls, no significant relations were observed in any genetic models. Our results indicated that MMP-9?1562 C>T polymorphism was not a risk factor for stroke. Further studies should focus on gene–gene and gene–environment interactions, and provide a more convincing explanation for this association.     

Uexküllian <Emphasis Type="Italic">Umwelt</Emphasis> as science and as ideology: the light and the dark side of a concept

The concept of Umwelt, in particular the interpretation originally developed by Jakob von Uexküll, played an important role in the development of biological thought of the first half of the twentieth century. The theory of Umwelt (Umweltlehre) was one of the most original ideas that appeared in German biology at that time. It was the first attempt to introduce subjectivity into a science about organisms; it laid down the foundations of behavioural research and inspired the development of ethology. However, the theory of Umwelt has also been used to support more sinister activities and even some dangerous ideologies. The concept of Umwelt is of interest not only to historians: within some intellectual circles, it is still broadly used today. Our aim was to analyse the notion’s historic development within the context of biological thought of the first half of the 20th century. In particular, we focus (1) on how the concept was adopted and adapted for various, often widely diverging purposes; (2) on interactions between the Umweltlehre and other contemporary worldviews. We argue that in order to understand the developments that occurred in twentieth century biology, one needs to properly appreciate the role which Umweltlehre played in these. Even more importantly, the Umweltlehre is a worldview that influenced not only science but also politics and social affairs. In this respect it functioned rather like a number of other scientific and ideological frameworks of that time, such as Synthetic Darwinism.     

Object Depots in the Genus <Emphasis Type="Italic">Pogonomyrmex</Emphasis>: Exploring the “Who,” What,When, and Where

Harvester ants of the genus Pogonomyrmex collect and deposit many items on top of their nests. The depots of P. badius consist mostly of small charcoal fragments, while those of other species are primarily pebbles. Mature colonies can have hundreds of thousands of objects in their depot. In P. badius, the distributions of midden and charcoal about the mound are not completely overlapping, but are positively correlated in areas of overlap. Charcoal depots are isometric with colony size, but the amount of charcoal per colony size varies with season and site. The absence of the depot stimulates collection of nonfood objects. Recruitment to objects only occurs in the presence of food, and foragers choose objects based on size, but not color. An overview of current knowledge concerning depots in the genus indicates that depot formation is likely the ancestral state in the North American species. Furthermore, it is likely that selection is operating indirectly on these depots through selection on many dependent tasks.     

When is a ‘forest’ a savanna,and why does it matter?

Savannas are defined based on vegetation structure, the central concept being a discontinuous tree cover in a continuous grass understorey. However, at the high‐rainfall end of the tropical savanna biome, where heavily wooded mesic savannas begin to structurally resemble forests, or where tropical forests are degraded such that they open out to structurally resemble savannas, vegetation structure alone may be inadequate to distinguish mesic savanna from forest. Additional knowledge of the functional differences between these ecosystems which contrast sharply in their evolutionary and ecological history is required. Specifically, we suggest that tropical mesic savannas are predominantly mixed tree–C₄ grass systems defined by fire tolerance and shade intolerance of their species, while forests, from which C₄ grasses are largely absent, have species that are mostly fire intolerant and shade tolerant. Using this framework, we identify a suite of morphological, physiological and life‐history traits that are likely to differ between tropical mesic savanna and forest species. We suggest that these traits can be used to distinguish between these ecosystems and thereby aid their appropriate management and conservation. We also suggest that many areas in South Asia classified as tropical dry forests, but characterized by fire‐resistant tree species in a C₄ grass‐dominated understorey, would be better classified as mesic savannas requiring fire and light to maintain the unique mix of species that characterize them.     

Antigenic similarity between the β-subunits of the ATPases of a bacterium,a yeast and a higher plant

Antiserum raised against the β-subunit of wheat (Triticum aestivum) chloroplast ATPase cross-reacts with a 51000 protein located in the membrane fraction of Escherichia coli. The differential solubility of this polypeptide after chloroform treatment of unc⁺ and uncD409 strains indicates that this cross-reacting polypeptide is the bacterial β-subunit of ATPase. Thus a high degree of conservation of antigenic determinant sites exists between a bacterial β-subunit and the β-subunit of a monocot. This conservation also seems to extend to the β-subunit of mitochondrial ATPase of yeast (Saccharomyces cerevisiae).     

Aging in vertebrates,and the effect of caloric restriction: a mitochondrial free radical production–DNA damage mechanism?

Oxygen is toxic to aerobic animals because it is univalently reduced inside cells to oxygen free radicals. Studies dealing with the relationship between oxidative stress and aging in different vertebrate species and in caloric-restricted rodents are discussed in this review. Healthy tissues mainly produce reactive oxygen species (ROS) at mitochondria. These ROS can damage cellular lipids, proteins and, most importantly, DNA. Although antioxidants help to control this oxidative stress in cells in general, they do not decrease the rate of aging, because their concentrations are lower in long- than in short-lived animals and because increasing antioxidant levels does not increase vertebrate maximum longevity. However, long-lived homeothermic vertebrates consistently have lower rates of mitochondrial ROS production and lower levels of steady-state oxidative damage in their mitochondrial DNA than short-lived ones. Caloric-restricted rodents also show lower levels of these two key parameters than controls fed ad libitum. The decrease in mitochondrial ROS generation of the restricted animals has been recently localized at complex I and the mechanism involved is related to the degree of electronic reduction of the complex I ROS generator. Strikingly, the same site and mechanism have been found when comparing a long- with a short-lived animal species. It is suggested that a low rate of mitochondrial ROS generation extends lifespan both in long-lived and in caloric-restricted animals by determining the rate of oxidative attack and accumulation of somatic mutations in mitochondrial DNA.     

Stress and the developing hippocampus: a double-edged sword?

The mechanisms that regulate neuronal function are a sum of genetically determined programs and experience. The effect of experience on neuronal function is particularly important during development, because early-life positive and adverse experience (stress) may influence the still “plastic” nervous system long-term. Specifically, for hippocampal-mediated learning and memory processes, acute stress may enhance synaptic efficacy and overall learning ability, and conversely, chronic or severe stress has been shown to be detrimental. The mechanisms that enable stress to act as this “double-edged sword” are unclear. Here, we discuss the molecular mediators of the stress response in the hippocampus with an emphasis on novel findings regarding the role of the neuropeptide known as corticotropin-releasing hormone (CRH). We highlight the physiological and pathological roles of this peptide in the developing hippocampus, and their relevance to the long-term effects of early-life experience on cognitive function during adulthood.