Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium' in the phylum Nitrospirae

Magnetotactic bacteria (MTB) of the genus ‘Candidatus Magnetobacterium'' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named ‘Ca. Magnetobacterium casensis'' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood–Ljungdahl pathway for CO₂ fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood ‘Ca. Magnetobacterium'' genus.     

Microbiology of the fermentation of ‘iru pete’ and ‘iru woro’ obtained from local producers

Summary The microorganisms responsible for the fermentation of iru, obtained from local producers, were isolated and identified. Only bacteria were involved in the fermentation; the species areMicrococcus luteus, Staphylococcus aureus, Bacillus subtilis, Lactobacillus plantarum, Citrobacter freundii, Lactobacillus salivarius andStreptococcus pyogenes. Microbial population, temperature, pH and moisture content increased with increase in period of fermentation. A progressive in titratable acidity accompanied the fermentation.

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Resumen Se aislaron e identificaron los microorganismos responsables de la fermentación de iru obtenido de productores locales. En el proceso de fermentación unicamente estaban implicadas bacterias que se identificaron como:Micrococcus luteus, Staphylococcus aureus, Bacillus subtilis, Lactobacillus plantarum, Citrobacter freundii, Lactobacillus salivarius yStreptococcus pyogenes. La población microbiana, la temperatura, el pH y el contenido en humedad se incrementaron al aumentar el periodo de fermentación. Se observó un decremento progresivo del título de acidez a lo largo de la fermentación.

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Résumé Les microorganismes responsables de la fermentation des iru obtenus de producteurs locaux ont été isolés et identifiés. Seules des bactéries sont impliquées dans la fermentation. Les espèces sontMicrococcus luteus, Staphylococcus aureus, Bacillus subtilis, Lactobacillus plantarum, Citrobacter freundii, Lactobacillus salivarius etStreptococcus pyogenes. La population microbienne, la température, le pH et la teneur en eau agumentent avec l'augmentation du temps de fermentation. Une baisse progressive de l'acidité titrable accompagne la fermentation.

     

Rethinking translational nanomedicine: insights from the ‘bottom-up’ design of the Porphysome for guiding the clinical development of imageable nanomaterials

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Analyzing the structural and functional roles of residues from the ‘black’ and ‘gray’ clusters of human S100P protein

Two highly conserved structural motifs observed in members of the EF-hand family of calcium binding proteins. The motifs provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif represents a cluster of three amino acids called cluster I (‘black’ cluster) and cluster II (‘grey’ cluster). Cluster I is more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II is noticeably less conserved and includes a mix of aromatic, hydrophobic, and polar amino acids of different sizes. In the human calcium binding S100 P protein, these ‘black’ and ‘gray’ clusters include residues F15, F71, and F74 and L33, L58, and K30, respectively. To evaluate the effects of these clusters on structure and functionality of human S100 P, we have performed Ala scanning. The resulting mutants were studied by a multiparametric approach that included circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probes. Spectrofluorimetric Ca2+-titration of wild type S100 P showed that S100 P dimer has 1–2 strong calcium binding sites (K₁ = 4 × 106 M⁻¹) and two cooperative low affinity (K₂ = 4 × 104 M⁻¹) binding sites. Similarly, the S100 P mutants possess two types of calcium binding sites. This analysis revealed that the alanine substitutions in the clusters I and II caused comparable changes in the S100 P functional properties. However, analysis of heat- or GuHCl-induced unfolding of these proteins showed that the alanine substitutions in the cluster I caused notably more pronounced decrease in the protein stability compared to the changes caused by alanine substitutions in the cluster II. Opposite to literature data, the F15 A substitution did not cause the S100 P dimer dissociation, indicating that F15 is not crucial for dimer stability. Overall, similar to parvalbumins, the S100 P cluster I is more important for protein conformational stability than the cluster II.     

Finding the ‘lost years’ in green turtles: insights from ocean circulation models and genetic analysis

Organismal movement is an essential component of ecological processes and connectivity among ecosystems. However, estimating connectivity and identifying corridors of movement are challenging in oceanic organisms such as young turtles that disperse into the open sea and remain largely unobserved during a period known as ‘the lost years’. Using predictions of transport within an ocean circulation model and data from published genetic analysis, we present to our knowledge, the first basin-scale hypothesis of distribution and connectivity among major rookeries and foraging grounds (FGs) of green turtles (Chelonia mydas) during their ‘lost years’. Simulations indicate that transatlantic dispersal is likely to be common and that recurrent connectivity between the southwestern Indian Ocean and the South Atlantic is possible. The predicted distribution of pelagic juvenile turtles suggests that many ‘lost years hotspots’ are presently unstudied and located outside protected areas. These models, therefore, provide new information on possible dispersal pathways that link nesting beaches with FGs. These pathways may be of exceptional conservation concern owing to their importance for sea turtles during a critical developmental period.     

Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus Rhoicosphenia (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms

This study seeks to determine the phylogenetic position of the diatom genus Rhoicosphenia. Currently, four hypotheses based on the morphology of the siliceous valve and its various ultrastructural components, sexual reproduction, and chloroplasts have been proposed. Two previous morphological studies have tentatively placed Rhoicosphenia near members of the Achnanthidiaceae and Gomphonemataceae, and no molecular studies have been completed. The position of Rhoicosphenia as sister to ‘monoraphid’ diatoms is problematic due to the apparent non-monophyly of that group, so hypotheses of ‘monoraphid’ monophyly are also tested. Using an analysis of morphological and cytological features, as well as sequences from three genes, SSU, LSU, and rbcL, recovered from several freshwater Rhoicosphenia populations that have similar morphology to Rhoicosphenia abbreviata (Agardh) Lange-Bertalot, we have analyzed the phylogenetic position of Rhoicosphenia in the context of raphid diatoms. Further, we have used topology testing to determine the statistical likelihoods of these relationships. The hypothesis that Rhoicosphenia is a member of the Achnanthidiaceae cannot be rejected, while the hypothesis that it is a member of the Gomphonemataceae can be rejected. In our analyses, members of the Achnanthidiaceae are basal to Rhoicosphenia, and Rhoicosphenia is basal to the Cymbellales, or a basal member of the Cymbellales, which includes the Gomphonemataceae. Hypothesis testing rejects the monophyly of ‘monoraphid’ diatoms.     

Effects of inoculation methods on the incidence of ear-cockle and ‘tundu’ on wheat under field conditions

Wheat,Triticum aestivum L. cv. Mexipak was artificially inoculated withAnguina tritici (Steinb.) under field conditions. Nematode inocula: 0, 0.1, 0.2 and 0.3 g of seed galls/50 seeds or, germinated seeds of wheat (sown in a 1-m long row) were either added as intact seed galls or as a suspension of 2nd stage juveniles. Inoculation of ungerminated seeds with juveniles produced the highest incidence of ear-cockle disease. Whereas, intact seed galls inocula produced the highest incidence of tundu disease. Ear-cockle incidence was always greater than that of tundu at all treatments. The highest reduction in grain yield was associated with the treatments that caused the highest incidence of tundu disease.     

‘Placebos’ and the logic of placebo comparison

Robin Nunn has argued that we should stop using the terms ‘placebo’ and ‘placebo effect’. I argue in support of Nunn’s position by considering the logic of why we perform placebo comparisons. Like all comparisons, placebo comparison is just a case of comparing one thing with another, but it is a mistake, I argue, to think of placebo comparison as a case where something is compared to ‘a placebo’. Rather, placebo comparison should be understood as a situation which sets-up the treatment and control groups in a particular way; not as a case involving objects or procedures called ‘placebos’ employed in order to control for ‘placebo effects’.     

‘Gender’ and the Concerns of Carnal Self-Consumption

This article analyses the co-occurrence of two concerns often expressed by indigenous leaders involved with reparations for victims of paramilitaries in Colombia. These concerns revolve around discomfort with the intense use of hegemonic ‘gender’ discourses in the context of the reparations, and a feeling that leaders' involvement in the latter brings about a betrayal of the family and of themselves. By engaging with the local category of eirruku (flesh), I argue that ways of engaging women in reparations entail the commoditisation of caring relationships. This article, based on 13 months of fieldwork with an indigenous organisation and the communities integrated into it between 2007 and 2008, contributes to the understanding of the articulation of gender and ethnic/racial identification in the context of contemporary forms of governance of indigenous peoples, while delving into ‘carnality’ as a concept to understand gendered forms of reproduction, reparation and selfhood.     

Phylogeny and taxonomy of the ‘manna lichens’

We present ataxonomic revision of the ‘manna lichens’ based on morphological, chemical, ecological and molecular data. A large number of herbarium specimens and fresh collections were examined. Phylogenetic analyses were performed using nuclear ribosomal (nrITS, nrLSU) and mitochondrial small subunit (mtSSU) sequences. Some notable phenotypic characters were plotted on the phylogenetic tree, and the analysis reveals that some of these characters are useful for genus and species level distinction of certain ‘manna lichens.’ Phylogeny of the Megasporaceae was revised using a combined data set of nrLSU and mtSSU and performing parsimony and Bayesian analyses. Five genera (Aspicilia, Circinaria, Lobothallia, Megaspora and Sagedia) are recognized. Further, the relationships of five presumably closely related genera of ‘manna lichens’, namely Agrestia (vagrant), Aspicilia (crustose) Circinaria (crustose), Chlorangium (vagrant) and Sphaerothallia (vagrant) with different growth forms were analysed. The analyses revealed that ‘manna lichens’ do not form a monophyletic group but occur in different clades within the genus Circinaria. The genera Agrestia, Chlorangium and Sphaerothallia are assigned as new synonyms under the genus Circinaria and no vagrant or erratic species remain in the genus Aspicilia. The analyses also show that five new erratic, vagrant and crustose species can be recognized. In this study two ‘manna lichens’, viz. Circinaria rostamii sp. nov. (Azerbaijan, Iran and Turkey), and Circinaria gyrosa sp. nov. (Armenia, Azerbaijan, Iran, Turkey, Turkmenistan and Spain) are described as new to science. Three potentially new species with crustose and erratic forms need additional study. Aspicilia fruticolosofoliacea is reduced to synonymy under C. alpicola, and a lectotype is designated for C. aspera. Thirteen new combinations in Circinaria are presented. The phenomenon of vagrancy is briefly discussed, and the biogeography of the ‘manna lichens’ is outlined. Illustrations, distribution maps, and an identification key to the species are provided.     

Effects of Auxins and Cytokinins on Embryo Formation from Root-derived Callus of Oncidium ‘Gower Ramsey’

In an attempt to optimize somatic embryo formation in Oncidium ‘Gower Ramsey’, the effects of five auxins (2,4-D, IAA, IBA, NAA and picloram) and five cytokinins (2iP, BA, kinetin, TDZ and zeatin), used alone, was tested in vitro using root-derived callus. In general, kinetin (0.5 and 2 mg l⁻¹) and zeatin (0.5 mg l⁻¹) were found to be more effective than other auxin and cytokinin treatments to induce somatic embryogenesis from root-derived callus.     

Making sense of ‘mixture’: states and the classification of ‘mixed’ people

Caribbean diaspora intellectuals have contributed significantly to African-American political struggles over the years, despite arguments by some African-American intellectuals about what they discern as West Indian negativism, extremism, and divisiveness in American political life. This essay examines the legacy of a representative sample of diasporic Caribbean intellectuals since the time of the Harlem Renaissance in the 1920s and culminating in the 1970s, notably, Garvey, members of the African Blood Brotherhood [ABB], C.L.R. James, and Walter Rodney, to demonstrate the phenomenal ideological vision, organizational capability, and political activism they have brought into fostering solidarity with African Americans in the struggle for fundamental change. The focus here is on their respective contributions to the debate on the relationship between class and race in America and the black diaspora generally, which has helped to shape the form, and orient the direction of African-American and Caribbean diasporic struggles for the better part of the twentieth century.     

New teleostean fishes from the Jurassic of southern Germany and the systematic problems concerning the ‘pholidophoriforms’

A new genus,Siemensichthys, from the Upper Jurassic of southern Germany is described. The new genus includes two species,S. macrocephalus (Agassiz) which was formerly in the genusPholidophorus, andS. siemensi n. sp. The two species share synapomorphies such as only one supramaxillary bone covering the dorsal margin of the maxilla. Both species are described, and their phylogenetic position is analyzed. The phylogenetic analyses, based on 27 taxa and 141 characters, show thatAnkylophorus from the Kimmeridgian of Cerin,Siemensichthys andEurycormus from the Solnhofen Lithographic Limestone of Bavaria, form a monophyletic group. The new extinct clade (preliminarily identified as theSiemensichthys- group) is proposed as the sister-group ofPholidophorus s. str. plus more advanced teleosts. This sister-group relationship is supported by eight characters (e.g., supraoccipital bone extending forward in the roof of the otic region; articular bone fused with both the angular and retroarticular; presence of an elongated posteroventral process of quadrate; presence of dorsal processes at the base of the innermost caudal rays of upper lobe; mobile premaxillary bone). Comparisons with species ofPholidophorus s. str. provide a new understanding of the genusPholidophorus. At least four synapomorphies are proposed to support the monophyly ofPholidophorus. As a consequence of this new interpretation, the European Late Jurassic species previously assigned to the Pholidophoridae and to the genusPholidophorus (e.g., ‘Ph.’armatus, ‘Ph.’ falcifer, ‘Ph.’ micronyx, ‘Ph.’ microps) should be reexamined because they do not belong to the family nor to the genus. The order PholidophoriformesBerg is not a monophyletic group as currently constructed. Therefore, all so-called pholidophoriforms are in need of revision.     

Regeneration of plants from callus and embryos of ‘Royal’ apricot

Immature embryos of apricot (Prunus armeniaca L.) cv. Royal with a PF index of 25–100 were used to regenerate plants in vitro using two methods. In the first case, callus was initiated on MS medium with 4.5 M 2, 4-D plus 0.44 M BA and regeneration of shoots from the callus occurred on MS medium with 4.4 M BA plus 1.0 M 2, 4-D. In the second case, adventitious buds were directly regenerated from the cotyledons on MS medium with 4.4 M BA plus 1.0 M 2, 4-D.Abbreviations BA 6-benzyladenine - IBA dole-3-butyric acid - NAA -naphthylacetic acid - 2, 4-D 2, 4-dichlorophenoxyacetic acid - PF (embryo length/seed length) x 100     

Morphological and chemical studies on the crystalloid-forming ‘succulent protein’ from normal and ribosome-deficient Aeonium domesticum plastids

Aeonium domesticum cv. variegatum is a mesochimera of the constitution green/white/green with normal proplastids and chloroplasts in the unaffected tissues and ribosome-deficient colourless mutant plastids in the white leaf tissues. All the different plastid types contain succulent protein crystalloids (SPC). For more detailed characterization, the SPC elements were freed from the plastids and purified by gel filtration. Electron microscopy of different fractions revealed five levels of structural organization. Beginning with the most complex state, the levels are designated as succulent protein (SP) organizational state V (hexagonally arranged and closely packed tubules in the stroma of intact plastids) to I (globular protomers of 5 nm diameter as the basic structure of SPCs). Highly purified SP-fractions were shown by means of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to consist of two or three proteins of M_r 56 kdalton, 58 kdalton and 60 kdalton, depending on the buffer medium used for SP isolation and the duration of storage of leaves in the frozen state. In the urea/SDS-PAGE system, these proteins show similar mobilities to - and -tubulin, but no immunoreaction against antitubulin. The proteolytic cleavage pattern of tubulin subunits and SP proteins are different. Their locations on two-dimensional isoelectric focusing-SDS gels show some overlappings because of microheterogeneities in both proteins in the pH gradient from pH 4.5 to 6.5. Malatedehydrogenase activity could not be detected in the purified SP fractions.Abbreviations CAM Crassulacean acid metabolism - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis - SP succulent protein - SPC succulent protein crystalloid - SPOS succulent protein organizational state     

Influence of Prohexadione-Calcium on the Growth and Quality of Summer ‘Jen-Ju Bar’ Guava Fruit

A 2-year trial was conducted to investigate the influence of prohexadione-calcium (ProCa) on the fruit quality of summer ‘Jen-Ju Bar’ guava (Psidium guajava L.). ‘Jen-Ju Bar’ trees were treated with various concentrations of ProCa: 0 (as control), 125, 250, and 500 mg L^?1, which significantly inhibited spring shoot growth. Summer guava fruits of the trees subjected to ProCa exhibited higher levels of total soluble solids and higher values of total soluble solids to titratable acidity ratio compared with control fruits. Summer guava fruits from trees treated with ProCa were firmer than those from untreated trees. ProCa sprays significantly affected pulp weight, core weight, pulp thickness, and pulp-to-core ratio. No other fruit quality characteristics were significantly affected by ProCa treatment.     

Environmental and anthropogenic determinants of the spread of alien plant species: insights from South Africa’s quaternary catchments

Alien plants invasion has negative impacts on the structure and functionality of ecosystems. Understanding the determinants of this process is fundamental for addressing environmental issues, such as the water availability in South Africa’s catchments. Both environmental and anthropogenic factors determine the invasion of alien species; however, their relative importance has to be quantified. The aim of this paper was to estimate the importance of 32 explanatory variables in predicting the distribution of the major invasive alien plant species (IAPS) of South Africa, through the use of Species Distribution Models. We used data from the National Invasive Alien Plants Survey, delineated at a quaternary catchment level, coupled with climatic, land cover, edaphic, and anthropogenic variables. Using two-part generalized linear models, we compared the accuracy of two different sets of variables in predicting the spatial distribution of IAPS; the first included environmental correlates alone, and the second included both environmental and anthropogenic variables. Using Random Forest, we explored the relative importance of the variables in producing a map of potential distribution of IAPS. Results showed that the inclusion of anthropogenic variables did not significantly improve model predictions. The most important variables influencing the distribution of IAPS appeared to be the climatic ones. The modeled potential distribution was analyzed in relation to provinces, biomes, and species’ minimum residence time.     

A consensus ethnobotany of the Q’eqchi’ Maya of Southern Belize

An ethnobotany study in collaboration with Q’eqchi’ Maya healers of Southern Belize led to a collection of 169 medicinal plant species, belonging to 67 different families. The data show the use of a majority of species from primary or secondary semi-evergreen rainforests of Southern Belize, rather than weedy species. The medicinal uses of the plants were grouped into 17 usage categories. The frequency of use for each plant and the informant consensus factor for each usage category reveals a consensus among the healers on the use of plant species as well as on the diseases treated. These results suggest a well-defined medicinal tradition.