Maytenus obtusifolia Mart. (Celastraceae): a tropical woody species in a transitional evolutionary stage of the gynodioecy–dioecy pathway

‘Gynodioecy–dioecy’ is one of the pathways by which dioecy can arise from hermaphroditism. Studies on sex determination and development of gynodioecious systems have focused on temperate and/or annual species. Little is known about the evolutionary dynamics of gynodioecy and dioecy in perennial tropical species, where these systems have more frequently evolved. Maytenus obtusifolia is an abundant species in restingas in southeastern Brazil. The sexual system of M. obtusifolia was investigated by studying the floral structure and reproductive biology. We considered the sexual system as an intermediate step in the pathway gynodioecy-dioecy. The characterization of the hermaphrodite morph was complex, because of a gradient of variation in floral morphology and reproductive characteristics (sizes of the style and stigmatic surface, pollen viability, embryo sacs containing hypertrophied synergids, and fruit set). This variation leads to different proportions of functional male and female flowers among hermaphrodite plants and is responsible for the different levels of reproductive success. Female reproductive success and pollen viability were negatively correlated with the hermaphrodite morph (r = ?0.67). The higher fruiting intensity and fruit/flower ratio of females (41 %) compared to hermaphrodites (2 %) and the fact that female plants produce more and better-quality seeds support the female compensation. We suggest that female sterility may be linked to the set of changes in the carpels. The differences in the quality and quantity of pollen grains of hermaphrodite plants, and the similar individual rates of pollen viability observed for three consecutive flowering events, may indicate a relationship with nuclear cytoplasmic sex determination.     

An in silico biomechanical analysis of the stent–esophagus interaction

Despite all technological innovations in esophageal stent design over the past 20 years, the association between the stent design’s mechanical behavior and its effect on the clinical outcome has not yet been thoroughly explored. A parametric numerical model of a commercially available esophageal bioresorbable polymeric braided wire stent is set up, accounting for stent design aspects such as braiding angle, strut material, wire thickness, degradation and friction between the wires comprising a predictive tool on the device’s mechanical behavior. Combining this tool with complex multilayered numerical models of the pathological in vivo stressed, actively contracting and buckling esophagus could provide clinicians and engineers with a patient-specific window into the mechanical aspects of stent-based esophageal intervention. This study integrates device and soft tissue mechanics in one computational framework to potentially aid in the understanding of the occurrence of specific symptoms and complications after stent placement.     

An immunohistochemical analysis of SERT in the blood–brain barrier of the male rat brain

5-Hydroxytryptamine (5-HT) was originally discovered as a vasoconstrictor. 5-HT lowers blood pressure when administered peripherally to both normotensive and hypertensive male rats. Because the serotonin transporter (SERT) can function bidirectionally, we must consider whether 5-HT can be transported from the bloodstream to the central nervous system (CNS) in facilitating the fall in blood pressure. The blood–brain barrier (BBB) is a highly selective barrier that restricts movement of substances from the bloodstream to the CNS and vice versa, but the rat BBB has not been investigated in terms of SERT expression. This requires us to determine whether the BBB of the rat, the species in which we first observed a fall in blood pressure to infused 5-HT, expresses SERT. We hypothesized that SERT is present in the BBB of the male rat. To test this hypothesis, over 500 blood vessels were sampled from coronal slices of six male rat brains. Immunofluorescence of these coronal slices was used to determine whether SERT and RecA-1 (an endothelial cell marker) colocalized to the BBB. Blood vessels were considered to be capillaries if they were between 1.5 and 23 µm (intraluminal diameter). SERT was identified in the largest pial vessels of the BBB (mean ± SEM = 228.70 ± 18.71 µm, N = 9) and the smallest capillaries (mean ± SEM = 2.75 ± 0.12 µm, N = 369). SERT was not identified in the endothelium of blood vessels ranging from 20 to 135 µm (N = 45). The expression of SERT in the rat BBB means that 5-HT entry into the CNS must be considered a potential mechanism when investigating 5-HT-induced fall in blood pressure.     

Pocket analysis of the full-length cholix toxin. An assessment of the structure–dynamics of the apo catalytic domain

Cholix toxin from Vibrio cholerae is the third member of the diphtheria toxin (DT) group of mono-ADP-ribosyltransferase (mART) bacterial toxins. It shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae DT. Cholix toxin is an important model for the development of antivirulence approaches and therapeutics against these toxins from pathogenic bacteria. Herein, we have used the high-resolution X-ray structure of full-length cholix complexed with NAD⁺ to describe the properties of the NAD⁺-binding pocket at the residue level, including the role of crystallographic water molecules in the NAD⁺ substrate interaction. The full-length apo cholix structure is used to describe the putative NAD⁺-binding site(s) and to correlate biochemical with crystallographic data to study the stoichiometry and orientation of bound NAD⁺ molecules. We quantitatively describe the NAD⁺ substrate interactions on a residue basis for the main 22 pocket residues in cholix_f, a glycerol and 5 contact water molecules as part of the recognition surface by the substrate according to the conditions of crystallization. In addition, the dynamic properties of an in silico version of the catalytic domain were investigated in order to understand the lack of electronic density for one of the main flexible loops (R-loop) in the pocket of X-ray complexes. Implications for a rational drug design approach for mART toxins are derived.     

Haplotype analysis of eight genes of the monoubiquitinated FANCD2–DNA damage–repair pathway in breast cancer patients

Background: Ten genes are associated with increased susceptibility to inherited breast cancer have also been associated with population breast cancer risk, and all are involved directly or indirectly in the monoubiquitinated FANCD2–DNA damage repair pathway. We analyzed 13 haplotype blocks in eight of these genes to estimate the breast cancer risk conferred by individual haplotypes. Methods: Haplotype blocks were constructed with 48 tag single-nucleotide polymorphisms (tSNPs) identified in eight breast cancer susceptibility genes, TP53, PTEN, CHEK2, ATM, NBS1, RAD50, BRIP1, and PALB2. Genotyping was performed by SNPscan on 734 female patients and 672 female age-matched controls. Results: Forty-five tSNPs were successfully genotyped by SNPscan, and call rates for each tSNP were above 98.9%. Thirteen haplotype blocks of eight genes were constructed with 41 successfully genotyped tSNPs. We found that seven haplotypes from four haplotype blocks located within three genes (NBS1, PTEN, and BRIP1) were significantly associated with breast cancer risk. Among these, four haplotypes (ATC in block 1 of NBS1, GCCCC and GCCCT in block 2 of NBS1, and GCT in block 2 of BRIP1) were correlated with breast cancer risk in sporadic cases (OR (95% CI) 1.350(1.124–1.623), 0.752(0.584–0.969), 0.803(0.649–0.993), and 0.776(0.604–0.997), respectively), and only one haplotype (GGCCT in block 2 of NBS1) was significantly associated with breast cancer risk in familial and early-onset cases (OR(95% CI) 1.902(1.134–3.191)). Conclusions: Four haplotypes within two genes (NBS1 and BRIP1) involved in the monoubiquitinated FANCD2–DNA damage–repair pathway are significantly associated with increased sporadic breast cancer risk, while one haplotype within NBS1 is correlated with an increased risk of familial or early-onset breast cancer, indicating that specific haplotypes may be distinct predictors of breast cancer.     

Erratum to: An in silico biomechanical analysis of the stent–esophagus interaction

Biomechanics and Modeling in Mechanobiology - In the original publication of the article, Tables 2 and 3 were published with error. The correct tables are provided below (Tables 2, 3). The...     

An analysis of the ‘legal high’ mephedrone

‘Legal highs’ are compounds, plant or fungal material which can be readily bought from the internet without legal restriction and the single chemicals may be structurally related to illegal drugs of abuse such as the amphetamines. Several recent deaths in the UK have been attributed to these legal highs and unfortunately there is little chemical or biological literature on these materials or certified standards. Here, we detail the analysis of the widely consumed synthetic N-methyl-cathinone analogue known as mephedrone ((1) 2-aminomethyl-1-tolyl-propan-1-one (4′-methylmethcathinone)) and report its spectral data and molecular properties. Material was purchased from an internet site and examined by extensive one- and two-dimensional NMR studies, high-resolution mass spectrometry, elemental analysis and optical rotation, which demonstrated the sample to be of high purity and racemic in nature.Additionally, we report the molecular modelling properties of methyl-cathinones and compare them to their corresponding methyl-amphetamine series. This indicated that the methyl-cathinones are considerably more hydrophilic than the methyl-amphetamines which may account for the higher doses that are needed to demonstrate similar effects. The presence of a ketone in the side chain introduces a far more planar quality to the methyl-cathinones which is absent in the methyl-amphetamine series, and this planarity may contribute to toxicity.     

The molecular dissection of the chaperone–usher pathway

Secretion systems are specialized in transport of proteins, DNA or nutrients across the cell envelope of bacteria and enable them to communicate with their environment. The chaperone–usher (CU) pathway is used for assembly and secretion of a large family of long adhesive protein polymers, termed pili, and is widespread among Gram-negative pathogens [1]. Moreover, recent evidence has indicated that CU secretion systems are also involved in sporulation  and . In this review we focus on the structural biology of the paradigmatic type 1 and P pili CU systems encoded by uropathogenic Escherichia coli (UPEC), where recent progress has provided unprecedented insights into pilus assembly and secretion mechanism. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.     

Genetic analysis of the phosphinothricin-tripeptide biosynthetic pathway of Streptomyces viridochromogenes Tü494

Summary Streptomyces viridochromogenes Tü494 produces the antibiotic phosphinothricyl-alanyl-alanine (Ptt). Ptt-non-producing mutants were isolated following N-methyl-N-nitro-N-nitrosoguanidine (NTG) or UV light treatment of spore suspensions. In co-synthesis and bioconversion experiments the mutational blocks in the biosynthetic pathway were localized. The mutant NTG1 was analysed in detail. This mutant acts as a secretor for all other mutants. From bioconversion experiments with presumptive precursors circumstantial evidence was obtained that NTG1 is mutated in a gene involved in the alanylation of N-acetyl-demethyl-phosphinothricin. Using a cosmid gene library the DNA region complementing the defective gene of mutant NTG1 was isolated on a 4-kb BamHI fragment. Subcloning experiments showed that a 3-kb BglII/BamHI fragment is sufficient for complementation of mutant NTG1.Formerly Susanne MüllerOffprint requests to: W. Wohlleben     

An alternate insulin-like growth factor I receptor signaling pathway for the progression of endothelial–mesenchymal transition

Emerging evidence suggests that endothelial-to-mesenchymal transition (EndoMT) is an important contributor to cardiovascular diseases and to vascular development and pathologies as well as in cancer progression. As in epithelial–mesenchymal transition (EMT), EndoMT may involve several regulated steps: disassembly of adherence junctions or loss of cell–cell contacts, cytoskeletal reorganization, proteases, cytokines and growth factor synthesis and secretion, extracellular matrix remodeling, membrane receptor expression, cell detachment and cell migration and differentiation. Loss of cell–cell contacts is a necessary and sufficient step in the progression of EndoMT. In endothelial cells, adherence junctions are composed of transmembrane adhesive proteins belonging to the cadherin family, with the VE-cadherin being the most important. This protein interacts with β-catenin, which links cadherin to the actin cytoskeleton. Tyrosine phosphorylation of both VE-cadherin and β-catenin is considered an important mechanism associated to the disassembly of adherence junctions or loss of cell–cell contacts. Insulin-like growth factor receptor I (IGFIR) is a transmembrane tyrosine kinase that has been involved in the alterations of cell–cell contacts and in the expression of some genes during cancer development and progression. Here, it is hypothesized that IGFIR autophosphorylation may initiate a signaling pathway that would lead to the loss of cell–cell contacts or adherence junctions, remarkable remodeling of the cytoskeleton, increased cell motility, and finally to the progressive transition towards a mesenchymal phenotype. Data supporting this hypothesis are presented here.     

Function of the ubiquitin–proteosome pathway in auxin response

Proteolysis of important regulatory proteins by the ubiquitin–proteosome pathway is a key aspect of cellular regulation in eukaryotes. Genetic studies in Arabidopsis indicate that response to auxin depends on the function of proteins in this pathway. The auxin transport inhibitor resistant 1 (TIR1) protein is part of a ubiquitin–protein–ligase complex (E3), known as SKP1 CDC53 F-box^TIR1 (SCF^TIR1), that possibly directs ubiquitin-modification of protein regulators of the auxin response. In yeast, a similar E3 complex, SCF^CDC4, is regulated by conjugation of the ubiquitin-related protein Rub1 to the Cdc53 protein. In Arabidopsis, the auxin-resistant1 (AXR1) gene encodes a subunit of the RUB1-activating enzyme, the first enzyme in the RUB-conjugation pathway. Loss of AXR1 results in loss of auxin response. These results suggest a model in which RUB1 modification regulates the activity of SCF^TIR1, thereby directing the degradation of the repressors of the auxin response.     

An evolving paradigm for the secretory pathway?

The paradigm that the secretory pathway consists of a stable endoplasmic reticulum and Golgi apparatus, using discrete transport vesicles to exchange their contents, gained important support from groundbreaking biochemical and genetic studies during the 1980s. However, the subsequent development of new imaging technologies with green fluorescent protein introduced data on dynamic processes not fully accounted for by the paradigm. As a result, we may be seeing an example of how a paradigm is evolving to account for the results of new technologies and their new ways of describing cellular processes.     

Role of the pentose phosphate pathway and the Entner–Doudoroff pathway in glucose metabolism of Gluconobacter oxydans 621H

Glucose catabolism by the obligatory aerobic acetic acid bacterium Gluconobacter oxydans 621H proceeds in two phases comprising rapid periplasmic oxidation of glucose to gluconate (phase I) and oxidation of gluconate to 2-ketogluconate or 5-ketogluconate (phase II). Only a small amount of glucose and part of the gluconate is taken up into the cells. To determine the roles of the pentose phosphate pathway (PPP) and the Entner–Doudoroff pathway (EDP) for intracellular glucose and gluconate catabolism, mutants defective in either the PPP (Δgnd, Δgnd zwf*) or the EDP (Δedd–eda) were characterized under defined conditions of pH 6 and 15 % dissolved oxygen. In the presence of yeast extract, neither of the two pathways was essential for growth with glucose. However, the PPP mutants showed a reduced growth rate in phase I and completely lacked growth in phase II. In contrast, the EDP mutant showed the same growth behavior as the reference strain. These results demonstrate that the PPP is of major importance for cytoplasmic glucose and gluconate catabolism, whereas the EDP is dispensable. Reasons for this difference are discussed.     

Parametric analysis of the ratio-dependent predator–prey model

We present a complete parametric analysis of stability properties and dynamic regimes of an ODE model in which the functional response is a function of the ratio of prey and predator abundances. We show the existence of eight qualitatively different types of system behaviors realized for various parameter values. In particular, there exist areas of coexistence (which may be steady or oscillating), areas in which both populations become extinct, and areas of "conditional coexistence" depending on the initial values. One of the main mathematical features of ratio-dependent models, distinguishing this class from other predator-prey models, is that the Origin is a complicated equilibrium point, whose characteristics crucially determine the main properties of the model. This is the first demonstration of this phenomenon in an ecological model. The model is investigated with methods of the qualitative theory of ODEs and the theory of bifurcations. The biological relevance of the mathematical results is discussed both regarding conservation issues (for which coexistence is desired) and biological control (for which extinction is desired).     

Targeted mutagenesis of the Clostridium acetobutylicum acetone–butanol–ethanol fermentation pathway

The production of the chemical solvents acetone and butanol by the bacterium Clostridium acetobutylicum was one of the first large-scale industrial processes to be developed, and in the first part of the last century ranked second in importance only to ethanol production. After a steep decline in its industrial use, there has been a recent resurgence of interest in the acetone–butanol–ethanol (ABE) fermentation process, with a particular emphasis on butanol production. In order to generate strains suitable for efficient use on an industrial scale, metabolic engineering is required to alter the AB ratio in favour of butanol, and eradicate the production of unwanted products of fermentation. Using ClosTron technology, a large-scale targeted mutagenesis in C. acetobutylicum ATCC 824 was carried out, generating a set of 10 mutants, defective in alcohol/aldehyde dehydrogenases 1 and 2 (adhE1, adhE2), butanol dehydrogenases A and B (bdhA, bdhB), phosphotransbutyrylase (ptb), acetate kinase (ack), acetoacetate decarboxylase (adc), CoA transferase (ctfA/ctfB), and a previously uncharacterised putative alcohol dehydrogenase (CAP0059). However, inactivation of the main hydrogenase (hydA) and thiolase (thl) could not be achieved. Constructing such a series of mutants is paramount for the acquisition of information on the mechanism of solvent production in this organism, and the subsequent development of industrial solvent producing strains. Unexpectedly, bdhA and bdhB mutants did not affect solvent production, whereas inactivation of the previously uncharacterised gene CAP0059 resulted in increased acetone, butanol, and ethanol formation. Other mutants showed predicted phenotypes, including a lack of acetone formation (adc, ctfA, and ctfB mutants), an inability to take up acids (ctfA and ctfB mutants), and a much reduced acetate formation (ack mutant). The adhE1 mutant in particular produced very little solvents, demonstrating that this gene was indeed the main contributor to ethanol and butanol formation under the standard batch culture conditions employed in this study. All phenotypic changes observed could be reversed by genetic complementation, with exception of those seen for the ptb mutant. This mutant produced around 100 mM ethanol, no acetone and very little (7 mM) butanol. The genome of the ptb mutant was therefore re-sequenced, together with its parent strain (ATCC 824 wild type), and shown to possess a frameshift mutation in the thl gene, which perfectly explained the observed phenotype. This finding reinforces the need for mutant complementation and Southern Blot analysis (to confirm single ClosTron insertions), which should be obligatory in all further ClosTron applications.     

Rat β-glucuronidase as a reporter protein for the analysis of the plant secretory pathway

Abstract

E. coliβ-glucuronidase, a cytosolic enzyme, was found not to be a good reporter enzyme for secretion studies in plants. In this study, we chose to test and adapt an animal β-glucuronidase as a better reporter protein for the secretory pathway of plants. We modified rat β-glucuronidase to obtain secreted and vacuolar variants. Five different C-termini were produced: the original C-terminus of the rat enzyme, a 19 codon deletion (Δ19), a 15 codon deletion (Δ15) and fusions of the Δ19 or Δ15 termini with the last 6 or 7 codons of the vacuolar sorting determinant of tobacco chitinase A, respectively. The signal sequence of the rat β-glucuronidase polypeptide was replaced by the sequence encoding the signal peptide of tobacco chitinase A. In a transient expression system, the best enzymatic activity was found with β-glucuronidase having the 15 codons deletion, therefore Δ15 (secRGUS) and Δ15 + Chi (RGUS-Chi) were further evaluated and their efficiency of secretion or vacuolar targeting were tested under different conditions. To determine the correct targeting of reporter genes, we compared the localization of β-glucuronidase and of an endogenous marker, α-mannosidase. Treating cells with drugs that specifically affect different aspects of the secretory pathway also tested the validity of RGUS-based reporters. A non-specific inhibitor such as cytochalasin D and a wide range inhibitor such as BFA were compared with specific inhibitors such as wortmannin and bafilomycin A1. Finally, monensin and NH₄Cl were used to evaluate the role of vacuolar pH in correct RGUS-Chi targeting. The two new reporter proteins proved to be good tools for our studies in the transient expression system in tobacco protoplasts and for further applications.     

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Following a strategy similar to that used in baker’s yeast (Herrgård et al. Nat Biotechnol 26:1155–1160, 2008). A consensus yeast metabolic network obtained from a community approach to systems biology (Herrgård et al. 2008; Dobson et al. BMC Syst Biol 4:145, 2010). Further developments towards a genome-scale metabolic model of yeast (Dobson et al. 2010; Heavner et al. BMC Syst Biol 6:55, 2012). Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network (Heavner et al. 2012) and in Salmonella typhimurium (Thiele et al. BMC Syst Biol 5:8, 2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2 (Thiele et al. 2011), a recent paper (Thiele et al. Nat Biotechnol 31:419–425, 2013). A community-driven global reconstruction of human metabolism (Thiele et al. 2013) described a much improved ‘community consensus’ reconstruction of the human metabolic network, called Recon 2, and the authors (that include the present ones) have made it freely available via a database at http://humanmetabolism.org/ and in SBML format at Biomodels (http://identifiers.org/biomodels.db/MODEL1109130000). This short analysis summarises the main findings, and suggests some approaches that will be able to exploit the availability of this model to advantage.     

Molecular and enzymatic analysis of the “aldoxime–nitrile pathway” in the glutaronitrile degrader Pseudomonas sp. K-9

A gene cluster responsible for aldoxime metabolism in the glutaronitrile degrader Pseudomonas sp. K-9 was analyzed genetically and enzymatically. The cluster was composed of genes coding for aldoxime dehydratase (Oxd), nitrile hydratase (NHase), NHase activator, amidase, acyl-CoA ligase, and some regulatory and functionally unknown proteins, which were similar to proteins appearing in the “aldoxime–nitrile pathway” gene cluster from strains having Fe-containing NHase. A key enzyme in the cluster, OxdK, which has 32.7–90.3 % identity with known Oxds, was overexpressed in Escherichia coli cells under the control of a T7 promoter in its His₆-tagged form, purified, and characterized. The enzyme showed similar characteristics with the known Oxds coexisting with an Fe-containing NHase in its subunit structure, substrate specificity, and effects on various compounds. The enzyme can be classified into a group of “aliphatic aldoxime dehydratase (EC 4.99.1.5).” The existence of a gene cluster of enzymes responsible for aldoxime metabolism via the aldoxime–nitrile pathway (aldoxime→nitrile→amide→acid→acyl-CoA) in Pseudomonas sp. K-9, and the fact that the proteins comprising the cluster are similar to those acting on aliphatic type substrates, evidently clarified the alkylaldoxime-degrading pathway in that strain.     

An analysis of the loss of acroporid corals at Looe Key,Florida, USA: 1983–2000

The Caribbean reef-building corals Acropora palmata and Acropora cervicornis have undergone widespread declines in the past two decades, leading to their designation as candidates for listing under the United States Endangered Species Act. Whole-reef censuses in 1983 and 2000 at Looe Key National Marine Sanctuary in the Florida Keys provide estimates of areal loss of live Acropora spp. cover. Area (square meters) of live coral cover was quantified from depiction on scaled base maps of extent of coral cover observed by a snorkeler on each reef spur at each census. Certain thickets appear to have been persistent (though none expanded), but the total area of live A. palmata at Looe Key is estimated to have declined by 93% and A. cervicornis by 98% during this 17-year interval. It is likely that acroporid populations may have already undergone substantial decline prior to our initial census in 1983.