A phylogeny of Begoniaceae Bercht. & J. Presl

Begonia is one of the largest angiosperm genera, with 1400 species currently recognised. These were placed into 63 sections in the most recent taxonomic treatment. However, there is considerable uncertainty in both section inter-relationships and sectional composition, and there is no formalised phylogenetic hypothesis for the genus. Using the nuclear internal transcribed spacers (ITS) and partial large subunit (26S) sequences of ribosomal DNA, I have produced phylogenetic trees to form the basis of a cladistic framework for the interpretation of the evolution and sectional level systematics of Begonia. Maximum parsimony, maximum likelihood and minimum evolution cladograms were produced for 35 Begonia, one Symbegonia and two Datisca species, for partial 26S, ITS and combined sequence data. The results of the analyses suggest that African taxa are basal in Begonia, but that there is not sufficient information to elucidate the precise relationships among these basal lineages. The genus Symbegonia is nested deeply within Begonia. A far larger data set was constructed by sequencing the ITS region for 153 species. Different alignment methods (automated, elision and manual) were tested on these sequences, as were different search strategies. The topology which was taken to be the best estimate of the ITS phylogeny of Begoniaceae was constructed using manual alignment, culled of ambiguous regions, and adjusted to reflect the topologies of smaller, localised, compartment analyses. In the resulting tree, the African species of Begonia resolve as paraphyletic, with both Asian species (including Socotra) and American species (sister to southern African species) monophyletic. Comparisons were made between the ITS sequence data and trees produced from the chloroplast trnC - trnD inter-genic spacer. Parsimony analyses of trnC - trnD sequences support African taxa as basal in Begonia] however, in contrast to the ITS data, trnC - trnD suggests polyphyly / paraphyly of American taxa, albeit with little bootstrap support. A morphological data matrix (67 characters for 159 taxa) did not produce a phylogenetic hypothesis for Begonia that was congruent with any other available data. Using a combined morphology - ITS analysis, the fit of individual morphological characters to a fundamental tree was examined. Some characters fitted the combined topology well, although some of the characters which have traditionally been considered important in Begonia taxonomy (e.g. the number of placental branches) proved misleading. The ITS tree was used as a framework for reviewing chromosome evolution in the genus (604 published counts from 239 species). In contrast to sequence divergence, which was greatest among African species, chromosome number diversity was greatest among American species. The correlation between phylogenetic relationships implied by the ITS tree and the geographical distributions of species was explored to obtain biogeographic hypotheses which may explain the present-day distribution of Begonia. As a general rule, related species are geographically proximal, suggesting limited dispersal of lineages. This finding contradicts observations made on morphology, where the close affinities of morphologically disparate (but geographically proximal) taxa were previously unsuspected. Mechanisms responsible for the evolution of large genera were discussed, and Willis' 'age and area' hypothesis compared to the 'relict' hypothesis of Cronk. In Begonia, the morphological diversity of the genus, and most of the species, are encompassed among the putatively derived lineages, favouring the 'relict' hypothesis

How would you integrate the equations of motion in dissipative particle dynamics simulations?

In this work we assess the quality and performance of several novel dissipative particle dynamics integration schemes that have not previously been tested independently. Based on a thorough comparison we identify the respective methods of Lowe and Shardlow as particularly promising candidates for future studies of large-scale properties of soft matter systems

High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis

RNA interference (RNAi) is a set of mechanisms which regulate gene expression in eukaryotes. Key elements of RNAi are small sense and antisense RNAs from 19 to 26 nt generated from double-stranded RNAs. MicroRNAs (miRNAs) are a major type of RNAi-associated small RNAs and are found in most eukaryotes studied to date. To investigate whether small RNAs associated with RNAi appear to be present in all eukaryotic lineages, and therefore present in the ancestral eukaryote, we studied two deep-branching protozoan parasites, Giardia intestinalis and Trichomonas vaginalis. Little is known about endogenous small RNAs involved in RNAi of these organisms. Using Illumina Solexa sequencing and genome-wide analysis of small RNAs from these distantly related deep-branching eukaryotes, we identified 10 strong miRNA candidates from Giardia and 11 from Trichomonas. We also found evidence of Giardia short-interfering RNAs potentially involved in the expression of variant-specific surface proteins. In addition, eight new small nucleolar RNAs from Trichomonas are identified. Our results indicate that miRNAs are likely to be general in ancestral eukaryotes and therefore are likely to be a universal feature of eukaryotes

Ligand-Induced Movements of Inner Transmembrane Helices of Glut1 Revealed by Chemical Cross-Linking of Di-Cysteine Mutants

The relative orientation and proximity of the pseudo-symmetrical inner transmembrane helical pairs 5/8 and 2/11 of Glut1 were analyzed by chemical cross-linking of di-cysteine mutants. Thirteen functional di-cysteine mutants were created from a C-less Glut1 reporter construct containing cysteine substitutions in helices 5 and 8 or helices 2 and 11. The mutants were expressed in Xenopus oocytes and the sensitivity of each mutant to intramolecular cross-linking by two homobifunctional thiol-specific reagents was ascertained by protease cleavage followed by immunoblot analysis. Five of 9 mutants with cysteine residues predicted to lie in close proximity to each other were susceptible to cross-linking by one or both reagents. None of 4 mutants with cysteine substitutions predicted to lie on opposite faces of their respective helices was susceptible to cross-linking. Additionally, the cross-linking of a di-cysteine pair (A70C/M420C, helices 2/11) predicted to lie near the exoplasmic face of the membrane was stimulated by ethylidene glucose, a non-transported glucose analog that preferentially binds to the exofacial substrate-binding site, suggesting that the binding of this ligand stimulates the closure of helices at the exoplasmic face of the membrane. In contrast, the cross-linking of a second di-cysteine pair (T158C/L325, helices 5/8), predicted to lie near the cytoplasmic face of the membrane, was stimulated by cytochalasin B, a glucose transport inhibitor that competitively inhibits substrate efflux, suggesting that this compound recruits the transporter to a conformational state in which closure of inner helices occurs at the cytoplasmic face of the membrane. This observation provides a structural explanation for the competitive inhibition of substrate efflux by cytochalasin B. These data indicate that the binding of competitive inhibitors of glucose efflux or influx induce occluded states in the transporter in which substrate is excluded from the exofacial or endofacial binding site

Utilisation of an operative difficulty grading scale for laparoscopic cholecystectomy

Background A reliable system for grading operative difficulty of laparoscopic cholecystectomy would standardise description of findings and reporting of outcomes. The aim of this study was to validate a difficulty grading system (Nassar scale), testing its applicability and consistency in two large prospective datasets. Methods Patient and disease-related variables and 30-day outcomes were identified in two prospective cholecystectomy databases: the multi-centre prospective cohort of 8820 patients from the recent CholeS Study and the single-surgeon series containing 4089 patients. Operative data and patient outcomes were correlated with Nassar operative difficultly scale, using Kendall’s tau for dichotomous variables, or Jonckheere–Terpstra tests for continuous variables. A ROC curve analysis was performed, to quantify the predictive accuracy of the scale for each outcome, with continuous outcomes dichotomised, prior to analysis. Results A higher operative difficulty grade was consistently associated with worse outcomes for the patients in both the reference and CholeS cohorts. The median length of stay increased from 0 to 4 days, and the 30-day complication rate from 7.6 to 24.4% as the difficulty grade increased from 1 to 4/5 (both p < 0.001). In the CholeS cohort, a higher difficulty grade was found to be most strongly associated with conversion to open and 30-day mortality (AUROC = 0.903, 0.822, respectively). On multivariable analysis, the Nassar operative difficultly scale was found to be a significant independent predictor of operative duration, conversion to open surgery, 30-day complications and 30-day reintervention (all p < 0.001). Conclusion We have shown that an operative difficulty scale can standardise the description of operative findings by multiple grades of surgeons to facilitate audit, training assessment and research. It provides a tool for reporting operative findings, disease severity and technical difficulty and can be utilised in future research to reliably compare outcomes according to case mix and intra-operative difficulty

Aristophanes and De Ste. Croix: The value of old comedy as evidence for Athenian popular culture

De Ste. Croix famously argued that Aristophanes had a conservative political outlook and attempted to use his comedies to win over lower-class audiences to this minority point of view. The ongoing influence of his interpretation has meant that old comedy has been largely ignored in the historiography of Athenian popular culture. This article extends earlier critiques of de Ste. Croix by systematically comparing how Aristophanes and the indisputably popular genre of fourth-century oratory represented the social classes of the Athenians and political leaders. The striking parallels between the two suggest that Aristophanes, far from advocating a minority position, exploited the rich and, at times, contradictory views of lower-class citizens for comic and ultimately competitive ends. As a consequence his plays are valuable evidence for Athenian popular culture and help to correct the markedly fourth-century bias in the writing of Athenian cultural history

Current knowledge, status and future for plant and fungal diversity in Great Britain and the UK Overseas Territories

Societal Impact Statement We rely on plants and fungi for most aspects of our lives. Yet plants and fungi are under threat, and we risk losing species before we know their identity, roles, and potential uses. Knowing names, distributions, and threats are first steps toward effective conservation action. Accessible products like field guides and online resources engage society, harnessing collective support for conservation. Here, we review current knowledge of the plants and fungi of the UK and UK Overseas Territories, highlighting gaps to help direct future research efforts toward conserving these vital elements of biodiversity. Summary This review summarizes current knowledge of the status and threats to the plants and fungi of Great Britain and the UK Overseas Territories (UKOTs). Although the body of knowledge is considerable, the distribution of information varies substantially, and we highlight knowledge gaps. The UK vascular flora is the most well studied and we have a relatively clear picture of its 9,001 native and alien taxa. We have seedbanked 72% of the native and archaeophyte angiosperm taxa and 78% of threatened taxa. Knowledge of the UKOTs flora varies across territories and we report a UKOTs flora comprising 4,093 native and alien taxa. We have conserved 27% of the native flora and 51% of the threatened vascular plants in Kew's Millennium Seed Bank, UK. We need a better understanding of the conservation status of plants in the wild, and progress toward completion or updating national red lists varies. Site‐based protection of key plant assemblages is outlined, and progress in identifying Important Plant Areas analyzed. Knowledge of the non‐vascular flora, especially seaweeds remains patchy, particularly in many UKOTs. The biggest gaps overall are in fungi, particularly non‐lichenized fungi. Considerable investment is needed to fill these knowledge gaps and instigate effective conservation strategies

Effects of Blood Collection Conditions on Ovarian Cancer Serum Markers

Evaluating diagnostic and early detection biomarkers requires comparing serum protein concentrations among biosamples ascertained from subjects with and without cancer. Efforts are generally made to standardize blood processing and storage conditions for cases and controls, but blood sample collection conditions cannot be completely controlled. For example, blood samples from cases are often obtained from persons aware of their diagnoses, and collected after fasting or in surgery, whereas blood samples from some controls may be obtained in different conditions, such as a clinic visit. By measuring the effects of differences in collection conditions on three different markers, we investigated the potential of these effects to bias validation studies.We analyzed serum concentrations of three previously studied putative ovarian cancer serum biomarkers-CA 125, Prolactin and MIF-in healthy women, women with ovarian cancer undergoing gynecologic surgery, women undergoing surgery for benign ovary pathology, and women undergoing surgery with pathologically normal ovaries. For women undergoing surgery, a blood sample was collected either in the clinic 1 to 39 days prior to surgery, or on the day of surgery after anesthesia was administered but prior to the surgical procedure, or both. We found that one marker, prolactin, was dramatically affected by collection conditions, while CA 125 and MIF were unaffected. Prolactin levels were not different between case and control groups after accounting for the conditions of sample collection, suggesting that sample ascertainment could explain some or all of the previously reported results about its potential as a biomarker for ovarian cancer.Biomarker validation studies should use standardized collection conditions, use multiple control groups, and/or collect samples from cases prior to influence of diagnosis whenever feasible to detect and correct for potential biases associated with sample collection

Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands

© INRA, EDP Sciences 2002Leaf morphology was assessed in nine mixed oak stands (Quercus petraea and Q. robur ) located in eight European countries. Exhaustive sampling was used in an area of each stand where the two species coexisted in approximately equal proportions (about 170 trees/species/stand). Fourteen leaf characters were assessed on each of 5 to10 leaves collected from the upper part of each tree. Three multivariate statistical techniques (CDA, canonical discriminant analysis; PCA, principal component analysis; MCA, multiple correspondence analysis) were used in two different ways: first on the total set of leaves over all stands (global analysis) and second, separately within each stand (local analysis). There was a general agreement of the results among the statistical methods used and between the analyses conducted (global and local). The first synthetic variable derived by each multivariate analysis exhibited a clear and sharp bimodal distribution, with overlapping in the central part. The two modes were interpreted as the two species, and the overlapping region was interpreted as an area where the within-species variations were superimposed. There was no discontinuity in the distribution or no visible evidence of a third mode which would have indicated the existence of a third population composed of trees with intermediate morphologies. Based on petiole length and number of intercalary veins, an "easy to use" discriminant function applicable to a major part of the natural distribution of the species was constructed. Validation on an independent set of trees provided a 98% rate of correct identification. The results were interpreted in the light of earlier reports about extensive hybridization occurring in mixed oak stands. Maternal effects on morphological characters, as well as a lower frequency or fitness of hybrids in comparison with parent species could explain the maintenance of two modes, which might be composed of either pure species or pure species and introgressed forms.Antoine Kremer, Jean Luc Dupouey, J. Douglas Deans, Joan Cottrell, Ulrike Csaikl, Reiner Finkeldey, Santiago Espinel, Jan Jensen, Jochen Kleinschmit, Barbara Van Dam, Alexis Ducousso, Ian Forrest, U. Lopez de Heredia, Andrew J. Lowe, Marcela Tutkova, Robert C. Munro, Sabine Steinhoff and Vincent Badea