Data access for the 1,000 Plants (1KP) project

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

[Paediatric anaesthesia outside the operating theatre suite: the situation in Germany and Quebec]

The authors describe the way pediatric anesthesia is organized outside the operating theatre in their country. In Germany, children can be anesthetized outside the operating theater in the hospital but also outside the hospital according to the concept of office-based anesthesia. National recommendations have been published and their revision is currently underway. In Quebec, pediatric anesthesia outside the operating theatre is well organized in order to ensure quality of care, patient's safety and efficiency of the system.

Depressive symptoms after a sexual assault among women: understanding victim-perpetrator relationships and the role of social perceptions

OBJECTIVES

Although mental health impact of gender based violence has been documented for many decades, the impact of the socio-cultural dimensions and type of perpetrator on mental health outcomes has not been described outside of developed countries. We explore depression symptomatology four to six weeks post-rape in South Africa and examine whether this differs according to the circumstances of the rape.

METHOD

140 participants recruited from public hospital services in the Eastern and Western Cape provinces were interviewed within two weeks after completing the post exposure prophylaxis (PEP) medication. A structured questionnaire was used to collect data on socio-demographic and sexual assault characteristics including perpetrator. Depressive symptomatology was measured using the Centre for Epidemiological Studies Depression Scale.

RESULTS

84.3% (95% CI: 78.1-90.3) women were found to have high levels of depressive symptoms, but lower levels were found among women raped in circumstances in which there was a lesser likelihood of blame such as those raped by strangers rather than intimate partners (Odds Ratio: (OR) 0.28 (95% Confidence Intervals (CI): 0.11-0.69) and higher levels were associated with experiencing four or more side effects related to PEP medication (OR: 3.79: CI: 1.03-13.94). Receiving support and severe sexual assaults (involving weapons and multiple perpetrators) were not associated with depression.

CONCLUSION

The study does not support the general assumption that more violent rape causes more psychological harm. These results have important implications for individual treatment because it is more generally assumed that multiple perpetrator rapes, stranger rapes and those with weapons would result in more psychological trauma and thus more enduring symptoms. Our findings point to the importance of understanding the socio-cultural dimensions, including dynamics of blame and stigma, of rape on mental health sequelae.

Phylogeny and origins of holoparasitism in Orobanchaceae

PREMISE

Orobanchaceae are a family of angiosperms that range from fully autotrophic and free-living to completely heterotrophic and dependent on their hosts (holoparasites). Most of the ca. 2060 species are hemiparasites that photosynthesize throughout all or part of their life cycles. Certain family members are ecologically important due to direct impacts on community biomass and diversity, plant-herbivore interactions, and nutrient cycling. Other members are among the most economically damaging weeds in the world. Multiple trophic transitions within this family make it ideal for studying molecular evolutionary and physiological changes that accompany the evolution of parasitism. •

METHODS

To establish a phylogenetic framework for such work, we substantially increased taxonomic sampling at loci for which a significant amount of data already existed (nuclear ITS and PHYA, plastid matK and rps2) and added data from the low-copy nuclear locus, PHYB. •

KEY RESULTS

The data provide strong support for relationships among six major clades and for the position of Brandisia hancei Hook. f. The positions of Boschniakia himalaica Hook. f. & Thomson, Centranthera cochinchinensis (Lour.) Merr., Mannagettaea hummelii Harry Sm., and Pterygiella nigrescens Oliv. are confirmed or suggested for the first time. •

CONCLUSIONS

There is a single origin of parasitism, and from within the hemiparasites, holoparasitism has originated three times. Moving from the base to the tips of the Orobanchaceae tree, the successive major splits within the parasitic clade are: Cymbarieae + the rest; Orobancheae + the rest; Brandisia + the rest; Rhinantheae + the rest; and Pedicularideae + Buchnereae.

The evolution of reproductive structures in seed plants: a re-examination based on insights from developmental genetics

The study of developmental genetics is providing insights into how plant morphology can and does evolve, and into the fundamental nature of specific organs. This new understanding has the potential to revise significantly the way we think about seed plant evolution, especially with regard to reproductive structures. Here, we have sought to take a step in bridging the divide between genetic data and critical fields such as paleobotany and systematics. We discuss the evidence for several evolutionarily important interpretations, including the possibility that ovules represent meristematic axes with their own type of lateral determinate organs (integuments) and a model that considers carpels as analogs of complex leaves. In addition, we highlight the aspects of reproductive development that are likely to be highly labile and homoplastic, factors that have major implications for the understanding of seed plant relationships. Although these hypotheses may suggest that some long-standing interpretations are misleading, they also open up whole new avenues for comparative study and suggest concrete best practices for evolutionary analyses of development.

Chitosan enhances mineralization during osteoblast differentiation of human bone marrow-derived mesenchymal stem cells, by upregulating the associated genes

OBJECTIVES

  Chitosan is widely used as a scaffold for bone tissue engineering. However, up-to-date, no previous detailed study has been conducted to elucidate any mechanism of osteogenesis by chitosan itself. Here, we have evaluated effects of chitosan-coated tissue culture plates on adhesion and osteoblast differentiation processes of human mesenchymal stem cells (hMSCs), isolated from adult bone marrow.

MATERIALS AND METHODS

  Tissue culture plates coated with chitosan at different coating densities were used to evaluate the effects on hMSC adhesion and osteoblast differentiation. hMSCs were induced to differentiate into osteoblasts on the chitosan-coated plates and were evaluated using established techniques: alkaline phosphatase assay, demonstration of presence of calcium and real time PCR.

RESULTS

  The cells adhered to plates of lower coating density of chitosan, but formed viable cell aggregates at higher coating density (100 μg/sq.cm). Coating density of 25 μg/sq.cm, supporting cell adhesion was chosen for osteoblast differentiation experiments. Differentiating hMSCs showed higher mineral deposition and calcium content on chitosan-coated plates. Chitosan upregulated genes associated with calcium binding and mineralization such as collagen type 1 alpha 1, integrin-binding sialoprotein, osteopontin, osteonectin and osteocalcin, significantly.

CONCLUSIONS

  We demonstrate for the first time that chitosan enhanced mineralization by upregulating the associated genes. Thus, the study may help clinical situations promoting use of chitosan in bone mineralization, necessary for healing non-union fractures and more.

Overview of endocrinopathies associated with β-thalassaemia major

BACKGROUND

  Thalassaemia major is a common and serious medical problem worldwide that is associated with a range of complications, including effects on multiple endocrine pathways. Minimizing or preventing comorbidities is important for these individuals who need life-long multidisciplinary care and treatment. However, there are limited overviews of the endocrine complications associated with this illness, nor any consensus regarding management guidelines.

METHOD

  A retrospective cohort analysis of β-thalassaemia patients attending an ambulatory transfusion clinic at Royal Prince Alfred Hospital was conducted from June 2008.

RESULTS

  All of our subjects (n=29) had at least one endocrinopathy present with 16 patients (55%) having three or more (≥3) endocrinopathies. Hypogonadism was the most prevalent followed by osteoporosis and growth failure (less than 3rd centile) with a frequency of 16/29 (55%), 14/29 (48%) and 10/29 (35%) patients respectively. Those with more endocrinopathies (≥3) had a longer duration of transfusion therapy when compared with those with fewer endocrinopathies.

CONCLUSION

  A summary of our clinical guidelines, which have been used to monitor and manage these complications, is presented along with a discussion on the results and pathophysiology of the associated endocrinopathies.

A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants

Flowering plants represent the most significant branch in the tree of land plants, with respect to the number of extant species, their impact on the shaping of modern ecosystems and their economic importance. However, unlike so many persistent phylogenetic problems that have yielded to insights from DNA sequence data, the mystery surrounding the origin of angiosperms has deepened with the advent and advance of molecular systematics. Strong statistical support for competing hypotheses and recent novel trees from molecular data suggest that the accuracy of current molecular trees requires further testing. Analyses of phytochrome amino acids using a duplicate gene-rooting approach yield trees that unite cycads and angiosperms in a clade that is sister to a clade in which Gingko and Cupressophyta are successive sister taxa to gnetophytes plus Pinaceae. Application of a cycads + angiosperms backbone constraint in analyses of a morphological dataset yields better resolved trees than do analyses in which extant gymnosperms are forced to be monophyletic. The results have implications both for our assessment of uncertainty in trees from sequence data and for our use of molecular constraints as a way to integrate insights from morphological and molecular evidence.

Evolutionary studies illuminate the structural-functional model of plant phytochromes

A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red-induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful.

BAL27862: A Unique Microtubule Destabilizer Active Against Chemorefractory Breast Cancers

Background: BAL27862, a novel, synthetic, small molecule, is a potent inhibitor of tubulin polymerization that induces cancer cell death. BAL27862 elicits a unique microtubule (MT) phenotype, distinct from paclitaxel, vinblastine and colchicine, has broad in vitro anti-proliferative activity against a diverse range of human tumor lines (low nM IC50s) and induces significant antitumor responses in a range of animal models of human cancer when administered orally (p.o.) or intravenously (i.v.). In this study, BAL27862 activity in a panel of experimental breast cancer models was assessed.Materials and Methods: Anti-proliferative activity was analyzed using a monolayer (crystal violet) or soft agar (clonogenic) assay. Effects on MT phenotypes were assessed by immunofluorescence for α-tubulin. Efficacy was assessed in mouse xenograft models bearing chemosensitive and multidrug resistant human breast tumors.Results: The unique BAL27862-associated MT phenotype in interphase cells consisted of a partially collapsed MT network without peripheral MTs. In dividing cells, tiny MT asters were found scattered within the nuclear region. Potent anti-proliferative activity was demonstrated against 8 breast cancer cell lines (crystal violet assay IC50 range: 6.5 – 22 nM for the SKBR3, MCF7, BT474, T47D, BT549, MDA-MB231, MDA-MB453 and MDA-MB468 lines), although one line (HCC1937) appeared relatively insensitive (IC50: >1000 nM). Interestingly, two breast cancer lines were sensitive to BAL27862 treatment in a clonogenic assay (IC50/IC70: MAXF 401 = 13/18 nM; MAXF MX1 = 22/46 nM), despite one being relatively resistant to paclitaxel treatment (MAXF 401 = 11/48 nM; MAXF MX1 = 127/>3500 nM). Moreover, using monolayer assays, BAL27862 activity was retained against five tumor lines overexpressing the Pgp efflux pump (including MT-3/ADR mammary adenocarcinoma cells), which were up to several thousand-fold resistant to paclitaxel and vinblastine. BAL27862 showed little activity against human stem cells or peripheral blood mononucleocytes.When administered p.o or i.v. to mice at well tolerated doses, BAL27862 treatment elicited statistically significant antitumor activity (p≤0.05) in three chemosensitive human breast tumor xenograft models (including MAXF 401, MaCa 4049 and MT-3); resulting in a final %T/C (ratio of mean tumor volume of treated and control group x 100) equivalent to that observed with comparator cytotoxics using MTD schedules (e.g. final %T/C in MT-3 model: 36% BAL27862, 35% paclitaxel, 50% doxorubicin). Strikingly, significant antitumor activity was maintained in the Pgp-overexpressing MT-3/ADR xenograft model, where paclitaxel and doxorubicin were ineffective (final %T/C: 37% BAL27862, 112% paclitaxel, 108% doxorubicin).Conclusions: BAL27862 is a new tubulin-interacting agent with an apparently novel mechanism of action. A potent antitumor activity in experimental models of breast cancer, including chemorefractory models, strongly support further development of BAL27862 as a novel breast cancer treatment modality with a possibility for both i.v. and p.o. administration.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2093.

Integrating ELF4 into the circadian system through combined structural and functional studies

The circadian clock is a timekeeping mechanism that enables anticipation of daily environmental changes. In the plant Arabidopsis thaliana, the circadian system is a multiloop series of interlocked transcription-translation feedbacks. Several genes have been arranged in these oscillation loops, but the position of the core-clock gene ELF4 in this network was previously undetermined. ELF4 lacks sequence similarity to known domains, and functional homologs have not yet been identified. Here we show that ELF4 is functionally conserved within a subclade of related sequences, and forms an alpha-helical homodimer with a likely electrostatic interface that could be structurally modeled. We support this hypothesis by expression analysis of new elf4 hypomorphic alleles. These weak mutants were found to have expression level phenotypes of both morning and evening clock genes, implicating multiple entry points of ELF4 within the multiloop network. This could be mathematically modeled. Furthermore, morning-expression defects were particular to some elf4 alleles, suggesting predominant ELF4 action just preceding dawn. We provide a new hypothesis about ELF4 in the oscillator-it acts as a homodimer to integrate two arms of the circadian clock.

Differential transcriptional responses between the interferon-gamma-induction and iron-limitation models of persistence for Chlamydia pneumoniae

BACKGROUND AND PURPOSE

Chlamydia spp. are important pathogens of humans and animals that cause a wide range of acute and chronic infections. A persistence model has been developed in which Chlamydia spp. do not complete their developmental cycle, have significantly reduced infectivity for new host cells, and exhibit abnormal inclusion and reticulate body morphology. This study was performed to compare the interferon-gamma (IFN-gamma) induction and iron-limitation models of persistence for Chlamydia spp. to investigate the common and unique transcriptional pathways involved.

METHODS

A quantitative real time-polymerase chain reaction approach was used to compare the IFN-gamma induction and iron-limitation models of Chlamydia pneumoniae persistence at the transcriptional level by analyzing selected genes in each of 5 distinct, functionally relevant subcategories.

RESULTS

The models showed minimal evidence of a general transcriptional stress response in persistence, with only 1 of the 7 genes analyzed in the IFN-gamma induction model (htrA) and 4 of the genes in the iron-limitation model (htrA, clpB, clpP1, ahpC) showing increased mRNA levels. Both models showed similar responses in relation to the genes associated with lack of reticulate body to elementary body conversion (ctcB, lcrH1, and hctB levels were all unchanged or downregulated). The models also showed similar responses to the key cell wall/envelope genes, ompA, omcB, and crpA, exhibiting lower mRNA levels in both models.

CONCLUSIONS

These data show that several key transcriptional pathways (lack of late developmental cycle completion, key cell wall components) respond similarly between the models. However, other pathways appear to differ depending on the persistence-inducing mechanism. This result suggests that Chlamydia spp. have evolved more than 1 mechanism to respond to different persistence-inducing conditions, but ultimately the pathways probably converge through a common persistence regulon.

Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

Trees inferred from DNA sequence data provide only limited insight into the phylogeny of seed plants because the living lineages (cycads, Ginkgo, conifers, gnetophytes, and angiosperms) represent fewer than half of the major lineages that have been detected in the fossil record. Nevertheless, phylogenetic trees of living seed plants inferred from sequence data can provide a test of relationships inferred in analyses that include fossils. So far, however, significant uncertainty persists because nucleotide data support several conflicting hypotheses. It is likely that improved sampling of gymnosperm diversity in nucleotide data sets will help alleviate some of the analytical issues encountered in the estimation of seed plant phylogeny, providing a more definitive test of morphological trees. Still, rigorous morphological analyses will be required to answer certain fundamental questions, such as the identity of the angiosperm sister group and the rooting of crown seed plants. Moreover, it will be important to identify approaches for incorporating insights from data that may be accurate but less likely than sequence data to generate results supported by high bootstrap values. How best to weigh evidence and distinguish among hypotheses when some types of data give high support values and others do not remains an important problem.

Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8-kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.

Alpha-fetoprotein as a tumor marker in hepatocellular carcinoma: investigations in south Indian subjects with hepatotropic virus and aflatoxin etiologies

OBJECTIVES

The prevalence of hepatitis B virus (HBV) is reportedly the main cause of hepatocellular carcinoma (HCC) in India, where hepatitis C virus (HCV)-associated HCC is believed to be relatively less prevalent. We verified the usefulness of alpha-fetoprotein (AFP) as a tumor marker and analyzed the influence of viral etiology on AFP levels in HCC.

METHODS

Of a total of 1012 cases with liver disease, 202 were investigated for the presence of AFP (142 HCC cases, 30 cirrhosis cases, and 30 chronic liver disease (CLD) cases). In addition, serum samples from 30 healthy patients, 30 hepatitis B surface antigen (HBsAg) carriers, and 30 acute viral hepatitis cases were included as controls. AFP was quantitatively determined using a commercial ELISA (Quorum Diagnostics, Canada). Out of the 142 HCC cases screened for AFP, aflatoxin B1 (AFB1) detection was carried out in 38 HCC cases using an in-house immunoperoxidase test.

RESULTS

In HBV and HCV co-infected HCC cases, the AFP positivity was 85.7%. In HBV alone-associated HCC, the positivity was 62.9%, and 54.5% of AFB1 positive HCC cases showed AFP positivity. In HBV and HCV negative HCC cases, the positivity was 20.5%, and in HCV-associated HCC it was 17.6%. The HBV/HCV co-infected group and HBV alone positive HCC cases had significantly elevated levels of AFP. When AFP positivity was analyzed based on the marker profile of HBV, 89.7% of AFP positive cases were HBV-DNA positive.

CONCLUSIONS

The overall positivity pattern of AFP in HCC does indicate that higher levels of AFP are observed with hepatitis virus positivity, especially with HBV. Further studies must be carried out to correlate the serum levels of AFP with the size, number, and degree of differentiation of HCC nodules.