Response of breast carcinoma to endocrine therapy predicted using immunostained pelleted fine needle aspirates.

Fine needle aspirates from 82 patients with breast carcinoma were fixed in methacarn, double embedded in agar or gelatin, and then in paraffin wax. Sequential sections were stained with monoclonal antibodies to the oestrogen receptor-related protein P29 (antibody D5), carcinoembryonic antigen (CEA), epithelial membrane antigen (EMA) and cytokeratin (CAM 5.2). Sixty-one of 82 (74%) aspirates provided sections suitable for immunostaining. Twenty-six (43%) were D5 positive, 23 (38%) CEA positive, 59 (97%) EMA positive, and 54 (89%) CAM 5.2 positive. Twenty-six of these patients were treated with some form of endocrine therapy. Twelve (46%) showed positive staining for D5. Eleven (92%) of the 12 D5-positive patients responded or had static disease, and 8% progressed. Of the 14 D5-negative tumours 43% responded or remained static, and 57% progressed. The difference in response between the D5-positive and the D5-negative tumours was significant (P less than 0.05, Fisher's exact test). There was no correlation between staining for CEA, EMA or cytokeratin and response to endocrine therapy

Sustainability of crop production from polluted lands

Sustainable food production for a rapidly growing global population is a major challenge of this century. In order to meet the demand for food production, an additional land area of 2.7 to 4.9 Mha year -1 will be required for agriculture. However, one third of arable lands are already contaminated, therefore the use of polluted lands will have to feature highly in modern agriculture. The use of such lands comes however with additional challenges and suitable agrotechnological interventions are essential for ensuring the safety and sustainability of relevant production system. There are also other issues to consider such as, cost benefit analysis, the possible entry of pollutants into to the phytoproducts, certification and marketing of such products, in order to achieve a the large scale exploitation of polluted land

Decision and Discovery in Defining “Disease”

This version (May 17, 2005) was published in its final form as: Schwartz PH. Decision and discovery in defining 'disease'. In: Kincaid H, McKitrick J, editors. Establishing medical reality: essays in the metaphysics and epistemology of biomedical science. Dordrecht: Springer; 2007. p. 47-63. http://dx.doi.org/10.1007/1-4020-5216-2_5The debate over how to analyze the concept of disease has often centered on the question of whether to include a reference to values, in particular the ‘disvalue’of diseases, or whether to avoid such notions. ‘Normativists,’such as King ([1954], 1981) and Culver and Gert (1982) emphasize the undesirability of diseases, while ‘Naturalists,’ most prominently Christopher Boorse (1977, 1987, 1997), instead require just the presence of biological dysfunction. The debate between normativism and naturalism often deteriorates into stalemate, with each side able to point out significant problems with the other. It starts to look as if neither approach can work. In this paper, I argue that the standoff stems from deeply questionable assumptions that have been used to formulate the opposing positions and guide the debate. In the end, I propose an alternative set of guidelines that offer a more constructive way to devise and compare theories

Small RNAs Prevent Transcription-Coupled Loss of Histone H3 Lysine 9 Methylation in Arabidopsis thaliana

In eukaryotes, histone H3 lysine 9 methylation (H3K9me) mediates silencing of invasive sequences to prevent deleterious consequences including the expression of aberrant gene products and mobilization of transposons. In Arabidopsis thaliana, H3K9me maintained by SUVH histone methyltransferases (MTases) is associated with cytosine methylation (5meC) maintained by the CMT3 cytosine MTase. The SUVHs contain a 5meC binding domain and CMT3 contains an H3K9me binding domain, suggesting that the SUVH/CMT3 pathway involves an amplification loop between H3K9me and 5meC. However, at loci subject to read-through transcription, the stability of the H3K9me/5meC loop requires a mechanism to counteract transcription-coupled loss of H3K9me. Here we use the duplicated PAI genes, which stably maintain SUVH-dependent H3K9me and CMT3-dependent 5meC despite read-through transcription, to show that when PAI sRNAs are depleted by dicer ribonuclease mutations, PAI H3K9me and 5meC levels are reduced and remaining PAI 5meC is destabilized upon inbreeding. The dicer mutations confer weaker reductions in PAI 5meC levels but similar or stronger reductions in PAI H3K9me levels compared to a cmt3 mutation. This comparison indicates a connection between sRNAs and maintenance of H3K9me independent of CMT3 function. The dicer mutations reduce PAI H3K9me and 5meC levels through a distinct mechanism from the known role of dicer-dependent sRNAs in guiding the DRM2 cytosine MTase because the PAI genes maintain H3K9me and 5meC at levels similar to wild type in a drm2 mutant. Our results support a new role for sRNAs in plants to prevent transcription-coupled loss of H3K9me

Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function

<p>Abstract</p> <p>Background</p> <p>Plants contain numerous <it>Su(var)3-9 </it>homologues (<it>SUVH</it>) and related (<it>SUVR</it>) genes, some of which await functional characterization. Although there have been studies on the evolution of plant <it>Su(var)3-9 SET </it>genes, a systematic evolutionary study including major land plant groups has not been reported. Large-scale phylogenetic and evolutionary analyses can help to elucidate the underlying molecular mechanisms and contribute to improve genome annotation.</p> <p>Results</p> <p>Putative orthologs of plant Su(var)3-9 SET protein sequences were retrieved from major representatives of land plants. A novel clustering that included most members analyzed, henceforth referred to as core <it>Su(var)3-9 </it>homologues and related (<it>cSUVHR</it>) gene clade, was identified as well as all orthologous groups previously identified. Our analysis showed that plant Su(var)3-9 SET proteins possessed a variety of domain organizations, and can be classified into five types and ten subtypes. Plant <it>Su(var)3-9 SET </it>genes also exhibit a wide range of gene structures among different paralogs within a family, even in the regions encoding conserved PreSET and SET domains. We also found that the majority of SUVH members were intronless and formed three subclades within the SUVH clade.</p> <p>Conclusions</p> <p>A detailed phylogenetic analysis of the plant <it>Su(var)3-9 SET g</it>enes was performed. A novel deep phylogenetic relationship including most plant <it>Su(var)3-9 SET </it>genes was identified. Additional domains such as SAR, ZnF_C2H2 and WIYLD were early integrated into primordial PreSET/SET/PostSET domain organization. At least three classes of gene structures had been formed before the divergence of <it>Physcomitrella patens </it>(moss) from other land plants. One or multiple retroposition events might have occurred among <it>SUVH </it>genes with the donor genes leading to the V-2 orthologous group. The structural differences among evolutionary groups of plant <it>Su(var)3-9 SET </it>genes with different functions were described, contributing to the design of further experimental studies.</p

Olaparib in patients with metastatic castration-resistant prostate cancer with DNA repair gene aberrations (TOPARP-B): a multicentre, open-label, randomised, phase 2 trial

Background Metastatic castration-resistant prostate cancer is enriched in DNA damage response (DDR) gene aberrations. The TOPARP-B trial aims to prospectively validate the association between DDR gene aberrations and response to olaparib in metastatic castration-resistant prostate cancer. Methods In this open-label, investigator-initiated, randomised phase 2 trial following a selection (or pick-the-winner) design, we recruited participants from 17 UK hospitals. Men aged 18 years or older with progressing metastatic castration-resistant prostate cancer previously treated with one or two taxane chemotherapy regimens and with an Eastern Cooperative Oncology Group performance status of 2 or less had tumour biopsies tested with targeted sequencing. Patients with DDR gene aberrations were randomly assigned (1:1) by a computer-generated minimisation method, with balancing for circulating tumour cell count at screening, to receive 400 mg or 300 mg olaparib twice daily, given continuously in 4-week cycles until disease progression or unacceptable toxicity. Neither participants nor investigators were masked to dose allocation. The primary endpoint of confirmed response was defined as a composite of all patients presenting with any of the following outcomes: radiological objective response (as assessed by Response Evaluation Criteria in Solid Tumors 1.1), a decrease in prostate-specific antigen (PSA) of 50% or more (PSA50) from baseline, or conversion of circulating tumour cell count (from ≥5 cells per 7·5 mL blood at baseline to <5 cells per 7·5 mL blood). A confirmed response in a consecutive assessment after at least 4 weeks was required for each component. The primary analysis was done in the evaluable population. If at least 19 (43%) of 44 evaluable patients in a dose cohort responded, then the dose cohort would be considered successful. Safety was assessed in all patients who received at least one dose of olaparib. This trial is registered at ClinicalTrials.gov, NCT01682772. Recruitment for the trial has completed and follow-up is ongoing. Findings 711 patients consented for targeted screening between April 1, 2015, and Aug 30, 2018. 161 patients had DDR gene aberrations, 98 of whom were randomly assigned and treated (49 patients for each olaparib dose), with 92 evaluable for the primary endpoint (46 patients for each olaparib dose). Median follow-up was 24·8 months (IQR 16·7–35·9). Confirmed composite response was achieved in 25 (54·3%; 95% CI 39·0–69·1) of 46 evaluable patients in the 400 mg cohort, and 18 (39·1%; 25·1–54·6) of 46 evaluable patients in the 300 mg cohort. Radiological response was achieved in eight (24·2%; 11·1–42·3) of 33 evaluable patients in the 400 mg cohort and six (16·2%; 6·2–32·0) of 37 in the 300 mg cohort; PSA50 response was achieved in 17 (37·0%; 23·2–52·5) of 46 and 13 (30·2%; 17·2–46·1) of 43; and circulating tumour cell count conversion was achieved in 15 (53·6%; 33·9–72·5) of 28 and 13 (48·1%; 28·7–68·1) of 27. The most common grade 3–4 adverse event in both cohorts was anaemia (15 [31%] of 49 patients in the 300 mg cohort and 18 [37%] of 49 in the 400 mg cohort). 19 serious adverse reactions were reported in 13 patients. One death possibly related to treatment (myocardial infarction) occurred after 11 days of treatment in the 300 mg cohort. Interpretation Olaparib has antitumour activity against metastatic castration-resistant prostate cancer with DDR gene aberrations, supporting the implementation of genomic stratification of metastatic castration-resistant prostate cancer in clinical practice

Poplar maintains zinc homeostasis with heavy metal genes HMA4 and PCS1

Perennial woody species, such as poplar (Populus spp.) must acquire necessary heavy metals like zinc (Zn) while avoiding potential toxicity. Poplar contains genes with sequence homology to genes HMA4 and PCS1 from other species which are involved in heavy metal regulation. While basic genomic conservation exists, poplar does not have a hyperaccumulating phenotype. Poplar has a common indicator phenotype in which heavy metal accumulation is proportional to environmental concentrations but excesses are prevented. Phenotype is partly affected by regulation of HMA4 and PCS1 transcriptional abundance. Wild-type poplar down-regulates several transcripts in its Zn-interacting pathway at high Zn levels. Also, overexpressed PtHMA4 and PtPCS1 genes result in varying Zn phenotypes in poplar; specifically, there is a doubling of Zn accumulation in leaf tissues in an overexpressed PtPCS1 line. The genomic complement and regulation of poplar highlighted in this study supports a role of HMA4 and PCS1 in Zn regulation dictating its phenotype. These genes can be altered in poplar to change its interaction with Zn. However, other poplar genes in the surrounding pathway may maintain the phenotype by inhibiting drastic changes in heavy metal accumulation with a single gene transformation