Docking, synthesis, and in vitro evaluation of antimitotic estrone analogs

In the present study, Autodock 4.0 was employed to discover potential carbonic anhydrase IX inhibitors that are able to interfere with microtubule dynamics by binding to the Colchicine binding site of tubulin. Modifications at position 2’ of estrone were made to include moieties that are known to improve the antimitotic activity of estradiol analogs. 2-ethyl-3-O-sulphamoyl-estra-1,3,5(10),15-tetraen-3-ol-17-one estronem (C9) and 2-ethyl-3-O-sulphamoyl-estra-1,3,5(10)16-tetraene (C12) were synthesized and tested in vitro. Growth studies were conducted utilizing spectrophotometrical analysis with crystal violet as DNA stain. Compounds C9 and C12 were cytotoxic in MCF-7 and MDA-MB-231 tumorigenic and metastatic breast cancer cells, SNO non-keratinizing squamous epithelium cancer cells and HeLa cells after 48 h exposure. Compounds C9 inhibited cell proliferation to 50% of the vehicle-treated controls from 110-160 nM and C12 at concentrations ranging from 180-220 nM. Confocal microscopy revealed abnormal spindle morphology in mitotic cells. Cell cycle analysis showed an increase in the number of cells in the G2/M fraction after 24 h and an increase in the number of cell in the sub-G1 fraction after 48 h, indicating that the compounds are antimitotic and able to induce apoptosis.Medical Research Council of South Africa (AG374, AK076), the Cancer Association of South Africa (AK246), the Struwig-Germeshuysen Cancer Research Trust of South Africa (AJ038) and RESCOM University of Pretoria (A0R984).http://www3.interscience.wiley.com/journal/120118371/grouphome/home.htm

In vitro effects of a new and novel antimitotic compound in human breast adenocarcinoma metastatic epithelial cells

This study contributes to the understanding of molecular mechanisms and cell signaling events associated with in vitro anticancer responses of a new and novel antimitotic compound, 2-etiel-3-sulfamaat- 1,3,5(10)16-tetraeen (C19).This paper was initially delivered at the Annual Congress of the Biological Sciences Division of the South African Academy for Science and Art, ARC-Plant Protection Research Institute, Roodeplaat, Pretoria, South Africa on 01 October 2010.http://www.satnt.ac.zaam201

In vitro evaluation of a novel antimitotic estradiol analog and dichloroacetic acid on breast adenocarcinoma and breast non-tumorigenic cells

In vitro evaluation of a novel antimitotic estradiol analog and dichloroacetae, which restore mitochondrion function in breast adenocarcinoma and breast non-tumorigenic cells, will contribute to the field of combination therapy in cancer.This paper was initially delivered at the Annual Congress of the Biological Sciences Division of the South African Academy for Science and Art, ARC-Plant Protection Research Institute, Roodeplaat, Pretoria, South Africa on 01 October 2010.am201

Medical students’ use of caffeine for ‘academic purposes’ and their knowledge of its benefits, side-effects and withdrawal symptoms

Background: Caffeine is often used for its benefits, which include increased vigilance. It does have side-effects, however, such as palpitations andwithdrawal symptoms that include headaches and drowsiness. Tertiary education often requires students to study for extended hours, especiallyduring periods of increased workload prior to tests and examinations. Medical students, who have to master a very large volume of academic work ina limited period of time, are no exception. This cross-sectional study investigated caffeine use for ‘academic purposes’ by first- to third-year medicalstudents at the University of the Free State in 2006, and their knowledge of its benefits, side-effects and withdrawal symptoms.Methods: Data were collected by means of an anonymous, self-administered questionnaire that was completed by students during formal classtime, arranged in advance with the relevant lecturers. Questionnaires were available in Afrikaans and English. A pilot study was conducted on20 physiotherapy students to test the questionnaire. Chi-squared and Kruskall-Wallis tests were used to compare categorical and numerical variables,respectively. Ethical approval to perform the investigation was granted by the Ethics Committee of the Faculty of Health Sciences, University of theFree State.Results: A 90.5% (360/389) response rate was obtained. Ninety-four per cent of participants used caffeine, with academic purposes (62.6%) amongthe three most frequent reasons given for its consumption. Other reasons included social consumption (70%) and preference for the taste (72.4%).Coffee (88.2%) was the most commonly consumed caffeinated product among these students, followed by energy mixtures and tablets (37.9%),and soft drinks (36%). Third-year students were the heaviest consumers of coffee for academic purposes. An increase in caffeine consumptionfor academic purpose was directly related to progression from first- to third- year of the medical course. The average scores for questions on thebenefits, side-effects and withdrawal symptoms were all below 1.5 out of 5. Misconceptions about caffeine were also identified. With regard to thebenefits of caffeine, the most commonly cited misconception was that it could be used as a substitute for sleep (26.7% of respondents). The mostcommon misconception regarding its side-effects was that it caused hot flushes (21.9%), while aggression (27.2%) was cited as the most commonmisconception regarding caffeine withdrawal.Conclusions: The high percentage of caffeine usage and low scores in the caffeine knowledge test indicated that most participants were usingcaffeine without having sufficient knowledge of its benefits, side-effects and withdrawal symptoms. It is recommended that awareness programmeson the side-effects and symptoms of caffeine withdrawal should be implemented by the student health and counselling facilities on campus. Thedisplay of posters in strategic venues and distribution of pamphlets could assist in the dissemination of information on this extensively consumedsubstance

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq

<p>Abstract</p> <p>Background</p> <p><it>De novo </it>assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a <it>Eucalyptus </it>tree species (<it>E. grandis</it>) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs.</p> <p>Results</p> <p>We present an extensive expressed gene catalog for a commercially grown <it>E. grandis </it>× <it>E. urophylla </it>hybrid clone constructed using only Illumina mRNA-Seq technology and <it>de novo </it>assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any <it>Eucalyptus </it>tree. mRNA-Seq analysis furthermore allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions.</p> <p>Conclusions</p> <p><it>De novo </it>assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in <it>Eucalyptus </it>and other non-model organisms. The transcriptome resource (Eucspresso, <url>http://eucspresso.bi.up.ac.za/</url>) generated by this study will be of value for genomic analysis of woody biomass production in <it>Eucalyptus </it>and for comparative genomic analysis of growth and development in woody and herbaceous plants.</p

Germline sequence variants contributing to cancer susceptibility in South African breast cancer patients of African ancestry

Since the discovery of the breast cancer susceptibility genes, BRCA1 and BRCA2, various other genes conferring an increased risk for breast cancer have been identified. Studies to evaluate sequence variants in cancer predisposition genes among women of African ancestry are limited and mostly focused on BRCA1 and BRCA2. To characterize germline sequence variants in cancer susceptibility genes, we analysed a cohort of 165 South African women of self-identified African ancestry diagnosed with breast cancer, who were unselected for family history of cancer. With the exception of four cases, all others were previously investigated for BRCA1 and BRCA2 deleterious variants, and were negative for pathogenic variants. We utilized the Illumina TruSight cancer panel for targeted sequencing of 94 cancer susceptibility genes. A total of 3.6% of patients carried a pathogenic/likely pathogenic variant in a known breast cancer susceptibility gene: 1.2% in BRCA1, 0.6% in each of BRCA2, ATM, CHEK2 and PALB, none of whom had any family history of breast cancer. The mean age of patients who carried deleterious variant in BRCA1/BRCA2 was 39 years and 8 months compared to 47 years and 3 months among women who carried a deleterious variant in other breast cancer susceptibility genes.The University of Pretoria, Genomics Research Institute, the Cancer Association of South Africa, the South African Medical Research Council and the South African National Research Foundation.https://www.nature.com/srepBiochemistryGeneticsMicrobiology and Plant Patholog

MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters

<p>Abstract</p> <p>Background</p> <p>Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill.</p> <p>Description</p> <p>MADIBA (MicroArray Data Interface for Biological Annotation) facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for <it>Plasmodium</it>, rice and <it>Arabidopsis</it>. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied.</p> <p>Conclusion</p> <p>MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments – expression profiling of the <it>Plasmodium </it>life cycle, and salt stress treatments of <it>Arabidopsis </it>and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA. </p

Virus genome dynamics under different propagation pressures : reconstruction of whole genome haplotypes of West Nile viruses from NGS data

BACKGROUND : Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies population variants. These variants are not discernable in the consensus genome at the time of emergence, and the maintenance of mutationselection equilibria of population variants is greatly underestimated. The emergence of lineage 1 WNV strains has been studied extensively, but recent epidemics caused by lineage 2 WNV strains in Hungary, Austria, Greece and Italy emphasizes the increasing importance of this lineage to public health. In this study we explored the quasispecies dynamics of minority variants that contribute to cell-tropism and host determination, i.e. the ability to infect different cell types or cells from different species from Next Generation Sequencing (NGS) data of a historic lineage 2 WNV strain. RESULTS : Minority variants contributing to host cell membrane association persist in the viral population without contributing to the genetic change in the consensus genome. Minority variants are shown to maintain a stable mutation-selection equilibrium under positive selection, particularly in the capsid gene region. CONCLUSIONS : This study is the first to infer positive selection and the persistence of WNV haplotype variants that contribute to viral fitness without accompanying genetic change in the consensus genotype, documented solely from NGS sequence data. The approach used in this study streamlines the experimental design seeking viral minority variants accurately from NGS data whilst minimizing the influence of associated sequence error.The Agricultural Research Council (ARC) Onderstepoort Veterinary Institute (OVI) is thanked for providing the WNV strain and funding used in this study.CK was funded though an AgriSETA bursary.http://www.biomedcentral.com/bmcgenomicshb201