Analyzing DNA Microarrays with Undergraduate Statisticians

With advances in technology, biologists have been saddled with high dimensional data that need modern statistical methodology for analysis. DNA microarrays are able to simultaneously measure thousands of genes (and the activity of those genes) in a single sample. Biologists use microarrays to trace connections between pathways or to identify all genes that respond to a signal. The statistical tools we usually teach our undergraduates are inadequate for analyzing thousands of measurements on tens of samples. The project materials include readings on microarrays as well as computer lab activities. The topics covered include image analysis, filtering and normalization techniques, and statistical methods. The course materials are designed for someone with little or no statistical background, but due to the novel concepts covered, they could easily be adjusted to accommodate students with practically any background

Applying Failure Modes and Effects Analysis to Public Health Models: The Breathe Easy at Home Program

Failure Modes and Effects Analysis (FMEA) is a structured process used to identify and prioritize risks by ranking them based on severity, occurrence, and detectability. Historically, FMEA has been used within industries, including automotive and health care. This project explored the adaption of the FMEA template to a small public health program designed to improve asthma outcomes. The Breathe Easy at Home (BEAH) program is a multi-sector partnership that uses a web-based system to link clinical sites with housing code inspections and enforcement for patients with asthma. In July and August 2014, an FMEA was conducted to uncover risks within the BEAH process, and failures were prioritized for corrective action. The FMEA team prioritized risk based on severity, occurrence, and detectability to apply the FMEA process to a public health program. The FMEA team developed an action plan to improve failure modes that received the highest rankings. To fit the needs of a relatively small public health program, Joint Health Commission and U.S. Veterans Administration rating scales were adapted. The FMEA process can be adapted to a public health systems evaluation framework in order to prioritize areas for improvement

Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor

Background Carboxylesterases (CES) perform diverse metabolic roles in mammalian organisms in the detoxification of a broad range of drugs and xenobiotics and may also serve in specific roles in lipid, cholesterol, pheromone and lung surfactant metabolism. Five CES families have been reported in mammals with human CES1 and CES2 the most extensively studied. Here we describe the genetics, expression and phylogeny of CES isozymes in the opossum and report on the sequences and locations of CES1, CES2 and CES6 'like' genes within two gene clusters on chromosome one. We also discuss the likely sequence of gene duplication events generating multiple CES genes during vertebrate evolution. Results We report a cDNA sequence for an opossum CES and present evidence for CES1 and CES2 like genes expressed in opossum liver and intestine and for distinct gene locations of five opossum CES genes,CES1, CES2.1, CES2.2, CES2.3 and CES6, on chromosome 1. Phylogenetic and sequence alignment studies compared the predicted amino acid sequences for opossum CES with those for human, mouse, chicken, frog, salmon and Drosophila CES gene products. Phylogenetic analyses produced congruent phylogenetic trees depicting a rapid early diversification into at least five distinct CES gene family clusters: CES2, CES1, CES7, CES3, and CES6. Molecular divergence estimates based on a Bayesian relaxed clock approach revealed an origin for the five mammalian CES gene families between 328-378 MYA. Conclusion The deduced amino acid sequence for an opossum cDNA was consistent with its identity as a mammalian CES2 gene product (designated CES2.1). Distinct gene locations for opossum CES1 (1: 446,222,550-446,274,850), three CES2 genes (1: 677,773,395-677,927,030) and a CES6 gene (1: 677,585,520-677,730,419) were observed on chromosome 1. Opossum CES1 and multiple CES2 genes were expressed in liver and intestine. Amino acid sequences for opossum CES1 and three CES2 gene products revealed conserved residues previously reported for human CES1 involved in catalysis, ligand binding, tertiary structure and organelle localization. Phylogenetic studies indicated the gene duplication events which generated ancestral mammalian CES genes predated the common ancestor for marsupial and eutherian mammals, and appear to coincide with the early diversification of tetrapods.Full Tex

A Randomized, Double-Blinded, Phase II Trial of Gemcitabine and Nab-Paclitaxel Plus Apatorsen or Placebo in Patients with Metastatic Pancreatic Cancer: The RAINIER Trial.

Lessons learnedThe addition of the heat shock protein 27 (Hsp27)-targeting antisense oligonucleotide, apatorsen, to a standard first-line chemotherapy regimen did not result in improved survival in unselected patients with metastatic pancreatic cancer.Findings from this trial hint at the possible prognostic and predictive value of serum Hsp27 that may warrant further investigation.BackgroundThis randomized, double-blinded, phase II trial evaluated the efficacy of gemcitabine/nab-paclitaxel plus either apatorsen, an antisense oligonucleotide targeting heat shock protein 27 (Hsp27) mRNA, or placebo in patients with metastatic pancreatic cancer.MethodsPatients were randomized 1:1 to Arm A (gemcitabine/nab-paclitaxel plus apatorsen) or Arm B (gemcitabine/nab-paclitaxel plus placebo). Treatment was administered in 28-day cycles, with restaging every 2 cycles, until progression or intolerable toxicity. Serum Hsp27 levels were analyzed at baseline and on treatment. The primary endpoint was overall survival (OS).ResultsOne hundred thirty-two patients were enrolled, 66 per arm. Cytopenias and fatigue were the most frequent grade 3/4 treatment-related adverse events for both arms. Median progression-free survival (PFS) and OS were 2.7 and 5.3 months, respectively, for arm A, and 3.8 and 6.9 months, respectively, for arm B. Objective response rate was 18% for both arms. Patients with high serum level of Hsp27 represented a poor-prognosis subgroup who may have derived modest benefit from addition of apatorsen.ConclusionAddition of apatorsen to chemotherapy does not improve outcomes in unselected patients with metastatic pancreatic cancer in the first-line setting, although a trend toward prolonged PFS and OS in patients with high baseline serum Hsp27 suggests this therapy may warrant further evaluation in this subgroup

Which growth standards should be used to identify large- and small-for-gestational age infants of mothers with type 1 diabetes? A pre-specified analysis of the CONCEPTT trial.

BACKGROUND: Offspring of women with type 1 diabetes are at increased risk of fetal growth patterns which are associated with perinatal morbidity. Our aim was to compare rates of large- and small-for-gestational age (LGA; SGA) defined according to different criteria, using data from the Continuous Glucose Monitoring in Type 1 Diabetes Pregnancy Trial (CONCEPTT). METHODS: This was a pre-specified analysis of CONCEPTT involving 225 pregnant women and liveborn infants from 31 international centres ( ClinicalTrials.gov NCT01788527; registered 11/2/2013). Infants were weighed immediately at birth and GROW, INTERGROWTH and WHO centiles were calculated. Relative risk ratios, sensitivity and specificity were used to assess the different growth standards with respect to perinatal outcomes, including neonatal hypoglycaemia, hyperbilirubinaemia, respiratory distress, neonatal intensive care unit (NICU) admission and a composite neonatal outcome. RESULTS: Accelerated fetal growth was common, with mean birthweight percentiles of 82.1, 85.7 and 63.9 and LGA rates of 62, 67 and 30% using GROW, INTERGROWTH and WHO standards respectively. Corresponding rates of SGA were 2.2, 1.3 and 8.9% respectively. LGA defined according to GROW centiles showed stronger associations with preterm delivery, neonatal hypoglycaemia, hyperbilirubinaemia and NICU admission. Infants born > 97.7th centile were at highest risk of complications. SGA defined according to INTERGROWTH centiles showed slightly stronger associations with perinatal outcomes. CONCLUSIONS: GROW and INTERGROWTH standards performed similarly and identified similar numbers of neonates with LGA and SGA. GROW-defined LGA and INTERGROWTH-defined SGA had slightly stronger associations with neonatal complications. WHO standards underestimated size in preterm infants and are less applicable for use in type 1 diabetes. TRIAL REGISTRATION: This trial is registered with ClinicalTrials.gov . number NCT01788527 . Trial registered 11/2/2013

Advancing our understanding of the connectivity, evolution and management of marine lobsters through genetics

The genomic revolution has provided powerful insights into the biology and ecology of many non-model organisms. Genetic tools have been increasingly applied to marine lobster research in recent years and have improved our understanding of species delimitation and population connectivity. High resolution genomic markers are just beginning to be applied to lobsters and are now starting to revolutionise our understanding of fine spatial and temporal scales of population connectivity and adaptation to environmental conditions. Lobsters play an important role in the ecosystem and many species are commercially exploited but many aspects of their biology is still largely unknown. Genetics is a powerful tool that can further contribute to our understanding of their ecology and evolution and assist management. Here we illustrate how recent genetic advancements are (1) leading to a step change in our understanding of evolution and adaptation, (2) elucidating factors driving connectivity and recruitment, (3) revealing insights into ecological processes and can (4) potentially revolutionise management of this commercially important group. We discuss how improvements in sequencing technologies and statistical methods for genetic data analyses combined with increased sampling efforts and careful sampling design have transformed our understanding of lobsters biology in recent years. We also highlight possible future directions in the application of genomic tools to lobster research that can aid management, in particular, the close-kin-mark-recapture method. Finally, we identify gaps and challenges in lobster research, such as the lack of any reference genomes and predictions on how lobsters will respond to future environmental conditions

Salicylic acid treatment and expression of an RNA-dependent RNA polymerase 1 transgene inhibit lethal symptoms and meristem invasion during tobacco mosaic virus infection in Nicotiana benthamiana.

BACKGROUND: Host RNA-dependent RNA polymerases (RDRs) 1 and 6 contribute to antiviral RNA silencing in plants. RDR6 is constitutively expressed and was previously shown to limit invasion of Nicotiana benthamiana meristem tissue by potato virus X and thereby inhibit disease development. RDR1 is inducible by salicylic acid (SA) and several other phytohormones. But although it contributes to basal resistance to tobacco mosaic virus (TMV) it is dispensable for SA-induced resistance in inoculated leaves. The laboratory accession of N. benthamiana is a natural rdr1 mutant and highly susceptible to TMV. However, TMV-induced symptoms are ameliorated in transgenic plants expressing Medicago truncatula RDR1. RESULTS: In MtRDR1-transgenic N. benthamiana plants the spread of TMV expressing the green fluorescent protein (TMV.GFP) into upper, non-inoculated, leaves was not inhibited. However, in these plants exclusion of TMV.GFP from the apical meristem and adjacent stem tissue was greater than in control plants and this exclusion effect was enhanced by SA. TMV normally kills N. benthamiana plants but although MtRDR1-transgenic plants initially displayed virus-induced necrosis they subsequently recovered. Recovery from disease was markedly enhanced by SA treatment in MtRDR1-transgenic plants whereas in control plants SA delayed but did not prevent systemic necrosis and death. Following SA treatment of MtRDR1-transgenic plants, extractable RDR enzyme activity was increased and Western blot analysis of RDR extracts revealed a band cross-reacting with an antibody raised against MtRDR1. Expression of MtRDR1 in the transgenic N. benthamiana plants was driven by a constitutive 35S promoter derived from cauliflower mosaic virus, confirmed to be non-responsive to SA. This suggests that the effects of SA on MtRDR1 are exerted at a post-transcriptional level. CONCLUSIONS: MtRDR1 inhibits severe symptom development by limiting spread of virus into the growing tips of infected plants. Thus, RDR1 may act in a similar fashion to RDR6. MtRDR1 and SA acted additively to further promote recovery from disease symptoms in MtRDR1-transgenic plants. Thus it is possible that SA promotes MtRDR1 activity and/or stability through post-transcriptional effects.We thank Zhixiang Chen for his advice on the RDR assay protocol. Xiaoqiang Wang and Zhentian Lei at the Samuel Roberts Noble Foundation for the AKTA purification protocol and analysis of recombinant MBP:MtRDR1 fusion protein, respectively. David Baulcombe, Peter Palukaitis, Joel Milner and Lydia Hunter are thanked for stimulating discussions and useful advice and Adrienne Pate for expert technical assistance. FSF was funded by grants from the Cambridge Overseas Trust and the Ministry of Education of Taiwan, and WSL was funded by a studentship from the Biotechnology and Biological Sciences Research Council (BBSRC) and work in the Carr lab was funded by BBSRC grants (BB/D008204/1, BB/D014376/1, BB/J011762/1), The Leverhulme Trust (F/09 741/F, RPG-2012-667), and Cambridge University Isaac Newton Trust. RSN and SRC were funded by the Samuel Roberts Noble Foundation, Inc