A common phytoene synthase mutation underlies white petal varieties of the California poppy.

The California poppy (Eschscholzia californica) is renowned for its brilliant golden-orange flowers, though white petal variants have been described. By whole-transcriptome sequencing, we have discovered in multiple white petal varieties a single deletion leading to altered splicing and C-terminal truncation of phytoene synthase (PSY), a key enzyme in carotenoid biosynthesis. Our findings underscore the diverse roles of phytoene synthase in shaping horticultural traits, and resolve a longstanding mystery of the regaled golden poppy

Carbon Free Boston: Technical Summary

Part of a series of reports that includes: Carbon Free Boston: Summary Report; Carbon Free Boston: Social Equity Report; Carbon Free Boston: Buildings Technical Report; Carbon Free Boston: Transportation Technical Report; Carbon Free Boston: Waste Technical Report; Carbon Free Boston: Energy Technical Report; Carbon Free Boston: Offsets Technical Report; Available at http://sites.bu.edu/cfb/OVERVIEW: This technical summary is intended to argument the rest of the Carbon Free Boston technical reports that seek to achieve this goal of deep mitigation. This document provides below: a rationale for carbon neutrality, a high level description of Carbon Free Boston’s analytical approach; a summary of crosssector strategies; a high level analysis of air quality impacts; and, a brief analysis of off-road and street light emissions.Published versio

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data

Summary: DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage. However, only a subset of genes with altered dosage exhibit concordant changes in gene expression. This subset is likely to be enriched for oncogenes and tumor suppressor genes, and can be identified by integrating these two layers of genome-scale data. We introduce DNA/RNA-Integrator (DR-Integrator), a statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies genes with significant correlations between DNA copy number and gene expression, and implements a supervised analysis that captures genes with significant alterations in both DNA copy number and gene expression between two sample classes

A Tri-Marker Proliferation Index Predicts Biochemical Recurrence after Surgery for Prostate Cancer

Prostate cancer exhibits tremendous variability in clinical behavior, ranging from indolent to lethal disease. Better prognostic markers are needed to stratify patients for appropriately aggressive therapy. By expression profiling, we can identify a proliferation signature variably expressed in prostate cancers. Here, we asked whether one or more tissue biomarkers might capture that information, and provide prognostic utility. We assayed three proliferation signature genes: MKI67 (Ki-67; also a classic proliferation biomarker), TOP2A (DNA topoisomerase II, alpha), and E2F1 (E2F transcription factor 1). Immunohistochemical staining was evaluable on 139 radical prostatectomy cases (in tissue microarray format), with a median clinical follow-up of eight years. Each of the three proliferation markers was by itself prognostic. Notably, combining the three markers together as a “proliferation index” (0 or 1, vs. 2 or 3 positive markers) provided superior prognostic performance (hazard ratio = 2.6 (95% CI: 1.4–4.9); P = 0.001). In a multivariate analysis that included preoperative serum prostate specific antigen (PSA) levels, Gleason grade and pathologic tumor stage, the composite proliferation index remained a significant predictor (P = 0.005). Analysis of receiver-operating characteristic (ROC) curves confirmed the improved prognostication afforded by incorporating the proliferation index (compared to the clinicopathologic data alone). Our findings highlight the potential value of a multi-gene signature-based diagnostic, and define a tri-marker proliferation index with possible utility for improved prognostication and treatment stratification in prostate cancer

A DNA microarray survey of gene expression in normal human tissues

BACKGROUND: Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states. Comparatively little is known about the genes expressed across the gamut of normal human tissues. Systematic studies of global gene-expression patterns, by linking variation in the expression of specific genes to phenotypic variation in the cells or tissues in which they are expressed, provide clues to the molecular organization of diverse cells and to the potential roles of the genes. RESULTS: Here we describe a systematic survey of gene expression in 115 human tissue samples representing 35 different tissue types, using cDNA microarrays representing approximately 26,000 different human genes. Unsupervised hierarchical cluster analysis of the gene-expression patterns in these tissues identified clusters of genes with related biological functions and grouped the tissue specimens in a pattern that reflected their anatomic locations, cellular compositions or physiologic functions. In unsupervised and supervised analyses, tissue-specific patterns of gene expression were readily discernable. By comparative hybridization to normal genomic DNA, we were also able to estimate transcript abundances for expressed genes. CONCLUSIONS: Our dataset provides a baseline for comparison to diseased tissues, and will aid in the identification of tissue-specific functions. In addition, our analysis identifies potential molecular markers for detection of injury to specific organs and tissues, and provides a foundation for selection of potential targets for selective anticancer therapy

Pengembangan Modul Intervensi Untuk Meningkatkan Resiliensi Pada Individu Yang Mengalami Perubahan Fisik Menjadi Penyandang Disabilitas

Penelitian ini bertujuan untuk menindaklanjuti temuan sebelumnya dengan mengembangkan modul intervensi secara terperinci, yang selanjutnya dapat digunakan sebagai panduan dalam membantu meningkatkan resiliensi individu yang mengalami Perubahan kondisi fisik menjadi penyandang disabilitas. Penulis menyusun serta merinci rancangan implementasi awal yang direkomendasikan oleh penelitian sebelumnya kedalam langkah-langkah yang lebih sistematis dan operasional hingga memperoleh hasil akhir berupa modul. Metode yang digunakan berbasis tahapan riset aksi, meskipun proses yang dilakukan hanya sampai pada langkah ketiga, yaitu Perumusan solusi dari persoalan yang diangkat. Partisipan terdiri dari delapan individu yang mengalami Perubahan kondisi menjadi penyandang disabilitas. Selain partisipan, empat orang psikolog juga dilibatkan dalam penelitian ini sebagai penelaah modul. Hasil penelitian ini berupa sebuah paket modul intervensi untuk peningkatan resiliensi melalui penguatan faktor protektif serta pengembangan strategi koping dan adaptasi pada individu yang mengalami Perubahan kondisi fisik menjadi penyandang disabilitas. Paket modul tersebut terdiri dari 5 sub-modul yang telah disusun sedemikian rupa untuk memudahkan pelaksanaannya, terdiri dari modul: (1) memperkuat dukungan keluarga terhadap penyandang disabilitas; (2) pendampingan awal penyandang disabilitas; (3) intervensi lanjut 1 (penguatan faktor protektif internal); (4) intervensi lanjut 2 (pengembangan strategi koping); dan (5) intervensi lanjut 3 (langkah adaptasi positif)