Charles Hauser

Chlamydomonas reinhardtii Genome Project. A Guide to the Generation and Use of the cDNA Information

The National Science Foundation-funded Chlamydomonas reinhardtii genome project involves (a) construction and sequencing of cDNAs isolated from cells exposed to various environmental conditions, (b) construction of a high-density cDNA microarray, (c) generation of genomic contigs that are nucleated around specific physical and genetic markers, (d) generation of a complete chloroplast genome sequence and analyses of chloroplast gene expression, and (e) the creation of a Web-based resource that allows for easy access of the information in a format that can be readily queried. Phases of the project performed by the groups at the Carnegie Institution and Duke University involve the generation of normalized cDNA libraries, sequencing of cDNAs, analysis and assembly of these sequences to generate contigs and a set of predicted unique genes, and the use of this information to construct a high-density DNA microarray. In this paper, we discuss techniques involved in obtaining cDNA end-sequence information and the ways in which this information is assembled and analyzed. Descriptions of protocols for preparing cDNA libraries, assembling cDNA sequences and annotating the sequence information are provided (the reader is directed to Web sites for more detailed descriptions of these methods). We also discuss preliminary results in which the different cDNA libraries are used to identify genes that are potentially differentially expressed.

Bioaccumulation and Effects of CdTe/CdS Quantum Dots on Chlamydomonas reinhardtii – Nanoparticles or the Free Ions?

In order to properly assess the environmental risk of engineered nanoparticles (ENP), it is necessary to determine their fate (including dissolution, aggregation, and bioaccumulation) under representative environmental conditions. CdTe/CdS quantum dots (QD), such as those used in medical imaging, are known to release Cd(2+) due (mainly) to the dissolution of their outer shell. In this study, Chlamydomonas reinhardtii was exposed to either a soluble Cd salt or QD at similar concentrations of total Cd. Free Cd concentrations were measured using the Absence of Gradients and Nernstian Equilibrium Stripping technique. QD dissolution increased with decreasing pH and with increasing QD concentration. When exposed to QD, bioaccumulation was largely accounted for by dissolved Cd. Nonetheless, QD were shown to be taken up by the cells and to provoke unique biological effects. Whole transcriptome screening using RNA-Seq analysis showed that the free Cd and the QD had distinctly different biological effects.

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences, with students pooling their work to contribute to international databases.

Transcriptome Sequencing (RNA-seq) Analysis of the Effects of Metal Nanoparticle Exposure on the Transcriptome of Chlamydomonas reinhardtii

ABSTRACT The widespread use of nanoparticles (NPs) raises concern over their potential toxicological effects in humans and ecosystems. Here we used transcriptome sequencing (RNA-seq) to evaluate the effects of exposure to four different metal-based NPs, nano-Ag (nAg), nano-TiO2 (nTiO2), nano-ZnO (nZnO), and CdTe/CdS quantum dots (QDs), in the eukaryotic green alga Chlamydomonas reinhardtii. The transcriptome was characterized before and after exposure to each NP type. Specific toxicological effects were inferred from the functions of genes whose transcripts either increased or decreased. Data analysis resulted in important differences and also similarities among the NPs. Elevated levels of transcripts of several marker genes for stress were observed, suggesting that only nZnO caused nonspecific global stress to the cells under environmentally relevant conditions. Genes with photosynthesis-related functions were decreased drastically during exposure to nTiO2 and slightly during exposures to the other NP types. This pattern suggests either toxicological effects in the chloroplast or effects that mimic a transition from low to high light. nAg exposure dramatically elevated the levels of transcripts encoding known or predicted components of the cell wall and the flagella, suggesting that it damages structures exposed to the external milieu. Exposures to nTiO2, nZnO, and QDs elevated the levels of transcripts encoding subunits of the proteasome, suggesting proteasome inhibition, a phenomenon believed to underlie the development and progression of several major diseases, including Alzheimers disease, and used in chemotherapy against multiple myeloma.

A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students.

A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles.

Chapter 28 – Protein Synthesis in the Chloroplast

Publisher Summary Translational control functions in diverse biological processes including developmental pattern formation, intracellular protein targeting, the control of homeostasis, and a variety of stress responses. Since the discovery of genomes in plastids, Chlamydomonas research has played a central role in the development of our understanding of the plastid translation machinery and the mechanisms that regulate translation in chloroplasts, and this chapter reviews relevant findings and models. Protein synthesis rates in the Chlamydomonas chloroplast are routinely measured using pulse labeling of intact cells with 35SO4 or [14C] acetate, or isolated chloroplasts with [35S]methionine. This part, radioisotope pulse labeling of newly synthesized proteins, is described under methodologies of protein synthesis. Genetics has been used extensively for the identification and characterization of trans-acting factors and cis-acting sequences that function in the translation of chloroplast mRNAs. Chloroplast ribosomes are introduced and updated with recent research findings. Translation requires general translation factors (GTF), many of which are GTPases activated by the ribosome. The identities and properties of the Chlamydomonas GTFs are covered in this section. Chlamydomonas responds to light in a variety of ways, including changes in chloroplast gene expression at the translational level. This section reviews distinct translational regulatory responses during dark-to-light transitions and under high light stress. Reverse genetic approaches are used to address the functions of other translation factors originally identified through biochemical approaches.

Tyrosine kinase inhibition: Ligand binding and conformational change in c-Kit and c-Abl.

The conformational flexibility exhibited by protein kinases poses an enormous challenge to the design of cancer therapeutics. Additionally the high degree of structural conservation within the kinase superfamily often leads to inhibitors that exhibit little selectivity and substantial cross reactivity. This work investigates the conformational changes that accompany the binding of Gleevec, or imatinib mesylate, to the tyrosine kinases c‐Kit and c‐Abl. Our analysis is that this fit is driven, at least in part, by the need to exclude water from solvent‐exposed backbone hydrogen bonds. Both experimental and molecular modeling studies of the active state inhibitor of the tyrosine kinase c‐Abl indicate that solvent exclusion also plays a role in this system.

The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates.

The era of big data is also the era of abundant data, creating new opportunities for student-scientist research partnerships. By coordinating undergraduate efforts, the Genomics Education Partnership produces high-quality annotated data sets and analyses that could not be generated otherwise, leading to scientific publications while providing many students with research experience.