Microarray analysis of the in vivo sequence preferences of a minor groove binding drug

<p>Abstract</p> <p>Background</p> <p>Minor groove binding drugs (MGBDs) interact with DNA in a sequence-specific manner and can cause changes in gene expression at the level of transcription. They serve as valuable models for protein interactions with DNA and form an important class of antitumor, antiviral, antitrypanosomal and antibacterial drugs. There is a need to extend knowledge of the sequence requirements for MGBDs from <it>in vitro </it>DNA binding studies to living cells.</p> <p>Results</p> <p>Here we describe the use of microarray analysis to discover yeast genes that are affected by treatment with the MGBD berenil, thereby allowing the investigation of its sequence requirements for binding <it>in vivo</it>. A novel approach to sequence analysis allowed us to address hypotheses about genes that were directly or indirectly affected by drug binding. The results show that the sequence features of A/T richness and heteropolymeric character discovered by <it>in vitro </it>berenil binding studies are found upstream of genes hypothesized to be directly affected by berenil but not upstream of those hypothesized to be indirectly affected or those shown to be unaffected.</p> <p>Conclusion</p> <p>The data support the conclusion that effects of berenil on gene expression in yeast cells can be explained by sequence patterns discovered by <it>in vitro </it>binding experiments. The results shed light on the sequence and structural rules by which berenil binds to DNA and affects the transcriptional regulation of genes and contribute generally to the development of MGBDs as tools for basic and applied research.</p

Invasive Plants in U. S. National Wildlife Refuges: A Coordinated Research Project Using Undergraduate Ecology Students

Answering large-scale questions in ecology can involve time-consuming data compilation. We show how networks of undergraduate classes can make these projects more manageable and provide an authentic research experience for students. With this approach, we examined the factors associated with plant species richness in US national wildlife refuges. We found that the richness of harmful invasive plants and the richness of native plants were positively correlated in mainland refuges but negatively correlated in island refuges. Nonnative richness and invasive richness were also positively correlated with colonization pressure as indicated by nonnative richness around each refuge. Associations between refuge characteristics and invasive plants varied substantially among regions, with refuge area and habitat diversity important predictors of invasion in some regions but not in others. Our results serve to identify the refuges that are most susceptible to plant invasion and demonstrate the potential value of a new model for education and research integration

Improving treatment plan evaluation with automation

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135377/1/acm20016.pd

Progress toward understanding the ecological impacts of non-native species

A predictive understanding of the ecological impacts of nonnative species has been slow to develop, owing largely to an apparent dearth of clearly defined hypotheses and the lack of a broad theoretical framework. The context dependency of impact has fueled the perception that meaningful generalizations are nonexistent. Here, we identified and reviewed 19 testable hypotheses that explain temporal and spatial variation in impact. Despite poor validation of most hypotheses to date, evidence suggests that each can explain at least some impacts in some situations. Several hypotheses are broad in scope (applying to plants and animals in virtually all contexts) and some of them, intriguingly, link processes of colonization and impact. Collectively, these hypotheses highlight the importance of the functional ecology of the nonnative species and the structure, diversity, and evolutionary experience of the recipient community as general determinants of impact; thus, they could provide the foundation for a theoretical framework for understanding and predicting impact. Further substantive progress toward this goal requires explicit consideration of within-taxon and across-taxa variation in the per capita effect of invaders, and analyses of complex interactions between invaders and their biotic and abiotic environments

Invasion Ecology, 2nd ed.

This new edition of Invasion Ecology provides a comprehensive and updated introduction to all aspects of biological invasion by non-native species. Highlighting important research findings associated with each stage of invasion, the book provides an overview of the invasion process from transportation patterns and causes of establishment success to ecological impacts, invader management, and post-invasion evolution. The authors have produced new chapters on predicting and preventing invasion, managing and eradicating invasive species, and invasion dynamics in a changing climate. Modern global trade and travel have led to unprecedented movement of non-native species by humans with unforeseen, interesting, and occasionally devastating consequences. Increasing recognition of the problems associated with invasion has led to a rapid growth in research into the dynamics of non-native species and their adverse effects on native biota and human economies. This book provides a synthesis of this fast growing field of research and is an essential text for undergraduate and graduate students in ecology and conservation management