In eukaryotes, regulated RNA degradation is important for numerous processes, such as the modulation of gene expression, quality control during mRNA synthesis, and defense against RNA viruses. Since RNA degradation enzymes are ubiquitous, this process must be carefully controlled so that only the appropriate targets are recognized and degraded. Much remains to be learned about how this control is achieved, especially in multi-cellular organisms.

We have obtained evidence that Suppressor of sable protein [Su(s)] of Drosophila participates in nuclear RNA quality control. Su(s) is an RNA binding protein that associates with genes as they are being transcribed and inhibits the accumulation of specific aberrant transcripts—mutant alleles with transposon insertions that affect splicing; heat-shock inducible RNAs produced from tandemly-repeated transposons in the vicinity of a heat shock locus; and cryptic transcripts produced from a wild-type gene at an inappropriate time, when neighboring genes are being expressed. Other results indicate that Su(s) promotes degradation of these RNAs by the nuclear exosome.

Currently, we are further investigating the mechanism involved. There are at least two different RNA quality control systems in the nucleus, and one of our goals is to determine if Su(s) functions in one of the known pathways or some other process. In addition, we are working to define the RNA sequences that are bound by Su(s) and to determine if these sites are enriched in a particular region of RNAs, e.g. coding versus noncoding sequences. Our approach to these questions is multifaceted in that we use genetic, biochemical, molecular, cell biological and genomic methods.

The results of this research will provide new insights into nuclear RNA degradation mechanisms in multi-cellular organisms and help to clarify how defective RNAs are identified by the nuclear quality control machinery. The presence of multiple RNA quality control systems and the high degree of similarity in the general components of these systems indicate that this is a vitally important process for most, if not all, eukaryotic organisms.

Ted Salmon is a Cell Biologist and Biophysicist whose primary research is directed towards understanding the molecular mechanisms governing the assembly of spindle microtubules and the segregation of chromosomes during mitosis. Our working hypothesis is that mitosis will be explained by the molecular and structural properties of the centrosome which organizes and nucleates the polymerization of spindle microtubules, the assembly of microtubules which orient and participate in the generation of chromosome movements, and the microtubule motors such as the kinesin and dynein families of proteins which appear to generate polarized forces along the lattice of microtubules, at kinetochores, and within the spindle fibers. The laboratory has pioneered the development of video and digital imaging microscopy methods for analysis of molecular and structural dynamics in living cells and in vitro. We have developed fluorescently labeled tubulins to serve as tracers in studies of the dynamic pathways for microtubule assembly in vivo and in vitro using low light level fluorescence microscopy and digital image processing techniques. We have also developed high resolution video microscopy methods for visualizing the polymerization of individual microtubules and the motility of motors in living cells and reconstituted preparations. These functional assays provide the basis for determination of the basic mechanisms of microtubule polymerization and motor function, analysis of kinetochore motility, and the means of eventually achieving reconstitution of chromosome segregation in reconstituted preparations in vitro. There is also an interest in the lab in how hydrostatic pressure alters the assembly and function of the cytoskeleton and how organisms have adapted to the effects of deep sea pressures.

The Laederach Lab is interested in better understanding the relationship between RNA structure and folding dynamics. We use a combination of computational and experimental approaches to study the process of RNA folding and assembly. In particular, we develop novel computational approaches to analyze and interpret chemical mapping data. Most recently, we have begun investigating the relationship between disease-associated Single Nucleotide Polymorphisms (SNPs) occurring in Human UTRs and their effect on RNA structure. In particular, we have been investigating regulatory RNA elements called “RiboSNitches,” which like bacterial Riboswitches undergo a large conformational change and regulate translation post-transcriptionally. SNPs in the RiboSNitch cause the conformational change.

Selected publications

Google Scholar Profile

CV

My research activities are diverse and span aspects of vegetation science from plant interactions to global patterns. However, the four projects described below serve to illustrate my current primary research interests. Please note that I am retired to the rank of Research Professor and no longer accept graduate and postdoctoral students, but I am continuing my research projects, continue to collaborate with colleagues, and continue to advise undergraduate research projects.

Community dynamics. Much of my early research at UNC focused on plant community dynamics, a topic that I have continued to investigate throughout my career. With students and collaborators I have made extensive use of permanent plots to address these kinds of questions. We recently completed an additional resurvey of forest demography plots (some dating back to 1934) and are using these data to address a broad range of questions including urban impact, evolving successional dynamics reflecting local and global change, and changes in productivity resulting from factors such as successional dynamics and changes in atmospheric CO₂.

Ecoinformatics. Ecoinformatics arrived as a subdiscipline of ecology only around the start of the 21^st century. I have been active during this period in developing the necessary cyber-infrastructure and addressing science questions in the area of ecoinformatics that draws on the increasing availability of data that document attributes of places, attributes of biological taxa (species), and records of occurrence and co-occurrence of species in specific places. In the past, studies of ecological communities were largely local case studies and no one knew how generalizable they were; many simply reflected the idiosyncrasies of a particular combination of time and space. We are now in a position to analyze community patterns over very large scales and assess their generality and the impacts of local contingencies.

Vegetation Classification. Formal, widely-adopted vegetation classifications are important for many purposes ranging from inventory to mapping to management prescription to simply documenting the context within which research has been conducted. In 1994 I established a collaboration consisting of the Ecological Society of American, the Nature Conservancy, the USGS and the US Federal Geographic Data Committee (with the US Forest Service as lead agency) to develop an open and scientifically credible US National Vegetation Classification (USNVC). We proposed national standards and in 2008 the Federal Geographic Data Committee adopted the key components as the US national standard. My research group and collaborators built the USNVC data archive in the form of VegBank.org, developed a peer-review system, and have completed the first formal revision and documentation of a significant set of Associations for the National Vegetation Classification.

Vegetation of the Carolinas. I have always been fascinated by the patterns of vegetation and biodiversity across landscapes. The Carolinas are remarkably diverse and the factors responsible for the vegetation of the region are poorly understood. In 1988, I established a collaboration to systematically document the natural vegetation of the Carolinas. Subsequently we have acquired and databased over 10,000 vegetation plots covering most of the over 500 USNVC vegetation types of the Carolinas. The resulting data are summarized on our website (cvs.bio.unc.edu) for use by applied scientists and the general public. In addition, we provide digital tools for predicting the natural vegetation of sites to guide restoration efforts.

Professional Service. I have and continue to contribute to the scientific community in numerous ways. I have served the International Association for Vegetation Science as President (2007-2011) and Publications Officer (2011-2015), I co-founded the Journal of Vegetation Science and served as one of the original Coeditors-in-Chief (1990-1995), I organized of the North American Section, and am active in efforts to establish international standards for vegetation data. I have served the Ecological Society of America as Secretary (1992-1995), Editor-in-Chief of Ecology and Ecological Monographs (1995-2000), and co-organizer of the Vegetation Section and the Southeastern Chapter, in addition to participating in numerous other roles.

Links to websites maintained by Prof. Peet and his collaborators:

• Carolina Vegetation Survey
• VegBank
• Duke Forest LTREB Project

My research group investigates the community ecology of infectious disease. We study pathogens infecting wild plants, chiefly grasses. Our main current interest is interactions between fungal pathogens and the broader leaf microbiome.

Research in my laboratory is centered on the initial interactions of the plant pathogenic bacterium, Agrobacterium tumefaciens, with potential host cells. A. tumefaciens is a soil bacterium. Infections of wound sites of plants with this bacterium result in the formation of crown gall tumors. We are particularly interested in the initial attachment of the bacteria to plant host cells. This initial loose binding is required for bacterial virulence and T-DNA transfer to plant cells. Bacterial mutants which are unable to carry out this attachment are avirulent. We are currently engaged in cloning and sequencing the genes required for this attachment. Their expression is regulated by signals from the wounded plant tissue. We are characterizing the compounds which are involved in this signaling and the genes which are regulated. Our results suggest that there is an initial exchange of signals between the bacterium and the plant before the bacteria bind irreversibly to the plant and the transfer of T-DNA can begin. We are also interested in the plant receptor to which the bacteria bind. We have identified mutants of the plant Arabidopsis which appear to be unable to bind the bacteria and are in the process of identifying the plant genes and proteins involved in bacterial binding.

The double-stranded structure of DNA provides for an elegant mechanism allowing the accurate duplication and repair of DNA. However, to make use of the properties of complementary base pairing the hydrogen bonds holding the double helix together must be disrupted, and the helix unwound, to expose single-stranded DNA templates for use by DNA polymerases, primases and other DNA modifying enzymes. This unwinding reaction is accomplished by a class of enzymes called DNA helicases. These enzymes disrupt the double helical structure of DNA in an energy-requiring reaction that is dependent on the hydrolysis of nucleoside 5′-triphosphates. Examples of DNA helicase enzymes are now numerous in phage, bacteria, eukaryotic viruses, and in eukaryotic cells suggesting that these enzymes are ubiquitous. In addition, we now know that helicases are involved in all aspects of DNA metabolism. Individual cells contain multiple DNA helicases; each helicase apparently has a unique biochemical role in the cell.

For the last several years we have focused our studies on the enzymatic mechanisms and biological roles of DNA helicases. The bacterium E. coli and the budding yeast S. cerevisiae provide attractive systems in which to pursue these studies due to the ease of genetic manipulation and the ability to isolate enzymes for biochemical studies. A large body of literature now exists for the enzymes found in E. coli. Yeast, however, remains largely unexplored. We are directing our efforts toward characterizing DNA helicases from both E. coli and yeast. The long-range goal of the research program is to understand, in enzymatic and molecular terms, the mechanism of action of several helicase enzymes, and to define their individual roles in DNA metabolism.

The lab also has an interest in the process of DNA transfer by bacterial conjugation, defined as the unidirectional and horizontal transmission of genetic information between bacterial cells. Conjugation was discovered more than 50 years ago yet we still have only a rudimentary knowledge of the molecular details surrounding this important mechanism for DNA transfer. Previous studies have shown that DNA transfer begins at a site- and strand-specific nick in the conjugative plasmid. The double-stranded DNA molecule is then unwound from this nick, presumably by a DNA helicase, and a single-strand of DNA is transferred into the recipient cell. This laboratory has demonstrated, using the F plasmid as a paradigm, the participation of two F plasmid-encoded proteins, TraIp and TraYp, and one host-encoded protein, integration host factor (IHF), in the nicking reaction; subsequent unwinding has not yet been reconstituted in any system. The goal of this project is to arrive at a more detailed understanding of this key process.

Adaptations are central to the study of evolution. Thus it is surprising that we know so little about the molecular basis of adaptive evolution. The goal of my research is to identify, clone, and characterize the evolution of genes underlying natural adaptations in order to determine the types of genes involved, how many and what types of genetic changes occurred, and the evolutionary history of these changes. These data will address key questions. For example, do adaptations involve many genetic changes or only a few? How important are regulatory versu! s amino acid changes in adaptation? How often are “new” gene s involved in adaptations? Are most adaptive alleles new mutations or pre-existing alleles segregating at low to moderate frequency within a species? Clearly, a deeper understanding of how genes change during adaptation will give insight into the potential and limits of adaptive evolution.

Spatial patterns of genomic features

I am also using genomic data to address important evolutionary questions. Recently, I used D. melanogaster genome sequence data to estimate genome-wide levels of gene clustering and to contrast the amount of clustering among genes with similar motifs to the levels of clustering in general. All chromosomes, except the fourth, showed substantial levels of gene clusteri! ng. Although not more clustered than the average pair of adjacent genes, genes with the same primary motif occur adjacent to one another more often than expected by chance. These results may mean that these small local groups of genes share regulatory elements and evolutionary histories.

Detecting natural selection in DNA sequence data

Molecular evolutionists have long sought to determine which changes within the protein coding and regulatory regions of a gene were shap! ed by natural selection. If an adaptive substitution has occurred in the recent past, there should be a paucity of DNA polymorphism surrounding the site under selection. Taking advantage of this fact, Andrew Kern and I have developed a permutation approach for detecting selected sites using polarized DNA polymorphism and divergence data. This method is especially useful for detecting the effects of weak selected forces across several loci. We used this approach to analyze a large DNA polymorphism and divergence data set of D. simulans genes. Surprisingly, although replacement fixations do not on average appear to be driven by selection, preferred codons – those codons that use the most abundant tRNA – have on average been fixed by selection. We plan to apply this method to additional data sets and to look at spatial patterns of nucleotide fixation within and around genes. For instance, one could see if there is a bias in the types of polymorphism (sy! nonymous vs. non-synonymous) nearest to a type of fixation. This would give insight into the dynamics of the fixation process and its impacts on adjoining variation.

The organization of genetic information in eukaryotes is far from straightforward. The interspersion of coding and non-coding regions makes genes up to tens of times larger than they “need” to be if protein coding were the only prerequisite. The presence of untranslated regions in mature mRNAs and the positioning of cis-acting enhancers at considerable distances all contribute to expand the effective size of genes and diminish the apparent informational density of eukaryotic genomes. The relative size of these non-coding elements is quite diverse in distantly related eukaryotes and their distribution does not appear random. Comparing details of gene organization in different groups of organisms provides clues of the possible adaptive significance of some of these differences and may suggest mechanistic explanations to relate a particular type of gene organization to a corresponding functional mode.

Selected References   |   Curriculum Vitae  |   Open Positions  |   Currently Seeking Postdocs  |
Dept. Pharmacology Web Page | Potential Students Interested in Joining the Lab

We are interested in cell-to-cell communication. At present, our efforts are focused on signaling that depends on the heterotrimeric G protein complex. Much of our work is devoted to understanding novel mechanisms for activating this pathway therefore we are looking at organisms quite divergent to animal cells where much is already understood about G protein signaling. Using the diversity of life to discover the diversity of cell signaling is a powerful approach.

The JonesLab showed that most eukaryotic cells outside of the animal group have a very different mechanism for activation mechanism. Whereas, the rate-limiting step for G protein activation is nucleotide exchange on the Galpha subunit of the complex, in plant cells and protists, this step is spontaneous. Therefore, the need for a G protein coupled receptor to catalyze this GTP for GDP nucleotide exchange is not needed in plant cells and protists. We showed that the reaction that returns G protein activation (GTP-bound) to the inactive state is the rate-limiting step and is mediated by a receptor like protein that accelerates this “off” reaction. However, this is not the only mechanism to control the pool size of the activated G protein. The JonesLab takes a wide variety of experimental and theoretical approaches to solve central basic problems in cell biology with the intent that our work will translate into improved quality of life, create sustainable agriculture, and make us better stewards of the Earth. Mathematical modelers, biochemists, microscopists, physiologists, geneticists are welcomed to join the JonesLab team. Please see the available positions by clicking the link above.