Over the years, IGBB scientists have gained a reputation for publishing papers that are widely cited. Below are papers that are (a) authored/co-authored by an IGBB employee, faculty fellow, or affiliate and (b) fall within the top ten percent of scientific publications with regard to citation impact. Citation benchmarking values are from Scopus. Papers in the 99th percentile are in the top 1% globally. Citation benchmarking takes into account
the date of publication, the document type, and discipline-specific factors. For a particular IGBB fellow/affiliate/staff member, only those papers published while at MS State are included. The list below is updated periodically.
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Characterization of virulent and avirulent Listeria monocytogenes strains by PCR amplification of putative transcriptional regulator and internalin genes
Liu D, Ainsworth AJ, Austin FW, Lawrence ML (2003) Characterization of virulent and avirulent Listeria monocytogenes strains by PCR amplification of putative transcriptional regulator and internalin genes. Journal of Medical Microbiology 52(Pt 12): 1065-1070.
ABSTRACT Listeria monocytogenes is an opportunistic bacterial pathogen that is an important cause of human food-borne illness worldwide. However, L. monocytogenes strains demonstrate considerable variation in pathogenic potential. In this report, virulent and avirulent L. monocytogenes isolates were compared by using a comparative screening strategy. Two clones were identified that contained DNA that was only present in virulent L. monocytogenes strains. PCR primers were designed for three genes from these clones and for five other selected L. monocytogenes genes. All eight primer sets predominantly detected virulent L. monocytogenes isolates, as determined by a mouse virulence assay; one of the putative internalin genes, lmo2821, was detected in all strains that were considered to be virulent. Primers from these eight genes were then tested by PCR against a larger panel of bacterial strains; each of the genes was detected predominantly in clinical or food L. monocytogenes isolates, rather than environmental isolates. The findings from this study suggest that virulent L. monocytogenes strains may possess genes that are not present in avirulent isolates, which could serve as markers for PCR assessment of L. monocytogenes virulence.
Precocious flowering in trees: the FLOWERING LOCUS T gene as a research and breeding tool in Populus
Zhang H, Harry DE, Ma C, Yuceer C, Hsu CY, Vikram V, Shevchenko O, Etherington E,Strauss SH (2010) Precocious flowering in trees: the FLOWERING LOCUS T gene as a research and breeding tool in Populus. Journal of Experimental Botany 61(10): 2549-2560.
ABSTRACT Expression of FLOWERING LOCUS T (FT) and its homologues has been shown to accelerate the onset of flowering in a number of plant species, including poplar (Populus spp.). The application of FT should be of particular use in forest trees, as it could greatly accelerate and enable new kinds of breeding and research. Recent evidence showing the extent to which FT is effective in promoting flowering in trees is discussed, and its effectiveness in poplar is reported. Results using one FT gene from Arabidopsis and two from poplar, all driven by a heat-inducible promoter, transformed into two poplar genotypes are also described. Substantial variation in flowering response was observed depending on the FT gene and genetic background. Heat-induced plants shorter than 30 cm failed to flower as well as taller plants. Plants exposed to daily heat treatments lasting 3 weeks tended to produce fewer abnormal flowers than those in heat treatments of shorter durations; increasing the inductive temperature from 37 degrees C to 40 degrees C produced similar benefits. Using optimal induction conditions, approximately 90% of transgenic plants could be induced to flower. When induced FT rootstocks were grafted with scions that lacked FT, flowering was only observed in rootstocks. The results suggest that a considerable amount of species- or genotype-specific adaptation will be required to develop FT into a reliable means for shortening the generation cycle for breeding in poplar.
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
ABSTRACT We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.
AgBase: a unified resource for functional analysis in agriculture
IGBB Authors: Fiona M. McCarthy, Susan M. Bridges, Nan Wang, G. Bryce Magee, Bindu Nanduri, Mark L. Lawrence, Shane C. Burgess
McCarthy FM, Bridges SM, Wang N, Magee GB, Williams WP, Luthe DS, Burgess SC (2007) AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Research 35(Database issue): D599-D603.
ABSTRACT Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation. To facilitate systems biology in these species we have established the curated, web-accessible, public resource 'AgBase' (www.agbase.msstate.edu). We have improved the structural annotation of agriculturally important genomes by experimentally confirming the in vivo expression of electronically predicted proteins and by proteogenomic mapping. Proteogenomic data are available from the AgBase proteogenomics link. We contribute Gene Ontology (GO) annotations and we provide a two tier system of GO annotations for users. The 'GO Consortium' gene association file contains the most rigorous GO annotations based solely on experimental data. The 'Community' gene association file contains GO annotations based on expert community knowledge (annotations based directly from author statements and submitted annotations from the community) and annotations for predicted proteins. We have developed two tools for proteomics analysis and these are freely available on request. A suite of tools for analyzing functional genomics datasets using the GO is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an online mechanism for agricultural researchers to submit requests for GO annotations.
Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads
Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AG,Roger AJ (2013) Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proceedings of the Royal Society B: Biological Sciences 280(1769): 20131755.
ABSTRACT Most eukaryotic lineages belong to one of a few major groups. However, several protistan lineages have not yet been robustly placed in any of these groups. Both the breviates and apusomonads are two such lineages that appear to be related to the Amoebozoa and Opisthokonta (i.e. the 'unikonts' or Amorphea); however, their precise phylogenetic positions remain unclear. Here, we describe a novel microaerophilic breviate, Pygsuia biforma gen. nov. sp. nov., isolated from a hypoxic estuarine sediment. Ultrastructurally, this species resembles the breviate genera Breviata and Subulatomonas but has two cell morphologies, adherent and swimming. Phylogenetic analyses of the small sub-unit rRNA gene show that Pygsuia is the sister to the other breviates. We constructed a 159-protein supermatrix, including orthologues identified in RNA-seq data from Pygsuia. Phylogenomic analyses of this dataset show that breviates, apusomonads and Opisthokonta form a strongly supported major eukaryotic grouping we name the Obazoa. Although some phylogenetic methods disagree, the balance of evidence suggests that the breviate lineage forms the deepest branch within Obazoa. We also found transcripts encoding a nearly complete integrin adhesome from Pygsuia, indicating that this protein complex involved in metazoan multicellularity may have evolved earlier in eukaryote evolution than previously thought.
Differential detergent fractionation for non-electrophoretic eukaryote cell proteomics
ABSTRACT Differential detergent fractionation (DDF), which relies on detergents to sequentially extract proteins from eukaryotic cells, has been used to increase proteome coverage of 2D-PAGE. Here, we used DDF extraction in conjunction with the nonelectrophoretic proteomics method of liquid chromatography and electrospray ionization tandem mass spectrometry. We demonstrate that DDF can be used with 2D-LC ESI MS2 for comprehensive cellular proteomics, including a large proportion of membrane proteins. Compared to some published methods designed to isolate membrane proteins specifically, DDF extraction yields comprehensive proteomes which include twice as many membrane proteins. Two-thirds of these membrane proteins have more than one trans-membrane domain. Since DDF separates proteins based upon their physicochemistry and subcellular localization, this method also provides data useful for functional genome annotation. As more genome sequences are completed, methods which can aid in functional annotation will become increasingly important.
Pharmacological targets in the ubiquitin system offer new ways of treating cancer, neurodegenerative disorders and infectious diseases
Edelmann MJ, Nicholson B, Kessler BM (2011) Pharmacological targets in the ubiquitin system offer new ways of treating cancer, neurodegenerative disorders and infectious diseases. Expert Reviews in Molecular Medicine 13: e35.
ABSTRACT Recent advances in the development and discovery of pharmacological interventions within the ubiquitin-proteasome system (UPS) have uncovered an enormous potential for possible novel treatments of neurodegenerative disease, cancer, immunological disorder and microbial infection. Interference with proteasome activity, although initially considered unlikely to be exploitable clinically, has already proved to be very effective against haematological malignancies, and more specific derivatives that target subsets of proteasomes are emerging. Recent small-molecule screens have revealed inhibitors against ubiquitin-conjugating and -deconjugating enzymes, many of which have been evaluated for their potential use as therapeutics, either as single agents or in synergy with other drugs. Here, we discuss recent advances in the characterisation of novel UPS modulators (in particular, inhibitors of ubiquitin-conjugating and -deconjugating enzymes) and how they pave the way towards new therapeutic approaches for the treatment of proteotoxic disease, cancer and microbial infection.
Removal of listeria monocytogenes biofilms with bacteriophage P100
ABSTRACT Listeria monocytogenes is an important foodborne pathogen with a persistent ability to form biofilm matrices in the food processing environments. In this study, we have determined the ability of bacteriophage P100 to reduce L. monocytogenes cell populations under biofilm conditions by using 21 L. monocytogenes strains representing 13 different serotypes. There were considerable differences in the ability of various strains of L. monocytogenes to form biofilms, with strains of serotype l/2a showing maximum biofilm formation. Irrespective of the serotype, growth conditions, or biofilm levels, the phage P100 treatment significantly reduced L. monocytogenes cell populations under biofilm conditions. On the stainless steel coupon surface, there was a 3.5- to 5.4-log/cm2 reduction in L. monocytogenes cells by phage treatment. These findings illustrate that phage P100 is active against a wide range of L. monocytogenes strains in biofilm conditions.
Evidence for a physical association of the COP9 signalosome, the proteasome, and specific SCF E3 ligases in vivo
Peng Z, Shen Y, Feng S, Wang X, Chitteti BR, Vierstra RD, Deng XW (2003) Evidence for a physical association of the COP9 signalosome, the proteasome, and specific SCF E3 ligases in vivo. Current Biology 13(13): R504-R505.
ABSTRACT Cell penetrating peptides (CPPs) are those peptides that can transverse cell membranes to enter cells. Once inside the cell, different CPPs can localize to different cellular components and perform different roles. Some generate pore-forming complexes resulting in the destruction of cells while others localize to various organelles. Use of machine learning methods to predict potential new CPPs will enable more rapid screening for applications such as drug delivery. We have investigated the influence of the composition of training datasets on the ability to classify peptides as cell penetrating using support vector machines (SVMs). We identified 111 known CPPs and 34 known non-penetrating peptides from the literature and commercial vendors and used several approaches to build training data sets for the classifiers. Features were calculated from the datasets using a set of basic biochemical properties combined with features from the literature determined to be relevant in the prediction of CPPs. Our results using different training datasets confirm the importance of a balanced training set with approximately equal number of positive and negative examples. The SVM based classifiers have greater classification accuracy than previously reported methods for the prediction of CPPs, and because they use primary biochemical properties of the peptides as features, these classifiers provide insight into the properties needed for cell-penetration. To confirm our SVM classifications, a subset of peptides classified as either penetrating or non-penetrating was selected for synthesis and experimental validation. Of the synthesized peptides predicted to be CPPs, 100% of these peptides were shown to be penetrating.
ABSTRACT Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world's conifer forests.
Wing patterning gene redefines the mimetic history of Heliconius butterflies
Hines HM, Counterman BA, Papa R, Albuquerque de Moura P, Cardoso MZ, Linares M, Mallet J, Reed RD, Jiggins CD, Kronforst MR,McMillan WO (2011) Wing patterning gene redefines the mimetic history of Heliconius butterflies. Proceedings of the National Academy of Sciences of the United States of America 108(49): 19666-19671.
ABSTRACT The mimetic butterflies Heliconius erato and Heliconius melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing-pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries, and therefore might not represent the history of the adaptive traits as accurately as markers linked to color pattern genes. To assess the evolutionary histories across different loci, we compared relationships among races within H. erato and within H. melpomene using a series of unlinked genes, genes linked to color pattern loci, and optix, a gene recently shown to control red color-pattern variation. We found that although unlinked genes partition populations by geographic region, optix had a different history, structuring lineages by red color patterns and supporting a single origin of red-rayed patterns within each species. Genes closely linked (80-250 kb) to optix exhibited only weak associations with color pattern. This study empirically demonstrates the necessity of examining phenotype-determining genomic regions to understand the history of adaptive change in rapidly radiating lineages. With these refined relationships, we resolve a long-standing debate about the origins of the races within each species, supporting the hypothesis that the red-rayed Amazonian pattern evolved recently and expanded, causing disjunctions of more ancestral patterns.
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