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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Dielectrophoretic characterization of erythrocytes: positive ABO blood types
ABSTRACT Dielectrophoretic manipulation of erythrocytes/red blood cells is investigated as a tool to identify blood type for medical diagnostic applications. Positive blood types of the ABO typing system (A+, B+, AB+ and O+) were tested and cell responses quantified. The dielectrophoretic response of each blood type was observed in a platinum electrode microdevice, delivering a field of 0.025V(pp)/microm at 1 MHz. Responses were recorded via video microscopy for 120 s and erythrocyte positions were tabulated at 20-30 s intervals. Both vertical and horizontal motions of erythrocytes were quantified via image object recognition, object tracking in MATLAB, binning into appropriate electric field contoured regions (wedges) and statistical analysis. Cells of O+ type showed relatively attenuated response to the dielectrophoretic field and were distinguished with greater than 95% confidence from all the other three blood types. AB+ cell responses differed from A+ and B+ blood types likely because AB+ erythrocytes express both the A and B glycoforms on their membrane. This research suggests that dielectrophoresis of untreated erythrocytes beyond simple dilution depends on blood type and could be used in portable blood typing devices.
Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis
ABSTRACT Cell dedifferentiation is a cell fate switching process in which a differentiated cell reverts to a status with competence for cell division and organ regeneration like an embryonic stem cell. Although the phenomenon of cell dedifferentiation has been known for over two and a half centuries in plants, little is known of the underlying mechanisms. Here, we have established the proteome map of Arabidopsis cotyledons and investigated the dynamic change of the cotyledon proteome in the time course of cell dedifferentiation. Among the 353 distinct genes, corresponding to 500 2-DE gel protein spots identified with high confidence, 12% have over twofold differential regulations within the first 48 h of induction of cell dedifferentiation. The distributions of these genes among different Gene Ontology categories and gene differential regulations within each of the categories have been examined. In addition, we have investigated the cotyledon phosphoproteome using Pro-Q Diamond Phosphoprotein in Gel Stain followed by mass spectrometry analyses. Among the 53 identified putative phosphoproteins, nine are differentially regulated during cell dedifferentiation. These studies have provided significant new insight into protein and phosphoprotein differential expression during cell dedifferentiation in plants.
Effects of F-strain Mycoplasma gallisepticum inoculation at twelve weeks of age on performance and egg characteristics of commercial egg-laying hens
Burnham MR, Branton SL, Peebles ED, Lott BD, Gerard PD (2002) Effects of F-strain Mycoplasma gallisepticum inoculation at twelve weeks of age on performance and egg characteristics of commercial egg-laying hens. Poultry Science 81(10): 1478-1485.
ABSTRACT The effects of F-strain Mycoplasma gallisepticum (FMG) inoculation during the pullet period on the subsequent performance and egg characteristics of commercial Single Combed White Leghorn hens were evaluated. In two trials, BW, feed consumption, egg production (EP), egg weight, egg size class, relative eggshell water vapor conductance, and relative percentages of eggshell, yolk and albumen weights were determined through approximately 60 wk of age. In each trial, pullets at 12 wk of age were randomly assigned to negative pressure biological isolation units. Birds in one-half of the total units were inoculated with FMG, and the other half were sham-inoculated with sterile media. In both trials, onset of lay was delayed approximately 1 wk in layers inoculated with FMG. Control birds that had not been previously inoculated with FMG laid their first egg at 18 wk of age, while birds that had been previously inoculated with FMG laid their first egg at 19 wk of age. In Trial 1, FMG-inoculated hens laid significantly fewer total eggs, which became apparent at each week after Week 42. In Trial 2, a numerical decrease in total EP occurred, and the percentage of undersized eggs laid by FMG-inoculated birds was significantly lower at 19 wk of age but was higher at 20 and 21 wk when compared to controls. Mortality was not significantly different between the treatments in either trial. These data demonstrate that when birds are housed in isolation facilities and inoculated with FMG at 12 wk of age, onset of lay is delayed. These data also suggest that FMG may lead to delays in undersize EP and decreases in total EP. However, because significant FMG effects on these parameters were observed in only one trial, additional studies may be necessary to verify these effects.
Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility
Feugang JM, Kaya A, Page GP, Chen L, Mehta T, Hirani K, Nazareth L, Topper E, Gibbs R, Memili E (2009) Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility. BMC Genomics 10: 176.
ABSTRACT BACKGROUND: Fertility is one of the most critical factors controlling biological and financial performance of animal production systems and genetic improvement of lines. The objective of this study was to identify molecular defects in the sperm that are responsible for uncompensable fertility in Holstein bulls. We performed a comprehensive genome wide analysis of single nucleotide polymorphisms (SNP) for bull fertility followed by a second-stage replication in additional bulls for a restricted set of markers. RESULTS: In the Phase I association study, we genotyped the genomic sperm DNA of 10 low-fertility and 10 high-fertility bulls using Bovine SNP Gene Chips containing approximately 10,000 random SNP markers. In these animals, 8,207 markers were found to be polymorphic, 97 of which were significantly associated with fertility (p<0.01). In the Phase II study, we tested the four most significant SNP from the Phase I study in 101 low-fertility and 100 high-fertility bulls, with two SNPs (rs29024867 and rs41257187) significantly replicated. Rs29024867 corresponds to a nucleotide change of C --> G 2,190 bp 3' of the collagen type I alpha 2 gene on chromosome 4, while the rs41257187 (C --> T) is in the coding region of integrin beta 5 gene on chromosome 1. The SNP rs41257187 induces a synonymous (Proline --> Proline), suggesting disequilibrium with the true causative locus (i), but we found that the incubation of bull spermatozoa with integrin beta 5 antibodies significantly decreased the ability to fertilize oocytes. Our findings suggest that the bovine sperm integrin beta 5 protein plays a role during fertilization and could serve as a positional or functional marker of bull fertility. CONCLUSION: We have identified molecular markers associated with bull fertility and established that at least one of the genes harboring such variation has a role in fertility. The findings are important in understanding mechanisms of uncompensatory infertility in bulls, and in other male mammals. The findings set the stage for more hypothesis-driven research aimed at discovering the role of variation in the genome that affect fertility and that can be used to identify molecular mechanisms of development.
Characterization of the last subunit of the arabidopsis COP9 signalosome: Implications for the overall structure and origin of the complex
Serino G, Su H, Peng Z, Tsuge T, Wei N, Deng XW (2003) Characterization of the last subunit of the arabidopsis COP9 signalosome: Implications for the overall structure and origin of the complex. Plant Cell 15(3): 719-731.
ABSTRACT The COP9 signalosome (CSN) is an evolutionarily conserved protein complex that resembles the lid subcomplex of proteasomes. Through its ability to regulate specific proteasome-mediated protein degradation events, CSN controls multiple aspects of development. Here, we report the cloning and characterization of AtCSN2, the last uncharacterized CSN subunit from Arabidopsis. We show that the AtCSN2 gene corresponds to the previously identified FUS12 locus and that AtCSN2 copurifies with CSN, confirming that AtCSN2 is an integral component of CSN. AtCSN2 is not only able to interact with the SCF(TIR1) subunit AtCUL1, which is partially responsible for the regulatory interaction between CSN and SCF(TIR1), but also interacts with AtCUL3, suggesting that CSN is able to regulate the activity of other cullin-based E3 ligases through conserved interactions. Phylogenetic analysis indicated that the duplication and subsequent divergence events that led to the genes that encode CSN and lid subunits occurred before the divergence of unicellular and multicellular eukaryotic organisms and that the CSN subunits were more conserved than the lid subunits during evolution. Comparative analyses of the subunit interaction of CSN revealed a set of conserved subunit contacts and resulted in a model of CSN subunit topology, some aspects of which were substantiated by in vivo cross-link tests.
Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
Nadeau NJ, Ruiz M, Salazar P, Counterman B, Medina JA, Ortiz-Zuazaga H, Morrison A, McMillan WO, Jiggins CD, Papa R (2014) Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato. Genome Research 24(8): 1316-1333.
ABSTRACT Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on color pattern. The comimetic species, H. erato and H. melpomene, have parallel hybrid zones in which both species undergo a change from one color pattern form to another. We use restriction-associated DNA sequencing to obtain several thousand genome-wide sequence markers and use these to analyze patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data-alignment to a reference genome and de novo assembly-and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ∼15% divergent) related to the reference sequence. Our results confirm that the color pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to color pattern differences. We also use association mapping to identify previously unmapped color pattern loci, in particular the Ro locus. Finally, we identify a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti.
A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice
La H, Ding B, Mishra GP, Zhou B, Yang H, Bellizzi Mdel R, Chen S, Meyers BC, Peng Z, Zhu JK,Wang GL (2011) A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proceedings of the National Academy of Sciences of the United States of America 108(37): 15498-15503.
ABSTRACT DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counteract transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.
Predictable convergence in hemoglobin function has unpredictable molecular underpinnings
Natarajan C, Hoffmann FG, Weber RE, Fago A, Witt CC, Storz JF (2016) Predictable convergence in hemoglobin function has unpredictable molecular underpinnings. Science 354(6310): 336-339.
ABSTRACT High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences. Bioinformatics, computational biology, and systems biology deal with biological problems using computational methods. Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level. Clearly, clustering can be used in many areas of biological data analysis. However, this paper presents a review of the current clustering algorithms designed especially for analyzing gene expression data. It is also intended to introduce one of the main problems in bioinformatics - clustering gene expression data - to the operations research community. -¬ 2012 Elsevier Ltd. All rights reserved.
ABSTRACT Somatic cell nuclear transfer (SCNT), the technique commonly known as cloning, permits transformation of a somatic cell into an undifferentiated zygote with the potential to develop into a newborn animal (i.e., a clone). In somatic cells, chromatin is programmed to repress most genes and express some, depending on the tissue. It is evident that the enucleated oocyte provides the environment in which embryonic genes in a somatic cell can be expressed. This process is controlled by a series of epigenetic modifications, generally referred to as "nuclear reprogramming," which are thought to involve the removal of reversible epigenetic changes acquired during cell differentiation. A similar process is thought to occur by overexpression of key transcription factors to generate induced pluripotent stem cells (iPSCs), bypassing the need for SCNT. Despite its obvious scientific and medical importance, and the great number of studies addressing the subject, the molecular basis of reprogramming in both reprogramming strategies is largely unknown. The present review focuses on the cellular and molecular events that occur during nuclear reprogramming in the context of SCNT and the various approaches currently being used to improve nuclear reprogramming. A better understanding of the reprogramming mechanism will have a direct impact on the efficiency of current SCNT procedures, as well as iPSC derivation.
Differential loss and retention of cytoglobin, myoglobin, and globin-E during the radiation of vertebrates
Hoffmann FG, Opazo JC, Storz JF (2011) Differential loss and retention of cytoglobin, myoglobin, and globin-E during the radiation of vertebrates. Genome Biology & Evolution 3(1): 588-600.
ABSTRACT If rates of postduplication gene retention are positively correlated with levels of functional constraint, then gene duplicates that have been retained in a restricted number of taxonomic lineages would be expected to exhibit relatively low levels of sequence conservation. Paradoxical patterns are presented by gene duplicates that have been retained in a small number of taxa but which are nonetheless subject to strong purifying selection relative to paralogous members of the same multigene family. This pattern suggests that such genes may have been co-opted for novel, lineage-specific functions. One possible example involves the enigmatic globin-E gene (GbE), which appears to be exclusively restricted to birds. Available data indicate that this gene is expressed exclusively in the avian eye, but its physiological function remains a mystery. In contrast to the highly restricted phyletic distribution of GbE, the overwhelming majority of jawed vertebrates (gnathostomes) possess copies of the related cytoglobin (Cygb) and myoglobin (Mb) genes. The purpose of the present study was 1) to assess the phyletic distribution of the Cygb, Mb, and GbE genes among vertebrates, 2) to elucidate the duplicative origins and evolutionary histories of these three genes, and 3) to evaluate the relative levels of functional constraint of these genes based on comparative sequence analysis. To accomplish these objectives, we conducted a combined phylogenetic and comparative genomic analysis involving taxa that represent each of the major lineages of gnathostome vertebrates. Results of synteny comparisons and phylogenetic topology tests revealed that GbE is clearly not the product of a recent, bird-specific duplication event. Instead, GbE originated via duplication of a proto-Mb gene in the stem lineage of gnathostomes. Unlike the Mb gene, which has been retained in all major gnathostome lineages other than amphibians, the GbE gene has been retained only in the lineage leading to modern birds and has been independently lost in at least four major lineages: teleost fish, amphibians, mammals, and nonavian reptiles. Despite the restricted phyletic distribution of this gene, our results indicate that GbE is one of the most highly conserved globins in the avian genome.
PTMs in Conversation: Activity and Function of Deubiquitinating Enzymes Regulated via Post-Translational Modifications
Kessler BM, Edelmann MJ (2011) PTMs in Conversation: Activity and Function of Deubiquitinating Enzymes Regulated via Post-Translational Modifications. Cell Biochemistry and Biophysics 60(1-2): 21-38.
ABSTRACT Deubiquitinating enzymes (DUBs) constitute a diverse protein family and their impact on numerous biological and pathological processes has now been widely appreciated. Many DUB functions have to be tightly controlled within the cell, and this can be achieved in several ways, such as substrate-induced conformational changes, binding to adaptor proteins, proteolytic cleavage, and post-translational modifications (PTMs). This review is focused on the role of PTMs including monoubiquitination, sumoylation, acetylation, and phosphorylation as characterized and putative regulative factors of DUB function. Although this aspect of DUB functionality has not been yet thoroughly studied, PTMs represent a versatile and reversible method of controlling the role of DUBs in biological processes. In several cases PTMs might constitute a feedback mechanism insuring proper functioning of the ubiquitin proteasome system and other DUB-related pathways.
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