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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Reduction of Listeria monocytogenes on the surface of fresh channel catfish fillets by bacteriophage Listex P100
Soni KA, Nannapaneni R, Hagens S (2010) Reduction of Listeria monocytogenes on the surface of fresh channel catfish fillets by bacteriophage Listex P100. Foodborne Pathogens & Disease 7(4): 427-434.
ABSTRACT Bacteriophage Listex P100 (phage P100) was approved by the U.S. Food and Drug Administration and U.S. Department of Agriculture's Food Safety and Inspection Service for Listeria monocytogenes control on both raw and ready-to-eat food products. In this article, we present the proof of concept on the influence of phage dose, phage contact time, and storage temperature on the listericidal activity of phage P100 in reducing the L. monocytogenes loads on the surface of fresh channel catfish fillet. The fresh catfish fillet samples were surface inoculated with approximately 4.3 log(10) colony forming units (CFU)/g of a two serotype mix (1/2a and 4b) of L. monocytogenes cells and then surface treated with phage P100. L. monocytogenes reduction was influenced by phage contact time and phage dose regardless of higher or lower temperature regimes tested on catfish fillet. The reduction in L. monocytogenes loads (p < 0.05) with the phage P100 dose of 2 x 10(7) plaque forming units (PFU)/g (7.3 log(10) PFU/g) was 1.4-2.0 log(10) CFU/g at 4 degrees C, 1.7-2.1 log(10) CFU/g at 10 degrees C, and 1.6-2.3 log(10) CFU/g at room temperature (22 degrees C) on raw catfish fillet. The phage contact time of 30 min was adequate to yield greater than 1 log(10) CFU/g reduction in L. monocytogenes, whereas 15 min contact time with phage yielded less than 1 log(10) CFU/g reduction in L. monocytogenes loads on catfish fillet. Phage P100 titer was stable on catfish fillet samples, and overall reductions in L. monocytogenes counts were still maintained over a 10-day shelf life at 4 degrees C or 10 degrees C by phage P100 treatment. These findings illustrate the effectiveness of an alternative generally recognized as safe antimicrobial such as bacteriophage Listex P100 in quantitatively reducing L. monocytogenes from fresh catfish fillet surfaces.
Listeria monocytogenes subgroups IIIA, IIIB, and IIIC delineate genetically distinct populations with varied pathogenic potential
ABSTRACT Listeria monocytogenes lineage III strains belonging to subgroups IIIA (n=8), IIIB (n=5), and IIIC (n=6) were examined along with other known serotype strains (n=11) by PCR and Southern hybridization using several recently described species-, virulence-, and serotype-specific primers and probes. The virulence of seven representative lineage III strains was then evaluated in mice via the intraperitoneal route. The results suggest that subgroup IIIA consists of typical rhamnose-positive avirulent serotype 4a and virulent serotype 4c strains, subgroup IIIC consists of atypical rhamnose-negative virulent serotype 4c strains, and subgroup IIIB consists of atypical rhamnose-negative virulent non-serotype 4a and non-serotype 4c strains, some of which may be related to serotype 7. It is possible that subgroup IIIB (including serotype 7) may represent a novel subspecies within L. monocytogenes.
Effect of developmental exposure to chlorpyrifos on the expression of neurotrophin growth factors and cell-specific markers in neonatal rat brain
Betancourt AM, Burgess SC, Carr RL (2006) Effect of developmental exposure to chlorpyrifos on the expression of neurotrophin growth factors and cell-specific markers in neonatal rat brain. Toxicological Sciences 92(2): 500-506.
ABSTRACT Chlorpyrifos (CPS), a known neurotoxicant, is a widely used agricultural organophosphorus insecticide. The effects of postnatal exposure to CPS on the expression of mRNA for two factors critical to brain development, nerve growth factor (NGF) and reelin, were investigated in the forebrain of rats. In addition, the expression of mRNA for the muscarinic acetylcholine receptor (mAChR) M(1) subtype and cell-specific markers for developing neurons (beta-III tubulin), astrocytes (glial fibrillary acidic protein, GFAP), and oligodendrocytes (myelin-associated glycoprotein, MAG) was also investigated. Oral administration of CPS (1.5 or 3.0 mg/kg) or the corn oil vehicle was performed daily from postnatal days (PNDs) 1 through 6. No signs of overt toxicity or of cholinergic hyperstimulation were observed after CPS administration. Body weight was significantly different from controls on PND7 in both males and females exposed to 3.0 mg/kg CPS. Quantitative PCR was performed on the forebrain. The expression of NGF, reelin, and M(1) mAChR mRNA was significantly reduced with both dosages of CPS in both sexes. beta-III Tubulin mRNA expression remained unchanged after exposure, whereas MAG mRNA expression was significantly decreased with both dosages of CPS in both sexes, suggesting effects on the developing oligodendrocytes. In contrast, GFAP mRNA levels were significantly increased with both dosages of CPS in both sexes, suggesting increased astrocyte reactivity. Our findings indicate that dosages of CPS which cause significant cholinesterase inhibition but do not exert overt toxicity can adversely affect the expression levels of critical genes involved in brain development during the early postnatal period in the rat.
Comparative assessment of acid, alkali and salt tolerance in Listeria monocytogenes virulent and avirulent strains
Liu D, Lawrence ML, Ainsworth AJ, Austin FW (2005) Comparative assessment of acid, alkali and salt tolerance in Listeria monocytogenes virulent and avirulent strains. FEMS Microbiology Letters 243(2): 373-378.
ABSTRACT Listeria monocytogenes is an opportunistic bacterial pathogen of man and animals that has the capacity to survive under extreme environmental conditions. While our knowledge on L. monocytogenes and its ability to sustain within wide pH and temperature ranges and salt concentrations has been largely built on the virulent strains of this species, relatively little is known about avirulent strains in this regard. In this study, we extend our analysis on avirulent L. monocytogenes strains. By subjecting three virulent (EGD, 874 and ATCC 19196) and three avirulent (ATCC 19114, HCC23 and HCC25) strains to various pH and salt concentrations, it was found that L. monocytogenes recovered well after treatment with 100 mM Tris at pH 12.0, and to a lesser extent at pH 3.0. Interestingly, avirulent L. monocytogenes strains showed a somewhat higher tolerance to alkali than virulent strains. This unique feature of avirulent L. monocytogenes strains may potentially be exploited for the development of a rapid technique for differentiation between avirulent and virulent strains. Furthermore, all L. monocytogenes strains tested were resistant to saturated NaCl (about 7 M, or 40% w/v) for a long period of time (20 h and possibly longer). Together, these results highlight that acid, alkali, and/or salt treatments commonly used in food product processing may not be sufficient to eliminate L. monocytogenes, and therefore stringent quality control measures at the beginning and end of the food manufacturing process is essential to ensure that such food products are free of listerial contamination.
Preliminary evaluation of laser-induced breakdown spectroscopy for tissue classification
ABSTRACT Laser-induced breakdown spectroscopy (LIBS) is an on-line, real-time technology that can produce immediate information about the elemental contents of tissue samples. We have previously shown that LIBS may be used to distinguish cancerous from non-cancerous tissue. In this work, we study LIBS spectra produced from chicken brain, lung, spleen, liver, kidney and skeletal muscle. Different data processing techniques were used to study if the information contained in these LIBS spectra is able to differentiate between different types of tissue samples and then identify unknown tissues. We have demonstrated a clear distinguishing between each of the known tissue types with only 21 selected analyte lines from each observed LIBS spectrum. We found that in order to produce an analytical model to work well with new sample we need to have representative training data to cover a wide range of spectral variation due to experimental or environmental changes.
Developmental potential of bovine oocytes cultured in different maturation and culture conditions
Sagirkaya H, Misirlioglu M, Kaya A, First NL, Parrish JJ, Memili E (2007) Developmental potential of bovine oocytes cultured in different maturation and culture conditions. Animal Reproduction Science 101(3-4): 225-240.
ABSTRACT Diverse groups of chemicals in culture media are needed for successful bovine oocyte maturation and embryo development during which dramatic cytoplasmic and nuclear reprogramming events take place. In vitro embryo production (IVP) procedures frequently include supplements such as serum and/or co-culture with various types of somatic cells. However, the presence of undefined serum in culture media introduces a variation from batch to batch, increases viral or prion contamination risk, and leads to problems during fetal development. The aim of the present study was to investigate the possibility of using chemically defined-synthetic serum substitute (SSS) in place of fetal calf serum (FCS) during maturation and long-term culture to stimulate in vitro maturation (IVM), fertilization (IVF) and subsequent embryo development. In Experiment I, the effect of the protein source on in vitro maturation was tested by maturing oocytes in culture media supplemented with 10% FCS (Control Group), 10% SSS (Group I) and 10% SSS+10 ng/ml epidermal growth factor (EGF) (Group II). In Experiment II, effects of SSS on both oocyte maturation and embryo development during in vitro culture (IVC) were tested by maturing oocytes in media supplemented with 10% FCS (FCS Group) or 10% SSS+10 ng/ml EGF (SSS Group), followed by IVF and IVC in SOF media supplemented with 10% FCS and 10% SSS on day 4 for FCS and SSS Groups, respectively. Even though rates for cleavage and development to blastocyst stage were not different, blastocyst cell numbers were higher in Group II containing SSS and EGF. The SSS supplementation group had higher apoptotic nuclei as compared to the FCS Group in Experiment II. Transcripts for heat shock protein 70 (Hsp70), interferon tau (IF-tau), DNA methyltransferase 3a (Dnmt3a), desmosomal glycoprotein desmocollin III (DcIII) and insulin-like growth factor II receptor (Igf-2r) were altered in different culture conditions in Experiment I. However, only glucose transporter-1 (Glut-1) mRNA was different in the SSS and FCS Groups in the second experiment. In summary, SSS and EGF in maturation medium and replacement of FCS with SSS alone in culture medium on day 4 of IVC support oocyte maturation and embryo development in vitro. However, significance of culture condition induced changes on the genome-wide abundance of messenger ribonucleic acid and the significance of the apoptotic nuclei during fetal development still remain to be determined.
Efficient capture of unique sequences from eukaryotic genomes
ABSTRACT Cot-based cloning and sequencing (CBCS), a synthesis of Cot analysis, DNA cloning and high-throughput sequencing, promises to accelerate the study of eukaryotic genomes. In particular, CBCS will (1) permit efficient gene discovery in species with substantial quantities of repetitive DNA, (2) allow the sequence complexity (i.e. all the unique sequence information) of large genomes to be elucidated at a fraction of the cost of shotgun sequencing, and (3) enhance genome sequencing efforts by facilitating capture of low-copy sequences not secured by EST sequencing. CBCS should accelerate comparative genomics research, especially in large genomes such as those of many crops.
Whole-Genome Duplications Spurred the Functional Diversification of the Globin Gene Superfamily in Vertebrates
ABSTRACT It has been hypothesized that two successive rounds of whole-genome duplication (WGD) in the stem lineage of vertebrates provided genetic raw materials for the evolutionary innovation of many vertebrate-specific features. However, it has seldom been possible to trace such innovations to specific functional differences between paralogous gene products that derive from a WGD event. Here, we report genomic evidence for a direct link between WGD and key physiological innovations in the vertebrate oxygen transport system. Specifically, we demonstrate that key globin proteins that evolved specialized functions in different aspects of oxidative metabolism (hemoglobin, myoglobin, and cytoglobin) represent paralogous products of two WGD events in the vertebrate common ancestor. Analysis of conserved macrosynteny between the genomes of vertebrates and amphioxus (subphylum Cephalochordata) revealed that homologous chromosomal segments defined by myoglobin + globin-E, cytoglobin, and the alpha-globin gene cluster each descend from the same linkage group in the reconstructed proto-karyotype of the chordate common ancestor. The physiological division of labor between the oxygen transport function of hemoglobin and the oxygen storage function of myoglobin played a pivotal role in the evolution of aerobic energy metabolism, supporting the hypothesis that WGDs helped fuel key innovations in vertebrate evolution.
Gene duplication, genome duplication, and the functional diversification of vertebrate globins
ABSTRACT The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto alpha- and beta-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (alpha(2)beta(2)). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of alpha- and beta-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.
Current perspectives on the use of alternative species in human health and ecological hazard assessments
Perkins EJ, Ankley GT, Crofton KM, Garcia-Reyero N, Lalone CA, Johnson MS, Tietge JE, Villeneuve DL (2013) Current perspectives on the use of alternative species in human health and ecological hazard assessments. Environmental Health Perspectives 121(9): 1002-1010.
ABSTRACT Background: Traditional animal toxicity tests can be time and resource intensive, thereby limiting the number of chemicals that can be comprehensively tested for potential hazards to humans and/or to the environment.Objective: We compared several types of data to demonstrate how alternative models can be used to inform both human and ecological risk assessment.Methods: We reviewed and compared data derived from high throughput in vitro assays to fish reproductive tests for seven chemicals. We investigated whether human-focused assays can be predictive of chemical hazards in the environment. We examined how conserved pathways enable the use of nonmammalian models, such as fathead minnow, zebrafish, and Xenopus laevis, to understand modes of action and to screen for chemical risks to humans.Results: We examined how dose-dependent responses of zebrafish embryos exposed to flusilazole can be extrapolated, using pathway point of departure data and reverse toxicokinetics, to obtain human oral dose hazard values that are similar to published mammalian chronic toxicity values for the chemical. We also examined how development/safety data for human health can be used to help assess potential risks of pharmaceuticals to nontarget species in the environment.Discussion: Using several examples, we demonstrate that pathway-based analysis of chemical effects provides new opportunities to use alternative models (nonmammalian species, in vitro tests) to support decision making while reducing animal use and associated costs.Conclusions: These analyses and examples demonstrate how alternative models can be used to reduce cost and animal use while being protective of both human and ecological health.Citation: Perkins EJ, Ankley GT, Crofton KM, Garcia-Reyero N, LaLone CA, Johnson MS, Tietge JE, Villeneuve DL. 2013. Current perspectives on the use of alternative species in human health and ecological hazard assessments. Environ Health Perspect 121:1002-1010; https://doi.org/10.1289/ehp.1306638.
Developmental and molecular correlates of bovine preimplantation embryos
Sagirkaya H, Misirlioglu M, Kaya A, First NL, Parrish JJ, Memili E (2006) Developmental and molecular correlates of bovine preimplantation embryos. Reproduction 131(5): 895-904.
ABSTRACT Expression of embryonic genes is altered in different culture conditions, which influence developmental potential both during preimplantation and fetal development. The objective of this study was to define the effects of culture conditions on: bovine embryonic development to blastocyst stage, blastocyst cell number, apoptosis and expression patterns of a panel of developmentally important genes. Bovine embryos were cultured in vitro in three culture media containing amino acids, namely potassium simplex optimization medium (KSOMaa), Charles Rosenkrans 1 (CR1aa) and synthetic oviductal fluid (SOFaa). Apoptosis in blastocysts was determined by TUNEL assay and expression profiles of developmentally important genes were assayed by real-time PCR. In vivo-produced bovine blastocysts were used as controls for experiments determining gene expression patterns. While the cleavage rates did not differ, embryos cultured in SOFaa had higher rates of development to blastocyst stage (p<0.05). Mean cell numbers and percentages of apoptotic cells per blastocyst did not differ among the groups. Expression of the heat shock protein 70 (Hsp70) gene was significantly up-regulated in both CR1aa and KSOMaa when compared with SOFaa (p<0.001). DNA methyltransferase 3a (Dnmt3a) expression was higher in embryos cultured in CR1aa than in those cultured in SOFaa (p<0.001). Expression of interferon tau (IF-tau) and insulin-like growth factor II receptor (Igf-2r) genes was significantly up-regulated in KSOMaa when compared with CR1aa (p<0.001). Gene expression did not differ between in vivo-derived blastocysts and their in vitro-derived counterparts. In conclusion, SOFaa supports higher development to blastocyst stage than KSOMaa and CR1aa, and the culture conditions influence gene expression.
Transcriptome analysis of bull spermatozoa: implications for male fertility
Feugang JM, Rodriguez-Osorio N, Kaya A, Wang H, Page GP, Ostermeier GC, Topper EK, Memili E (2010) Transcriptome analysis of bull spermatozoa: implications for male fertility. Reproductive BioMedicine Online 21(3): 312-324.
ABSTRACT Spermatozoa deliver more than the paternal genome into the oocyte; they also carry remnant messenger RNA from spermatogenesis. The RNA profiles of spermatozoa from high-fertility and a low-fertility Holstein bulls were analysed using Affymetrix bovine genechips. A total of 415 transcripts out of approximately 24,000 were differentially detected in spermatozoa collected from both bulls (fold change > or =2.0; P<0.01). These transcripts were associated with different cellular functions and biological processes. Spermatozoa from high-fertility bulls contained higher concentrations of transcripts for membrane and extracellular space protein locations, while spermatozoa from the low-fertility bulls were deficient of transcripts for transcriptional and translational factors. Quantitative real-time PCR was used on three low-fertility and four high-fertility bulls to validate the microarray data. Two highly represented transcripts in the microarray analysis (protamine 1 and casein beta 2) were validated, as well as a third transcript (thrombospondin receptor CD36 molecule) that showed a lower concentration in low-fertility bulls. This study presents the global analysis of spermatozoa originating from bulls with opposite fertility. These results provide some specific transcripts in spermatozoa that could be associated with bull fertility.
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