Little information exists on the microbiomes of livestock workers. A cross-sectional, epidemiolog... more Little information exists on the microbiomes of livestock workers. A cross-sectional, epidemiological study was conducted enrolling 59 participants (26 of which had livestock contact) in Iowa. Participants were enrolled in one of four ways: from an existing prospective cohort study (n = 38), from the Iowa Department of Natural Resources Animal Feeding Operations database (n = 17), through Iowa county fairs (n = 3), and through snowball sampling (n = 1). We collected swabs from the nares and oropharynx of each participant to assess the microbiome via 16s rRNA sequencing. We observed livestock workers to have greater diversity in their microbiomes compared to those with no livestock contact. In the nares, there were 27 operational taxonomic units found to be different between livestock workers and non-livestock workers with the greatest difference seen with Streptococcus and Proteobacteria. In the oropharynx, livestock workers with swine exposure were more likely to carry several pathogenic organisms. The results of this study are the first to characterize the livestock worker nasal and oropharyngeal microbiomes.
We analyzed microarray expression data to highlight biological pathways that respond to embryonic... more We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide ''knockdown'', recombinant Leptin-a ''rescue'', and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca 2+ /calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling.
Background: Staphylococcus aureus is a frequent cause of both infections globally. Colonization w... more Background: Staphylococcus aureus is a frequent cause of both infections globally. Colonization with the organism is known to increase the risk of developing infections and occurs in roughly one third of the general population. While many factors influence colonization, it has been demonstrated other members of the microbiome influence colonization with S. aureus. Here, we assessed the nasal and oropharyngeal microbiomes of healthy participants in relation to S. aureus colonization in a cross-sectional study using 16s rRNA sequencing of the v1-v3 region. As livestock workers have also been shown to be at an increased risk of carriage, we have also assessed microbiota differences in colonization status in a population of livestock workers. Results: In both the nares and oropharynx, there were no microbiota differentially abundant between colonized and non-colonized persons. However, there was a significant difference in the beta diversity (Bray-Curtis distances) between carriers and non-carriers (P=0.002). When considering carriage stratified by livestock exposure, there were a number of differences. Most notably, colonized livestock workers had significantly more Porphyomonas (2-fold change =-8.54, P = 0.03) than the non-colonized livestock workers. Conclusions: S. aureus is a frequent colonizer of the human upper respiratory tract, including the nares and oropharynx and causes a wide range of infections. Livestock workers are at increased risk for carriage. Interventions such as improving oral hygiene may lead to decreased S. aureus carriage by reducing other bacterial species such as Porphyomonas. Larger, longitudinal studies are needed to better explore what microorganisms may be associated with S. aureus colonization.
The PubMed database offers an extensive set of publication data that can be useful, yet inherentl... more The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS-Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.
Background: As context is important to gene expression, so is the preprocessing of microarray to ... more Background: As context is important to gene expression, so is the preprocessing of microarray to transcriptomics. Microarray data suffers from several normalization and significance problems. Arbitrary fold change (FC) cutoffs of >2 and significance p-values of <0.02 lead data collection to look only at genes which vary wildly amongst other genes. Therefore, questions arise as to whether the biology or the statistical cutoff are more important within the interpretation. In this paper, we reanalyzed a zebrafish (D. rerio) microarray data set using GeneSpring and different differential gene expression cutoffs and found the data interpretation was drastically different. Furthermore, despite the advances in microarray technology, the array captures a large portion of genes known but yet still leaving large voids in the number of genes assayed, such as leptin a pleiotropic hormone directly related to hypoxia-induced angiogenesis. Results: The data strongly suggests that the number of differentially expressed genes is more up-regulated than down-regulated, with many genes indicating conserved signalling to previously known functions. Recapitulated data from Marques et al. (2008) was similar but surprisingly different with some genes showing unexpected signalling which may be a product of tissue (heart) or that the intended response was transient. Conclusions: Our analyses suggest that based on the chosen statistical or fold change cutoff ; microarray analysis can provide essentially more than one answer, implying data interpretation as more of an art than a science, with follow up gene expression studies a must. Furthermore, gene chip annotation and development needs to maintain pace with not only new genomes being sequenced but also novel genes that are crucial to the overall gene chips interpretation.
Abstract The field of paleotempestology has gained more awareness in the past decade as a result ... more Abstract The field of paleotempestology has gained more awareness in the past decade as a result of increased hurricane intensity, quantity, and duration within the late Holocene. One of the best localities to find records of hurricane overwash deposits is in the Bahamian islands. San Salvador Island, Bahamas (SSI) is a small (150km2), isolated carbonate platform, that contains shallow (0.5-3m) saline lakes that occur in between interdune areas of arcuate dune ridges. Due to San Salvador Island&#x27;s location within the Bahamian ...
<p>Points represent OTUs with phyla represented by color. Negative values represent OTUs si... more <p>Points represent OTUs with phyla represented by color. Negative values represent OTUs significantly more abundant in swine workers and positive values represent OTUs significantly more abundant in all other livestock workers. The Benjamini-Hochberg correction was applied.</p
<p>The JAK-STAT signaling KEGG pathway shows the known interactions within the JAK-STAT sig... more <p>The JAK-STAT signaling KEGG pathway shows the known interactions within the JAK-STAT signaling cascade.</p
<p>Bi-directionality is removed from directed consensus networks by adding the edge weights... more <p>Bi-directionality is removed from directed consensus networks by adding the edge weights from both directions for each set of nodes in (A) and using an undirected edge with the new total in (B).</p
<p>a) alpha diversity of nasal samples by livestock exposure (b) alpha diversity of orophar... more <p>a) alpha diversity of nasal samples by livestock exposure (b) alpha diversity of oropharyngeal samples by livestock exposure. c) PCoA of the Bray-Curtis dissimilarity matrix all samples by livestock exposure. d) PCoA of the nasal samples. e) PCoA of the oropharyngeal samples. PC1 and PC2 = principle coordinates 1 and 2 respectively.</p
<p>Points represent OTUs with phyla represented by color. Negative values represent OTUs si... more <p>Points represent OTUs with phyla represented by color. Negative values represent OTUs significantly more abundant in livestock workers and positive values represent OTUs significantly more abundant in non-livestock workers. a) Differentially abundant OTUs in the nares of all participant by livestock and b) differentially abundant OTUs in the nares of male participants by livestock exposure. The Benjamini-Hochberg correction applied to all figures.</p
<p>Negative values represent OTUs significantly more abundant in livestock workers and posi... more <p>Negative values represent OTUs significantly more abundant in livestock workers and positive values represent OTUs significantly more abundant in non-livestock workers. a) Differentially abundant OTUs in the nares of those over 55 and b) Differentially abundant OTUs in the nares of those 55 and under. The Benjamini-Hochberg correction applied to all figures.</p
We investigated innate immune function in developing zebrafish with reduced leptin expression (vi... more We investigated innate immune function in developing zebrafish with reduced leptin expression (via antisense morpholino technology). Leptin is a pleiotropic, adipose derived hormone known to be involved in mammalian lipid mobilization and storage, as well as the maintenance of many peripheral systems such as immune function. Despite many well‐described effects in mammals, leptin's function(s) in lower vertebrates are still poorly resolved. A fluorescent strain of P. aeruginosa was used to challenge the immune system of developing zebrafish and to visualize the progression of infection. Leptin knockdown significantly reduced the ability to fight invading pathogens, which was reflected in both reduced survivability and increased bacterial load of leptin morphants. Overall, these data suggest that leptin signaling influences innate immune function in fishes as it does in mammals, and promotes zebrafish as another vertebrate model for studying leptin function.
Little information exists on the microbiomes of livestock workers. A cross-sectional, epidemiolog... more Little information exists on the microbiomes of livestock workers. A cross-sectional, epidemiological study was conducted enrolling 59 participants (26 of which had livestock contact) in Iowa. Participants were enrolled in one of four ways: from an existing prospective cohort study (n = 38), from the Iowa Department of Natural Resources Animal Feeding Operations database (n = 17), through Iowa county fairs (n = 3), and through snowball sampling (n = 1). We collected swabs from the nares and oropharynx of each participant to assess the microbiome via 16s rRNA sequencing. We observed livestock workers to have greater diversity in their microbiomes compared to those with no livestock contact. In the nares, there were 27 operational taxonomic units found to be different between livestock workers and non-livestock workers with the greatest difference seen with Streptococcus and Proteobacteria. In the oropharynx, livestock workers with swine exposure were more likely to carry several pathogenic organisms. The results of this study are the first to characterize the livestock worker nasal and oropharyngeal microbiomes.
We analyzed microarray expression data to highlight biological pathways that respond to embryonic... more We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide ''knockdown'', recombinant Leptin-a ''rescue'', and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca 2+ /calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling.
Background: Staphylococcus aureus is a frequent cause of both infections globally. Colonization w... more Background: Staphylococcus aureus is a frequent cause of both infections globally. Colonization with the organism is known to increase the risk of developing infections and occurs in roughly one third of the general population. While many factors influence colonization, it has been demonstrated other members of the microbiome influence colonization with S. aureus. Here, we assessed the nasal and oropharyngeal microbiomes of healthy participants in relation to S. aureus colonization in a cross-sectional study using 16s rRNA sequencing of the v1-v3 region. As livestock workers have also been shown to be at an increased risk of carriage, we have also assessed microbiota differences in colonization status in a population of livestock workers. Results: In both the nares and oropharynx, there were no microbiota differentially abundant between colonized and non-colonized persons. However, there was a significant difference in the beta diversity (Bray-Curtis distances) between carriers and non-carriers (P=0.002). When considering carriage stratified by livestock exposure, there were a number of differences. Most notably, colonized livestock workers had significantly more Porphyomonas (2-fold change =-8.54, P = 0.03) than the non-colonized livestock workers. Conclusions: S. aureus is a frequent colonizer of the human upper respiratory tract, including the nares and oropharynx and causes a wide range of infections. Livestock workers are at increased risk for carriage. Interventions such as improving oral hygiene may lead to decreased S. aureus carriage by reducing other bacterial species such as Porphyomonas. Larger, longitudinal studies are needed to better explore what microorganisms may be associated with S. aureus colonization.
The PubMed database offers an extensive set of publication data that can be useful, yet inherentl... more The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS-Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.
Background: As context is important to gene expression, so is the preprocessing of microarray to ... more Background: As context is important to gene expression, so is the preprocessing of microarray to transcriptomics. Microarray data suffers from several normalization and significance problems. Arbitrary fold change (FC) cutoffs of >2 and significance p-values of <0.02 lead data collection to look only at genes which vary wildly amongst other genes. Therefore, questions arise as to whether the biology or the statistical cutoff are more important within the interpretation. In this paper, we reanalyzed a zebrafish (D. rerio) microarray data set using GeneSpring and different differential gene expression cutoffs and found the data interpretation was drastically different. Furthermore, despite the advances in microarray technology, the array captures a large portion of genes known but yet still leaving large voids in the number of genes assayed, such as leptin a pleiotropic hormone directly related to hypoxia-induced angiogenesis. Results: The data strongly suggests that the number of differentially expressed genes is more up-regulated than down-regulated, with many genes indicating conserved signalling to previously known functions. Recapitulated data from Marques et al. (2008) was similar but surprisingly different with some genes showing unexpected signalling which may be a product of tissue (heart) or that the intended response was transient. Conclusions: Our analyses suggest that based on the chosen statistical or fold change cutoff ; microarray analysis can provide essentially more than one answer, implying data interpretation as more of an art than a science, with follow up gene expression studies a must. Furthermore, gene chip annotation and development needs to maintain pace with not only new genomes being sequenced but also novel genes that are crucial to the overall gene chips interpretation.
Abstract The field of paleotempestology has gained more awareness in the past decade as a result ... more Abstract The field of paleotempestology has gained more awareness in the past decade as a result of increased hurricane intensity, quantity, and duration within the late Holocene. One of the best localities to find records of hurricane overwash deposits is in the Bahamian islands. San Salvador Island, Bahamas (SSI) is a small (150km2), isolated carbonate platform, that contains shallow (0.5-3m) saline lakes that occur in between interdune areas of arcuate dune ridges. Due to San Salvador Island&#x27;s location within the Bahamian ...
<p>Points represent OTUs with phyla represented by color. Negative values represent OTUs si... more <p>Points represent OTUs with phyla represented by color. Negative values represent OTUs significantly more abundant in swine workers and positive values represent OTUs significantly more abundant in all other livestock workers. The Benjamini-Hochberg correction was applied.</p
<p>The JAK-STAT signaling KEGG pathway shows the known interactions within the JAK-STAT sig... more <p>The JAK-STAT signaling KEGG pathway shows the known interactions within the JAK-STAT signaling cascade.</p
<p>Bi-directionality is removed from directed consensus networks by adding the edge weights... more <p>Bi-directionality is removed from directed consensus networks by adding the edge weights from both directions for each set of nodes in (A) and using an undirected edge with the new total in (B).</p
<p>a) alpha diversity of nasal samples by livestock exposure (b) alpha diversity of orophar... more <p>a) alpha diversity of nasal samples by livestock exposure (b) alpha diversity of oropharyngeal samples by livestock exposure. c) PCoA of the Bray-Curtis dissimilarity matrix all samples by livestock exposure. d) PCoA of the nasal samples. e) PCoA of the oropharyngeal samples. PC1 and PC2 = principle coordinates 1 and 2 respectively.</p
<p>Points represent OTUs with phyla represented by color. Negative values represent OTUs si... more <p>Points represent OTUs with phyla represented by color. Negative values represent OTUs significantly more abundant in livestock workers and positive values represent OTUs significantly more abundant in non-livestock workers. a) Differentially abundant OTUs in the nares of all participant by livestock and b) differentially abundant OTUs in the nares of male participants by livestock exposure. The Benjamini-Hochberg correction applied to all figures.</p
<p>Negative values represent OTUs significantly more abundant in livestock workers and posi... more <p>Negative values represent OTUs significantly more abundant in livestock workers and positive values represent OTUs significantly more abundant in non-livestock workers. a) Differentially abundant OTUs in the nares of those over 55 and b) Differentially abundant OTUs in the nares of those 55 and under. The Benjamini-Hochberg correction applied to all figures.</p
We investigated innate immune function in developing zebrafish with reduced leptin expression (vi... more We investigated innate immune function in developing zebrafish with reduced leptin expression (via antisense morpholino technology). Leptin is a pleiotropic, adipose derived hormone known to be involved in mammalian lipid mobilization and storage, as well as the maintenance of many peripheral systems such as immune function. Despite many well‐described effects in mammals, leptin's function(s) in lower vertebrates are still poorly resolved. A fluorescent strain of P. aeruginosa was used to challenge the immune system of developing zebrafish and to visualize the progression of infection. Leptin knockdown significantly reduced the ability to fight invading pathogens, which was reflected in both reduced survivability and increased bacterial load of leptin morphants. Overall, these data suggest that leptin signaling influences innate immune function in fishes as it does in mammals, and promotes zebrafish as another vertebrate model for studying leptin function.
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