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Carl Schmidt

University of Delaware, Animal & Food Sciences, Faculty Member

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My research interests focus largely on evolution, particularly using the chicken to determine the impact of human selection for production traits. Several approaches are used including basic morphometrics to establish the physical changes that have occurred in various selected and unselected lines. In addition we are making extensive use of microarrays and DNA sequencing to identify transcription and genomic changes.

To support this effort, my group is developing bioinformatics resources to support archosaurian (birds, crocodilians) comparative genomics (http://birdbase.net)

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Cesare Castellini

University of Perugia

Shanmugam Murugesan

Directorate of Poultry Research

Juan Manuel Cantet

USDA Agricultural Research Service

North Carolina State University

JOHN KING LAYOS

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Papers by Carl Schmidt

Integrated Genomic Approaches to Characterize and Mitigate Heat Stress in Poultry

Annual Review of Animal Biosciences, 2025

With the burgeoning human population, climate change, and expansion of poultry production in hot ... more With the burgeoning human population, climate change, and expansion of poultry production in hot climates, it is imperative to aid global food security by enhancing the resilience of thermally challenged poultry. As a complement to management approaches used to mitigate heat stress, we give selected examples of recent studies on heat stress in poultry using various ‘omics technologies. An integrated analysis of positional and functional candidate genes is provided, highlighting the most prominent pathways involved in the heat stress response. We finish by discussing efficient strategies to enhance thermal tolerance of poultry by genomics approaches, advocating for preservation of biodiversity that may provide beneficial allelic variation, and identifying current and future challenges in producing climate-resilient poultry.

Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken

by Carl Schmidt and Heidi Van Every

BMC Genomics, 2021

Background: Artificial selection of modern meat-producing chickens (broilers) for production char... more Background: Artificial selection of modern meat-producing chickens (broilers) for production characteristics has led to dramatic changes in phenotype, yet the impact of this selection on metabolic and molecular mechanisms is poorly understood. The first 3 weeks post-hatch represent a critical period of adjustment, during which the yolk lipid is depleted and the bird transitions to reliance on a carbohydrate-rich diet. As the liver is the major organ involved in macronutrient metabolism and nutrient allocatytion, a combined transcriptomics and metabolomics approach has been used to evaluate hepatic metabolic reprogramming between Day 4 (D4) and Day 20 (D20) post-hatch. Results: Many transcripts and metabolites involved in metabolic pathways differed in their abundance between D4 and D20, representing different stages of metabolism that are enhanced or diminished. For example, at D20 the first stage of glycolysis that utilizes ATP to store or release glucose is enhanced, while at D4, the ATP-generating phase is enhanced to provide energy for rapid cellular proliferation at this time point. This work has also identified several metabolites, including citrate, phosphoenolpyruvate, and glycerol, that appear to play pivotal roles in this reprogramming. Conclusions: At Day 4, metabolic flexibility allows for efficiency to meet the demands of rapid liver growth under oxygen-limiting conditions. At Day 20, the liver's metabolism has shifted to process a carbohydrate-rich diet that supports the rapid overall growth of the modern broiler. Characterizing these metabolic changes associated with normal post-hatch hepatic development has generated testable hypotheses about the involvement of specific genes and metabolites, clarified the importance of hypoxia to rapid organ growth, and contributed to our understanding of the molecular changes affected by decades of artificial selection.

Distinct genes and pathways associated with transcriptome differences in early cardiac development between fast-and slow-growing broilers

by Jibin Zhang and Carl Schmidt

PLOS ONE, 2018

Modern fast-growing broilers are susceptible to cardiac dysfunctions because their relatively sma... more Modern fast-growing broilers are susceptible to cardiac dysfunctions because their relatively small hearts cannot adequately meet the increased need of pumping blood through a large body mass. To improve cardiac health in broilers through breeding, we need to identify the genes and pathways that contribute to imbalanced cardiac development and occurrence of heart dysfunction. Two broiler lines–Ross 708 and Illinois–were included in this study as models of modern fast-growing and heritage slow-growing broilers, respectively. The left ventricular transcriptome were compared between the two broiler lines at day 6 and 21 post hatch through RNA-seq analysis to identify genes and pathways regulating compromised cardiac development in modern broilers. Number of differentially expressed genes (DEGs, p<0.05) between the two broiler lines increased from 321 at day 6 to 819 at day 21. As the birds grew, Ross broilers showed more DEGs (n = 1879) than Illinois broilers (n = 1117). Both broilers showed significant change of muscle related genes and immune genes, but Ross broilers showed remarkable change of expression of several lipid transporter genes including APOA4, APOB, APOH, FABP4 and RBP7. Ingenuity pathway analysis (IPA) suggested that increased cell apoptosis and inhibited cell cycle due to increased lipid accumulation , oxidative stress and endoplasmic reticulum stress may be related to the increased cardiac dysfunctions in fast-growing broilers. Cell cycle regulatory pathways like " Mitotic Roles of Polo-like Kinases " are ranked as the top changed pathways related to the cell apo-ptosis. These findings provide further insight into the cardiac dysfunction in modern broilers and also potential targets for improvement of their cardiac health through breeding.

TransAtlasDB: an integrated database connecting expression data, metadata and variants

by Carl Schmidt and Modupeore O. Adetunji

High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-fr... more High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful function-alities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis.

Chicken hepatic response to chronic heat stress using integrated transcriptome and metabolome analysis

The liver plays a central role in metabolism and is important in maintaining homeostasis througho... more The liver plays a central role in metabolism and is important in maintaining homeostasis throughout the body. This study integrated transcriptomic and metabolomic data to understand how the liver responds under chronic heat stress. Chickens from a rapidly growing broiler line were heat stressed for 8 hours per day for one week and liver samples were collected at 28 days post hatch. Transcriptome analysis reveals changes in genes responsible for cell cycle regulation, DNA replication, and DNA repair along with immune function. Integrating the metabolome and transcriptome data highlighted multiple pathways affected by heat stress including glucose, amino acid, and lipid metabolism along with glutathione production and beta-oxidation.

The chicken gene nomenclature committee report

by Carl Schmidt and Shane C Burgess

BMC Genomics, 2009

Comparative genomics is an essential component of the post-genomic era. The chicken genome is the... more Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species. Moreover, due to its unique evolutionary niche, the chicken genome can be used to understand evolution of functional elements and gene regulation in mammalian species. However comparative biology both within avian species and within amniotes is hampered due to the difficulty of recognising functional orthologs. This problem is compounded as different databases and sequence repositories proliferate and the names they assign to functional elements proliferate along with them. Currently, genes can be published under more than one name and one name sometimes refers to unrelated genes. Standardized gene nomenclature is necessary to facilitate communication between scientists and genomic resources. Moreover, it is important that this nomenclature be based on existing nomenclature efforts where possible to truly facilitate studies between different species. We report here the formation of the Chicken Gene Nomenclature Committee (CGNC), an international and centralized effort to provide standardized nomenclature for chicken genes. The CGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees for human and mouse. The CGNC will develop standardized nomenclature in consultation with the research community and relies on the support of the research community to ensure that the nomenclature facilitates comparative and genomic studies.

WebGIVI: a web-based gene enrichment analysis and visualization tool

by Carl Schmidt and Liang Sun

Background: A major challenge of high throughput transcriptome studies is presenting the data to ... more Background: A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task.

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast-and slow-growing broilers under heat stress

by Jibin Zhang and Carl Schmidt

Background: Modern fast-growing broilers are susceptible to heart failure under heat stress becau... more Background: Modern fast-growing broilers are susceptible to heart failure under heat stress because their relatively small hearts cannot meet increased need of blood pumping. To improve the cardiac tolerance to heat stress in modern broilers through breeding, we need to find the important genes and pathways that contribute to imbalanced cardiac development and frequent occurrence of heat-related heart dysfunction. Two broiler lines – Ross 708 and Illinois – were included in this study as a fast-growing model and a slow-growing model respectively. Each broiler line was separated to two groups at 21 days posthatch. One group was subjected to heat stress treatment in the range of 35–37 °C for 8 h per day, and the other was kept in thermoneutral condition. Body and heart weights were measured at 42 days posthatch, and gene expression in left ventricles were compared between treatments and broiler lines through RNA-seq analysis.

Transcriptomic changes throughout post-hatch development in Gallus gallus pituitary

by Carl Schmidt and Elizabeth Pritchett

The pituitary gland is a neuroendocrine organ that works closely with the hypothalamus to affect ... more The pituitary gland is a neuroendocrine organ that works closely with the hypothalamus to affect multiple processes within the body including the stress response, metabolism, growth and immune function. Relative tissue expression (rEx) is a transcriptome analysis method that compares the genes expressed in a particular tissue to the genes expressed in all other tissues with available data. Using rEx, the aim of this study was to identify genes that are uniquely or more abundantly expressed in the pituitary when compared to all other collected chicken tissues. We applied rEx to define genes enriched in the chicken pituitaries at days 21, 22 and 42 post-hatch. rEx analysis identified 25 genes shared between all time points, 295 genes shared between days 21 and 22 and 407 genes unique to day 42. The 25 genes shared by all time points are involved in morphogenesis and general nervous tissue development. The 295 shared genes between days 21 and 22 are involved in neurogenesis and nervous system development and differentiation. The 407 unique day 42 genes are involved in pituitary development, endocrine system development and other hormonally related gene ontology terms. Overall, rEx analysis indicates a focus on nervous system/tissue development at days 21 and 22. By day 42, in addition to nervous tissue development, there is expression of genes involved in the endocrine system, possibly for maturation and preparation for reproduction. This study defines the transcriptome of the chicken pituitary gland and aids in understanding the expressed genes critical to its function and maturation.

Liver transcriptome response to hyperthermic stress in three distinct chicken lines

Background: High ambient temperatures cause stress in poultry, especially for broiler lines, whic... more Background: High ambient temperatures cause stress in poultry, especially for broiler lines, which are genetically selected for rapid muscle growth. RNA-seq technology provides powerful insights into environmental response from a highly metabolic tissue, the liver. We investigated the effects of acute (3 h, 35 °C) and chronic (7d of 35 °C for 7 h/d) heat stress on the liver transcriptome of 3-week-old chicks of a heat-susceptible broiler line, a heat-resistant Fayoumi line, and their advanced intercross line (AIL). Results: Transcriptome sequencing of 48 male chickens using Illumina HiSeq 2500 technology yielded an average of 33.9 million, 100 base-pair, single-end reads per sample. There were 8 times more differentially expressed genes (DEGs) (FDR < 0.05) in broilers (n = 627) than Fayoumis (n = 78) when comparing the acute-heat samples to the control (25 °C) samples. Contrasting genetic lines under similar heat treatments, the highest number of DEGs appeared between Fayoumi and broiler lines. Principal component analysis of gene expression and analysis of the number of DEGs suggested that the AIL had a transcriptomic response more similar to the Fayoumi than the broiler line during acute heat stress. The number of DEGs also suggested that acute heat stress had greater impact on the broiler liver transcriptome than chronic heat stress. The angiopoietin-like 4 (ANGPTL4) gene was identified as differentially expressed among all 6 contrasts. Ingenuity Pathway Analysis (IPA) created a novel network that combines the heat shock protein family with immune response genes.

Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences

Background: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed... more Background: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within-and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation.

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

by M. Nefedov and Carl Schmidt

PLoS Biology, 2010

A synergistic combination of two next-generation sequencing platforms with a detailed comparative... more A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (,1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Identification of quantitative trait loci for body temperature, body weight, breast yield, and digestibility in an advanced intercross line of chickens under heat stress

Background: Losses in poultry production due to heat stress have considerable negative economic c... more Background: Losses in poultry production due to heat stress have considerable negative economic consequences. Previous studies in poultry have elucidated a genetic influence on response to heat. Using a unique chicken genetic resource, we identified genomic regions associated with body temperature (BT), body weight (BW), breast yield, and digestibility measured during heat stress. Identifying genes associated with a favorable response during high ambient temperature can facilitate genetic selection of heat-resilient chickens. Methods: Generations F18 and F19 of a broiler (heat-susceptible) × Fayoumi (heat-resistant) advanced intercross line (AIL) were used to fine-map quantitative trait loci (QTL). Six hundred and thirty-one birds were exposed to daily heat cycles from 22 to 28 days of age, and phenotypes were measured before heat treatment, on the 1st day and after 1 week of heat treatment. BT was measured at these three phases and BW at pre-heat treatment and after 1 week of heat treatment. Breast muscle yield was calculated as the percentage of BW at day 28. Ileal feed digestibility was assayed from digesta collected from the ileum at day 28. Four hundred and sixty-eight AIL were genotyped using the 600 K Affymetrix chicken SNP (single nucleotide polymorphism) array. Trait heritabilities were estimated using an animal model. A genome-wide association study (GWAS) for these traits and changes in BT and BW was conducted using Bayesian analyses. Candidate genes were identified within 200-kb regions around SNPs with significant association signals. Results: Heritabilities were low to moderate (0.03 to 0.35). We identified QTL for BT on Gallus gallus chromosome (GGA)14, 15, 26, and 27; BW on GGA1 to 8, 10, 14, and 21; dry matter digestibility on GGA19, 20 and 21; and QTL of very large effect for breast muscle yield on GGA1, 15, and 22 with a single 1-Mb window on GGA1 explaining more than 15 % of the genetic variation. Conclusions: This is the first study to estimate heritabilities and perform GWAS using this AIL for traits measured during heat stress. Significant QTL as well as low to moderate heritabilities were found for each trait, and these QTL may facilitate selection for improved animal performance in hot climatic conditions.

Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress

Background: Heat stress in poultry results in considerable economic losses and is a concern for b... more Background: Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO 2 , pO 2 , base excess, HCO 3 , TCO 2 , K, Na, ionized Ca, hematocrit, hemoglobin, sO 2 , and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. Results: There were significant increases in pH, base excess, HCO 3 , TCO 2 , ionized Ca, hematocrit, hemoglobin, and sO 2 , and significant decreases in pCO 2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12–14, 17, 18, 21–28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress. Conclusions: The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.

Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array

Background: Indigenous populations of animals have developed unique adaptations to their local en... more Background: Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study's goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments. Results: Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0. 15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions. Conclusions: The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture.

Distinct functional responses to stressors of bone marrow derived dendritic cells from diverse inbred chicken lines

Differences in responses of chicken bone marrow derived dendritic cells (BMDC) to in vitro treatm... more Differences in responses of chicken bone marrow derived dendritic cells (BMDC) to in vitro treatment with lipopolysaccharide (LPS), heat, and LPS þ heat were identified. The Fayoumi is more disease resistant and heat tolerant than the Leghorn line. Nitric Oxide (NO) production, phagocytic ability, MHC II surface expression and mRNA expression were measured. NO was induced in BMDC from both lines in response to LPS and LPS þ heat stimulation; Fayoumi produced more NO with LPS treatment. Fayoumi had higher phagocytic ability and MHC II surface expression. Gene expression for the heat-related genes BAG3, HSP25, HSPA2, and HSPH1 was strongly induced with heat and few differences existed between lines. Expression for the immune-related genes CCL4, CCL5, CD40, GM-CSF, IFN-g, IL-10, IL-12b, IL-1b, IL-6, IL-8, and iNOS was highly induced in response to LPS and different between lines. This research contributes to the sparse knowledge of genetic differences in chicken BMDC biology and function.

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

by Jacqueline Smith and Carl Schmidt

PLoS Biology, 2010

A synergistic combination of two next-generation sequencing platforms with a detailed comparative... more A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Specificity of G protein β and γ subunit interactions

Journal of Biological Chemistry

Multiple heterotrimeric guanine nucleotide binding protein (G protein) subunits have evolved to c... more Multiple heterotrimeric guanine nucleotide binding protein (G protein) subunits have evolved to couple a large variety of receptors to intracellular effectors. G protein beta gamma subunits are essential for efficient coupling of alpha subunits to receptors, and they are also important for modulation of effectors. Several different beta and gamma subunits exist, but it is not known whether all possible combinations of beta and gamma can form functional dimers. To answer this question, we have compared the ability of in vitro translated beta 1, beta 2, and beta 3 to form dimers with either gamma 1 or gamma 2. Dimerization was monitored by gel filtration, resistance to tryptic digestion, and chemical cross-linking. The results indicate that beta 1 binds both gamma subunits, beta 2 binds only gamma 2, and beta 3 will bind neither gamma 1 or gamma 2. Hence, the occurrence of beta gamma dimers may be partially regulated by the ability of the subunits to associate. Specificity of dimeriza...

PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways

by Liang Sun, Carl Schmidt, and Yongnan Zhu

BMC bioinformatics, 2015

High-throughput methods are generating biological data on a vast scale. In many instances, genomi... more High-throughput methods are generating biological data on a vast scale. In many instances, genomic, transcriptomic, and proteomic data must be interpreted in the context of signaling and metabolic pathways to yield testable hypotheses. Since humans can interpret visual information rapidly, a means for interactive visual exploration that lets biologists interpret such data in a comprehensive and exploratory manner would be invaluable. However, humans have limited memory capacity. Current visualization tools have limited viewing and manipulation capabilities to address complex data analysis problems, and visual exploratory tools are needed to reduce the high mental workload imposed on biologists. We present PathRings, a new interactive web-based, scalable biological pathway visualization tool for biologists to explore and interpret biological pathways. PathRings integrates metabolic and signaling pathways from Reactome in a single compound graph visualization, and uses color to highli...

The G protein gamma subunit. Requirements for dimerization with beta subunits

The Journal of biological chemistry, Jan 30, 1995

Guanine nucleotide-binding protein beta and gamma subunits form a tightly bound complex that can ... more Guanine nucleotide-binding protein beta and gamma subunits form a tightly bound complex that can only be separated by denaturation. Assembly of beta and gamma subunits is a complicated process. The beta 1 and gamma 2 subunits can be synthesized in vitro in rabbit reticulocyte lysate and then assembled into dimers, but beta 1 cannot form beta gamma dimers when synthesized in a wheat germ extract. In contrast, gamma 2 translated in either system can dimerize with beta 1, suggesting that dimerization-competent gamma 2 can be synthesized without the aid of specific chaperonins or other cofactors. Dimerization-competent gamma 2 in solution forms an asymmetric particle with a Stokes radius of about 21 +/- 0.4 A (n = 4), s20,w of 0.9 S (range 0.8-1.0 S, n = 2), and frictional ratio of 1.57 (assuming no hydration). To define the part of gamma 2 that is needed for native beta gamma dimer formation, a series of N- and C-terminal truncations were generated, synthesized in vitro, and incubated ...

Integrated Genomic Approaches to Characterize and Mitigate Heat Stress in Poultry

Annual Review of Animal Biosciences, 2025

With the burgeoning human population, climate change, and expansion of poultry production in hot ... more With the burgeoning human population, climate change, and expansion of poultry production in hot climates, it is imperative to aid global food security by enhancing the resilience of thermally challenged poultry. As a complement to management approaches used to mitigate heat stress, we give selected examples of recent studies on heat stress in poultry using various ‘omics technologies. An integrated analysis of positional and functional candidate genes is provided, highlighting the most prominent pathways involved in the heat stress response. We finish by discussing efficient strategies to enhance thermal tolerance of poultry by genomics approaches, advocating for preservation of biodiversity that may provide beneficial allelic variation, and identifying current and future challenges in producing climate-resilient poultry.

Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken

by Carl Schmidt and Heidi Van Every

BMC Genomics, 2021

Background: Artificial selection of modern meat-producing chickens (broilers) for production char... more Background: Artificial selection of modern meat-producing chickens (broilers) for production characteristics has led to dramatic changes in phenotype, yet the impact of this selection on metabolic and molecular mechanisms is poorly understood. The first 3 weeks post-hatch represent a critical period of adjustment, during which the yolk lipid is depleted and the bird transitions to reliance on a carbohydrate-rich diet. As the liver is the major organ involved in macronutrient metabolism and nutrient allocatytion, a combined transcriptomics and metabolomics approach has been used to evaluate hepatic metabolic reprogramming between Day 4 (D4) and Day 20 (D20) post-hatch. Results: Many transcripts and metabolites involved in metabolic pathways differed in their abundance between D4 and D20, representing different stages of metabolism that are enhanced or diminished. For example, at D20 the first stage of glycolysis that utilizes ATP to store or release glucose is enhanced, while at D4, the ATP-generating phase is enhanced to provide energy for rapid cellular proliferation at this time point. This work has also identified several metabolites, including citrate, phosphoenolpyruvate, and glycerol, that appear to play pivotal roles in this reprogramming. Conclusions: At Day 4, metabolic flexibility allows for efficiency to meet the demands of rapid liver growth under oxygen-limiting conditions. At Day 20, the liver's metabolism has shifted to process a carbohydrate-rich diet that supports the rapid overall growth of the modern broiler. Characterizing these metabolic changes associated with normal post-hatch hepatic development has generated testable hypotheses about the involvement of specific genes and metabolites, clarified the importance of hypoxia to rapid organ growth, and contributed to our understanding of the molecular changes affected by decades of artificial selection.

Distinct genes and pathways associated with transcriptome differences in early cardiac development between fast-and slow-growing broilers

by Jibin Zhang and Carl Schmidt

PLOS ONE, 2018

Modern fast-growing broilers are susceptible to cardiac dysfunctions because their relatively sma... more Modern fast-growing broilers are susceptible to cardiac dysfunctions because their relatively small hearts cannot adequately meet the increased need of pumping blood through a large body mass. To improve cardiac health in broilers through breeding, we need to identify the genes and pathways that contribute to imbalanced cardiac development and occurrence of heart dysfunction. Two broiler lines–Ross 708 and Illinois–were included in this study as models of modern fast-growing and heritage slow-growing broilers, respectively. The left ventricular transcriptome were compared between the two broiler lines at day 6 and 21 post hatch through RNA-seq analysis to identify genes and pathways regulating compromised cardiac development in modern broilers. Number of differentially expressed genes (DEGs, p<0.05) between the two broiler lines increased from 321 at day 6 to 819 at day 21. As the birds grew, Ross broilers showed more DEGs (n = 1879) than Illinois broilers (n = 1117). Both broilers showed significant change of muscle related genes and immune genes, but Ross broilers showed remarkable change of expression of several lipid transporter genes including APOA4, APOB, APOH, FABP4 and RBP7. Ingenuity pathway analysis (IPA) suggested that increased cell apoptosis and inhibited cell cycle due to increased lipid accumulation , oxidative stress and endoplasmic reticulum stress may be related to the increased cardiac dysfunctions in fast-growing broilers. Cell cycle regulatory pathways like " Mitotic Roles of Polo-like Kinases " are ranked as the top changed pathways related to the cell apo-ptosis. These findings provide further insight into the cardiac dysfunction in modern broilers and also potential targets for improvement of their cardiac health through breeding.

TransAtlasDB: an integrated database connecting expression data, metadata and variants

by Carl Schmidt and Modupeore O. Adetunji

High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-fr... more High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful function-alities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis.

Chicken hepatic response to chronic heat stress using integrated transcriptome and metabolome analysis

The liver plays a central role in metabolism and is important in maintaining homeostasis througho... more The liver plays a central role in metabolism and is important in maintaining homeostasis throughout the body. This study integrated transcriptomic and metabolomic data to understand how the liver responds under chronic heat stress. Chickens from a rapidly growing broiler line were heat stressed for 8 hours per day for one week and liver samples were collected at 28 days post hatch. Transcriptome analysis reveals changes in genes responsible for cell cycle regulation, DNA replication, and DNA repair along with immune function. Integrating the metabolome and transcriptome data highlighted multiple pathways affected by heat stress including glucose, amino acid, and lipid metabolism along with glutathione production and beta-oxidation.

The chicken gene nomenclature committee report

by Carl Schmidt and Shane C Burgess

BMC Genomics, 2009

Comparative genomics is an essential component of the post-genomic era. The chicken genome is the... more Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species. Moreover, due to its unique evolutionary niche, the chicken genome can be used to understand evolution of functional elements and gene regulation in mammalian species. However comparative biology both within avian species and within amniotes is hampered due to the difficulty of recognising functional orthologs. This problem is compounded as different databases and sequence repositories proliferate and the names they assign to functional elements proliferate along with them. Currently, genes can be published under more than one name and one name sometimes refers to unrelated genes. Standardized gene nomenclature is necessary to facilitate communication between scientists and genomic resources. Moreover, it is important that this nomenclature be based on existing nomenclature efforts where possible to truly facilitate studies between different species. We report here the formation of the Chicken Gene Nomenclature Committee (CGNC), an international and centralized effort to provide standardized nomenclature for chicken genes. The CGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees for human and mouse. The CGNC will develop standardized nomenclature in consultation with the research community and relies on the support of the research community to ensure that the nomenclature facilitates comparative and genomic studies.

WebGIVI: a web-based gene enrichment analysis and visualization tool

by Carl Schmidt and Liang Sun

Background: A major challenge of high throughput transcriptome studies is presenting the data to ... more Background: A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task.

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast-and slow-growing broilers under heat stress

by Jibin Zhang and Carl Schmidt

Background: Modern fast-growing broilers are susceptible to heart failure under heat stress becau... more Background: Modern fast-growing broilers are susceptible to heart failure under heat stress because their relatively small hearts cannot meet increased need of blood pumping. To improve the cardiac tolerance to heat stress in modern broilers through breeding, we need to find the important genes and pathways that contribute to imbalanced cardiac development and frequent occurrence of heat-related heart dysfunction. Two broiler lines – Ross 708 and Illinois – were included in this study as a fast-growing model and a slow-growing model respectively. Each broiler line was separated to two groups at 21 days posthatch. One group was subjected to heat stress treatment in the range of 35–37 °C for 8 h per day, and the other was kept in thermoneutral condition. Body and heart weights were measured at 42 days posthatch, and gene expression in left ventricles were compared between treatments and broiler lines through RNA-seq analysis.

Transcriptomic changes throughout post-hatch development in Gallus gallus pituitary

by Carl Schmidt and Elizabeth Pritchett

The pituitary gland is a neuroendocrine organ that works closely with the hypothalamus to affect ... more The pituitary gland is a neuroendocrine organ that works closely with the hypothalamus to affect multiple processes within the body including the stress response, metabolism, growth and immune function. Relative tissue expression (rEx) is a transcriptome analysis method that compares the genes expressed in a particular tissue to the genes expressed in all other tissues with available data. Using rEx, the aim of this study was to identify genes that are uniquely or more abundantly expressed in the pituitary when compared to all other collected chicken tissues. We applied rEx to define genes enriched in the chicken pituitaries at days 21, 22 and 42 post-hatch. rEx analysis identified 25 genes shared between all time points, 295 genes shared between days 21 and 22 and 407 genes unique to day 42. The 25 genes shared by all time points are involved in morphogenesis and general nervous tissue development. The 295 shared genes between days 21 and 22 are involved in neurogenesis and nervous system development and differentiation. The 407 unique day 42 genes are involved in pituitary development, endocrine system development and other hormonally related gene ontology terms. Overall, rEx analysis indicates a focus on nervous system/tissue development at days 21 and 22. By day 42, in addition to nervous tissue development, there is expression of genes involved in the endocrine system, possibly for maturation and preparation for reproduction. This study defines the transcriptome of the chicken pituitary gland and aids in understanding the expressed genes critical to its function and maturation.

Liver transcriptome response to hyperthermic stress in three distinct chicken lines

Background: High ambient temperatures cause stress in poultry, especially for broiler lines, whic... more Background: High ambient temperatures cause stress in poultry, especially for broiler lines, which are genetically selected for rapid muscle growth. RNA-seq technology provides powerful insights into environmental response from a highly metabolic tissue, the liver. We investigated the effects of acute (3 h, 35 °C) and chronic (7d of 35 °C for 7 h/d) heat stress on the liver transcriptome of 3-week-old chicks of a heat-susceptible broiler line, a heat-resistant Fayoumi line, and their advanced intercross line (AIL). Results: Transcriptome sequencing of 48 male chickens using Illumina HiSeq 2500 technology yielded an average of 33.9 million, 100 base-pair, single-end reads per sample. There were 8 times more differentially expressed genes (DEGs) (FDR < 0.05) in broilers (n = 627) than Fayoumis (n = 78) when comparing the acute-heat samples to the control (25 °C) samples. Contrasting genetic lines under similar heat treatments, the highest number of DEGs appeared between Fayoumi and broiler lines. Principal component analysis of gene expression and analysis of the number of DEGs suggested that the AIL had a transcriptomic response more similar to the Fayoumi than the broiler line during acute heat stress. The number of DEGs also suggested that acute heat stress had greater impact on the broiler liver transcriptome than chronic heat stress. The angiopoietin-like 4 (ANGPTL4) gene was identified as differentially expressed among all 6 contrasts. Ingenuity Pathway Analysis (IPA) created a novel network that combines the heat shock protein family with immune response genes.

Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences

Background: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed... more Background: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within-and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation.

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

by M. Nefedov and Carl Schmidt

PLoS Biology, 2010

A synergistic combination of two next-generation sequencing platforms with a detailed comparative... more A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (,1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Identification of quantitative trait loci for body temperature, body weight, breast yield, and digestibility in an advanced intercross line of chickens under heat stress

Background: Losses in poultry production due to heat stress have considerable negative economic c... more Background: Losses in poultry production due to heat stress have considerable negative economic consequences. Previous studies in poultry have elucidated a genetic influence on response to heat. Using a unique chicken genetic resource, we identified genomic regions associated with body temperature (BT), body weight (BW), breast yield, and digestibility measured during heat stress. Identifying genes associated with a favorable response during high ambient temperature can facilitate genetic selection of heat-resilient chickens. Methods: Generations F18 and F19 of a broiler (heat-susceptible) × Fayoumi (heat-resistant) advanced intercross line (AIL) were used to fine-map quantitative trait loci (QTL). Six hundred and thirty-one birds were exposed to daily heat cycles from 22 to 28 days of age, and phenotypes were measured before heat treatment, on the 1st day and after 1 week of heat treatment. BT was measured at these three phases and BW at pre-heat treatment and after 1 week of heat treatment. Breast muscle yield was calculated as the percentage of BW at day 28. Ileal feed digestibility was assayed from digesta collected from the ileum at day 28. Four hundred and sixty-eight AIL were genotyped using the 600 K Affymetrix chicken SNP (single nucleotide polymorphism) array. Trait heritabilities were estimated using an animal model. A genome-wide association study (GWAS) for these traits and changes in BT and BW was conducted using Bayesian analyses. Candidate genes were identified within 200-kb regions around SNPs with significant association signals. Results: Heritabilities were low to moderate (0.03 to 0.35). We identified QTL for BT on Gallus gallus chromosome (GGA)14, 15, 26, and 27; BW on GGA1 to 8, 10, 14, and 21; dry matter digestibility on GGA19, 20 and 21; and QTL of very large effect for breast muscle yield on GGA1, 15, and 22 with a single 1-Mb window on GGA1 explaining more than 15 % of the genetic variation. Conclusions: This is the first study to estimate heritabilities and perform GWAS using this AIL for traits measured during heat stress. Significant QTL as well as low to moderate heritabilities were found for each trait, and these QTL may facilitate selection for improved animal performance in hot climatic conditions.

Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress

Background: Heat stress in poultry results in considerable economic losses and is a concern for b... more Background: Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO 2 , pO 2 , base excess, HCO 3 , TCO 2 , K, Na, ionized Ca, hematocrit, hemoglobin, sO 2 , and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. Results: There were significant increases in pH, base excess, HCO 3 , TCO 2 , ionized Ca, hematocrit, hemoglobin, and sO 2 , and significant decreases in pCO 2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12–14, 17, 18, 21–28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress. Conclusions: The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.

Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array

Background: Indigenous populations of animals have developed unique adaptations to their local en... more Background: Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study's goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments. Results: Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0. 15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions. Conclusions: The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture.

Distinct functional responses to stressors of bone marrow derived dendritic cells from diverse inbred chicken lines

Differences in responses of chicken bone marrow derived dendritic cells (BMDC) to in vitro treatm... more Differences in responses of chicken bone marrow derived dendritic cells (BMDC) to in vitro treatment with lipopolysaccharide (LPS), heat, and LPS þ heat were identified. The Fayoumi is more disease resistant and heat tolerant than the Leghorn line. Nitric Oxide (NO) production, phagocytic ability, MHC II surface expression and mRNA expression were measured. NO was induced in BMDC from both lines in response to LPS and LPS þ heat stimulation; Fayoumi produced more NO with LPS treatment. Fayoumi had higher phagocytic ability and MHC II surface expression. Gene expression for the heat-related genes BAG3, HSP25, HSPA2, and HSPH1 was strongly induced with heat and few differences existed between lines. Expression for the immune-related genes CCL4, CCL5, CD40, GM-CSF, IFN-g, IL-10, IL-12b, IL-1b, IL-6, IL-8, and iNOS was highly induced in response to LPS and different between lines. This research contributes to the sparse knowledge of genetic differences in chicken BMDC biology and function.

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

by Jacqueline Smith and Carl Schmidt

PLoS Biology, 2010

A synergistic combination of two next-generation sequencing platforms with a detailed comparative... more A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Specificity of G protein β and γ subunit interactions

Journal of Biological Chemistry

Multiple heterotrimeric guanine nucleotide binding protein (G protein) subunits have evolved to c... more Multiple heterotrimeric guanine nucleotide binding protein (G protein) subunits have evolved to couple a large variety of receptors to intracellular effectors. G protein beta gamma subunits are essential for efficient coupling of alpha subunits to receptors, and they are also important for modulation of effectors. Several different beta and gamma subunits exist, but it is not known whether all possible combinations of beta and gamma can form functional dimers. To answer this question, we have compared the ability of in vitro translated beta 1, beta 2, and beta 3 to form dimers with either gamma 1 or gamma 2. Dimerization was monitored by gel filtration, resistance to tryptic digestion, and chemical cross-linking. The results indicate that beta 1 binds both gamma subunits, beta 2 binds only gamma 2, and beta 3 will bind neither gamma 1 or gamma 2. Hence, the occurrence of beta gamma dimers may be partially regulated by the ability of the subunits to associate. Specificity of dimeriza...

PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways

by Liang Sun, Carl Schmidt, and Yongnan Zhu

BMC bioinformatics, 2015

High-throughput methods are generating biological data on a vast scale. In many instances, genomi... more High-throughput methods are generating biological data on a vast scale. In many instances, genomic, transcriptomic, and proteomic data must be interpreted in the context of signaling and metabolic pathways to yield testable hypotheses. Since humans can interpret visual information rapidly, a means for interactive visual exploration that lets biologists interpret such data in a comprehensive and exploratory manner would be invaluable. However, humans have limited memory capacity. Current visualization tools have limited viewing and manipulation capabilities to address complex data analysis problems, and visual exploratory tools are needed to reduce the high mental workload imposed on biologists. We present PathRings, a new interactive web-based, scalable biological pathway visualization tool for biologists to explore and interpret biological pathways. PathRings integrates metabolic and signaling pathways from Reactome in a single compound graph visualization, and uses color to highli...

The G protein gamma subunit. Requirements for dimerization with beta subunits

The Journal of biological chemistry, Jan 30, 1995

Guanine nucleotide-binding protein beta and gamma subunits form a tightly bound complex that can ... more Guanine nucleotide-binding protein beta and gamma subunits form a tightly bound complex that can only be separated by denaturation. Assembly of beta and gamma subunits is a complicated process. The beta 1 and gamma 2 subunits can be synthesized in vitro in rabbit reticulocyte lysate and then assembled into dimers, but beta 1 cannot form beta gamma dimers when synthesized in a wheat germ extract. In contrast, gamma 2 translated in either system can dimerize with beta 1, suggesting that dimerization-competent gamma 2 can be synthesized without the aid of specific chaperonins or other cofactors. Dimerization-competent gamma 2 in solution forms an asymmetric particle with a Stokes radius of about 21 +/- 0.4 A (n = 4), s20,w of 0.9 S (range 0.8-1.0 S, n = 2), and frictional ratio of 1.57 (assuming no hydration). To define the part of gamma 2 that is needed for native beta gamma dimer formation, a series of N- and C-terminal truncations were generated, synthesized in vitro, and incubated ...

Heart Transcriptome Response of Fast-versus Slow-growing Broilers under Heat Stress

by Jibin Zhang and Carl Schmidt

Modern broilers with rapid growth and large body size are highly susceptible to heart failure due... more Modern broilers with rapid growth and large body size are highly susceptible to heart failure due to imbalanced development of hearts relative to muscle. When exposed to high temperature, broilers have increased mortality due to cardiovascular dysfunction. To improve cardiac function of modern broilers under heat stress through breeding, we must identify significant genes and critical pathways that are responsible for susceptibility to heat stress. We compared cardiac transcriptome response to heat stress in a modern broiler line with fast growth rate (Ross 708) and a legacy broiler line with slow growth rate (Illinois). After heat stress treatment at 39℃ for 8 hours/day from 21 days to 42 days posthatch, only the Ross broilers showed reduced normalized heart weight compared to the control-temperature group at the same age. In RNAseq study of left ventricles, 325 differentially expressed (DE) genes were found between the heat stress and control group of Ross broilers, but only 3 DE genes were found in Illinois broilers. Ingenuity pathway analysis indicates significant downregulation (P<0.05) of multiple regulator effects involved in cell proliferation, cell movement, angiogenesis and quantity of immune cells, and upregulation of regulator effects involved in cardiac hypertrophy, heart contraction and heart rate in Ross broilers under heat stress compared to control temperature. In addition, the comparisons between the two broiler lines indicates that cell cycle activity is higher in Ross than in Illinois birds under normal temperature, but lower in Ross than in Illinois under heat stress. Among the top ranked canonical pathways, mitotic role of polo-like kinase pathway is the most significant one in all comparisons. This result indicates that the increased susceptibility to heart failure of modern broilers under heat stress may be due to impaired heart development induced by retarded cell cycle activity, thus revealing a potential target for genetic improvement.

Different Cardiac Development Revealed by Transcriptomic Analysis between Legacy and Modern Broiler Chickens

by Jibin Zhang, Carl Schmidt, and Susan Lamont

Fast-growing modern broilers are susceptible to cardiac arrhythmia and heart failure. To understa... more Fast-growing modern broilers are susceptible to cardiac arrhythmia and heart failure. To understand the developmental regulation related to these problems, cardiac gene expression in Illinois and Ross broilers was investigated at 6 and 21 days post hatch (dph) using RNA-seq (n=5-6 for each group). Because Illinois is a legacy broiler line with isometric heart growth, and Ross is a modern broiler line with a negative allometric heart growth, comparison of gene expression between the two lines and the two time points provides an avenue to understand genetic regulation underlying their different cardiac development.
Sequence data were mapped to the Galgal5 reference genome and differential expression analysis was performed using edgeR software, with false discovery rate (FDR) < 0.05 and Log2 fold change (Log2FC) > 1. A total of 501 and 388 differentially expressed genes (DEGs) were found between times in Ross and Illinois broilers, respectively, with 138 DEGs shared between the two lines. A total of 170 and 210 DEGs were found between the broiler lines at 6 and 21 dph, respectively, with 28 DEGs shared between the two time points. Among these DEGs, granzyme K always showed the highest, and hemoglobin the lowest, Log2FC in the 21 dph vs. 6 dph contrast. Ribosome Assembly Factor MRTO4 always showed distinctly higher expression in Ross than Illinois broilers.
Ingenuity Pathway Analysis (IPA) predicted development of immune cells from 6 to 21 dph in both broiler lines. A significant decrease in cell proliferation was predicted in Ross but not Illinois broilers from 6 to 21 dph. Cell quantity, apoptosis, and activation of immune cells were all predicted to be higher in Ross than Illinois broilers at 6 dph, whereas only differentiation of connective tissue cells was predicted to be higher in Ross than Illinois broilers at 21 dph. These identified DEGs and pathways related to cardiac development provide potential targets for improving cardiac function in modern broilers through breeding for favorable genetic variants.

Gene Expression Response to Heat Stress in Two Broiler Lines

by Jibin Zhang, Carl Schmidt, and Susan Lamont

The fast growth rate and increased body weight of modern broilers makes them susceptible to heart... more The fast growth rate and increased body weight of modern broilers makes them susceptible to heart failure and sensitive to heat stress. To find the genetic causes of these problems, gene expression was measured in hearts of two broiler lines that differed in their response to heat stress.
Each line was separated into two groups that were kept under heat stress or at ambient temperature. The comparison of gene expression between the two lines and heat
treatments suggests that expression of 325 genes were significantly changed in modern broilers under heat stress, while only 3 genes changed their expression in heritage broilers that adapt well to heat stress. Through identification of genes that regulate cardiac response to heat stress in different broiler lines, we can find potential ways to breed heat-tolerant broilers to mitigate both poverty in Africa and the effects of climate change on the global broiler industry.