Susan Lamont - Academia.edu (original) (raw)

Papers by Susan Lamont

Identification of specific gene or quantitative trait locus that responds to specific stimulus is... more Identification of specific gene or quantitative trait locus that responds to specific stimulus is an important goal for genetic improvement programs. In a heat stress experiment with 3 distinct chicken lines, we found Angiopoietin-like 4 (ANGPTL4) to be differentially expressed in all 3 lines during acute and chronic heat stress. This outcome suggests the need to further explore ANGPTL4 as a potential candidate gene for selection to improve chicken response to heat stress.

Bone marrow antigen presenting cells (BM-APC), from Fayoumis (disease resistant and heat tolerant... more Bone marrow antigen presenting cells (BM-APC), from Fayoumis (disease resistant and heat tolerant) and Leghorn (disease susceptible) chicken lines were evaluated for response to an inflammatory stimulus and heat stress. BM-APC from Fayoumis produced more nitric oxide (NO) and had higher Major Histocompatibility Complex (MHC) class II cell surface expression compared to those from Leghorn, indicating that BM-APC studied in vitro may be a useful tool to evaluate molecular effects of disease and/or heat tolerance in chickens.

 As a major infectious disease in poultry, Newcastle disease has caused: I. Considerable economi... more  As a major infectious disease in poultry, Newcastle disease has caused: I. Considerable economic loss in poultry industry worldwide II. Serious problem in some rural areas where chickens are a significant source of income and nutrition [1]  Vaccination is an important strategy to prevent the disease but is not always executable or effective due to: I. Lack of cold chain and proper management in rural communities in African and Asia [2] II. Evolution and diversity of Newcastle disease virus (NDV) [3]  Selection and breeding provides a promising approach to enhance resistance to the disease so that [4] I. Global poultry industry productivity will be increased II. Poverty and food insecurity in developing countries will be alleviated  Two objectives of this study: I. Identify genes and pathways regulating host response to NDV II. Identify genes and pathways related to distinct genetic resistance between the two inbred chicken lines

and Implications Heat stress (HS) is a major environmental stressor to chickens because chickens ... more and Implications Heat stress (HS) is a major environmental stressor to chickens because chickens lack sufficient physical ability to mitigate heat. One of the potential results of heat stress is the "leaky gut syndrome", which allows gut bacteria to escape into the host and release toxins including lipopolysaccharide (LPS). To model the chicken immune response to bacteria toxins under heat stress, a chicken macrophage-like cell line, HD11, was subjected to HS, LPS, or HS + LPS treatments. Expression of a gene panel of heat shock proteins, stressrelated molecules, signaling molecules, and immune response molecules were measured and analyzed at 4 time points across the 3 conditions. As expected, heat shock proteins and immune response molecules increased in expression during HS and LPS challenge, respectively. Treatment of HS + LPS increased the expression of these responsive genes even more than either treatment alone. This suggests that heat stress proteins not only mitigate heat stress, but also trigger a higher level of immune response in chickens.

and Implications Selection of chickens for resilience to heat stress could be a valid strategy to... more and Implications Selection of chickens for resilience to heat stress could be a valid strategy to reduce the negative economic impact of climate change. A heat-susceptible broiler line and a heat-resistant Fayoumi line were evaluated for response to heat stress using RNA-seq technology. We found that 278 genes were differentially expressed (False Discovery Rate (FDR) <0.05) between broilers and Fayoumi that were subjected to high ambient temperatures. GO Term Finder analysis revealed that differentially expressed genes (DEGs) were enriched in biological regulation process and catalytic activity function. Many novel key genes and biological networks related to heat stress response were identified and may be biomarkers used to breed chickens that are better able to adapt to heat stress.

The liver plays a variety of roles in energy metabolism, digestion, and immune response. During t... more The liver plays a variety of roles in energy metabolism, digestion, and immune response. During the challenge by an environmental stressor, such as heat, the liver is one of the key organs that determines the chicken's ability to cope with the hostile environment. Sequencing RNA extracted from liver samples from a heat-susceptible broiler line and a heatresistant Fayoumi line, we have identified a set of genes that were differentially expressed due to an acute heat stress challenge. Analysis of these genes in context of the biological pathways showed opposite responses by the broiler and Fayoumi chickens, but there was activation of immune signaling pathways for both lines. This result suggests that despite mechanistic differences in heat stress response, selection for improvement in heat tolerance may also cause alteration to immune response.

and Implications As one of the most severe infectious diseases in the poultry industry, Newcastle... more and Implications As one of the most severe infectious diseases in the poultry industry, Newcastle disease (ND) causes a significant economic loss worldwide even with the extensive implementation of vaccine. To find targets to improve genetic resistance to ND to enhance protection in chickens, gene expression was analyzed in spleen of two chicken lines which differed in their resistance to ND. The comparison of gene expression between two treatments (challenged or non-challenged) in the two chicken lines at 2 and 6 days post-inoculation (dpi) suggests that that the most dramatic changes of gene expression occurred in Leghorn chickens at 2dpi. The identified differentially expressed genes that regulate splenic response to NDV provide potential avenues to breed NDV-resistant chickens in the future.

PLOS ONE, Sep 23, 2019

The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, how... more The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome. Given the ability of RNA-seq to reveal active regions of the genome, detection of RNA-seq SNPs can prove valuable in understanding the phenotypic diversity between populations. Thus, we present a novel computational workflow named VAP (Variant Analysis Pipeline) that takes advantage of multiple RNA-seq splice aware aligners to call SNPs in non-human models using RNA-seq data only. We applied VAP to RNA-seq from a highly inbred chicken line and achieved high accuracy when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post transcriptional modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. The source code and user manuals are available at https://modupeore.github.io/VAP/.

Poultry Science, Oct 1, 2015

Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of Effects of dieta... more Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks broiler and laying-hen chicks

Poultry Science, Oct 1, 1991

Three in vivo assays were used to measure the immunocompetence of chickens in two generations of ... more Three in vivo assays were used to measure the immunocompetence of chickens in two generations of a selection experiment. The obtained data were used to estimate the variance components for sire and dam for antibody production to Pasteurella multocida and Mycoplasma gallisepticum vaccines, for Tcell-mediated immunity evaluated by a phytohemagglutinin wing web assay, and for clearance of foreign particles from the circulatory system. Heritabilities of and genetic correlations among these immunological traits were calculated from the sire variance components. Heritability estimates of the immunological traits based on the sire component of variance ranged from .06 to .53, and genetic correlations among immunological traits were generally negative.

Poultry Science, Apr 1, 1989

Body weights at 8, 20, and 32 wk, total egg production, average egg weight, egg production during... more Body weights at 8, 20, and 32 wk, total egg production, average egg weight, egg production during a 4-wk period, and age at first egg laid were measured in 652 female progeny of heterozygous × heterozygous (F1) or heterozygous × homozygous (backcross) matings of the Iowa State University S1 White Leghorn chicken line. Hens were classified by B-haplotypes (B1 or B19) and haplotype-associated immune responses (high or low) to the amino acid polymer glutamic acid-alanine-tyrosine (Ir-GAT). Body weights were affected by parental mating group, sire, and dam, but they were not affected by haplotype (B/Ir-GAT). Sexual maturity and egg production were not affected by any factors except hatch. Average egg weight was affected by parental mating group, sire, dam, and genotype, with homozygous B19B19 birds having a heavier mean egg weight (41.71 g ± .20) than homozygous B1B1Ir-GAT-high and-low birds (40.8 g ± .38 and 39.2 g ± .54, respectively); mean egg weights of heterozygous birds were approximately intermediate to the others.

The effects of increasing concentrations of dietary fiber through the addition of dried distiller... more The effects of increasing concentrations of dietary fiber through the addition of dried distiller's grains with solubles (DDGS) and wheat bran to a corn-soy bean meal were evaluated for commercial broiler and layer chicks separated into 4 groups during a 21 d trial. Diets were formulated to be isocaloric and meet or exceed nutrient recommendations. Birds had unlimited access to feed and water. The increased dietary fiber had opposite effects on the production of short chain fatty acids for broilers and layers due to differences of the microbial community in the ceca. The change also included signs of decreased cecal health of the chicks, suggesting that it is not a good idea to increase dietary fiber past nutrient recommendations in chicken feed.

Developmental and Comparative Immunology, Oct 1, 2016

BMC Genomics, Nov 22, 2016

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. Conclusions: This study extends our understanding of the liver transcriptome response to different heat exposure treatments in distinct genetic chicken lines and provides information necessary for breeding birds to be more resilient to the negative impacts of heat. The data strongly suggest ANGPTL4 as a candidate gene for improvement of heat tolerance in chickens.

PLOS ONE, Oct 13, 2016

Acute heat stress requires immediate adjustment of the stressed individual to sudden changes of a... more Acute heat stress requires immediate adjustment of the stressed individual to sudden changes of ambient temperatures. Chickens are particularly sensitive to heat stress due to development of insufficient physiological mechanisms to mitigate its effects. One of the symptoms of heat stress is endotoxemia that results from release of the lipopolysaccharide (LPS) from the guts. Heat-related cytotoxicity is mitigated by the innate immune system, which is comprised mostly of phagocytic cells such as monocytes and macrophages. The objective of this study was to analyze the molecular responses of the chicken macrophagelike HD11 cell line to combined heat stress and lipopolysaccharide treatment in vitro. The cells were heat-stressed and then allowed a temperature-recovery period, during which the gene expression was investigated. LPS was added to the cells to mimic the heat-stressrelated endotoxemia. Semi high-throughput gene expression analysis was used to study a gene panel comprised of heat shock proteins, stress-related genes, signaling molecules and immune response genes. HD11 cell line responded to heat stress with increased mRNA abundance of the HSP25, HSPA2 and HSPH1 chaperones as well as DNAJA4 and DNAJB6 co-chaperones. The anti-apoptotic gene BAG3 was also highly up-regulated, providing evidence that the cells expressed pro-survival processes. The immune response of the HD11 cell line to LPS in the heat stress environment (up-regulation of CCL4, CCL5, IL1B, IL8 and iNOS) was higher than in thermoneutral conditions. However, the peak in the transcriptional regulation of the immune genes was after two hours of temperature-recovery. Therefore, we propose the potential influence of the extracellular heat shock proteins not only in mitigating effects of abiotic stress but also in triggering the higher level of the immune responses. Finally, use of correlation networks for the data analysis aided in discovering subtle differences in the gene expression (i.e. the role of the CASP3 and CASP9 genes).

PLOS ONE, Jul 31, 2017

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.

Journal of Molecular Endocrinology, 2017

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.

Research Square (Research Square), Feb 22, 2023

Background Poultry production is vulnerable to increasing temperatures in terms of animal welfare... more Background Poultry production is vulnerable to increasing temperatures in terms of animal welfare and in economic losses. With the predicted increase in global temperature and the number and severity of heat waves, it is important to understand how chickens raised for food respond to heat stress. This knowledge can be used to determine how to select chickens that are adapted to thermal challenge. As neuroendocrine organs, the hypothalamus and pituitary provide systemic regulation of the heat stress response. Methods and Results Here we report a transcriptome analysis of the pituitary response to acute heat stress. Chickens were stressed for 2 hours at 35˚C (HS) and transcriptomes compared with birds maintained in thermoneutral temperatures (25˚C). Conclusions The observations were evaluated in the context of ontology terms and pathways to describe the pituitaries response to heat stress. The pituitaries of heat stressed birds exhibited responses to hyperthermia through altered expression of genes coding for chaperones, cell cycle regulators, cholesterol synthesis, transcription factors, along with the secreted peptide hormones. prolactin, and proopiomelanocortin.

Identification of specific gene or quantitative trait locus that responds to specific stimulus is... more Identification of specific gene or quantitative trait locus that responds to specific stimulus is an important goal for genetic improvement programs. In a heat stress experiment with 3 distinct chicken lines, we found Angiopoietin-like 4 (ANGPTL4) to be differentially expressed in all 3 lines during acute and chronic heat stress. This outcome suggests the need to further explore ANGPTL4 as a potential candidate gene for selection to improve chicken response to heat stress.

Bone marrow antigen presenting cells (BM-APC), from Fayoumis (disease resistant and heat tolerant... more Bone marrow antigen presenting cells (BM-APC), from Fayoumis (disease resistant and heat tolerant) and Leghorn (disease susceptible) chicken lines were evaluated for response to an inflammatory stimulus and heat stress. BM-APC from Fayoumis produced more nitric oxide (NO) and had higher Major Histocompatibility Complex (MHC) class II cell surface expression compared to those from Leghorn, indicating that BM-APC studied in vitro may be a useful tool to evaluate molecular effects of disease and/or heat tolerance in chickens.

 As a major infectious disease in poultry, Newcastle disease has caused: I. Considerable economi... more  As a major infectious disease in poultry, Newcastle disease has caused: I. Considerable economic loss in poultry industry worldwide II. Serious problem in some rural areas where chickens are a significant source of income and nutrition [1]  Vaccination is an important strategy to prevent the disease but is not always executable or effective due to: I. Lack of cold chain and proper management in rural communities in African and Asia [2] II. Evolution and diversity of Newcastle disease virus (NDV) [3]  Selection and breeding provides a promising approach to enhance resistance to the disease so that [4] I. Global poultry industry productivity will be increased II. Poverty and food insecurity in developing countries will be alleviated  Two objectives of this study: I. Identify genes and pathways regulating host response to NDV II. Identify genes and pathways related to distinct genetic resistance between the two inbred chicken lines

and Implications Heat stress (HS) is a major environmental stressor to chickens because chickens ... more and Implications Heat stress (HS) is a major environmental stressor to chickens because chickens lack sufficient physical ability to mitigate heat. One of the potential results of heat stress is the "leaky gut syndrome", which allows gut bacteria to escape into the host and release toxins including lipopolysaccharide (LPS). To model the chicken immune response to bacteria toxins under heat stress, a chicken macrophage-like cell line, HD11, was subjected to HS, LPS, or HS + LPS treatments. Expression of a gene panel of heat shock proteins, stressrelated molecules, signaling molecules, and immune response molecules were measured and analyzed at 4 time points across the 3 conditions. As expected, heat shock proteins and immune response molecules increased in expression during HS and LPS challenge, respectively. Treatment of HS + LPS increased the expression of these responsive genes even more than either treatment alone. This suggests that heat stress proteins not only mitigate heat stress, but also trigger a higher level of immune response in chickens.

and Implications Selection of chickens for resilience to heat stress could be a valid strategy to... more and Implications Selection of chickens for resilience to heat stress could be a valid strategy to reduce the negative economic impact of climate change. A heat-susceptible broiler line and a heat-resistant Fayoumi line were evaluated for response to heat stress using RNA-seq technology. We found that 278 genes were differentially expressed (False Discovery Rate (FDR) <0.05) between broilers and Fayoumi that were subjected to high ambient temperatures. GO Term Finder analysis revealed that differentially expressed genes (DEGs) were enriched in biological regulation process and catalytic activity function. Many novel key genes and biological networks related to heat stress response were identified and may be biomarkers used to breed chickens that are better able to adapt to heat stress.

The liver plays a variety of roles in energy metabolism, digestion, and immune response. During t... more The liver plays a variety of roles in energy metabolism, digestion, and immune response. During the challenge by an environmental stressor, such as heat, the liver is one of the key organs that determines the chicken's ability to cope with the hostile environment. Sequencing RNA extracted from liver samples from a heat-susceptible broiler line and a heatresistant Fayoumi line, we have identified a set of genes that were differentially expressed due to an acute heat stress challenge. Analysis of these genes in context of the biological pathways showed opposite responses by the broiler and Fayoumi chickens, but there was activation of immune signaling pathways for both lines. This result suggests that despite mechanistic differences in heat stress response, selection for improvement in heat tolerance may also cause alteration to immune response.

and Implications As one of the most severe infectious diseases in the poultry industry, Newcastle... more and Implications As one of the most severe infectious diseases in the poultry industry, Newcastle disease (ND) causes a significant economic loss worldwide even with the extensive implementation of vaccine. To find targets to improve genetic resistance to ND to enhance protection in chickens, gene expression was analyzed in spleen of two chicken lines which differed in their resistance to ND. The comparison of gene expression between two treatments (challenged or non-challenged) in the two chicken lines at 2 and 6 days post-inoculation (dpi) suggests that that the most dramatic changes of gene expression occurred in Leghorn chickens at 2dpi. The identified differentially expressed genes that regulate splenic response to NDV provide potential avenues to breed NDV-resistant chickens in the future.

PLOS ONE, Sep 23, 2019

The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, how... more The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome. Given the ability of RNA-seq to reveal active regions of the genome, detection of RNA-seq SNPs can prove valuable in understanding the phenotypic diversity between populations. Thus, we present a novel computational workflow named VAP (Variant Analysis Pipeline) that takes advantage of multiple RNA-seq splice aware aligners to call SNPs in non-human models using RNA-seq data only. We applied VAP to RNA-seq from a highly inbred chicken line and achieved high accuracy when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post transcriptional modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. The source code and user manuals are available at https://modupeore.github.io/VAP/.

Poultry Science, Oct 1, 2015

Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of Effects of dieta... more Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks broiler and laying-hen chicks

Poultry Science, Oct 1, 1991

Three in vivo assays were used to measure the immunocompetence of chickens in two generations of ... more Three in vivo assays were used to measure the immunocompetence of chickens in two generations of a selection experiment. The obtained data were used to estimate the variance components for sire and dam for antibody production to Pasteurella multocida and Mycoplasma gallisepticum vaccines, for Tcell-mediated immunity evaluated by a phytohemagglutinin wing web assay, and for clearance of foreign particles from the circulatory system. Heritabilities of and genetic correlations among these immunological traits were calculated from the sire variance components. Heritability estimates of the immunological traits based on the sire component of variance ranged from .06 to .53, and genetic correlations among immunological traits were generally negative.

Poultry Science, Apr 1, 1989

Body weights at 8, 20, and 32 wk, total egg production, average egg weight, egg production during... more Body weights at 8, 20, and 32 wk, total egg production, average egg weight, egg production during a 4-wk period, and age at first egg laid were measured in 652 female progeny of heterozygous × heterozygous (F1) or heterozygous × homozygous (backcross) matings of the Iowa State University S1 White Leghorn chicken line. Hens were classified by B-haplotypes (B1 or B19) and haplotype-associated immune responses (high or low) to the amino acid polymer glutamic acid-alanine-tyrosine (Ir-GAT). Body weights were affected by parental mating group, sire, and dam, but they were not affected by haplotype (B/Ir-GAT). Sexual maturity and egg production were not affected by any factors except hatch. Average egg weight was affected by parental mating group, sire, dam, and genotype, with homozygous B19B19 birds having a heavier mean egg weight (41.71 g ± .20) than homozygous B1B1Ir-GAT-high and-low birds (40.8 g ± .38 and 39.2 g ± .54, respectively); mean egg weights of heterozygous birds were approximately intermediate to the others.

The effects of increasing concentrations of dietary fiber through the addition of dried distiller... more The effects of increasing concentrations of dietary fiber through the addition of dried distiller's grains with solubles (DDGS) and wheat bran to a corn-soy bean meal were evaluated for commercial broiler and layer chicks separated into 4 groups during a 21 d trial. Diets were formulated to be isocaloric and meet or exceed nutrient recommendations. Birds had unlimited access to feed and water. The increased dietary fiber had opposite effects on the production of short chain fatty acids for broilers and layers due to differences of the microbial community in the ceca. The change also included signs of decreased cecal health of the chicks, suggesting that it is not a good idea to increase dietary fiber past nutrient recommendations in chicken feed.

Developmental and Comparative Immunology, Oct 1, 2016

BMC Genomics, Nov 22, 2016

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. Conclusions: This study extends our understanding of the liver transcriptome response to different heat exposure treatments in distinct genetic chicken lines and provides information necessary for breeding birds to be more resilient to the negative impacts of heat. The data strongly suggest ANGPTL4 as a candidate gene for improvement of heat tolerance in chickens.

PLOS ONE, Oct 13, 2016

Acute heat stress requires immediate adjustment of the stressed individual to sudden changes of a... more Acute heat stress requires immediate adjustment of the stressed individual to sudden changes of ambient temperatures. Chickens are particularly sensitive to heat stress due to development of insufficient physiological mechanisms to mitigate its effects. One of the symptoms of heat stress is endotoxemia that results from release of the lipopolysaccharide (LPS) from the guts. Heat-related cytotoxicity is mitigated by the innate immune system, which is comprised mostly of phagocytic cells such as monocytes and macrophages. The objective of this study was to analyze the molecular responses of the chicken macrophagelike HD11 cell line to combined heat stress and lipopolysaccharide treatment in vitro. The cells were heat-stressed and then allowed a temperature-recovery period, during which the gene expression was investigated. LPS was added to the cells to mimic the heat-stressrelated endotoxemia. Semi high-throughput gene expression analysis was used to study a gene panel comprised of heat shock proteins, stress-related genes, signaling molecules and immune response genes. HD11 cell line responded to heat stress with increased mRNA abundance of the HSP25, HSPA2 and HSPH1 chaperones as well as DNAJA4 and DNAJB6 co-chaperones. The anti-apoptotic gene BAG3 was also highly up-regulated, providing evidence that the cells expressed pro-survival processes. The immune response of the HD11 cell line to LPS in the heat stress environment (up-regulation of CCL4, CCL5, IL1B, IL8 and iNOS) was higher than in thermoneutral conditions. However, the peak in the transcriptional regulation of the immune genes was after two hours of temperature-recovery. Therefore, we propose the potential influence of the extracellular heat shock proteins not only in mitigating effects of abiotic stress but also in triggering the higher level of the immune responses. Finally, use of correlation networks for the data analysis aided in discovering subtle differences in the gene expression (i.e. the role of the CASP3 and CASP9 genes).

PLOS ONE, Jul 31, 2017

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.

Journal of Molecular Endocrinology, 2017

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.

Research Square (Research Square), Feb 22, 2023

Background Poultry production is vulnerable to increasing temperatures in terms of animal welfare... more Background Poultry production is vulnerable to increasing temperatures in terms of animal welfare and in economic losses. With the predicted increase in global temperature and the number and severity of heat waves, it is important to understand how chickens raised for food respond to heat stress. This knowledge can be used to determine how to select chickens that are adapted to thermal challenge. As neuroendocrine organs, the hypothalamus and pituitary provide systemic regulation of the heat stress response. Methods and Results Here we report a transcriptome analysis of the pituitary response to acute heat stress. Chickens were stressed for 2 hours at 35˚C (HS) and transcriptomes compared with birds maintained in thermoneutral temperatures (25˚C). Conclusions The observations were evaluated in the context of ontology terms and pathways to describe the pituitaries response to heat stress. The pituitaries of heat stressed birds exhibited responses to hyperthermia through altered expression of genes coding for chaperones, cell cycle regulators, cholesterol synthesis, transcription factors, along with the secreted peptide hormones. prolactin, and proopiomelanocortin.

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.

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.

Prolonged exposure to high temperature can significantly increase metabolism, depress appetite, r... more Prolonged exposure to high temperature can significantly increase metabolism, depress appetite, reduce meat production and raise mortality in broilers. Because the cardiovascular system plays an important role to dissipate heat and transport oxygen, strong cardiac function is indispensable for birds to survive under heat stress. However, due to small hearts relative to body weight, modern broilers have high risk of heart failure at high temperature.

In this study, a Ross 708 line (modern broilers) and a Heritage broiler line (relaxed selection since the 1950s) were subjected to heat stress at 35℃ for 7 hours/day from 21 to 42 days posthatch and compared to control groups kept at ambient temperature. Twenty-three libraries generated from left ventricles averaged 10 million 50-base pair single-end reads after transcriptome sequencing, trimming and filtering.

After differential expression analysis, more than 300 differentially expressed genes between heat-stressed and control birds were identified in modern broilers, while only three genes were differentially expressed in heritage broilers at a significance level of False Discovery Rate (FDR)<0.1 and log2 fold-change (LFC)>1. By Ingenuity Pathway Analysis (IPA), the significantly differentially expressed genes in modern broilers are mainly involved in apoptosis, cell proliferation, cell migration and inflammatory response. In heart disease, those genes are highly related to ventricular hypotrophy, cardiac arrhythmia and tachycardia. This information provides insights into mechanisms of susceptibility of modern broilers’ heart to heat stress and a foundation for future genomic selection in broilers to improve their adaptation to global climate change.