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Kaur G, Quilici DR, Woolsey RJ, Petereit J, Nuss AB. Starvation-Induced Changes to the Midgut Proteome and Neuropeptides in Manduca sexta. Insects 2024; 15:325. [PMID: 38786882 DOI: 10.3390/insects15050325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
Starvation is a complex physiological state that induces changes in protein expression to ensure survival. The insect midgut is sensitive to changes in dietary content as it is at the forefront of communicating information about incoming nutrients to the body via hormones. Therefore, a DIA proteomics approach was used to examine starvation physiology and, specifically, the role of midgut neuropeptide hormones in a representative lepidopteran, Manduca sexta. Proteomes were generated from midguts of M. sexta fourth-instar caterpillars, starved for 24 h and 48 h, and compared to fed controls. A total of 3047 proteins were identified, and 854 of these were significantly different in abundance. KEGG analysis revealed that metabolism pathways were less abundant in starved caterpillars, but oxidative phosphorylation proteins were more abundant. In addition, six neuropeptides or related signaling cascade proteins were detected. Particularly, neuropeptide F1 (NPF1) was significantly higher in abundance in starved larvae. A change in juvenile hormone-degrading enzymes was also detected during starvation. Overall, our results provide an exploration of the midgut response to starvation in M. sexta and validate DIA proteomics as a useful tool for quantifying insect midgut neuropeptide hormones.
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Affiliation(s)
- Gurlaz Kaur
- Cell and Molecular Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - David R Quilici
- Mick Hitchcock, Ph.D. Nevada Proteomics Center, University of Nevada, Reno, NV 89557, USA
| | - Rebekah J Woolsey
- Mick Hitchcock, Ph.D. Nevada Proteomics Center, University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | - Andrew B Nuss
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada, Reno, NV 89557, USA
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Payen SH, Adhikari K, Petereit J, Uppal T, Rossetto CC, Verma SC. SARS-CoV-2 superinfection in CD14 + monocytes with latent human cytomegalovirus (HCMV) promotes inflammatory cascade. Virus Res 2024; 345:199375. [PMID: 38642618 PMCID: PMC11061749 DOI: 10.1016/j.virusres.2024.199375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), has posed significant challenges to global health. While much attention has been directed towards understanding the primary mechanisms of SARS-CoV-2 infection, emerging evidence suggests co-infections or superinfections with other viruses may contribute to increased morbidity and mortality, particularly in severe cases of COVID-19. Among viruses that have been reported in patients with SARS-CoV-2, seropositivity for Human cytomegalovirus (HCMV) is associated with increased COVID-19 risk and hospitalization. HCMV is a ubiquitous beta-herpesvirus with a seroprevalence of 60-90 % worldwide and one of the leading causes of mortality in immunocompromised individuals. The primary sites of latency for HCMV include CD14+ monocytes and CD34+ hematopoietic cells. In this study, we sought to investigate SARS-CoV-2 infection of CD14+ monocytes latently infected with HCMV. We demonstrate that CD14+ cells are susceptible and permissive to SARS-CoV-2 infection and detect subgenomic transcripts indicative of replication. To further investigate the molecular changes triggered by SARS-CoV-2 infection in HCMV-latent CD14+ monocytes, we conducted RNA sequencing coupled with bioinformatic differential gene analysis. The results revealed significant differences in cytokine-cytokine receptor interactions and inflammatory pathways in cells superinfected with replication-competent SARS-CoV-2 compared to the heat-inactivated and mock controls. Notably, there was a significant upregulation in transcripts associated with pro-inflammatory response factors and a decrease in anti-inflammatory factors. Taken together, these findings provide a basis for the heightened inflammatory response, offering potential avenues for targeted therapeutic interventions among HCMV-infected severe cases of COVID-19. SUMMARY: COVID-19 patients infected with secondary viruses have been associated with a higher prevalence of severe symptoms. Individuals seropositive for human cytomegalovirus (HCMV) infection are at an increased risk for severe COVID-19 disease and hospitalization. HCMV reactivation has been reported in severe COVID-19 cases with respiratory failure and could be the result of co-infection with SARS-CoV-2 and HCMV. In a cell culture model of superinfection, HCMV has previously been shown to increase infection of SARS-CoV-2 of epithelial cells by upregulating the human angiotensin-converting enzyme-2 (ACE2) receptor. In this study, we utilize CD14+ monocytes, a major cell type that harbors latent HCMV, to investigate co-infection of SARS-CoV-2 and HCMV. This study is a first step toward understanding the mechanism that may facilitate increased COVID-19 disease severity in patients infected with SARS-CoV-2 and HCMV.
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Affiliation(s)
- Shannon Harger Payen
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Kabita Adhikari
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Juli Petereit
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, United States
| | - Timsy Uppal
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Cyprian C Rossetto
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Subhash C Verma
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States.
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Petereit J, Lannig G, Baßmann B, Bock C, Buck BH. Circadian rhythm in turbot (Scophthalmus maximus): daily variation of blood metabolites in recirculating aquaculture systems. Metabolomics 2024; 20:23. [PMID: 38347335 PMCID: PMC10861666 DOI: 10.1007/s11306-023-02077-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
INTRODUCTION Animal welfare in aquaculture is becoming increasingly important, and detailed knowledge of the species concerned is essential for further optimization on farms. Every organism is controlled by an internal clock, the circadian rhythm, which is crucial for metabolic processes and is partially influenced by abiotic factors, making it important for aquaculture practices. OBJECTIVE In order to determine the circadian rhythm of adult turbot (Scophthalmus maximus), blood samples were collected over a 24-h period and plasma metabolite profiles were analyzed by 1H-NMR spectroscopy. METHODS The fish were habituated to feeding times at 9 am and 3 pm and with the NMR spectroscopy 46 metabolites could be identified, eight of which appeared to shift throughout the day. RESULTS We noted exceptionally high values around 3 pm for the amino acids isoleucine, leucine, valine, phenylalanine, lysine, and the stress indicator lactate. These metabolic peaks were interpreted as either habituation to the usual feeding time or as natural peak levels in turbot in a 24-h circle because other indicators for stress (glucose, cortisol and lysozymes) showed a stable baseline, indicating that the animals had no or very little stress during the experimental period. CONCLUSION This study provides initial insights into the diurnal variation of metabolites in adult turbot; however, further studies are needed to confirm present findings of possible fluctuations in amino acids and sugars. Implementing optimized feeding times (with high levels of sugars and low levels of stress metabolites) could lead to less stress, fewer disease outbreaks and overall improved fish welfare in aquaculture facilities.
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Affiliation(s)
- J Petereit
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI), Am Handelshafen 12, 27570, Bremerhaven, Germany.
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Aquaculture and Sea-Ranching, Justus-Von-Liebig-Weg 6, 18059, Rostock, Germany.
| | - G Lannig
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI), Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - B Baßmann
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Aquaculture and Sea-Ranching, Justus-Von-Liebig-Weg 6, 18059, Rostock, Germany
| | - C Bock
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI), Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - B H Buck
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI), Am Handelshafen 12, 27570, Bremerhaven, Germany
- University of Applied Sciences Bremerhaven, An Der Karlstadt 8, 27568, Bremerhaven, Germany
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Habibian JS, Bolino M, Qian A, Woolsey R, Quilici D, Petereit J, Ferguson BS. Class I HDAC inhibitors attenuate dexamethasone-induced muscle atrophy via increased protein kinase C (PKC) delta phosphorylation. Cell Signal 2023; 110:110815. [PMID: 37478958 PMCID: PMC10528066 DOI: 10.1016/j.cellsig.2023.110815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Skeletal muscle atrophy is defined by wasting or decrease in muscle mass owing to injury, aging, malnutrition, chronic disuse, or physical consequences of chronic illness. Under normal physiological conditions, a network of signal transduction pathways serves to balance muscle protein synthesis and proteolysis; however, metabolic shifts occur from protein synthesis to protein degradation that leads to a reduction in cross-sectional myofibers and can result in loss of skeletal muscle mass (atrophy) over time. Recent evidence highlights posttranslational modifications (PTMs) such as acetylation and phosphorylation in contractile dysfunction and muscle wasting. Indeed, histone deacetylase (HDAC) inhibitors have been shown to attenuate muscle atrophy and delay muscle damage in response to nutrient deprivation, in models of metabolic dysfunction and genetic models of muscle disease (e.g., muscle dystrophy). Despite our current understanding of lysine acetylation in muscle physiology, a role for HDACs in the regulation of muscle signal transduction remains a 'black box.' Using C2C12 myotubes stimulated with dexamethasone (Dex) as a model of muscle atrophy, we report that protein kinase C delta (PKCδ) phosphorylation decreased at threonine 505 (T505) and serine 643 (S643) in myotubes in response to muscle atrophy; these residues are important for PKCδ activity. Interestingly, PKCδ phosphorylation was restored/increased in myotubes treated with a pan-HDAC inhibitor or a class I selective HDAC inhibitor targeting HDACs1, -2, and - 3 in response to Dex. Moreover, we observed that Dex induced atrophy in skeletal muscle tissue in mice; this reduction in atrophy occurred rapidly, with weight loss noted by day 3 post-Dex and muscle weight loss noted by day 7. Similar to our findings in C2C12 myotubes, Dex attenuated phosphorylation of PKCδ at S643, while HDAC inhibition restored or increased PKCδ phosphorylation at both T505 and S643 in the tibialis anterior. Consistent with this hypothesis, we report that HDAC inhibition could not restore myotube size in response to Dex in the presence of a PKCδ inhibitor or when overexpressing a dominant negative PKCδ. Additionally, the overexpression of a constitutively active PKCδ prevented Dex-induced myotube atrophy. Combined, these data suggest that HDACs regulate muscle physiology via changes in intracellular signaling, namely PKCδ phosphorylation. Whether HDACs regulate PKCδ through canonical (e.g. gene-mediated regulation of phosphatases) or non-canonical (e.g. direct deacetylation of PKCδ to change phosphorylation states) mechanisms remain unclear and future research is needed to clarify this point.
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Affiliation(s)
- Justine S Habibian
- Department of Nutrition, The University of Nevada Reno, Reno, NV 89557, United States of America; Cellular and Molecular Biology, The University of Nevada Reno, Reno, NV 89557, United States of America; Cellular and Molecular Pharmacology and Physiology, The University of Nevada Reno, Reno, NV 89557, USA
| | - Matthew Bolino
- Department of Nutrition, The University of Nevada Reno, Reno, NV 89557, United States of America; Cellular and Molecular Biology, The University of Nevada Reno, Reno, NV 89557, United States of America
| | - Anthony Qian
- Cellular and Molecular Pharmacology and Physiology, The University of Nevada Reno, Reno, NV 89557, USA
| | - Rebekah Woolsey
- Mick Hitchcock, Ph.D. Nevada Proteomics Center (RRID:SCR_017761), The University of Nevada Reno, Reno, NV 89557, USA
| | - David Quilici
- Mick Hitchcock, Ph.D. Nevada Proteomics Center (RRID:SCR_017761), The University of Nevada Reno, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center (RRID:SCR_017802), The University of Nevada Reno, Reno, NV 89557, USA
| | - Bradley S Ferguson
- Department of Nutrition, The University of Nevada Reno, Reno, NV 89557, United States of America; Cellular and Molecular Biology, The University of Nevada Reno, Reno, NV 89557, United States of America; Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, The University of Nevada Reno, Reno, NV 89557, United States of America.
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Chrisman B, He C, Jung JY, Stockham N, Paskov K, Washington P, Petereit J, Wall DP. Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity. Genome Res 2023; 33:1734-1746. [PMID: 37879860 PMCID: PMC10691534 DOI: 10.1101/gr.277175.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 05/25/2023] [Indexed: 10/27/2023]
Abstract
Although it is ubiquitous in genomics, the current human reference genome (GRCh38) is incomplete: It is missing large sections of heterochromatic sequence, and as a singular, linear reference genome, it does not represent the full spectrum of human genetic diversity. To characterize gaps in GRCh38 and human genetic diversity, we developed an algorithm for sequence location approximation using nuclear families (ASLAN) to identify the region of origin of reads that do not align to GRCh38. Using unmapped reads and variant calls from whole-genome sequences (WGSs), ASLAN uses a maximum likelihood model to identify the most likely region of the genome that a subsequence belongs to given the distribution of the subsequence in the unmapped reads and phasings of families. Validating ASLAN on synthetic data and on reads from the alternative haplotypes in the decoy genome, ASLAN localizes >90% of 100-bp sequences with >92% accuracy and ∼1 Mb of resolution. We then ran ASLAN on 100-mers from unmapped reads from WGS from more than 700 families, and compared ASLAN localizations to alignment of the 100-mers to the recently released T2T-CHM13 assembly. We found that many unmapped reads in GRCh38 originate from telomeres and centromeres that are gaps in GRCh38. ASLAN localizations are in high concordance with T2T-CHM13 alignments, except in the centromeres of the acrocentric chromosomes. Comparing ASLAN localizations and T2T-CHM13 alignments, we identified sequences missing from T2T-CHM13 or sequences with high divergence from their aligned region in T2T-CHM13, highlighting new hotspots for genetic diversity.
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Affiliation(s)
- Brianna Chrisman
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA;
- Nevada Bioinformatics Center, University of Nevada, Reno, Nevada 89557, USA
| | - Chloe He
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
| | - Jae-Yoon Jung
- Department of Pediatrics (Systems Medicine), Stanford University, Stanford, California 94305, USA
| | - Nate Stockham
- Department of Neuroscience, Stanford University, Stanford, California 94305, USA
| | - Kelley Paskov
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
| | - Peter Washington
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, Nevada 89557, USA
| | - Dennis P Wall
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
- Department of Pediatrics (Systems Medicine), Stanford University, Stanford, California 94305, USA
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Schneider BS, Petereit J, Zhang L, Voss JG. Crush Injury and Simulated Flight Effects on Muscle Gene Expression in Female Mice. Nurs Res 2023; 72:363-370. [PMID: 37625178 PMCID: PMC10542909 DOI: 10.1097/nnr.0000000000000667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND Aeromedical evacuation provides critical care during long-distance transport of injured victims between medical facilities. Often, these victims sustain muscle trauma related to mechanical insults, such as crush. Understanding the effects of flight on injured muscle is important because the aircraft cabin represents an external environment with mild hypoxia-the cabin's altitude is 2,438 m instead of sea level. Because mild hypobaric hypoxia can alter gene expression in normal muscle and affect recovery patterns, it is beneficial to examine whether this type of hypoxia may also alter injury-related genes. OBJECTIVE The objective of this study was to verify the hypothesis that differential gene expression occurs in response to mild hypobaric hypoxia exposure in crush-injured muscle during two early recovery (preregeneration stage) time points. METHODS Twenty-four female mice were anesthetized, and the right gastrocnemius muscle underwent crush injury. Approximately 24 hours later, mice were exposed to normobaric normoxia or hypobaric hypoxia for 8-9 hours. After 32 or 48 hours of recovery, the mice were euthanized, and the right and left lateral gastrocnemius muscles were collected for microarray and bioinformatics analyses. RESULTS The study hypothesis was verified. There were 353 highly upregulated, differentially expressed genes identified in the injured muscle compared to the uninjured muscle. Mid1 was upregulated in both pressure conditions regardless of injury status. There were 52 and 15 differentially expressed genes at 32 and 48 hours postinjury, respectively, in the hypobaric hypoxia-exposed, injured muscle compared to the normobaric normoxia-exposed, injured muscle. The macrophage gene Cd68 correlated with other leukocyte-related genes. DISCUSSION These findings expand our understanding of the genetic changes that occur in muscle in response to a crush injury, including those related to the macrophage protein CD68. Nursing interventions addressing adequate functioning after crush muscle injury may need to consider the effects on Cd68 and its closely related genes. In addition, our results suggest a responsiveness of the gene Mid1 to flight-relevant hypobaric hypoxia. Changes in the expression of Mid1 may be appropriate in assessing the long-term health of flight crew members.
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Miller AJ, Gass J, Jo MC, Bishop L, Petereit J, Woodhams DC, Voyles J. Towards the generation of gnotobiotic larvae as a tool to investigate the influence of the microbiome on the development of the amphibian immune system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220125. [PMID: 37305911 PMCID: PMC10258664 DOI: 10.1098/rstb.2022.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/28/2022] [Indexed: 06/13/2023] Open
Abstract
The immune equilibrium model suggests that exposure to microbes during early life primes immune responses for pathogen exposure later in life. While recent studies using a range of gnotobiotic (germ-free) model organisms offer support for this theory, we currently lack a tractable model system for investigating the influence of the microbiome on immune system development. Here, we used an amphibian species (Xenopus laevis) to investigate the importance of the microbiome in larval development and susceptibility to infectious disease later in life. We found that experimental reductions of the microbiome during embryonic and larval stages effectively reduced microbial richness, diversity and altered community composition in tadpoles prior to metamorphosis. In addition, our antimicrobial treatments resulted in few negative effects on larval development, body condition, or survival to metamorphosis. However, contrary to our predictions, our antimicrobial treatments did not alter susceptibility to the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) in the adult life stage. While our treatments to reduce the microbiome during early development did not play a critical role in determining susceptibility to disease caused by Bd in X. laevis, they nevertheless indicate that developing a gnotobiotic amphibian model system may be highly useful for future immunological investigations. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
| | - Jordan Gass
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Myung Chul Jo
- Environmental Health and Safety, University of Nevada, Reno, NV 89557, USA
| | - Lucas Bishop
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | | | - Jamie Voyles
- Department of Biology, University of Nevada, Reno, NV 89557, USA
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Khan M, Li L, Haak L, Payen SH, Carine M, Adhikari K, Uppal T, Hartley PD, Vasquez-Gross H, Petereit J, Verma SC, Pagilla K. Significance of wastewater surveillance in detecting the prevalence of SARS-CoV-2 variants and other respiratory viruses in the community - A multi-site evaluation. One Health 2023; 16:100536. [PMID: 37041760 PMCID: PMC10074727 DOI: 10.1016/j.onehlt.2023.100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/13/2023] Open
Abstract
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends of virus prevalence within the community. The surveillance also provides precise and early detection of any new and circulating variants, which aids in response to viral outbreaks. Site-specific monitoring of SARS-CoV-2 variants provides valuable information on the prevalence of new or emerging variants in the community. We sequenced the genomic RNA of viruses present in the wastewater samples and analyzed for the prevalence of SARS-CoV-2 variants as well as other respiratory viruses for a period of one year to account for seasonal variations. The samples were collected from the Reno-Sparks metropolitan area on a weekly basis between November 2021 to November 2022. Samples were analyzed to detect the levels of SARS-CoV-2 genomic copies and variants identification. This study confirmed that wastewater monitoring of SARS-CoV-2 variants can be used for community surveillance and early detection of circulating variants and supports wastewater-based epidemiology (WBE) as a complement to clinical respiratory virus testing as a healthcare response effort. Our study showed the persistence of the SARS-CoV-2 virus throughout the year compared to a seasonal presence of other respiratory viruses, implicating SARS-CoV-2's broad genetic diversity and strength to persist and infect susceptible hosts. Through secondary analysis, we further identified antimicrobial resistance (AMR) genes in the same wastewater samples and found WBE to be a feasible tool for community AMR detection and monitoring.
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Affiliation(s)
- Majid Khan
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Shannon Harger Payen
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Madeline Carine
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Kabita Adhikari
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Paul D. Hartley
- Nevada Genomics Center, University of Nevada, Reno, NV 89557, USA
| | - Hans Vasquez-Gross
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Krishna Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
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Petereit J, Hoerterer C, Krause G. Country-specific food culture and scientific knowledge transfer events - Do they influence the purchasing behaviour of seafood products? Aquaculture 2022; 560:738590. [PMID: 36398056 PMCID: PMC9484271 DOI: 10.1016/j.aquaculture.2022.738590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/13/2022] [Accepted: 07/04/2022] [Indexed: 05/13/2023]
Abstract
A positive perception of aquaculture products is essential to boost production by using more sustainable and eco-friendly solutions. However, consumer perception and resulting purchasing decisions remain poorly understood. In most European countries, the consumer perception tends to be rather negative, which is reinforced by knowledge gaps and misleading information from the media. This is believed to have the greatest impact on the current low consumption rate of farmed fish across Europe. Previous research has suggested that consumers may often be reluctant to change their seafood purchasing behaviour despite having a solid scientific understanding of aquaculture products and their mode of production. In this study, we investigated the extent to which country-specific contexts and degree of scientific knowledge contribute to the purchasing behaviour of consumers across Europe. To this end, interactive poster surveys and semi-structured interviews were conducted at eight different knowledge transfer events (KTEs) across three countries, targeting 383 participants. The application of a yet underutilized method, an interactive poster survey, underscored the need to use new approaches to tackle consumer behaviour. Our results indicate that increased scientific knowledge does not lead to changes in purchasing behaviour per se. Perceptions and purchasing habits are very contextual and vary from culture to culture. This points to the highly interlinked nature of country-specific marine food culture that ranges between individual awareness, scientific knowledge, and socio-cultural contexts, all of which renders in resulting individual purchasing decisions. Our results suggest focusing more on the sustainability of a product and emphasising the ongoing transition towards a circular economy approach in the aquaculture sector may be a promising pathway to foster more sustainability-driven purchasing decisions in the seafood sector. Our findings also question whether trying to educate the public about more sustainable purchasing criteria is really the key to foster more sustainable consumption patterns or whether we are working from misleading assumptions that lead to wrong approaches. In conclusion, a lack of clear and easily accessible information appears to be the main barrier to social acceptance of sustainable aquaculture products in Europe.
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Affiliation(s)
- J. Petereit
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Corresponding author.
| | - C. Hoerterer
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - G. Krause
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Institute for Advanced Sustainability Studies (IASS), Potsdam, Germany
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Mhatre SD, Iyer J, Petereit J, Dolling-Boreham RM, Tyryshkina A, Paul AM, Gilbert R, Jensen M, Woolsey RJ, Anand S, Sowa MB, Quilici DR, Costes SV, Girirajan S, Bhattacharya S. Artificial gravity partially protects space-induced neurological deficits in Drosophila melanogaster. Cell Rep 2022; 40:111279. [PMID: 36070701 PMCID: PMC10503492 DOI: 10.1016/j.celrep.2022.111279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/16/2022] [Accepted: 08/05/2022] [Indexed: 02/03/2023] Open
Abstract
Spaceflight poses risks to the central nervous system (CNS), and understanding neurological responses is important for future missions. We report CNS changes in Drosophila aboard the International Space Station in response to spaceflight microgravity (SFμg) and artificially simulated Earth gravity (SF1g) via inflight centrifugation as a countermeasure. While inflight behavioral analyses of SFμg exhibit increased activity, postflight analysis displays significant climbing defects, highlighting the sensitivity of behavior to altered gravity. Multi-omics analysis shows alterations in metabolic, oxidative stress and synaptic transmission pathways in both SFμg and SF1g; however, neurological changes immediately postflight, including neuronal loss, glial cell count alterations, oxidative damage, and apoptosis, are seen only in SFμg. Additionally, progressive neuronal loss and a glial phenotype in SF1g and SFμg brains, with pronounced phenotypes in SFμg, are seen upon acclimation to Earth conditions. Overall, our results indicate that artificial gravity partially protects the CNS from the adverse effects of spaceflight.
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Affiliation(s)
- Siddhita D Mhatre
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA; COSMIAC Research Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Janani Iyer
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA; Universities Space Research Association, Mountain View, CA 94043, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | - Roberta M Dolling-Boreham
- Department of Electrical and Biomedical Engineering, McMaster University, Hamilton, ON L8S 4L8, Canada; Blue Marble Space Institute of Science, Seattle, WA 94035, USA
| | - Anastasia Tyryshkina
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Amber M Paul
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Universities Space Research Association, Mountain View, CA 94043, USA; Blue Marble Space Institute of Science, Seattle, WA 94035, USA; NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USA; Embry-Riddle Aeronautical University, Department of Human Factors and Behavioral Neurobiology, Daytona Beach, FL 32114, USA
| | - Rachel Gilbert
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Matthew Jensen
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Sulekha Anand
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
| | - Marianne B Sowa
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - David R Quilici
- Nevada Proteomics Center, University of Nevada, Reno, NV 89557, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Santhosh Girirajan
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sharmila Bhattacharya
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Biological and Physical Sciences Division, NASA Headquarters, Washington DC 20024, USA.
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Chen J, Banerjee A, Petereit J. Pathways relevant to Alzheimer’s disease are identified during proinflammatory activation from a microglial model derived from human monocytes. Alzheimers Dement 2021. [DOI: 10.1002/alz.056355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Nguyen H, Tran D, Galazka JM, Costes SV, Beheshti A, Petereit J, Draghici S, Nguyen T. CPA: a web-based platform for consensus pathway analysis and interactive visualization. Nucleic Acids Res 2021; 49:W114-W124. [PMID: 34037798 PMCID: PMC8262702 DOI: 10.1093/nar/gkab421] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/16/2021] [Accepted: 05/05/2021] [Indexed: 01/06/2023] Open
Abstract
In molecular biology and genetics, there is a large gap between the ease of data collection and our ability to extract knowledge from these data. Contributing to this gap is the fact that living organisms are complex systems whose emerging phenotypes are the results of multiple complex interactions taking place on various pathways. This demands powerful yet user-friendly pathway analysis tools to translate the now abundant high-throughput data into a better understanding of the underlying biological phenomena. Here we introduce Consensus Pathway Analysis (CPA), a web-based platform that allows researchers to (i) perform pathway analysis using eight established methods (GSEA, GSA, FGSEA, PADOG, Impact Analysis, ORA/Webgestalt, KS-test, Wilcox-test), (ii) perform meta-analysis of multiple datasets, (iii) combine methods and datasets to accurately identify the impacted pathways underlying the studied condition and (iv) interactively explore impacted pathways, and browse relationships between pathways and genes. The platform supports three types of input: (i) a list of differentially expressed genes, (ii) genes and fold changes and (iii) an expression matrix. It also allows users to import data from NCBI GEO. The CPA platform currently supports the analysis of multiple organisms using KEGG and Gene Ontology, and it is freely available at http://cpa.tinnguyen-lab.com.
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Affiliation(s)
- Hung Nguyen
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
| | - Duc Tran
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
| | - Jonathan M Galazka
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Sylvain V Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Afshin Beheshti
- KBR, NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Juli Petereit
- University of Nevada Reno, Nevada Bioinformatics Center, Reno, NV 89557, USA
| | - Sorin Draghici
- Wayne State University, Department of Computer Science, Detroit, MI 48202, USA
| | - Tin Nguyen
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
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Speth Z, Kaur G, Mazolewski D, Sisomphou R, Siao DDC, Pooraiiouby R, Vasquez-Gross H, Petereit J, Gulia-Nuss M, Mathew D, Nuss AB. Characterization of Anopheles stephensi Odorant Receptor 8, an Abundant Component of the Mouthpart Chemosensory Transcriptome. Insects 2021; 12:593. [PMID: 34208911 PMCID: PMC8304465 DOI: 10.3390/insects12070593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/22/2021] [Accepted: 06/26/2021] [Indexed: 01/25/2023]
Abstract
Several mosquito species within the genus Anopheles are vectors for human malaria, and the spread of this disease is driven by the propensity of certain species to feed preferentially on humans. The study of olfaction in mosquitoes is important to understand dynamics of host-seeking and host-selection; however, the majority of these studies focus on Anopheles gambiae or An. coluzzii, both vectors of malaria in Sub-Saharan Africa. Other malaria vectors may recognize different chemical cues from potential hosts; therefore, in this study, we investigated An. stephensi, the south Asian malaria mosquito. We specifically focused on the mouthparts (primarily the maxillary palp and labella) that have been much less investigated compared to the antennae but are also important for host-seeking. To provide a broad view of chemoreceptor expression, RNAseq was used to examine the transcriptomes from the mouthparts of host-seeking females, blood-fed females, and males. Notably, AsOr8 had a high transcript abundance in all transcriptomes and was, therefore, cloned and expressed in the Drosophila empty neuron system. This permitted characterization with a panel of odorants that were selected, in part, for their presence in the human odor profile. The responsiveness of AsOr8 to odorants was highly similar to An. gambiae Or8 (AgOr8), except for sulcatone, which was detected by AsOr8 but not AgOr8. Subtle differences in the receptor sensitivity to specific odorants may provide clues to species- or strain-specific approaches to host-seeking and host selection. Further exploration of the profile of An. stephensi chemosensory proteins may yield a better understanding of how different malaria vectors navigate host-finding and host-choice.
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Affiliation(s)
- Zachary Speth
- Cell and Molecular Biology Graduate Program, University of Nevada, Reno, NV 89557, USA; (Z.S.); (G.K.); (D.M.)
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Gurlaz Kaur
- Cell and Molecular Biology Graduate Program, University of Nevada, Reno, NV 89557, USA; (Z.S.); (G.K.); (D.M.)
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Devin Mazolewski
- Cell and Molecular Biology Graduate Program, University of Nevada, Reno, NV 89557, USA; (Z.S.); (G.K.); (D.M.)
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Rayden Sisomphou
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Danielle Denise C. Siao
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Rana Pooraiiouby
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Hans Vasquez-Gross
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA; (H.V.-G.); (J.P.)
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA; (H.V.-G.); (J.P.)
| | - Monika Gulia-Nuss
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA;
| | - Dennis Mathew
- Department of Biology, University of Nevada, Reno, NV 89557, USA;
| | - Andrew B. Nuss
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA;
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Fisher KE, Tillett RL, Fotoohi M, Caldwell C, Petereit J, Schlauch K, Tittiger C, Blomquist GJ, MacLean M. RNA-Seq used to identify ipsdienone reductase (IDONER): A novel monoterpene carbon-carbon double bond reductase central to Ips confusus pheromone production. Insect Biochem Mol Biol 2021; 129:103513. [PMID: 33388375 PMCID: PMC7909325 DOI: 10.1016/j.ibmb.2020.103513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
The pinyon ips beetle, Ips confusus (LeConte) is a highly destructive pest in pine forests in western North America. When colonizing a new host tree, I. confusus beetles coordinate a mass attack to overcome the tree's defenses using aggregation pheromones. Ips confusus, as with other Ips spp. beetles, biosynthesize ipsdienol and ipsenol in a specific enantiomeric blend and ratio as aggregation pheromones. While several of the initial steps in the pheromone biosynthetic pathway have been well defined, the final steps were unknown. We used comparative RNA-Seq analysis between fed and unfed male I. confusus midgut tissue to identify candidate genes involved in pheromone biosynthesis. The 12,995 potentially unique transcripts showed a clear separation based on feeding state. Differential expression analysis identified gene groups that were tightly connected. This analysis identified all known pheromone biosynthetic genes and suggested a novel monoterpene double bond reductase, ipsdienone reductase (IDONER), with pheromone biosynthetic gene expression patterns. IDONER cDNA was cloned, expressed, and functionally characterized. The coding DNA sequence has an ORF of 1101 nt with a predicted translation product of 336 amino acids. The enzyme has a molecular weight of 36.7 kDa with conserved motifs of the medium chain dehydrogenases/reductase (MDR) superfamily in the leukotriene B4 dehydrogenases/reductases (LTB4R) family. Tagged recombinant protein was expressed and purified. Enzyme assays and GC/MS analysis showed IDONER catalyzed the reduction of ipsdienone to form ipsenone. This study shows that IDONER is a monoterpene double bond reductase involved in I. confusus pheromone biosynthesis.
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Affiliation(s)
- Katherine E Fisher
- Phigenics Research and Innovation Laboratory, Nevada Center for Applied Research, 1664 N. Virginia St., Reno, NV, 89557, USA.
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, 89154, USA.
| | - Misha Fotoohi
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 N. Virginia St., Reno, NV, 89557, USA.
| | - Cody Caldwell
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 N. Virginia St., Reno, NV, 89557, USA.
| | - Juli Petereit
- Nevada Center for Bioinformatics, University of Nevada, Reno, NV, 89557, USA.
| | - Karen Schlauch
- Desert Research Institute, Northern Nevada Science Center Campus, 2215 Raggio Parkway, Reno, NV, 89512, USA.
| | - Claus Tittiger
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 N. Virginia St., Reno, NV, 89557, USA.
| | - Gary J Blomquist
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 N. Virginia St., Reno, NV, 89557, USA.
| | - Marina MacLean
- Department of Biochemistry and Molecular Biology, University of Nevada, 1664 N. Virginia St., Reno, NV, 89557, USA.
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Matthews JJ, Olszewski A, Petereit J. Knowledge, Training, and Attitudes of Students and Speech-Language Pathologists About Providing Communication Services to Individuals Who Are Transgender. Am J Speech Lang Pathol 2020; 29:597-610. [PMID: 32320622 PMCID: PMC7842867 DOI: 10.1044/2020_ajslp-19-00148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Purpose Little is known about the professional knowledge, training, and attitudes of current and future speech-language pathologists (SLPs) toward serving people who are transgender. The purpose of this study was to understand the current climate of students and professionals in delivering voice and communications services to people who are transgender. An understanding of these areas is necessary to help practicing and aspiring SLPs work toward cultural competence in serving this population. Method A survey was completed by 386 speech-language pathology students and SLPs at three professional conferences. The survey assessed the professional and ethical knowledge, training experiences, and attitudes of the participants in relation to communication services for people who are transgender. Results In terms of professional knowledge, the majority of students and experienced SLP respondents agreed or strongly agreed (77.8%) that treating clients who are transgender was within the SLP scope of practice and was their ethical responsibility (82.2%). Regarding training, approximately 20% of survey respondents received training for working with people who are transgender, whereas approximately 8% of survey respondents reported having experience working with clients who are transgender. With respect to attitude, approximately 54% of survey respondents reported being comfortable treating clients who are transgender, and 37% of survey respondents reported they were likely to pursue training for treating clients who are transgender. Additional analyses were completed comparing students and experienced SLPs as well as the influence of geographic region. Discussion Students and SLPs were generally knowledgeable of professional guidelines and standards regarding serving people who are transgender. However, in this survey, very few clinicians indicated they had received training to serve this population. Recommendations to address this gap are discussed.
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Affiliation(s)
| | - Abbie Olszewski
- Department of Speech Pathology and Audiology, University of Nevada, Reno
| | - Juli Petereit
- Nevada Center for Bioinformatics, University of Nevada, Reno
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16
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Ghan R, Petereit J, Tillett RL, Schlauch KA, Toubiana D, Fait A, Cramer GR. The common transcriptional subnetworks of the grape berry skin in the late stages of ripening. BMC Plant Biol 2017; 17:94. [PMID: 28558655 PMCID: PMC5450095 DOI: 10.1186/s12870-017-1043-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/22/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock. CONCLUSIONS A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.
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Affiliation(s)
- Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Juli Petereit
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Richard L. Tillett
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - Karen A. Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV 89557 USA
| | - David Toubiana
- Telekom Innovation, Laboratories and Cyber Security Research Center, Department of Information, Systems Engineering, Ben Gurion University, Beer Sheva, Israel
| | - Aaron Fait
- Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, 84990 Midreshet Ben-Gurion, Israel
| | - Grant R. Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
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Nadeau JA, Petereit J, Tillett RL, Jung K, Fotoohi M, MacLean M, Young S, Schlauch K, Blomquist GJ, Tittiger C. Comparative transcriptomics of mountain pine beetle pheromone-biosynthetic tissues and functional analysis of CYP6DE3. BMC Genomics 2017; 18:311. [PMID: 28427347 PMCID: PMC5397757 DOI: 10.1186/s12864-017-3696-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/11/2017] [Indexed: 12/14/2022] Open
Abstract
Background The mountain pine beetle (MPB, Dendroctonus ponderosae Hopkins) is a highly destructive pest of pine forests in western North America. During flight to a new host tree and initiation of feeding, mountain pine beetles release aggregation pheromones. The biosynthetic pathways of these pheromones are sex-specific and localized in the midgut and fat body, but the enzymes involved have not all been identified or characterized. Results We used a comparative RNA-Seq analysis between fed and unfed male and female MPB midguts and fat bodies to identify candidate genes involved in pheromone biosynthesis. The 13,407 potentially unique transcripts showed clear separation based on feeding state and gender. Gene co-expression network construction and examination using petal identified gene groups that were tightly connected. This, as well as other co-expression and gene ontology analyses, identified all four known pheromone biosynthetic genes, confirmed the tentative identification of four others from a previous study, and suggested nine novel candidates. One cytochrome P450 monooxygenase, CYP6DE3, identified as a possible exo-brevicomin-biosynthetic enzyme in this study, was functionally characterized and likely is involved in resin detoxification rather than pheromone biosynthesis. Conclusions Our analysis supported previously characterized pheromone-biosynthetic genes involved in exo-brevicomin and frontalin biosynthesis and identified a number of candidate cytochrome P450 monooxygenases and a putative cyclase for further studies. Functional analyses of CYP6DE3 suggest its role in resin detoxification and underscore the limitation of using high-throughput data to tentatively identify candidate genes. Further functional analyses of candidate genes found in this study should lead to the full characterization of MPB pheromone biosynthetic pathways and the identification of molecular targets for possible pest management strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3696-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J A Nadeau
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - J Petereit
- Biomedical Engineering Department, University of Nevada, Reno, NV, 89557, USA
| | - R L Tillett
- Nevada INBRE Bioinformatics Core, University of Nevada, Reno, NV, 89557, USA
| | - K Jung
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - M Fotoohi
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - M MacLean
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - S Young
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - K Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - G J Blomquist
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - C Tittiger
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.
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Cserne Szappanos H, Petereit J, Millar H, Ingley E, Hool L. Clarifying a Novel PKA Phosphorylation Site on the L-type Calcium Channel. Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Background Networks provide effective models to study complex biological systems, such as gene and protein interaction networks. With the advent of new sequencing technologies, many life scientists are grasping for user-friendly methods and tools to examine biological components at the whole-systems level. Gene co-expression network analysis approaches are frequently used to successfully associate genes with biological processes and demonstrate great potential to gain further insights into the functionality of genes, thus becoming a standard approach in Systems Biology. Here the objective is to construct biologically meaningful and statistically strong co-expression networks, the identification of research dependent subnetworks, and the presentation of self-contained results. Results We introduce petal, a novel approach to generate gene co-expression network models based on experimental gene expression measures. petal focuses on statistical, mathematical, and biological characteristics of both, input data and output network models. Often over-looked issues of current co-expression analysis tools include the assumption of data normality, which is seldom the case for hight-throughput expression data obtained from RNA-seq technologies. petal does not assume data normality, making it a statistically appropriate method for RNA-seq data. Also, network models are rarely tested for their known typical architecture: scale-free and small-world. petal explicitly constructs networks based on both these characteristics, thereby generating biologically meaningful models. Furthermore, many network analysis tools require a number of user-defined input variables, these often require tuning and/or an understanding of the underlying algorithm; petal requires no user input other than experimental data. This allows for reproducible results, and simplifies the use of petal. Lastly, this approach is specifically designed for very large high-throughput datasets; this way, petal’s network models represent as much of the entire system as possible to provide a whole-system approach. Conclusion petal is a novel tool for generating co-expression network models of whole-genomics experiments. It is implemented in R and available as a library. Its application to several whole-genome experiments has generated novel meaningful results and has lead the way to new testing hypothesizes for further biological investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0298-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juli Petereit
- University of Nevada, Reno, 1664 N. Virginia Street, Reno, 89557, USA.
| | - Sebastian Smith
- University of Nevada, Reno, 1664 N. Virginia Street, Reno, 89557, USA
| | | | - Karen A Schlauch
- University of Nevada, Reno, 1664 N. Virginia Street, Reno, 89557, USA
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Schlauch KA, Khaiboullina SF, De Meirleir KL, Rawat S, Petereit J, Rizvanov AA, Blatt N, Mijatovic T, Kulick D, Palotás A, Lombardi VC. Genome-wide association analysis identifies genetic variations in subjects with myalgic encephalomyelitis/chronic fatigue syndrome. Transl Psychiatry 2016; 6:e730. [PMID: 26859813 PMCID: PMC4872418 DOI: 10.1038/tp.2015.208] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/28/2015] [Accepted: 11/05/2015] [Indexed: 12/21/2022] Open
Abstract
Myalgic encephalomyelitis, also known as chronic fatigue syndrome or ME/CFS, is a multifactorial and debilitating disease that has an impact on over 4 million people in the United States alone. The pathogenesis of ME/CFS remains largely unknown; however, a genetic predisposition has been suggested. In the present study, we used a DNA single-nucleotide polymorphism (SNP) chip representing over 906,600 known SNPs to analyze DNA from ME/CFS subjects and healthy controls. To the best of our knowledge, this study represents the most comprehensive genome-wide association study (GWAS) of an ME/CFS cohort conducted to date. Here 442 SNPs were identified as candidates for association with ME/CFS (adjusted P-value<0.05). Whereas the majority of these SNPs are represented in non-coding regions of the genome, 12 SNPs were identified in the coding region of their respective gene. Among these, two candidate SNPs resulted in missense substitutions, one in a pattern recognition receptor and the other in an uncharacterized coiled-coil domain-containing protein. We also identified five SNPs that cluster in the non-coding regions of T-cell receptor loci. Further examination of these polymorphisms may help identify contributing factors to the pathophysiology of ME/CFS, as well as categorize potential targets for medical intervention strategies.
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Affiliation(s)
- K A Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - S F Khaiboullina
- Nevada Center for Biomedical Research, University of Nevada, Reno, NV, USA
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - K L De Meirleir
- Nevada Center for Biomedical Research, University of Nevada, Reno, NV, USA
| | - S Rawat
- Nevada Center for Biomedical Research, University of Nevada, Reno, NV, USA
| | - J Petereit
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - A A Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - N Blatt
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | | | - D Kulick
- Mayo Clinic, Scottsdale, AZ, USA
| | - A Palotás
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- Asklepios-Med (private medical practice and research center), Szeged, Hungary
| | - V C Lombardi
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
- Nevada Center for Biomedical Research, University of Nevada, Reno, NV, USA
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Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA, Owen NA, Griffiths H, Smith JAC, De Paoli HC, Weston DJ, Cottingham R, Hartwell J, Davis SC, Silvera K, Ming R, Schlauch K, Abraham P, Stewart JR, Guo HB, Albion R, Ha J, Lim SD, Wone BWM, Yim WC, Garcia T, Mayer JA, Petereit J, Nair SS, Casey E, Hettich RL, Ceusters J, Ranjan P, Palla KJ, Yin H, Reyes-García C, Andrade JL, Freschi L, Beltrán JD, Dever LV, Boxall SF, Waller J, Davies J, Bupphada P, Kadu N, Winter K, Sage RF, Aguilar CN, Schmutz J, Jenkins J, Holtum JAM. A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytol 2015; 207:491-504. [PMID: 26153373 DOI: 10.1111/nph.13393] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI, 02912, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Nick A Owen
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Henrique C De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Robert Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Sarah C Davis
- Voinovich School of Leadership and Public Affairs and Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Katia Silvera
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Karen Schlauch
- Nevada Center for Bioinformatics, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Paul Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - J Ryan Stewart
- Department of Plant and Wildlife Sciences, Brigham Young University, 4105 Life Sciences Building, Provo, UT, 84602, USA
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rebecca Albion
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Jungmin Ha
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Bernard W M Wone
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Travis Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Juli Petereit
- Nevada Center for Bioinformatics, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Sujithkumar S Nair
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - Erin Casey
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Johan Ceusters
- Department of M²S, Faculty of Engineering Technology, TC Bioengineering Technology, KU Leuven, Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Hengfu Yin
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400, China
| | - Casandra Reyes-García
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, México
| | - José Luis Andrade
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, México
| | - Luciano Freschi
- Department of Botany, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Juan D Beltrán
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jade Waller
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jack Davies
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Phaitun Bupphada
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nirja Kadu
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S3B2, Canada
| | - Cristobal N Aguilar
- Department of Food Research, School of Chemistry, Universidad Autónoma de Coahuila, Saltillo, México
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Joseph A M Holtum
- College of Marine and Environmental Sciences, James Cook University, Townsville, 4811, QLD, Australia
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