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Reese TC, Blakeslee AMH, Crane LC, Fletcher LS, Repetto MF, Smith N, Stancil C, Tepolt CK, Toscano BJ, Griffen BD. Shift from income breeding to capital breeding with latitude in the invasive Asian shore crab Hemigrapsus sanguineus. Sci Rep 2024; 14:6654. [PMID: 38509340 PMCID: PMC10954667 DOI: 10.1038/s41598-024-57434-y] [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: 06/30/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Organisms vary in the timing of energy acquisition and use for reproduction. Thus, breeding strategies exist on a continuum, from capital breeding to income breeding. Capital breeders acquire and store energy for breeding before the start of the reproductive season, while income breeders finance reproduction using energy acquired during the reproductive season. Latitude and its associated environmental drivers are expected to heavily influence breeding strategy, potentially leading to latitudinal variation in breeding strategies within a single species. We examined the breeding strategy of the Asian shore crab Hemigrapsus sanguineus at five sites spanning nearly 10° of latitude across its invaded United States range. We hypothesized that the primary breeding strategy of this species would shift from income breeding to capital breeding as latitude increases. We found that though this species' breeding strategy is dominated by capital breeding throughout much of the range, income breeding increases in importance at lower latitudes. This latitudinal pattern is likely heavily influenced by the duration of the foraging and breeding seasons, which also vary with latitude. We also found that reproductive characteristics at the northern and southern edges of the invaded range were consistent with continued range expansion. We suggest that the reproductive flexibility of the Asian shore crab is a key facilitator of its continued invasion success. Our results highlight the influence of latitude on the breeding strategy of a species and emphasize the need for further research regarding the ecological importance and implications of flexibility in breeding strategies within species.
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Affiliation(s)
- Tanner C Reese
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | | | - Laura C Crane
- Wells National Estuarine Research Reserve, Wells, ME, 04090, USA
| | - Laura S Fletcher
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Michele F Repetto
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Nanette Smith
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Carter Stancil
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | | | - Blaine D Griffen
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
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2
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Reese TC, Devineni A, Smith T, Lalami I, Ahn JM, Raj GV. Evaluating physiochemical properties of FDA-approved orally administered drugs. Expert Opin Drug Discov 2024; 19:225-238. [PMID: 37921049 DOI: 10.1080/17460441.2023.2275617] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
INTRODUCTION Analyses of orally administered FDA-approved drugs from 1990 to 1993 enabled the identification of a set of physiochemical properties known as Lipinski's Rule of Five (Ro5). The original Ro5 and extended versions still remain the reference criteria for drug development programs. Since many bioactive compounds do not conform to the Ro5, we validated the relevance of and adherence to these rulesets in a contemporary cohort of FDA-approved drugs. AREAS COVERED The authors noted that a significant proportion of FDA-approved orally administered parent compounds from 2011 to 2022 deviate from the original Ro5 criteria (~38%) or the Ro5 with extensions (~53%). They then evaluated if a contemporary Ro5 criteria (cRo5) could be devised to better predict oral bioavailability. Furthermore, they discuss many case studies showcasing the need for and benefit of increasing the size of certain compounds and cover several evolving strategies for improving oral bioavailability. EXPERT OPINION Despite many revisions to the Ro5, the authors find that no single proposed physiochemical rule has universal concordance with absolute oral bioavailability. Innovations in drug delivery and formulation have dramatically expanded the range of physicochemical properties and the chemical diversity for oral administration.
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Affiliation(s)
- Tanner C Reese
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Anvita Devineni
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Tristan Smith
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Ismail Lalami
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, USA
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3
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Collier AB, Viswanadhapalli S, Gopalam R, Lee TK, Kassees K, Parra K, Sharma G, Reese TC, Liu X, Yang X, Ebrahimi B, Pratap UP, Mahajan M, Arnold WC, Baker A, Chen CY, Elmore ST, Subbarayalu P, Sareddy GR, Valente PT, Kost ER, Ahn JM, Vadlamudi RK. Novel LIPA-Targeted Therapy for Treating Ovarian Cancer. Cancers (Basel) 2024; 16:500. [PMID: 38339252 PMCID: PMC10854701 DOI: 10.3390/cancers16030500] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Ovarian cancer (OCa) is the most lethal form of gynecologic cancer, and the tumor heterogeneities at the molecular, cellular, and tissue levels fuel tumor resistance to standard therapies and pose a substantial clinical challenge. Here, we tested the hypothesis that the heightened basal endoplasmic reticulum stress (ERS) observed in OCa represents an exploitable vulnerability and may overcome tumor heterogeneity. Our recent studies identified LIPA as a novel target to induce ERS in cancer cells using the small molecule ERX-41. However, the role of LIPA and theutility of ERX-41 to treat OCa remain unknown. Expression analysis using the TNMplot web tool, TCGA data sets, and immunohistochemistry analysis using a tumor tissue array showed that LIPA is highly expressed in OCa tissues, compared to normal tissues. ERX-41 treatment significantly reduced the cell viability and colony formation ability and promoted the apoptosis of OCa cells. Mechanistic studies revealed a robust and consistent induction of ERS markers, including CHOP, elF2α, PERK, and ATF4, upon ERX-41 treatment. In xenograft and PDX studies, ERX-41 treatment resulted in a significant reduction in tumor growth. Collectively, our results suggest that ERX-41 is a novel therapeutic agent that targets the LIPA with a unique mechanism of ERS induction, which could be exploited to treat heterogeneity in OCa.
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Affiliation(s)
- Alexia B. Collier
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Suryavathi Viswanadhapalli
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Rahul Gopalam
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Tae-Kyung Lee
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA; (T.-K.L.); (K.K.); (C.-Y.C.); (S.T.E.); (J.-M.A.)
| | - Kara Kassees
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA; (T.-K.L.); (K.K.); (C.-Y.C.); (S.T.E.); (J.-M.A.)
| | - Karla Parra
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; (K.P.); (G.S.); (T.C.R.); (X.L.)
| | - Gaurav Sharma
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; (K.P.); (G.S.); (T.C.R.); (X.L.)
| | - Tanner C. Reese
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; (K.P.); (G.S.); (T.C.R.); (X.L.)
| | - Xihui Liu
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; (K.P.); (G.S.); (T.C.R.); (X.L.)
| | - Xue Yang
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Behnam Ebrahimi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Uday P. Pratap
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Megharani Mahajan
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - William C. Arnold
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Adriana Baker
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Chia-Yuan Chen
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA; (T.-K.L.); (K.K.); (C.-Y.C.); (S.T.E.); (J.-M.A.)
| | - Scott Terry Elmore
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA; (T.-K.L.); (K.K.); (C.-Y.C.); (S.T.E.); (J.-M.A.)
| | - Panneerdoss Subbarayalu
- Greehey Children’s Cancer Research Institute, Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA;
| | - Gangadhara R. Sareddy
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Philip T. Valente
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Edward R. Kost
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA; (T.-K.L.); (K.K.); (C.-Y.C.); (S.T.E.); (J.-M.A.)
| | - Ratna K. Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (A.B.C.); (S.V.); (R.G.); (X.Y.); (B.E.); (U.P.P.); (M.M.); (W.C.A.); (A.B.); (G.R.S.); (P.T.V.); (E.R.K.)
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Audie L. Murphy Division, South Texas Veterans Health Care System, San Antonio, TX 78229, USA
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Kim K, Huang H, Parida PK, He L, Marquez-Palencia M, Reese TC, Kapur P, Brugarolas J, Brekken RA, Malladi S. Cell Competition Shapes Metastatic Latency and Relapse. Cancer Discov 2023; 13:85-97. [PMID: 36098678 PMCID: PMC9839468 DOI: 10.1158/2159-8290.cd-22-0236] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 02/28/2022] [Revised: 07/21/2022] [Accepted: 09/06/2022] [Indexed: 01/17/2023]
Abstract
Cell competition, a fitness-sensing process, is essential for tissue homeostasis. Using cancer metastatic latency models, we show that cell competition results in the displacement of latent metastatic (Lat-M) cells from the primary tumor. Lat-M cells resist anoikis and survive as residual metastatic disease. A memodeled extracellular matrix facilitates Lat-M cell displacement and survival in circulation. Disrupting cell competition dynamics by depleting secreted protein and rich in cysteine (SPARC) reduced displacement from orthotopic tumors and attenuated metastases. In contrast, depletion of SPARC after extravasation in lung-resident Lat-M cells increased metastatic outgrowth. Furthermore, multiregional transcriptomic analyses of matched primary tumors and metachronous metastases from patients with kidney cancer identified tumor subclones with Lat-M traits. Kidney cancer enriched for these Lat-M traits had a rapid onset of metachronous metastases and significantly reduced disease-free survival. Thus, an unexpected consequence of cell competition is the displacement of cells with Lat-M potential, thereby shaping metastatic latency and relapse. SIGNIFICANCE We demonstrate that cell competition within the primary tumor results in the displacement of Lat-M cells. We further show the impact of altering cell competition dynamics on metastatic incidence that may guide strategies to limit metastatic recurrences. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Kangsan Kim
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas.,Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Huocong Huang
- Hamon Center for Therapeutic Oncology Research and Department of Surgery, UT Southwestern Medical Center, Dallas, Texas
| | - Pravat Kumar Parida
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas.,Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Lan He
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mauricio Marquez-Palencia
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas.,Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Tanner C Reese
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Department of Urology, UT Southwestern Medical Center, Dallas, Texas
| | - Payal Kapur
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas.,Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, UT Southwestern Medical Center, Dallas, Texas
| | - James Brugarolas
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, UT Southwestern Medical Center, Dallas, Texas.,Hematology-Oncology Division, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas
| | - Rolf A Brekken
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Hamon Center for Therapeutic Oncology Research and Department of Surgery, UT Southwestern Medical Center, Dallas, Texas
| | - Srinivas Malladi
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas.,Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
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5
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Quezada-Villa K, Cannizzo ZJ, Carver J, Dunn RP, Fletcher LS, Kimball ME, McMullin AL, Orocu B, Pfirrmann BW, Pinkston E, Reese TC, Smith N, Stancil C, Toscano BJ, Griffen BD. Predicting diet in brachyuran crabs using external morphology. PeerJ 2023; 11:e15224. [PMID: 37065690 PMCID: PMC10100828 DOI: 10.7717/peerj.15224] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Morphological traits have often been used to predict diet and trophic position of species across many animal groups. Variation in gut size of closely related animals is known to be a good predictor of dietary habits. Species that are more herbivorous or that persist on low-quality diets often have larger stomachs than their carnivorous counterparts. This same pattern exists in crabs and in most species, individuals exhibit external markings on the dorsal side of their carapace that appear to align with the position and size of their gut. We hypothesized that these external markings could be used as an accurate estimate of the crab's cardiac stomach size, allowing an approximation of crab dietary strategies without the need to sacrifice and dissect individual animals. We used literature values for mean diet and standardized external gut size markings taken from crab photographs across 50 species to show that percent herbivory in the diet increases non-linearly across species of brachyuran crab with the external estimate of gut size. We also used data from dissections in four species to show that external gut markings were positively correlated with gut sizes, though the strength of this correlation differed across species. We conclude that when rough approximations of diet quality such as percent herbivory will suffice, measuring external carapace markings in crabs presents a quick, free, non-lethal alternative to dissections. Our results also provide important insights into tradeoffs that occur in crab morphology and have implications for crab evolution.
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Affiliation(s)
| | - Zachary J. Cannizzo
- National Oceanic and Atmospheric Administration Office of National Marine Sanctuaries—National Marine Protected Areas Center, Washington DC, United States
| | - Jade Carver
- Department of Biology, Brigham Young University, Provo, Utah, United States
| | - Robert P. Dunn
- Baruch Marine Field Laboratory, University of South Carolina, Georgetown, South Carolina, United States
- North Inlet-Winyah Bay National Estuarine Research Reserve, Georgetown, South Carolina, United States
| | - Laura S. Fletcher
- Department of Biology, Brigham Young University, Provo, Utah, United States
| | - Matthew E. Kimball
- Baruch Marine Field Laboratory, University of South Carolina, Georgetown, South Carolina, United States
| | | | - Brenden Orocu
- Department of Biology, Brigham Young University, Provo, Utah, United States
| | - Bruce W. Pfirrmann
- Baruch Marine Field Laboratory, University of South Carolina, Georgetown, South Carolina, United States
| | - Emily Pinkston
- Department of Biology, Brigham Young University, Provo, Utah, United States
| | - Tanner C. Reese
- Department of Biology, Brigham Young University, Provo, Utah, United States
| | - Nanette Smith
- Department of Biology, Brigham Young University, Provo, Utah, United States
| | - Carter Stancil
- Department of Biology, Brigham Young University, Provo, Utah, United States
| | - Benjamin J. Toscano
- Department of Biology, Trinity College, Hartford, Connecticut, United States
| | - Blaine D. Griffen
- Department of Biology, Brigham Young University, Provo, Utah, United States
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6
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Fletcher LS, Bolander M, Reese TC, Asay EG, Pinkston E, Griffen BD. Metabolic rates of the Asian shore crab Hemigrapsus sanguineus in air as a function of body size, location, and injury. Ecol Evol 2022; 12:e9297. [PMID: 36177136 PMCID: PMC9463042 DOI: 10.1002/ece3.9297] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 11/07/2022] Open
Abstract
Rapid warming in the Gulf of Maine may influence the success or invasiveness of the Asian shore crab, Hemigrapsus sanguineus. To better predict the effects of climate change on this invasive species, it is necessary to measure its energy dynamics under a range of conditions. However, previous research has only focused on the metabolism of this intertidal species in water. We sampled adult crabs from three different sites and measured their metabolic rates in the air. We show that metabolic rate increases with body mass and the number of missing limbs, but decreases with the number of regenerating limbs, possibly reflecting the timing of energy allocation to limb regeneration. Importantly, metabolic rates measured here in the air are ~4× higher than metabolic rates previously measured for this species in water. Our results provide baseline measurements of aerial metabolic rates across body sizes, which may be affected by climate change. With a better understanding of respiration in H. sanguineus, we can make more informed predictions about the combined effects of climate change and invasive species on the northeast coasts of North America.
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Affiliation(s)
| | | | | | | | - Emily Pinkston
- Department of BiologyBrigham Young UniversityProvoUtahUSA
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7
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Pantaleón García J, Kulkarni VV, Reese TC, Wali S, Wase SJ, Zhang J, Singh R, Caetano MS, Kadara H, Moghaddam S, Johnson FM, Wang J, Wang Y, Evans S. OBIF: an omics-based interaction framework to reveal molecular drivers of synergy. NAR Genom Bioinform 2022; 4:lqac028. [PMID: 35387383 PMCID: PMC8982434 DOI: 10.1093/nargab/lqac028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 01/08/2023] Open
Abstract
Bioactive molecule library screening may empirically identify effective combination therapies, but molecular mechanisms underlying favorable drug–drug interactions often remain unclear, precluding further rational design. In the absence of an accepted systems theory to interrogate synergistic responses, we introduce Omics-Based Interaction Framework (OBIF) to reveal molecular drivers of synergy through integration of statistical and biological interactions in synergistic biological responses. OBIF performs full factorial analysis of feature expression data from single versus dual exposures to identify molecular clusters that reveal synergy-mediating pathways, functions and regulators. As a practical demonstration, OBIF analyzed transcriptomic and proteomic data of a dyad of immunostimulatory molecules that induces synergistic protection against influenza A and revealed unanticipated NF-κB/AP-1 cooperation that is required for antiviral protection. To demonstrate generalizability, OBIF analyzed data from a diverse array of Omics platforms and experimental conditions, successfully identifying the molecular clusters driving their synergistic responses. Hence, unlike existing synergy quantification and prediction methods, OBIF is a phenotype-driven systems model that supports multiplatform interrogation of synergy mechanisms.
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Affiliation(s)
- Jezreel Pantaleón García
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Vikram V Kulkarni
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Tanner C Reese
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- Rice University, Houston, TX 77005, USA
| | - Shradha Wali
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Saima J Wase
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ratnakar Singh
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Mauricio S Caetano
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Faye M Johnson
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongxing Wang
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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