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Full-Text Articles in Life Sciences

How Viruses Grant Superpowers To Their Hosts: Investigating Prophage-Dependent Immunity In Cluster F Phages Through Genetic Engineering Of The Immunity Repressor Gene, Kassidy Espinosa, Kirk Anders Oct 2024

How Viruses Grant Superpowers To Their Hosts: Investigating Prophage-Dependent Immunity In Cluster F Phages Through Genetic Engineering Of The Immunity Repressor Gene, Kassidy Espinosa, Kirk Anders

Biology Student Scholarship

Using genetic engineering to clone the immunity repressor gene in Cluster F phages has provided insights into prophage-dependent immunity. My research builds on the work of previous students, offering a deeper understanding of how bacteriophages confer immunity to their bacterial hosts.


Fire And Ant Interactions Mediated By Honeydew And Extrafloral Nectar In An Australian Tropical Savanna, Fernanda M. P. Oliveira, Carlos H. F Silva, Melinda L. Moir, Inara R. Leal, Alan N. Andersen Oct 2024

Fire And Ant Interactions Mediated By Honeydew And Extrafloral Nectar In An Australian Tropical Savanna, Fernanda M. P. Oliveira, Carlos H. F Silva, Melinda L. Moir, Inara R. Leal, Alan N. Andersen

Natural Resources Research Articles

Fire is a major disturbance affecting ecosystems globally, but its impact on mutualisms has received minimal attention. Here, we use a long-term field experiment to investigate the impact of different fire regimes on globally important ant–honeydew and ant–extrafloral nectar (EFN) mutualistic interactions in an Australian tropical savanna. These interactions provide ants with a key energy source, while their plant and hemipteran hosts receive protection services. We examined ant interactions on species of Eucalyptus (lacking EFNs) and Acacia (with EFNs) in three replicate plots each of burning every 2 and 3 years early in the dry season, burning late in the …


Sars-Cov-2 Vaccine Improved Hemostasis Of A Patient With Protein S Deficiency: A Case Report, Mohammad A. Mohammad, Alaa Malik, Lekha Thangada, Diana Polanía-Villanueva, Jovanny Zabaleta, Rinku Majumder Oct 2024

Sars-Cov-2 Vaccine Improved Hemostasis Of A Patient With Protein S Deficiency: A Case Report, Mohammad A. Mohammad, Alaa Malik, Lekha Thangada, Diana Polanía-Villanueva, Jovanny Zabaleta, Rinku Majumder

School of Medicine Faculty Publications

A 16-year-old patient, while an infant, incurred right-sided hemiparesis and had difficulty breast feeding. She was later diagnosed with a neonatal stroke and her genetic testing showed a missense mutation in her PROS1 (Protein S) gene. Both her grandfather and father, but not her mother, had hereditary Protein S (PS) deficiency. The patient was not prescribed any mediation due to her young age but was frequently checked by her physician. The patient’s plasma was first collected at the age of 13, and the isolated plasma from the patient and her father were analyzed by aPTT, thrombin generation, and enzyme-linked immunosorbent …


Multiregional Transcriptomic Profiling Provides Improved Prognostic Insight In Localized Non-Small Cell Lung Cancer, Chenyang Li, Thinh T Nguyen, Jian-Rong Li, Xingzhi Song, Junya Fujimoto, Curtis Gumb, Ignacio I Wistuba, Andrew P Futreal, Jianhua Zhang, Shawna M Hubert, John V Heymach, Jia Wu, Christopher I Amos, Jianjun Zhang, Chao Cheng Oct 2024

Multiregional Transcriptomic Profiling Provides Improved Prognostic Insight In Localized Non-Small Cell Lung Cancer, Chenyang Li, Thinh T Nguyen, Jian-Rong Li, Xingzhi Song, Junya Fujimoto, Curtis Gumb, Ignacio I Wistuba, Andrew P Futreal, Jianhua Zhang, Shawna M Hubert, John V Heymach, Jia Wu, Christopher I Amos, Jianjun Zhang, Chao Cheng

Faculty, Staff and Student Publications

Lung Cancer remains the leading cause of cancer deaths in the USA and worldwide. Non-small cell lung cancer (NSCLC) harbors high transcriptomic intratumor heterogeneity (RNA-ITH) that limits the reproducibility of expression-based prognostic models. In this study, we used multiregional RNA-seq data (880 tumor samples from 350 individuals) from both public (TRACERx) and internal (MDAMPLC) cohorts to investigate the effect of RNA-ITH on prognosis in localized NSCLC at the gene, signature, and tumor microenvironment levels. At the gene level, the maximal expression of hazardous genes (expression negatively associated with survival) but the minimal expression of protective genes (expression positively associated with …


Uroplectes Ebogo Sp. N. (Scorpiones: Buthidae) From Cameroon, František Kovařík, František Šťáhlavský, Valeriy Govorov Oct 2024

Uroplectes Ebogo Sp. N. (Scorpiones: Buthidae) From Cameroon, František Kovařík, František Šťáhlavský, Valeriy Govorov

Euscorpius

A new species Uroplectes ebogo sp. n. is described from Cameroon, fully illustrated with color photos showing its morphology and habitus. Uroplectes ebogo sp. n. is the only species of the genus with a combination two characters: metasoma without carinae and metasoma V and telson without punctuation. In addition to morphology and hemispermatophore, we also present the information about the karyotype of Uroplectes ebogo sp. n. (2n=24).


Resolving The Contradictory Conclusions From Three Reviews Of Controlled Longitudinal Studies Of Physical Punishment: A Meta-Analysis, C.J. Ferguson, J. Pritsker, M.L. Gunnoe, R.E. Larzelere Oct 2024

Resolving The Contradictory Conclusions From Three Reviews Of Controlled Longitudinal Studies Of Physical Punishment: A Meta-Analysis, C.J. Ferguson, J. Pritsker, M.L. Gunnoe, R.E. Larzelere

University Faculty Publications and Creative Works

Larzelere, R.E., Gunnoe, M.L., Pritsker, J., & Ferguson, C.J. (2024). Resolving the Contradictory Conclusions from Three Reviews of Controlled Longitudinal Studies of Physical Punishment: A Meta-Analysis. Marriage & Family Review, 60 (7), 395-433. https://doi.org/10.1080/01494929.2024.2392672


Aridity Drives The Response Of Soil Total And Particulate Organic Carbon To Drought In Temperate Grasslands And Shrublands, Baoku Shi, Manuel Delgado-Baquerizo, Alan K. Knapp, Melinda D. Smith, Sasha Reed, Brooke Osborne, Yolima Carrillo, Fernando T. Maestre, Yu Zhu, Anping Chen, Kate Wilkins, Martin C. Holdrege, Andrew Kulmatiski, Catherine Picon-Cochard, Christiane Roscher, Sally Power, Kerry M. Byrne, Amber C. Churchill, Anke Jentsch, Hugh A. L. Henry, Karen H. Beard, Max A. Schuchardt, Nico Eisenhauer, Rafael Otfinowski, Yann Hautier, Huitao Shen, Yonghui Wang, Zhongwu Wang, Chengliang Wang, Daniela Francis Cusack, Alessandro Petraglia, Michele Carbognani, T’Ai G.W. Forte, S. Luke Flory, Pengli Hou, Tao Zhang, Weifeng Gao, Wei Sun Oct 2024

Aridity Drives The Response Of Soil Total And Particulate Organic Carbon To Drought In Temperate Grasslands And Shrublands, Baoku Shi, Manuel Delgado-Baquerizo, Alan K. Knapp, Melinda D. Smith, Sasha Reed, Brooke Osborne, Yolima Carrillo, Fernando T. Maestre, Yu Zhu, Anping Chen, Kate Wilkins, Martin C. Holdrege, Andrew Kulmatiski, Catherine Picon-Cochard, Christiane Roscher, Sally Power, Kerry M. Byrne, Amber C. Churchill, Anke Jentsch, Hugh A. L. Henry, Karen H. Beard, Max A. Schuchardt, Nico Eisenhauer, Rafael Otfinowski, Yann Hautier, Huitao Shen, Yonghui Wang, Zhongwu Wang, Chengliang Wang, Daniela Francis Cusack, Alessandro Petraglia, Michele Carbognani, T’Ai G.W. Forte, S. Luke Flory, Pengli Hou, Tao Zhang, Weifeng Gao, Wei Sun

Wildland Resources Faculty Publications

The increasing prevalence of drought events in grasslands and shrublands worldwide potentially has impacts on soil organic carbon (SOC). We leveraged the International Drought Experiment to study how SOC, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) concentrations, responds to extreme drought treatments (1-in-100-year) for 1 to 5 years at 19 sites worldwide. In more mesic areas (aridity index > 0.65), SOC and POC concentrations decreased by 7.9% (±3.9) and 15.9% (±6.2) with drought, respectively, but there were no impacts on MAOC concentrations. However, drought had no impact on SOC, POC, or MAOC concentrations in drylands (aridity index < 0.65). The response of SOC to drought varied along an aridity gradient, concomitant with interannual precipitation variability and standing SOC concentration gradients. These findings highlight the differing response magnitudes of POC and MAOC concentrations to drought and the key regulating role of aridity.


Two New Species Of Agrilus Curtis From Arizona With Some New Distributional And Host Records Of Buprestids From The Southwest Usa (Coleoptera: Buprestidae), Norman E. Woodley Oct 2024

Two New Species Of Agrilus Curtis From Arizona With Some New Distributional And Host Records Of Buprestids From The Southwest Usa (Coleoptera: Buprestidae), Norman E. Woodley

Insecta Mundi

Two new species of Agrilus Curtis (Coleoptera: Buprestidae), A. botzi Woodley, new species and A. vachellia Woodley new species, both from southeastern Arizona, are described. Agrilus barri Hespenheide and Westcott and Taphrocerus leoni Dugès are recorded from Arizona and represent new U.S. records. Sixteen new state distributional records are presented, along with a few other significant records.


Oregon State Rank Assessment For Nerite Ramshorn (Vorticifex Neritoides), Jesse Laney Oct 2024

Oregon State Rank Assessment For Nerite Ramshorn (Vorticifex Neritoides), Jesse Laney

Institute for Natural Resources Publications

Oregon state conservation status assessment for nerite ramshorn (Vorticifex neritoides) using NatureServe methodology, 2024.


Oregon State Rank Assessment For Mann's Mollusk-Eating Ground Beetle (Scaphinotus Mannii), Jesse Laney Oct 2024

Oregon State Rank Assessment For Mann's Mollusk-Eating Ground Beetle (Scaphinotus Mannii), Jesse Laney

Institute for Natural Resources Publications

Oregon state conservation status assessment for Mann's mollusk-eating ground beetle (Scaphinotus mannii) using NatureServe methodology, 2024.


Oregon State Rank Assessment For Yuma Myotis (Myotis Yumanensis), Jesse Laney Oct 2024

Oregon State Rank Assessment For Yuma Myotis (Myotis Yumanensis), Jesse Laney

Institute for Natural Resources Publications

Oregon state conservation status assessment for Yuma myotis (Myotis yumanensis) using NatureServe methodology, 2024.


Integrating Multiple Biodiversity Metrics To Assess Diatom Diversity And Diatom/Macrophyte Host Specificity In Four Florida Benchmark Lakes, Alana Jade Bronk Oct 2024

Integrating Multiple Biodiversity Metrics To Assess Diatom Diversity And Diatom/Macrophyte Host Specificity In Four Florida Benchmark Lakes, Alana Jade Bronk

USF Tampa Graduate Theses and Dissertations

Biodiversity is declining across all natural environments, however, freshwater systems are thought to be among the most threatened. Quantifying and understanding trends in freshwater biodiversity has become more urgent as rapid biodiversity loss continues. To provide a robust ecological assessment, more than one bioindicator should be used, along with multiple biodiversity metrics. Macrophytes and diatoms are important components of aquatic systems, especially in shallow lakes. The relationship between macrophytes and epiphytic diatoms, though, is not clearly understood, and has not been well-studied, particularly in Florida, which has the largest abundance of natural freshwater lakes in the southeastern U.S This study …


A Multivariate Approach To Assessing Landscape Structure Effects On Wildlife Crossing Structure Use, Thomas J. Yamashita, Humberto L. Perotto-Baldivieso, David B. Wester, Kevin W. Ryer, Richard J. Kline, Michael E. Tewes, John H. Young Jr., Jason V. Lombardi Oct 2024

A Multivariate Approach To Assessing Landscape Structure Effects On Wildlife Crossing Structure Use, Thomas J. Yamashita, Humberto L. Perotto-Baldivieso, David B. Wester, Kevin W. Ryer, Richard J. Kline, Michael E. Tewes, John H. Young Jr., Jason V. Lombardi

School of Earth, Environmental, & Marine Sciences Faculty Publications

Background

Complexity in landscape structure is often assessed using individual metrics related to ecological processes. However, this rarely incorporates important relationships among metrics and may miss landscape structure effects. Multivariate statistics provide techniques for assessing overall landscape structure effects. We assessed how multivariate statistics could be used to connect landscape structure with an ecological process [bobcat (Lynx rufus) wildlife crossing structure (WCS) use]. We tested how landscape structure at WCS sites compared to the surrounding landscape and how structure affected detections at WCS sites. Our study was conducted in Cameron County, Texas, USA where WCSs are in various …


Strategic Light Use Efficiency Optimization Of Hydroponic Lettuce Exposed To Different Photosynthetic Photon Flux Densities, Peyton Lou Palsha, Marc W, Van Iersel, Ryan W. Dickson, Lynne Seymour, Kuan Qin, Rhuanito Saranz Ferrarezi Oct 2024

Strategic Light Use Efficiency Optimization Of Hydroponic Lettuce Exposed To Different Photosynthetic Photon Flux Densities, Peyton Lou Palsha, Marc W, Van Iersel, Ryan W. Dickson, Lynne Seymour, Kuan Qin, Rhuanito Saranz Ferrarezi

Horticulture Faculty Publications and Presentations

Light use efficiency characterizes the ability of a crop to convert radiation into biomass. Determining optimum cultivar-specific photosynthetic photon flux density (PPFD) values from sole-source lighting can be used to optimize leaf expansion, maximize biomass, and shorten the production period. This study evaluated the growth of hydroponic lettuce (Lactuca sativa) ‘Rex’ cultivated under different PPFD levels using sole-source lighting. At lower PPFD levels of 201 to 292 µmol·m−2·s−1, the plant projected canopy size (PCS) and specific leaf area increased to enhance light capture by 36.2% as compared to higher PPFD levels (333 and 413 µmol·m−2 …


Encyclopedia Of Scale Insect Pests: Corrigenda And Additions, Takumasa Kondo, Gillian W. Watson Oct 2024

Encyclopedia Of Scale Insect Pests: Corrigenda And Additions, Takumasa Kondo, Gillian W. Watson

Insecta Mundi

The Encyclopedia of Scale Insect Pests was published in 2022 by CABI Publishing. Some errors and omissions in Chapter 2, Table 2 have been brought to the attention of the Encyclopedia editors; since some of them have plant quarantine implications, they are corrected in this article.


Biology Of Aproida Balyi Pascoe, 1863 (Coleoptera: Chrysomelidae: Cassidinae: Aproidini) On Its Host Plant, Eustrephus Latifolius R. Br. Ex Ker-Gawl (Asparagaceae) In Australia, Caroline Simmrita Chaboo, Vivian E., Mariana Campos, Geoff B. Monteith Oct 2024

Biology Of Aproida Balyi Pascoe, 1863 (Coleoptera: Chrysomelidae: Cassidinae: Aproidini) On Its Host Plant, Eustrephus Latifolius R. Br. Ex Ker-Gawl (Asparagaceae) In Australia, Caroline Simmrita Chaboo, Vivian E., Mariana Campos, Geoff B. Monteith

Insecta Mundi

Within the leaf-beetle subfamily Cassidinae (Coleoptera: Chrysomelidae), Aproida Pascoe, 1863 (Aproidini) from Australia has been considered a transitional genus between mining cassidines (“hispines”) and exophagous cassidines (“tortoise beetles”). To illuminate this transition, a detailed study was conducted over one year of the biology of Aproida balyi Pascoe, 1863 on the host plant, Eustrephus latifolius R. Br. ex Ker-Gawl (Asparagaceae). Distribution maps of the host plant and three Aproida species are provided. The life cycle of A. balyi comprises single eggs in a foamy ootheca, three larval instars that feed openly, a pupa suspended from the larva III exuvia, and …


Cd28 Costimulation Augments Car Signaling In Nk Cells Via The Lck/Cd3Ζ/Zap70 Signaling Axis, Sunil Acharya, Rafet Basar, May Daher, Hind Rafei, Ping Li, Emily Ensley, Bijender Kumar, Pinaki P Banerjee, Luciana Melo Garcia, Paul Lin, Vakul Mohanty, Kun H Kim, Xianli Jiang, Yuchen Pan, Ye Li, Bin Liu, Ana K Nunez Cortes, Chenyu Zhang, Mohsen Fathi, Ali Rezvan, Melisa J Montalvo, Sophia L Cha, Francia Reyes-Silva, Rejeena Shrestha, Xingliang Guo, Kiran Kundu, Alexander Biederstädt, Luis Muniz-Feliciano, Gary M Deyter, Mecit Kaplan, Xin R Jiang, Enli Liu, Antrix Jain, Janos Roszik, Natalie W Fowlkes, Luisa M Solis Soto, Maria G Raso, Joseph D Khoury, Pei Lin, Francisco Vega, Navin Varadarajan, Ken Chen, David Marin, Elizabeth J Shpall, Katayoun Rezvani Oct 2024

Cd28 Costimulation Augments Car Signaling In Nk Cells Via The Lck/Cd3Ζ/Zap70 Signaling Axis, Sunil Acharya, Rafet Basar, May Daher, Hind Rafei, Ping Li, Emily Ensley, Bijender Kumar, Pinaki P Banerjee, Luciana Melo Garcia, Paul Lin, Vakul Mohanty, Kun H Kim, Xianli Jiang, Yuchen Pan, Ye Li, Bin Liu, Ana K Nunez Cortes, Chenyu Zhang, Mohsen Fathi, Ali Rezvan, Melisa J Montalvo, Sophia L Cha, Francia Reyes-Silva, Rejeena Shrestha, Xingliang Guo, Kiran Kundu, Alexander Biederstädt, Luis Muniz-Feliciano, Gary M Deyter, Mecit Kaplan, Xin R Jiang, Enli Liu, Antrix Jain, Janos Roszik, Natalie W Fowlkes, Luisa M Solis Soto, Maria G Raso, Joseph D Khoury, Pei Lin, Francisco Vega, Navin Varadarajan, Ken Chen, David Marin, Elizabeth J Shpall, Katayoun Rezvani

Faculty, Staff and Student Publications

Multiple factors in the design of a chimeric antigen receptor (CAR) influence CAR T-cell activity, with costimulatory signals being a key component. Yet, the impact of costimulatory domains on the downstream signaling and subsequent functionality of CAR-engineered natural killer (NK) cells remains largely unexplored. Here, we evaluated the impact of various costimulatory domains on CAR-NK cell activity, using a CD70-targeting CAR. We found that CD28, a costimulatory molecule not inherently present in mature NK cells, significantly enhanced the antitumor efficacy and long-term cytotoxicity of CAR-NK cells both in vitro and in multiple xenograft models of hematologic and solid tumors. Mechanistically, …


Tissue-Agnostic Targeting Of Neurotrophic Tyrosine Receptor Kinase Fusions: Current Approvals And Future Directions, Mohamed A Gouda, Kyaw Z Thein, David S Hong Oct 2024

Tissue-Agnostic Targeting Of Neurotrophic Tyrosine Receptor Kinase Fusions: Current Approvals And Future Directions, Mohamed A Gouda, Kyaw Z Thein, David S Hong

Faculty, Staff and Student Publications

NTRK fusions are oncogenic drivers for multiple tumor types. Therefore, the development of selective tropomyosin receptor kinase (TRK) inhibitors, including larotrectinib and entrectinib, has been transformative in the context of clinical management, given the high rates of responses to these drugs, including intracranial responses in patients with brain metastases. Given their promising activity in pan-cancer cohorts, larotrectinib and entrectinib received U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA) approval for tissue-agnostic indications in patients with advanced solid tumors harboring NTRK fusions. The safety profiles for both drugs are quite manageable, although neurotoxicity driven by the on-target inhibition …


Biologic And Clinical Analysis Of Childhood Gamma Delta T-All Identifies Lmo2/Stag2 Rearrangements As Extremely High Risk, Shunsuke Kimura, Chun Shik Park, Lindsey E Montefiori, Ilaria Iacobucci, Petri Pölönen, Elizabeth D Arnold, Anthony Brown, Barbara Buldini, Kenneth J Caldwell, Yunchao Chang, Chelsey Chen, Cheng Cheng, Zhongshan Cheng, John Choi, Valentino Conter, Kristine R Crews, Hester A De Groot-Kruseman, Takao Deguchi, Mariko Eguchi, Hannah E Muhle, Sarah Elitzur, Gabriele Escherich, Burgess B Freeman, Zhaohui Gu, Katie Han, Keizo Horibe, Toshihiko Imamura, Sima Jeha, Motohiro Kato, Kean H Chiew, Tanya Khan, Michal Kicinski, Stefan Köhrer, Steven M Kornblau, Rishi S Kotecha, Chi-Kong Li, Yen-Chun Liu, Franco Locatelli, Selina M Luger, Elisabeth M Paietta, Atsushi Manabe, Hanne V Marquart, Riccardo Masetti, Mellissa Maybury, Pauline Mazilier, Jules P P Meijerink, Sharnise Mitchell, Takako Miyamura, Andrew S Moore, Koichi Oshima, Katarzyna Pawinska-Wasikowska, Rob Pieters, Mollie S Prater, Shondra M Pruett-Miller, Ching-Hon Pui, Chunxu Qu, Michaela Reiterova, Noemi Reyes, Kathryn G Roberts, Jacob M Rowe, Atsushi Sato, Kjeld Schmiegelow, Martin Schrappe, Shuhong Shen, Szymon Skoczeń, Orietta Spinelli, Jan Stary, Michael Svaton, Masatoshi Takagi, Junko Takita, Yanjing Tang, David T Teachey, Paul G Thomas, Daisuke Tomizawa, Jan Trka, Elena Varotto, Tiffaney L Vincent, Jun J Yang, Allen E J Yeoh, Yinmei Zhou, Martin Zimmermann, Hiroto Inaba, Charles G Mullighan Oct 2024

Biologic And Clinical Analysis Of Childhood Gamma Delta T-All Identifies Lmo2/Stag2 Rearrangements As Extremely High Risk, Shunsuke Kimura, Chun Shik Park, Lindsey E Montefiori, Ilaria Iacobucci, Petri Pölönen, Elizabeth D Arnold, Anthony Brown, Barbara Buldini, Kenneth J Caldwell, Yunchao Chang, Chelsey Chen, Cheng Cheng, Zhongshan Cheng, John Choi, Valentino Conter, Kristine R Crews, Hester A De Groot-Kruseman, Takao Deguchi, Mariko Eguchi, Hannah E Muhle, Sarah Elitzur, Gabriele Escherich, Burgess B Freeman, Zhaohui Gu, Katie Han, Keizo Horibe, Toshihiko Imamura, Sima Jeha, Motohiro Kato, Kean H Chiew, Tanya Khan, Michal Kicinski, Stefan Köhrer, Steven M Kornblau, Rishi S Kotecha, Chi-Kong Li, Yen-Chun Liu, Franco Locatelli, Selina M Luger, Elisabeth M Paietta, Atsushi Manabe, Hanne V Marquart, Riccardo Masetti, Mellissa Maybury, Pauline Mazilier, Jules P P Meijerink, Sharnise Mitchell, Takako Miyamura, Andrew S Moore, Koichi Oshima, Katarzyna Pawinska-Wasikowska, Rob Pieters, Mollie S Prater, Shondra M Pruett-Miller, Ching-Hon Pui, Chunxu Qu, Michaela Reiterova, Noemi Reyes, Kathryn G Roberts, Jacob M Rowe, Atsushi Sato, Kjeld Schmiegelow, Martin Schrappe, Shuhong Shen, Szymon Skoczeń, Orietta Spinelli, Jan Stary, Michael Svaton, Masatoshi Takagi, Junko Takita, Yanjing Tang, David T Teachey, Paul G Thomas, Daisuke Tomizawa, Jan Trka, Elena Varotto, Tiffaney L Vincent, Jun J Yang, Allen E J Yeoh, Yinmei Zhou, Martin Zimmermann, Hiroto Inaba, Charles G Mullighan

Faculty, Staff and Student Publications

Acute lymphoblastic leukemia expressing the gamma delta T-cell receptor (γδ T-ALL) is a poorly understood disease. We studied 200 children with γδ T-ALL from 13 clinical study groups to understand the clinical and genetic features of this disease. We found age and genetic drivers were significantly associated with outcome. γδ T-ALL diagnosed in children under 3 years of age was extremely high-risk and enriched for genetic alterations that result in both LMO2 activation and STAG2 inactivation. Mechanistically, using patient samples and isogenic cell lines, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping, resulting in …


The History Of Chromosomal Instability In Genome-Doubled Tumors, Toby M Baker, Siqi Lai, Andrew R Lynch, Tom Lesluyes, Haixi Yan, Annelien Verfaillie, Amy L Bowes, Nischalan Pillay, Adrienne M Flanagan, Charles Swanton, Paul T Spellman, Maxime Tarabichi, Peter Van Loo Oct 2024

The History Of Chromosomal Instability In Genome-Doubled Tumors, Toby M Baker, Siqi Lai, Andrew R Lynch, Tom Lesluyes, Haixi Yan, Annelien Verfaillie, Amy L Bowes, Nischalan Pillay, Adrienne M Flanagan, Charles Swanton, Paul T Spellman, Maxime Tarabichi, Peter Van Loo

Faculty, Staff and Student Publications

Tumors frequently display high chromosomal instability and contain multiple copies of genomic regions. Here, we describe Gain Route Identification and Timing In Cancer (GRITIC), a generic method for timing genomic gains leading to complex copy number states, using single-sample bulk whole-genome sequencing data. By applying GRITIC to 6,091 tumors, we found that non-parsimonious evolution is frequent in the formation of complex copy number states in genome-doubled tumors. We measured chromosomal instability before and after genome duplication in human tumors and found that late genome doubling was followed by an increase in the rate of copy number gain. Copy number gains …


Multi-Ancestry Gwas Meta-Analyses Of Lung Cancer Reveal Susceptibility Loci And Elucidate Smoking-Independent Genetic Risk, Bryan R Gorman, Sun-Gou Ji, Michael Francis, Anoop K Sendamarai, Yunling Shi, Uma Saxena, Andrea K Devito, Jinyoung Byun, Younghun Han, Xiangjun Xiao, Don D Sin, Wim Timens, Jennifer Moser, Sumitra Muralidhar, Rachel Ramoni, Rayjean J Hung, James D Mckay, Yohan Bossé, Ryan Sun, Christopher I Amos, Va Million Veteran Program, Saiju Pyarajan Oct 2024

Multi-Ancestry Gwas Meta-Analyses Of Lung Cancer Reveal Susceptibility Loci And Elucidate Smoking-Independent Genetic Risk, Bryan R Gorman, Sun-Gou Ji, Michael Francis, Anoop K Sendamarai, Yunling Shi, Uma Saxena, Andrea K Devito, Jinyoung Byun, Younghun Han, Xiangjun Xiao, Don D Sin, Wim Timens, Jennifer Moser, Sumitra Muralidhar, Rachel Ramoni, Rayjean J Hung, James D Mckay, Yohan Bossé, Ryan Sun, Christopher I Amos, Va Million Veteran Program, Saiju Pyarajan

Faculty, Staff and Student Publications

Lung cancer remains the leading cause of cancer mortality, despite declining smoking rates. Previous lung cancer GWAS have identified numerous loci, but separating the genetic risks of lung cancer and smoking behavioral susceptibility remains challenging. Here, we perform multi-ancestry GWAS meta-analyses of lung cancer using the Million Veteran Program cohort (approximately 95% male cases) and a previous study of European-ancestry individuals, jointly comprising 42,102 cases and 181,270 controls, followed by replication in an independent cohort of 19,404 cases and 17,378 controls. We then carry out conditional meta-analyses on cigarettes per day and identify two novel, replicated loci, including the 19p13.11 …


An Experiment Study On Implementing Syngas On A Small Generator Set, Bui Van Chinh, Khong Vu Quang, Khanh Nguyen Duc Oct 2024

An Experiment Study On Implementing Syngas On A Small Generator Set, Bui Van Chinh, Khong Vu Quang, Khanh Nguyen Duc

ASEAN Journal on Science and Technology for Development

This paper presents an experiment on syngas's influence on the performance and pollutant characteristics of a mechanical diesel engine generator set. Using syngas as an external fuel is good for medium and light loads of less than 80%. While a moderate substitution of syngas will contribute to good performance at high loads, a larger level of syngas provided may degrade engine performance. The brake-specific energy consumption rises as the replacement syngas flow increases. Using syngas as an external fuel to substitute for a part of the diesel might cause the engine to perform unstablely. The more syngas replacements, the greater …


Temperature Affects Nest Box Selection, Nest Success, And Nestling Size In A Southeastern Population Of Eastern Bluebirds, Katie Stumpf Oct 2024

Temperature Affects Nest Box Selection, Nest Success, And Nestling Size In A Southeastern Population Of Eastern Bluebirds, Katie Stumpf

Georgia Journal of Science

Given the critical role of temperature in avian reproduction, rising global temperatures will likely impact reproductive success of many bird populations. We examined the effect of nest box temperature, nest box color, entrance orientation, distance to forest cover, and distance to water on net box selection, nest success, and nestling size in eastern bluebirds (Sialia sialis) in central Georgia. White painted nest boxes had significantly cooler temperatures than control nest boxes (P < 0.05). However, model selection revealed that eastern bluebird females selected control boxes, despite their overall warmer temperatures. Nest success was associated with year, likely because of high nest predation during the warmer 2022 breeding season (P < 0.05). Nest success was also associated with cooler nest boxes, possibly because incubating females spend more time incubating which can reduce predation risks. Larger nestlings fledged from painted nest boxes, nest boxes with cooler temperatures, and nests from 2021, which we attribute to decreased thermoregulatory demands enabling faster nestling growth in cooler boxes and years. These seemingly opposing results suggest there may be an optimal temperature range where nest box temperature maximizes reproductive fitness while minimizing energetic demands on incubating adults. Determining this temperature range can help target management efforts to ensure specific goals are met.


Albinism In Olivierus Martensii (Karsch, 1879) (Scorpiones: Buthidae), Victoria Tang, Zhenbang Liu Oct 2024

Albinism In Olivierus Martensii (Karsch, 1879) (Scorpiones: Buthidae), Victoria Tang, Zhenbang Liu

Euscorpius

This is a formal case report for the albinism in Olivierus martensii (Karsch, 1879). Albino phenotype is compared with its normal counterpart in terms of their morphology and behavior by cursory experiments. The examined 7 albino individuals (5 of which were adults) were smaller and more slender than their normal counterparts. However, these quantitative differences were not statistically significant and should be treated with caution due to the low sample size. Their abilities to detect both white light and UV light or UV-excited fluorescence were not significantly undermined, although their tendency to ensure a clear vision through self-cleaning behavior appeared …


Oregon State Rank Assessment For Flightless Haliplid Beetle (Apteraliplus Parvulus), Eleanor P. Gaines Oct 2024

Oregon State Rank Assessment For Flightless Haliplid Beetle (Apteraliplus Parvulus), Eleanor P. Gaines

Institute for Natural Resources Publications

Oregon state conservation status assessment for flightless haliplid beetle (Apteraliplus parvulus) using NatureServe methodology, 2024.


Cultivation In Long-Term Simulated Microgravity Is Detrimental To Pyocyanin Production And Subsequent Biofilm Formation Ability Of Pseudomonas Aeruginosa, K. Z. M. Chen, L. M. Vu, Amy Cheng Vollmer Oct 2024

Cultivation In Long-Term Simulated Microgravity Is Detrimental To Pyocyanin Production And Subsequent Biofilm Formation Ability Of Pseudomonas Aeruginosa, K. Z. M. Chen, L. M. Vu, Amy Cheng Vollmer

Biology Faculty Works

Pseudomonas aeruginosa forms aggregates known as biofilms. Previous studies have shown that when P. aeruginosa is cultivated in space, thicker and structurally different biofilms are formed than from those grown on Earth. We investigated how microgravity, simulated in a laboratory setting, influenced the growth, colonization, and virulence potentials of a P. aeruginosa PA14 wild-type strain, as well as two surface attachment-defective (sad) mutants altered at crucial biofilm-forming steps: flgK and pelA. Using high-aspect ratio rotating-wall vessel (HARV) bioreactors, P. aeruginosa bacteria were grown to stationary phase under prolonged (6 days) exposure to simulated microgravity or normal gravity …


Oregon State Rank Assessment For Obscure Bumblebee (Bombus Caliginosus), Jesse Laney, Eleanor P. Gaines Oct 2024

Oregon State Rank Assessment For Obscure Bumblebee (Bombus Caliginosus), Jesse Laney, Eleanor P. Gaines

Institute for Natural Resources Publications

Oregon state conservation status assessment for obscure bumblebee (Bombus caliginosus) using NatureServe methodology, 2024.


Arid1a-Baf Coordinates Zic2 Genomic Occupancy For Epithelial-To-Mesenchymal Transition In Cranial Neural Crest Specification, Samantha M. Barnada, Aida Giner De Gracia, Cruz Morenilla-Palao, Maria Teresa López-Cascales, Chiara Scopa, Francis J. Waltrich, Harald M.M. Mikkers, Maria Elena Cicardi, Jonathan Karlin, Davide Trotti, Kevin A. Peterson, Samantha A. Brugmann, Gijs W.E. Santen, Steven B. Mcmahon, Eloísa Herrera, Marco Trizzino Oct 2024

Arid1a-Baf Coordinates Zic2 Genomic Occupancy For Epithelial-To-Mesenchymal Transition In Cranial Neural Crest Specification, Samantha M. Barnada, Aida Giner De Gracia, Cruz Morenilla-Palao, Maria Teresa López-Cascales, Chiara Scopa, Francis J. Waltrich, Harald M.M. Mikkers, Maria Elena Cicardi, Jonathan Karlin, Davide Trotti, Kevin A. Peterson, Samantha A. Brugmann, Gijs W.E. Santen, Steven B. Mcmahon, Eloísa Herrera, Marco Trizzino

Department of Biochemistry and Molecular Biology Faculty Papers

The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of individuals with CSS harbor variants in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS-patient-derived ARID1A induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from …


Oregon State Rank Assessment For Goose Lake Tui Chub (Siphateles Bicolor Thalassinus), Jesse Laney Oct 2024

Oregon State Rank Assessment For Goose Lake Tui Chub (Siphateles Bicolor Thalassinus), Jesse Laney

Institute for Natural Resources Publications

Oregon state conservation status assessment for Goose Lake tui chub (Siphateles bicolor thalassinus) using NatureServe methodology, 2024.


Two Lives, Shruti Trehan Mbbs Oct 2024

Two Lives, Shruti Trehan Mbbs

Journal of Wellness

A busy oncologist makes a decision to leave her busy, thriving, community practice in the Mid-West and moves to a Veterans Affairs hospital in South Florida in the quest for a better work-life balance.