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7. Index

Author

Adams, Peter

Published
2023

8. Notes

Author

Adams, Peter

Published
2023

9. Cover

Author

Adams, Peter

Published
2023

12. Epilogue

Author

Adams, Peter

Published
2023

23. Senescent glia link mitochondrial dysfunction and lipid accumulation

Author

Byrns, China N., Perlegos, Alexandra E., Miller, Karl N., Jin, Zhecheng, Carranza, Faith R., Manchandra, Palak, Beveridge, Connor H., Randolph, Caitlin E., Chaluvadi, V. Sai, Zhang, Shirley L., Srinivasan, Ananth R., Bennett, F. C., Sehgal, Amita, Adams, Peter D., Chopra, Gaurav, and Bonini, Nancy M.

Published
2024
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24. Unravelling the fluorescence kinetics of light-harvesting proteins with simulated measurements

Author

Gray, Callum, Kailas, Lekshmi, Adams, Peter G., and Duffy, Christopher D. P.

Subjects
Quantitative Biology - Molecular Networks, Quantitative Biology - Biomolecules, Quantitative Biology - Subcellular Processes
Abstract

The plant light-harvesting pigment-protein complex LHCII is the major antenna sub-unit of PSII and is generally (though not universally) accepted to play a role in photoprotective energy dissipation under high light conditions, a process known Non-Photochemical Quenching (NPQ). The underlying mechanisms of energy trapping and dissipation within LHCII are still debated. Various proposed models differ considerably in their molecular and kinetic detail, but are often based on different interpretations of very similar transient absorption measurements of isolated complexes. Here we present a simulated measurement of the fluorescence decay kinetics of quenched LHCII aggregates to determine whether this relatively simple measurement can discriminate between different potential NPQ mechanisms. We simulate not just the underlying physics (excitation, energy migration, quenching and singlet-singlet annihilation) but also the signal detection and typical experimental data analysis. Comparing this to a selection of published fluorescence decay kinetics we find that: (1) Different proposed quenching mechanisms produce noticeably different fluorescence kinetics even at low (annihilation free) excitation density, though the degree of difference is dependent on pulse width. (2) Measured decay kinetics are consistent with most LHCII trimers becoming relatively slow excitation quenchers. A small sub-population of very fast quenchers produces kinetics which do not resemble any observed measurement. (3) It is necessary to consider at least two distinct quenching mechanisms in order to accurately reproduce experimental kinetics, supporting the idea that NPQ is not a simple binary switch switch., Comment: 5 figures, original research article submitted to BBA-Bioenergetics

Published
2023

29. Simulations of near-source wind development and pollution dispersion over complex terrain under different thermal conditions

Author

Li, Zhihao, Tanzer-Gruener, Rebecca, Presto, Albert, Adams, Peter, and Singh, Satbir

Subjects
Physics - Fluid Dynamics, Physics - Computational Physics
Abstract

A computational fluid dynamics (CFD) model that solves the steady-state Reynolds-Averaged Navier-Stokes (RANS) equations for buoyant compressible pollution dispersion under different meteorological conditions is developed. A 6.4 km by 6.4 km computational domain over a complex terrain with a height of 1 km above the ground surface is created. Meteorological data from multiple available sources are utilized to obtain boundary conditions of wind speed, air temperature, turbulent kinetic energy (TKE), and its dissipation rate. To evaluate the model, a monitoring network of four anemometers is deployed. Model predictions are compared with measurements of wind speed and the concentration of SO2 emitted by a local coke plant. Comparisons show that the predicted wind speeds are reasonably close to the measured mean wind speeds and the average error is within 10 percent at one location where relative fast wind speeds are recorded. The CFD model also predicts the correct trend of varying wind speeds across multiple sites of different elevations. The model also provides good predictions of SO2 concentrations for multiple cases, considering the complex nature of the terrain and meteorological conditions.

Published
2022

30. Apoptotic stress causes mtDNA release during senescence and drives the SASP

Author

Victorelli, Stella, Salmonowicz, Hanna, Chapman, James, Martini, Helene, Vizioli, Maria Grazia, Riley, Joel S., Cloix, Catherine, Hall-Younger, Ella, Machado Espindola-Netto, Jair, Jurk, Diana, Lagnado, Anthony B., Sales Gomez, Lilian, Farr, Joshua N., Saul, Dominik, Reed, Rebecca, Kelly, George, Eppard, Madeline, Greaves, Laura C., Dou, Zhixun, Pirius, Nicholas, Szczepanowska, Karolina, Porritt, Rebecca A., Huang, Huijie, Huang, Timothy Y., Mann, Derek A., Masuda, Claudio Akio, Khosla, Sundeep, Dai, Haiming, Kaufmann, Scott H., Zacharioudakis, Emmanouil, Gavathiotis, Evripidis, LeBrasseur, Nathan K., Lei, Xue, Sainz, Alva G., Korolchuk, Viktor I., Adams, Peter D., Shadel, Gerald S., Tait, Stephen W. G., and Passos, João F.

Published
2023
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33. Guidelines for minimal information on cellular senescence experimentation in vivo

Author

Ogrodnik, Mikolaj, Carlos Acosta, Juan, Adams, Peter D., d’Adda di Fagagna, Fabrizio, Baker, Darren J., Bishop, Cleo L., Chandra, Tamir, Collado, Manuel, Gil, Jesus, Gorgoulis, Vassilis, Gruber, Florian, Hara, Eiji, Jansen-Dürr, Pidder, Jurk, Diana, Khosla, Sundeep, Kirkland, James L., Krizhanovsky, Valery, Minamino, Tohru, Niedernhofer, Laura J., Passos, João F., Ring, Nadja A.R., Redl, Heinz, Robbins, Paul D., Rodier, Francis, Scharffetter-Kochanek, Karin, Sedivy, John M., Sikora, Ewa, Witwer, Kenneth, von Zglinicki, Thomas, Yun, Maximina H., Grillari, Johannes, and Demaria, Marco

Published
2024
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35. Spatial mapping of cellular senescence: emerging challenges and opportunities

Author

Gurkar, Aditi U., Gerencser, Akos A., Mora, Ana L., Nelson, Andrew C., Zhang, Anru R., Lagnado, Anthony B., Enninful, Archibald, Benz, Christopher, Furman, David, Beaulieu, Delphine, Jurk, Diana, Thompson, Elizabeth L., Wu, Fei, Rodriguez, Fernanda, Barthel, Grant, Chen, Hao, Phatnani, Hemali, Heckenbach, Indra, Chuang, Jeffrey H., Horrell, Jeremy, Petrescu, Joana, Alder, Jonathan K., Lee, Jun Hee, Niedernhofer, Laura J., Kumar, Manoj, Königshoff, Melanie, Bueno, Marta, Sokka, Miiko, Scheibye-Knudsen, Morten, Neretti, Nicola, Eickelberg, Oliver, Adams, Peter D., Hu, Qianjiang, Zhu, Quan, Porritt, Rebecca A., Dong, Runze, Peters, Samuel, Victorelli, Stella, Pengo, Thomas, Khaliullin, Timur, Suryadevara, Vidyani, Fu, Xiaonan, Bar-Joseph, Ziv, Ji, Zhicheng, and Passos, João F.

Published
2023
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36. Giving Hope to the American Dream: Implementing a Corequisite Model of Developmental Writing

Author

Adams, Peter

Abstract

It has been twenty-seven years since a small group of faculty at the Community College of Baltimore County, faced with the discovery that two-thirds of students placed in our upper-level basic writing course never passed first year composition, began the development of the Accelerated Learning Program (ALP), one of the earliest corequisite programs in the country. This article traces that development of the ALP model and identifies the features of ALP that have now resulted in 74% of our basic writers passing first year composition. In addition, after exploring the growing phenomenon of top-down mandates concerning basic writing, it provides guidance for departments engaged in selecting the best corequisite model for their context.

Published
2020

37. Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells

Author

Missinato, Maria A., Murphy, Sean, Lynott, Michaela, Yu, Michael S., Kervadec, Anaïs, Chang, Yu-Ling, Kannan, Suraj, Loreti, Mafalda, Lee, Christopher, Amatya, Prashila, Tanaka, Hiroshi, Huang, Chun-Teng, Puri, Pier Lorenzo, Kwon, Chulan, Adams, Peter D., Qian, Li, Sacco, Alessandra, Andersen, Peter, and Colas, Alexandre R.

Published
2023
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42. Transcriptional control of leukemogenesis by the chromatin reader SGF29

Author

Barbosa, Karina, Deshpande, Anagha, Perales, Marlenne, Xiang, Ping, Murad, Rabi, Pramod, Akula Bala, Minkina, Anna, Robertson, Neil, Schischlik, Fiorella, Lei, Xue, Sun, Younguk, Brown, Adam, Amend, Diana, Jeremias, Irmela, Doench, John G., Humphries, R. Keith, Ruppin, Eytan, Shendure, Jay, Mali, Prashant, Adams, Peter D., and Deshpande, Aniruddha J.

Published
2024
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47. Author Correction: Apoptotic stress causes mtDNA release during senescence and drives the SASP

Author

Victorelli, Stella, Salmonowicz, Hanna, Chapman, James, Martini, Helene, Vizioli, Maria Grazia, Riley, Joel S., Cloix, Catherine, Hall-Younger, Ella, Machado Espindola-Netto, Jair, Jurk, Diana, Lagnado, Anthony B., Sales Gomez, Lilian, Farr, Joshua N., Saul, Dominik, Reed, Rebecca, Kelly, George, Eppard, Madeline, Greaves, Laura C., Dou, Zhixun, Pirius, Nicholas, Szczepanowska, Karolina, Porritt, Rebecca A., Huang, Huijie, Huang, Timothy Y., Mann, Derek A., Masuda, Claudio Akio, Khosla, Sundeep, Dai, Haiming, Kaufmann, Scott H., Zacharioudakis, Emmanouil, Gavathiotis, Evripidis, LeBrasseur, Nathan K., Lei, Xue, Sainz, Alva G., Korolchuk, Viktor I., Adams, Peter D., Shadel, Gerald S., Tait, Stephen W. G., and Passos, João F.

Published
2024
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49. The San Diego Nathan Shock Center: tackling the heterogeneity of aging

Author

Shadel, Gerald S, Adams, Peter D, Berggren, W Travis, Diedrich, Jolene K, Diffenderfer, Kenneth E, Gage, Fred H, Hah, Nasun, Hansen, Malene, Hetzer, Martin W, Molina, Anthony JA, Manor, Uri, Marek, Kurt, O’Keefe, David D, Pinto, Antonio FM, Sacco, Alessandra, Sharpee, Tatyana O, Shokriev, Maxim N, and Zambetti, Stefania

Subjects
Stem Cell Research - Nonembryonic - Non-Human, Aging, Biotechnology, Stem Cell Research, 1.1 Normal biological development and functioning, Underpinning research, Good Health and Well Being, Frailty, Geroscience, Humans, Heterogeneity, Organoids, Human cohort, Single-cell analysis, Machine learning
Abstract

Understanding basic mechanisms of aging holds great promise for developing interventions that prevent or delay many age-related declines and diseases simultaneously to increase human healthspan. However, a major confounding factor in aging research is the heterogeneity of the aging process itself. At the organismal level, it is clear that chronological age does not always predict biological age or susceptibility to frailty or pathology. While genetics and environment are major factors driving variable rates of aging, additional complexity arises because different organs, tissues, and cell types are intrinsically heterogeneous and exhibit different aging trajectories normally or in response to the stresses of the aging process (e.g., damage accumulation). Tackling the heterogeneity of aging requires new and specialized tools (e.g., single-cell analyses, mass spectrometry-based approaches, and advanced imaging) to identify novel signatures of aging across scales. Cutting-edge computational approaches are then needed to integrate these disparate datasets and elucidate network interactions between known aging hallmarks. There is also a need for improved, human cell-based models of aging to ensure that basic research findings are relevant to human aging and healthspan interventions. The San Diego Nathan Shock Center (SD-NSC) provides access to cutting-edge scientific resources to facilitate the study of the heterogeneity of aging in general and to promote the use of novel human cell models of aging. The center also has a robust Research Development Core that funds pilot projects on the heterogeneity of aging and organizes innovative training activities, including workshops and a personalized mentoring program, to help investigators new to the aging field succeed. Finally, the SD-NSC participates in outreach activities to educate the general community about the importance of aging research and promote the need for basic biology of aging research in particular.

Published
2021

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