119 results on '"Adams, Peter"'
Search Results
2. METTL3-mediated chromatin contacts promote stress granule phase separation through metabolic reprogramming during senescence.
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Wang, Chen, Tanizawa, Hideki, Hill, Connor, Havas, Aaron, Zhang, Qiang, Liao, Liping, Hao, Xue, Lei, Xue, Wang, Lu, Nie, Hao, Qi, Yuan, Tian, Bin, Gardini, Alessandro, Kossenkov, Andrew V., Goldman, Aaron, Berger, Shelley L., Noma, Ken-ichi, Adams, Peter D., and Zhang, Rugang
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METABOLIC reprogramming ,STRESS granules ,PHASE separation ,CHROMATIN ,GENE expression ,CELLULAR aging - Abstract
METTL3 is the catalytic subunit of the methyltransferase complex, which mediates m
6 A modification to regulate gene expression. In addition, METTL3 regulates transcription in an enzymatic activity-independent manner by driving changes in high-order chromatin structure. However, how these functions of the methyltransferase complex are coordinated remains unknown. Here we show that the methyltransferase complex coordinates its enzymatic activity-dependent and independent functions to regulate cellular senescence, a state of stable cell growth arrest. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 expression through the three-dimensional chromatin organization during senescence. Elevated Hexokinase 2 expression subsequently promotes liquid-liquid phase separation, manifesting as stress granule phase separation, by driving metabolic reprogramming. This correlates with an impairment of translation of cell-cycle related mRNAs harboring polymethylated m6 A sites. In summary, our results report a coordination of m6 A-dependent and -independent function of the methyltransferase complex in regulating senescence through phase separation driven by metabolic reprogramming. Here, the authors report that METTL3 orchestrates cellular senescence by coordinating its enzymatic activity-dependent and independent functions. METTL3-mediated chromatin loops induce phase separation via metabolic reprogramming. [ABSTRACT FROM AUTHOR]- Published
- 2024
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3. Senescent glia link mitochondrial dysfunction and lipid accumulation.
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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.
- Abstract
Senescence is a cellular state linked to ageing and age-onset disease across many mammalian species1,2. Acutely, senescent cells promote wound healing3,4 and prevent tumour formation5; but they are also pro-inflammatory, thus chronically exacerbate tissue decline. Whereas senescent cells are active targets for anti-ageing therapy6–11, why these cells form in vivo, how they affect tissue ageing and the effect of their elimination remain unclear12,13. Here we identify naturally occurring senescent glia in ageing Drosophila brains and decipher their origin and influence. Using Activator protein 1 (AP1) activity to screen for senescence14,15, we determine that senescent glia can appear in response to neuronal mitochondrial dysfunction. In turn, senescent glia promote lipid accumulation in non-senescent glia; similar effects are seen in senescent human fibroblasts in culture. Targeting AP1 activity in senescent glia mitigates senescence biomarkers, extends fly lifespan and health span, and prevents lipid accumulation. However, these benefits come at the cost of increased oxidative damage in the brain, and neuronal mitochondrial function remains poor. Altogether, our results map the trajectory of naturally occurring senescent glia in vivo and indicate that these cells link key ageing phenomena: mitochondrial dysfunction and lipid accumulation.The authors identify naturally occurring senescent glia in aged Drosophila brains and decipher their origin and influence, determining that they can appear in response to neuronal mitochondrial dysfunction and that they promote lipid accumulation, indicating that these cells link key ageing phenomena. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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4. Collective Motivational Interviewing for Substance Use Problems: Concept and Implications.
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Tse, Nick, Tse, Samson, Wong, Paul, and Adams, Peter
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MOTIVATIONAL interviewing ,SUBSTANCE abuse ,MOTIVATION (Psychology) ,SOCIAL networks ,SOCIAL support - Abstract
Collective motivational interviewing (CMI) breaks new ground by extending the theory of motivational interviewing (MI) beyond the individual to include the social network. We explain the core concepts of the six-process model of CMI, which involves multiple parties in the motivational process in embodying a spirit of "neutrality." The semi-structured manual-guided CMI was trialed in persons with substance use with the support of concerned significant others (CSOs), which demonstrated positive outcomes on motivation, social support, frequency of drug use, and adherence to long-term drug treatments. Our developed CMI approach makes a clear contribution to the theory of MI and can potentially benefit people with substance use problems with complex needs. Presently, we are refining CMI and have been applying this approach to additional clients and CSOs. We call for more studies to monitor its fidelity and wider application in populations of individuals affected by substance use disorders. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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5. Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells.
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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.
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TRANSCRIPTION factors ,HEART size ,MYOCARDIAL infarction ,ENDOTHELIAL cells ,MULTIOMICS - Abstract
Defining the mechanisms safeguarding cell fate identity in differentiated cells is crucial to improve 1) - our understanding of how differentiation is maintained in healthy tissues or altered in a disease state, and 2) - our ability to use cell fate reprogramming for regenerative purposes. Here, using a genome-wide transcription factor screen followed by validation steps in a variety of reprogramming assays (cardiac, neural and iPSC in fibroblasts and endothelial cells), we identified a set of four transcription factors (ATF7IP, JUNB, SP7, and ZNF207 [AJSZ]) that robustly opposes cell fate reprogramming in both lineage and cell type independent manners. Mechanistically, our integrated multi-omics approach (ChIP, ATAC and RNA-seq) revealed that AJSZ oppose cell fate reprogramming by 1) - maintaining chromatin enriched for reprogramming TF motifs in a closed state and 2) - downregulating genes required for reprogramming. Finally, KD of AJSZ in combination with MGT overexpression, significantly reduced scar size and improved heart function by 50%, as compared to MGT alone post-myocardial infarction. Collectively, our study suggests that inhibition of barrier to reprogramming mechanisms represents a promising therapeutic avenue to improve adult organ function post-injury. Transdifferentiation has been proposed as an approach for regenerative medicine, but the mechanisms that safeguard cell identity are not well established. Here they identify transcription factors that oppose transdifferentiation and show that knockdown of these genes improves recovery after myocardial infarction. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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6. Hematopoiesis: a BETter understanding.
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Dasgupta, Nirmalya and Adams, Peter D
- Abstract
Epigenetic modifications are known to be crucial for hematopoietic stem cell (HSC) differentiation, with the BET family member BRD4 playing a vital role in this as an epigenetic reader. In this issue of EMBO reports, Yang et al (2023) demonstrate that the absence of BRD4 leads to senescence in HSCs and hematopoietic progenitor cells (HPCs), affecting the expression of crucial genes involved in myeloid and erythroid development. These data suggest that BRD4 has a protective role in preserving histone tails, thereby sustaining normal HSC/HPC functions. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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7. Foxes at your front door? Habitat selection and home range estimation of suburban red foxes (Vulpes vulpes).
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Kobryn, Halina T., Swinhoe, Edward J., Bateman, Philip W., Adams, Peter J., Shephard, Jill M., and Fleming, Patricia A.
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HABITAT selection ,SUBURBS ,FOXES ,HOMESITES ,INTRODUCED animals ,RED fox ,CITIES & towns ,RESOURCE exploitation ,NATIVE plants - Abstract
The red fox (Vulpes vulpes) is one of the most adaptable carnivorans, thriving in cities across the globe. We used GPS-tracking of five suburban foxes across high-density residential suburbs of Perth, Western Australia to quantify (1) their habitat selection and (2) home range area. All five foxes showed statistically significant avoidance of residential locations (p < 0.001) and preference for parkland (p < 0.001), with native vegetation reserves, golf courses, and water reserves showing disproportionately greater use. Landuse category also influenced their movements, with foxes moving quickest (i.e., commuting) in proximity to roads and slowest (i.e., foraging) when they were further from roads. Three females had core home ranges (50% autocorrelated-corrected kernel density estimate; AKDE
c ) averaging 37 ± 20 ha or 95% AKDEc averaging 208 ± 196 ha. One male had a 95 ha core home range and 349 ha 95% AKDEc but the other male covered an area ~ 20 times this: using a 371 ha core home range and 7,368 ha 95% AKDEc . The extensive movement patterns we describe are likely to be common for urban foxes, with half of published home range estimates for urban foxes (principally based on VHF data) excluding data for 'lost' individuals or animals that showed 'excursions'. It is likely that the home range estimates for these urban exploiters have therefore been grossly underestimated to date. Further application of GPS trackers that allow remote download will vastly improve our understanding of habitat preference and exploitation of resources by urban foxes. [ABSTRACT FROM AUTHOR]- Published
- 2023
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8. Morphological and Functional Divergence of the Lower Jaw Between Native and Invasive Red Foxes.
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Brassard, Colline, Forbes-Harper, Jesse L., Crawford, Heather M., Stuart, John-Michael, Warburton, Natalie M., Calver, Michael C., Adams, Peter, Monchâtre-Leroy, Elodie, Barrat, Jacques, Lesellier, Sandrine, Guintard, Claude, Garès, Hélène, Larralle, Arnaud, Triquet, Raymond, Merlin, Marilaine, Cornette, Raphaël, Herrel, Anthony, and Fleming, Patricia A.
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RED fox ,MANDIBLE ,TEMPORALIS muscle ,FOXES ,GEOMETRIC approach ,EUCLIDEAN distance ,INTRODUCED species - Abstract
The introduction of European red foxes in Australia in the late mid-nineteenth century has resulted in the spread of this invasive species across the continent. The morphological and functional divergence of this relatively recently introduced population has not been explored to date, yet it may provide unique insights into adaptability of this widespread carnivore to very different environments. Here we used three-dimensional geometric morphometric approaches and dissections to explore differences in mandible form and function between two populations: one from France and the other from Western Australia. Bite force was predicted for Australian foxes using partial least squares (PLS) regression models based on the observed covariation between estimated bite force (from muscle dissections) and mandible form in French foxes. Muscle contributions were estimated based on Euclidean distances between landmarks that provide insights into muscle lever arms. Despite the greater sample size, Australian foxes show reduced variability in mandible shape compared with French foxes. The mandibles of adult French foxes tend to be slightly smaller and they also strongly differ in shape from the Australian foxes in functionally important areas of the mandible such as muscle insertion areas. This is accompanied by significant differences in the predicted bite force, even relative to size, and muscle contribution: the bite of Australian foxes is weaker and they show greater use of their temporalis muscle compared to French foxes. The reduced variability suggests a founder effect or stabilizing selection on a specific morphology, which was supported by statistical tests. The corresponding anatomical traits suggest different functional demands likely due to differences in diet or competition. Future studies investigating the drivers of variation in mandible shape in native and invasive populations, including data from the original source of the Australian introductions, are needed to better understand the observed differences. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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9. The San Diego Nathan Shock Center: tackling the heterogeneity of aging.
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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 J. A., Manor, Uri, Marek, Kurt, O'Keefe, David D., Pinto, Antonio F. M., Sacco, Alessandra, Sharpee, Tatyana O., Shokriev, Maxim N., and Zambetti, Stefania
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AGING ,MENTORING ,CELLULAR aging ,AGE ,NATURE & nurture ,ECOLOGICAL genetics - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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10. Author Correction: Senescent glia link mitochondrial dysfunction and lipid accumulation.
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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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11. MYC regulates fatty acid metabolism through a multigenic program in claudin-low triple negative breast cancer.
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Casciano, Jessica C., Perry, Caroline, Cohen-Nowak, Adam J., Miller, Katelyn D., Vande Voorde, Johan, Zhang, Qifeng, Chalmers, Susan, Sandison, Mairi E., Liu, Qin, Hedley, Ann, McBryan, Tony, Tang, Hsin-Yao, Gorman, Nicole, Beer, Thomas, Speicher, David W., Adams, Peter D., Liu, Xuefeng, Schlegel, Richard, McCarron, John G., and Wakelam, Michael J. O.
- Abstract
Background: Recent studies have suggested that fatty acid oxidation (FAO) is a key metabolic pathway for the growth of triple negative breast cancers (TNBCs), particularly those that have high expression of MYC. However, the underlying mechanism by which MYC promotes FAO remains poorly understood.Methods: We used a combination of metabolomics, transcriptomics, bioinformatics, and microscopy to elucidate a potential mechanism by which MYC regulates FAO in TNBC.Results: We propose that MYC induces a multigenic program that involves changes in intracellular calcium signalling and fatty acid metabolism. We determined key roles for fatty acid transporters (CD36), lipases (LPL), and kinases (PDGFRB, CAMKK2, and AMPK) that each contribute to promoting FAO in human mammary epithelial cells that express oncogenic levels of MYC. Bioinformatic analysis further showed that this multigenic program is highly expressed and predicts poor survival in the claudin-low molecular subtype of TNBC, but not other subtypes of TNBCs, suggesting that efforts to target FAO in the clinic may best serve claudin-low TNBC patients.Conclusion: We identified critical pieces of the FAO machinery that have the potential to be targeted for improved treatment of patients with TNBC, especially the claudin-low molecular subtype. [ABSTRACT FROM AUTHOR]- Published
- 2020
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12. Modifiable Factors to Prevent Prolonged Length of Stay after Sleeve Gastrectomy.
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Meneveau, Max, Mehaffey, J. Hunter, Adams, Peter D., Turrentine, Florence E., Schirmer, Bruce, and Hallowell, Peter T.
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SLEEVE gastrectomy ,LENGTH of stay in hospitals ,BODY mass index ,PREOPERATIVE education ,LOGISTIC regression analysis - Abstract
Background: Early discharge after laparoscopic sleeve gastrectomy (SG) is common and safe, but two-thirds of patients are still hospitalized longer than 1 day. The purpose of this study was to evaluate factors associated with early discharge at a single institution with intention to discharge on postoperative day 1. Methods: Retrospective review of preoperative, intraoperative, and postoperative factors was performed for all patients undergoing SG at an academic hospital between 2010 and 2016. The primary outcome measure was length of stay (LOS). Multivariate logistic regression was used to identify independent predictors of prolonged LOS. Results: A total of 367 patients undergoing SG were included. Two hundred eighty-seven (78%) were women and 294 (80%) were Caucasian. Mean age was 45.5 years and mean body mass index (BMI) was 48.7 kg/m2. One hundred twenty-three patients (33.5%) had a LOS ≤ 1 day. Compared to patients staying ≥ 2 days, early discharge patients had significantly lower BMI, creatinine, and American Society of Anesthesiologists class, were more likely to be White, married, have private insurance, and were more likely to have a morning start and no postoperative upper gastrointestinal (UGI) swallow study. Regression analysis demonstrated several independent predictors of prolonged LOS including institutional experience (OR 0.5, p < 0.001), case start time (OR 0.6, p = 0.04), and routine UGI swallow (OR 8.8, p < 0.0001) postoperatively. Conclusions: LOS after SG is affected by multiple factors, including patient health, socioeconomic status, case order, and postoperative management. Optimization of these may allow for improvement in preoperative education and streamlined postoperative pathways, resulting in reduced LOS. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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13. Workplace harassment among staff in higher education: a systematic review.
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Henning, Marcus, Zhou, Chen, Adams, Peter, Moir, Fiona, Hobson, Jennifer, Hallett, Charlene, and Webster, Craig
- Abstract
Workplace harassment in higher education adversely impacts workforce productivity and has deleterious health effects on victims. The aim of this study was to review the literature pertaining to workplace harassment in higher education. This systematic literature search was conducted in December 2013 and completed in January 2014. Refereed journal publications from 1994 to 2013 inclusive were identified. The strategy was conducted on seven major databases. A total of 3278 articles were initially screened, and after review 51 refereed journal articles were included in the final analysis. A thematic analysis identified six themes: causation, types, employee roles, measurement, consequences and interventions. The published evidence, mainly from North America, suggests that workplace harassment is prevalent in higher education, such as gender harassment, workplace bullying, and mobbing. This review highlighted issues associated with: (1) confirming direct causation of harassment due to the high prevalence of correlational research in this area; (2) establishing and standardising measures of harassment that would have cross-cultural applicability and validity; (3) the demand for more comparative research to cater for the globally mobile workforce; (4) the requirement for greater monitoring and evaluation of the efficacy of policies and programmes purporting to be effective in dealing with harassment in the higher education workplace; and (5) the need for more contextually laden research to examine the unique nuances operating in countries, such as those in the Asia Pacific region, not well represented in the literature. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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14. Switching to a Social Approach to Addiction: Implications for Theory and Practice.
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Adams, Peter
- Subjects
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SUBSTANCE abuse & psychology , *VERSTEHEN - Abstract
The concept of addiction is complex and shaped by a range of understandings including how the recipient of an addiction is interpreted. This paper examines how concepts of self and concepts of addiction interact. Two fundamentally different understandings of self are considered: one which focuses on the self as a bio-psychological individual, the 'particle' self, and another that focuses on the self as a nexus of relationships, the 'social' self. The effect these have on understandings of addiction is examined along with implications for service interventions. Particle-informed understandings of addiction are seen as dominating services and leading to intervention responses that focus on the individual and de-emphasize the role of family, community and culture. The absence of social understandings limits both the range and quality of services offered. Particle and social approaches to addiction could operate side-by-side in offering a broader range of effective service responses to addiction. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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15. Autophagy mediates degradation of nuclear lamina.
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Dou, Zhixun, Xu, Caiyue, Donahue, Greg, Shimi, Takeshi, Pan, Ji-An, Zhu, Jiajun, Ivanov, Andrejs, Capell, Brian C., Drake, Adam M., Shah, Parisha P., Catanzaro, Joseph M., Daniel Ricketts, M., Lamark, Trond, Adam, Stephen A., Marmorstein, Ronen, Zong, Wei-Xing, Johansen, Terje, Goldman, Robert D., Adams, Peter D., and Berger, Shelley L.
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AUTOPHAGY ,CYTOLOGICAL research ,NEOPLASTIC cell transformation ,PROTEIN research ,BIOLOGICAL transport - Abstract
Macroautophagy (hereafter referred to as autophagy) is a catabolic membrane trafficking process that degrades a variety of cellular constituents and is associated with human diseases. Although extensive studies have focused on autophagic turnover of cytoplasmic materials, little is known about the role of autophagy in degrading nuclear components. Here we report that the autophagy machinery mediates degradation of nuclear lamina components in mammals. The autophagy protein LC3/Atg8, which is involved in autophagy membrane trafficking and substrate delivery, is present in the nucleus and directly interacts with the nuclear lamina protein lamin B1, and binds to lamin-associated domains on chromatin. This LC3-lamin B1 interaction does not downregulate lamin B1 during starvation, but mediates its degradation upon oncogenic insults, such as by activated RAS. Lamin B1 degradation is achieved by nucleus-to-cytoplasm transport that delivers lamin B1 to the lysosome. Inhibiting autophagy or the LC3-lamin B1 interaction prevents activated RAS-induced lamin B1 loss and attenuates oncogene-induced senescence in primary human cells. Our study suggests that this new function of autophagy acts as a guarding mechanism protecting cells from tumorigenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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16. Dendrobium bigibbum (sect. Phalaenanthe) in Australia - analysis of diagnostic characters, review of taxa and a new classification.
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Adams, Peter
- Abstract
Dendrobium bigibbum Lindl. has a long confused history, with taxa variously described as separate species, subspecies, varieties and forms. This paper records morphological variation in 160 representative plants in north Queensland and Torres Strait. The distribution range is delineated. ITS-DNA results did not show significant differences between populations. The evidence supports a single species D. bigibbum Lindl. with three intergrading varieties: vars bigibbum, superbum and compactum. Some types have uncertain provenance, particularly D. phalaenopsis, which is reduced to synonymy under D. bigibbum var. superbum. A combination of characters can be used to identify varieties. A new combination of D. bigibbum var. compactum reduces D. phalaenopsis var. compactum to synonymy. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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17. Exploring Free Will and Consciousness in the Light of Quantum Physics and Neuroscience.
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Adams, Peter and Suarez, Antoine
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- 2013
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18. Introduction.
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Adams, Peter and Suarez, Antoine
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- 2013
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19. Mathematics and the Pharmacokinetics of Alcohol.
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Jennings, Michael and Adams, Peter
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- 2013
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20. Chromatin in Senescent Cells: A Conduit for the Anti-Aging Effects of Wnt Signaling?
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Banumathy, Gowrishankar and Adams, Peter D.
- Abstract
Cellular senescence is thought to contribute to tissue aging. The role of Wnt signaling in aging is little studied and poorly understood, but there is evidence that Wnt signaling can be both pro- and anti-aging. Here we discuss the idea that, in at least some cell and tissue contexts, Wnt signaling might antagonize aging through its ability to regulate chromatin structure in senescent cells. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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21. Regional Air Quality-Atmospheric Nucleation Interactions.
- Author
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O'Dowd, Colin D., Wagner, Paul E., Jung, JaeGun, Adams, Peter J., and Pandis, Spyros N.
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The creation of new atmospheric particles from in situ nucleation influences climate through cloud-aerosol interactions and may negatively impact human health. Although recent observations show that nucleation is widespread over most continents, the corresponding pathways remain uncertain. A computationally efficient multicomponent aerosol dynamics model (DMAN) that simulates the full aerosol size distribution and composition starting at a diameter of 0.8 nm has been developed. Several proposed nucleation rate expressions for binary (H2SO4-H2O), ternary (NH3-H2SO4-H2O), and ion-induced nucleation are evaluated using DMAN against ambient measurements from the Pittsburgh Air Quality Study (PAQS). The ternary NH3-H2SO4-H2O nucleation model is successful in predicting the presence or lack of nucleation on 19 out of 19 days with complete data sets in July 2001 and on 25 out of 29 days in January 2002. DMAN has been added to the three-dimensional (3D) Chemical Transport Model PMCAMx-UF and is tested in the Eastern USA. Reductions of ammonia emissions are predicted to decrease the frequency of nucleation events during both summer and winter, with a more dramatic effect during the summer. The response to changes in emissions of sulfur dioxide during the summer is counterintuitive. Reductions of sulfur dioxide and the resulting sulfate by up to 40% actually increase the frequency of the summer nucleation events. Modeling predicts the opposite effect in winter, with reductions of sulfur dioxide leading to fewer nucleation events. Keywords Ultrafine PM, tropospheric aerosols, ammonia, Eastern United States, PMCAMx-UF [ABSTRACT FROM AUTHOR]
- Published
- 2008
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22. Looking Ahead.
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Adams, Peter J.
- Abstract
When I first sat down to write this book I was unsure how it would unfold. Ideas had been swirling around in my head off and on for the 20 years since I first began working with people affected by addictive relationships, but for various reasons I had not been in the position to commit them to paper2. While on study leave for the first half of 2006 I began writing these ideas down and to my surprise they emerged with more coherence than I had anticipated. Looking back, what appears to have held the work together is the focus on intimacy. The impact of addictive relationships on intimacy can be observed at every level: when people enter addictive relationships they take on an alternative form of intimacy, when they struggle to change they are struggling with very strong interpersonal processes, when they attempt to reintegrate they are faced with the challenge of rebuilding and mending intimate connections, and, most importantly, addictive relationships create distortions and asymmetries for surrounding intimates. This I find is the most disturbing aspect of addictive contexts. Those who live with a person in an addictive relationship are invariably affected and, for many, affected in profound ways that persist through their lives. The addictive relationship appears to cut through the connections between intimates, impoverishing the lives of most of those involved and leaving behind them a trail of alienation, hurt, and shame. In contrast to this destructive potential, I have also watched many people rally all the strength and courage they possess to take on the enormous task of disengaging from an addictive relationship and reforming their connections into a world of multiple intimacies. Their journey invariably involves the ups and downs of hope and disappointment and the heartbreak of separations and reversions. What's more, the forming and reforming of intimacies is a very slow and fickle process and, as illustrated throughout this book, requires support at the level of individuals, family, community, and society. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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23. Applications to Practice.
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Adams, Peter J.
- Abstract
The initiation of a therapeutic relationship between an addiction practitioner and someone in an addictive relationship often provides the first step in the processes of resocialization and reintegration. But in many circumstances introducing a therapeutic relationship—a relationship with high intimacy potential—adds further fragmentation into the addictive social system. Family members who are bewildered and frustrated by their loved one's deteriorating behavior, and are buoyed up by expectations and hope that these services can fix addictions, are only too willing to hand over their involvement to addiction professionals. The practitioner's presence and the prospect of quick solutions provide them with some reprieve, and they willingly withdraw to allow the practitioner to exercise his or her knowledge and skills. While family members may have little idea of what is happening during a mysterious sequence of counseling sessions, they are reassured by the prospect of change and their confidence is reinforced when after several sessions the behavior of their loved one seems to improve. However, a little later their confidence is rocked when, following a series of sessions or time in a residential rehabilitation program the therapeutic relationship draws to a close and by implication the responsibility is handed back to the family. Their loved one returns, and acts differently for a while, but in time returns to old routines, which leads on eventually to the addictive relationship reasserting itself. Now, facing a full reversion, the intimates are left wondering whether there is any real prospect for change. What hope is there when not even addiction services with all their wisdom and resources are able to make things different? In their despondency they continue to distance themselves from their loved one, and their fragmented world seems more solid and powerful than ever. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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24. Mobilizing Communities.
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Adams, Peter J.
- Abstract
The discussion of the opportunities for collective action in Chapter 9 identified the key role community empowerment and social connectedness can play in engaging the strength of neighborhoods and communities. The quotation above by a leading Samoan academic captures the way in which social connectedness and personal identity are intertwined. This chapter explores how these broader layers of social connectedness can contribute to collective actions that challenge addictive relationships. It focuses on three quite different examples of community approaches that have been used to assist and support the long process of reintegration. The first example examines the use of volunteers as a way for addiction services to link in ongoing community support for reintegration. The second example emerged within Croatian and Italian communities as a widespread and organized network aimed at providing long-term support for families undertaking reintegration. The third example describes the application of indigenous understandings of the central value of relationships to develop a variety of strategies to support changes in Māori communities in Aotearoa-New Zealand. Each example was chosen to highlight the diversity of ways that a community might incorporate social approaches in their response to addictive relationships. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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25. Family Resources.
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Adams, Peter J.
- Abstract
The previous three parts of the book have stepped out from under the mantle of particle orientations and explored what it might mean to interpret addictions in a social frame. Part IV explores how this work might be applied to assist people in their struggles with addictive relationships and their attempts at reintegration. This chapter provides an overview of the approaches and resources that an individual or family can make use of in challenging an addictive relationship (namely the relationship between a person and an addictive substance/process). The chapter is divided into three sections, starting with what is currently available and moving toward what is desirable for the future. The first section examines the social components that already exist in various self-help approaches to reintegration. The second section summarizes family and other social interventions that have been developed by researchers in conjunction with addiction services. The third section makes use of the content developed in earlier chapters to outline how people in an addictive social system can monitor their own response through the phases of reappraisal, reconnection, and collective action. The family situation with Jack, Danny and Julie, and their two children, Adrienne and Luke, will be used to illustrate the different opportunities. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
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26. Reintegration.
- Author
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Adams, Peter J.
- Abstract
As outlined in Chapter 4, reintegration is the slow process of reestablishing intimacies in social system previously dominated by an addictive relationship. For the person leaving this all-consuming involvement, reintegration involves journeying from a singular asymmetrical intimacy to a social world of multiple symmetrical relationships. It is a long and difficult voyage that will require many steps both forward and backward before balanced and multiple connections can be achieved. For intimates, there are two paths of reintegration depending on whether or not they choose to remain associated with the addictive system. For those who choose to stay, reintegration focuses primarily on steadily intensifying the relationship with their affected loved one as he or she moves progressively out of the addictive relationship. For those who choose to leave, the pathway can also engage them in a long voyage focusing on establishing a new array of connections. While separation is an important process in itself, the following discussion will focus on intimate reintegration for those who choose to remain in the integrating social system. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
27. Collective Opportunities.
- Author
-
Adams, Peter J.
- Abstract
Earlier chapters have examined the various ways in which the intensifying strength of intimacy in an addictive relationship is paralleled by reducing levels of intensity in other intimacies. The emphasis on the strength of these processes risks giving the impression that addictive relationships become too strongly embedded to allow any change. But this impression is certainly not what is intended; people in addictive social systems can and do—throug considerable effort—make changes to these systems. Since social processes have played a critical role in the emergence of addictive relationships, this book contends that social processes also offer opportunities for restoring people into an interconnected, nonaddictive social world. The big opportunity that will be explored in this and subsequent chapters concerns the potential of collective strength between people in counteracting and reversing the trend toward fragmentation. It proposes that groups of people associated with the addictive relationship can connect with each other in ways that override fragmentation processes. In a world of improving social relationships the addictive relationship becomes increasingly isolated; it has no real currency and spins by itself like an unattached cog. The person in the addictive relationship can no longer manage both worlds. He or she is confronted with having to choose between intimacy with the addictive substance/process or intimacy with people. Pursuit of both intimacies becomes increasingly less viable. Furthermore, even when the choice is made in favor of the addictive substance/process, improved social integration lessens the impact of the addictive relationship on other intimates, thereby freeing intimates to pursue their own pathways to improved well-being. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
28. Becoming Intimate.
- Author
-
Adams, Peter J.
- Abstract
In the above extract F. Scott Fitzgerald illustrates the subtle interpersonal dynamics that are often intertwined in lifestyles associated with addictive processes. Part I of this book introduced the switch from viewing addiction in terms of human particles to viewing addiction as a social event. Part II moves in closer to the core of addictive relationships and examines the processes associated with forming, maintaining, and ending social connections in addictive systems. In particular, Part II explores the nature of intimacy as a special form of social connectedness. Addictions understood within a social world operate most strongly in the zone of intense sociality, namely at those points of contact between people where they experience their strongest and most intimate involvements. In doing so it identifies intimacy as the primary site for addictive processes, the site at which the destructiveness of addictive relationships is most active2: the place where the action happens. However, before proceeding into this zone, a conceptual framework is required in order to talk sensibly about the relationship between addiction and intimacy. This chapter establishes a simple set of concepts that can be used to understand how addictive relationships and intimacies interact. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
29. Fragmented Lives.
- Author
-
Adams, Peter J.
- Abstract
Frank McCourt's memoir of his early years in New York and Ireland provides a heart-wrenching account of the consequences to a family of a father's unrelenting commitment to a relationship with alcohol. It is hard to read the book and not feel some frustration, some anger, perhaps even some resentment at the father's ongoing allegiance to his drinking. If he had stopped, all would have been different; he would have found employment, the family would have had money for food and clothing, more of the children would have survived, and the family may have stayed together. But his relationship to alcohol continued on, uninterrupted by the chaos and the fragmentation it was creating. The remainder of the family found themselves progressively isolated from each other and distanced from the world around them. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
30. Intimacy and Power.
- Author
-
Adams, Peter J.
- Abstract
The previous chapter surveyed the general ways in which fragmenting asymmetries evolve in addictive systems, but the observation that these asymmetries occur does not explain how they are achieved. Attention now shifts to the processes and techniques that make these asymmetries possible. The passage above describes a critical point in Huckleberry Finn where Huck's father (Pap), who is in an addictive relationship to alcohol, attempts to kill Huck. Huck responds by leaving town to pursue his life on the river. While this level of physical violence does not occur within every addictive system, abuse and other forms of controlling behavior are commonplace. Such controlling tactics vary in degree—from slaps to fatal stabbings—and in kind—from verbal threats to ongoing surveillance. What is common to all these strategies is that they involve an attempt of one person in a relationship to impose a level of power over the other person. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
31. Intimacies in Addictive Contexts.
- Author
-
Adams, Peter J.
- Abstract
In previous chapters, addictive relationships (those connecting a person with an addictive substance/process) were viewed from above, looking down on connecting objects. As signaled by the passage from Anne Brontë's book, this chapter delves more into the intricacies and dynamics faced with intimacies in addictive contexts. It takes the analysis of intimacy developed in the previous chapter and applies it in detail to addictive systems. Since the lived experience of such systems differ for those who are in an addictive relationship and for those who live around them, this chapter approaches intimacy from two separate angles: first, from the point of view of inside the addictive relationship, that is, between the person and the addictive substance/process; and second, from the point of view of other intimates, that is, between other people in the immediate social system with the person in the addictiverelationship. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
32. Responding to Addiction.
- Author
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Adams, Peter J.
- Abstract
James K. Baxter struggled throughout his life with his addictive relationship to alcohol. His concept of a "cold hub" or inner nothingness captures something of the social emptiness that lies at the core of addictive systems. The previous chapter outlined how within a social system the rising dominance of an addictive relationship feeds off deteriorations in relationships elsewhere. This leads to experiences of fragmentation for other people in the system. This chapter explores the prospect of change. It outlines change as a slow and difficult journey involving periods of crisis, moving forward and reverting back and rethinking before the pathway for reintegration is established. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
33. Addiction and Connecting.
- Author
-
Adams, Peter J.
- Abstract
The previous two chapters have outlined the importance of addictions and introduced the basic assumptions underlying the social paradigm that comprises the orientation for this book. This chapter explains the vital role of social connections in forming identity, the process of entering into an addictive relationship, and how this is likely to impact on other people. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
34. A Social World.
- Author
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Adams, Peter J.
- Abstract
When Captain James Cook and his crew landed in Tahiti on April 13, 1769, after sailing through the bitter weather of the South Pacific, a whole new world opened up not only to them but also to the many people in different parts of Europe who subsequently read accounts of their voyages. Cook himself represented the best of the British Royal Navy; he was a brilliant cartographer, a strong leader, and someone who was deeply respectful of other people and their cultures. Others on board included artists, botanists and one key ambassador of European culture, Joseph Banks. He was a man of aristocratic upbringing and with broad interests in both the arts and the sciences and it was his writings that provided Europe with a window on a new way of interpreting this and their own world. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
35. Addiction in Perspective.
- Author
-
Adams, Peter J.
- Abstract
In these early years of the twenty-first century we find ourselves constantly immersed in talk about addictions. Newspapers and television regularly present disturbing items on the rising negative effects of addiction. When the country is not waging a "war on drugs," it is struggling with drunken driving, youth drug crime, increases in pathological gambling, alcohol destroying families, spates of Internet addiction, and so forth. Increasing numbers of popular books on addiction appear in book stores with titles such as, Codependent No More; Woman, Sex, and Addiction: A Search for Love and Power, and Workaholics: The Respectable Addicts.2 Many people with high media profiles regularly succumb to addictions; the tabloids and magazines revel in details on fallen movie stars, television celebrities, sports heroes, community leaders, and politicians. Self-professed alcoholics and drug addicts often bare their souls on syndicated television talk shows, detailing stories on the horrors of being addicted and its impact on loved ones. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
36. Design and Application of a shRNA-Based Gene Replacement Retrovirus.
- Author
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Walker, John M., Ochs, Michael F., Rugang Zhang, Adams, Peter D., and Xiaofen Ye
- Abstract
To perform structure/function analyses of a protein in vivo, ideally one should be able to simultaneously abolish expression of the endogenous wild-type protein, substitute it with a form of the protein containing a targeted mutation, and analyze the functional consequences. Until recently, this was a highly challenging and/or laborious approach in mammalian systems, requiring a targeted gene knockin in a human cell line or mouse. Herein is described a RNA interference (RNAi)-based approach to achieve this much more simply in mammalian cells. A single retrovirus has been constructed, which directs expression of a short hairpin RNA (shRNA) to knockdown expression of the endogenous protein of interest; a cDNA coding for a wild-type or mutant version of the same protein that also contains "silent mutations" that do not affect the protein sequence, but do make the mRNA resistant to the shRNA; and a puromycin-resistance gene to allow rapid drug selection of the virus-infected cells. Using this virus, expression of the endogenous Anti-Silencing Function 1a (ASF1a) histone chaperone has been efficiently replaced in primary human cells, by an ectopically expressed epitope-tagged version. Moreover, the virus is designed so that other shRNA and shRNA-resistant cDNA cassettes can easily be substituted, making the approach readily applicable to other protein targets. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
37. Application of Magnetic Beads to Purify Cells Transiently Transfected With Plasmids Encoding Short Hairpin RNAs.
- Author
-
Walker, John M., Humphrey, Tim, Brooks, Gavin, and Adams, Peter D.
- Abstract
Short interfering (si) RNAs are commonly used to knock down expression of proteins in mammalian cells and thereby investigate protein function. siRNAs were originally introduced into mammalian cells by transient transfection of short, synthetic, double-stranded RNA oligo nucleotides. More recently, a convenient, more cost-effective approach has been developed that makes use of plasmids encoding short hairpin (sh) RNAs, which are transiently or stably transfected into cells. After expression in cells, shRNAs are processed by the cell to the corresponding siRNAs. However, most protocols for transient transfection of plasmid DNAs introduce the DNA into a minority of the total cells. Therefore, to investigate the biochemical effects of protein knockdown, it is necessary to purify the transfected cells. This can be done by cotransfection of a plasmid encoding the cell surface marker protein, CD19 or CD20, followed by immunopurification of the CD19- or CD20-expressing cells with magnetic beads. The purified cells can then be used for a wide range of biochemical analyses. In addition, since the CD19/CD20 cell surface marker approach can be readily combined with analysis of cell cycle distribution of propidium iodide-stained cells, it is straightforward to determine simultaneously the biochemical and cell cycle effects of a knocked-down protein. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
38. Biochemical Analysis of the Cell Cycle and Cell Cycle Checkpoints in Transiently Transfected Cells After Collection With Magnetic Beads.
- Author
-
Walker, John M., Schönthal, Axel H., Ye, Xiaofen, Poustovoitov, Maxim, Santos, Hidelita, Nelson, David M., and Adams, Peter D.
- Abstract
It is frequently necessary to examine the biochemical effects of ectopically expressed proteins or short hairpin (sh) RNA-mediated protein knock-down in intact cells. Plasmids that direct the expression of ectopic proteins or shRNAs can be conveniently introduced into cells by transient transfection of plasmid DNAs. However, most protocols used for the transient transfection of plasmid DNAs introduce the foreign DNA into only a minority of the total cells. Therefore, to investigate the biochemical effects of the foreign DNA it is necessary to purify the transfected cells away from the untransfected cells. This can be easily achieved by cotransfection of a plasmid encoding the cell surface marker protein CD19 or CD20, followed by immunopurification of the CD19- or CD20-expressing cells with magnetic beads coated with an anti-CD19 or anti-CD20 antibody. The purified cells can be used for a wide range of biochemical analyses, including protein extraction for Western blot and immunoprecipitation, RNA extraction for Northern blot, and DNA and chromatin extraction for nuclease digestion. Since the CD19/CD20 cell surface marker approach can be readily combined with analysis of cell cycle distribution of propidium-iodide-stained cells, it is straightforward to simultaneously determine the biochemical and cell cycle effects of an ectopically expressed or knocked-down protein. [ABSTRACT FROM AUTHOR]
- Published
- 2004
- Full Text
- View/download PDF
39. Development of the Coastal Storm Modeling System (CoSMoS) for predicting the impact of storms on high-energy, active-margin coasts.
- Author
-
Barnard, Patrick, Ormondt, Maarten, Erikson, Li, Eshleman, Jodi, Hapke, Cheryl, Ruggiero, Peter, Adams, Peter, and Foxgrover, Amy
- Subjects
STORM damage ,COASTAL development ,CLIMATE change ,PILOT projects ,MORPHOLOGY - Abstract
The Coastal Storm Modeling System (CoSMoS) applies a predominantly deterministic framework to make detailed predictions (meter scale) of storm-induced coastal flooding, erosion, and cliff failures over large geographic scales (100s of kilometers). CoSMoS was developed for hindcast studies, operational applications (i.e., nowcasts and multiday forecasts), and future climate scenarios (i.e., sea-level rise + storms) to provide emergency responders and coastal planners with critical storm hazards information that may be used to increase public safety, mitigate physical damages, and more effectively manage and allocate resources within complex coastal settings. The prototype system, developed for the California coast, uses the global WAVEWATCH III wave model, the TOPEX/Poseidon satellite altimetry-based global tide model, and atmospheric-forcing data from either the US National Weather Service (operational mode) or Global Climate Models (future climate mode), to determine regional wave and water-level boundary conditions. These physical processes are dynamically downscaled using a series of nested Delft3D-WAVE (SWAN) and Delft3D-FLOW (FLOW) models and linked at the coast to tightly spaced XBeach (eXtreme Beach) cross-shore profile models and a Bayesian probabilistic cliff failure model. Hindcast testing demonstrates that, despite uncertainties in preexisting beach morphology over the ~500 km alongshore extent of the pilot study area, CoSMoS effectively identifies discrete sections of the coast (100s of meters) that are vulnerable to coastal hazards under a range of current and future oceanographic forcing conditions, and is therefore an effective tool for operational and future climate scenario planning. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
40. A comparison of oncogene-induced senescence and replicative senescence: implications for tumor suppression and aging.
- Author
-
Nelson, David, McBryan, Tony, Jeyapalan, Jessie, Sedivy, John, and Adams, Peter
- Subjects
GENETICS of aging ,TUMOR suppressor genes ,CELLULAR aging ,INHIBITION of cellular proliferation ,ONCOGENES - Abstract
Cellular senescence is a stable proliferation arrest associated with an altered secretory pathway, the senescence-associated secretory phenotype. However, cellular senescence is initiated by diverse molecular triggers, such as activated oncogenes and shortened telomeres, and is associated with varied and complex physiological endpoints, such as tumor suppression and tissue aging. The extent to which distinct triggers activate divergent modes of senescence that might be associated with different physiological endpoints is largely unknown. To begin to address this, we performed gene expression profiling to compare the senescence programs associated with two different modes of senescence, oncogene-induced senescence (OIS) and replicative senescence (RS [in part caused by shortened telomeres]). While both OIS and RS are associated with many common changes in gene expression compared to control proliferating cells, they also exhibit substantial differences. These results are discussed in light of potential physiological consequences, tumor suppression and aging. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
41. Potential for dissemination of Phytophthora cinnamomi by feral pigs via ingestion of infected plant material.
- Author
-
Li, Andrew, Williams, Nari, Fenwick, Stanley, Hardy, Giles, and Adams, Peter
- Abstract
Feral pigs have long been implicated as potential vectors in the spread of the devastating plant pathogen Phytophthora cinnamomi due to their rooting and wallowing activities which may predispose them as vectors of infested soil. In this study, we aim to determine whether feral pigs have the potential to act as vectors of plant pathogens such as P. cinnamomi through their feeding activity. The typically omnivorous diet of feral pigs may also lead to the passage of P. cinnamomi infected plant material through their digestive system. This study investigates the potential for feral pigs to pass viable P. cinnamomi in their faeces following the ingestion of millet seeds, pine plugs and Banksia leptophilia roots inoculated with P. cinnamomi. Recovery rates of P. cinnamomi from the millet seeds, pine plugs and B. leptophilia roots following a single ingested bolus were 33.2, 94.9 and 10.4 %, respectively supported by quantitative PCR analysis. These results demonstrate that P. cinnamomi remain viable within infected plant material following passage through the pig digestive tract, although the digestive processes reduce the pathogen's viability. An inverse relationship was observed between the viability of infected material and passage time, suggesting that partially digested plant material provides protection for P. cinnamomi against the adverse environmental conditions of the pig digestive tract. Phytophthora cinnamomi remained viable for up to 7 days in larger pieces of colonised woody plant material such as the pine plugs. A plant infection trial using passaged P. cinnamomi colonised pine plugs showed that even material that remained in the digestive tract for 7 days was capable of infecting and killing healthy plants, susceptible to P. cinnamomi. This study provides compelling evidence that feral pigs have the ability to transport viable P. cinnamomi in their digestive tract. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
42. p53 status determines the role of autophagy in pancreatic tumour development.
- Author
-
Rosenfeldt, Mathias T., O'Prey, Jim, Morton, Jennifer P., Nixon, Colin, MacKay, Gillian, Mrowinska, Agata, Au, Amy, Rai, Taranjit Singh, Zheng, Liang, Ridgway, Rachel, Adams, Peter D., Anderson, Kurt I., Gottlieb, Eyal, Sansom, Owen J., and Ryan, Kevin M.
- Subjects
P53 antioncogene ,TUMOR growth ,AUTOPHAGY ,HOMEOSTASIS ,LABORATORY mice ,ADENOCARCINOMA ,GENETICS ,MAMMALS - Abstract
Macroautophagy (hereafter referred to as autophagy) is a process in which organelles termed autophagosomes deliver cytoplasmic constituents to lysosomes for degradation. Autophagy has a major role in cellular homeostasis and has been implicated in various forms of human disease. The role of autophagy in cancer seems to be complex, with reports indicating both pro-tumorigenic and tumour-suppressive roles. Here we show, in a humanized genetically-modified mouse model of pancreatic ductal adenocarcinoma (PDAC), that autophagy's role in tumour development is intrinsically connected to the status of the tumour suppressor p53. Mice with pancreases containing an activated oncogenic allele of Kras (also called Ki-Ras)-the most common mutational event in PDAC-develop a small number of pre-cancerous lesions that stochastically develop into PDAC over time. However, mice also lacking the essential autophagy genes Atg5 or Atg7 accumulate low-grade, pre-malignant pancreatic intraepithelial neoplasia lesions, but progression to high-grade pancreatic intraepithelial neoplasias and PDAC is blocked. In marked contrast, in mice containing oncogenic Kras and lacking p53, loss of autophagy no longer blocks tumour progression, but actually accelerates tumour onset, with metabolic analysis revealing enhanced glucose uptake and enrichment of anabolic pathways, which can fuel tumour growth. These findings provide considerable insight into the role of autophagy in cancer and have important implications for autophagy inhibition in cancer therapy. In this regard, we also show that treatment of mice with the autophagy inhibitor hydroxychloroquine, which is currently being used in several clinical trials, significantly accelerates tumour formation in mice containing oncogenic Kras but lacking p53. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
43. Senescent cells harbour features of the cancer epigenome.
- Author
-
Cruickshanks, Hazel A., McBryan, Tony, Nelson, David M., VanderKraats, Nathan D., Shah, Parisha P., van Tuyn, John, Singh Rai, Taranjit, Brock, Claire, Donahue, Greg, Dunican, Donncha S., Drotar, Mark E., Meehan, Richard R., Edwards, John R., Berger, Shelley L., and Adams, Peter D.
- Subjects
DNA methylation ,CELLULAR aging ,CANCER cells ,NUCLEOTIDE sequence ,DNA methyltransferases ,CPG nucleotides - Abstract
Altered DNA methylation and associated destabilization of genome integrity and function is a hallmark of cancer. Replicative senescence is a tumour suppressor process that imposes a limit on the proliferative potential of normal cells that all cancer cells must bypass. Here we show by whole-genome single-nucleotide bisulfite sequencing that replicative senescent human cells exhibit widespread DNA hypomethylation and focal hypermethylation. Hypomethylation occurs preferentially at gene-poor, late-replicating, lamin-associated domains and is linked to mislocalization of the maintenance DNA methyltransferase (DNMT1) in cells approaching senescence. Low-level gains of methylation are enriched in CpG islands, including at genes whose methylation and silencing is thought to promote cancer. Gains and losses of methylation in replicative senescence are thus qualitatively similar to those in cancer, and this 'reprogrammed' methylation landscape is largely retained when cells bypass senescence. Consequently, the DNA methylome of senescent cells might promote malignancy, if these cells escape the proliferative barrier. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
44. Effects of climate change and wave direction on longshore sediment transport patterns in Southern California.
- Author
-
Adams, Peter, Inman, Douglas, and Lovering, Jessica
- Subjects
- *
CLIMATE change & society , *WAVES (Physics) , *SEDIMENT transport , *COASTAL changes , *SEDIMENTATION analysis , *BATHYMETRIC maps ,EL Nino - Abstract
Changes in deep-water wave climate drive coastal morphologic change according to unique shoaling transformation patterns of waves over local shelf bathymetry. The Southern California Bight has a particularly complex shelf configuration, of tectonic origin, which poses a challenge to predictions of wave driven, morphologic coastal change. Northward shifts in cyclonic activity in the central Pacific Ocean, which may arise due to global climate change, will significantly alter the heights, periods, and directions of waves approaching the California coasts. In this paper, we present the results of a series of numerical experiments that explore the sensitivity of longshore sediment transport patterns to changes in deep water wave direction, for several wave height and period scenarios. We outline a numerical modeling procedure, which links a spectral wave transformation model (SWAN) with a calculation of gradients in potential longshore sediment transport rate (CGEM), to project magnitudes of potential coastal erosion and accretion, under proscribed deep water wave conditions. The sediment transport model employs two significant assumptions: (1) quantity of sediment movement is calculated for the transport-limited case, as opposed to supply-limited case, and (2) nearshore wave conditions used to evaluate transport are calculated at the 5-meter isobath, as opposed to the wave break point. To illustrate the sensitivity of the sedimentary system to changes in deep-water wave direction, we apply this modeling procedure to two sites that represent two different coastal exposures and bathymetric configurations. The Santa Barbara site, oriented with a roughly west-to-east trending coastline, provides an example where the behavior of the coastal erosional/accretional character is exacerbated by deep-water wave climate intensification. Where sheltered, an increase in wave height enhances accretion, and where exposed, increases in wave height and period enhance erosion. In contrast, all simulations run for the Torrey Pines site, oriented with a north-to-south trending coastline, resulted in erosion, the magnitude of which was strongly influenced by wave height and less so by wave period. At both sites, the absolute value of coastal accretion or erosion strongly increases with a shift from northwesterly to westerly waves. These results provide some examples of the potential outcomes, which may result from increases in cyclonic activity, El Niño frequency, or other changes in ocean storminess that may accompany global climate change. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
45. Estimating the potential economic impacts of climate change on Southern California beaches.
- Author
-
Pendleton, Linwood, King, Philip, Mohn, Craig, Webster, D., Vaughn, Ryan, and Adams, Peter
- Subjects
ECONOMICS ,CLIMATE change ,BEACHES ,ABSOLUTE sea level change ,BEACHGOERS ,BEACH erosion - Abstract
Climate change could substantially alter the width of beaches in Southern California. Climate-driven sea level rise will have at least two important impacts on beaches: (1) higher sea level will cause all beaches to become more narrow, all things being held constant, and (2) sea level rise may affect patterns of beach erosion and accretion when severe storms combine with higher high tides. To understand the potential economic impacts of these two outcomes, this study examined the physical and economic effects of permanent beach loss caused by inundation due to sea level rise of one meter and of erosion and accretion caused by a single, extremely stormy year (using a model of beach change based on the wave climate conditions of the El Niño year of 1982/1983.) We use a random utility model of beach attendance in Southern California that estimates the impacts of changes on beach width for different types of beach user visiting public beaches in Los Angeles and Orange Counties. The model allows beachgoers to have different preferences for beach width change depending on beach size. We find that the effect of climate-driven beach change differs for users that participate in bike path activities, sand-based activities, and water-based activities. We simulate the effects of climate-related beach loss on attendance patterns at 51 public beaches, beach-related expenditures at those beaches, and the non-market (consumer surplus) value of beach going to those beaches. We estimate that increasing sea level will cause an overall reduction of economic value in beach going, with some beaches experiencing increasing attendance and beach-related earnings while attendance and earnings at other beaches would be lower. We also estimate that the potential annual economic impacts from a single stormy year may be as large as those caused by permanent inundation that would result from a rise in sea level of one meter. The economic impacts of both permanent inundation and storm-related erosion are distributed unevenly across the region. To put the economic impacts of these changes in beach width in perspective, the paper provides simple estimates of the cost of mitigating beach loss by nourishing beaches with sand. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
46. Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions.
- Author
-
Tran, Tran T., Kulis, Christina, Long, Steven M., Bryant, Darryn, Adams, Peter, and Smythe, Mark L.
- Subjects
CONTINUOUS geometries ,PROTEINS ,ORGANIC compounds ,COORDINATION compounds ,MOLECULAR biology - Abstract
Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
47. The generalized almost resolvable cycle system problem.
- Author
-
Adams, Peter, Billington, Elizabeth, Hoffman, D., and Lindner, C.
- Subjects
VERTEX operator algebras ,STEINER systems ,QUASIGROUPS ,INTEGRAL theorems ,DIFFERENCE algebra - Abstract
Let ( X, C) be a k-cycle system of order n, with vertex set X (of cardinality n) and collection of k-cycles C. Suppose n= kq+ r where r< k. An almost parallel class of C is a collection of q=( n−r)/ k pairwise vertex-disjoint k-cycles of C. Each almost parallel class thus will miss r of the n vertices in X. The k-cycle system ( X,C) is said to be almost resolvable if C can be partitioned into almost parallel classes such that the remaining k-cycles are vertex disjoint. (These remaining k-cycles are referred to as a short parallel class.) In this paper we (a) construct an almost resolvable 10-cycle system of every order congruent to 5 (mod 20), and (b) construct an almost resolvable 10-cycle system of order 41, thus completing the result that the spectrum for almost resolvable 10-cycle systems consists of all orders congruent to 1 or 5 (mod 20). [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
48. Providing Post-Treatment Support in an Outpatient Alcohol and Other Drug Treatment Context: A Qualitative Study of Staff Opinion.
- Author
-
Pulford, Justin, Black, Stella, Wheeler, Amanda, Sheridan, Janie, and Adams, Peter
- Subjects
OUTPATIENT medical care ,HEALTH facility employees ,PHYSICIAN-patient relations ,DISCUSSION ,QUALITATIVE research - Abstract
This paper examines the post-treatment support practices, attitudes and preferences of outpatient alcohol and other drug (AOD) treatment staff as well as perceived barriers to implementing a post-treatment support service in an outpatient AOD treatment context. Data were collected via semi-structured interview and group discussion ( n = 23). Findings suggest that post-treatment support was rarely provided by participating AOD treatment staff or their respective services. However, there was widespread support for implementing such services, and it was generally believed that implementation would be most successful if: multiple post-treatment support options were made available; if one or more of these options were based on the maintenance of an established client/clinician relationship; and if one of the options involved proactive (service-led) telephone support. A number of barriers to possible implementation were identified, although none were considered insurmountable. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
49. Providing Post-treatment Support in an Outpatient Alcohol and other Drug Treatment Context: A Survey of Client Opinion.
- Author
-
Pulford, Justin, Black, Stella, Wheeler, Amanda, Sheridan, Janie, and Adams, Peter
- Subjects
AFTERCARE services ,PATIENTS ,DRUG therapy ,OUTPATIENT medical care ,TELECOMMUNICATION systems ,ALCOHOL drinking - Abstract
This paper presents findings from a survey that sought the post-treatment support preferences of a group of outpatient alcohol and other drug treatment clients. The client group ( n = 83) were presented with six possible models of post-treatment support and were asked to express their level of interest in using or receiving each model and, if interested, by what means they could best be provided. The six models included a range of pro-active (service initiated) and passive (client initiated) support services, variously accessible by telephone, mail, text-message, computer or in-person. Participants were also afforded an opportunity to identify alternative approaches. The results suggest pro-active telephone- and mail-based approaches to post-treatment support are favoured over passive in-person approaches and that computer and text-message approaches (whether passive or pro-active) may be least favourable in the contemporary environment. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
50. Client/Clinician Discrepancies in Perceived Problem Improvement and the Potential Influence on Dropout Response.
- Author
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Pulford, Justin, Adams, Peter, and Sheridan, Janie
- Subjects
- *
MEDICAL personnel , *TREATMENT effectiveness , *SCHOOL dropouts , *MENTAL health services , *REHABILITATION counseling - Abstract
This paper examines the possibility that clinicians working in an alcohol and other drug (AOD) treatment service may lack appreciation of problem improvement in clients who choose to dropout against clinical advice. Underlying this investigation is the belief that if clinicians are indeed unperceptive of problem improvement amongst this population then this may explain why retention based responses to client dropout continue to be promoted, despite evidence to suggest that they are ineffective and/or unnecessary. Outcome data obtained from a sample of 75 AOD treatment clients and their respective clinicians at baseline and 2-month follow-up are reported. Analysis of these data suggest a client/clinician discrepancy in perceived problem improvement was evident in the study setting: clinicians reported significantly less problem improvement in the first 2 months of service attendance as compared to their clients and this discrepancy was most pronounced if the client had dropped out of treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
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