1
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Huang Y, Wang Y, Deng J, Gao S, Qiu J, He J, Yang T, Tan N, Cheng S, Song Z. Research on the anti-oxidant and anti-aging effects of Polygonatum kingianum saponins in Caenorhabditis elegans. Heliyon 2024; 10:e35556. [PMID: 39170193 PMCID: PMC11336756 DOI: 10.1016/j.heliyon.2024.e35556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
Oxidative stress and its impact on aging are critical areas of research. Natural anti-oxidants, such as saponins found in Polygonatum sibiricum, hold promise as potential clinical interventions against aging. In this study, we utilized the nematode model organism, Caenorhabditis elegans, to investigate the pharmacological effects of Polygonatum sibiricum saponins (PKS) on antioxidation and anti-aging. The results demonstrated a significant anti-aging biological activity associated with PKS. Through experiments involving lifespan and stress, lipofuscin, q-PCR, and ROS measurement, we found that PKS effectively mitigated aging-related processes. Furthermore, the mechanism underlying these anti-aging effects was linked to the SKN-1 signaling pathway. PKS increased the nuclear localization of the SKN-1 transcription factor, leading to the up-regulation of downstream anti-oxidant genes, such as gst-4 and sod-3, and a substantial reduction in intracellular ROS levels within the nematode. In conclusion, our study sheds light on the anti-oxidant and anti-aging properties of PKS in C. elegans. This research not only contributes to understanding the biological mechanisms involved but also highlights the potential therapeutic applications of these natural compounds in combating aging-related processes.
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Affiliation(s)
- Yaqi Huang
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Yetong Wang
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Jia Deng
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Sijie Gao
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Jiakang Qiu
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Jiawei He
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Tong Yang
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Nianhua Tan
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Shaowu Cheng
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Zhenyan Song
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
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2
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Zheng X. An Introductory Guide to Using Bloomington Drosophila Stock Center and FlyBase for Aging Research. Cells 2024; 13:1192. [PMID: 39056774 PMCID: PMC11275189 DOI: 10.3390/cells13141192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Studies on numerous species have demonstrated strikingly conserved mechanisms that determine the aging process, from yeasts to worms, flies, zebrafish, mice, and humans. The fruit fly Drosophila melanogaster is an excellent model organism for studying the biological basis of normal aging and etiology of age-related diseases. Since its inception in 1967, the Bloomington Drosophila Stock Center (BDSC) has grown into the largest collection of documented D. melanogaster strains (currently > 91,000). This paper aims to briefly review conserved mechanisms of aging and provides a guide to help users understand the organization of stock listings on the BDSC website and familiarize themselves with the search functions on BDSC and FlyBase, with an emphasis on using genes in conserved pathways as examples to find stocks for aging studies.
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Affiliation(s)
- Xiangzhong Zheng
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
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3
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Georgievskaya A, Tlyachev T, Kiselev K, Hillebrand G, Chekanov K, Danko D, Golodyaev A, Majmudar G. Predicting human chronological age via AI analysis of dorsal hand versus facial images: A study in a cohort of Indian females. Exp Dermatol 2024; 33:e15045. [PMID: 38509744 DOI: 10.1111/exd.15045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/22/2024]
Abstract
Predicting a person's chronological age (CA) from visible skin features using artificial intelligence (AI) is now commonplace. Often, convolutional neural network (CNN) models are built using images of the face as biometric data. However, hands hold telltale signs of a person's age. To determine the utility of using only hand images in predicting CA, we developed two deep CNNs based on 1) dorsal hand images (H) and 2) frontal face images (F). Subjects (n = 1454) were Indian women, 20-80 years, across three geographic cohorts (Mumbai, New Delhi and Bangalore) and having a broad variation in skin tones. Images were randomised: 70% of F and 70% of H were used to train CNNs. The remaining 30% of F and H were retained for validation. CNN validation showed mean absolute error for predicting CA using F and H of 4.1 and 4.7 years, respectively. In both cases correlations of predicted and actual age were statistically significant (r(F) = 0.93, r(H) = 0.90). The CNNs for F and H were validated for dark and light skin tones. Finally, by blurring or accentuating visible features on specific regions of the hand and face, we identified those features that contributed to the CNN models. For the face, areas of the inner eye corner and around the mouth were most important for age prediction. For the hands, knuckle texture was a key driver for age prediction. Collectively, for AI estimates of CA, CNNs based solely on hand images are a viable alternative and comparable to CNNs based on facial images.
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Affiliation(s)
| | | | | | - Greg Hillebrand
- James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio, USA
| | | | | | | | - Gopa Majmudar
- James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio, USA
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4
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Duffy A, Lawler F, Dalton C, Connolly M. Setting up a journal club for healthcare professionals in an older people's residential care setting. Nurs Older People 2023; 35:21-27. [PMID: 37850272 DOI: 10.7748/nop.2023.e1448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 10/19/2023]
Abstract
With the rise in the number of older people in the population and new developments in older people's services such as integrated care hubs, there is a need for healthcare professionals working with older people to keep up to date with the latest research. This article describes the process of establishing a multidisciplinary journal club in a residential care setting and recognising the potential of such clubs to develop staff members' critical thinking, presentation and communication skills. The authors emphasise the importance of fostering a culture of learning in older people's services and describe how a journal club can support healthcare professionals to maintain their knowledge and improve care.
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Affiliation(s)
- Anita Duffy
- Our Lady's Hospice & Care Services, Dublin; School of Nursing, Midwifery and Health Systems, University College Dublin, Republic of Ireland
| | - Fiona Lawler
- Education and Research, Our Lady's Hospice & Care Services, Dublin, Republic of Ireland
| | - Christine Dalton
- Older Person's Services, Our Lady's Hospice & Care Services, Dublin, Republic of Ireland
| | - Michael Connolly
- School of Nursing, Midwifery and Health Systems, University College Dublin; Our Lady's Hospice & Care Services, Dublin, Republic of Ireland
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5
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Vignali V, Hines PA, Cruz AG, Ziętek B, Herold R. Health horizons: Future trends and technologies from the European Medicines Agency's horizon scanning collaborations. Front Med (Lausanne) 2022; 9:1064003. [PMID: 36569125 PMCID: PMC9772004 DOI: 10.3389/fmed.2022.1064003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
In medicines development, the progress in science and technology is accelerating. Awareness of these developments and their associated challenges and opportunities is essential for medicines regulators and others to translate them into benefits for society. In this context, the European Medicines Agency uses horizon scanning to shine a light on early signals of relevant innovation and technological trends with impact on medicinal products. This article provides the results of systematic horizon scanning exercises conducted by the Agency, in collaboration with the World Health Organization (WHO) and the European Commission's Joint Research Centre's (DG JRC). These collaborative exercises aim to inform policy-makers of new trends and increase preparedness in responding to them. A subset of 25 technological trends, divided into three clusters were selected and reviewed from the perspective of medicines regulators. For each of these trends, the expected impact and challenges for their adoption are discussed, along with recommendations for developers, regulators and policy makers.
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Affiliation(s)
- Valentina Vignali
- European Medicines Agency, Amsterdam, Netherlands
- Department of Biomedical Engineering, W.J. Kolff Institute, University Medical Center Groningen, Groningen, Netherlands
| | - Philip A. Hines
- European Medicines Agency, Amsterdam, Netherlands
- Faculty of Health Medicines and Life Sciences, Maastricht University, Maastricht, Netherlands
| | | | | | - Ralf Herold
- European Medicines Agency, Amsterdam, Netherlands
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6
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Samad N, Nasir A, Rehman MHU, Bhatti SA, Imran I. Adenosine protects D-galactose induced alterations in rat model of aging via attenuating neurochemical profile and redox status. Metab Brain Dis 2022; 37:2483-2496. [PMID: 35870061 DOI: 10.1007/s11011-022-01049-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 07/07/2022] [Indexed: 10/16/2022]
Abstract
Aging is the process that every organism faces. The aging model of brain has been developed by the use of d-galactose (d-Gal). Adenosine (Ad) being a neuroprotective agent that has been utilized in treatment of various neurological disorders. The aim of current study is to evaluate the outcome of Ad on d-Gal induced neurotoxicity which caused behavioral deficits, memory impairment and oxidative stress. Rats were treated with d-Gal at a dose of 300 mg/ml/kg and Ad 1 mg/ml/kg; intraperitoneally for 28 days. Behavioral assessment was performed after the treatment period. Animals were sacrificed after behavioral tests and their brains were collected, hippocampus were removed for biochemical and neurochemical analysis. The results showed that administration of Ad ameliorates the negative effects of d-Gal induced aging in various behavioral tests and increased the time spent in the open arm and light box in elevated plus maze (EPM) and light dark activity (LDA) tests respectively indicate anxiolytic effect; increased the mobility time in tail suspension test (TST) shows antidepressant effect; decreased escape latencies in Morris water maze (MWM) acquisition trials, increase entries and time spent in the target quadrant suggests improvement in learning ability of animals. Administration of Ad also decreased malondialdehyde (MDA) levels, increased antioxidant enzymes activity; decreased acetylcholinesterase (AChE) activity, increased 5-hydroxytryptamine (5-HT, serotonin) metabolism and normalized histopathological alteration in the hippocampus. It is concluded that anxiety, depression and memory impairment induced by d-Gal were protected by Ad through its antioxidant and neuro-modulatory effects.
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Affiliation(s)
- Noreen Samad
- Department of Biochemistry, Faculty of Science, Bahauddin Zakariya University, Multan, 60800, Pakistan.
| | - Arooj Nasir
- Department of Biochemistry, Faculty of Science, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | | | - Sheraz Ahmed Bhatti
- Department of Pathobiology, Faculty of Veterinary Science, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Imran Imran
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60800, Pakistan
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7
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Britton R, Liu AT, Rege SV, Adams JM, Akrapongpisak L, Le D, Alcantara-Lee R, Estrada RA, Ray R, Ahadi S, Gallager I, Yang CF, Minami SS, Braithwaite SP, Czirr E, Campbell MK. Molecular and histological correlates of cognitive decline across age in male C57BL/6J mice. Brain Behav 2022; 12:e2736. [PMID: 35971662 PMCID: PMC9480918 DOI: 10.1002/brb3.2736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 07/01/2022] [Accepted: 07/20/2022] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Increasing age is the number one risk factor for developing cognitive decline and neurodegenerative disease. Aged humans and mice exhibit numerous molecular changes that contribute to a decline in cognitive function and increased risk of developing age-associated diseases. Here, we characterize multiple age-associated changes in male C57BL/6J mice to understand the translational utility of mouse aging. METHODS Male C57BL/6J mice from various ages between 2 and 24 months of age were used to assess behavioral, as well as, histological and molecular changes across three modalities: neuronal, microgliosis/neuroinflammation, and the neurovascular unit (NVU). Additionally, a cohort of 4- and 22-month-old mice was used to assess blood-brain barrier (BBB) breakdown. Mice in this cohort were treated with a high, acute dose of lipopolysaccharide (LPS, 10 mg/kg) or saline control 6 h prior to sacrifice followed by tail vein injection of 0.4 kDa sodium fluorescein (100 mg/kg) 2 h later. RESULTS Aged mice showed a decline in cognitive and motor abilities alongside decreased neurogenesis, proliferation, and synapse density. Further, neuroinflammation and circulating proinflammatory cytokines were increased in aged mice. Additionally, we found changes at the BBB, including increased T cell infiltration in multiple brain regions and an exacerbation in BBB leakiness following chemical insult with age. There were also a number of readouts that were unchanged with age and have limited utility as markers of aging in male C57BL/6J mice. CONCLUSIONS Here we propose that these changes may be used as molecular and histological readouts that correspond to aging-related behavioral decline. These comprehensive findings, in the context of the published literature, are an important resource toward deepening our understanding of normal aging and provide an important tool for studying aging in mice.
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Affiliation(s)
| | - Angela T Liu
- Alkahest, Inc., San Carlos, California, USA.,Coda Biotherapeutics, South San Francisco, California, USA
| | | | | | - Lily Akrapongpisak
- Alkahest, Inc., San Carlos, California, USA.,University of Queensland, Herston, Queensland, Australia
| | - David Le
- Alkahest, Inc., San Carlos, California, USA.,Fountain Therapeutics, South San Francisco, California, USA
| | | | | | - Rebecca Ray
- Alkahest, Inc., San Carlos, California, USA.,202 Chives Way, Walnut Creek, California, USA
| | - Sara Ahadi
- Alkahest, Inc., San Carlos, California, USA
| | | | | | | | | | - Eva Czirr
- Alkahest, Inc., San Carlos, California, USA.,Confluence Therapeutics, South San Francisco, California, USA
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8
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Marchetti B, Giachino C, Tirolo C, Serapide MF. "Reframing" dopamine signaling at the intersection of glial networks in the aged Parkinsonian brain as innate Nrf2/Wnt driver: Therapeutical implications. Aging Cell 2022; 21:e13575. [PMID: 35262262 PMCID: PMC9009237 DOI: 10.1111/acel.13575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/11/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022] Open
Abstract
Dopamine (DA) signaling via G protein‐coupled receptors is a multifunctional neurotransmitter and neuroendocrine–immune modulator. The DA nigrostriatal pathway, which controls the motor coordination, progressively degenerates in Parkinson's disease (PD), a most common neurodegenerative disorder (ND) characterized by a selective, age‐dependent loss of substantia nigra pars compacta (SNpc) neurons, where DA itself is a primary source of oxidative stress and mitochondrial impairment, intersecting astrocyte and microglial inflammatory networks. Importantly, glia acts as a preferential neuroendocrine–immune DA target, in turn, counter‐modulating inflammatory processes. With a major focus on DA intersection within the astrocyte–microglial inflammatory network in PD vulnerability, we herein first summarize the characteristics of DA signaling systems, the propensity of DA neurons to oxidative stress, and glial inflammatory triggers dictating the vulnerability to PD. Reciprocally, DA modulation of astrocytes and microglial reactivity, coupled to the synergic impact of gene–environment interactions, then constitute a further level of control regulating midbrain DA neuron (mDAn) survival/death. Not surprisingly, within this circuitry, DA converges to modulate nuclear factor erythroid 2‐like 2 (Nrf2), the master regulator of cellular defense against oxidative stress and inflammation, and Wingless (Wnt)/β‐catenin signaling, a key pathway for mDAn neurogenesis, neuroprotection, and immunomodulation, adding to the already complex “signaling puzzle,” a novel actor in mDAn–glial regulatory machinery. Here, we propose an autoregulatory feedback system allowing DA to act as an endogenous Nrf2/Wnt innate modulator and trace the importance of DA receptor agonists applied to the clinic as immune modifiers.
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Affiliation(s)
- Bianca Marchetti
- Department of Biomedical and Biotechnological Sciences (BIOMETEC) Pharmacology Section Medical School University of Catania Catania Italy
- OASI Research Institute‐IRCCS, Troina (EN), Italy Troina Italy
| | | | - Cataldo Tirolo
- OASI Research Institute‐IRCCS, Troina (EN), Italy Troina Italy
| | - Maria F. Serapide
- Department of Biomedical and Biotechnological Sciences (BIOMETEC) Pharmacology Section Medical School University of Catania Catania Italy
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9
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Garay RP. Investigational drugs and nutrients for human longevity. Recent clinical trials registered in ClinicalTrials.gov and clinicaltrialsregister.eu. Expert Opin Investig Drugs 2021; 30:749-758. [PMID: 34081543 DOI: 10.1080/13543784.2021.1939306] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction:Several pharmacological drugs have shown proof of concept for longevity in animal models. I aimed to identify and review those longevity drug candidates that are undergoing clinical trials.Areas covered:Recent (post-2017) longevity clinical trials were found in US and EU clinical trial registries. Longevity drug candidates are the antidiabetic drugs metformin and acarbose, and the immunosuppressant rapamycin. These medicinal drugs are tested on biochemical and clinical markers of aging. In addition, vitamin D supplementation is being investigated in two mega-trials (sample size> 5000) for its efficacy in reducing all-cause mortality.Expert opinion:Anti-aging effects of longevity drug candidates suggest, but do not demonstrate that they prolong life. The two megatrials with vitamin D supplementation make it possible to detect differences in life expectancy between vitamin D and placebo. Therefore, a protocol similar to that for vitamin D could be used to demonstrate pro-longevity effects of metformin, acarbose, and rapamycin.
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Affiliation(s)
- Ricardo P Garay
- Pharmacology and Therapeutics, Craven, Villemoisson-sur-Orge, France.,CNRS, National Centre of Scientific Research, Paris, France
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10
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Gibbs NH, Michalski H, Promislow DEL, Kaeberlein M, Creevy KE. Reasons for Exclusion of Apparently Healthy Mature Adult and Senior Dogs From a Clinical Trial. Front Vet Sci 2021; 8:651698. [PMID: 34150883 PMCID: PMC8206478 DOI: 10.3389/fvets.2021.651698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/27/2021] [Indexed: 11/14/2022] Open
Abstract
Background: Interventional clinical trials intended to maintain health in aging dogs are unusual and require particular attention to exclusion criteria. Objectives: To describe reasons for exclusion when a mature adult and senior canine population with normal health status was sought. Animals: Fifty six companion dogs nominated for a randomized controlled trial (RCT). Procedures: Exclusions occurred within Stage 1 (S1): owner-provided survey information; Stage 2 (S2): medical records review; and Stage 3 (S3): screening examination and within Owner, Dog, or Other factor categories. Results: Of 56 nominated dogs, 39 were excluded at S1 (n = 19), S2 (n = 5), and S3 (n = 15), respectively. Dogs were excluded for Owner (n = 4), Dog (n = 27), Other (n = 6), and concurrent (Owner + Dog; n = 2) factors. The most common exclusion period was S1 (n = 19), with weight outside the target range being the most common exclusion factor in that stage (n = 10). Heart murmurs were the second most common exclusion factor (S1: n = 1; S3: n = 5); suspected or confirmed systemic illness was third most common (S1: n = 2; S2: n = 3; S3: n = 2). Among dogs who passed S1 and S2 screening (n = 32), 15 dogs (48%) were excluded at S3, for heart murmur > grade II/VI (n = 5), cardiac arrhythmias (n = 2), and clinicopathologic abnormalities (n = 2). Conclusions and Clinical Relevance: Dogs nominated for a clinical trial for healthy mature adult and senior dogs were excluded for size, previous diagnoses, and newly discovered cardiac abnormalities. For future interventions in mature adult and senior dogs of normal health status, it is important to define expected age-related abnormalities to ensure that meaningful exclusion criteria are used.
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Affiliation(s)
- Nicole H Gibbs
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Hannah Michalski
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Daniel E L Promislow
- Department of Laboratory Medicine & Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Department of Biology, University of Washington, Seattle, WA, United States
| | - Matt Kaeberlein
- Department of Laboratory Medicine & Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Kate E Creevy
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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11
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Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:1-53. [PMID: 34340765 DOI: 10.1016/bs.apcsb.2021.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of molecular pathway activation is the recent instrument that helps to quantize activities of various intracellular signaling, structural, DNA synthesis and repair, and biochemical processes. This may have a deep impact in fundamental research, bioindustry, and medicine. Unlike gene ontology analyses and numerous qualitative methods that can establish whether a pathway is affected in principle, the quantitative approach has the advantage of exactly measuring the extent of a pathway up/downregulation. This results in emergence of a new generation of molecular biomarkers-pathway activation levels, which reflect concentration changes of all measurable pathway components. The input data can be the high-throughput proteomic or transcriptomic profiles, and the output numbers take both positive and negative values and positively reflect overall pathway activation. Due to their nature, the pathway activation levels are more robust biomarkers compared to the individual gene products/protein levels. Here, we review the current knowledge of the quantitative gene expression interrogation methods and their applications for the molecular pathway quantization. We consider enclosed bioinformatic algorithms and their applications for solving real-world problems. Besides a plethora of applications in basic life sciences, the quantitative pathway analysis can improve molecular design and clinical investigations in pharmaceutical industry, can help finding new active biotechnological components and can significantly contribute to the progressive evolution of personalized medicine. In addition to the theoretical principles and concepts, we also propose publicly available software for the use of large-scale protein/RNA expression data to assess the human pathway activation levels.
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12
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Sorokin M, Borisov N, Kuzmin D, Gudkov A, Zolotovskaia M, Garazha A, Buzdin A. Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways. Front Genet 2021; 12:617059. [PMID: 33633781 PMCID: PMC7900570 DOI: 10.3389/fgene.2021.617059] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Current methods of high-throughput molecular and genomic analyses enabled to reconstruct thousands of human molecular pathways. Knowledge of molecular pathways structure and architecture taken along with the gene expression data can help interrogating the pathway activation levels (PALs) using different bioinformatic algorithms. In turn, the pathway activation profiles can characterize molecular processes, which are differentially regulated and give numeric characteristics of the extent of their activation or inhibition. However, different pathway nodes may have different functions toward overall pathway regulation, and calculation of PAL requires knowledge of molecular function of every node in the pathway in terms of its activator or inhibitory role. Thus, high-throughput annotation of functional roles of pathway nodes is required for the comprehensive analysis of the pathway activation profiles. We proposed an algorithm that identifies functional roles of the pathway components and applied it to annotate 3,044 human molecular pathways extracted from the Biocarta, Reactome, KEGG, Qiagen Pathway Central, NCI, and HumanCYC databases and including 9,022 gene products. The resulting knowledgebase can be applied for the direct calculation of the PALs and establishing large scale profiles of the signaling, metabolic, and DNA repair pathway regulation using high throughput gene expression data. We also provide a bioinformatic tool for PAL data calculations using the current pathway knowledgebase.
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Affiliation(s)
- Maxim Sorokin
- Omicsway Corp., Walnut, CA, United States.,Laboratory of Clinical Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nicolas Borisov
- Omicsway Corp., Walnut, CA, United States.,Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Denis Kuzmin
- Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alexander Gudkov
- Laboratory of Clinical Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Marianna Zolotovskaia
- Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | | | - Anton Buzdin
- Omicsway Corp., Walnut, CA, United States.,Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia.,Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
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13
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Jarrell ZR, Smith MR, Hu X, Orr M, Liu KH, Quyyumi AA, Jones DP, Go YM. Plasma acylcarnitine levels increase with healthy aging. Aging (Albany NY) 2020; 12:13555-13570. [PMID: 32554854 PMCID: PMC7377890 DOI: 10.18632/aging.103462] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
Acylcarnitines transport fatty acids into mitochondria and are essential for β-oxidation and energy metabolism. Decreased mitochondrial activity results in increased plasma acylcarnitines, and increased acylcarnitines activate proinflammatory signaling and associate with age-related disease. Changes in acylcarnitines associated with healthy aging, however, are not well characterized. In the present study, we examined the associations of plasma acylcarnitines with age (range: 20-90) in 163 healthy, non-diseased individuals from the predictive medicine research cohort (NCT00336570) and tested for gender-specific differences. The results show that long-chain and very long-chain acylcarnitines increased with age, while many odd-chain acylcarnitines decreased with age. Gender-specific differences were observed for several acylcarnitines, e.g., eicosadienoylcarnitine varied with age in males, and hydroxystearoylcarnitine varied in females. Metabolome-wide association study (MWAS) of age-associated acylcarnitines with all untargeted metabolic features showed little overlap between genders. These results show that plasma concentrations of acylcarnitines vary with age and gender in individuals selected for criteria of health. Whether these variations reflect mitochondrial dysfunction with aging, mitochondrial reprogramming in response to chronic environmental exposures, early pre-disease change, or an adaptive response to healthy aging, is unclear. The results highlight a potential utility for untargeted metabolomics research to elucidate gender-specific mechanisms of aging and age-related disease.
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Affiliation(s)
- Zachery R. Jarrell
- Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322, USA
| | - M. Ryan Smith
- Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322, USA
| | - Xin Hu
- Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322, USA
| | - Michael Orr
- Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322, USA
| | - Ken H. Liu
- Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322, USA
| | - Arshed A. Quyyumi
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322, USA
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