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Book: Techniques in quantification and localization of gene expression

Patterson, Bruce K.

2000

Author's details	ed. by Bruce K. Patterson
Keywords	Genexpression ; Forschungsmethode
Subject	Forschung
Language	English
Size	XVII, 150 S. : Ill., graph. Darst.
Publisher	Birkhäuser
Publishing place	Boston
Publishing country	United States
Document type	Book
HBZ-ID	HT011266851
ISBN	0-8176-4034-7 ; 3-7643-4034-7 ; 978-0-8176-4034-7 ; 978-3-7643-4034-6
Database	Catalogue ZB MED Medicine, Health

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Article: Genetic diversity of lion populations in Kenya: Evaluating past management practices and recommendations for future conservation actions.

Chege, Mumbi / Sewalt, Bobbie / Lesilau, Francis / de Snoo, Geert / Patterson, Bruce D / Kariuki, Linus / Otiende, Moses / Omondi, Patrick / de Iongh, Hans / Vrieling, K / Bertola, Laura D

Evolutionary applications

2024 Volume 17, Issue 3, Page(s) e13676

Abstract: The decline of lions ( ...

Abstract	The decline of lions (
Language	English
Publishing date	2024-03-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2405496-3
ISSN	1752-4563 ; 1752-4571
ISSN (online)	1752-4563
ISSN	1752-4571
DOI	10.1111/eva.13676
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Article ; Online: Rationalising development of classification systems describing livestock production systems for disease burden analysis within the Global Burden of Animal Diseases programme.

Li, Yin / McIntyre, K Marie / Rasmussen, Philip / Gilbert, William / Chaters, Gemma / Raymond, Kassy / Jemberu, Wudu T / Larkins, Andrew / Patterson, Grace T / Kwok, Stephen / Kappes, Alexander James / Mayberry, Dianne / Schrobback, Peggy / Acosta, Mario Herrero / Stacey, Deborah A / Huntington, Benjamin / Bruce, Mieghan / Knight-Jones, Theodore / Rushton, Jonathan

Research in veterinary science

2024 Volume 168, Page(s) 105102

Abstract: The heterogeneity that exists across the global spectrum of livestock production means that livestock productivity, efficiency, health expenditure and health outcomes vary across production systems. To ensure that burden of disease estimates are specific ...

Abstract	The heterogeneity that exists across the global spectrum of livestock production means that livestock productivity, efficiency, health expenditure and health outcomes vary across production systems. To ensure that burden of disease estimates are specific to the represented livestock population and people reliant upon them, livestock populations need to be systematically classified into different types of production system, reflective of the heterogeneity across production systems. This paper explores the data currently available of livestock production system classifications and animal health through a scoping review as a foundation for the development of a framework that facilitates more specific estimates of livestock disease burdens. A top-down framework to classification is outlined based on a systematic review of existing classification methods and provides a basis for simple grouping of livestock at global scale. The proposed top-down classification framework, which is dominated by commodity focus of production along with intensity of resource use, may have less relevance at the sub-national level in some jurisdictions and will need to be informed and adapted with information on how countries themselves categorize livestock and their production systems. The findings in this study provide a foundation for analysing animal health burdens across a broad level of production systems. The developed framework will fill a major gap in how livestock production and health are currently approached and analysed.
MeSH term(s)	Animals ; Livestock ; Animal Diseases/epidemiology ; Cost of Illness
Language	English
Publishing date	2024-01-06
Publishing country	England
Document type	Systematic Review ; Journal Article
ZDB-ID	840961-4
ISSN	1532-2661 ; 0034-5288
ISSN (online)	1532-2661
ISSN	0034-5288
DOI	10.1016/j.rvsc.2023.105102
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Article ; Online: Cardiometabolic characteristics of people with metabolically healthy and unhealthy obesity.

Petersen, Max C / Smith, Gordon I / Palacios, Hector H / Farabi, Sarah S / Yoshino, Mihoko / Yoshino, Jun / Cho, Kevin / Davila-Roman, Victor G / Shankaran, Mahalakshmi / Barve, Ruteja A / Yu, Jinsheng / Stern, Jennifer H / Patterson, Bruce W / Hellerstein, Marc K / Shulman, Gerald I / Patti, Gary J / Klein, Samuel

Cell metabolism

2024 Volume 36, Issue 4, Page(s) 745–761.e5

Abstract: There is considerable heterogeneity in the cardiometabolic abnormalities associated with obesity. We evaluated multi-organ system metabolic function in 20 adults with metabolically healthy obesity (MHO; normal fasting glucose and triglycerides, oral ... ...

Abstract	There is considerable heterogeneity in the cardiometabolic abnormalities associated with obesity. We evaluated multi-organ system metabolic function in 20 adults with metabolically healthy obesity (MHO; normal fasting glucose and triglycerides, oral glucose tolerance, intrahepatic triglyceride content, and whole-body insulin sensitivity), 20 adults with metabolically unhealthy obesity (MUO; prediabetes, hepatic steatosis, and whole-body insulin resistance), and 15 adults who were metabolically healthy lean. Compared with MUO, people with MHO had (1) altered skeletal muscle biology (decreased ceramide content and increased expression of genes involved in BCAA catabolism and mitochondrial structure/function); (2) altered adipose tissue biology (decreased expression of genes involved in inflammation and extracellular matrix remodeling and increased expression of genes involved in lipogenesis); (3) lower 24-h plasma glucose, insulin, non-esterified fatty acids, and triglycerides; (4) higher plasma adiponectin and lower plasma PAI-1 concentrations; and (5) decreased oxidative stress. These findings provide a framework of potential mechanisms responsible for MHO and the metabolic heterogeneity of obesity. This study was registered at ClinicalTrials.gov (NCT02706262).
MeSH term(s)	Adult ; Humans ; Obesity/metabolism ; Insulin Resistance ; Obesity, Metabolically Benign ; Triglycerides ; Cardiovascular Diseases ; Metabolic Syndrome/metabolism ; Body Mass Index ; Risk Factors
Chemical Substances	Triglycerides
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2176834-1
ISSN	1932-7420 ; 1550-4131
ISSN (online)	1932-7420
ISSN	1550-4131
DOI	10.1016/j.cmet.2024.03.002
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Article: Case series: Maraviroc and pravastatin as a therapeutic option to treat long COVID/Post-acute sequelae of COVID (PASC).

Patterson, Bruce K / Yogendra, Ram / Guevara-Coto, Jose / Mora-Rodriguez, Rodrigo A / Osgood, Eric / Bream, John / Parikh, Purvi / Kreimer, Mark / Jeffers, Devon / Rutland, Cedric / Kaplan, Gary / Zgoda, Michael

Frontiers in medicine

2023 Volume 10, Page(s) 1122529

Abstract: Post-acute sequelae of COVID (PASC), or long COVID, is a multisystem complication of SARS-CoV-2 infection that continues to debilitate millions worldwide thus highlighting the public health importance of identifying effective therapeutics to alleviate ... ...

Abstract	Post-acute sequelae of COVID (PASC), or long COVID, is a multisystem complication of SARS-CoV-2 infection that continues to debilitate millions worldwide thus highlighting the public health importance of identifying effective therapeutics to alleviate this illness. One explanation behind PASC may be attributed to the recent discovery of persistent S1 protein subunit of SARS-CoV-2 in CD16+ monocytes up to 15 months after infection. CD16+ monocytes, which express both CCR5 and fractalkine receptors (CX3CR1), play a role in vascular homeostasis and endothelial immune surveillance. We propose targeting these receptors using the CCR5 antagonist, maraviroc, along with pravastatin, a fractalkine inhibitor, could disrupt the monocytic-endothelial-platelet axis that may be central to the etiology of PASC. Using five validated clinical scales (NYHA, MRC Dyspnea, COMPASS-31, modified Rankin, and Fatigue Severity Score) to measure 18 participants' response to treatment, we observed significant clinical improvement in 6 to 12 weeks on a combination of maraviroc 300 mg per oral twice a day and pravastatin 10 mg per oral daily. Subjective neurological, autonomic, respiratory, cardiac and fatigue symptoms scores all decreased which correlated with statistically significant decreases in vascular markers sCD40L and VEGF. These findings suggest that by interrupting the monocytic-endothelial-platelet axis, maraviroc and pravastatin may restore the immune dysregulation observed in PASC and could be potential therapeutic options. This sets the framework for a future double-blinded, placebo-controlled randomized trial to further investigate the drug efficacy of maraviroc and pravastatin in treating PASC.
Language	English
Publishing date	2023-02-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2023.1122529
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Article ; Online: Simultaneous ultrasensitive subpopulation staining/hybridization in situ (SUSHI) in HIV-1 disease monitoring.

Patterson, Bruce K

Methods in molecular biology (Clifton, N.J.)

2010 Volume 659, Page(s) 337–346

Abstract: The field of virology is undergoing a revolution as diagnostic tests and new therapies are allowing clinicians to treat, monitor, and predict outcomes of viral diseases. The majority of these techniques, however, destroy the factory of viral production ... ...

Abstract	The field of virology is undergoing a revolution as diagnostic tests and new therapies are allowing clinicians to treat, monitor, and predict outcomes of viral diseases. The majority of these techniques, however, destroy the factory of viral production and the information inherent in the reservoir - the cell. In this chapter, we describe a technique that combines cell surface immunophenotyping (to unequivocally identify cell types) and ultrasensitive fluorescence in situ hybridization (U-FISH) for HIV-1 to detect productively infected cells. Identification of virus and host (cells) allows earlier detection of changes in viral production and viral suppression but most importantly allows clinicians to monitor response to anti-viral therapy on a cell-by-cell and tissue-by-tissue basis taking into account the fact that the human body consists of very different, distinct compartments with unique selection pressures exerted on the viral life cycle.
MeSH term(s)	Cell Line ; Flow Cytometry ; HIV-1/genetics ; HIV-1/physiology ; Humans ; In Situ Hybridization, Fluorescence/methods ; RNA, Viral/analysis ; RNA, Viral/biosynthesis ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; Tissue Fixation ; Virus Replication
Chemical Substances	RNA, Viral
Language	English
Publishing date	2010
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-60761-789-1_26
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Case series

Bruce K. Patterson / Ram Yogendra / Jose Guevara-Coto / Rodrigo A. Mora-Rodriguez / Eric Osgood / John Bream / Purvi Parikh / Mark Kreimer / Devon Jeffers / Cedric Rutland / Gary Kaplan / Michael Zgoda

Frontiers in Medicine, Vol

Maraviroc and pravastatin as a therapeutic option to treat long COVID/Post-acute sequelae of COVID (PASC)

2023 Volume 10

Abstract	Post-acute sequelae of COVID (PASC), or long COVID, is a multisystem complication of SARS-CoV-2 infection that continues to debilitate millions worldwide thus highlighting the public health importance of identifying effective therapeutics to alleviate this illness. One explanation behind PASC may be attributed to the recent discovery of persistent S1 protein subunit of SARS-CoV-2 in CD16+ monocytes up to 15 months after infection. CD16+ monocytes, which express both CCR5 and fractalkine receptors (CX3CR1), play a role in vascular homeostasis and endothelial immune surveillance. We propose targeting these receptors using the CCR5 antagonist, maraviroc, along with pravastatin, a fractalkine inhibitor, could disrupt the monocytic-endothelial-platelet axis that may be central to the etiology of PASC. Using five validated clinical scales (NYHA, MRC Dyspnea, COMPASS-31, modified Rankin, and Fatigue Severity Score) to measure 18 participants’ response to treatment, we observed significant clinical improvement in 6 to 12 weeks on a combination of maraviroc 300 mg per oral twice a day and pravastatin 10 mg per oral daily. Subjective neurological, autonomic, respiratory, cardiac and fatigue symptoms scores all decreased which correlated with statistically significant decreases in vascular markers sCD40L and VEGF. These findings suggest that by interrupting the monocytic-endothelial-platelet axis, maraviroc and pravastatin may restore the immune dysregulation observed in PASC and could be potential therapeutic options. This sets the framework for a future double-blinded, placebo-controlled randomized trial to further investigate the drug efficacy of maraviroc and pravastatin in treating PASC.
Keywords	long COVID ; maraviroc ; CCR5 antagonist ; PASC ; statins ; fractalkine (CX3CR1) ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Protein kinetics of superoxide dismutase-1 in familial and sporadic amyotrophic lateral sclerosis.

Ly, Cindy V / Ireland, Margaret D / Self, Wade K / Bollinger, James / Jockel-Balsarotti, Jennifer / Herzog, Hillary / Allred, Peggy / Miller, Leah / Doyle, Michael / Anez-Bruzual, Isabel / Trikamji, Bhavesh / Hyman, Ted / Kung, Tyler / Nicholson, Katherine / Bucelli, Robert C / Patterson, Bruce W / Bateman, Randall J / Miller, Timothy M

Annals of clinical and translational neurology

2023 Volume 10, Issue 6, Page(s) 1012–1024

Abstract: Objective: Accumulation of misfolded superoxide dismutase-1 (SOD1) is a pathological hallmark of SOD1-related amyotrophic lateral sclerosis (ALS) and is observed in sporadic ALS where its role in pathogenesis is controversial. Understanding in vivo ... ...

Abstract	Objective: Accumulation of misfolded superoxide dismutase-1 (SOD1) is a pathological hallmark of SOD1-related amyotrophic lateral sclerosis (ALS) and is observed in sporadic ALS where its role in pathogenesis is controversial. Understanding in vivo protein kinetics may clarify how SOD1 influences neurodegeneration and inform optimal dosing for therapies that lower SOD1 transcripts. Methods: We employed stable isotope labeling paired with mass spectrometry to evaluate in vivo protein kinetics and concentration of soluble SOD1 in cerebrospinal fluid (CSF) of SOD1 mutation carriers, sporadic ALS participants and controls. A deaminated SOD1 peptide, SDGPVKV, that correlates with protein stability was also measured. Results: In participants with heterozygous SOD1 Interpretation: These results highlight the ability of stable isotope labeling approaches and peptide deamidation to discern the influence of disease mutations on protein kinetics and stability and support implementation of this method to optimize clinical trial design of gene and molecular therapies for neurological disorders. Trial registration: Clinicaltrials.gov: NCT03449212.
MeSH term(s)	Humans ; Superoxide Dismutase-1/genetics ; Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/cerebrospinal fluid ; Superoxide Dismutase/genetics ; Kinetics
Chemical Substances	Superoxide Dismutase-1 (EC 1.15.1.1) ; Superoxide Dismutase (EC 1.15.1.1)
Language	English
Publishing date	2023-04-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2740696-9
ISSN	2328-9503 ; 2328-9503
ISSN (online)	2328-9503
ISSN	2328-9503
DOI	10.1002/acn3.51784
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Article ; Online: Persistence of S1 Spike Protein in CD16+ Monocytes up to 245 Days in SARS-CoV-2 Negative Post COVID-19 Vaccination Individuals with Post-Acute Sequalae of COVID-19 (PASC)-Like Symptoms

Patterson, Bruce K. / Yogendra, Ram / Francisco, Edgar B. / Long, Emily / Pise, Amruta / Osgood, Eric / Bream, John / Kreimer, Mark / Jeffers, Devon / Beaty, Christopher / Heide, Richard Vander / Guevara-Coto, Jose / Mora-Rodríguez, Rodrigo A

medRxiv

Abstract: There have been concerning reports about people experiencing new onset persistent complications (greater than 30 days) following approved SARS-CoV-2 vaccines (BNT162b2 (Pfizer), mRNA-1273 (Moderna), Janssen (Johnson and Johnson), and ChAdOx1 nCoV-19 ( ... ...

Abstract	There have been concerning reports about people experiencing new onset persistent complications (greater than 30 days) following approved SARS-CoV-2 vaccines (BNT162b2 (Pfizer), mRNA-1273 (Moderna), Janssen (Johnson and Johnson), and ChAdOx1 nCoV-19 (AstraZeneca)). We sought to determine the immunologic abnormalities in these patients and to investigate whether the potential etiology was similar to Post-Acute Sequalae of COVID (PASC), or long COVID. We studied 50 individuals who received one of the approved COVID-19 vaccines and who experienced new onset PASC-like symptoms along with 45 individuals post-vaccination without symptoms as controls. We performed multiplex cytokine/chemokine profiling with machine learning as well as SARS-CoV-2 S1 protein detection on CD16+ monocyte subsets using flow cytometry and mass spectrometry. We determined that post-vaccination individuals with PASC-like symptoms had similar symptoms to PASC patients. When analyzing their immune profile, Post-vaccination individuals had statistically significant elevations of sCD40L (p<0.001), CCL5 (p=0.017), IL-6 (p=0.043), and IL-8 (p=0.022). Machine learning characterized these individuals as PASC using previously developed algorithms. Of the S1 positive post-vaccination patients, we demonstrated by liquid chromatography/ mass spectrometry that these CD16+ cells from post-vaccination patients from all 4 vaccine manufacturers contained S1, S1 mutant and S2 peptide sequences. Post-COVID vaccination individuals with PASC-like symptoms exhibit markers of platelet activation and pro-inflammatory cytokine production, which may be driven by the persistence of SARS-CoV-2 S1 proteins in intermediate and non-classical monocytes. The data from this study also cannot make any inferences on epidemiology and prevalence for persistent post-COVID vaccine symptoms. Thus, further studies and research need to be done to understand the risk factors, likelihood and prevalence of these symptoms.
Keywords	covid19
Language	English
Publishing date	2024-03-24
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.03.24.24304286
Database	COVID19

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Article ; Online: Persistence of S1 Spike Protein in CD16+ Monocytes up to 245 Days in SARS-CoV-2 Negative Post COVID-19 Vaccination Individuals with Post-Acute Sequalae of COVID-19 (PASC)-Like Symptoms

Yogendra, Ram / Patterson, Bruce K / Francisco, Brian / Long, Emily / Pise, Amruta / Osgood, Eric / Bream, John / Kreimer, Mark / Jeffers, Devin / Beaty, Christopher / Vander Heide, Richard / Guevara, Jose / Mora-Rodriguez, Rodrigo

medRxiv

Abstract	There have been concerning reports about people experiencing new onset persistent complications (greater than 30 days) following approved SARS-CoV-2 vaccines (BNT162b2 (Pfizer), mRNA-1273 (Moderna), Janssen (Johnson and Johnson), and ChAdOx1 nCoV-19 (AstraZeneca)). We sought to determine the immunologic abnormalities in these patients and to investigate whether the potential etiology was similar to Post-Acute Sequalae of COVID (PASC), or long COVID. We studied 50 individuals who received one of the approved COVID-19 vaccines and who experienced new onset PASC-like symptoms along with 45 individuals post-vaccination without symptoms as controls. We performed multiplex cytokine/chemokine profiling with machine learning as well as SARS-CoV-2 S1 protein detection on CD16+ monocyte subsets using flow cytometry and mass spectrometry. We determined that post-vaccination individuals with PASC-like symptoms had similar symptoms to PASC patients. When analyzing their immune profile, Post-vaccination individuals had statistically significant elevations of sCD40L (p<0.001), CCL5 (p=0.017), IL-6 (p=0.043), and IL-8 (p=0.022). Machine learning characterized these individuals as PASC using previously developed algorithms. Of the S1 positive post-vaccination patients, we demonstrated by liquid chromatography/ mass spectrometry that these CD16+ cells from post-vaccination patients from all 4 vaccine manufacturers contained S1, S1 mutant and S2 peptide sequences. Post-COVID vaccination individuals with PASC-like symptoms exhibit markers of platelet activation and pro-inflammatory cytokine production, which may be driven by the persistence of SARS-CoV-2 S1 proteins in intermediate and non-classical monocytes. The data from this study also cannot make any inferences on epidemiology and prevalence for persistent post-COVID vaccine symptoms. Thus, further studies and research need to be done to understand the risk factors, likelihood and prevalence of these symptoms.
Keywords	covid19
Language	English
Publishing date	2024-03-24
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.03.24.24304286
Database	COVID19

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