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Article ; Online: Expression of V-nitrogenase and Fe-nitrogenase in

Chanderban, Melissa / Hill, Christopher A / Dhamad, Ahmed E / Lessner, Daniel J

2023 Volume 89, Issue 9, Page(s) e0103323

Abstract: All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen ( ... ...

Abstract	All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N
MeSH term(s)	Nitrogenase/genetics ; Nitrogenase/metabolism ; Molybdenum/metabolism ; Methanosarcina/genetics ; Methanosarcina/metabolism ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Archaea/metabolism
Chemical Substances	Nitrogenase (EC 1.18.6.1) ; Molybdenum (81AH48963U) ; Nitrogen (N762921K75)
Language	English
Publishing date	2023-09-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/aem.01033-23
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Article ; Online: A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans.

Dhamad, Ahmed E / Lessner, Daniel J

Applied and environmental microbiology

2020 Volume 86, Issue 21

Abstract: CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. ... ...

Abstract	CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The
MeSH term(s)	Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; CRISPR-Cas Systems ; Gene Expression ; Genes, Archaeal/genetics ; Methanosarcina/genetics ; Methanosarcina/metabolism ; Nitrogen Fixation/genetics
Chemical Substances	Archaeal Proteins
Language	English
Publishing date	2020-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.01402-20
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Article: COVID-19: molecular and serological detection methods.

Dhamad, Ahmed E / Abdal Rhida, Muna A

PeerJ

2020 Volume 8, Page(s) e10180

Abstract: Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to ... ...

Abstract	Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods.
Keywords	covid19
Language	English
Publishing date	2020-10-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.10180
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Article ; Online: COVID-19

Ahmed E. Dhamad / Muna A. Abdal Rhida

PeerJ, Vol 8, p e

molecular and serological detection methods

2020 Volume 10180

Abstract	Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods.
Keywords	COVID-19 ; SARS-CoV-2 ; rRT-PCR ; ID NOW COVID-19 ; Isothermal amplification ; CRISPR-Cas12 ; Medicine ; R ; Biology (General) ; QH301-705.5 ; covid19
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: COVID-19: molecular and serological detection methods

Dhamad, Ahmed E / Abdal Rhida, Muna A

PeerJ

Abstract	Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #884024
Database	COVID19

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Article ; Online: Diffuse reflectance spectroscopy reveals heat stress-induced changes in hemoglobin concentration in chicken breast.

Dadgar, Sina / Greene, Elizabeth / Dhamad, Ahmed / Mallmann, Barbara / Dridi, Sami / Rajaram, Narasimhan

Scientific reports

2021 Volume 11, Issue 1, Page(s) 3649

Abstract: Heat stress (HS) is devastating to the poultry industry due to its adverse effects on animal well-being and performance. The effects of heat stress are typically measured using a portable i-STAT blood analyzer that quantifies circulatory hemoglobin ... ...

Abstract	Heat stress (HS) is devastating to the poultry industry due to its adverse effects on animal well-being and performance. The effects of heat stress are typically measured using a portable i-STAT blood analyzer that quantifies circulatory hemoglobin concentration and other blood chemistry parameters. Here, we used diffuse reflectance spectroscopy (DRS) as a novel non-invasive method to directly determine changes in hematological parameters in the breast tissues of live heat-stressed broilers. Three-week-old male broilers were randomly subjected to two environmental conditions (thermoneutral, TN, 24 °C vs. cyclic heat stress, HS, 35 °C, 12 h/day). Optical spectra were acquired using DRS to monitor breast hemoglobin (Hb) concentration and vascular oxygen saturation (sO
MeSH term(s)	Animal Feed ; Animals ; Breast/metabolism ; Chickens/metabolism ; Female ; Heat-Shock Response ; Hemoglobins/metabolism ; Hot Temperature/adverse effects ; Meat/analysis ; Poultry ; Spectrum Analysis
Chemical Substances	Hemoglobins
Language	English
Publishing date	2021-02-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-83293-y
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Article ; Online: Systematic Proteomic Identification of the Heat Shock Proteins (Hsp) that Interact with Estrogen Receptor Alpha (ERα) and Biochemical Characterization of the ERα-Hsp70 Interaction.

Dhamad, Ahmed E / Zhou, Zhenqi / Zhou, Jianhong / Du, Yuchun

PloS one

2016 Volume 11, Issue 8, Page(s) e0160312

Abstract: ... Among the reported Hsp cochaperones, we detected prostaglandin E synthase 3 (p23 ...

Abstract	Heat shock proteins (Hsps) are known to associate with estrogen receptors (ER) and regulate ER-mediated cell proliferation. Historically, the studies in this area have focused on Hsp90. However, some critical aspects of the Hsp-ERα interactions remain unclear. For example, we do not know which Hsps are the major or minor ERα interactants and whether or not different Hsp isoforms associate equally with ERα. In the present study, through a quantitative proteomic method we found that 21 Hsps and 3 Hsp cochaperones were associated with ERα in human 293T cells that were cultured in a medium containing necessary elements for cell proliferation. Four Hsp70s (Hsp70-1, Hsc70, Grp75, and Grp78) were the most abundant Hsps identified to associate with ERα, followed by two Hsp90s (Hsp90α and Hsp90β) and three Hsp110s (Hsp105, HspA4, and HspA4L). Hsp90α was found to be 2-3 times more abundant than Hsp90β in the ERα-containing complexes. Among the reported Hsp cochaperones, we detected prostaglandin E synthase 3 (p23), peptidyl-prolyl cis-trans isomerase FKBP5 (FKBP51), and E3 ubiquitin-protein ligase CHIP (CHIP). Studies with the two most abundant ERα-associated Hsps, Hsp70-1 and Hsc70, using human breast cancer MCF7 cells demonstrate that the two Hsps interacted with ERα in both the cytoplasm and nucleus when the cells were cultured in a medium supplemented with fetal bovine serum and phenol red. Interestingly, the ERα-Hsp70-1/Hsc70 interactions were detected only in the cytoplasm but not in the nucleus under hormone starvation conditions, and stimulation of the starved cells with 17β-estradiol (E2) did not change this. In addition, E2-treatment weakened the ERα-Hsc70 interaction but had no effect on the ERα-Hsp70-1 interaction. Further studies showed that significant portions of Hsp70-1 and Hsc70 were associated with transcriptionally active chromatin and inactive chromatin, and the two Hsps interacted with ERα in both forms of the chromatins in MCF7 cells.
MeSH term(s)	Cell Nucleus/drug effects ; Cell Nucleus/metabolism ; Chromatin/chemistry ; Chromatin/metabolism ; Cytoplasm/drug effects ; Cytoplasm/metabolism ; Estradiol/pharmacology ; Estrogen Receptor alpha/genetics ; Estrogen Receptor alpha/metabolism ; Gene Expression ; HEK293 Cells ; HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Heat-Shock Proteins/genetics ; Heat-Shock Proteins/metabolism ; Humans ; MCF-7 Cells ; Prostaglandin-E Synthases/genetics ; Prostaglandin-E Synthases/metabolism ; Protein Binding ; Protein Interaction Mapping ; Proteomics/methods ; Tacrolimus Binding Proteins/genetics ; Tacrolimus Binding Proteins/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Chromatin ; ESR1 protein, human ; Estrogen Receptor alpha ; HSP70 Heat-Shock Proteins ; Heat-Shock Proteins ; Hspa14 protein, human ; Estradiol (4TI98Z838E) ; STUB1 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Tacrolimus Binding Proteins (EC 5.2.1.-) ; tacrolimus binding protein 5 (EC 5.2.1.8) ; PTGES3 protein, human (EC 5.3.99.3) ; Prostaglandin-E Synthases (EC 5.3.99.3)
Language	English
Publishing date	2016-08-02
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0160312
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Hypoxia further exacerbates woody breast myopathy in broilers via alteration of satellite cell fate.

Emami, Nima K / Cauble, Reagan N / Dhamad, Ahmed E / Greene, Elizabeth S / Coy, Cynthia S / Velleman, Sandra G / Orlowski, Sara / Anthony, Nicholas / Bedford, Mike / Dridi, Sami

Poultry science

2021 Volume 100, Issue 7, Page(s) 101167

Abstract: Woody breast (WB) condition has created a variety of challenges for the global poultry industry. To date, there are no effective treatments or preventative measures due to its unknown (undefined) etiology. Several potential mechanisms including oxidative ...

Abstract	Woody breast (WB) condition has created a variety of challenges for the global poultry industry. To date, there are no effective treatments or preventative measures due to its unknown (undefined) etiology. Several potential mechanisms including oxidative stress, fiber-type switching, cellular damage, and altered intracellular calcium levels have been proposed to play a key role in the progression of the WB myopathy. In a previous study, we have shown that WB is associated with hypoxia-like status and dysregulated oxygen homeostasis. As satellite cells (SC) play a pivotal role in muscle fiber repair and remodeling under stress conditions, we undertook the present study to determine satellite cell fate in WB-affected birds when reared in either normoxic or hypoxic conditions. Modern random bred broilers from 2015 (n = 200) were wing banded and reared under standard brooding practices for the first 2 wk post-hatch. At 15 d, chicks were divided in 2 body weight-matched groups and reared to 6 wk in either control local altitude or hypobaric chambers with simulated altitude of 6,000 ft. Birds were provided ad libitum access to water and feed, according to the Cobb recommendations. At 6 wk of age, birds were processed and scored for WB, and breast samples were collected from WB-affected and unaffected birds for molecular analyses (n = 10/group). SCs were isolated from normal breast muscle, cultured in vitro, and exposed to normoxia or hypoxia for 2 h. The expression of target genes was determined by qPCR using 2
MeSH term(s)	Animals ; Chickens ; Hypoxia/veterinary ; Muscle Development ; Muscular Diseases/veterinary ; Pectoralis Muscles
Language	English
Publishing date	2021-03-27
Publishing country	England
Document type	Journal Article
ZDB-ID	242586-5
ISSN	1525-3171 ; 0032-5791
ISSN (online)	1525-3171
ISSN	0032-5791
DOI	10.1016/j.psj.2021.101167
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Article: Muscle Metabolome Profiles in Woody Breast-(un)Affected Broilers: Effects of Quantum Blue Phytase-Enriched Diet.

Greene, Elizabeth / Cauble, Reagan / Dhamad, Ahmed E / Kidd, Michael T / Kong, Byungwhi / Howard, Sara M / Castro, Hector F / Campagna, Shawn R / Bedford, Mike / Dridi, Sami

Frontiers in veterinary science

2020 Volume 7, Page(s) 458

Abstract: Woody breast (WB) myopathy is significantly impacting modern broilers and is imposing a huge economic burden on the poultry industry worldwide. Yet, its etiology is not fully defined. In a previous study, we have shown that hypoxia and the activation of ... ...

Abstract	Woody breast (WB) myopathy is significantly impacting modern broilers and is imposing a huge economic burden on the poultry industry worldwide. Yet, its etiology is not fully defined. In a previous study, we have shown that hypoxia and the activation of its upstream mediators (AKT/PI3K/mTOR) played a key role in WB myopathy, and supplementation of quantum blue (QB) can help to reduce WB severity via modulation of hypoxia-related pathways. To gain further insights, we undertook here a metabolomics approach to identify key metabolite signatures and outline their most enriched biological functions. Ultra performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS) identified a total of 108 known metabolites. Of these, mean intensity differences at
Language	English
Publishing date	2020-08-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2020.00458
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Article ; Online: Systematic Proteomic Identification of the Heat Shock Proteins (Hsp) that Interact with Estrogen Receptor Alpha (ERα) and Biochemical Characterization of the ERα-Hsp70 Interaction.

Ahmed E Dhamad / Zhenqi Zhou / Jianhong Zhou / Yuchun Du

PLoS ONE, Vol 11, Iss 8, p e

2016 Volume 0160312

Abstract: ... Among the reported Hsp cochaperones, we detected prostaglandin E synthase 3 (p23 ...

Abstract	Heat shock proteins (Hsps) are known to associate with estrogen receptors (ER) and regulate ER-mediated cell proliferation. Historically, the studies in this area have focused on Hsp90. However, some critical aspects of the Hsp-ERα interactions remain unclear. For example, we do not know which Hsps are the major or minor ERα interactants and whether or not different Hsp isoforms associate equally with ERα. In the present study, through a quantitative proteomic method we found that 21 Hsps and 3 Hsp cochaperones were associated with ERα in human 293T cells that were cultured in a medium containing necessary elements for cell proliferation. Four Hsp70s (Hsp70-1, Hsc70, Grp75, and Grp78) were the most abundant Hsps identified to associate with ERα, followed by two Hsp90s (Hsp90α and Hsp90β) and three Hsp110s (Hsp105, HspA4, and HspA4L). Hsp90α was found to be 2-3 times more abundant than Hsp90β in the ERα-containing complexes. Among the reported Hsp cochaperones, we detected prostaglandin E synthase 3 (p23), peptidyl-prolyl cis-trans isomerase FKBP5 (FKBP51), and E3 ubiquitin-protein ligase CHIP (CHIP). Studies with the two most abundant ERα-associated Hsps, Hsp70-1 and Hsc70, using human breast cancer MCF7 cells demonstrate that the two Hsps interacted with ERα in both the cytoplasm and nucleus when the cells were cultured in a medium supplemented with fetal bovine serum and phenol red. Interestingly, the ERα-Hsp70-1/Hsc70 interactions were detected only in the cytoplasm but not in the nucleus under hormone starvation conditions, and stimulation of the starved cells with 17β-estradiol (E2) did not change this. In addition, E2-treatment weakened the ERα-Hsc70 interaction but had no effect on the ERα-Hsp70-1 interaction. Further studies showed that significant portions of Hsp70-1 and Hsc70 were associated with transcriptionally active chromatin and inactive chromatin, and the two Hsps interacted with ERα in both forms of the chromatins in MCF7 cells.
Keywords	Medicine ; R ; Science ; Q
Subject code	610 ; 616
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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