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Article ; Online: Looking deeper into tissue elongation.

Williams, Audrey M / Horne-Badovinac, Sally

2020 Volume 21, Issue 6, Page(s) 305

MeSH term(s)	Animals ; Cell Division ; Drosophila ; Germ Cells
Language	English
Publishing date	2020-02-18
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	2031313-5
ISSN	1471-0080 ; 1471-0072
ISSN (online)	1471-0080
ISSN	1471-0072
DOI	10.1038/s41580-020-0226-z
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Article ; Online: Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX.

Lau, Edmond Y / Enright, Heather A / Lao, Victoria / Malfatti, Michael A / Mayer, Brian P / Williams, Audrey M / Valdez, Carlos A

PloS one

2023 Volume 18, Issue 3, Page(s) e0283181

Abstract: The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S-[2-[Di(propan-2-yl)amino]ethyl] O-ethyl methylphosphonothioate (VX) has been studied using 31P-nuclear magnetic resonance (NMR) ...

Abstract	The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S-[2-[Di(propan-2-yl)amino]ethyl] O-ethyl methylphosphonothioate (VX) has been studied using 31P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t1/2 ~ 2 hrs) relative over background (t1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent's degradation profile was identical to that of background degradation (t1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (PGF⋯OOxime ~ 4-5 Å) to the phosphorus center of GF in the 'downGF' orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the 'downGF' orientation than in the 'upGF' orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the 'downGD' orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (PGD⋯OOxime ~ 4-5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12-14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.
MeSH term(s)	Soman ; Nerve Agents ; Oximes ; Molecular Dynamics Simulation ; Cyclodextrins ; Medical Countermeasures ; Organophosphorus Compounds/chemistry ; Chemical Warfare Agents ; Phosphorus
Chemical Substances	cyclohexyl methylphosphonofluoridate (VM36F9N236) ; VX (9A4381183B) ; Soman (96-64-0) ; Nerve Agents ; Oximes ; Cyclodextrins ; Organophosphorus Compounds ; Chemical Warfare Agents ; Phosphorus (27YLU75U4W)
Language	English
Publishing date	2023-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0283181
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Article ; Online: Toward Machine Learning-Driven Mass Spectrometric Identification of Trichothecenes in the Absence of Standard Reference Materials.

Mayer, Brian P / Dreyer, Mark L / Prieto Conaway, Maria C / Valdez, Carlos A / Corzett, Todd / Leif, Roald / Williams, Audrey M

Analytical chemistry

2023 Volume 95, Issue 35, Page(s) 13064–13072

Abstract: While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both ... ...

Abstract	While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both analytical reference standards and associated mass spectral databases, identification of these modified compounds reflects both a challenge and a critical gap from forensic and public health perspectives. We report here the application of machine learning (ML) techniques toward identification of discriminative fragment ions from mass spectrometric data that can be exploited to detect evidence of type A and B trichothecenes. The goal of this work is to establish a new method for the identification of unknown, though structurally similar trichothecenes, by leveraging objective ML techniques. Discriminative fragments derived from a series of gradient-boosted machine learners are then used to develop ML-driven precursor ion scan (PIS) methods on a triple quadrupole mass spectrometer (QQQ) for screening of "unknown unknown" trichothecenes. Specifically, we apply the PIS method to a laboratory-synthesized trichothecene, a first step in demonstrating the power of alternative, machine learning-driven mass spectrometric methods.
MeSH term(s)	Databases, Factual ; Forensic Medicine ; Machine Learning ; Trichothecenes
Chemical Substances	trichothecene (7OO57LYZ5I) ; Trichothecenes
Language	English
Publishing date	2023-08-22
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	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c01474
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Article ; Online: Toward Machine Learning-Driven Mass Spectrometric Identification of Trichothecenes in the Absence of Standard Reference Materials

Mayer, Brian P. / Dreyer, Mark L. / Prieto Conaway, Maria C. / Valdez, Carlos A. / Corzett, Todd / Leif, Roald / Williams, Audrey M.

Analytical Chemistry. 2023 Aug. 22, v. 95, no. 35 p.13064-13072

2023

Abstract	While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both analytical reference standards and associated mass spectral databases, identification of these modified compounds reflects both a challenge and a critical gap from forensic and public health perspectives. We report here the application of machine learning (ML) techniques toward identification of discriminative fragment ions from mass spectrometric data that can be exploited to detect evidence of type A and B trichothecenes. The goal of this work is to establish a new method for the identification of unknown, though structurally similar trichothecenes, by leveraging objective ML techniques. Discriminative fragments derived from a series of gradient-boosted machine learners are then used to develop ML-driven precursor ion scan (PIS) methods on a triple quadrupole mass spectrometer (QQQ) for screening of “unknown unknown” trichothecenes. Specifically, we apply the PIS method to a laboratory-synthesized trichothecene, a first step in demonstrating the power of alternative, machine learning-driven mass spectrometric methods.
Keywords	analytical chemistry ; forensic sciences ; mass spectrometry ; public health ; spectrometers ; trichothecenes
Language	English
Dates of publication	2023-0822
Size	p. 13064-13072.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c01474
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Article ; Online: Modulators of calcium signalling at fertilization.

Stein, Paula / Savy, Virginia / Williams, Audrey M / Williams, Carmen J

Open biology

2020 Volume 10, Issue 7, Page(s) 200118

Abstract: ... Calcium ( ... ...

Abstract	Calcium (Ca
MeSH term(s)	Calcium/metabolism ; Calcium Release Activated Calcium Channels/genetics ; Calcium Signaling/genetics ; Endoplasmic Reticulum/genetics ; Fertilization/genetics ; Humans ; Inositol 1,4,5-Trisphosphate Receptors/genetics
Chemical Substances	Calcium Release Activated Calcium Channels ; Inositol 1,4,5-Trisphosphate Receptors ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2020-07-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.200118
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Article ; Online: Part 3: Solid phase extraction of Russian VX and its chemical attribution signatures in food matrices and their detection by GC-MS and LC-MS.

Williams, Audrey M / Vu, Alexander K / Mayer, Brian P / Hok, Saphon / Valdez, Carlos A / Alcaraz, Armando

Talanta

2018 Volume 186, Page(s) 607–614

Abstract: Chemical attribution signatures indicative of O-isobutyl S-(2-diethylaminoethyl) methylphosphonothioate (Russian VX) synthetic routes were investigated in spiked food samples. Attribution signatures were identified using a multifaceted approach: Russian ... ...

Abstract	Chemical attribution signatures indicative of O-isobutyl S-(2-diethylaminoethyl) methylphosphonothioate (Russian VX) synthetic routes were investigated in spiked food samples. Attribution signatures were identified using a multifaceted approach: Russian VX was synthesized using six synthetic routes and the chemical attribution signatures identified by GC-MS and LC-MS. Three synthetic routes were then down selected and spiked into complex matrices: bottled water, baby food, milk, liquid eggs, and hot dogs. Sampling and extraction methodologies were developed for these materials and used to isolate the attribution signatures and Russian VX from each matrix. Recoveries greater than 60% were achieved for most signatures in all matrices; some signatures provided recoveries greater than 100%, indicating some degradation during sample preparation. A chemometric model was then developed and validated with the concatenated data from GC-MS and LC-MS analyses of the signatures; the classification results of the model were > 75% for all samples. This work is part three of a three-part series in this issue of the United States-Sweden collaborative efforts towards the understanding of the chemical attribution signatures of Russian VX in crude materials and in food matrices.
MeSH term(s)	Animals ; Chemical Warfare Agents/chemistry ; Chemical Warfare Agents/isolation & purification ; Chromatography, Liquid ; Drinking Water/chemistry ; Food Analysis ; Food Contamination/analysis ; Gas Chromatography-Mass Spectrometry ; Humans ; Infant ; Infant Food/analysis ; Mass Spectrometry ; Milk/chemistry ; Organothiophosphorus Compounds/chemistry ; Organothiophosphorus Compounds/isolation & purification ; Solid Phase Extraction
Chemical Substances	Chemical Warfare Agents ; Drinking Water ; Organothiophosphorus Compounds ; S-(N,N-diethylaminoethyl) isobutyl methylphosphothiolate (LG34LSI9IU)
Language	English
Publishing date	2018-03-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2018.03.044
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Article ; Online: Statistical analysis of the chemical attribution signatures of 3-methylfentanyl and its methods of production.

Mayer, Brian P / Valdez, Carlos A / DeHope, Alan J / Spackman, Paul E / Williams, Audrey M

Talanta

2018 Volume 186, Page(s) 645–654

Abstract: Chemical attribution of the origin of an illegal drug is a key component of forensic efforts aimed at combating illicit and clandestine manufacture of drugs and pharmaceuticals. The results of these studies yield detailed information on synthesis ... ...

Abstract	Chemical attribution of the origin of an illegal drug is a key component of forensic efforts aimed at combating illicit and clandestine manufacture of drugs and pharmaceuticals. The results of these studies yield detailed information on synthesis byproducts, reagents, and precursors that can be used to identify the method of manufacture. In the present work, chemical attribution signatures (CAS) associated with the synthesis of the analgesic 3-methylfentanyl, N-(3-methyl-1-phenethylpiperidin-4-yl)-N-phenylpropanamide, were investigated. Eighteen crude samples from six synthesis methods were generated, the analysis of which was used to identify signatures (i.e. chemical compounds) that were important in the discrimination of synthetic route. These methods were carefully selected to minimize the use of scheduled precursors, complicated laboratory equipment, number of steps, and extreme reaction conditions. Using gas and liquid chromatographies combined with time-of-flight mass spectrometry (GC-QTOF and LC-QTOF) over 160 distinct species were monitored. Analysis of this combined data set was performed using modern machine learning techniques capable of reducing the size of the data set, prioritizing key chemical attribution signatures, and identifying the method of production for blindly synthesized 3-methylfentanyl materials.
Language	English
Publishing date	2018-08-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2018.02.026
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Article: Part 3: Solid phase extraction of Russian VX and its chemical attribution signatures in food matrices and their detection by GC-MS and LC-MS

Williams, Audrey M / Vu, Alexander K / Mayer, Brian P / Hok, Saphon / Valdez, Carlos A / Alcaraz, Armando

Elsevier B.V. Talanta. 2018 Aug. 15, v. 186

2018

Abstract	Chemical attribution signatures indicative of O-isobutyl S-(2-diethylaminoethyl) methylphosphonothioate (Russian VX) synthetic routes were investigated in spiked food samples. Attribution signatures were identified using a multifaceted approach: Russian VX was synthesized using six synthetic routes and the chemical attribution signatures identified by GC-MS and LC-MS. Three synthetic routes were then down selected and spiked into complex matrices: bottled water, baby food, milk, liquid eggs, and hot dogs. Sampling and extraction methodologies were developed for these materials and used to isolate the attribution signatures and Russian VX from each matrix. Recoveries greater than 60% were achieved for most signatures in all matrices; some signatures provided recoveries greater than 100%, indicating some degradation during sample preparation. A chemometric model was then developed and validated with the concatenated data from GC-MS and LC-MS analyses of the signatures; the classification results of the model were > 75% for all samples. This work is part three of a three-part series in this issue of the United States-Sweden collaborative efforts towards the understanding of the chemical attribution signatures of Russian VX in crude materials and in food matrices.
Keywords	bottled water ; chemometrics ; eggs ; food matrix ; gas chromatography-mass spectrometry ; hot dogs ; infant foods ; liquid chromatography ; liquids ; milk ; models ; solid phase extraction
Language	English
Dates of publication	2018-0815
Size	p. 607-614.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2018.03.044
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Article: Statistical analysis of the chemical attribution signatures of 3-methylfentanyl and its methods of production

Mayer, Brian P / Valdez, Carlos A / DeHope, Alan J / Spackman, Paul E / Williams, Audrey M

Elsevier B.V. Talanta. 2018 Aug. 15, v. 186

2018

Abstract	Chemical attribution of the origin of an illegal drug is a key component of forensic efforts aimed at combating illicit and clandestine manufacture of drugs and pharmaceuticals. The results of these studies yield detailed information on synthesis byproducts, reagents, and precursors that can be used to identify the method of manufacture. In the present work, chemical attribution signatures (CAS) associated with the synthesis of the analgesic 3-methylfentanyl, N-(3-methyl-1-phenethylpiperidin-4-yl)-N-phenylpropanamide, were investigated. Eighteen crude samples from six synthesis methods were generated, the analysis of which was used to identify signatures (i.e. chemical compounds) that were important in the discrimination of synthetic route. These methods were carefully selected to minimize the use of scheduled precursors, complicated laboratory equipment, number of steps, and extreme reaction conditions. Using gas and liquid chromatographies combined with time-of-flight mass spectrometry (GC-QTOF and LC-QTOF) over 160 distinct species were monitored. Analysis of this combined data set was performed using modern machine learning techniques capable of reducing the size of the data set, prioritizing key chemical attribution signatures, and identifying the method of production for blindly synthesized 3-methylfentanyl materials.
Keywords	analgesics ; artificial intelligence ; byproducts ; chemical compounds ; data collection ; forensic sciences ; laboratory equipment ; liquid chromatography ; manufacturing ; mass spectrometry ; statistical analysis
Language	English
Dates of publication	2018-0815
Size	p. 645-654.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2018.02.026
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Article ; Online: Planar-Polarized Semaphorin-5c and Plexin A Promote the Collective Migration of Epithelial Cells in Drosophila.

Stedden, Claire G / Menegas, William / Zajac, Allison L / Williams, Audrey M / Cheng, Shouqiang / Özkan, Engin / Horne-Badovinac, Sally

Current biology : CB

2019 Volume 29, Issue 6, Page(s) 908–920.e6

Abstract: Collective migration of epithelial cells is essential for morphogenesis, wound repair, and the spread of many cancers, yet how individual cells signal to one another to coordinate their movements is largely unknown. Here, we introduce a tissue-autonomous ...

Abstract	Collective migration of epithelial cells is essential for morphogenesis, wound repair, and the spread of many cancers, yet how individual cells signal to one another to coordinate their movements is largely unknown. Here, we introduce a tissue-autonomous paradigm for semaphorin-based regulation of collective cell migration. Semaphorins typically regulate the motility of neuronal growth cones and other migrating cell types by acting as repulsive cues within the migratory environment. Studying the follicular epithelial cells of Drosophila, we discovered that the transmembrane semaphorin, Sema-5c, promotes collective cell migration by acting within the migrating cells themselves, not the surrounding environment. Sema-5c is planar polarized at the basal epithelial surface such that it is enriched at the leading edge of each cell. This location places it in a prime position to send a repulsive signal to the trailing edge of the cell ahead to communicate directional information between neighboring cells. Our data show that Sema-5c can signal across cell-cell boundaries to suppress protrusions in neighboring cells and that Plexin A is the receptor that transduces this signal. Finally, we present evidence that Sema-5c antagonizes the activity of Lar, another transmembrane guidance cue that operates along leading-trailing cell-cell interfaces in this tissue, via a mechanism that appears to be independent of Plexin A. Together, our results suggest that multiple transmembrane guidance cues can be deployed in a planar-polarized manner across an epithelium and work in concert to coordinate individual cell movements for collective migration.
MeSH term(s)	Animals ; Cell Movement/genetics ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/physiology ; Epithelial Cells/physiology ; Membrane Glycoproteins/genetics ; Membrane Glycoproteins/metabolism ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Receptor-Like Protein Tyrosine Phosphatases/genetics ; Receptor-Like Protein Tyrosine Phosphatases/metabolism ; Receptors, Cell Surface/genetics ; Receptors, Cell Surface/metabolism ; Semaphorins/genetics ; Semaphorins/metabolism
Chemical Substances	Drosophila Proteins ; Membrane Glycoproteins ; Nerve Tissue Proteins ; Receptors, Cell Surface ; Sema5c protein, Drosophila ; Semaphorins ; plexA protein, Drosophila ; Lar protein, Drosophila (EC 3.1.3.48) ; Receptor-Like Protein Tyrosine Phosphatases (EC 3.1.3.48)
Language	English
Publishing date	2019-02-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2019.01.049
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