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Article ; Online: Mutational scans reveal differential evolvability of

Li, Xueying C / Fuqua, Timothy / van Breugel, Maria Elize / Crocker, Justin

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2023 Volume 378, Issue 1877, Page(s) 20220054

Abstract: Rapid enhancer and slow promoter evolution have been demonstrated through comparative genomics. However, it is not clear how this information is encoded genetically and if this can be used to place evolution in a predictive context. Part of the challenge ...

Abstract	Rapid enhancer and slow promoter evolution have been demonstrated through comparative genomics. However, it is not clear how this information is encoded genetically and if this can be used to place evolution in a predictive context. Part of the challenge is that our understanding of the potential for regulatory evolution is biased primarily toward natural variation or limited experimental perturbations. Here, to explore the evolutionary capacity of promoter variation, we surveyed an unbiased mutation library for three promoters in
MeSH term(s)	Animals ; Drosophila/genetics ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Transcription Factors/metabolism ; Drosophila Proteins/genetics ; Enhancer Elements, Genetic ; Gene Expression Regulation, Developmental ; Mutation
Chemical Substances	Transcription Factors ; Drosophila Proteins
Language	English
Publishing date	2023-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2022.0054
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Book ; Conference proceedings: Conference on health effects of atmospheric salts and gases of sulfur and nitrogen in association with photochemical oxidant

Crocker, T. Timothy

executive summary ; Januar 7 - 8 1974, Newport Beach, Calif

(PB / National Technical Information Service ; 248178)

1974

Event/congress	Conference on Health Effects of Atmospheric Salts and Gases of Sulfur and Nitrogen in Association with Photochemical Oxidant (1, 1974, NewportCalif.)
Author's details	T. Timothy Crocker, ed
Series title	PB / National Technical Information Service ; 248178
Collection
Language	English
Publisher	Nat. Technical Inform. Service
Publishing place	Springfield, Ill
Publishing country	United States
Document type	Book ; Conference proceedings
HBZ-ID	HT012912263
Database	Catalogue ZB MED Medicine, Health

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Shelf mark	Loan status	Location
Se 201 -248148-	verfügbar in Königswinter	Königswinter

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Book: Transport of macromolecules and particles at target sites for deposition of air pollutants

Crocker, T. Timothy / Bhalla, Deepak K.

includes the report of the Institute's Health Review Committee

(Research report / Health Effects Institute ; 3 ; PB / [National Technical Information Service] ; 86-209855)

1986

Author's details	T. T. Crocker and D. K. Bhalla
Series title	Research report / Health Effects Institute ; 3 PB / [National Technical Information Service] ; 86-209855 PB / National Technical Information Service
Collection	PB / National Technical Information Service
Keywords	Air Pollutants, Environmental / toxicity ; Nitrogen Dioxide / pharmacokinetics ; Ozone / pharmacokinetics ; Formaldehyde / pharmacokinetics ; Respiratory System / metabolism ; Biological Transport ; Cell Membrane Permeability ; Epithelium ; Macromolecular Systems ; Rats, Inbred Strains
Language	English
Size	III, 57 S. : Ill.
Publisher	Health Effects Inst
Publishing place	Cambridge, Mass
Publishing country	United States
Document type	Book
Remark	Kopie erschienen im Verl. NTIS, Springfield, Va., 1986
HBZ-ID	HT007569302
Database	Catalogue ZB MED Medicine, Health

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Se 201 -86-209855-	verfügbar in Königswinter	Königswinter

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Article ; Online: An open-source semi-automated robotics pipeline for embryo immunohistochemistry.

Fuqua, Timothy / Jordan, Jeff / Halavatyi, Aliaksandr / Tischer, Christian / Richter, Kerstin / Crocker, Justin

Scientific reports

2021 Volume 11, Issue 1, Page(s) 10314

Abstract: A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their ... ...

Abstract	A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.
MeSH term(s)	Animals ; Automation ; Embryo, Mammalian ; Immunohistochemistry/methods ; Microscopy, Confocal ; Robotics/methods
Language	English
Publishing date	2021-05-13
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/s41598-021-89676-5
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Article ; Online: Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development.

Galupa, Rafael / Alvarez-Canales, Gilberto / Borst, Noa Ottilie / Fuqua, Timothy / Gandara, Lautaro / Misunou, Natalia / Richter, Kerstin / Alves, Mariana R P / Karumbi, Esther / Perkins, Melinda Liu / Kocijan, Tin / Rushlow, Christine A / Crocker, Justin

Developmental cell

2023 Volume 58, Issue 1, Page(s) 51–62.e4

Abstract: Developmental enhancers bind transcription factors and dictate patterns of gene expression during development. Their molecular evolution can underlie phenotypical evolution, but the contributions of the evolutionary pathways involved remain little ... ...

Abstract	Developmental enhancers bind transcription factors and dictate patterns of gene expression during development. Their molecular evolution can underlie phenotypical evolution, but the contributions of the evolutionary pathways involved remain little understood. Here, using mutation libraries in Drosophila melanogaster embryos, we observed that most point mutations in developmental enhancers led to changes in gene expression levels but rarely resulted in novel expression outside of the native pattern. In contrast, random sequences, often acting as developmental enhancers, drove expression across a range of cell types; random sequences including motifs for transcription factors with pioneer activity acted as enhancers even more frequently. Our findings suggest that the phenotypic landscapes of developmental enhancers are constrained by enhancer architecture and chromatin accessibility. We propose that the evolution of existing enhancers is limited in its capacity to generate novel phenotypes, whereas the activity of de novo elements is a primary source of phenotypic novelty.
MeSH term(s)	Animals ; Drosophila/metabolism ; Drosophila melanogaster/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Chromatin/genetics ; Chromatin/metabolism ; Enhancer Elements, Genetic/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Evolution, Molecular ; Phenotype ; Gene Expression Regulation, Developmental
Chemical Substances	Drosophila Proteins ; Chromatin ; Transcription Factors
Language	English
Publishing date	2023-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2022.12.003
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Article ; Online: Therapeutic activation of endothelial sphingosine-1-phosphate receptor 1 by chaperone-bound S1P suppresses proliferative retinal neovascularization.

Niaudet, Colin / Jung, Bongnam / Kuo, Andrew / Swendeman, Steven / Bull, Edward / Seno, Takahiro / Crocker, Reed / Fu, Zhongjie / Smith, Lois E H / Hla, Timothy

EMBO molecular medicine

2023 Volume 15, Issue 5, Page(s) e16645

Abstract: Sphingosine-1-phosphate (S1P), the circulating HDL-bound lipid mediator that acts via S1P receptors (S1PR), is required for normal vascular development. The role of this signaling axis in vascular retinopathies is unclear. Here, we show in a mouse model ... ...

Abstract	Sphingosine-1-phosphate (S1P), the circulating HDL-bound lipid mediator that acts via S1P receptors (S1PR), is required for normal vascular development. The role of this signaling axis in vascular retinopathies is unclear. Here, we show in a mouse model of oxygen-induced retinopathy (OIR) that endothelial overexpression of S1pr1 suppresses while endothelial knockout of S1pr1 worsens neovascular tuft formation. Furthermore, neovascular tufts are increased in Apom
MeSH term(s)	Mice ; Animals ; Sphingosine-1-Phosphate Receptors ; Retinal Neovascularization ; Receptors, Lysosphingolipid/genetics ; Receptors, Lysosphingolipid/agonists ; Lipoproteins, HDL ; Sphingosine ; Lysophospholipids
Chemical Substances	Sphingosine-1-Phosphate Receptors ; sphingosine 1-phosphate (26993-30-6) ; Receptors, Lysosphingolipid ; Lipoproteins, HDL ; Sphingosine (NGZ37HRE42) ; Lysophospholipids
Language	English
Publishing date	2023-03-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.15252/emmm.202216645
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Article ; Online: Dense and pleiotropic regulatory information in a developmental enhancer.

Fuqua, Timothy / Jordan, Jeff / van Breugel, Maria Elize / Halavatyi, Aliaksandr / Tischer, Christian / Polidoro, Peter / Abe, Namiko / Tsai, Albert / Mann, Richard S / Stern, David L / Crocker, Justin

Nature

2020 Volume 587, Issue 7833, Page(s) 235–239

Abstract: Changes in gene regulation underlie much of phenotypic ... ...

Abstract	Changes in gene regulation underlie much of phenotypic evolution
MeSH term(s)	Animals ; Base Sequence ; Binding Sites ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Drosophila melanogaster/growth & development ; Enhancer Elements, Genetic/genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental/genetics ; Homeodomain Proteins/genetics ; Larva/genetics ; Larva/growth & development ; Mutation ; Phenotype ; Transcription Factors/genetics
Chemical Substances	Drosophila Proteins ; Homeodomain Proteins ; Transcription Factors ; Ubx protein, Drosophila
Language	English
Publishing date	2020-10-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2816-5
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Article ; Online: Similar foraging energetics of two sympatric albatrosses despite contrasting life histories and wind-mediated foraging strategies.

Kroeger, Caitlin E / Crocker, Daniel E / Orben, Rachael A / Thompson, David R / Torres, Leigh G / Sagar, Paul M / Sztukowski, Lisa A / Andriese, Timothy / Costa, Daniel P / Shaffer, Scott A

The Journal of experimental biology

2020 Volume 223, Issue Pt 23

Abstract: Understanding the environmental and behavioral factors that influence how organisms maintain energy balance can inform us about their potential resiliency to rapid environmental changes. Flexibility in maintaining energy balance is particularly important ...

Abstract	Understanding the environmental and behavioral factors that influence how organisms maintain energy balance can inform us about their potential resiliency to rapid environmental changes. Flexibility in maintaining energy balance is particularly important to long-lived, central-place foraging seabirds that are constrained when locating food for offspring in a dynamic ocean environment. To understand the role of environmental interactions, behavioral flexibility and morphological constraints on energy balance, we used doubly labeled water to measure the at-sea daily energy expenditure (DEE) of two sympatrically breeding seabirds, Campbell (
MeSH term(s)	Animals ; Birds ; Female ; Male ; Seasons ; Sympatry ; Wind ; Wings, Animal
Language	English
Publishing date	2020-12-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218085-6
ISSN	1477-9145 ; 0022-0949
ISSN (online)	1477-9145
ISSN	0022-0949
DOI	10.1242/jeb.228585
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Article: Extracranial displacement of a ventricular catheter following trauma.

Sergides, Ioannis / Crocker, Matthew / Hampton, Timothy / Bassi, Sanj

British journal of neurosurgery

2006 Volume 20, Issue 4, Page(s) 257–258

Abstract: We report a case of complete extracranial displacement of the proximal part of a ventriculo-peritoneal shunt following trauma. The possible mechanism of the delayed displacement of the shunt is discussed. The importance of early recognition of this ... ...

Abstract	We report a case of complete extracranial displacement of the proximal part of a ventriculo-peritoneal shunt following trauma. The possible mechanism of the delayed displacement of the shunt is discussed. The importance of early recognition of this unusual cause of shunt dysfunction is considered.
MeSH term(s)	Adult ; Catheters, Indwelling ; Craniocerebral Trauma/complications ; Equipment Failure ; Humans ; Male ; Ventriculoperitoneal Shunt/instrumentation
Language	English
Publishing date	2006-08
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	639029-8
ISSN	0268-8697
ISSN	0268-8697
DOI	10.1080/02688690600852779
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Book ; Online: Marine gas-phase sulfur emissions during an induced phytoplankton bloom

Kilgour, Delaney B. / Novak, Gordon A. / Sauer, Jon S. / Moore, Alexia N. / Dinasquet, Julie / Amiri, Sarah / Franklin, Emily B. / Mayer, Kathryn / Winter, Margaux / Morris, Clare K. / Price, Tyler / Malfatti, Francesca / Crocker, Daniel R. / Lee, Christopher / Cappa, Christopher D. / Goldstein, Allen H. / Prather, Kimberly A. / Bertram, Timothy H.

eISSN: 1680-7324

2021

Abstract: The oxidation of dimethyl sulfide (DMS; CH 3 SCH 3 ), emitted from the surface ocean, contributes to the formation of Aitken mode particles and their growth to cloud condensation nuclei (CCN) sizes in remote marine environments. It is not clear whether ... ...

Abstract	The oxidation of dimethyl sulfide (DMS; CH 3 SCH 3 ), emitted from the surface ocean, contributes to the formation of Aitken mode particles and their growth to cloud condensation nuclei (CCN) sizes in remote marine environments. It is not clear whether other, less commonly measured marine-derived, sulfur-containing gases share similar dynamics to DMS and contribute to secondary marine aerosol formation. Here, we present measurements of gas-phase volatile organosulfur molecules taken with a Vocus proton transfer reaction high resolution time-of-flight mass spectrometer during a mesocosm phytoplankton bloom experiment using coastal seawater. We show that DMS, methanethiol (MeSH; CH 3 SH), and benzothiazole (C 7 H 5 NS) account for on average over 90 % of total gas-phase sulfur emissions, with non-DMS sulfur sources representing 36.8 ± 7.7 % of sulfur emissions during the first nine days of the experiment in the pre-bloom phase prior to major biological growth, before declining to 14.5 ± 6.0 % in the latter half of the experiment when DMS dominates during the bloom and decay phases. The molar ratio of DMS to MeSH during the pre-bloom phase (DMS : MeSH = 4.60 ± 0.93) was consistent with the range of previously calculated ambient DMS to MeSH sea-to-air flux ratios. As the experiment progressed, the DMS to MeSH emission ratio increased significantly, reaching 31.8 ± 18.7 during the bloom and decay. Measurements of dimethylsulfoniopropionate (DMSP), heterotrophic bacteria, and enzyme activity in the seawater suggest the DMS : MeSH ratio is a sensitive indicator of the bacterial sulfur demand and the composition and magnitude of available sulfur sources in seawater. The evolving DMS : MeSH ratio and the emission of a new aerosol precursor gas, benzothiazole, have important implications for secondary sulfate formation pathways in coastal marine environments.
Subject code	660
Language	English
Publishing date	2021-08-06
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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