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Article ; Online: Successful repair of coracoid and femur fractures in a Eurasian eagle owl (

Kim, Hee-Jong / Kim, Kyoo-Tae

2023 Volume 24, Issue 1, Page(s) e17

Abstract: To our knowledge, this is the first case of concurrent diaphyseal left coracoid and left femoral fractures in a Eurasian eagle owl and its post-release survival in Korea. The femur was surgically repaired using an external skeletal fixator-intramedullary ...

Abstract	To our knowledge, this is the first case of concurrent diaphyseal left coracoid and left femoral fractures in a Eurasian eagle owl and its post-release survival in Korea. The femur was surgically repaired using an external skeletal fixator-intramedullary (IM) pin tie-in method, and the coracoid was repaired solely with an IM pin on day 6 after femur surgery. The eagle owl underwent a gradual rehabilitation process. The bird was successfully rehabilitated and released 101 d after initial presentation. The bird was monitored using a wildlife tracking device and was confirmed to have survived for over 5 mon in the wild.
MeSH term(s)	Animals ; Strigiformes ; Fractures, Bone/veterinary ; Animals, Wild ; Femur/surgery
Language	English
Publishing date	2023-02-01
Publishing country	Korea (South)
Document type	Case Reports
ZDB-ID	2125308-0
ISSN	1976-555X ; 1976-555X
ISSN (online)	1976-555X
ISSN	1976-555X
DOI	10.4142/jvs.22240
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A case of rickets in an artificially raised white-tailed eagle (Haliaeetus albicilla) chick at a zoo.

Kim, Hee-Jong / Kim, Kyoo-Tae

The Journal of veterinary medical science

2023 Volume 85, Issue 5, Page(s) 584–586

Abstract: A two-week-old white-tailed eagle presented with an inability to stand and flex its limbs. Despite hatching naturally and owing to lack of parental attention, the bird was raised indoors by zookeepers with no access to sunlight. Palpation and ... ...

Abstract	A two-week-old white-tailed eagle presented with an inability to stand and flex its limbs. Despite hatching naturally and owing to lack of parental attention, the bird was raised indoors by zookeepers with no access to sunlight. Palpation and radiographic examination of the bilateral tibiotarsus and femur bone revealed pronounced deformation and curvature, and bilateral decreased bone densities, respectively. The reduced calcium concentration in the blood was treated with calcium gluconate injections and calcium-supplemented feeds. Chopped mouse tails were fed directly, and whole pink-skinned nude mice were fed weekly. The zookeeper also gently massaged the bird and dressed it with a bandage. Sunlight exposure was provided daily. Saliva containing chicken feed was obtained from the mother. The bird could stand properly after four weeks of treatment, and the blood calcium concentration was restored to normal levels.
MeSH term(s)	Animals ; Mice ; Eagles ; Chickens ; Calcium ; Mice, Nude ; Rickets/veterinary
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2023-03-17
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1071753-5
ISSN	1347-7439 ; 0916-7250
ISSN (online)	1347-7439
ISSN	0916-7250
DOI	10.1292/jvms.22-0516
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Article ; Online: Application of 3D-printed prosthetic lower beak in an Oriental stork (Ciconia boyciana).

Kim, Hee-Jong / Cho, Cheongwoon / Kim, Kyoo-Tae

The Journal of veterinary medical science

2023 Volume 85, Issue 11, Page(s) 1190–1194

Abstract: To our knowledge, ours is the first case of applying a 3D-printed prosthetic beak to an Oriental stork (Ciconia boyciana). A stork in captivity underwent several surgeries for beak fractures, but the lower-mandible fractures failed to be repaired. ... ...

Abstract	To our knowledge, ours is the first case of applying a 3D-printed prosthetic beak to an Oriental stork (Ciconia boyciana). A stork in captivity underwent several surgeries for beak fractures, but the lower-mandible fractures failed to be repaired. Therefore, we applied a patient-specific beak prosthesis of titanium alloy and nylon. Because the prosthetic beak could not be maintained due to mandible and soft-tissue inflammation, the stork was euthanized. Still, we confirmed typical behavior and feeding for ~3 months after surgery. This report highlights some of the challenges we encountered and identifies process improvements required for a more successful surgery.
MeSH term(s)	Animals ; Beak/surgery ; Birds ; Printing, Three-Dimensional
Language	English
Publishing date	2023-09-12
Publishing country	Japan
Document type	Case Reports ; Journal Article
ZDB-ID	1071753-5
ISSN	1347-7439 ; 0916-7250
ISSN (online)	1347-7439
ISSN	0916-7250
DOI	10.1292/jvms.23-0231
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Article ; Online: Structural basis of a transcription pre-initiation complex on a divergent promoter.

Gorbea Colón, Jose J / Palao, Leon / Chen, Shin-Fu / Kim, Hee Jong / Snyder, Laura / Chang, Yi-Wei / Tsai, Kuang-Lei / Murakami, Kenji

Molecular cell

2023 Volume 83, Issue 4, Page(s) 574–588.e11

Abstract: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. ... ...

Abstract	Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
MeSH term(s)	RNA Polymerase II/metabolism ; Cryoelectron Microscopy ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Promoter Regions, Genetic ; Transcription, Genetic ; Mediator Complex/genetics ; Transcription Initiation, Genetic
Chemical Substances	RNA Polymerase II (EC 2.7.7.-) ; Saccharomyces cerevisiae Proteins ; Mediator Complex
Language	English
Publishing date	2023-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.01.011
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Article ; Online: Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography.

Lauman, Richard / Kim, Hee Jong / Pino, Lindsay K / Scacchetti, Alessandro / Xie, Yixuan / Robison, Faith / Sidoli, Simone / Bonasio, Roberto / Garcia, Benjamin A

Analytical chemistry

2023 Volume 95, Issue 12, Page(s) 5187–5195

Abstract: Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next- ... ...

Abstract	Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in the fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before MS identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA MS increases both coverage and throughput, while EMLC LC-MS orthogonally separates RNA molecules of different lengths and charges. The combination of the two methods offers a broadly applicable platform to improve the length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.
MeSH term(s)	Base Sequence ; Mass Spectrometry/methods ; Chromatography, Liquid ; Ion Mobility Spectrometry/methods ; RNA
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04114
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Article ; Online: Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography

Lauman, Richard / Kim, Hee Jong / Pino, Lindsay K. / Scacchetti, Alessandro / Xie, Yixuan / Robison, Faith / Sidoli, Simone / Bonasio, Roberto / Garcia, Benjamin A.

Analytical Chemistry. 2023 Mar. 14, v. 95, no. 12 p.5187-5195

2023

Abstract	Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in the fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before MS identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA MS increases both coverage and throughput, while EMLC LC–MS orthogonally separates RNA molecules of different lengths and charges. The combination of the two methods offers a broadly applicable platform to improve the length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.
Keywords	RNA ; analytical chemistry ; electrochemistry ; liquid chromatography ; mass spectrometry
Language	English
Dates of publication	2023-0314
Size	p. 5187-5195.
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.2c04114
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Article: A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences,

Kramer, Marianne C / Kim, Hee Jong / Palos, Kyle R / Garcia, Benjamin A / Lyons, Eric / Beilstein, Mark A / Nelson, Andrew D L / Gregory, Brian D

Frontiers in plant science

2022 Volume 13, Page(s) 906603

Abstract: Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified ... ...

Abstract	Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in
Language	English
Publishing date	2022-05-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2022.906603
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Article ; Online: Harnessing the intrinsic photochemistry of isoxazoles for the development of chemoproteomic crosslinking methods.

Lougee, Marshall G / Pagar, Vinayak Vishnu / Kim, Hee Jong / Pancoe, Samantha X / Chia, W Kit / Mach, Robert H / Garcia, Benjamin A / Petersson, E James

Chemical communications (Cambridge, England)

2022 Volume 58, Issue 65, Page(s) 9116–9119

Abstract: The intrinsic photochemistry of the isoxazole, a common heterocycle in medicinal chemistry, can be applied to offer an alternative to existing strategies using more perturbing, extrinsic photo-crosslinkers. The utility of isoxazole photo-crosslinking is ... ...

Abstract	The intrinsic photochemistry of the isoxazole, a common heterocycle in medicinal chemistry, can be applied to offer an alternative to existing strategies using more perturbing, extrinsic photo-crosslinkers. The utility of isoxazole photo-crosslinking is demonstrated in a wide range of biologically relevant experiments, including common proteomics workflows.
MeSH term(s)	Chemistry, Pharmaceutical ; Isoxazoles ; Photochemistry
Chemical Substances	Isoxazoles
Language	English
Publishing date	2022-08-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d2cc02263j
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Article ; Online: Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics.

Barshop, William D / Rayatpisheh, Shima / Kim, Hee Jong / Wohlschlegel, James A

Journal of proteome research

2019 Volume 18, Issue 4, Page(s) 1893–1901

Abstract: The standard approach for proteomic data acquisition of isobaric-tagged samples by mass spectrometry is data-dependent acquisition. This semistochastic, identification-first paradigm generates a wealth of peptide-level data without regard to relative ... ...

Abstract	The standard approach for proteomic data acquisition of isobaric-tagged samples by mass spectrometry is data-dependent acquisition. This semistochastic, identification-first paradigm generates a wealth of peptide-level data without regard to relative abundance. We introduce a data acquisition concept called sequential windowed acquisition of reporter masses (SWARM). This approach performs quantitation first, thereby allowing subsequent acquisition decisions to be predicated on user-defined patterns of reporter ion intensities. The efficacy of this approach is validated through experiments with both synthetic mixtures of Escherichia coli ribosomes spiked into human cell lysates at known ratios and the quantitative evaluation of the human proteome's response to the inhibition of cullin-based protein ubiquitination via the small molecule MLN4924. We find that SWARM-informed parallel reaction monitoring acquisitions display effective acquisition biasing toward analytes displaying quantitative characteristics of interest, resulting in an improvement in the detection of differentially abundant analytes. The SWARM concept provides a flexible platform for the further development of new acquisition methods.
MeSH term(s)	Bacterial Proteins/analysis ; Bacterial Proteins/chemistry ; Escherichia coli/chemistry ; HEK293 Cells ; Humans ; Peptides/analysis ; Peptides/chemistry ; Proteome/analysis ; Proteome/chemistry ; Proteomics/methods ; Tandem Mass Spectrometry
Chemical Substances	Bacterial Proteins ; Peptides ; Proteome
Language	English
Publishing date	2019-03-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.8b00884
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Article: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II

Yang, Chun / Fujiwara, Rina / Kim, Hee Jong / Basnet, Pratik / Zhu, Yunye / Gorbea Colón, Jose J. / Steimle, Stefan / Garcia, Benjamin A. / Kaplan, Craig D. / Murakami, Kenji

Molecular cell. 2022 Feb. 03, v. 82, no. 3

2022

Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we ... ...

Abstract	Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
Keywords	DNA-directed RNA polymerase ; Saccharomyces cerevisiae ; oligonucleotides ; transcription initiation ; yeasts
Language	English
Dates of publication	2022-0203
Size	p. 660-676.e9.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.12.020
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