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Article: Suite of methods for assessing inner retinal temporal dynamics across spatial and temporal scales in the living human eye.

Kurokawa, Kazuhiro / Crowell, James A / Zhang, Furu / Miller, Donald T

2020 Volume 7, Issue 1, Page(s) 15013

Abstract: Significance: ...

Abstract	Significance:
Language	English
Publishing date	2020-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2781943-7
ISSN	2329-4248 ; 2329-423X
ISSN (online)	2329-4248
ISSN	2329-423X
DOI	10.1117/1.NPh.7.1.015013
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Article ; Online: Underwater hearing in sea ducks with applications for reducing gillnet bycatch through acoustic deterrence.

McGrew, Kathleen A / Crowell, Sarah E / Fiely, Jonathan L / Berlin, Alicia M / Olsen, Glenn H / James, Jennifer / Hopkins, Heather / Williams, Christopher K

The Journal of experimental biology

2022 Volume 225, Issue 20

Abstract: As diving foragers, sea ducks are vulnerable to underwater anthropogenic activity, including ships, underwater construction, seismic surveys and gillnet fisheries. Bycatch in gillnets is a contributing source of mortality for sea ducks, killing hundreds ... ...

Abstract	As diving foragers, sea ducks are vulnerable to underwater anthropogenic activity, including ships, underwater construction, seismic surveys and gillnet fisheries. Bycatch in gillnets is a contributing source of mortality for sea ducks, killing hundreds of thousands of individuals annually. We researched underwater hearing in sea duck species to increase knowledge of underwater avian acoustic sensitivity and to assist with possible development of gillnet bycatch mitigation strategies that include auditory deterrent devices. We used both psychoacoustic and electrophysiological techniques to investigate underwater duck hearing in several species including the long-tailed duck (Clangula hyemalis), surf scoter (Melanitta perspicillata) and common eider (Somateria mollissima). Psychoacoustic results demonstrated that all species tested share a common range of maximum auditory sensitivity of 1.0-3.0 kHz, with the long-tailed ducks and common eiders at the high end of that range (2.96 kHz), and surf scoters at the low end (1.0 kHz). In addition, our electrophysiological results from 4 surf scoters and 2 long-tailed ducks, while only tested at 0.5, 1 and 2 kHz, generally agree with the audiogram shape from our psychoacoustic testing. The results from this study are applicable to the development of effective acoustic deterrent devices or pingers in the 2-3 kHz range to deter sea ducks from anthropogenic threats.
MeSH term(s)	Humans ; Animals ; Ducks/physiology ; Fisheries ; Acoustics ; Hearing
Language	English
Publishing date	2022-10-28
Publishing country	England
Document type	Journal Article
ZDB-ID	218085-6
ISSN	1477-9145 ; 0022-0949
ISSN (online)	1477-9145
ISSN	0022-0949
DOI	10.1242/jeb.243953
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Article ; Online: The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica.

Crowell, Roseanna M / Nienow, James A / Cahoon, Aubrey Bruce

Journal of phycology

2019 Volume 55, Issue 2, Page(s) 352–364

Abstract: Nitzschia palea is a common freshwater diatom used as a bioindicator because of its tolerance of polluted waterways. There is also evidence it may be the tertiary endosymbiont within the "dinotom" dinoflagellate Durinskia baltica. A putative strain of N. ...

Abstract	Nitzschia palea is a common freshwater diatom used as a bioindicator because of its tolerance of polluted waterways. There is also evidence it may be the tertiary endosymbiont within the "dinotom" dinoflagellate Durinskia baltica. A putative strain of N. palea was collected from a pond on the University of Virginia's College at Wise campus and cultured. For initial identification, three markers were sequenced-nuclear 18S rDNA, the chloroplast 23S rDNA, and rbcL. Morphological characteristics were determined using light and scanning electron microscopy; based on these observations the cells were identified as N. palea and named strain "Wise." DNA from N. palea was deep sequenced and the chloroplast and mitochondrial genomes assembled. Single gene phylogenies grouped N. palea-Wise within a clearly defined N. palea clade and showed it was most closely related to the strain "SpainA3." The chloroplast genome of N. palea is 119,447 bp with a quadripartite structure, 135 protein-coding, 28 tRNA, and 3 rRNA genes. The mitochondrial genome is 37,754 bp with a single repeat region as found in other diatom chondriomes, 37 protein-coding, 23 tRNA, and 2 rRNA genes. The chloroplast genomes of N. palea and D. baltica have identical gene content, synteny, and a 92.7% pair-wise sequence similarity with most differences occurring in intergenic regions. The N. palea mitochondrial genome and D. baltica's endosymbiont mitochondrial genome also have identical gene content and order with a sequence similarity of 90.7%. Genome-based phylogenies demonstrated that D. baltica is more similar to N. palea than any other diatom sequence currently available. These data provide the genome sequences of two organelles for a widespread diatom and show they are very similar to those of Durinskia baltica's endosymbiont.
MeSH term(s)	Chloroplasts ; Diatoms ; Dinoflagellida ; Genome, Chloroplast ; Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA
Language	English
Publishing date	2019-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	281226-5
ISSN	1529-8817 ; 0022-3646
ISSN (online)	1529-8817
ISSN	0022-3646
DOI	10.1111/jpy.12824
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Article ; Online: Analysis of Caenorhabditis elegans acetylcholine synthesis mutants reveals a temperature-sensitive requirement for cholinergic neuromuscular function.

Duerr, Janet S / McManus, John R / Crowell, John A / Rand, James B

Genetics

2021 Volume 218, Issue 4

Abstract: In Caenorhabditis elegans, the cha-1 gene encodes choline acetyltransferase (ChAT), the enzyme that synthesizes the neurotransmitter acetylcholine. We have analyzed a large number of cha-1 hypomorphic mutants, most of which are missense alleles. Some ... ...

Abstract	In Caenorhabditis elegans, the cha-1 gene encodes choline acetyltransferase (ChAT), the enzyme that synthesizes the neurotransmitter acetylcholine. We have analyzed a large number of cha-1 hypomorphic mutants, most of which are missense alleles. Some homozygous cha-1 mutants have approximately normal ChAT immunoreactivity; many other alleles lead to consistent reductions in synaptic immunostaining, although the residual protein appears to be stable. Regardless of protein levels, neuromuscular function of almost all mutants is temperature-sensitive, i.e., neuromuscular function is worse at 25° than at 14°. We show that the temperature effects are not related to acetylcholine release, but specifically to alterations in acetylcholine synthesis. This is not a temperature-dependent developmental phenotype, because animals raised at 20° to young adulthood and then shifted for 2 h to either 14° or 25° had swimming and pharyngeal pumping rates similar to animals grown and assayed at either 14° or 25°, respectively. We also show that the temperature-sensitive phenotypes are not limited to missense alleles; rather, they are a property of most or all severe cha-1 hypomorphs. We suggest that our data are consistent with a model of ChAT protein physically, but not covalently, associated with synaptic vesicles; and there is a temperature-dependent equilibrium between vesicle-associated and cytoplasmic (i.e., soluble) ChAT. Presumably, in severe cha-1 hypomorphs, increasing the temperature would promote dissociation of some of the mutant ChAT protein from synaptic vesicles, thus removing the site of acetylcholine synthesis (ChAT) from the site of vesicular acetylcholine transport. This, in turn, would decrease the rate and extent of vesicle-filling, thus increasing the severity of the behavioral deficits.
MeSH term(s)	Acetylcholine/biosynthesis ; Animals ; Caenorhabditis elegans ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Choline O-Acetyltransferase/genetics ; Choline O-Acetyltransferase/metabolism ; Cholinergic Neurons/metabolism ; Mutation, Missense ; Neuromuscular Junction/metabolism ; Thermotolerance
Chemical Substances	Caenorhabditis elegans Proteins ; Choline O-Acetyltransferase (EC 2.3.1.6) ; Acetylcholine (N9YNS0M02X)
Language	English
Publishing date	2021-06-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyab078
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Article ; Online: Mitigating Mismatch Compression in Differential Local Field Potentials.

Tiruvadi, Vineet / James, Samuel / Howell, Bryan / Obatusin, Mosadoluwa / Crowell, Andrea / Riva-Posse, Patricio / Gross, Robert E / McIntyre, Cameron C / Mayberg, Helen S / Butera, Robert

IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society

2023 Volume 31, Page(s) 68–77

Abstract: Deep brain stimulation (DBS) devices capable of measuring differential local field potentials ( ∂ LFP) enable neural recordings alongside clinical therapy. Efforts to identify oscillatory correlates of various brain disorders, or disease readouts, are ... ...

Abstract	Deep brain stimulation (DBS) devices capable of measuring differential local field potentials ( ∂ LFP) enable neural recordings alongside clinical therapy. Efforts to identify oscillatory correlates of various brain disorders, or disease readouts, are growing but must proceed carefully to ensure readouts are not distorted by brain environment. In this report we identified, characterized, and mitigated a major source of distortion in ∂ LFP that we introduce as mismatch compression (MC). Using in vivo, in silico, and in vitro models of MC, we showed that impedance mismatches in the two recording electrodes can yield incomplete rejection of stimulation artifact and subsequent gain compression that distorts oscillatory power. We then developed and validated an opensource mitigation pipeline that mitigates the distortions arising from MC. This work enables more reliable oscillatory readouts for adaptive DBS applications.
MeSH term(s)	Humans ; Deep Brain Stimulation ; Brain
Language	English
Publishing date	2023-01-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1166307-8
ISSN	1558-0210 ; 1063-6528 ; 1534-4320
ISSN (online)	1558-0210
ISSN	1063-6528 ; 1534-4320
DOI	10.1109/TNSRE.2022.3217469
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Article ; Online: Multi-reference global registration of individual A-lines in adaptive optics optical coherence tomography retinal images.

Kurokawa, Kazuhiro / Crowell, James A / Do, Nhan / Lee, John J / Miller, Donald T

Journal of biomedical optics

2021 Volume 26, Issue 1

Abstract: Significance: Adaptive optics optical coherence tomography (AO-OCT) technology enables non-invasive, high-resolution three-dimensional (3D) imaging of the retina and promises earlier detection of ocular disease. However, AO-OCT data are corrupted by eye- ...

Abstract	Significance: Adaptive optics optical coherence tomography (AO-OCT) technology enables non-invasive, high-resolution three-dimensional (3D) imaging of the retina and promises earlier detection of ocular disease. However, AO-OCT data are corrupted by eye-movement artifacts that must be removed in post-processing, a process rendered time-consuming by the immense quantity of data. Aim: To efficiently remove eye-movement artifacts at the level of individual A-lines, including those present in any individual reference volume. Approach: We developed a registration method that cascades (1) a 3D B-scan registration algorithm with (2) a global A-line registration algorithm for correcting torsional eye movements and image scaling and generating global motion-free coordinates. The first algorithm corrects 3D translational eye movements to a single reference volume, accelerated using parallel computing. The second algorithm combines outputs of multiple runs of the first algorithm using different reference volumes followed by an affine transformation, permitting registration of all images to a global coordinate system at the level of individual A-lines. Results: The 3D B-scan algorithm estimates and corrects 3D translational motions with high registration accuracy and robustness, even for volumes containing microsaccades. Averaging registered volumes improves our image quality metrics up to 22 dB. Implementation in CUDA™ on a graphics processing unit registers a 512 × 512 × 512 volume in only 10.6 s, 150 times faster than MATLAB™ on a central processing unit. The global A-line algorithm minimizes image distortion, improves regularity of the cone photoreceptor mosaic, and supports enhanced visualization of low-contrast retinal cellular features. Averaging registered volumes improves our image quality up to 9.4 dB. It also permits extending the imaging field of view (∼2.1 × ) and depth of focus (∼5.6 × ) beyond what is attainable with single-reference registration. Conclusions: We can efficiently correct eye motion in all 3D at the level of individual A-lines using a global coordinate system.
MeSH term(s)	Artifacts ; Imaging, Three-Dimensional ; Optics and Photonics ; Retina/diagnostic imaging ; Tomography, Optical Coherence
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1309154-2
ISSN	1560-2281 ; 1083-3668
ISSN (online)	1560-2281
ISSN	1083-3668
DOI	10.1117/1.JBO.26.1.016001
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Article ; Online: Cone photoreceptor dysfunction in retinitis pigmentosa revealed by optoretinography.

Lassoued, Ayoub / Zhang, Furu / Kurokawa, Kazuhiro / Liu, Yan / Bernucci, Marcel T / Crowell, James A / Miller, Donald T

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 47

Abstract: Retinitis pigmentosa (RP) is the most common group of inherited retinal degenerative diseases, whose most debilitating phase is cone photoreceptor death. Perimetric and electroretinographic methods are the gold standards for diagnosing and monitoring RP ... ...

Abstract	Retinitis pigmentosa (RP) is the most common group of inherited retinal degenerative diseases, whose most debilitating phase is cone photoreceptor death. Perimetric and electroretinographic methods are the gold standards for diagnosing and monitoring RP and assessing cone function. However, these methods lack the spatial resolution and sensitivity to assess disease progression at the level of individual photoreceptor cells, where the disease originates and whose degradation causes vision loss. High-resolution retinal imaging methods permit visualization of human cone cells in vivo but have only recently achieved sufficient sensitivity to observe their function as manifested in the cone optoretinogram. By imaging with phase-sensitive adaptive optics optical coherence tomography, we identify a biomarker in the cone optoretinogram that characterizes individual cone dysfunction by stimulating cone cells with flashes of light and measuring nanometer-scale changes in their outer segments. We find that cone optoretinographic responses decrease with increasing RP severity and that even in areas where cone density appears normal, cones can respond differently than those in controls. Unexpectedly, in the most severely diseased patches examined, we find isolated cones that respond normally. Short-wavelength-sensitive cones are found to be more vulnerable to RP than medium- and long-wavelength-sensitive cones. We find that decreases in cone response and cone outer-segment length arise earlier in RP than changes in cone density but that decreases in response and length are not necessarily correlated within single cones.
MeSH term(s)	Electroretinography ; Eye Proteins/metabolism ; Humans ; Ophthalmoscopy/methods ; Retina/metabolism ; Retinal Cone Photoreceptor Cells/metabolism ; Retinitis Pigmentosa/metabolism
Chemical Substances	Eye Proteins ; RPGR protein, human
Language	English
Publishing date	2021-11-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2107444118
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Article ; Online: Revealing How Color Vision Phenotype and Genotype Manifest in Individual Cone Cells.

Zhang, Furu / Kurokawa, Kazuhiro / Bernucci, Marcel T / Jung, Hae Won / Lassoued, Ayoub / Crowell, James A / Neitz, Jay / Neitz, Maureen / Miller, Donald T

Investigative ophthalmology & visual science

2021 Volume 62, Issue 2, Page(s) 8

Abstract: Purpose: Psychophysical and genetic testing provide substantial information about color vision phenotype and genotype. However, neither reveals how color vision phenotypes and genotypes manifest themselves in individual cones, where color vision and its ...

Abstract	Purpose: Psychophysical and genetic testing provide substantial information about color vision phenotype and genotype. However, neither reveals how color vision phenotypes and genotypes manifest themselves in individual cones, where color vision and its anomalies are thought to originate. Here, we use adaptive-optics phase-sensitive optical coherence tomography (AO-PSOCT) to investigate these relationships. Methods: We used AO-PSOCT to measure cone function-optical response to light stimulation-in each of 16 human subjects with different phenotypes and genotypes of color vision (five color-normal, three deuteranopic, two protanopic, and six deuteranomalous trichromatic subjects). We classified three spectral types of cones (S, M, and L), and we measured cone structure-namely cone density, cone mosaic arrangement, and spatial arrangement of cone types. Results: For the different phenotypes, our cone function results show that (1) color normals possess S, M, and L cones; (2) deuteranopes are missing M cones but are normal otherwise; (3) protanopes are missing L cones but are normal otherwise; and (4) deuteranomalous trichromats are missing M cones but contain evidence of at least two subtypes of L cones. Cone function was consistent with the subjects' genotype in which only the first two M and L genes in the gene array are expressed and was correlated with the estimated spectral separation between photopigments, including in the deuteranomalous trichromats. The L/M cone ratio was highly variable in the color normals. No association was found between cone density and the genotypes and phenotypes investigated, and the cone mosaic arrangement was altered in the dichromats. Conclusions: AO-PSOCT is a novel method for assessing color vision phenotype and genotype in single cone cells.
MeSH term(s)	Adult ; Color Perception/physiology ; Color Vision/genetics ; Color Vision Defects/genetics ; Color Vision Defects/metabolism ; Color Vision Defects/pathology ; Female ; Genotype ; Humans ; Male ; Middle Aged ; Phenotype ; Retinal Cone Photoreceptor Cells/metabolism ; Retinal Cone Photoreceptor Cells/pathology ; Retinal Pigments/metabolism ; Tomography, Optical Coherence/methods ; Young Adult
Chemical Substances	Retinal Pigments
Language	English
Publishing date	2021-02-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	391794-0
ISSN	1552-5783 ; 0146-0404
ISSN (online)	1552-5783
ISSN	0146-0404
DOI	10.1167/iovs.62.2.8
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Article ; Online: Multi-reference global registration of individual A-lines in adaptive optics optical coherence tomography retinal images (Publisher's Note).

Kurokawa, Kazuhiro / Crowell, James / Do, Nhan / Lee, John / Miller, Donald

Journal of biomedical optics

2021 Volume 26, Issue 1

Abstract: The note corrects an error that appeared in Equation 14 of the originally published article. ...

Abstract	The note corrects an error that appeared in Equation 14 of the originally published article.
Language	English
Publishing date	2021-01-25
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	1309154-2
ISSN	1560-2281 ; 1083-3668
ISSN (online)	1560-2281
ISSN	1083-3668
DOI	10.1117/1.JBO.26.1.019803
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Article: The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica

Crowell, Roseanna M / Cahoon, Aubrey Bruce / Nienow, James A

Journal of phycology. 2019 Apr., v. 55, no. 2

2019

Abstract: Nitzschia palea is a common freshwater diatom used as a bioindicator because of its tolerance of polluted waterways. There is also evidence it may be the tertiary endosymbiont within the “dinotom” dinoflagellate Durinskia baltica. A putative strain of N. ...

Abstract	Nitzschia palea is a common freshwater diatom used as a bioindicator because of its tolerance of polluted waterways. There is also evidence it may be the tertiary endosymbiont within the “dinotom” dinoflagellate Durinskia baltica. A putative strain of N. palea was collected from a pond on the University of Virginia's College at Wise campus and cultured. For initial identification, three markers were sequenced—nuclear 18S rDNA, the chloroplast 23S rDNA, and rbcL. Morphological characteristics were determined using light and scanning electron microscopy; based on these observations the cells were identified as N. palea and named strain “Wise.” DNA from N. palea was deep sequenced and the chloroplast and mitochondrial genomes assembled. Single gene phylogenies grouped N. palea—Wise within a clearly defined N. palea clade and showed it was most closely related to the strain “SpainA3.” The chloroplast genome of N. palea is 119,447 bp with a quadripartite structure, 135 protein‐coding, 28 tRNA, and 3 rRNA genes. The mitochondrial genome is 37,754 bp with a single repeat region as found in other diatom chondriomes, 37 protein‐coding, 23 tRNA, and 2 rRNA genes. The chloroplast genomes of N. palea and D. baltica have identical gene content, synteny, and a 92.7% pair‐wise sequence similarity with most differences occurring in intergenic regions. The N. palea mitochondrial genome and D. baltica's endosymbiont mitochondrial genome also have identical gene content and order with a sequence similarity of 90.7%. Genome‐based phylogenies demonstrated that D. baltica is more similar to N. palea than any other diatom sequence currently available. These data provide the genome sequences of two organelles for a widespread diatom and show they are very similar to those of Durinskia baltica's endosymbiont.
Keywords	chloroplast genome ; chloroplasts ; endosymbionts ; genes ; intergenic DNA ; Miozoa ; mitochondrial genome ; Nitzschia ; nucleotide sequences ; phylogeny ; ribosomal DNA ; ribosomal RNA ; scanning electron microscopy ; sequence homology ; transfer RNA ; waterways ; Virginia
Language	English
Dates of publication	2019-04
Size	p. 352-364.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	281226-5
ISSN	1529-8817 ; 0022-3646
ISSN (online)	1529-8817
ISSN	0022-3646
DOI	10.1111/jpy.12824
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