Article
Chemistry, Analytical
Anhui Liang, Kexin Yu, Xiaolin Min, Jing Li, Jianyu Li, Xiaoling Zuo, Youli Yao
Summary: In this paper, we studied the coupling effect of seven cone fiber couplers using four-part cone models. This is the first study to explore the coupling effect of four layers of biological couplers in animals and other biological lives. Our simulation results showed that the coupling effect of the cone couplers is strongest in two wavelength regions, with most power transferring from the central cone to the surrounding cones. Additionally, we found that the splitting ratios of the central cones in the yellow-green wavelength range are greater than the sum of the splitting ratios of the surrounding cones. This research is important for understanding color preprocessing and the photopic luminous efficiency of the human eye.
Article
Computer Science, Artificial Intelligence
Thomas Mensink, Jasper Uijlings, Alina Kuznetsova, Michael Gygli, Vittorio Ferrari
Summary: This paper conducts extensive experimental exploration of transfer learning across different image domains and task types. The study reveals that for most tasks, there exists a source task that outperforms ILSVRC'12 pre-training. The image domain is found to be the most important factor for achieving positive transfer, and the source dataset should include the image domain of the target dataset for best results. Additionally, transfer across task types can be beneficial, but its success depends on both the source and target task types.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2022)
Article
Multidisciplinary Sciences
Yeon Jin Kim, Orin Packer, Andreas Pollreisz, Paul R. Martin, Ulrike Grunert, Dennis M. Dacey
Summary: The connectivity of visual processing in human, macaque monkey and marmoset retina was examined. The circuitry arising from S cones exhibited distinct features in each species. These findings imply that the early-stage chromatic signals are unique in the human retina and emphasize the necessity of understanding human connectome at the level of synaptic wiring for comprehending human color vision.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Genetics & Heredity
Claudius F. Kratochwil, Ricardo Mallarino
Summary: This review focuses on the general principles governing the formation and evolution of color patterns in different vertebrate groups. It discusses the types of patterns, molecular and developmental mechanisms by which they originate, and their role in evolutionary change. The review also outlines outstanding questions and proposes different approaches for further research.
ANNUAL REVIEW OF GENETICS
(2023)
Article
Multidisciplinary Sciences
Michihiko Aramaki, Xuefeng Wu, Hong Liu, Ye Liu, Young-Wook Cho, Mina Song, Yulong Fu, Lily Ng, Douglas Forrest
Summary: Cone photoreceptor diversity is crucial for color vision, but little is known about the control of diversity in these neurons. In this study, the researchers derived a Cre driver to isolate individual M and S opsin-enriched cones in mice and identified expression gradients for groups of genes. They found that thyroid hormone receptor ss 2 (TR ss 2) plays a role in controlling the expression of these genes and promoting cone diversity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Goosang Yu, Hui Kwon Kim, Jinman Park, Hyunjong Kwak, Yumin Cheong, Dongyoung Kim, Jiyun Kim, Jisung Kim, Hyongbum Henry Kim
Summary: In this study, the efficiency of prime editing was evaluated for a large number of pegRNAs. Computational models, DeepPrime and DeepPrime-FT, were developed to predict editing efficiencies for different prime editing systems and cell types. The study also included profiling of editing efficiencies at mismatched targets and the development of a computational model for predicting editing efficiencies at such targets. These findings and models will greatly enhance the applications of prime editing.
Article
Multidisciplinary Sciences
Hao Wang, Jiaxin Yang, Yu Zhang, Jianliang Qian, Jianrong Wang
Summary: The team introduces a computational method called FLAMINGO, which can generate high-resolution 3D chromosomal structures for all chromosomes in the human genome across multiple cell-types with superior accuracy and scalability compared to other methods.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Subha Nasir-Ahmad, Sammy C. S. Lee, Paul R. Martin, Ulrike Grunert
Summary: The study investigates the expression of Satb2 in ganglion cells in three primate species, revealing a low proportion of Satb2 cells in the ganglion cell population with species-specific differences. The findings suggest rapid species-specific adaptations in Satb2 expression during primate evolution, as the expression is not conserved across Old World and New World suborders.
JOURNAL OF COMPARATIVE NEUROLOGY
(2021)
Article
Biology
Ya-tang Li, Markus Meister
Summary: The superior colliculus in the brain is a crucial visual processing station that receives input from various types of retinal ganglion cells. Through recording mouse superficial SC neurons, we identified 24 functional types using an unsupervised clustering algorithm. These types can be grouped into two categories: one that responds similarly to retinal ganglion cells and another with more diverse and specialized stimulus selectivity. Cells of the same functional type tend to cluster together in anatomical space, and the visual representation in the SC has lower dimensionality compared to the retina, suggesting a sifting process along the visual pathway.
Article
Endocrinology & Metabolism
Jihong Zheng, Wenqi Song, Yihang Zhou, Xuan Li, Meng Wang, Chao Zhang
Summary: This study provides a detailed examination of the evolutionary transition of the pineal gland from a photoreceptive organ in fish to a neuroendocrine organ in mammals at the single-cell resolution. The comparative analysis of single-cell transcriptomic datasets from zebrafish, rats, and monkeys reveals distinct cellular compositions, gene expressions, and signaling processes in the pineal gland of each species. The study identifies key factors responsible for the anatomical and functional transformation of the pineal gland, including the involvement of specific genes, ligand-receptor interactions, and transcription factors. The findings enhance our understanding of the pineal gland's role in phototransduction, melatonin production, and circadian rhythms in vertebrates.
JOURNAL OF PINEAL RESEARCH
(2023)
Article
Pharmacology & Pharmacy
Jongmin Kim, Jeong Sik Kong, Hyeonji Kim, Wonil Han, Jae Yon Won, Dong-Woo Cho
Summary: This study developed a RdECM extracted from porcine retina and formulated it into a bioink suitable for 3D cell printing. The RdECM bioink was found to affect the differentiation of Muller cells and showed a protective effect on the retina in a retinal degeneration animal model, suggesting its potential for retinal tissue engineering.
Article
Biochemistry & Molecular Biology
Kyle J. McCulloch, Aide Macias-Munoz, Ali Mortazavi, Adriana D. Briscoe
Summary: The evolution of color vision is often studied in terms of receptor gain and loss. This study examines the visual systems of butterflies that have either retained or lost a specific photoreceptor subtype, known as UV2. The researchers identify various mechanisms through which these butterflies modulate their color vision, such as chromatin reorganization and gene truncation. They also find that species lacking the UV2 receptor shift the peak sensitivity of their UV1 receptor cells to longer wavelengths. Additionally, the widespread use of filtering pigments and co-expression of two opsins in the same photoreceptor cells contribute to the diversity and adaptability of the visual systems in Heliconius butterflies.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Endocrinology & Metabolism
Hong Liu, Ailing Lu, Kevin A. Kelley, Douglas Forrest
Summary: The study investigates the physiological significance of an enhancer for the induction of thyroid hormone receptor beta 2 (TR beta 2). Mutations in the enhancer region of the endogenous Thrb gene in mice show that e-box sites affect TR beta 2 expression in cones, while nearby sequences affect expression in pituitary. Furthermore, the study reveals the importance of studying enhancers in their natural chromosomal context and the influence of noncoding sequences on thyroid hormone functions.
Article
Meteorology & Atmospheric Sciences
Shihua Liu, Joshua-Xiouhua Fu, Zhiping Wen, Peng Zhang
Summary: In this diagnostic study, three distinctive MJO types in boreal winter are documented and their controlling mechanisms and teleconnections are investigated with a synergetic global approach. It is revealed that the diverse nature of the MJO primarily results from different tropical-extratropical interactions and associated internal atmospheric processes.
Article
Developmental Biology
Joanna F. D. Hagen, Natalie S. Roberts, Robert J. Johnston Jr
Summary: This article describes the evolution of visual opsin proteins in vertebrates and the mechanisms of vision. By studying the loss, duplication, and expression regulation of opsin genes, it reveals that opsin proteins have different sensitivities to wavelengths of light in different species. Understanding how these molecular changes allow animals to adapt to different environments is a major goal in the field. This review provides a comprehensive overview of our current understanding of opsin evolution in vertebrates.
DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sujun Li, Shyamtanu Datta, Emily Brabbit, Zoe Love, Victoria Woytowicz, Kyle Flattery, Jessica Capri, Katie Yao, Siqi Wu, Michael Imboden, Arun Upadhyay, Rasappa Arumugham, Wallace B. Thoreson, Margaret M. DeAngelis, Neena B. Haider
Summary: Recent advancements in viral vector engineering and understanding of retinal diseases have led to the development of novel gene therapy approaches, with Nr2e3 showing promise as a broad-spectrum therapy for various forms of retinitis pigmentosa (RP). Nr2e3 administered therapy resulted in reduced retinal degeneration and improved retinal homeostasis in diseased tissue, indicating its potential as a therapeutic option for RP patients.
Article
Ophthalmology
Donny W. Suh, Helen H. Song, Hozhabr Mozafari, Wallace B. Thoreson
Summary: The study utilized a computer simulation model to simulate the formation of retinal hemorrhage in AHT, finding that similar stress forces were generated in different layers of the retina.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2021)
Article
Neurosciences
Chi Zhang, Yeon Jin Kim, Ana R. Silverstein, Akina Hoshino, Thomas A. Reh, Dennis M. Dacey, Rachel O. Wong
Review
Physiology
Wallace B. Thoreson
Summary: The review explores the conversion of light-evoked voltage responses of rod and cone photoreceptor cells in the vertebrate retina to synaptic vesicle release events for transmission to downstream neurons. It discusses processes, proteins, and structures involved in this early step in vision, focusing on studies from salamander retina with comparisons to other experimental animals. Many mechanisms are conserved across species, highlighting the importance of understanding the intricate details of synaptic transmission in the visual system.
PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY
(2021)
Article
Biology
Cassandra L. Hays, Asia L. Sladek, Greg D. Field, Wallace B. Thoreson
Summary: Rods achieve the transmission of single-photon responses by enhancing release regularity and sensitivity to small voltage changes. The regularly timed, multivesicular release promotes efficient transmission to post-synaptic rod-bipolar cells, requiring lower overall release rates than uniquantal release governed by Poisson statistics.
Article
Pathology
Aicha Saadane, Yunpeng Du, Wallace B. Thoreson, Masaru Miyagi, Emma M. Lessieur, Jianying Kiser, Xiangyi Wen, Bruce A. Berkowitz, Timothy S. Kern
Summary: This study demonstrated that diabetes increases cytosolic calcium level in rod cells, activating a Ca2+-sensitive protease called calpain, leading to oxidative stress and inflammation in the retina. Inhibiting calpain activity or reducing Wwox up-regulation could be novel therapeutic targets for early diabetic retinopathy.
AMERICAN JOURNAL OF PATHOLOGY
(2021)
Article
Multidisciplinary Sciences
Yuchen Wang, Yan Cao, Cassandra L. Hays, Thibaut Laboute, Thomas A. Ray, Debbie Guerrero-Given, Abhimanyu S. Ahuja, Dipak Patil, Olga Rivero, Naomi Kamasawa, Jeremy N. Kay, Wallace B. Thoreson, Kirill A. Martemyanov
Summary: This study identified a molecular player, Latrophilin3 (LPHN3), operating selectively at cone synapses to modulate the effects of horizontal cells on synaptic release. The findings demonstrate the critical role of alternative splicing in adhesion GPCRs for their physiological function, as a gain-of-function mouse model of a specific splice isoform of LPHN3 profoundly disrupted synaptic release by cones and resulted in synaptic transmission deficits.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Yeon Jin Kim, Beth B. Peterson, Joanna D. Crook, Hannah R. Joo, Jiajia Wu, Christian Puller, Farrel R. Robinson, Paul D. Gamlin, King-Wai Yau, Felix Viana, John B. Troy, Robert G. Smith, Orin S. Packer, Peter B. Detwiler, Dennis M. Dacey
Summary: The neural coding of motion direction has been extensively studied in the visual cortex of non-human primates. In this study, the authors identified various direction-selective cell types in the retina of macaque monkeys, providing insights into the precortical circuitry responsible for computing motion direction in the primate visual system.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Chris S. Mesnard, Cody L. Barta, Asia L. Sladek, David Zenisek, Wallace B. Thoreson
Summary: The release of glutamate from rod and cone photoreceptor cells is facilitated by presynaptic ribbons composed mainly of the protein RIBEYE. The absence of ribbons in these cells leads to reduced temporal resolution, contrast sensitivity, and b-waves. The readily releasable pool of vesicles and the speed of vesicle replenishment are also reduced in cells lacking ribbons. Our findings suggest that synaptic ribbons play a crucial role in enhancing the release of vesicles and maintaining proper visual responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Ophthalmology
C. S. Mesnard, C. L. Hays, C. L. Barta, A. L. Sladek, J. J. Grassmeyer, K. K. Hinz, R. M. Quadros, C. B. Gurumurthy, W. B. Thoreson
Summary: This study found that Syt7 is present in mouse rod terminals and contributes to release evoked by long depolarizing steps. Additionally, it was found that Syt1 is the principal sensor shaping rod and cone inputs to bipolar cells in response to light flashes.
EXPERIMENTAL EYE RESEARCH
(2022)
Correction
Biochemistry & Molecular Biology
Chris S. S. Mesnard, Cody L. L. Barta, Asia L. L. Sladek, David Zenisek, Wallace B. B. Thoreson
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Haitao Luan, Timothy A. Bielecki, Bhopal C. Mohapatra, Namista Islam, Insha Mushtaq, Aaqib M. Bhat, Sameer Mirza, Sukanya Chakraborty, Mohsin Raza, Matthew D. Storck, Michael S. Toss, Jane L. Meza, Wallace B. Thoreson, Donald W. Coulter, Emad A. Rakha, Vimla Band, Hamid Band
Summary: Understanding the cellular adaptations that promote metastasis in cancer could lead to new therapeutic targets. In this study, overexpression of EHD2 protein was found in breast cancers, particularly in the triple-negative and HER2+ subtypes, and correlated with shorter patient survival. EHD2 was linked to the stability of caveolae and the store-operated calcium entry (SOCE) pathway, promoting tumorigenesis and metastasis in breast cancer. Targeting the EHD2-SOCE axis may have potential therapeutic implications for breast cancer patients with EHD2 and CAV1/2 overexpression.
Article
Multidisciplinary Sciences
Yeon Jin Kim, Orin Packer, Andreas Pollreisz, Paul R. Martin, Ulrike Grunert, Dennis M. Dacey
Summary: The connectivity of visual processing in human, macaque monkey and marmoset retina was examined. The circuitry arising from S cones exhibited distinct features in each species. These findings imply that the early-stage chromatic signals are unique in the human retina and emphasize the necessity of understanding human connectome at the level of synaptic wiring for comprehending human color vision.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Meeting Abstract
Ophthalmology
Cassandra Hays, Asia Sladek, Greg Field, Wallace Thoreson
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Ophthalmology
Andreas Pollreisz, Martina Neschi, Kenneth R. Sloan, Michael Pircher, Tamara Mittermueller, Dennis M. Dacey, Ursula Schmidt-Erfurth, Christine A. Curcio
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2020)