Visual predation during springtime foraging of the North Atlantic right whale (Eubalaena glacialis)

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Mammal Science 33 (2017): 991–1013, doi:10.1111/mms.12417.To assess the role that vision plays in the ability of the North Atlantic right whale (Eubalaena glacialis) to detect its primary prey species, the calanoid copepod Calanus finmarchicus, we have compared the absorbance spectrum of the E. glacialis rod visual pigment, the transmittance spectra of C. finmarchicus carotenoid pigments, as well as the downwelling irradiance and horizontal radiance spectra collected during springtime at three locations in the western Gulf of Maine. The E. glacialis rod visual pigment absorbs light maximally at 493 nm, while microspectrophotometric measurements of the C. finmarchicus carotenoid pigments reveal transmission spectra with minima matching very well with the E. glacialis rod visual pigment absorbance spectra maximum. Springtime spectral downwelling irradiance and horizontal radiance values from the surface waters of Cape Cod Bay and at all depths in Great South Channel overlap the E. glacialis rod absorbance spectrum, allowing C. finmarchicus to appear as a high-contrast dark silhouette against a bright background space-light, thus facilitating visually-guided contrast foraging. In contrast, spectral downwelling irradiance and horizontal radiance at depth in Cape Cod Bay, and all depths in Wilkinson Basin, do not overlap the E. glacialis rod absorbance spectrum, providing little if any useful light for contrast vision.This work was supported by Wildlife Bycatch Reduction at the New England Aquarium under U.S. Department of Commerce NOAA Award #NA09NMF4520413 (J.I.F.). T.W.C. was supported by the National Science Foundation (IOS0721608) and the Air Force Office of Scientific Research (FA9550-09-1-0149). Additional support comes from NIH grant 2RO1EY009514 (D.D.Oprian)

Aryl hydrocarbon receptor deficiency causes the development of chronic obstructive pulmonary disease through the integration of multiple pathogenic mechanisms

Emphysema, a component of chronic obstructive pulmonary disease (COPD), is characterized by irreversible alveolar destruction that results in a progressive decline in lung function. This alveolar destruction is caused by cigarette smoke, the most important risk factor for COPD. Only 15%-20% of smokers develop COPD, suggesting that unknown factors contribute to disease pathogenesis. We postulate that the aryl hydrocarbon receptor (AHR), a receptor/transcription factor highly expressed in the lungs, may be a new susceptibility factor whose expression protects against COPD. Here, we report that Ahr-deficient mice chronically exposed to cigarette smoke develop airspace enlargement concomitant with a decline in lung function. Chronic cigarette smoke exposure also increased cleaved caspase-3, lowered SOD2 expression, and altered MMP9 and TIMP-1 levels in Ahr-deficient mice. We also show that people with COPD have reduced expression of pulmonary and systemic AHR, with systemic AHR mRNA levels positively correlating with lung function. Systemic AHR was also lower in never-smokers with COPD. Thus, AHR expression protects against the development of COPD by controlling interrelated mechanisms involved in the pathogenesis of this disease. This study identifies the AHR as a new, central player in the homeostatic maintenance of lung health, providing a foundation for the AHR as a novel therapeutic target and/or predictive biomarker in chronic lung disease

Exploring Structural and Functional Variation Among Opsin Classes

Opsins comprise a family of proteins belonging to the superfamily of G-protein coupled receptors (GPCRs). The opsins combined with vitamin-A derived chromophores make up the photopigments responsible for such diverse functions as image- and nonimage-forming vision, entrainment of circadian cycles, and the pupillary light response. The elucidation of the structural and biochemical properties of photopigments is of extreme importance to understanding the biological processes that they control. Currently the crystal structure of two photopigments have been solved; bovine rhodopsin from the vertebrate visual opsins, and squid rhodopsin from the invertebrate visual opsins. In the vertebrate visual opsins, five main subclasses exist; the RH1 class containing bovine rhodopsin makes up the rod based opsins, and the SWS1, SWS2, RH2, and M/LWS classes make up the cone based opsins. I question how similar structurally and biochemically the cone opsin classes are to the RH1 class. Using in vitro G-protein activation assays it is shown that mutations targeting key structural bonds within the cone opsin classes, compared to the RH1 class, result in different profiles of biochemical behavior reflective of structural variation surrounding the chromophore-binding pocket. This structural variation is further explored through the use of spin-labeling techniques aimed at analyzing the helical arrangement within the M/LWS cone opsin class compared to the RH1 class. In addition, a sixth class of opsins, the melanopsins, which maintains greater sequence identity to the invertebrate visual opsins than to the vertebrate visual opsins, is analyzed to identify the location of the counterion to the protonated Schiff base. The counterion is a key functional residue within the opsin family responsible for stabilizing the inactive dark state pigment as well as tuning the wavelength absorbance into the visible spectrum. Through spectroscopic analysis of various melanopsin mutants, evidence is presented that shows the counterion residue is not conserved across opsin groups. Through the evolution of the opsins, the location of the counterion has changed at least twice. This work highlights the large level of complexity that exists in the structure of the opsin family emphasizing the need for further structural analysis

Deep-sea and pelagic rod visual pigments identified in the mysticete whales

Our current understanding of the spectral sensitivities of the mysticete whale rod-based visual pigments is based on two species, the gray whale (Eschrichtius robustus) and the humpback whale (Megaptera novaeangliae) possessing absorbance maxima determined from difference spectra to be 492 and 497 nm, respectively. These absorbance maxima values are blueshifted relative to those from typical terrestrial mammals (≈500 nm) but are redshifted when compared to those identified in the odontocetes (479-484 nm). Although these mysticete species represent two of the four mysticete families, they do not fully represent the mysticete whales in terms of foraging strategy and underwater photic environments where foraging occurs. In order to better understand the spectral sensitivities of the mysticete whale rod visual pigments, we have examined the rod opsin genes from 11 mysticete species and their associated amino acid substitutions. Based on the amino acids occurring at positions 83, 292, and 299 along with the directly determined dark spectra from expressed odontocete and mysticete rod visual pigments, we have determined that the majority of mysticete whales possess deep-sea and pelagic like rod visual pigments with absorbance maxima between 479 and 484 nm. Finally, we have defined the five amino acid substitution events that determine the resulting absorbance spectra and associated absorbance maxima for the mysticete whale rod visual pigments examined here. Copyright © Cambridge University Press 2012

Unexpected diversity and photoperiod dependence of the zebrafish melanopsin system.

Animals have evolved specialized photoreceptors in the retina and in extraocular tissues that allow them to measure light changes in their environment. In mammals, the retina is the only structure that detects light and relays this information to the brain. The classical photoreceptors, rods and cones, are responsible for vision through activation of rhodopsin and cone opsins. Melanopsin, another photopigment first discovered in Xenopus melanophores (Opn4x), is expressed in a small subset of retinal ganglion cells (RGCs) in the mammalian retina, where it mediates non-image forming functions such as circadian photoentrainment and sleep. While mammals have a single melanopsin gene (opn4), zebrafish show remarkable diversity with two opn4x-related and three opn4-related genes expressed in distinct patterns in multiple neuronal cell types of the developing retina, including bipolar interneurons. The intronless opn4.1 gene is transcribed in photoreceptors as well as in horizontal cells and produces functional photopigment. Four genes are also expressed in the zebrafish embryonic brain, but not in the photoreceptive pineal gland. We discovered that photoperiod length influences expression of two of the opn4-related genes in retinal layers involved in signaling light information to RGCs. Moreover, both genes are expressed in a robust diurnal rhythm but with different phases in relation to the light-dark cycle. The results suggest that melanopsin has an expanded role in modulating the retinal circuitry of fish

Deep-sea and pelagic rod visual pigments identified in the mysticete whales

Our current understanding of the spectral sensitivities of the mysticete whale rod-based visual pigments is based on two species, the gray whale (Eschrichtius robustus) and the humpback whale (Megaptera novaeangliae) possessing absorbance maxima determined from difference spectra to be 492 and 497 nm, respectively. These absorbance maxima values are blueshifted relative to those from typical terrestrial mammals (≈500 nm) but are redshifted when compared to those identified in the odontocetes (479-484 nm). Although these mysticete species represent two of the four mysticete families, they do not fully represent the mysticete whales in terms of foraging strategy and underwater photic environments where foraging occurs. In order to better understand the spectral sensitivities of the mysticete whale rod visual pigments, we have examined the rod opsin genes from 11 mysticete species and their associated amino acid substitutions. Based on the amino acids occurring at positions 83, 292, and 299 along with the directly determined dark spectra from expressed odontocete and mysticete rod visual pigments, we have determined that the majority of mysticete whales possess deep-sea and pelagic like rod visual pigments with absorbance maxima between 479 and 484 nm. Finally, we have defined the five amino acid substitution events that determine the resulting absorbance spectra and associated absorbance maxima for the mysticete whale rod visual pigments examined here. Copyright © Cambridge University Press 2012

HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study

Understanding the characteristics of human immunodeficiency virus (HIV) necessary for infection in a new host is a critical goal for acquired immunodeficiency syndrome (AIDS) research. We studied the characteristics of HIV-1 envelope genes in 38 men in the Multicenter AIDS Cohort Study cohort before seroconversion. We found a range of diversity (0.2%-5.6% [median, 0.86%]), V1-V2 loop length (58-93 aa), and potential N-linked glycosylation sites (n = 2-9). However, at least 46% of the men had replicating virus that appeared to have been derived from a single viral variant. Nearly all variants were predicted to be CCR5 tropic. We found no correlation between these viral characteristics and the HIV outcomes of time to clinical AIDS or death and/or a CD4 cell count <200 cells/micro