Collagenase predigestion on paraffin sections enhances collagen immunohistochemical detection without distorting tissue morphology

Reliable immunohistochemical detection of collagen in formalin fixed, paraffin embedded tissues requires protease digestion. While these pan-proteases (pepsin, trypsin, protease K, etc.) enhance collagen detection, they also digest many other tissue proteins and produce poor cellular morphology and unrecognizable cellular structures. Balancing the conditions (protease type, concentration, incubation time and temperature) to digest some, but not all, proteins in a tissue section while optimizing collagen detection requires one to compromise improved collagen immunolabeling with adequate cellular morphology. Furthermore, optimal conditions for digesting tissue proteins to enhance collagen detection vary among tissue types and their fixation. Although brain is not typically subject to these deleterious consequences, structures such as epithelium, spermatids, stroma etc. and other tissues with complicated histology are profoundly affected. To resolve this technical dilemma, we discovered a novel use for collagenase to enhance collagen immunodetection without affecting the noncollagen proteins, thereby preserving tissue morphology. Collagenase, which is typically used in vitro for disassociation of cells, has never been used reliably on formalin fixed, paraffin embedded tissue sections. This new use of collagenase for immunohistochemistry promotes increased collagen immunolabeling, is easy to use, is versatile, and allows preservation of tissue structure that provides maximal and accurate histological information.     

High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian archipelago

In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100-400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N=1,222) collected across 17,000 km from Hawai'i to the western Indian Ocean. Results indicate that P. filamentosus is a highly dispersive species with low but significant population structure (mtDNA Φ(ST)=0.029, microsatellite F(ST)=0.029) due entirely to the isolation of Hawai'i. No population structure was detected across 14,000 km of the Indo-Pacific from Tonga in the Central Pacific to the Seychelles in the western Indian Ocean, a pattern rarely observed in reef species. Despite a long pelagic phase (60-180 days), interisland dispersal as adults, and extensive gene flow across the Indo-Pacific, P. filamentosus is unable to maintain population connectivity with Hawai'i. Coalescent analyses indicate that P. filamentosus may have colonized Hawai'i 26 K-52 K y ago against prevailing currents, with dispersal away from Hawai'i dominating migration estimates. P. filamentosus harbors low genetic diversity in Hawai'i, a common pattern in marine fishes, and our data indicate a single archipelago-wide stock. However, like the Hawaiian Grouper, Hyporthodus quernus, this snapper had several significant pairwise comparisons (F(ST)) clustered around the middle of the archipelago (St. Rogatien, Brooks Banks, Gardner) indicating that this region may be isolated or (more likely) receives input from Johnston Atoll to the south.     

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range‐restricted butterflyfishes across the Red Sea and Arabian Sea using genome‐wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.     

Does color matter? Molecular and ecological divergence in four sympatric color morphs of a coral reef fish

Non‐sex‐linked color polymorphism is common in animals and can be maintained in populations via balancing selection or, when under diversifying selection, can promote divergence. Despite their potential importance in ecological interactions and the evolution of biodiversity, their function and the mechanisms by which these polymorphisms are maintained are still poorly understood. Here, we combine field observations with life history and molecular data to compare four sympatric color morphs of the coral reef fish Paracirrhites forsteri (family Cirrhitidae) in the central Red Sea. Our findings verify that the color morphs are not sex‐limited, inhabit the same reefs, and do not show clear signs of avoidance or aggression among them. A barcoding approach based on 1,276 bp of mitochondrial DNA could not differentiate the color morphs. However, when 36,769 SNPs were considered, we found low but significant population structure. Focusing on 1,121 F_ST outliers, we recovered distinct population clusters that corresponded to shifts in allele frequencies with each color morph harboring unique alleles. Genetic divergence at these outlier loci is accompanied by differences in growth and marginal variation in microhabitat preference. Together, life history and molecular analysis suggest subtle divergence between the color morphs in this population, the causes for which remain elusive.     

MK-STYX, a catalytically inactive phosphatase regulating mitochondrially dependent apoptosis

Evasion of apoptosis is a significant problem affecting an array of cancers. In order to identify novel regulators of apoptosis, we performed an RNA interference (RNAi) screen against all kinases and phosphatases in the human genome. We identified MK-STYX (STYXL1), a catalytically inactive phosphatase with homology to the mitogen-activated protein kinase (MAPK) phosphatases. Despite this homology, MK-STYX knockdown does not significantly regulate MAPK signaling in response to growth factors or apoptotic stimuli. Rather, RNAi-mediated knockdown of MK-STYX inhibits cells from undergoing apoptosis induced by cellular stressors activating mitochondrion-dependent apoptosis. This MK-STYX phenotype mimics the loss of Bax and Bak, two potent guardians of mitochondrial apoptotic potential. Similar to loss of both Bax and Bak, cells without MK-STYX expression are unable to release cytochrome c. Proapoptotic members of the BCL-2 family (Bax, Bid, and Bim) are unable to trigger cytochrome c release in MK-STYX-depleted cells, placing the apoptotic deficiency at the level of mitochondrial outer membrane permeabilization (MOMP). MK-STYX was found to localize to the mitochondria but is neither released from the mitochondria upon apoptotic stress nor proximal to the machinery currently known to control MOMP, indicating that MK-STYX regulates MOMP using a distinct mechanism.     

Two deep evolutionary lineages in the circumtropical glasseye Heteropriacanthus cruentatus (Teleostei,Priacanthidae) with admixture in the south‐western Indian Ocean

A phylogeographic study of the circumtropical glasseye Heteropriacanthus cruentatus was conducted. Molecular analyses indicate two mitochondrial cytochrome c oxidase subunit I (coI) lineages that are 10·4% divergent: one in the western Atlantic (Caribbean) and another that was detected across the Indo‐Pacific. A fixed single nucleotide polymorphism (SNP) was detected at a nuclear locus (S7 ribosomal protein) and is consistent with this finding. There is evidence of recent dispersal from the Atlantic to the Indian Ocean with individuals of mixed lineages detected in South Africa and the Mozambique Channel. Using coalescent analyses of the mitochondrial dataset, time of divergence between lineages was estimated to be c. 15·3 million years. The deep divergence between these two lineages indicates distinct evolutionary units, however, due to the lack of morphological differences and evidence of hybridization between lineages, taxonomic revision is not suggested at this time.     

Variomics Screen Identifies the Re-entrant Loop of the Calcium-activated Chloride Channel ANO1 That Facilitates Channel Activation

The calcium-activated chloride channel ANO1 regulates multiple physiological processes. However, little is known about the mechanism of channel gating and regulation of ANO1 activity. Using a high-throughput, random mutagenesis-based variomics screen, we generated and functionally characterized ∼6000 ANO1 mutants and identified novel mutations that affected channel activity, intracellular trafficking, or localization of ANO1. Mutations such as S741T increased ANO1 calcium sensitivity and rendered ANO1 calcium gating voltage-independent, demonstrating a critical role of the re-entrant loop in coupling calcium and voltage sensitivity of ANO1 and hence in regulating ANO1 activation. Our data present the first unbiased and comprehensive study of the structure-function relationship of ANO1. The novel ANO1 mutants reported have diverse functional characteristics, providing new tools to study ANO1 function in biological systems, paving the path for a better understanding of the function of ANO1 and its role in health and diseases.     

Videotaped Behavior as a Predictor of Clinical Outcome in Rhesus Macaques (Macaca mulatta)

Understanding the behavior of laboratory NHP facilitates health assessment and clinical care. We sought to characterize the behavior of critically ill rhesus macaques (Macaca mulatta) and determine whether specific behaviors or behavioral changes might facilitate the determination of prognosis and clinical endpoints. Twenty-two critically-ill subjects were videorecorded after they were removed from the outdoor breeding colony for diagnostic work-up and treatment. Subjects were categorized as survivors (n = 15) and those that were euthanized according to existing clinical endpoints (n = 7). Behavior before, during, and after cageside examination was compared between these groups with regard to the presence or absence of direct observation. This approach allowed us to determine whether these settings revealed differences between groups or masking of behaviors during direct observation. Before cageside examination, several behaviors (for example, self-grooming and anxiety behaviors) were significantly more common in surviving subjects than in euthanized subjects. Few significant differences in behavior were detectable during or after the examination. Subjects that were eventually euthanized showed more illness-related behaviors; however, not all animals requiring euthanasia showed these signs when an observer was present. Furthermore, euthanized animals spent more time in an alert posture during direct observation than at other times. Therefore, direct observation of critically ill rhesus macaques may not yield the most accurate assessment of illness severity, and using video to assess behavior may be helpful for prognosis.The assessment and recognition of pain and distress in laboratory animals is crucial to ensure welfare and high-quality research.^{6,10,12,20,23,26,28} Difficulty in identifying species-specific signs of pain and distress suggests that cageside assessment of clinical condition by an observer, as a stand-alone method, may not be an optimal method of determining prognosis in critically ill animals of some species.^10,24,26,27 The behavior of NHP, including rhesus macaques (Macaca mulatta), can be especially difficult to interpret due to their relatively stoic nature and tendency to mask clinical signs of illness in the presence of human observers.^{8,10,12,14,17} Two explanations for the tendency to mask pain, which is also observed in other species, are their status as a prey species and the need to hide weaknesses from group members.^3,17,22,23 According to the 2009 Institute for Laboratory Animal Research (ILAR) recommendations for recognizing pain and distress in nonhuman primates, “[v]iewing an animal from a distance or by video can aid in detecting subtle clinical changes.”¹² The goal of the current study was to evaluate the use of videotaped behavioral data to increase accuracy in predicting prognoses for rhesus macaques that are critically ill.A humane endpoint is defined as the earliest time at which an animal may experience unnecessary pain or distress, undue suffering, or impending death.^4,12 Both subjective and objective diagnostic criteria are currently used to define clinical and research endpoints.^{6,7,10,12,21,26,29}A myriad of diagnostics can be used for this purpose, including physical examination, cageside examination, blood assays (CBC and serum biochemistry), imaging (radiographs, ultrasound, CT, and MRI), bacterial culture and sensitivity, urinalysis, and collection of tissue samples (fine-needle aspiration and biopsy). One specific example of using clinical diagnostics to aid in the prediction of mortality in NHP involved using acid-base levels in animals with severe social trauma.¹¹ Behavioral assessment may be an important and underutilized diagnostic method for assessing pain and distress. Recent studies have evaluated the behavior, specifically facial expression, of mice to detect and assess pain.^16,19 Methods for evaluating behavior typically involve cageside examination, but assessment of behavior via videotape in the absence of an observer may also be useful.Endpoints may vary depending on species, nature of the research conducted, and assessment of degree of pain or distress. At our facility, experimental endpoints (those defined as part of a specific study) are differentiated from clinical endpoints (those determined by an animal''s health and quality of life). The veterinarian has the authority to elect euthanasia for an animal that is assessed to have reached an endpoint by either or both classifications. IACUC-approved endpoint policies have been established to aid in this decision. Criteria included in these guidelines include weight loss (excluding postpartum females and intended weight loss for obese animals), anorexia that is not responsive to treatment, diarrhea that is not responsive to treatment, and major organ failure that is not responsive to treatment. Veterinarians use cageside examination in the overall assessment of animals and to aid in the decision to euthanize.To our knowledge, the current study is the first to assess the behavior of critically ill rhesus macaques that controls for the cause of clinical presentation and to use observer presence or absence as an independent variable. To obtain information that may assist in refining clinical endpoints, we compared the behavior of critically ill rhesus macaques while an observer was absent, present, and recently present (labeled as preobservation, observation, and postobservation, respectively, in this text).We hypothesized that in comparison to in-person observation of critically ill rhesus macaques, the use of videotaping in the absence of direct observation would be more accurate in detecting differences in the behavior between those animals that eventually required euthanasia and those that did not. In addition, we hypothesized that behaviors would be suppressed (‘masked’) during direct observation, accounting for the reduced information available to the direct observer. If our hypothesis is supported, then videotaped behavior may be useful as a prognostic indicator that could be incorporated into development of clinical endpoints.