scholarly journals Multiple ancestral duplications of the red-sensitive opsin gene (LWS) in teleost fishes and convergent spectral shifts to green vision in gobies

2021 ◽  
Author(s):  
Fabio Cortesi ◽  
Daniel Escobar Camacho ◽  
Martin Luehrmann ◽  
Gina Maria Sommer ◽  
Zuzana Musilova
Keyword(s):  
Genome Duplication ◽  
In Situ Hybridisation ◽  
Bright Light ◽  
Opsin Gene ◽  
Colour Perception ◽  
Long Wavelength ◽  
Cone Opsin ◽  
Spectral Shifts ◽  
Functional Replacement

Photopigments, consisting of an opsin protein bound to a light-sensitive chromophore, are at the centre of vertebrate vision. The vertebrate ancestor already possessed four cone opsin classes involved in colour perception during bright-light conditions, which are sensitive from the ultraviolet to the red-wavelengths of light. Teleosts experienced an extra round of whole genome duplication (3R) at their origin, and while most teleosts maintained only one long-wavelength-sensitive opsin gene (LWS1), the second ancestral copy (LWS2) persisted in characins and osteoglossomorphs. Following 3R, teleost opsins have continued to expand and diversify, which is thought to be a consequence of the different light environment fishes inhabit, from clear streams to the relative darkness of the deep-sea. Although many recent and a few ancestral opsin duplicates can be found, none predating the 3R were thought to exist. In this study we report on a second, previously unnoticed ancestral duplication of the red-sensitive opsin (LWS3), which predates the teleost-specific genome duplication and only persists in gobiid fishes. This is surprising, since it implies that LWS3 has been lost at least 19-20 times independently along the teleost phylogeny. Mining 109 teleost genomes we also uncover a third lineage, the elopomorphs, that maintained the LWS2 copy. We identify convergent amino acid changes that green-shift ancestral and recent LWS copies, leading to adaptive differentiation and the functional replacement of the original green-sensitive RH2 opsin. Retinal transcriptomes and in-situ hybridisation show that LWS3 is expressed to various extents in gobies and in the case of the whitebarred goby, Amblygobius phalaena, it occurs in a separate photoreceptor to LWS1. Our study highlights the importance of comparative studies to comprehend evolution of gene function.

scholarly journals Functional preservation and variation in the cone opsin genes of nocturnal tarsiers

2017 ◽  
Vol 372 (1717) ◽  
pp. 20160075 ◽  
Author(s):  
Gillian L. Moritz ◽  
Perry S. Ong ◽  
George H. Perry ◽  
Nathaniel J. Dominy
Keyword(s):  
Colour Vision ◽  
Purifying Selection ◽  
Opsin Gene ◽  
Long Wavelength ◽  
Cone Opsin ◽  
Light Levels ◽  
Tarsius Bancanus ◽  
Dim Light ◽  
Two Stages ◽  
Functional Preservation

The short-wavelength sensitive (S-) opsin gene OPN1SW is pseudogenized in some nocturnal primates and retained in others, enabling dichromatic colour vision. Debate on the functional significance of this variation has focused on dark conditions, yet many nocturnal species initiate activity under dim (mesopic) light levels that can support colour vision. Tarsiers are nocturnal, twilight-active primates and exemplary visual predators; they also express different colour vision phenotypes, raising the possibility of discrete adaptations to mesopic conditions. To explore this premise, we conducted a field study in two stages. First, to estimate the level of functional constraint on colour vision, we sequenced OPN1SW in 12 wild-caught Philippine tarsiers ( Tarsius syrichta ). Second, to explore whether the dichromatic visual systems of Philippine and Bornean ( Tarsius bancanus ) tarsiers—which express alternate versions of the medium/long-wavelength sensitive (M/L-) opsin gene OPN1MW / OPN1LW —confer differential advantages specific to their respective habitats, we used twilight and moonlight conditions to model the visual contrasts of invertebrate prey. We detected a signature of purifying selection for OPN1SW , indicating that colour vision confers an adaptive advantage to tarsiers. However, this advantage extends to a relatively small proportion of prey–background contrasts, and mostly brown arthropod prey amid leaf litter. We also found that the colour vision of T. bancanus is advantageous for discriminating prey under twilight that is enriched in shorter (bluer) wavelengths, a plausible idiosyncrasy of understorey habitats in Borneo. This article is part of the themed issue ‘Vision in dim light’.

South American Weakly Electric Fish (Gymnotiformes) Are Long-Wavelength-Sensitive Cone Monochromats

2016 ◽  
Vol 88 (3-4) ◽  
pp. 204-212 ◽  
Author(s):  
Da-Wei Liu ◽  
Ying Lu ◽  
Hong Young Yan ◽  
Harold H. Zakon
Keyword(s):  
Short Wavelength ◽  
Electric Fish ◽  
Sister Group ◽  
Weakly Electric Fish ◽  
Opsin Gene ◽  
South American ◽  
Long Wavelength ◽  
Cone Opsin ◽  
Opsin Genes ◽  
Weakly Electric

Losses of cone opsin genes are noted in animals that are nocturnal or rely on senses other than vision. We investigated the cone opsin repertoire of night-active South American weakly electric fish. We obtained opsin gene sequences from genomic DNA of 3 gymnotiforms (Eigenmannia virescens, Sternopygus macrurus, Apteronotus albifrons) and the assembled genome of the electric eel (Electrophorus electricus). We identified genes for long-wavelength-sensitive (LWS) and medium-wavelength-sensitive cone opsins (RH2) and rod opsins (RH1). Neither of the 2 short-wavelength-sensitive cone opsin genes were found and are presumed lost. The fact that Electrophorus has a complete repertoire of extraretinal opsin genes and conservation of synteny with the zebrafish (Danio rerio) for genes flanking the 2 short-wavelength-sensitive opsin genes supports the supposition of gene loss. With microspectrophotometry and electroretinograms we observed absorption spectra consistent with RH1 and LWS but not RH2 opsins in the retinal photoreceptors of E. virescens. This profile of opsin genes and their retinal expression is identical to the gymnotiform's sister group, the catfish, which are also nocturnally active and bear ampullary electroreceptors, suggesting that this pattern likely occurred in the common ancestor of gymnotiforms and catfish. Finally, we noted an unusual N-terminal motif lacking a conserved glycosylation consensus site in the RH2 opsin of gymnotiforms, a catfish and a characin (Astyanax mexicanus). Mutations at this site influence rhodopsin trafficking in mammalian photoreceptors and cause retinitis pigmentosa. We speculate that this unusual N terminus may be related to the absence of the RH2 opsin in the cones of gymnotiforms and catfish.

Bio-P and non-bio-P bacteria identification by a novel microbial approach

1999 ◽  
Vol 39 (6) ◽  
pp. 13-20 ◽  
Author(s):  
Philip L. Bond ◽  
Jürg Keller ◽  
Linda L. Blackall
Keyword(s):  
In Situ Hybridisation ◽  
Microbial Populations ◽  
Biological Phosphorus Removal ◽  
Gram Positive Bacteria ◽  
P Content ◽  
Identification Of Bacteria ◽  
Widespread Belief ◽  
Biological Phosphorus ◽  
P Removal

Culturing bacteria from activated sludge with enhanced biological phosphorus removal (EBPR) has strongly implicated Acinetobacter with the process. However, using fluorescent in-situ hybridisation (FISH) probing to analyse microbial populations, we have shown evidence opposing this widespread belief. We describe the phosphorus (P) removing performance and microbial population analyses of sludges obtained in a laboratory scale EBPR reactor. Two sludges with extremely high P removing capabilities were examined, the P content of these sludges was 8.6% (P sludge) and 12.3% (S sludge) of the MLSS. Identification of bacteria using FISH probing indicated both sludges were dominated by microbes from the beta proteobacteria and high mol% G+C Gram positive bacteria. Acinetobacter could make up only a small proportion of the cells in these sludges. Sludge with extremely poor P removal (P content of 1.5%, referred to as T sludge) was then generated by reducing the P in the influent. Bacteria resembling the G-bacteria became abundant in this sludge and these were identified using FISH probing. The anaerobic transformations of the T and P sludges correlated well with that of the non-EBPR and EBPR biological models respectively, indicating that bacteria in the T sludge have the potential to inhibit P removal in EBPR systems.

scholarly journals Wheat, Rye, and Barley Genomes Can Associate during Meiosis in Newly Synthesized Trigeneric Hybrids

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 113
Author(s):  
María-Dolores Rey ◽  
Carmen Ramírez ◽  
Azahara C. Martín
Keyword(s):  
Chromosome Segregation ◽  
Genome Duplication ◽  
Triticum Turgidum ◽  
Aegilops Tauschii ◽  
Genomic In Situ Hybridization ◽  
Hordeum Chilense ◽  
Genomic Constitution ◽  
Chromosome Associations ◽  
High Level

Polyploidization, or whole genome duplication (WGD), has an important role in evolution and speciation. One of the biggest challenges faced by a new polyploid is meiosis, in particular, discriminating between multiple related chromosomes so that only homologs recombine to ensure regular chromosome segregation and fertility. Here, we report the production of two new hybrids formed by the genomes of species from three different genera: a hybrid between Aegilops tauschii (DD), Hordeum chilense (HchHch), and Secale cereale (RR) with the haploid genomic constitution HchDR (n = 7× = 21); and a hybrid between Triticum turgidum spp. durum (AABB), H. chilense, and S. cereale with the constitution ABHchR (n = 7× = 28). We used genomic in situ hybridization and immunolocalization of key meiotic proteins to establish the chromosome composition of the new hybrids and to study their meiotic behavior. Interestingly, there were multiple chromosome associations at metaphase I in both hybrids. A high level of crossover (CO) formation was observed in HchDR, which shows the possibility of meiotic recombination between the different genomes. We succeeded in the duplication of the ABHchR genome, and several amphiploids, AABBHchHchRR, were obtained and characterized. These results indicate that recombination between the genera of three economically important crops is possible.

Positive selection of the long-wavelength opsin gene in South American cichlid fishes

Hydrobiologia ◽  
2021 ◽  
Author(s):  
Thomaz Mansini Carrenho Fabrin ◽  
Luciano Seraphim Gasques ◽  
Rodrigo Junio da Graça ◽  
Sônia Maria Alves Pinto Prioli ◽  
Weferson Júnio da Graça ◽  
...  
Keyword(s):  
Positive Selection ◽  
Opsin Gene ◽  
South American ◽  
Long Wavelength ◽  
Cichlid Fishes ◽  
Selection Of

scholarly journals Rapid Multi-Hybridisation FISH Screening for Balanced Porcine Reciprocal Translocations Suggests a Much Higher Abnormality Rate Than Previously Appreciated

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 250
Author(s):  
Rebecca E O’Connor ◽  
Lucas G Kiazim ◽  
Claudia C Rathje ◽  
Rebecca L Jennings ◽  
Darren K Griffin
Keyword(s):  
Semen Analysis ◽  
In Situ Hybridisation ◽  
Economic Loss ◽  
Environmental Damage ◽  
Fluorescence In Situ Hybridisation ◽  
Reciprocal Translocations ◽  
Chromosome Translocations ◽  
Farrowing Rate ◽  
Significant Economic Loss

With demand rising, pigs are the world’s leading source of meat protein; however significant economic loss and environmental damage can be incurred if boars used for artificial insemination (AI) are hypoprolific (sub-fertile). Growing evidence suggests that semen analysis is an unreliable tool for diagnosing hypoprolificacy, with litter size and farrowing rate being more applicable. Once such data are available, however, any affected boar will have been in service for some time, with significant financial and environmental losses incurred. Reciprocal translocations (RTs) are the leading cause of porcine hypoprolificacy, reportedly present in 0.47% of AI boars. Traditional standard karyotyping, however, relies on animal specific expertise and does not detect more subtle (cryptic) translocations. Previously, we reported development of a multiple hybridisation fluorescence in situ hybridisation (FISH) strategy; here, we report on its use in 1641 AI boars. A total of 15 different RTs were identified in 69 boars, with four further animals XX/XY chimeric. Therefore, 4.5% had a chromosome abnormality (4.2% with an RT), a 0.88% incidence. Revisiting cases with both karyotype and FISH information, we reanalysed captured images, asking whether the translocation was detectable by karyotyping alone. The results suggest that chromosome translocations in boars may be significantly under-reported, thereby highlighting the need for pre-emptive screening by this method before a boar enters a breeding programme.

scholarly journals α-Fetoprotein mRNA in situ hybridisation is a highly specific marker of hepatocellular carcinoma: a multi-centre study

2021 ◽  
Author(s):  
Shi-Xun Lu ◽  
Yu-Hua Huang ◽  
Li-Li Liu ◽  
Chris Zhiyi Zhang ◽  
Xia Yang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
In Situ Hybridisation ◽  
Diagnostic Value ◽  
Detection Sensitivity ◽  
Specific Marker ◽  
Specific Method ◽  
Multi Centre Study ◽  
Arginase 1 ◽  
Afp Mrna

Abstract Background Pathologic diagnosis of hepatocellular carcinoma (HCC) can be challenging in differentiating from benign and non-hepatocytic malignancy lesions. The aim of this study was to investigate the potential utility of α-fetoprotein (AFP) mRNA RNAscope, a sensitive and specific method, in the diagnosis of HCC. Methods Three independent retrospective cohorts containing 2216 patients with HCC, benign liver lesions, and non-hepatocytic tumours were examined. AFP was detected using ELISA, IHC (Immunohistochemistry), and RNAscope. Glypican3 (GPC3), hepatocyte paraffin-1 (HepPar-1), and arginase-1 (Arg-1) proteins were detected using IHC. Results AFP RNAscope improved the HCC detection sensitivity by 24.7–32.7% compared with IHC. In two surgical cohorts, a panel of AFP RNAscope and GPC3 provided the best diagnostic value in differentiating HCC from benign hepatocytic lesions (AUC = 0.905 and 0.811), and a panel including AFP RNAscope, GPC3, HepPar-1, and Arg-1 yielded the best AUC (0.971 and 0.977) when distinguishing HCC from non-hepatocytic malignancies. The results from the liver biopsy cohort were similar, and additional application of AFP RNAscope improved the sensitivity by 18% when distinguishing HCC from benign hepatocytic lesions. Conclusions AFP mRNA detected by RNAscope is highly specific for hepatocytic malignancy and may serve as a novel diagnostic biomarker for HCC.

scholarly journals Abnormal mucus in cap polyposis

Gut ◽  
1998 ◽  
Vol 42 (1) ◽  
pp. 135-138 ◽  
Author(s):  
M P Buisine ◽  
J F Colombel ◽  
M Lecomte-Houcke ◽  
P Gower ◽  
J P Aubert ◽  
...  
Keyword(s):  
In Situ Hybridisation ◽  
Clinical Manifestations ◽  
Goblet Cells ◽  
Biopsy Specimens ◽  
Mucin Genes ◽  
Cap Polyposis ◽  
Abnormal Glycosylation ◽  
Histochemical Examination ◽  
Mrna In Situ Hybridisation

Background—Cap polyposis is a rare disease characterised by mucoid and bloody diarrhoea, with polyps covered by a cap of mucoid and fibrinopurulent exudate. The pathogenesis is not known.Aims—To pour some light on cap polyposis pathogenesis, by examining the mucus of patients and analysing the expression of five mucin genes, MUC2, MUC3,MUC4, MUC5AC, and MUC5B.Patient and methods—The study was performed on biopsy specimens taken from a patient with recurrent cap polyposis. Histochemical examination, electron microscopy, and mRNA in situ hybridisation were used.Results—The mucus of cap polyposis differed in three respects from that of normal adult colon: abnormal ultrastructure of the mucus in the goblet cells, predominance of non-sulphated mucins, abnormal expression of the MUC4, MUC3, andMUC5AC genes.Conclusions—Most of these abnormalities have been reported for other pathological situations, suggesting that the abnormalities observed in the mucus of this patient with cap polyposis are probably secondary phenomena rather than primary. However, the mucin abnormalities detected, which reflect deregulation of the expression of three apomucin genes, abnormal glycosylation, and abnormalities of the secretion process, are also probably involved in the clinical manifestations of cap polyposis.

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