scholarly journals Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)

2019 ◽  
Author(s):  
Martin Luehrmann ◽  
Fabio Cortesi ◽  
Karen L. Cheney ◽  
Fanny de Busserolles ◽  
N. Justin Marshall
Keyword(s):  
Gene Expression ◽  
Mate Selection ◽  
Opsin Gene ◽  
Small Scale ◽  
Microhabitat Use ◽  
List Type ◽  
Light Spectrum ◽  
Feeding Mode ◽  
Eye Size ◽  
Visual Systems

AbstractVertebrates exhibit diverse visual systems that vary in terms of morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and gene expression levels.In fish, such adaptations are driven by two main factors: differences in the light environment and behavioural tasks, including foraging, predator avoidance and mate selection. Whether visual systems also adapt to small-scale spectral differences in light, between microhabitats, is less clear.We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) on coral reefs drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology.We found that cardinalfishes display six types of partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix.Using data on visual opsin gene expression previously characterized in this family, it was discovered that species in exposed habitats had increased expression of the short-wavelength sensitive violet opsin (SWS2B) and decreased expression of the dim-light active rod opsin (RH1). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue-green central part of the light spectrum (SWS2As and RH2s), while fishes entirely hidden in the reef substrate had an increased expression of the long-wavelength sensitive red opsin (LWS).We found that eye size relative to body size significantly differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure.Retinal topography did not show co-adaptation with microhabitat use, but instead with feeding mode.We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems are also adapted to both the light intensity and the light spectrum of their preferred diurnal microhabitat.

scholarly journals Opsin gene evolution in amphibious and terrestrial combtooth blennies (Blenniidae)

2018 ◽  
Author(s):  
Fabio Cortesi ◽  
Karen M Cheney ◽  
Georgina M Cooke ◽  
Terry Ord
Keyword(s):  
Gene Expression ◽  
Gene Evolution ◽  
Opsin Gene ◽  
Light Spectrum ◽  
Cone Opsin ◽  
Visual Systems ◽  
Morphological Adaptations ◽  
Opsin Genes ◽  
Or Gene ◽  
Main Food Source

Evolutionary adaptations to life on land include changes to the physiology, morphology and behaviour of an animal in response to physical differences between water and air. The visual systems of amphibious species show pronounced morphological adaptations; yet, whether molecular changes also occur remains largely unknown. Here, we investigated the molecular evolution of visual pigment genes (opsins) in amphibious and terrestrial fishes belonging to the Salariini division of blennies (Blenniidae). We hypothesized that when conquering land, blenny opsins adapt, in terms of sequence variation and/or gene expression, to match both higher light intensities as well as the broader light spectrum. Using retinal transcriptomes in six species ranging from fully aquatic to fully terrestrial, we found very little variation in opsin gene sequences or gene expression between species. All blennies expressed a single rod opsin gene as well as two cone opsin genes sensitive to longer-wavelengths of light: RH2A-1 (green-sensitive) and LWS (red-sensitive). They also expressed one or two short-wavelength-sensitive cone opsin genes (SWS2Aα, SWS2Aβ; blue-sensitive) in a phylogenetically inert manner. However, based on amino acid predictions, both SWS2A proteins confer similar peak spectral sensitivities and differential expression is therefore unlikely to be ecologically significant. Red-sensitivity is likely beneficial for feeding on algae and detritus, the main food source of Salariini blennies, and could be co-adapted to perceive visual displays in terrestrial species, which often use red dorsal fins to signal during aggressive disputes and courtship. Our data suggests that on the molecular level, the visual systems that evolved in aquatic blennies have been retained in species that have transitioned onto land.

scholarly journals Intra-retinal variation of opsin gene expression in the guppy (Poecilia reticulata)

2011 ◽  
Vol 214 (19) ◽  
pp. 3248-3254 ◽  
Author(s):  
D. J. Rennison ◽  
G. L. Owens ◽  
W. T. Allison ◽  
J. S. Taylor
Keyword(s):  
Gene Expression ◽  
Poecilia Reticulata ◽  
Opsin Gene

Abstract 5953: Flow Pulsation Affect Distal Pulmonary Artery Endothelial Cell mRNA Expression

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Min Li ◽  
Kurt Stenmark ◽  
Robin Shandas ◽  
Wei Tan
Keyword(s):  
Gene Expression ◽  
Pulmonary Artery ◽  
Pulsatile Flow ◽  
Static Condition ◽  
Flow Chamber ◽  
Physical Characteristics ◽  
List Type ◽  
Flow Pulsation ◽  
Individual Gene ◽  
Speed Flow

Background: Due to the development of pulmonary arterial hypertension (PAH), distal pulmonary artery endothelial cells (dPAEC) are exposed to wall shear stress (SS) that is different in physical characteristics compared to normal condition. The effect of individual components of SS on PAEC biology has not been thoroughly examined. Thus the current study was designed to examine how dPAEC respond to different component of SS in regarding to gene expression including adhesion molecules: ICAM, VCAM, E-selectin; chemokine: MCP-1 and growth factors:VEGF, Flt-1. Methods: Bovine dPAEC were cultured and placed on fibronectin-coated slides till confluent. Cells were then exposed to SS with different frequency (1Hz, 2Hz), pulsation (low, medium and high with an average SS of 14 dynes/cm 2 ) and time (1hr or 6hrs). The flow studies were carried out using a flow chamber connected to a variable speed flow pump. All data was represented as fold change relative to static condition. Results: As shown in table below, The effect of flow frequency on gene expression depends on individual gene. There was no difference of ICAM expression between 1Hz and 2Hz. Frequency of 2Hz significantly increased VCAM and MCP-1 expression compared to frequency of 1Hz. Compared to static condition, steady flow increased all gene expression. One hour pulsatile flow further increased ICAM, VCAM, E-selectin and MCP-1 but not VEGF or Flt-1 expression as pulsation increased. 3) Prolonged pulsatile flow further increased all gene expression. Conclusion: Physical characteristics of flow, especially flow pulsation stimulate dPAEC gene expression which can contribute to the development of PAH.

scholarly journals 77 Prevalence of secondary immunotherapeutic targets in the absence of established immune biomarkers in solid tumors

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A86-A86
Author(s):  
Paul DePietro ◽  
Mary Nesline ◽  
Yong Hee Lee ◽  
RJ Seager ◽  
Erik Van Roey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Reference Population ◽  
List Type ◽  
Tumor Type ◽  
Genomic Profiling ◽  
Rna Seq ◽  
Immune Biomarkers ◽  
Cancer Types ◽  
Immune Related Genes

BackgroundImmune checkpoint inhibitor-based therapies have achieved impressive success in the treatment of several cancer types. Predictive immune biomarkers, including PD-L1, MSI and TMB are well established as surrogate markers for immune evasion and tumor-specific neoantigens across many tumors. Positive detection across cancer types varies, but overall ~50% of patients test negative for these primary immune markers.1 In this study, we investigated the prevalence of secondary immune biomarkers outside of PD-L1, TMB and MSI.MethodsComprehensive genomic and immune profiling, including PD-L1 IHC, TMB, MSI and gene expression of 395 immune related genes was performed on 6078 FFPE tumors representing 34 cancer types, predominantly composed of lung cancer (36.7%), colorectal cancer (11.9%) and breast cancer (8.5%). Expression levels by RNA-seq of 36 genes targeted by immunotherapies in solid tumor clinical trials, identified as secondary immune biomarkers, were ranked against a reference population. Genes with a rank value ≥75th percentile were considered high and values were associated with PD-L1 (positive ≥1%), MSI (MSI-H or MSS) and TMB (high ≥10 Mut/Mb) status. Additionally, secondary immune biomarker status was segmented by tumor type and cancer immune cycle roles.ResultsIn total, 41.0% of cases were PD-L1+, 6.4% TMB+, and 0.1% MSI-H. 12.6% of cases were positive for >2 of these markers while 39.9% were triple negative (PD-L1-/TMB-/MSS). Of the PD-L1-/TMB-/MSS cases, 89.1% were high for at least one secondary immune biomarker, with 69.3% having ≥3 markers. PD-L1-/TMB-/MSS tumor types with ≥50% prevalence of high secondary immune biomarkers included brain, prostate, kidney, sarcoma, gallbladder, breast, colorectal, and liver cancer. High expression of cancer testis antigen secondary immune biomarkers (e.g., NY-ESO-1, LAGE-1A, MAGE-A4) was most commonly observed in bladder, ovarian, sarcoma, liver, and prostate cancer (≥15%). Tumors demonstrating T-cell priming (e.g., CD40, OX40, CD137), trafficking (e.g., TGFB1, TLR9, TNF) and/or recognition (e.g., CTLA4, LAG3, TIGIT) secondary immune biomarkers were most represented by kidney, gallbladder, and sarcoma (≥40%), with melanoma, esophageal, head & neck, cervical, stomach, and lung cancer least represented (≥15%).ConclusionsOur studies show comprehensive tumor profiling that includes gene expression can detect secondary immune biomarkers targeted by investigational therapies in ~90% of PD-L1-/TMB-/MSS cases. While genomic profiling could also provide therapeutic choices for a percentage of these patients, detection of secondary immune biomarkers by RNA-seq provides additional options for patients without a clear therapeutic path as determined by PD-L1 testing and genomic profiling alone.ReferenceHuang R S P, Haberberger J, Severson E, et al. A pan-cancer analysis of PD-L1 immunohistochemistry and gene amplification, tumor mutation burden and microsatellite instability in 48,782 cases. Mod Pathol 2021;34: 252–263.

scholarly journals A comprehensive analysis of vomeronasal organ transcriptome reveals variable gene expression depending on age and function in rabbits

2020 ◽  
Author(s):  
PR Villamayor ◽  
D Robledo ◽  
C Fernández ◽  
J Gullón ◽  
L Quintela ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transient Receptor Potential ◽  
Expression Patterns ◽  
Vomeronasal Organ ◽  
Receptor Potential ◽  
Transient Receptor Potential Channel ◽  
List Type ◽  
Gene Repertoire ◽  
Behavioural Responses ◽  
Transient Receptor

ABSTRACTThe vomeronasal organ (VNO) is a chemosensory organ specialized in the detection of pheromones and consequently the regulation of behavioural responses mostly related to reproduction. VNO shows a broad variation on its organization, functionality and gene expression in vertebrates, and although the species analyzed to date have shown very specific features, its expression patterns have only been well-characterized in mice. Despite rabbits represent a model of chemocommunication, unfortunately no genomic studies have been performed on VNO of this species to date. The capacity of VNO to detect a great variety of different stimuli suggests a large number of genes with complex organization to support this function. Here we provide the first comprehensive gene expression analysis of the rabbit VNO through RNA-seq across different sexual maturation stages. We characterized the VNO transcriptome, updating the number of the two main vomeronasal receptor (VR) families, 129 V1R and 70 V2R. Among others, the expression of transient receptor potential channel 2 (TRPC2), a crucial cation channel generating electrical responses to sensory stimulation in vomeronasal neurons, along with the specific expression of some fomyl-peptide receptors and H2-Mv genes, both known to have specific roles in the VNO, revealed a the particular gene expression repertoire of this organ, but also its singularity in rabbits. Moreover, juvenile and adult VNO transcriptome showed consistent differences, which may indicate that these receptors are tuned to fulfill specific functions depending on maturation age. We also identified VNO-specific genes, including most VR and TRPC2, thus confirming their functional association with the VNO. Overall, these results represent the genomic baseline for future investigations which seek to understand the genetic basis of behavioural responses canalized through the VNO.HIGHLIGHTSFirst description of the rabbit vomeronasal organ (VNO) transcriptomeVNO contains a unique gene repertoire depending on the speciesHigh fluctuation of the VNO gene expression reveals changes dependent on age and specific functionsMost vomeronasal-receptors (VR) and transient receptor potential channel 2 (TRPC2) genes are VNO-specificReproduction-related genes shows a wide expression pattern

scholarly journals SP1 Evaluating medicines use reviews (MURs) in children

2020 ◽  
Vol 105 (9) ◽  
pp. e1.1-e1
Author(s):  
Rebecca Venables ◽  
Eirini Iliopoulou ◽  
Tania Cork
Keyword(s):  
Child Anxiety ◽  
Community Pharmacists ◽  
Education Institution ◽  
Service Evaluation ◽  
Small Scale ◽  
List Type ◽  
Medicines Use ◽  
Medicines Use Reviews ◽  
Framework Approach ◽  
And Training

AimTo evaluate Medicines Use Reviews (MURs) in community pharmacies, with a focus on MURs conducted with children alone and with their guardian(s).MethodA service evaluation of MURs was conducted using a questionnaire proforma. The questionnaire proforma design was informed by current literature and MUR guidance (PSNC)1 and included both quantitative and qualitative questions in order to understand how pharmacists approach and perceive conducting MURs, with a specific focus on those with children alone and with their guardian(s). Participants were community pharmacists holding an MUR accreditation by a Higher Education Institution, whom had already performed at least one MUR. Quantitative data formed descriptive statistics and this was supported by the qualitative data which was analysed using a thematic framework approach. Ethics was not required; this work was a service evaluation.ResultsIn total, 16 community pharmacists participated. The majority 81% (13/16) reported that they did not conduct any MURs in patients younger than 18 years. All participants reported feeling confident when conducting MURs in adults; whilst 56% (9/16) of participants reported feeling confident in conducting an MUR with a child with their parent/guardian present and only 25% (4/16) feeling confident with a child alone. Lack of confidence regarding child MURs was linked to paucity of opportunity, insufficient experience and training, and the need to amend question technique. Regarding consent, 75% (12/16) of participants reported that they were not confident in taking MUR consent from children, and 31% (5/16) from adolescents. Reasons for low confidence in gaining child/adolescent consent included never conducting MURs in children - so no experience in gaining consent, concern regarding child understanding, and always wanting a responsible adult present. Further barriers to MURs in children included: issues surrounding safeguarding, children possibly not having the necessary knowledge to participate if parents are responsible for medicines management, child ability to provide full consent and child anxiety, thus impact on aptitude to communicate effectively.ConclusionThis was a small-scale evaluation exploring MURs in children. Supporting anecdotal evidence prior to this study, study findings suggest that very few MURs are conducted in patients less than 18 years. Community pharmacists discussed poorer confidence in conducting MURs with children and adolescents compared to adults. Reports highlighted that the major barriers to conducting MURs in this patient cohort may be related to pharmacists’ concerns surrounding child consent and potential lack of experience and training. This study should be used to inform larger studies exploring barriers to gaining consent in children, and also conducting appropriate services with children. Analogous studies with other healthcare professional groups would be beneficial, and this data could be compared. Findings should also help to shape future education and training for pharmacists and allied healthcare professionals in order to optimise future patient services, thus patient care.ReferencePSNC. 2018. MURs: the basics. [online] Available at: https://psnc.org.uk/servicescommissioning/advanced-services/murs/murs-the-basics/ [Accessed 19 Nov. 2018]

scholarly journals Ontogenetic changes in photoreceptor opsin gene expression in coho salmon (Oncorhynchus kisutch, Walbaum)

2008 ◽  
Vol 211 (24) ◽  
pp. 3879-3888 ◽  
Author(s):  
S. E. Temple ◽  
K. M. Veldhoen ◽  
J. T. Phelan ◽  
N. J. Veldhoen ◽  
C. W. Hawryshyn
Keyword(s):  
Gene Expression ◽  
Coho Salmon ◽  
Oncorhynchus Kisutch ◽  
Opsin Gene ◽  
Ontogenetic Changes

scholarly journals RNA interactions with CTCF are essential for its proper function

2019 ◽  
Author(s):  
Ricardo Saldaña-Meyer ◽  
Javier Rodriguez-Hernaez ◽  
Mayilaadumveettil Nishana ◽  
Karina Jácome-López ◽  
Elphege P. Nora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Ctcf Binding ◽  
Proper Function ◽  
List Type ◽  
Transcriptional Inhibition ◽  
Local Insulation

SummaryThe function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms of how CTCF dynamically contributes to genome organization is not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs; promoting its oligomerization. Here we found that inhibition of transcription or interfering with CTCF ability to bind RNA through mutations of two of its 11 zinc fingers that are not involved with CTCF binding to its cognate site in vitro, zinc finger-1 (ZF1) or −10 (ZF10), disrupt CTCF association to chromatin. These mutations alter gene expression profiles as CTCF mutants lose their ability to promote local insulation. Our results highlight the importance of RNA as a structural component of the genome, in part by affecting the association of CTCF with chromatin and likely its interaction with other factors.Transcriptional inhibition disrupts CTCF binding to chromatinRNA-binding regions (RBR) in CTCF are found within ZF1 and ZF10Local insulation is markedly decreased in ZF1∆ and ZF10∆ mutant rescuesGene expression and chromatin organization are disrupted by RBR mutants

scholarly journals Fantastic beasts and how to sequence them: genomic approaches for obscure model organisms

2017 ◽  
Author(s):  
Mikhail V. Matz
Keyword(s):  
Gene Expression ◽  
Frequency Spectrum ◽  
Gene Expression Analysis ◽  
Genomic Analysis ◽  
Reference Sequence ◽  
Model Organisms ◽  
List Type ◽  
Allele Frequency Spectrum ◽  
Specific Restriction ◽  
Genomic Basis

SummaryApplication of genomic approaches to “obscure model organisms” (OMOs), meaning species with little or no genomic resources, enables increasingly sophisticated studies of genomic basis of evolution, acclimatization and adaptation in real ecological contexts. Here, I highlight sequencing solutions and data handling techniques most suited for genomic analysis of OMOs.Glossary-Allele Frequency Spectrum, AFS(same as Site Frequency Spectrum, SFS): histogram of the number of segregating variants depending on their frequency in one or more populations.-Restriction site-Associated DNA (RAD) sequencing: family of diverse genotyping methods that sequence short fragments of the genome adjacent to recognition site(s) for specific restriction endonuclease(s).-Linkage Disequilibrium (LD): in this review, correlation of genotypes at a pair of markers across individuals.-LD block: typical distance between markers in the genome across which their genotypes remain correlated.-Genome scan:profiling of genotypes along the genome looking for unusual patterns. Often used to look for signatures of natural selection or introgression.-“Denser-than-LD” genotyping: genotyping of several polymorphic markers per LD block.-Highly contiguous reference: genome or transcriptome reference sequence containing the least amount of fragmentation.-Phased data: data showing which SNP alleles belong to the same homologous chromosome copy.-Cross-tissue gene expression analysis: looking for individual-specific shifts in gene expression detectable across multiple tissues. Such shifts are predominantly genetic in nature.

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