Global omics study of Tetraselmis chuii reveals time-related metabolic adaptations upon oxidative stress

Microalgae species encounter oxidative stress in their natural environments, prompting the development of species-specific adaptation mechanisms. Understanding these mechanisms can offer valuable insights for biotechnological applications in microalgal metabolic manipulation. In this study, we investigated the response of Tetraselmis chuii, an industrially important microalga, to H2O2-induced oxidative stress. Exposure to 0.5-mM H2O2 resulted in reduced cell viability, and higher concentrations led to a drastic decline. After 1 h of exposure to H2O2, photosynthetic capacity (Qy) was negatively impacted, and this reduction intensified after 6 h of continuous stress. Global multi-omics analysis revealed that T. chuii rapidly responded to H2O2-induced oxidative stress within the first hour, causing significant changes in both transcriptomic and metabolomic profiles. Among the cellular functions negatively affected were carbon and energy flow, with photosynthesis-related PSBQ having a 2.4-fold downregulation, pyruvate kinase decreased by 1.5-fold, and urea content reduced by threefold. Prolonged exposure to H2O2 incurred a high energy cost, leading to unsuccessful attempts to enhance carbon metabolism, as depicted, for example, by the upregulation of photosystems-related PETC and PETJ by more than twofold. These findings indicate that T. chuii quickly responds to oxidative stress, but extended exposure can have detrimental effects on its cellular functions. KEY POINTS: • 0.5-mM H2O2-induced oxidative stress strongly affects T. chuii • Distinct short- and long-term adaptation mechanisms are induced • Major metabolic adaptations occur within the first hour of exposure.

Similar Patient Satisfaction and Quality of Life Improvement Achieved with TKA and THA According to the Goodman Scale: A Comparative Study

Background: Total knee arthroplasty (TKA) and total hip arthroplasty (THA) are effective treatments for severe knee and hip osteoarthritis. Historically, TKA has been associated with lower satisfaction than THA, but recent advances in knee surgery have led to lower dissatisfaction rates. This study aimed to compare the satisfaction and self-reported improvement in the quality of life of two cohorts of patients who underwent TKA and THA, respectively. Methods: This observational study compared two previously published cohorts of patients who underwent THA and TKA in a single university center. The Goodman scale was used to assess satisfaction and self-perception of improved quality of life after TKA and THA at a minimum one-year follow-up. Propensity score matching was used to balance age, gender, and follow-up between groups. Significance was set at 0.05. Results: The study included a total of 105 THAs and 131 TKAs. Both groups had high levels of satisfaction with pain relief, ability to do house/yard work, and overall satisfaction, with above 90% satisfaction rates. Regarding improvement in quality of life, both groups had 86% of patients reporting improvement as "much better." After propensity score matching, no significant difference was found between THA and TKA for any of the comparisons made using the Goodman scale. Conclusions: The study showed that both TKA and THA resulted in high levels of satisfaction and improvement in quality of life. There was no significant difference in satisfaction rates between TKA and THA, contrary to the historical trend of lower satisfaction rates for TKA.

Anterior knee pain and sit-up tests predicts patients' satisfaction and improvement in quality of life after anterior stabilized total knee replacement without patellar resurfacing

PURPOSE

The purpose of this study was to assess patient satisfaction and identify risk factors for dissatisfaction after anterior stabilised conventional total knee arthroplasty (TKA) without patellar resurfacing, using the Goodman score.

METHODS

We conducted a cross-sectional study using data from our institutional database from 1 January 2018 to 1 March 2021. Patients who underwent TKA with the Vanguard® Cruciate Retaining Anterior Stabilized Knee System (Zimmer Biomet, Warsaw, Indiana, USA) without patellar replacement were included. Patients with other bearing surfaces (posterior stabilised or medial congruent) or diagnosed with infection or instability were excluded. Patients' reported outcomes, body mass index (BMI), passive range of motion, the timed up-and-go test, sit-up test, and algometry were assessed. Patients were also asked if they had anterior knee pain. Satisfaction was assessed using the Goodman scale, and logistic multivariate regression was used to identify variables associated with dissatisfaction and perceived improvement in quality of life.

RESULTS

A total of 131 TKA patients were included in the study. The median satisfaction score was 100 (interquartile range [IQR], 87.5 to 100), with the 75-point threshold at the 90th percentile according to Section A of Goodman. Section B of Goodman showed that 113 TKA patients (86.26%) reported "great improvement" or "more than I ever dreamed." Multivariate logistic regression revealed that anterior knee pain (OR 5.16, 95% CI 1.24 to 21.39), the sit-up test (OR 0.63, 95% CI 0.49 to 0.81), and BMI (OR 0.84, 95% CI 0.70 to 0.99) were significantly associated with patient dissatisfaction and a worse perceived improvement in quality of life. The receiver operating characteristics curve for the models had areas under the curve of 0.83 (95% CI 0.69 to 0.97) and 0.82 (95% CI 0.70 to 0.94), respectively.

CONCLUSION

Anterior stabilised TKA without patellar resurfacing can achieve 90% satisfaction and 86% improvement in quality of life. To improve these results, it is essential to prevent and treat anterior knee pain and enhance quadriceps strength.

LEVEL OF EVIDENCE

Level III (retrospective cohort study).

[Unicompartmental knee prosthesis]

In a patient with severe unicompartmental knee osteoarthritis where conservative treatments have been exhausted, with painful symptoms located on the affected side and with a reducible axis, the unicompartmental knee prosthesis (UKP) is the first option for our work group. Within the study to confirm the diagnosis and plan the surgery, weight-bearing knee x-rays, Rosenberg x-rays, and teleradiographs of the lower extremities stand out. The objective of surgery is to replace the affected area, restoring the anatomy with an adequate balance of soft tissues. Regarding alignment, the challenge is not to overload the opposite side or that of the prosthesis. There are mobile and fixed plates and although the clinical and survival results are similar, in recent years with the incorporation of robotic surgery, the balance has tipped towards the use of fixed plates. The clinical and functional results are better and there are fewer complications than when total knee prostheses (TKP) are used in the same type of patients. The survival studied in registries is lower than for TKP, but when used in high-flow centers where the percentage of UKP is close to a third of the total with strict patient selection, the duration is as good as in PTR.

Estimación de la eficiencia del uso de pabellones electivos en el sistema de salud público chileno entre 2018 y 2021

Objective

The efficient use of wards intended for elective surgeries is essential to resolve cases on the surgical waiting list. This study aims to estimate the efficiency of ward use in the Chilean public health system between 2018 and 2021.

Methods

The design was an ecological study. Section A.21 of the database constructed by the monthly statistical summaries that each public health network facility reported to the Ministry of Health between 2018 and 2021 was analyzed. Data from subsections A, E and F were extracted: ward staffing, total elective surgeries by specialty, number and causes of suspension of elective surgeries. Then, the surgical performance during working hours and the percentage of hourly occupancy for a working day was estimated. Additionally, an analysis was made by region with data from 2021.

Results

The percentage of elective wards in use ranged from 81.1% to 94.1%, while those enabled for those staffing ranged from 70.5% to 90.4% during 2018 and 2021. The total number of surgeries was highest in 2019 (n = 416 339), but for 2018, 2020, and 2021 it ranged from 259 000 to 297 000. Suspensions varied between 10.8% (2019) and 6.9% (2021), with the leading cause being patient-related. When analyzing the number of cases canceled monthly by facility, we saw that the leading cause was trade union-related. The maximum throughput of a ward intended for elective surgery was reached in 2019 and was 2.5 surgeries; in 2018, 2020 and 2021, the throughput borders on two surgeries per ward enabled for elective surgery. The percentage of ward time occupied during working hours by contract day varies between 80.7% (2018) and 56.8% (2020).

Conclusions

All the parameters found and estimated in this study show that there is an inefficient utilization of operating rooms in Chilean public healthcare facilities.

Access to knee arthroplasty among National Health Fund beneficiaries in Chile between 2004 and 2021

Introduction: Knee osteoarthritis affects the quality of life, with knee arthroplasty being a cost-effective treatment for the severe stage of this disease. Access to knee arthroplasty is a health indicator of the Organisation for Economic Co-operation and Development. The objectives of this study are to determine the incidence of knee arthroplasty between 2004 and 2021 in beneficiaries of the National Health Fund in Chile, the proportion of patients who underwent surgery in the private system, and to estimate the patient's out-of-pocket expenditure for surgery. Methods: Cross-sectional study. We used the Department of Statistics and Health Information database. Patients discharged from a Chilean health center who underwent knee arthroplasty surgery between 2004 and 2021 were investigated. We analyzed the proportion of patients by their National Health Fund category and whether their surgery was performed in public or private network facilities. Results: Of the 31 526 knee arthroplasty procedures, 21 248 (67.38%) were performed on National Health Fund patients and 16 238 in public institutions (51.49%). Patients from the National Health Fund showed a systematic increase in knee arthroplasty volume until 2019 but decreased in 2020 and 2021 by 68% and 51%. Of the total number of patients in the public system operated on for knee arthroplasty, 856 (9%) belonged to group A1, 12 806 (60%) to group B, 2044 (10%) to group C, and 4421 (21%) to group D. The expenditure incurred by these patients was estimated to vary between 24.4% and 27.2%. The historical proportions of access to this surgery in private institutions are 7% in group A, 13% in group B, 24% in group C, and 52% in group D. Conclusion: Fifty percent of knee arthroplasty surgeries are performed in public institutions, and two-thirds are performed on patients of the National Health Fund. Forty-six percent of the C and D groups were operated in the private system. The pandemic has increased the access gap, leading to a substantial increase in the proportion of patients from the National Health Fund of the B, C, and D groups who have migrated to the private system to access this surgery.

Metabolic pathways for biosynthesis and degradation of starch in Tetraselmis chui during nitrogen deprivation and recovery

Tetraselmis chui is known to accumulate starch when subjected to stress. This phenomenon is widely studied for the purpose of industrial production and process development. Yet, knowledge about the metabolic pathways involved is still immature. Hence, in this study, transcription of 27 starch-related genes was monitored under nitrogen deprivation and resupply in 25 L tubular photobioreactors. T. chui proved to be an efficient starch producer under nitrogen deprivation, accumulating starch up to 56% of relative biomass content. The prolonged absence of nitrogen led to an overall down-regulation of the tested genes, in most instances maintained even after nitrogen replenishment when starch was actively degraded. These gene expression patterns suggest post-transcriptional regulatory mechanisms play a key role in T. chui under nutrient stress. Finally, the high productivity combined with an efficient recovery after nitrogen restitution makes this species a suitable candidate for industrial production of high-starch biomass.

Impact of COVID-19 outbreak in knee arthroplasty in Chile: a cross-sectional, national registry-based analysis

Introduction The need for beds and health personnel to treat coronavirus (COVID- 19) patients has led to the suspension of many elective sur-geries in Chile, including knee arthroplasties. This study aims to determine the incidence of knee arthroplasty in 2020, reflecting the effect of the COVID- 19 pandemic, and estimate the cost and time it would take to recover the waiting list prior to March 2020. Methods A cross- sectional study was designed. We analyzed databases from The Department of Statistics and Health Information databases from Chile for 2019 and 2020, identifying patients with surgical discharges associated with knee arthroplasty codes. We estimated the time it would take to recover the surgeries unperformed in 2020 by simulating a monthly workload increase from the 2019 baseline. The costs of knee arthroplasty paid by the National Health Fund to institutions were estimated by diagnosis-related groups. Results We found that the incidence rate of knee arthroplasty in 2020 decreased by 64% compared with 2019. The impact was higher in the public system (68%) and the National Health Found (63%). A simulated increase in knee arthroplasty productivity by 30% would allow recovering the postponed knee arthroplasty surgeries in 27 months, at a monthly cost to the public system of 318 million Chilean pesos (378 thousand US dollars). Conclusions The incidence rate of knee arthroplasty during 2020 decreased by 64%, revealing the extensive waiting line for people with knee osteoarthritis. An increase between 20- 40% in productivity compared with 2019 would allow recovering the unperformed surgeries in 20 to 41 months, at a monthly cost to the public network between 210 and 425 million Chilean pesos (250 to 506 thousand US dollars). 10.5867/medwave.2022.04.002511 https://www.medwave.cl/link.cgi/English/Reviews/Analysis/8732.act Reflections on death in the time of Covid-19 Donovan Casas Patiño The pandemic of COVID- 19 filled the world with sorrow as death was an ever- present menace everywhere. This document aims to rescue some reflective facts about death marked by a socio- historical context that revealed breaking points. These points work around three specific aspects: the agony of the dying, funeral and religious rituals, and the pilgrimage between doubt and guilt. Death in times of pandemic revealed the need to humanize and guarantee a dignified death. Likewise, the pandemic reinvented funeral rituals by globalizing them using technology and social networks. Finally, we saw that the pilgrimage preludes death and awakens the most negative feelings in the face of rejection and frustration.

Impact of COVID-19 outbreak in knee arthroplasty in Chile: a cross-sectional, national registry-based analysis

Introduction

The need for beds and health personnel to treat coronavirus (COVID- 19) patients has led to the suspension of many elective sur-geries in Chile, including knee arthroplasties. This study aims to determine the incidence of knee arthroplasty in 2020, reflecting the effect of the COVID- 19 pandemic, and estimate the cost and time it would take to recover the waiting list prior to March 2020.

Methods

A cross- sectional study was designed. We analyzed databases from The Department of Statistics and Health Information databases from Chile for 2019 and 2020, identifying patients with surgical discharges associated with knee arthroplasty codes. We estimated the time it would take to recover the surgeries unperformed in 2020 by simulating a monthly workload increase from the 2019 baseline. The costs of knee arthroplasty paid by the National Health Fund to institutions were estimated by diagnosis-related groups.

Results

We found that the incidence rate of knee arthroplasty in 2020 decreased by 64% compared with 2019. The impact was higher in the public system (68%) and the National Health Found (63%). A simulated increase in knee arthroplasty productivity by 30% would allow recovering the postponed knee arthroplasty surgeries in 27 months, at a monthly cost to the public system of 318 million Chilean pesos (378 thousand US dollars).

Conclusions

The incidence rate of knee arthroplasty during 2020 decreased by 64%, revealing the extensive waiting line for people with knee osteoarthritis. An increase between 20- 40% in productivity compared with 2019 would allow recovering the unperformed surgeries in 20 to 41 months, at a monthly cost to the public network between 210 and 425 million Chilean pesos (250 to 506 thousand US dollars).

Robotic-assisted vs conventional surgery in medial unicompartmental knee arthroplasty: a clinical and radiological study

BACKGROUND

The use of unicompartmental knee arthroplasty (UKA) has increased and new technologies have been developed to improve patient survival and satisfaction, soft tissue balance, alignment, and component size. Robot-assisted systems offer an increase in surgical precision and accuracy. The purpose of this study is to evaluate the precision of component position using five radiological parameters in conventional and robotic-assisted medial UKA using the NAVIO system.

METHODS

A cohort study was designed for patients who underwent medial UKA between April 2017 and March 2019 in a single center. Patients were allocated in the conventional (UKA-C) or robotic-assisted (UKA-R) group. The variables analyzed were age, gender, affected knee side, length of hospital stay, surgical time, and radiological measurements such as anatomical medial distal femoral angle (aMDFA), anatomical medial proximal tibial angle (aMPTA), tibial slope, the sagittal femoral angle, and the component size. A target was defined for each measurement, and a successful UKA was defined if at least four radiological measures were on target after surgery. Also, patients' reported outcomes were evaluated using the Oxford Knee Score (OKS) and a numeric rating scale (NRS) for pain.

RESULTS

Thirty-four patients were included, 18 of them underwent UKA-R. The success rate for UKA in the UKA-R group was 87%; meanwhile, in the UKA-C group this was 28%, this difference was significant and powered (Fisher's exact test, p = 0.001; 1 - β = 0.95). Also, a 5-point difference in favor of the UKA-R group in the median OKS (p = 0.01), and a significantly lower median NRS for pain (p < 0.000) were found after surgery.

CONCLUSIONS

UKA-R achieved more precision in the radiological parameters' measure in this study. Also, UKA-R has a trend towards a better OKS and a lower NRS for pain at short-term follow-up.

Selection and validation of reference genes for quantitative real-time PCR in the green microalgae Tetraselmis chui

Quantitative real-time reverse transcription PCR (RT-qPCR) is a highly sensitive technique that can be applied to analyze how genes are modulated by culture conditions, but identification of appropriate reference genes for normalization is a critical factor to be considered. For this reason, the expression stability of 18 candidate reference genes was evaluated for the green microalgae Tetraselmis chui using the widely employed algorithms geNorm, NormFinder, BestKeeper, the comparative ΔCT method, and RefFinder. Microalgae samples were collected from large scale outdoor photobioreactors during the growing phase (OUT_GP), and during the semi-continuous phase at different times of the day (OUT_DC). Samples from standard indoor cultures under highly controlled conditions (IND) were also collected to complement the other data. Different rankings for the candidate reference genes were obtained depending on the culture conditions and the algorithm employed. After comparison of the achieved ranks with the different methods, the references genes selected for samples from specific culture conditions were ALD and EFL in OUT_GP, RPL32 and UBCE in OUT_DC, and cdkA and UBCE in IND. Moreover, the genes EFL and cdkA or EFL and UBCE appeared as appropriate combinations for pools generated from all samples (ALL). Examination in the OUT_DC cultures of genes encoding the large and small subunits of ADP-glucose pyrophosphorylase (AGPL and AGPS, respectively) confirmed the reliability of the identified reference genes, RPL32 and UBCE. The present study represents a useful contribution for studies of gene expression in T. chui, and also represents the first step to set-up an RT-qPCR platform for quality control of T. chui biomass production in industrial facilities.

Robotic-assisted Unicompartmental knee Arthroplasty optimizes joint line restitution better than conventional surgery

Purpose

To compare joint line restoration after unicompartmental knee arthroplasty (UKA) between conventional and robotic-assisted surgery. Previous studies have shown that joint line distalization can lead to higher failure rates. The hypothesis was that robotic-assisted UKA is associated with less femoral component distalization and a precise tibial cut, which allows a more anatomical restitution of the knee joint line.

Methods

Retrospective cohort study of patients undergoing medial or lateral UKA between May 2018 and March 2020. Preoperative and postoperative radiologic assessment of the joint line was performed by two observers, using three different methods, one for tibial slope and one for tibial resection. Robotic assisted UKA and conventional UKA groups were compared.

Results

Sixty UKA were included, of which 48 (77.42%) were medial. Robotic-assisted UKA were 40 (64.52%) and 22(35.48%) were conventional

The distalization of the femoral component was higher in the conventional group despite the method of measurement used In both Weber methods, the difference was statistically different: Conventional 2.3 (0.9 to 5.6) v/s Robotic 1.5 (− 1.1 to 4.1) (p =0.0025*). A higher proportion of patients achieved a femoral component position ≤ two millimeters from the joint line using robotic-assisted UKA compared to the conventional technique .

No statistical difference between robotic-assisted and conventional UKA was found in tibial resection and slope.

Conclusion

Robotic-assisted UKA shows a better rate of joint line restoration due to less femoral component distalization than conventional UKA. No difference was found in the amount of tibial resection between groups in this study.

Level of evidence

III

Administering copper reduces hyper-excitability generated by penicillin G in motor cortex neurons from rat brain slices

Recording synaptic activity of layer III neurons from motor cortex slices, which was provoked by stimulating layer IV, generated synaptic responses of the field potential (FP) that went from mean 100 μV to 600 μV when the stimulus was increased up to twice the threshold. Administering 100 μM or 200 μM of copper, increased the responses to mean 800 μV and 820 μV, respectively. The response to 200 μM was not significantly greater than that to 100 μM. However, all FP responses were significantly lower to a copper concentration of 500 μM. The basal FP was slowly restored by removing the copper with Krebs-Ringer(K-R), resulting in similar characteristics to those observed before copper administration. Then, neurons were perfused with penicillin (2000 UI) to increase cortical excitability and to assess the depressing effect of high concentrations of copper. Administering 500 μM of copper significantly reduced the activity generated by penicillin, while removing by wash(K-R) penicillin and copper generated FP responses similar to those obtained at baseline. Our data indicate that depending on the concentration, copper can behave as an activating or blocking agent for cortical activity.

Multiplex-Polymerase Chain Reaction Assay for the Authentication of the Mackerel Scomber colias in Commercial Canned Products

A multiplex-polymerase chain reaction (PCR) system was developed for the authentication of the mackerel Scomber colias in commercial canned products. This novel method consists of an S. colias-specific fragment [159 base pairs (bp)] located in the nontranscribed spacer (NTS) sequence, and a Scomber genus-specific PCR product in the 5S rRNA gene (196201 bp) as a positive amplification control. The system was assayed using 18 different canned products labeled as S. colias. A positive identification was made in all but one sample, revealing this methodology as a potential molecular tool for direct application in the authentication of S. colias canned products.

Randomized comparison between interscalene and costoclavicular blocks for arthroscopic shoulder surgery

BACKGROUND

This randomized trial compared ultrasound-guided interscalene block (ISB) and costoclavicular brachial plexus block (CCB) for arthroscopic shoulder surgery. We hypothesized that CCB would provide equivalent analgesia to ISB 30 min after surgery without the risk of hemidiaphragmatic paralysis.

METHODS

All 44 patients received an ultrasound-guided block of the intermediate cervical plexus. Subsequently, they were randomized to ISB or CCB. The local anesthetic agent (20 mL of levobupivacaine 0.5% and epinephrine 5 µg/mL) and pharmacological block adjunct (4 mg of intravenous dexamethasone) were identical for all study participants. After the block performance, a blinded investigator assessed ISBs and CCBs every 5 min until 30 min using a composite scale that encompassed the sensory function of the supraclavicular nerves, the sensorimotor function of the axillary nerve and the motor function of the suprascapular nerve. A complete block was defined as one displaying a minimal score of six points (out of a maximum of eight points) at 30 min. Onset time was defined as the time required to reach the six-point minimal composite score. The blinded investigator also assessed the presence of hemidiaphragmatic paralysis at 30 min with ultrasonography.Subsequently, all patients underwent general anesthesia. Postoperatively, a blinded investigator recorded pain scores at rest at 0.5, 1, 2, 3, 6, 12, and 24 hours. Patient satisfaction at 24 hours, consumption of intraoperative and postoperative narcotics, and opioid-related side effects (eg, nausea/vomiting, pruritus) were also tabulated.

RESULTS

Both groups displayed equivalent postoperative pain scores at 0.5, 1, 2, 3, 6, 12, and 24 hours. ISB resulted in a higher incidence of hemidiaphragmatic paralysis (100% vs 0%; P < 0.001) as well as a shorter onset time (14.0 (5.0) vs 21.6 (6.4) minutes; p<0.001). However, no intergroup differences were found in terms of proportion of patients with minimal composite scores of 6 points at 30 min, intraoperative/postoperative opioid consumption, side effects, and patient satisfaction at 24 hours.

CONCLUSION

Compared to ISB, CCB results in equivalent postoperative analgesia while circumventing the risk of hemidiaphragmatic paralysis. Further confirmatory trials are required. Future studies should also investigate if CCB can provide surgical anesthesia for arthroscopic shoulder surgery.

CLINICAL TRIALS REGISTRATION

NCT03411343.

Antioxidant capacity and immunomodulatory effects of a chrysolaminarin-enriched extract in Senegalese sole

The microalgae are an important source of bioactive molecules including β-glucans that can be used as immunostimulants in aquaculture. In the present study, the antioxidant capacity, cytotoxicity and immunomodulatory activity of a chrysolaminarin-enriched extract obtained from the diatom Phaeodactylum tricornutum was evaluated. The extract showed a higher total antioxidant activity as determined by ORAC and FRAP assays and a lower DPPH scavenging activity than particulate yeast-β-glucan. The cytotoxicity test indicated that extract concentrations higher than 0.01% w/v could impair cell viability of human dermal fibroblasts. To evaluate the immunomodulatory activity, juvenile soles were intraperitoneally injected with the chrysolaminarin-enriched extract suspended in coconut oil (1 mg/fish) followed by a reinjection at 7 days. A sham group injected with the carrier solution was maintained as a negative control. Cumulated mortality of fish injected with the chrysolaminarin-enriched extract was 29.4% after six days and no mortality was recorded after extract reinjection. Expression analyses of fifteen genes related to the innate immune system in kidney, spleen and intestine showed temporal and organ-specific responses. A rapid (2 days post-injection; dpi) and strong induction of the pro-inflammatory il1b and the antimicrobial peptide hamp1 in the three immunological organs, the hsp90aa in kidney and spleen, irf3 in intestine and c3 in spleen was observed indicating a potent inflammatory response. The recovery of steady-state levels for all activated genes at 5 dpi, and the down-regulation of c-lectin receptor as well as some interferon-related genes (ifn1, irf1, irf3, irf8, irf9 and mx) in kidney and cxc10 in spleen indicated that the soles were able to activate a homeostatic response against the β-glucan insult. The reinjection of the chrysolaminarin-enriched extract did not activate a new inflammatory response but reduced the mRNA levels of hsp90aa and irf3 indicating that soles developed some resistance to β-glucans. Overall, these results reveal this enriched extract as a novel and potent source of β-glucans with antioxidant and immunomodulatory capacity suitable for immunostimulation in aquaculture.

De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray

Background

Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution.

Results

A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB.

Conclusions

Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-952) contains supplementary material, which is available to authorized users.

Distribution of red-spotted grouper nervous necrosis virus (RGNNV) antigens in nervous and non-nervous organs of European seabass(Dicentrarchus labrax) during the course of an experimental challenge

The distribution of red-spotted grouper nervous necrosis virus (RGNNV) antigens was examined by immunohistochemistry in the nervous and non-nervous organs of juvenile European seabass (Dicentrarchus labrax) during the course of an intramuscular infection. Histological changes resulting from the infection were evaluated from 3 days to 2 months post-infection. The specific antibody response was also studied 2 months post-challenge. Viral proteins were present throughout the experimental period in the retina (inner nuclear layer, ganglion layer, outer limiting membrane, and outer plexiform layer), brain (cerebellum and tectum opticum), and liver (hepatocytes and endothelial cells). These proteins were also observed in the renal tubular cells, white pulp of spleen, and in fibroblasts and cartilage of caudal fin. This is the first report of RGNNV proteins appearing in these organs, where the immunostaining was only detected at certain sampling times after the onset of mortality. Brain and retina of virus-exposed fish showed high levels of vacuolation, while accumulation of fat vacuoles was observed in the liver. RGNNV infection also induced a specific antibody response as measured by an ELISA. In summary, this is the first study demonstrating the presence of viral proteins in cells of caudal fin, kidney and spleen of European seabass.

Developmental origins of a novel gut morphology in frogs

Phenotypic variation is a prerequisite for evolution by natural selection, yet the processes that give rise to the novel morphologies upon which selection acts are poorly understood. We employed a chemical genetic screen to identify developmental changes capable of generating ecologically relevant morphological variation as observed among extant species. Specifically, we assayed for exogenously applied small molecules capable of transforming the ancestral larval foregut of the herbivorous Xenopus laevis to resemble the derived larval foregut of the carnivorous Lepidobatrachus laevis. Appropriately, the small molecules that demonstrate this capacity modulate conserved morphogenetic pathways involved in gut development, including downregulation of retinoic acid (RA) signaling. Identical manipulation of RA signaling in a species that is more closely related to Lepidobatrachus, Ceratophrys cranwelli, yielded even more similar transformations, corroborating the relevance of RA signaling variation in interspecific morphological change. Finally, we were able to recover the ancestral gut phenotype in Lepidobatrachus by performing a reverse chemical manipulation to upregulate RA signaling, providing strong evidence that modifications to this specific pathway promoted the emergence of a lineage-specific phenotypic novelty. Interestingly, our screen also revealed pathways that have not yet been implicated in early gut morphogenesis, such as thyroid hormone signaling. In general, the chemical genetic screen may be a valuable tool for identifying developmental mechanisms that underlie ecologically and evolutionarily relevant phenotypic variation.

Total substitution of fish oil by vegetable oils in Senegalese sole (Solea senegalensis) diets: effects on fish performance, biochemical composition, and expression of some glucocorticoid receptor-related genes

To study the substitution of fish oil by vegetable oils in fish diets, juveniles Senegalese sole (Solea senegalensis) were fed diets (56 % crude protein, 12 % crude lipid) containing either linseed (100LO) or soybean (100SO) oils in comparison with a 100 % fish oil-based diet (100FO) for 90 days. Samples of muscle, liver, and intestine were collected for biochemical analysis and for glucocorticoid receptor-related genes, including GR1 and GR2, and the associated heat shock proteins HSP70, HSP90AA, and HSP90AB. Besides, basal levels of plasma cortisol were also determined. After the feeding period, a stress test, consisting on 5 min of net chasing, was applied to a selected population of each dietary group. Total replacement of fish oil by vegetable oils did not induced changes in fish growth and performance, but affected fatty acid profile of muscle, liver, and intestine, reflecting those tissues the characteristic fatty acids of each type of dietary oil. A tendency to conserve the ARA/EPA ratio could be observed in the different tissues, despite of the level of these fatty acids in diet. Chasing stress induced an increase of muscle GR1 and a reduction in intestinal GR2 relative expressions at any of the experimental diets assayed. In liver, chasing stress induced an increase in both GR1 and GR2 gene expression in fish fed fish oil diets. Similarly, chasing stress induced an increase of muscle HSP70 and decrease of HSP90AB in liver at any of the experimental diet assayed. Besides, vegetable oils decreased the expression of HSP70 in intestine, being the relative expression of liver HSP90AA increased by the inclusion of linseed oil in the diet, at any of the experimental conditions assayed.

Dexamethasone modulates expression of genes involved in the innate immune system, growth and stress and increases susceptibility to bacterial disease in Senegalese sole (Solea senegalensis Kaup, 1858)

Cortisol, the main glucocorticoid in fish, undertakes pleiotropic biological effects in response to stressors to maintain homeostasis. It can exert several actions on the immune system, growth and cellular metabolism, establishing a fine-tune regulation stress response and cross-talk interactions with other regulatory pathways. In this study, we investigated a causal relationship between high levels of glucocorticoids and susceptibility to pathogens and modification of gene expression profiles in Senegalese sole. For this purpose, we carried out two experiments using post-metamorphic individuals (21 days after hatching) that were exposed to dexamethasone (DXM), a potent glucocorticoid, in order to mimic cortisol effects. We quantified transcript levels of a wide set of genes involved in innate immune system (g-type lysozyme and hepcidin (hamp1)), HPI axis (crf, crfbp, pomcα, pomcβ, gr1 and gr2), HPT axis (tgb), cellular stress defense system (hsp70 and hsp90aa), GH/IGF axis (igf-I and igf-Ir) and the neuropeptide trh. Short-term exposure to 0.1, 1 and 10 ppm DXM provoked a reduction of pomcβ transcripts and an increase of crfbp mRNAs in a dose-dependent manner at 48 and 72 h after treatment. Moreover, g-type lysozyme transcript levels decreased significantly at 72 h whereas hamp1 mRNA levels increased at 48 h after exposure. Long-term DXM treatment (10 ppm DXM) affected negatively weight of soles (~20% lower than controls). Moreover, reduced mRNA levels were observed for pomcβ after 1 week and igf-I and hamp1 after 2 weeks. In contrast, crfbp and crf increased mRNA levels after 2 weeks. hsp70 exhibited a dual response increasing transcript levels at 1 week after treatment and reducing thereafter. No significant changes in gene expression were observed at any time during this study for tgb, trh, hsp90aa, pomcα, gr1 and gr2. Finally, a challenge experiment using the pathogen Photobacterium damselae subsp piscicida confirmed earlier and higher mortalities in DXM-treated animals. Taken together, these data indicate that a prolonged exposure to DXM increases the susceptibility to pathogens and reduces growth. Moreover, DXM can trigger a wide cellular response modulating the expression of genes involved in the innate immune system, HPI and GH/IGF axes as well as cellular stress defense. These results are highly valuable to evaluate responses associated to aquaculture stressful conditions and discriminate specific glucocorticoid-mediated effects.

Genomic characterization, phylogeny and gene regulation of g-type lysozyme in sole (Solea senegalensis)

The g-type lysozyme is a key protein of the innate immune system to fight bacterial infections. In this study we cloned and characterized the gene encoding for g-type lysozyme in Senegalese sole (Solea senegalensis). The deduced amino acid sequence comprised 195 residues containing the three conserved catalytic residues and two cysteines. A BAC analysis revealed that the gene is structured in 5 exons and 4 introns. Also, two polyadenylation signals that generate two cDNAs differing in 3'-UTR length were detected. Promoter analysis showed the presence of the main cis-acting elements involved in the transcriptional regulation of the gene. At genomic level, the g-type lysozyme was associated with mucolipin 1 and the peptidoglycan recognition protein 2 conforming a cluster of antidefensive genes with a well-conserved synteny across Percomorpha. FISH analysis using the BAC clone revealed a single hybridization signal located in an acrocentric chromosome pair. The phylogenetic analysis confirmed that the g-type lysozyme represents a complex group in fish that has been shaped by gene duplications and diversification with several positions under Darwinian selection. Expression analysis in juvenile tissues indicated that transcript levels were higher in gills, spleen and heart. During development, gene expression activated just at the beginning of metamorphosis, increasing progressively until climax. Hormonal treatments demonstrated that this gene was regulated positively by thyroid hormones during development and negatively by dexamethasone. In contrast, no response was observed after all-trans retinoic acid or 4-diethylaminobenzaldehyde treatments. Finally, treatments using lipopolysaccharide, lipoteichoic acid, peptidoglycan, zymosan and poly(I:C) activated gene expression in a time- and tissue-specific manner. Taken together, data indicate that g-type lysozyme is a high evolutionary conserved gene that diversified to adapt to changing environment and pathogen conditions. Gene expression can be activated by diverse pathogen stimuli and modulated by physiological factors with important consequences for the aquaculture of this species.

Molecular characterization and transcriptional regulation of the sodium-dependent vitamin C transporter genes (slc23a1 and slc23a2) in a teleost fish, the Senegalese sole (Solea senegalensis)

Vitamin C (ascorbic acid, AA) is an antioxidant that acts as a free radical scavenger and cofactor for several important enzymatic reactions, thus being important for normal cellular functions, growth and development. Accumulation of AA in cells depends on two types of sodium-dependent vitamin C transporters (SVCTs), designed as SVCT1 and SVCT2. In human, they are the products of SLC23A1 and SLC23A2 genes, respectively. In the present work, the molecular cloning of the cDNAs corresponding to slc23a1 and slc23a2 in a teleost fish, the Senegalese sole (Solea senegalensis Kaup, 1858) is first described. Sequence analysis of the predicted polypeptides revealed a conserved topology with those of mammals with important motifs involved in structure and function, being also present in svct1 and svct2. Phylogenetic analyses including a range of vertebrate SVCTs suggest that both transporters are the result of an ancient gene duplication event that occurred prior to the divergence of tetrapods and teleosts, which took place 450 million years ago. Expression profiles in juvenile tissues and during larval development were analyzed using a real-time PCR approach. In juvenile fish, slc23a1 was strongly expressed in intestine, whereas slc23a2 exhibited a widespread distribution in tissues. Transcripts of both genes were detected at early developmental stages, probably representing mRNAs of maternal origin. A possible regulation by their own substrate was detected after first uptakes of AA from diet in both genes. During metamorphosis, both slc23a1 and slc23a2 were down-regulated, the former in a thyroid hormone (TH) dependent way. This pattern coincided with a significant reduction in the AA content of larvae during metamorphosis. These results are interpreted in a physiological context of general reduction in the metabolism of metamorphic larvae. Data presented here provide the first step toward a better understanding of the physiological role of SVCTs in teleost fish.

Tissue distribution of Red Spotted Grouper Nervous Necrosis Virus (RGNNV) genome in experimentally infected juvenile European seabass (Dicentrarchus labrax)

The distribution of viral genome in the tissues of juvenile European seabass (Dicentrarchus labrax) during the course of a Red Spotted Grouper Nervous Necrosis Virus (RGNNV) infection has not yet been described. The present study addresses this and indicates which target organs may be involved in viral replication. This information should enable more accurate detection of virus in asymptomatic carriers, and in turn help to control the spread of the disease. The aim of this study was to examine the pattern of expression of viral genomic segments RNA1 and RNA2, using two absolute real-time PCRs (RT-qPCR), over the course of a RGNNV infection after administering the virus by intramuscular injection. In situ hybridization was also used to locate the RNA2 viral segment in different organs throughout the infection. The experimental challenge provoked an acute form of viral nervous necrosis (VNN), with a resulting cumulative mortality of 37%. The RT-qPCRs designed allowed the detection of both genomic segments in all the organs tested (nervous and non-nervous tissues) at all sampling times examined. The highest viral RNA copy number was found in eyes, although viral replication appeared to begin in the brain. Viral replication was also recorded in pooled internal organs and in caudal fin. However, the increase in the viral RNA copy number in these organs did not result in an increased viral titre, which may indicate that a productive infection does not take place in non-nervous tissues, possibly due to a failure in a viral post-replication step.

Molecular characterization and gene expression of thyrotropin receptor (TSHR) and a truncated TSHR-like in Senegalese sole

Thyroid hormones (THs) play a key role in larval development, growth and metamorphosis in flatfish. Their synthesis is tightly regulated by the hypothalamic-pituitary-thyroid axis. Thyroid-stimulating hormone receptor (TSHR) is a key protein in the control of thyroid function stimulating TH synthesis after binding its ligand, the thyrotropin. In teleost fish, numerous reports have associated the TSHR with gametogenesis. However, little information about its role during larval development is available. In this study, we report the cloning of two different cDNAs with high similarity to TSHR. Phylogenetic analysis clustered both cDNAs separately. One of them (referred to TSHR) grouped with TSHR orthologs in tetrapods and teleost fish and possessed the three typical conserved domains and regulatory motifs. The second receptor (referred to as TSHRtr-like) represented a novel truncated cDNA bearing the extracellular and part of the transmembrane domain. TSHRtr-like orthologs were only found in teleosts, which suggests that it could have appeared after fish-specific 3R genome duplication. Expression profiles of both genes are analyzed in juvenile tissues and during larval development using a real-time PCR approach. In juvenile fish, TSHR and TSHRtr-like are expressed ubiquitously although transcript levels varied between organs. In both cases, the highest mRNAs levels are detected in brain. During larval development, both genes are expressed to a high level during the first stages (2-3days after hatching) reducing progressively their abundance in the whole larvae during metamorphosis. This reduction in mRNA abundance is more accentuated for the TSHRtr-like gene. To evaluate the possible regulation of both receptors by T4 during sole metamorphosis, larvae are exposed to the goitrogen thiourea (TU). Only TSHRtr-like modifies its expression, increasing its transcripts at 11days after treatment. Moreover, adding exogenous T4 hormone to TU-treated larvae restores the TSHRtr-like steady-state levels similar to the untreated control. Overall, these results demonstrate the existence of two thyrotropin receptors differentially regulated by THs in teleosts.

A combined RT-PCR and dot-blot hybridization method reveals the coexistence of SJNNV and RGNNV betanodavirus genotypes in wild meagre (Argyrosomus regius)

AIMS

To detect the possible coexistence of striped jack nervous necrosis virus (SJNNV) and red-spotted grouper nervous necrosis virus (RGNNV) genotypes in a single fish, a methodology based on the combination of PCR amplification and blot hybridization has been developed and applied in this study.

METHODS AND RESULTS

The degenerate primers designed for the PCR procedure target the T4 region within the capsid gene, resulting in the amplification of both genotypes. The subsequent hybridization of these amplification products with two different specific digoxigenin-labelled probes resulted in the identification of both genotypes separately. The application of the RT-PCR protocol to analyse blood samples from asymptomatic wild meagre (Argyrosomus regius) specimens has shown a 46.87% of viral nervous necrosis virus carriers. The combination of RT-PCR and blot hybridization increases the detection rate up to 90.62%, and, in addition, it has shown the coexistence of both genotypes in 18 out of the 32 specimens analysed (56.25%).

CONCLUSIONS

This study reports the coexistence of betanodaviruses belonging to two different genotypes (SJNNV and RGNNV) in wild fish specimens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report demonstrating the presence of SJNNV and RGNNV genotypes in the same specimen. This study also demonstrates a carrier state in this fish species for the first time.

Detection of infectious pancreatic necrosis virus (IPNV) from asymptomatic redbanded seabream, Pagrus auriga Valenciennes, and common seabream, Pagrus pagrus (L.), using a non-destructive procedure

A non-destructive procedure based on nested RT-PCR and dot-blot hybridization has been developed for the detection of asymptomatic IPNV-carrier fish. The pair of primers designed for RT-PCR amplified a 599-bp fragment of the pVP2 region within the polyprotein gene, resulting in the detection of IPNV genotype III.1. The use of a nested RT-PCR allowed the amplification of IPNV genotypes III.1 and I.2. In addition, a 191-bp probe was designed for hybridization studies used in combination with the nested RT-PCR. The application of the nested RT-PCR to analyse blood samples from asymptomatic redbanded seabream, Pagrus auriga, and common seabream, P. pagrus, specimens showed a 53.1% and 77.8% prevalence of IPNV-carriers, respectively. The combination of nested RT-PCR and dot-blot hybridization increased the detection rates up to 100% for redbanded seabream and 94.4% for common seabream. Therefore, the protocol described in this study is highly sensitive and specific for the detection of IPNV in asymptomatic carrier fish, and, in addition, the results demonstrate the carrier state in two newly cultured sparid species in southern Spain.

Effects of stocking density and feed ration on growth and gene expression in the Senegalese sole (Solea senegalensis): potential effects on the immune response

Stocking density and ration size are two major factors influencing aquaculture production. To evaluate their effects on growth and immune system in Senegalese sole (Solea senegalensis) juveniles, a 2 x 2 experimental design using two rations (1.0% and 0.25% of the total fish biomass) and two different initial stocking densities (7 and 30 kg m(-2)) was performed throughout a 60 days culture period. Soles fed 1.0% showed a higher specific growth rate (SGR) than those fed 0.25% (3.3-fold). No differences in SGR at 60 days were found between densities in spite of reduced values were detected at high density after 20 days (soles fed 0.25%) and 40 days (soles fed 1%) suggesting a compensatory growth. Physiologically, plasma cortisol levels were elevated in soles at high density (45-fold higher than at 7 kg m(-2)) whereas no differences associated to the feeding ration were observed. To assess the effects at a molecular level, the mRNA levels of genes involved in cellular stress (heat shock proteins HSP70 and HSP90), growth (insulin-like growth factors IGF-I, the spliced variants IGF-Ia and IGFI-b, and IGF-II) and innate immune system (g-type lysozyme and hepcidin (HAMP1)) were quantified. No differences in HSP90 expression were detected between densities or rations. In contrast, IGF-I, IGF-Ia and IGF-II showed reduced transcript levels in liver and HSP70 in liver and kidney at high density. Finally, g-type lysozyme and HAMP1 expression was greatly affected by both factors exhibiting an important reduction in the transcript levels at high density and low ration. Overall, our results show that S. senegalensis juveniles might exhibit satisfactory SGR at high density although the high plasma cortisol levels indicate a crowding stress that could negatively affect the expression levels of some of the genes studied.

Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species

Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.

Genomic characterization and gene expression analysis of four hepcidin genes in the redbanded seabream (Pagrus auriga)

Hepcidin antimicrobial peptides (HAMPs) are key molecules of the innate immune system against bacterial infections and in iron metabolism. In this study we report the molecular cloning and genomic characterization of four HAMP genes (referred to as HAMP1, HAMP2, HAMP3 and HAMP4) in the redbanded seabream (Pagrus auriga). All these genes possessed the eight characteristic cysteine residues involved in protein folding. No canonical sequence for convertase-mediated processing of the HAMP3 propeptide was identified. At the genomic level, all four HAMP genes consisted of two introns and three exons. Phylogenetic analysis revealed that HAMPs could group in two main clusters with HAMP2, HAMP3 and HAMP4 belonging to the more complex and diversified HAMP2-like group of acanthopterygians. Quantitation of mRNA levels in adult tissues showed that HAMP1 was ubiquitously expressed, HAMP2 mainly in kidney, spleen and intestine, whereas HAMP3 and HAMP4 in liver. During development, HAMP2 and HAMP3 were expressed at a high level in embryos. Moreover, the expression levels of the four HAMP genes increased between 5 and 15 days after hatching when larvae started external feeding. Induction experiments with lipopolysaccharide revealed significant changes in gene expression of the four HAMP genes in kidney, liver and spleen. However, expression profiles differed in magnitude and time course response. HAMP1 mRNAs increased rapidly in kidney at 1 h p.i. whereas HAMP2 did later at 24 h. Moreover, HAMP4 transcripts increased more than 5000-fold in liver whereas HAMP2 mRNAs dropped significantly in spleen at 3 h p.i. All these data suggest that HAMPs are involved in the response against bacterial infections although additional functions in iron regulation and embryogenesis in fish should be considered.

Molecular characterization, gene expression and transcriptional regulation of thyroid hormone receptors in Senegalese sole

Thyroid hormones (THs) play a key role in larval development, growth and metamorphosis in flatfish. Their genomic effects are mediated by thyroid hormone receptors (TRs). In this study, cDNAs encoding for TRalphaA, TRalphaB, and TRbeta have been sequenced in Senegalese sole (Soleasenegalensis). Main domains and conserved motifs were identified. Also, a truncated TRalphaB isoform (referred to as TRalphaBtr) and a spliced TRbeta variant (referred to as TRbetav) were detected. A phylogenetic analysis grouped both TRalpha and TRbeta genes into two separate clusters with their fish and mammalian counterparts. Expression profiles during larval development and in juvenile tissues were analyzed using a real-time PCR approach. In juvenile fish, TRalphaA, TRalphaB, TRbetav, and TRbeta showed distinct transcript levels in tissues. During metamorphosis, only TRbetav and TRbeta modified their mRNA levels in a similar way to the T4 contents. To evaluate the possible regulation of TRs by their cognate ligand T4 during sole metamorphosis, larvae were exposed to the goitrogen thiourea (TU). TRbeta transcripts decreased significantly at 11 and 15 days after treatment. Moreover, adding exogenous T4 hormone to TU-treated larvae restored the steady-state levels or even increased TRbeta and TRbetav mRNAs with respect to the untreated control. Overall, these results demonstrate that TRbeta transcription is up-regulated by THs playing a major role during metamorphosis in Senegalese sole.

Translational machinery of senegalese sole (Solea senegalensis Kaup) and Atlantic halibut (Hippoglossus hippoglossus L.): comparative sequence analysis of the complete set of 60s ribosomal proteins and their expression

Ribosomal proteins (RPs) comprise a large set of highly evolutionarily conserved proteins that are often over-represented in complementary DNA libraries. They have become very useful markers in comparative genomics, genome evolution, and phylogenetic studies across taxa. In this study, we report the sequences of the complete set of 60S RPs in Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus), two commercially important flatfish species. Amino-acid sequence comparisons of the encoded proteins showed a high similarity both between these two flatfish species and with respect to other fish and human counterparts. Expressed sequence tag analysis revealed the existence of paralogous genes for RPL3, RPL7, RPL41, and RPLP2 in Atlantic halibut and RPL13a in Senegalese sole as well as RPL19 and RPL22 in both species. Phylogenetic analysis of paralogs revealed distinct evolutionary histories for each RP in agreement with three rounds of genome duplications and lineage-specific duplications during flatfish evolution. Steady-state transcript levels for RPL19 and RPL22 RPs were quantitated during larval development and in different tissues of sole and halibut using a real-time polymerase chain reaction approach. All paralogs were expressed ubiquitously although at different levels in different tissues. Most RP transcripts increased coordinately after larval first-feeding in both species but decreased progressively during the metamorphic process. In all cases, expression profiles and transcript levels of orthologous genes in Senegalese sole and Atlantic halibut were highly congruent. The genomic resources and knowledge developed in this survey will be useful for the study of Pleuronectiformes evolution.

Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

Background

The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species.

Results

Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data.

Conclusion

New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.

Molecular characterization, phylogeny, and expression of c-type and g-type lysozymes in brill (Scophthalmus rhombus)

Lysozymes are key proteins of the innate immune system against bacterial infections. In this study we report the molecular cloning and characterization of the c-type and g-type lysozymes in brill (Scophthalmus rhombus). Catalytic and other conserved residues required for functionality were identified. Phylogenetic analysis revealed distinct evolutionary histories for each lysozyme type. Expression profiles of both lysozyme genes were studied in juvenile tissues using a real-time PCR approach. c-Type lysozyme was expressed mainly in stomach and liver, whereas the g-type was detected in all tissues with highest mRNA levels observed in the spleen. Induction experiments revealed that g-type transcripts increased significantly in head kidney after lipopolysaccharide (25- and 23-fold at 12 and 24h, respectively) and Photobacterium damselae subsp. piscicida (17-fold at 24h) treatments. In contrast, no induction was observed for c-type lysozyme. All these data suggest that g-type lysozyme is involved in the response against bacterial infections, whereas c-type lysozyme may also play a role in digestion.

Molecular characterization and gene expression analysis of insulin-like growth factors I and II in the redbanded seabream, Pagrus auriga: transcriptional regulation by growth hormone

Insulin-like growth factors (IGFs) I and II (IGF-I and IGF-II) play important roles in fish growth and development. The present study was aimed at isolating cDNAs encoding both IGF-I and IGF-II in the redbanded seabream (Pagrus auriga), and at measuring relative gene expression levels in different organs and during larval development. A fragment of 1321 nucleotides coding for IGF-I was cloned from liver using 3' and 5' RACE techniques. It included an open reading frame of 558 nucleotides, encoding a 185-amino acid preproIGF-I. With respect to IGF-II, a fragment of 1544 nucleotides was cloned as well. The open reading frame spanned 648 nucleotides, rendering a 215-amino acid preproIGF-II. The deduced mature 67-amino acid IGF-I and 70-amino acid IGF-II exhibited high sequence identities with their corresponding fish counterparts, ranging between 88.6-100% and 79.1-98.5%, respectively. Real-time PCR showed the highest IGF-I transcripts in liver ( approximately 200-fold higher than head-kidney). In contrast, the highest IGF-II mRNAs were detected in gills and heart ( approximately 16-fold higher than head-kidney). In addition, both IGFs exhibited different gene expression patterns during larval development suggesting that their expression is developmentally regulated. IGF-I reached the highest expression levels at 18 days after hatching (11.6-fold higher than 1 day after hatching), whereas IGF-II expression did not change significantly. Both hepatic IGF-I and IGF-II mRNA levels increased sharply (3.1- and 19-fold higher than control, respectively) 3 h after injection of porcine growth hormone, but remained unchanged from 6 to 24 h after treatment. Our results are discussed in relation to those previously reported for other bony fish.

Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR

Background

Flatfish metamorphosis involves major physiological and morphological changes. Due to its importance in aquaculture and as a model for developmental studies, some gene expression studies have focused on the understanding of this process using quantitative real-time PCR (qRT-PCR) technique. Therefore, adequate reference genes for accurate normalization are required.

Results

The stability of 12 potential reference genes was examined during larval development in Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus) to determine the most suitable genes for qRT-PCR analysis. Transcription levels of genes encoding β-Actin (ACTB), glyceraldehyde-3P-dehydrogenase (GAPDH), annexin A2 (ANXA2), glutathione S-transferase (GST), ornithine decarboxylase (ODC), hypoxanthine phosphoribosyltransferase (HPRT1), ubiquitin (UBQ), elongation factor 1 alpha (eEF1A1), 18S ribosomal RNA, and the ribosomal proteins S4 (RPS4) and L13a (RPL13a) were quantitated. Two paralogous genes for ACTB were analyzed in each of both flatfish species. In addition, two paralogous genes for GAPDH were studied in Senegalese sole. RPL13a represented non-orthologous genes between both flatfish species. GeNorm and NormFinder analyses for expression stability revealed RPS4, UBQ and eEF1A1 as the most stable genes in Senegalese sole, Atlantic halibut and in a combined analysis. In all cases, paralogous genes exhibited differences in expression stability.

Conclusion

This work suggests RPS4, UBQ, and eEF1A1 genes as useful reference genes for accurate normalization in qRT-PCR studies in Senegalese sole and Atlantic halibut larvae. The congruent results between both species in spite of the drastic differences in larval development suggest that selected housekeeping genes (HKGs) could be useful in other flatfish species. However, the finding of paralogous gene copies differentially expressed during development in some HKGs underscores the necessity to identify orthologous genes.