Identification of potential CD8+ epitopes in pp62 polyprotein of African swine fever virus using computational immunology.

The highly infectious African swine fever virus (ASFV) is currently the only known DNA arbovirus within the Asfarviridae family which primarily infects domestic pigs and wild boars. African swine fever (ASF) leads to a mortality rate of up to 100% which has caused massive socio-economic losses worldwide. Previous research indicates that ASFV's virulence can be attributed to polyprotein pp62, which plays a crucial role in viral assembly and core maturation. This particular study utilized in silico analysis to identify highly conserved cytotoxic T-cell epitopes in pp62 that can potentially serve as key components for future ASFV vaccines. To achieve this, the researchers retrieved, clustered, and aligned the peptide sequences of pp62. Subsequently, the aligned sequences were analyzed to identify epitopes that bind promiscuously to the swine major histocompatibility complex I (MHC I) alleles and exhibiting MHC IC50 values < 500 nM. Additionally, peptide sequences with positive proteasome and TAP scores were considered. Potential cross-reactivity was assessed by comparing the peptide sequences against available proteome sequences of Sus scrofa domesticus in various databases. Furthermore, molecular docking was conducted to evaluate the binding of candidate epitopes with swine leukocyte antigen-1*0401 (SLA-1*0401). The dissociation constants, binding energies, root mean square deviation, and root mean square fluctuation values for the SLA-epitope complexes were compared with a positive reference. In the course of the study, 21 highly conserved CD8+ epitopes were identified, out of which four were further assessed for their potential immunogenicity. The results demonstrated that the highly conserved CD8+ epitopes discovered in this study are promising for integration into future ASFV vaccine formulations. As preliminary data, it is anticipated that these findings will subsequently undergo in vitro and in vivo studies in the future.

Diving into the vertical dimension of elasmobranch movement ecology.

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements.

Biomechanical Analysis of the Slow-Twitch (Red) Muscle Force Transmission Pathways in Tunas.

In tunas, the slow-twitch red muscle, which has an elevated temperature, powers thunniform locomotion, a stiff-bodied swimming style. The anatomical placement and operating temperatures of red muscle vary widely among teleosts: in tunas, the red muscle is located centrally in the body, adjacent to the spine, and maintains an elevated temperature. In the majority of ectothermic teleosts, red muscle is located laterally in the body, adjacent to the skin, and operates at ambient temperature. The specialized physiology and biomechanics of red muscle in tunas are often considered important adaptations to their high-performance pelagic lifestyle; however, the mechanics of how muscular work is transmitted to the tail remains largely unknown. The red muscle has a highly pennate architecture and is connected to the spine through a network of bones (epicentral bones) and long tendons (posterior oblique tendons). The network of long tendons has been hypothesized to enhance the power transmitted to the tail. Here, we investigate the morphology and biomechanics of the tuna's red muscle and tendons to determine whether elasticity is exploited to reduce the cost of transport, as is the case in many terrestrial vertebrates. To address this question, we evaluate two hypotheses: (1) tendons stretch during red-muscle-actuated swimming and (2) tendons comprise the primary load transmission pathway from the red muscle to the spine. To evaluate these hypotheses, we measured the mechanical properties of the posterior oblique tendons and performed novel dissections to estimate the peak force that the red muscle can generate. The force-generating capacity of the red muscle is calculated to be much greater than the load-bearing capacity of the posterior oblique tendons. Thus, the long tendons likely stretch under force from the red muscle, but they are not strong enough to be the primary force transmission pathway. These results suggest that other pathways, such as serial load transmission through the red muscle myomeres to the great lateral tendon and/or the anterior oblique tendons to the skin, transmit appreciable force to the tail.

Direct measurement of swimming and diving kinematics of giant Atlantic bluefin tuna (Thunnus thynnus).

Tunas possess a range of physiological and mechanical adaptations geared towards high-performance swimming that are of considerable interest to physiologists, ecologists and engineers. Advances in biologging have provided significant improvements in understanding tuna migrations and vertical movement patterns, yet our understanding of the locomotion and swimming mechanics of these fish under natural conditions is limited. We equipped Atlantic bluefin tuna (Thunnus thynnus) with motion-sensitive tags and video cameras to quantify the gaits and kinematics used by wild fish. Our data reveal significant variety in the locomotory kinematics of Atlantic bluefin tuna, ranging from continuous locomotion to two types of intermittent locomotion. The tuna sustained swimming speeds in excess of 1.5 m s-1 (0.6 body lengths s-1), while beating their tail at a frequency of approximately 1 Hz. While diving, some descents were entirely composed of passive glides, with slower descent rates featuring more gliding, while ascents were primarily composed of active swimming. The observed swimming behaviour of Atlantic bluefin tuna is consistent with theoretical models predicting such intermittent locomotion to result in mechanical and physiological advantages. Our results confirm that Atlantic bluefin tuna possess behavioural specializations to increase their locomotory performance, which together with their unique physiology improve their capacity to use pelagic and mesopelagic habitats.

Temperature dependent pre- and postprandial activity in Pacific bluefin tuna (Thunnus orientalis).

Bluefin tunas are highly specialized fish with unique hydrodynamic designs and physiological traits. In this study, we present results in a captive population that demonstrate strong effects of ambient temperature on the tail beat frequency and swimming speed of a pelagic fish in both pre- and post-prandial states. We measured the responses of a ram ventilator, the Pacific bluefin tuna (Thunnus orientalis), after digestion of a meal to explore the impacts of the metabolic costs of digestion on behavior and respiration. A combination of respirometry, physiological biologging of visceral temperatures, and activity monitoring with accelerometry were used to explore the metabolic costs of digestion and the impacts on ventilation and swimming speed. Experiments were conducted at temperatures that are within the metabolic optimum for Pacific bluefin tuna (17 °C), and at a second temperature corresponding to the upper distributional limit of the species in the California Current (24 °C). Warmer temperatures resulted in higher tail-beat frequency and greater elevation of body temperature in pre-prandial Pacific bluefin tuna. Specific dynamic action (SDA) events resulted in a significant postprandial increase in tail-beat frequency of ~0.2 Hz, compared to pre-prandial levels of 1.5 Hz (17 °C) and 1.75 Hz (24 °C), possibly resulting from ventilatory requirements. Data of fish exercised in a swim-tunnel respirometer suggest that the observed increase in tail-beat frequency comprise 5.5 and 6.8% of the oxygen demand during peak SDA at 24 °C and 17 °C respectively. The facultative increase in swimming speed might increase oxygen uptake at the gills to meet the increasing demand by visceral organs involved in the digestive process, potentially decreasing the available energy of each meal for other metabolic processes, such as growth, maturation, and reproduction. We hypothesize that these post-prandial behaviors allow tuna to evacuate their guts more quickly, ultimately permitting fish to feed more frequently when prey is available.

Sediment structure and physicochemical changes following tidal inundation at a large open coast managed realignment site.

Managed realignment (MR) schemes are being implemented to compensate for the loss of intertidal saltmarsh habitats by breaching flood defences and inundating the formerly defended coastal hinterland. However, studies have shown that MR sites have lower biodiversity than anticipated, which has been linked with anoxia and poor drainage resulting from compaction and the collapse of sediment pore space caused by the site's former terrestrial land use. Despite this proposed link between biodiversity and soil structure, the evolution of the sediment sub-surface following site inundation has rarely been examined, particularly over the early stages of the terrestrial to marine or estuarine transition. This paper presents a novel combination of broad- and intensive-scale analysis of the sub-surface evolution of the Medmerry Managed Realignment Site (West Sussex, UK) in the three years following site inundation. Repeated broad-scale sediment physiochemical datasets are analysed to assess the early changes in the sediment subsurface and the preservation of the former terrestrial surface, comparing four locations of different former land uses. Additionally, for two of these locations, high-intensity 3D-computed X-ray microtomography and Itrax micro-X-ray fluorescence spectrometry analyses are presented. Results provide new data on differences in sediment properties and structure related to the former land use, indicating that increased agricultural activity leads to increased compaction and reduced porosity. The presence of anoxic conditions, indicative of poor hydrological connectivity between the terrestrial and post-inundation intertidal sediment facies, was only detected at one site. This site has experienced the highest rate of accretion over the terrestrial surface (ca. 7 cm over 36 months), suggesting that poor drainage is caused by the interaction (or lack of) between sediment facies rather than the former land use. This has significant implications for the design of future MR sites in terms of preparing sites, their anticipated evolution, and the delivery of ecosystem services.

The effect of temperature on postprandial metabolism of yellowfin tuna (Thunnus albacares).

Specific dynamic action (SDA), the increase in metabolic expenditure associated with consumption of a meal, represents a substantial portion of fish energy budgets and is highly influenced by ambient temperature. The effect of temperature on SDA has not been studied in yellowfin tuna (Thunnus albacares, Bonnaterre 1788), an active pelagic predator that occupies temperate and subtropical waters. The energetic cost and duration of SDA were calculated by comparing routine and post-prandial oxygen consumption rates. Mean routine metabolic rates in yellowfin tuna increased with temperature, from 136 mg O2 kg(-1)h(-1) at 20 °C to 211 mg O2 kg(-1)h at 24 °C. The mean duration of SDA decreased from 40.2h at 20 °C to 33.1h at 24 °C, while mean SDA coefficient, the percentage of energy in a meal that is consumed during digestion, increased from 5.9% at 20 °C to 12.7% at 24 °C. Digestion in yellowfin tuna is faster at a higher temperature but requires additional oxidative energy. Enhanced characterization of the role of temperature in SDA of yellowfin tuna deepens our understanding of tuna physiology and can help improve management of aquaculture and fisheries.

Exposure to Deepwater Horizon weathered crude oil increases routine metabolic demand in chub mackerel, Scomber japonicus.

During the 2010 Deepwater Horizon incident, the continuous release of crude oil from the damaged Macondo 252 wellhead on the ocean floor contaminated surface water habitats for pelagic fish for more than 12weeks. The spill occurred across pelagic, neritic and benthic waters, impacting a variety of ecosystems. Chemical components of crude oil are known to disrupt cardiac function in juvenile fish, and here we investigate the effects of oil on the routine metabolic rate of chub mackerel, Scomber japonicus. Mackerel were exposed to artificially weathered Macondo 252 crude oil, prepared as a Water Accommodated Fraction (WAF), for 72 or 96h. Routine metabolic rates were determined pre- and post-exposure using an intermittent-flow, swim tunnel respirometer. Routine energetic demand increased in all mackerels in response to crude oil and reached statistical significance relative to unexposed controls at 96h. Chemical analyses of bile from exposed fish revealed elevated levels of fluorescent metabolites, confirming the bioavailability of polycyclic aromatic hydrocarbons (PAHs) in the exposure WAF. The observed increase in metabolic demand is likely attributable to the bioenergetic costs of contaminant detoxification. These results indicate that short-term exposure (i.e. days) to oil has sub-lethal toxicity to mackerel and results in physiological stress during the active spill phase of the incident.

Hearing thresholds of swimming Pacific bluefin tuna Thunnus orientalis.

Pacific bluefin tuna (Thunnus orientalis) is a highly migratory, commercially valuable species potentially vulnerable to acoustic noise generated from human activities which could impact behavior and fitness. Although significant efforts have been made to understand hearing abilities of fishes, the large size and need to continuously swim for respiration have hindered investigations with tuna and other large pelagic species. In this study, Pacific bluefin tuna were trained to respond to a pure tone sound stimulus ranging 325-800 Hz and their hearing abilities quantified using a staircase psychophysical technique. Hearing was most sensitive from 400 to 500 Hz in terms of particle motion (radial acceleration -88 dB re 1 m s(-2); vertical acceleration -86 dB re 1 m s(-2)) and sound pressure (83 dB re 1 µPa). Compared to yellowfin tuna (Thunnus albacares) and kawakawa (Euthynnus affinis), Pacific bluefin tuna has a similar bandwidth of hearing and best frequency, but greater sensitivity overall. Careful calibration of the sound stimulus and experimental tank environment, as well as the adoption of behavioral methodology, demonstrates an experimental approach highly effective for the study of large fish species in the laboratory.

CD8+DR+ T-Cells and C3 Complement Serum Concentration as Potential Biomarkers in Thrombotic Antiphospholipid Syndrome.

Purpose. To assess complement factors and T lymphocyte activation subset abnormalities in patients with thrombotic antiphospholipid syndrome (APS) as potential biomarkers for development of clinical complications. Methods. We assessed C3, C4, factor B concentrations (nephelometry), complement haemolytic functional activity (CH100, radial immune diffusion), and the activation status of CD4+ and CD8+ T-cells (three-colour flow cytometry) in patients with thrombotic APS. Antiphospholipid (aPL) positive patients without APS-related clinical criteria, systemic lupus erythematosus (SLE) patients, and healthy individuals were evaluated as controls. A clinical followup was performed to assess the potential relationship between the immunological parameters and development of APS-related complications. Results. Lower concentrations of C3 and higher levels of CD8+DR+ cells were risk factors for development of APS-related complications during followup, including rethrombosis and neuropsychiatric symptoms. Patients with diagnosed thrombotic APS had significantly lower levels of C3, C4, and CH100 as well as higher percentages of activated CD4+DR+ and of CD8+DR+ T-cells than healthy controls but similar to that observed in autoimmune disease controls. Conclusion. Lower C3 and C4 complement levels and higher percentages of CD8+DR+ T-cells were observed in thrombotic APS patients. The potential role of these abnormalities as biomarkers of clinical outcome warrants further evaluation in a multicenter study.

Growth and maximum size of tiger sharks (Galeocerdo cuvier) in Hawaii.

Tiger sharks (Galecerdo cuvier) are apex predators characterized by their broad diet, large size and rapid growth. Tiger shark maximum size is typically between 380 & 450 cm Total Length (TL), with a few individuals reaching 550 cm TL, but the maximum size of tiger sharks in Hawaii waters remains uncertain. A previous study suggested tiger sharks grow rather slowly in Hawaii compared to other regions, but this may have been an artifact of the method used to estimate growth (unvalidated vertebral ring counts) compounded by small sample size and narrow size range. Since 1993, the University of Hawaii has conducted a research program aimed at elucidating tiger shark biology, and to date 420 tiger sharks have been tagged and 50 recaptured. All recaptures were from Hawaii except a single shark recaptured off Isla Jacques Cousteau (24°13'17″N 109°52'14″W), in the southern Gulf of California (minimum distance between tag and recapture sites  =  approximately 5,000 km), after 366 days at liberty (DAL). We used these empirical mark-recapture data to estimate growth rates and maximum size for tiger sharks in Hawaii. We found that tiger sharks in Hawaii grow twice as fast as previously thought, on average reaching 340 cm TL by age 5, and attaining a maximum size of 403 cm TL. Our model indicates the fastest growing individuals attain 400 cm TL by age 5, and the largest reach a maximum size of 444 cm TL. The largest shark captured during our study was 464 cm TL but individuals >450 cm TL were extremely rare (0.005% of sharks captured). We conclude that tiger shark growth rates and maximum sizes in Hawaii are generally consistent with those in other regions, and hypothesize that a broad diet may help them to achieve this rapid growth by maximizing prey consumption rates.

Intravenous immunoglobulin treatment increased live birth rate in a Spanish cohort of women with recurrent reproductive failure and expanded CD56(+) cells.

PROBLEM: Natural killer (NK, CD3(-)CD56(+)/CD16(+)) and NKT-like cells (CD3(+)CD56(+)/CD16(+)) activity is considered among the key factors for reproductive success. In the absence of immunological screening, beneficial effects of intravenous immunoglobulin (IVIG) in preventing recurrent reproductive failure (RRF) have not been reported. Here, we analyse the IVIG influence on pregnancy success in women with RRF and circulating NK or/and NKT-like cells expansion. METHOD OF STUDY: One hundred fifty-seven women with previous recurrent miscarriage and/or recurrent implantation failure after in vitro fertilization were consecutively studied. Sixty-four patients with CD56(+) cell expansion, no apparent underlying disease and who maintained their desire to conceive were selected. Forty of them received IVIG during pregnancy. RESULTS: Overall, the clinical pregnancy rate for the women under IVIG therapy was 92.5% and the live birth rate was 82.5%. Significantly lower pregnancy and live birth rates (25% and 12.5%, respectively) were observed for the patients with recurrent pregnancy loss and NK/NKT-like cells expansion without IVIG. After three cycles of IVIG, NK cell percentages decreased significantly and these values persisted throughout gestation. CONCLUSION: Intravenous immunoglobulin therapy for women with RRF and NK or NKT-like cell expansion was a safe and beneficial therapeutic strategy that associated with high clinical pregnancy and live birth rates.

The shark assemblage at French Frigate Shoals atoll, Hawai'i: species composition, abundance and habitat use.

Empirical data on the abundance and habitat preferences of coral reef top predators are needed to evaluate their ecological impacts and guide management decisions. We used longline surveys to quantify the shark assemblage at French Frigate Shoals (FFS) atoll from May to August 2009. Fishing effort consisted of 189 longline sets totaling 6,862 hook hours of soak time. A total of 221 sharks from 7 species were captured, among which Galapagos (Carcharhinus galapagensis, 36.2%), gray reef (Carcharhinus amblyrhynchos, 25.8%) and tiger (Galeocerdo cuvier, 20.4%) sharks were numerically dominant. A lack of blacktip reef sharks (Carcharhinus melanopterus) distinguished the FFS shark assemblage from those at many other atolls in the Indo-Pacific. Compared to prior underwater visual survey estimates, longline methods more accurately represented species abundance and composition for the majority of shark species. Sharks were significantly less abundant in the shallow lagoon than adjacent habitats. Recaptures of Galapagos sharks provided the first empirical estimate of population size for any Galapagos shark population. The overall recapture rate was 5.4%. Multiple closed population models were evaluated, with Chao M(h) ranking best in model performance and yielding a population estimate of 668 sharks with 95% confidence intervals ranging from 289-1720. Low shark abundance in the shallow lagoon habitats suggests removal of a small number of sharks from the immediate vicinity of lagoonal islets may reduce short-term predation on endangered monk seal (Monachus schauinslandi) pups, but considerable fishing effort would be required to catch even a small number of sharks. Additional data on long-term movements and habitat use of sharks at FFS are required to better assess the likely ecological impacts of shark culling.

The acute effects of heavy back squats on mechanical variables during a series of bilateral hops.

The purpose of the present study was to investigate the acute effects of performing a heavy resistance exercise (HRE) protocol on the mechanical variables during a series of bilateral hops. In a block-randomized design, 10 strength trained men performed an HRE or a control treatment before performing 5 series of bilateral hops separated by 2 minutes of passive recovery. Each series of bilateral hops was performed for 15 seconds on a force platform with the subject hopping at a frequency of 2.0 Hz. From the vertical force trace, the vertical force during the countermovement phase of each hop, the negative displacement during the countermovement phase, and the vertical stiffness were calculated. The HRE treatment consisted of performing parallel back squats with 40, 50, 60, and 80% of each subject's 1-repetition maximum after a series of dynamic stretches. The control treatment consisted of the dynamic stretches only. No significant differences in any of the mechanical variables were reported after the 2 treatments (p > 0.05). There were no significant correlations between the absolute maximal strength values and the percent change in any of the mechanical variables after the 2 treatments. Despite the lack of significant changes reported for the group, there were some notable individual responses. It is possible that increases in vertical stiffness during bilateral hops can be achieved after an HRE protocol in certain individuals. However, practitioners should be aware of the specificity issues and the individual nature of the responses to such protocols.