Diverse mutational spectrum in the 13q14 chromosomal region in a Brazilian cohort of retinoblastoma

Retinoblastoma is a rare childhood tumor caused by the inactivation of both copies of the RB1 gene. Early diagnosis and identification of heritable RB1 mutation carriers can improve the disease outcome and management via genetic counseling. We used the Multiplex Ligation-dependent Probe Amplification (MLPA) method to analyze the RB1 gene and flanking regions in blood samples from 159 retinoblastoma patients previously negative for RB1 point mutations via Sanger sequencing. We detected a wide spectrum of germline chromosomal alterations, ranging from partial loss or duplication of RB1 to large deletions spanning RB1 and adjacent genes. Mutations were validated via karyotyping, fluorescent in situ hybridization (FISH), SNP-arrays (Single Nucleotide Polymorphism-arrays) and/or quantitative relative real-time PCR. Patients with leukocoria as a presenting symptom showed reduced death rate (p = 0.013) and this sign occurred more frequently among carriers of two breakpoints within RB1 (p = 0.05). All unilateral cases presented both breakpoints outside of RB1 (p = 0.0075). Patients with one breakpoint within RB1 were diagnosed at earlier ages (p = 0.017). Our findings characterize the mutational spectrum of a Brazilian cohort of retinoblastoma patients and point to a possible relationship between the mutation breakpoint location and tumor outcome, contributing to a better prospect of the genotype/phenotype correlation and adding to the wide diversity of germline mutations involving RB1 and adjacent regions in retinoblastoma.

Salt stress and organic fertilization on the growth and biochemical metabolism of Hylocereus costaricensis (red pitaya) seedlings

Red pitaya (Hylocereus costaricensis) is a promising species, with high cultivation potential due to the organoleptic and functional qualities of its fruits. However, irrigation water salinity can affect the crop yield. Therefore, materials rich in organic substances can minimize the damage caused by excess salts in soil and/or water. Thus, the objective of this study was to evaluate the influence of organic matter sources as attenuators of salt stress on the production and biochemical responses of red pitaya seedlings. A completely randomized design in 4 × 5 factorial scheme, with five sources of organic matter (humus, sheep manure, biofertilizer, organic compost and sand + soil) and four salinities (0.6, 2.6, 4.6 and 6.6 dS m-1) with four replicates and two plants per plot was used. The shoot length, root length, cladode diameter, number of cladodes, number of sprotus, root volume, shoot dry mass, root dry mass and total dry mass, root and shoot dry mass ratio, chlorophyll a, b and total, amino acids and soluble sugars were evaluated at 120 days after the treatments began to be applied. Red pitaya is moderately tolerant to salinity (ECw from 4.0 to 6.0 dS m-1). Organic compost and sheep manure attenuate the harmful effects of salinity on red pitaya seedlings. Under salt stress conditions, red pitaya plants increase their levels of proline, amino acids and total sugars.

Subcutaneous facial emphysema secondary to a dental procedure

Subcutaneous emphysema is a possible but infrequent consequence of dental procedures. We present the case of a 6-year-old healthy boy transferred from a dental clinic immediately after local anaesthesia for tooth extraction, due to sudden orbital and facial swelling. On physical examination, oedema of the left upper eyelid with fine crepitus on palpation and left hemiface oedema with local pain were observed. Ophthalmologic observation was normal. CT scan of the face and orbits documented extensive infiltration of the subcutaneous tissue planes of the left face by air, with extension to the external part of the body of the mandible, retromaxillary fat, masticatory muscle spaces, parapharyngeal space and adjacent to the orbital roof. After completing initial evaluation, the dentist confirmed the use of an air-driven device during local anaesthesia administration. The patient improved with conservative treatment. Early recognition of this condition is essential to provide an adequate clinical assessment with exclusion of possible life-threatening complications.

Reported quality of life in countries with cases of COVID19: a systematic review

INTRODUCTION

Considering the relevance of the quality of life (QoL) and the consequences of the 2019 new coronavirus disease (COVID-19) due to the social distancing, this systematic review aimed to summarize effects of the COVID-19 in the QoL of the studied populations.

AREAS COVERED

Four databases, the methodological quality and the risk of bias in selected publications were investigated. Seven thousand and fifty-one individuals from Italy, Saudi Arabia, China, and Vietnam. Online system and printed questionnaires were used to assess the QoL, as patients affected by primary antibody deficiencies, residents, people from endemic and no endemic regions, and individuals with COVID-19. Different types of questionnaires are utilized to evaluate health-related quality of life (HRQOL). The methodological quality of three papers was good with low risk of bias and a decrease in the QoL.

EXPERT OPINION

The QoL of studies populations where COVID-19 was reported, worsened. Nevertheless, considering some indicators (infant mortality, average income, life expectancy, health coverage, and average schooling years), the standard of life and subsequently the quality of life among the presented countries (China, Vietnam, Italy, and Saudi Arabia) are different. Therefore, the simple comparison of these populations and the conclusions from this comparison must be done carefully.

Seasonal proteome variation in intertidal shrimps under a natural setting: Connecting molecular networks with environmental fluctuations

The ability of intertidal organisms to maintain their performance via molecular and physiological adjustments under low tide, seasonal fluctuations and extreme events ultimately determines population viability. Analyzing this capacity in the wild is extremely relevant since intertidal communities are under increased climate variability owing to global changes. We addressed the seasonal proteome signatures of a key intertidal species, the shrimp Palaemon elegans, in a natural setting. Shrimps were collected during spring and summer seasons at low tides and were euthanized in situ. Environmental variability was also assessed using hand-held devices and data loggers. Muscle samples were taken for 2D gel electrophoresis and protein identification through mass spectrometry. Proteome data revealed that 55 proteins (10.6% of the proteome) significantly changed between spring and summer collected shrimps, 24 of which were identified. These proteins were mostly involved in cytoskeleton remodelling, energy metabolism and transcription regulation. Overall, shrimps modulate gene expression leading to metabolic and structural adjustments related to seasonal differences in the wild (i.e. abiotic variation and possibly intrinsic cycles of reproduction and growth). This potentially promotes performance and fitness as suggested by the higher condition index in summer-collected shrimps. However, inter-individual variation (% coefficient of variation) in protein levels was quite low (min-max ranges were 0.6-8.3% in spring and 1.2-4.8% in summer), possibly suggesting reduced genetic diversity or physiological canalization. Protein plasticity is relevant to cope with present and upcoming environmental variation related to anthropogenic forcing (e.g. global change, pollution) but low inter-individual variation may limit evolutionary potential of shrimp populations.

Molecular assessment of wild populations in the marine realm: Importance of taxonomic, seasonal and habitat patterns in environmental monitoring

Scientists are currently faced with the challenge of assessing the effects of anthropogenic stressors on aquatic ecosystems. Cellular stress response (CSR) biomarkers are ubiquitous and phylogenetically conserved among metazoans and have been successfully applied in environmental monitoring but they can also vary according to natural biotic and abiotic factors. The reported variability may thus limit the wide application of biomarkers in monitoring, imposing the need to identify variability levels in the field. Our aim was to carry out a comprehensive in situ assessment of the CSR (heat shock protein 70 kDa, ubiquitin, antioxidant enzymes) and oxidative damage (lipid peroxidation) in wild populations across marine taxa by collecting fish, crustaceans, mollusks and cnidarians during two different seasons (spring and summer) and two habitat types (coast and estuary). CSR end-point patterns were different between taxa with mollusks having higher biomarker levels, followed by the cnidarians, while fish and crustaceans showed lower biomarker levels. The PCA showed clear clusters related to mobility/sessile traits with sessile organisms showing greater levels (>2-fold) of CSR proteins and oxidative damage. Mean intraspecific variability in the CSR measured by the coefficient of variation (% CV) (including data from all seasons and sites) was elevated (35-94%). Overall, there was a seasonal differentiation in biomarker patterns across taxonomic groups, especially evident in fish and cnidarians. A differentiation in biomarker patterns between habitat types was also observed and associated with phenotypic plasticity or local adaptation. Overall, specimens collected in the estuary had lower biomarker levels when compared to specimens collected in the coast. This work highlights the importance of assessing baseline biomarker levels across taxa, seasons and habitats prior to applying biomarker analyses in environmental monitoring. Selecting bioindicator species, defining sampling strategies, and identifying confounding factors are crucial preliminary steps that ensure the success of biomarkers as powerful tools in biomonitoring.

Environmental health assessment of warming coastal ecosystems in the tropics - Application of integrative physiological indices

According to climate science, ocean warming is one of the current and future greatest threats to coastal ecosystems. Projection scenarios for the end of this century show that tropical intertidal ecosystems are particularly at risk. In this study we optimized and tested a holistic method for bio-monitoring present and projected thermal pressure in such ecosystems, in order to assess organism vulnerability to ocean warming. Several species representative of different animal groups (fish, crustaceans and gastropods) were collected from the field and subjected to an experimental trial for 28 days, testing two temperatures: control (present seawater summer temperature) and elevated temperature (+3 °C, projected seawater temperature anomaly for 2100). Muscle samples were collected weekly to quantify several biomarkers of: i) macromolecular damage (protein unfolding and denaturation, and lipid peroxidation), ii) reactive oxygen species (ROS) scavengers (antioxidant enzymes), and iii) body condition (energy reserves and body mass). These biomarkers were combined in integrated biomarker response (IBR) indices, either in three separate stress response categories (as previously defined) or in a unique combined analysis of overall physiological performance. Both approaches suggest that temperature affected IBRs, with increasing temperatures significantly impairing the overall health of individuals. Biomarkers of lower levels of biological organization indicated deleterious effects of temperature, whereas biomarkers of higher levels suggested maintenance of performance after chronic exposure. Overall indices combining the estimates of biomarkers across levels of biological organization are essential to predict the vulnerability of species, or populations, to climate warming. Such indices may assist managers and stakeholders in the establishment of monitoring programs and environmental policies toward the conservation of fragile coastal systems.

What's in a tide pool? Just as much food web network complexity as in large open ecosystems

Understanding the fundamental laws that govern complex food web networks over large ecosystems presents high costs and oftentimes unsurmountable logistical challenges. This way, it is crucial to find smaller systems that can be used as proxy food webs. Intertidal rock pool environments harbour particularly high biodiversity over small areas. This study aimed to analyse their food web networks to investigate their potential as proxies of larger ecosystems for food web networks research. Highly resolved food webs were compiled for 116 intertidal rock pools from cold, temperate, subtropical and tropical regions, to ensure a wide representation of environmental variability. The network properties of these food webs were compared to that of estuaries, lakes and rivers, as well as marine and terrestrial ecosystems (46 previously published complex food webs). The intertidal rock pool food webs analysed presented properties that were in the same range as the previously published food webs. The niche model predictive success was remarkably high (73–88%) and similar to that previously found for much larger marine and terrestrial food webs. By using a large-scale sampling effort covering 116 intertidal rock pools in several biogeographic regions, this study showed, for the first time, that intertidal rock pools encompass food webs that share fundamental organizational characteristics with food webs from markedly different, larger, open and abiotically stable ecosystems. As small, self-contained habitats, intertidal rock pools are particularly tractable systems and therefore a large number of food webs can be examined with relatively low sampling effort. This study shows, for the first time that they can be useful models for the understanding of universal processes that regulate the complex network organization of food webs, which are harder or impossible to investigate in larger, open ecosystems, due to high costs and logistical difficulties.

Ecological traps in shallow coastal waters-Potential effect of heat-waves in tropical and temperate organisms

Mortality of fish has been reported in tide pools during warm days. That means that tide pools are potential ecological traps for coastal organisms, which happen when environmental changes cause maladaptive habitat selection. Heat-waves are predicted to increase in intensity, duration and frequency, making it relevant to investigate the role of tide pools as traps for coastal organisms. However, heat waves can also lead to acclimatization. If organisms undergo acclimatization prior to being trapped in tide pools, their survival chances may increase. Common tide pool species (46 species in total) were collected at a tropical and a temperate area and their upper thermal limits estimated. They were maintained for 10 days at their mean summer sea surface temperature +3°C, mimicking a heat-wave. Their upper thermal limits were estimated again, after this acclimation period, to calculate each species’ acclimation response. The upper thermal limits of the organisms were compared to the temperatures attained by tide pool waters to investigate if 1) tide pools could be considered ecological traps and 2) if the increase in upper thermal limits elicited by the acclimation period could make the organisms less vulnerable to this threat. Tropical tide pools were found to be ecological traps for an important number of common coastal species, given that they can attain temperatures higher than the upper thermal limits of most of those species. Tide pools are not ecological traps in temperate zones. Tropical species have higher thermal limits than temperate species, but lower acclimation response, that does not allow them to survive the maximum habitat temperature of tropical tide pools. This way, tropical coastal organisms seem to be, not only more vulnerable to climate warming per se, but also to an increase in the ecological trap effect of tide pools.

Seasonal changes in stress biomarkers of an exotic coastal species - Chaetopleura angulata (Polyplacophora) - Implications for biomonitoring

Knowledge on baseline values of stress biomarkers in natural conditions is urgent due to the need of reference values for monitoring purposes. Here we assessed the cellular stress response of the chiton Chaetopleura angulata in situ. Biomarkers commonly used in environmental monitoring (heat shock protein 70kDa, total ubiquitin, catalase, glutathione-S-transferase, superoxide-dismutase, lipid peroxidation) were analyzed in the digestive system, gills and muscle of C. angulata, under spring and summer conditions in order to assess seasonal tissue-specific responses. Season had an effect on all targeted organs, especially affecting the digestive system which displayed clear seasonal clusters. The respective Integrated Biomarker Response (IBR) showed a 7.2-fold seasonal difference. Muscle and gills showed similar IBRs between seasons making them appropriate organs to monitor chemical pollution as they were less responsive to seasonal variation. The most stable biomarkers in these organs were ubiquitin and superoxide-dismutase thus being reliable for monitoring purposes.

Comparing de novo and reference-based transcriptome assembly strategies by applying them to the blood-sucking bug Rhodnius prolixus

High Throughput Sequencing capabilities have made the process of assembling a transcriptome easier, whether or not there is a reference genome. But the quality of a transcriptome assembly must be good enough to capture the most comprehensive catalog of transcripts and their variations, and to carry out further experiments on transcriptomics. There is currently no consensus on which of the many sequencing technologies and assembly tools are the most effective. Many non-model organisms lack a reference genome to guide the transcriptome assembly. One question, therefore, is whether or not a reference-based genome assembly gives better results than de novo assembly. The blood-sucking insect Rhodnius prolixus-a vector for Chagas disease-has a reference genome. It is therefore a good model on which to compare reference-based and de novo transcriptome assemblies. In this study, we compared de novo and reference-based genome assembly strategies using three datasets (454, Illumina, 454 combined with Illumina) and various assembly software. We developed criteria to compare the resulting assemblies: the size distribution and number of transcripts, the proportion of potentially chimeric transcripts, how complete the assembly was (completeness evaluated both through CEGMA software and R. prolixus proteome fraction retrieved). Moreover, we looked for the presence of two chemosensory gene families (Odorant-Binding Proteins and Chemosensory Proteins) to validate the assembly quality. The reference-based assemblies after genome annotation were clearly better than those generated using de novo strategies alone. Reference-based strategies revealed new transcripts, including new isoforms unpredicted by automatic genome annotation. However, a combination of both de novo and reference-based strategies gave the best result, and allowed us to assemble fragmented transcripts.

Food web of the intertidal rocky shore of the west Portuguese coast - Determined by stable isotope analysis

The characterization of food web structure, energy pathways and trophic linkages is essential for the understanding of ecosystem functioning. Isotopic analysis was performed on food web components of the rocky intertidal ecosystem in four sites along the Portuguese west coast. The aim was to 1) determine the general food web structure, 2) estimate the trophic level of the dominant organisms and 3) track the incorporation of organic carbon of different origins in the diet of the top consumers. In this food web, fish are top consumers, followed by shrimp. Anemones and gastropods are intermediate consumers, while bivalves and zooplankton are primary consumers. Macroalgae Bifurcaria bifurcata, Ulva lactuca, Fucus vesiculosus, Codium sp. and phytoplankton are the dominant producers. Two energy pathways were identified, pelagic and benthic. Reliance on the benthic energy pathway was high for many of the consumers but not as high as previously observed in subtidal coastal food webs. The maximum TL was 3.3, which is indicative of a relatively short food web. It is argued that the diet of top consumers relies directly on low levels of the food web to a considerable extent, instead of on intermediate levels, which shortens the trophic length of the food web.

Physiological, cellular and biochemical thermal stress response of intertidal shrimps with different vertical distributions: Palaemon elegans and Palaemon serratus

The ability to cope with high temperature variations is a critical factor in intertidal communities. Two species of intertidal rocky shore shrimps (Palaemon sp.) with different vertical distributions were collected from the Portuguese coast in order to test if they were differentially sensitive to thermal stress. Three distinct levels of biological organization (organismal, biochemical, and cellular) were surveyed. The shrimp were exposed to a constant rate of temperature increase of 1°C x h(-1), starting at 20°C until reaching the CTMax (critical thermal maximum). During heat stress, two biomarkers of protein damage were quantified in the muscle via enzyme-linked immunosorbent assays: heat shock proteins HSP70 (hsp70/hsc70) and total ubiquitin. Muscle histopathological alterations caused by temperature were also evaluated. CTMax values were not significantly different between the congeners (P. elegans 33.4 ± 0.5 °C; P. serratus 33.0 ± 0.5 °C). Biomarker levels did not increase along the temperature trial, but P. elegans (higher intertidal) showed higher amounts of HSP70 and total ubiquitin than P. serratus (lower intertidal). HSP70 and total ubiquitin levels showed a positive significant correlation in both species, suggesting that their association is important in thermal tolerance. Histopathological observations of muscle tissue in P. serratus showed no gross alterations due to temperature but did show localized atrophy of muscle fibers at CTMax. In P. elegans, alterations occurred at a larger scale, showing multiple foci of atrophic muscular fascicles caused by necrotic or autolytic processes. In conclusion, Palaemon congeners displayed different responses to stress at a cellular level, with P. elegans having greater biomarker levels and histopathological alterations.

Effect of warming rate on the critical thermal maxima of crabs, shrimp and fish

The threat of global warming has prompted numerous recent studies on the thermal tolerance of marine species. A widely used method to determine the upper thermal limit has been the Critical Thermal Maximum (CTMax), a dynamic method, meaning that temperature is increased gradually until a critical point is reached. This method presents several advantages over static methods, however, there is one main issue that hinders interpretation and comparison of CTMax results: the rate at which the temperature is increased. This rate varies widely among published protocols. The aim of the present work was to determine the effect of warming rate on CTMax values, using different animal groups. The influence of the thermal niche occupied by each species (intertidal vs subtidal) and habitat (intertidal vs subtidal) was also investigated. CTMax were estimated at three different rates: 1°Cmin(-1), 1°C30min(-1) and 1°Ch(-1), in two species of crab, Eurypanopeus abbreviatus and Menippe nodifrons, shrimp Palaemon northropi and Hippolyte obliquimanus and fish Bathygobius soporator and Parablennius marmoreus. While there were significant differences in the effect of warming rates for some species, for other species warming rate produced no significant differences (H. obliquimanus and B. soporator). While in some species slower warming rates lead to lower CTMax values (P. northropi and P. marmoreus) in other species the opposite occurred (E. abbreviatus and M. nodifrons). Biological group has a significant effect with crabs' CTMax increasing at slower warming rates, which did not happen for shrimp and fish. Subtidal species presented lower CTMax, at all warming rates tested. This study highlights the importance of estimating CTMax values at realistic rates that species encounter in their environment and thus have an ecological value.

Effect of increasing temperature in the differential activity of oxidative stress biomarkers in various tissues of the Rock goby, Gobius paganellus

Oxidative stress biomarkers have been widely used in the development of ecological indices and in the assessment of exposure of aquatic organisms to contaminants from agricultural, industrial and urban pollution. However, temperature is known to also have a significant effect on oxidative stress biomarkers. This way, temperature is a confounding factor that may result in difficulties in the interpretation of oxidative stress biomarkers response patterns. Since climate change is expected to result in more frequent and intense heat wave events it is pertinent to investigate the effect of increasing temperature in the oxidative stress response of common aquatic organisms. It is also important to assess the differential response of different body tissues, given that they are differently exposed to temperature depending on their location and physiological function. This study investigates the effect of increasing temperature (20 °C-34 °C) in the response of multiple biomarkers of oxidative stress: lipid peroxidation, glutathione-S-transferase, superoxide dismutase and catalase activities, in the muscle, liver and gills of a common coastal fish, the Rock goby, Gobius paganellus. The response of the oxidative stress biomarkers analysed were always higher in the gills than in the other tissues. Muscle generally presented the lower levels of any of the biomarkers tested when compared to other tissues. Nevertheless, muscle tissue always responded significantly to temperature, as did the liver, while the gills were unresponsive in terms of lipid peroxidation and glutathione-S-transferase. Unresponsive tissues to temperature may be particularly interesting as indicators of pollution, given that temperature will not be a confounding variable in their oxidative stress response.

Effect of temperature in multiple biomarkers of oxidative stress in coastal shrimp

Various studies in captivity and in the wild have pointed to the effect of season, and temperature in particular, in the levels of the oxidative stress biomarkers currently used for environmental quality assessment. However, knowledge on how temperature affects the oxidative stress response is unavailable for most species. This study investigated the effect of increasing temperature on lipid peroxidation, catalase activity, superoxide dismutase and glutathione-S-transferase in the shrimps, Palaemon elegans and Palaemon serratus. It was concluded that increasing temperatures significantly affect all the biomarkers tested in both species, with the exception of superoxide dismutase in P. serratus which was not affected by temperature. The oxidative stress response was more intense in P. elegans, than in P. serratus, producing higher peaks of all biomarkers at temperatures between 22°C and 26°C, followed by low levels at higher temperatures. It was concluded that monitoring of ecosystems using oxidative stress biomarkers should take into account the species and thermal history of the organisms. Sampling should be avoided during heat waves and immediately after heat waves.