Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes.

Behavior is critical for animal survival and reproduction, and possibly for diversification and evolutionary radiation. However, the genetics behind adaptive variation in behavior are poorly understood. In this work, we examined a fundamental and widespread behavioral trait, exploratory behavior, in one of the largest adaptive radiations on Earth, the cichlid fishes of Lake Tanganyika. By integrating quantitative behavioral data from 57 cichlid species (702 wild-caught individuals) with high-resolution ecomorphological and genomic information, we show that exploratory behavior is linked to macrohabitat niche adaptations in Tanganyikan cichlids. Furthermore, we uncovered a correlation between the genotypes at a single-nucleotide polymorphism upstream of the AMPA glutamate-receptor regulatory gene cacng5b and variation in exploratory tendency. We validated this association using behavioral predictions with a neural network approach and CRISPR-Cas9 genome editing.

Integrative Taxonomy of Prosogonotrema bilabiatum Vigueras, 1940 (Digenea: Sclerodistomidae): A Parasite in Atlantic Spadefish Chaetodipterus faber (Broussonet, 1782) (Acanthuriformes: Ephippidae) from Brazil.

OBJECTIVES: The present work aims to expand the knowledge of the digenean species Prosogonotrema bilabiatum (Sclerodistomidae), a parasite of Chaetodipterus faber (Acanthuriformes) from Brazil, with an integrative taxonomic approach, using light microscopy, scanning electron microscopy, histology, and molecular biology. METHODS: Forty-one digenean specimens were stained with hydrochloric carmine for morphological studies. Eleven parasites were dehydrated through a graded ethanol series, critical point dried with carbon dioxide, and coated with gold for scanning electron microscopy analysis. Four specimens were processed following histological routine and stained with hematoxylin and eosin and Gomori trichrome. DNA extracted was amplified using 28S partial primer D1-D3. Maximum likelihood and Bayesian inference were performed for phylogenetic analysis. RESULTS: Morphometric and morphological data of the specimens studied ranged in accordance as observed in previous descriptions of the species. Observations from scanning electron microscopy and histology corroborated with those observed in stained whole mounts. Molecular analysis showed that specimens of P. bilabiatum from Brazil clustered with another two sequences of this species from different hosts and localities, with a high node support value. CONCLUSIONS: The integrative taxonomic approach allowed to record and describe new characteristics of P. bilabiatum related to the tegument, the structure and the arrangement of its tissues. The use of molecular markers confirmed that specimens identified as P. bilabiatum from different hosts and localities are all conspecific. Further studies, mainly molecular with less conserved genetic markers, should be carried out to better understand the phylogenetic relationships of Prosogonotrema with Hemiuroidea.

Validation of a 3D Local-Scale Adaptive Solar Radiation Model by Using Pyranometer Measurements and a High-Resolution Digital Elevation Model.

The result of the multidisciplinary collaboration of researchers from different areas of knowledge to validate a solar radiation model is presented. The MAPsol is a 3D local-scale adaptive solar radiation model that allows us to estimate direct, diffuse, and reflected irradiance for clear sky conditions. The model includes the adaptation of the mesh to complex orography and albedo, and considers the shadows cast by the terrain and buildings. The surface mesh generation is based on surface refinement, smoothing and parameterization techniques and allows the generation of high-quality adapted meshes with a reasonable number of elements. Another key aspect of the paper is the generation of a high-resolution digital elevation model (DEM). This high-resolution DEM is constructed from LiDAR data, and its resolution is two times more accurate than the publicly available DEMs. The validation process uses direct and global solar irradiance data obtained from pyranometers at the University of Salamanca located in an urban area affected by systematic shading from nearby buildings. This work provides an efficient protocol for studying solar resources, with particular emphasis on areas of complex orography and dense buildings where shadows can potentially make solar energy production facilities less efficient.

Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds.

This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.

Developmental plasticity and variability in the formation of egg-spots, a pigmentation ornament in the cichlid Astatotilapia calliptera.

Vertebrate pigmentation patterns are highly diverse, yet we have a limited understanding of how evolutionary changes to genetic, cellular, and developmental mechanisms generate variation. To address this, we examine the formation of a sexually-selected male ornament exhibiting inter- and intraspecific variation, the egg-spot pattern, consisting of circular yellow-orange markings on the male anal fins of haplochromine cichlid fishes. We focus on Astatotilapia calliptera, the ancestor-type species of the Malawi cichlid adaptive radiation of over 850 species. We identify a key role for iridophores in initializing egg-spot aggregations composed of iridophore-xanthophore associations. Despite adult sexual dimorphism, aggregations initially form in both males and females, with development only diverging between the sexes at later stages. Unexpectedly, we found that the timing of egg-spot initialization is plastic. The earlier individuals are socially isolated, the earlier the aggregations form, with iridophores being the cell type that responds to changes to the social environment. Furthermore, we observe apparent competitive interactions between adjacent egg-spot aggregations, which strongly suggests that egg-spot patterning results mostly from cell-autonomous cellular interactions. Together, these results demonstrate that A. calliptera egg-spot development is an exciting model for investigating pigment pattern formation at the cellular level in a system with developmental plasticity, sexual dimorphism, and intraspecific variation. As A. calliptera represents the ancestral bauplan for egg-spots, these findings provide a baseline for informed comparisons across the incredibly diverse Malawi cichlid radiation.

Effect of Calcium Hydroxide and Antioxidant Agents Filling the Pulp Chamber after Internal Bleaching.

To evaluate the effect of calcium hydroxide (CH), sodium ascorbate (SA) and sodium thiosulfate (ST) filling the pulp chamber on color stability and longevity of teeth after internal bleaching. Crowns of bovine incisors were submitted to internal bleaching and divided into groups according the material used in the pulp chamber: Control, CH, SA, ST. Each group was divided into two subgroups according to the time to perform restorative procedures (7 or 15 days). Color measurement was performed with a spectrophotometer at nine periods. The darkening (ΔE) values were calculated. The Mann-Whitney test was used to statistically analyze the data (p ⟨ 0.05). After bleaching, ΔE values were higher than 3.5, showing that the procedure was effective. After 24 hours, no difference was observed between groups. After 7 days, SA showed higher ΔE than the control group (p ⟨ 0.05). CH and TS did not differ from the control group. In restorations performed after 7/15 days, SA group showed higher values of darkening after 1 and 4 months than the control group (p ⟨ 0.05). SA induced perceptible darkening after bleaching and should not be used to fill the pulp chamber. ST and CH show color stability and longevity after 12 months.

Inheritance of genomic regions and genes associated with number of oocytes and embryos in Gir cattle through daughter design.

Over the past decades, daughter designs, including genotyped sires and their genotyped daughters, have been used as an approach to identify quantitative trait loci (QTL) related with economic traits. The aim of this study was to identify genomic regions inherited by Gir sire families and genes associated with number of viable oocytes (VO), total number of oocytes (TO) and number of embryos (EMBR) based on a daughter design approach. In total, 15 Gir sire families were selected. The number of daughters per family ranged from 26 to 395, which were genotyped with different SNP panels and imputed to the Illumina BovineHD BeadChip (777K) and had phenotypes for oocyte and embryo production. Daughters had phenotypic data for VO, TO, and EMBR. The search for QTL was performed through Genome-Wide Association Study (GWAS) based on genomic best linear unbiased prediction (gBLUP). QTL were found for each trait among and within families based on the top 10 genomic windows with the greatest genetic variance. For EMBR, genomic windows identified among families were located on BTA4, BTA5, BTA6, BTA7, BTA8, BTA13, BTA16 and BTA17, and they were most frequent on BTA7 within families. For VO, genomic windows were located on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA23 and BTA27 among families, being most frequent on BTA8 within families. For TO, top 10 genomic windows were identified on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA26 and BTA27, being most frequent on BTA7 and BTA8 within families. Considering all results, the greatest number of genomic windows was found on BTA7, where VCAN, XRCC4, TRNAC-ACA, HAPLN1 and EDIL3 genes were identified in the common regions. In conclusion, 15 Gir sire families with 26 to 395 daughters per family with phenotypes for oocyte and embryo production helped to identify the inheritance of several genomic regions, especially on BTA7, where EDIL3, HAPLN1 and VCAN candidate genes were associated with number of oocytes and embryos in Gir cattle families.

New Multitarget Rivastigmine-Indole Hybrids as Potential Drug Candidates for Alzheimer's Disease.

Alzheimer's disease (AD) is the most common form of dementia with no cure so far, probably due to the complexity of this multifactorial disease with diverse processes associated with its origin and progress. Several neuropathological hallmarks have been identified that encourage the search for new multitarget drugs. Therefore, following a multitarget approach, nine rivastigmine-indole (RIV-IND) hybrids (5a1-3, 5b1-3, 5c1-3) were designed, synthesized and evaluated for their multiple biological properties and free radical scavenging activity, as potential multitarget anti-AD drugs. The molecular docking studies of these hybrids on the active center of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) suggest their capacity to act as dual enzyme inhibitors with probable greater disease-modifying impact relative to AChE-selective FDA-approved drugs. Compounds 5a3 (IC50 = 10.9 µM) and 5c3 (IC50 = 26.8 µM) revealed higher AChE inhibition than the parent RIV drug. Radical scavenging assays demonstrated that all the hybrids containing a hydroxyl substituent in the IND moiety (5a2-3, 5b2-3, 5c2-3) have good antioxidant activity (EC50 7.8-20.7 µM). The most effective inhibitors of Aß42 self-aggregation are 5a3, 5b3 and 5c3 (47.8-55.5%), and compounds 5b2 and 5c2 can prevent the toxicity induced by Aß1-42 to cells. The in silico evaluation of the drug-likeness of the hybrids also showed that all the compounds seem to have potential oral availability. Overall, within this class of RIV-IND hybrids, 5a3 and 5c3 appear as lead compounds for anti-AD drug candidates, deserving further investigation.

Exposure to progesterone before an ovulation synchronization protocol increases the follicular diameter and fertility of multiparous suckled Bos taurus cows.

The objective of this study was to evaluate the effect of administering injectable progesterone (P4i) before a timed artificial insemination (TAI) protocol on the follicular growth, ovulation, and pregnancy rate of Bos taurus suckled cows. The effect of P4i administration before the TAI on the pregnancy rate (P/AI) was evaluated in 576 suckled Bos taurus cows at 30-90 days postpartum. In addition, the effect of P4i administration before TAI on follicular dynamics was evaluated in subgroup of 401 suckled Bos taurus cows. On Day -10 (D-10), cows were divided into two experimental groups (Control and P4i). In this moment, P4i cows received i.m. 150 mg of injectable long-action progesterone. After that, both experimental groups received a synchronization protocol (Day 0; D0) that consisted of administration i.m. of 2 mg of estradiol benzoate and a progesterone intravaginal insert on D0. On Day 8 (D8), the progesterone insert was removed, and the cows received 500 µg of cloprostenol, 400 IU of eCG, and 1 mg of estradiol cypionate. TAI was performed 48 h after the removal of the progesterone insert. The ultrasound exams were performed in a subgroup of cows on Days 0, 8, 10 and 12 to evaluate the diameter of the largest follicle, rate of follicular growth and risks of single and double ovulation. The pregnancy diagnosis was performed 30 days after TAI in all cows to determine the pregnancy rate. The diameter of the largest follicle, on D10 (P = 0.84), rate of follicular growth (P = 0.14), ovulation rate (P = 0.40) and double ovulation rates (P = 0.23) did not differ between experimental groups. The pregnancy rate was greater in the P4i group [Control 46.2 % (133/288) vs. P4i 55.6 % (160/288); P = 0.03]. The diameter of the largest follicles (LF) on D0 (Control 11.6 ± 0.2 vs. P4i 13.3 ± 0.3) was greater (P = 0.01) in the P4i group. In conclusion, injectable progesterone before the ovulation synchronization protocol increased the diameter of the largest follicle on the D0 and the pregnancy rate in multiparous Bos taurus suckled beef cows.

Variation in Neural Crest Development and Functional Divergence of sox10 Paralogs Contribute to Morphological Diversification in Cichlid Fishes.

Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains largely unexplored. Here, by leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the role of NC development in morphological diversification. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. Notably, several NC-related gene expression clusters showed both species-specific divergence in transcriptional landscapes and signatures of positive selection. Specifically, we identified two paralogs of the sox10 gene as prime NC-related candidates contributing to interspecific morphological variation, which displayed remarkable spatio-temporal expression variation in cichlids. Finally, through CRISPR-KO mutants, we experimentally validated the functional divergence between sox10 paralogs, with the acquisition of a novel role in cichlid skeletogenesis by sox10-like. Our study demonstrates the central role of NC-related processes - in particular those controlled by sox10s - in generating morphological diversification among closely-related species and lays the groundwork for further investigations into the mechanisms underpinning vertebrate NC diversification.

Lateral line system diversification during the early stages of ecological speciation in cichlid fish.

BACKGROUND: The mechanosensory lateral line system is an important sensory modality in fishes, informing multiple behaviours related to survival including finding food and navigating in dark environments. Given its ecological importance, we may expect lateral line morphology to be under disruptive selection early in the ecological speciation process. Here we quantify the lateral line system morphology of two ecomorphs of the cichlid fish Astatotilapia calliptera in crater Lake Masoko that have diverged from common ancestry within the past 1,000 years. RESULTS: Based on geometric morphometric analyses of CT scans, we show that the zooplanktivorous benthic ecomorph that dominates the deeper waters of the lake has large cranial lateral line canal pores, relative to those of the nearshore invertebrate-feeding littoral ecomorph found in the shallower waters. In contrast, fluorescence imaging revealed no evidence for divergence between ecomorphs in the number of either superficial or canal neuromasts. We illustrate the magnitude of the variation we observe in Lake Masoko A. calliptera in the context of the neighbouring Lake Malawi mega-radiation that comprises over 700 species. CONCLUSIONS: These results provide the first evidence of divergence in this often-overlooked sensory modality in the early stages of ecological speciation, suggesting that it may have a role in the broader adaptive radiation process.

Using a food web model to predict the effects of Hazardous and Noxious Substances (HNS) accidental spills on deep-sea hydrothermal vents from the Mid-Atlantic Ridge (MAR) region.

Deep-sea hydrothermal vents host unique ecosystems but face risks of incidents with Hazardous and Noxious Substances (HNS) along busy shipping lanes such as the transatlantic route. We developed an Ecopath with Ecosim (EwE) model of the Menez Gwen (MG) vent field (MG-EwE) (Mid-Atlantic Ridge) to simulate ecosystem effects of potential accidental spills of four different HNS, using a semi-Lagrangian Dispersion Model (sLDM) coupled with the Regional Ocean Modelling System (ROMS) calibrated for the study area. Food web modelling revealed a simplified trophic structure with low energy efficiency. The MG ecosystem was vulnerable to disruptions caused by all tested HNS, yet it revealed some long-term resilience. Understanding these impacts is vital for enhancing Spill Prevention, Control, and Countermeasure plans (SPCC) in remote marine areas and developing tools to assess stressors effects on these invaluable habitats.

Nutritional composition of ultra-processed plant-based foods in the out-of-home environment: a multi-country survey with plant-based burgers.

Ultra-processed plant-based foods, such as plant-based burgers, have gained in popularity. Particularly in the out-of-home (OOH) environment, evidence regarding their nutritional profile and environmental sustainability is still evolving. Plant-based burgers available at selected OOH sites were randomly sampled in Amsterdam, Copenhagen, Lisbon and London. Plant-based burgers (patty, bread and condiment) (n 41) were lab analysed for their energy, macronutrients, amino acids and minerals content per 100 g and serving and were compared with reference values. For the plant-based burgers, the median values per 100 g were 234 kcal, 20·8 g carbohydrates, 3·5 g dietary fibre and 12·0 g fat, including 0·08 g TFS and 2·2 g SFA. Protein content was 8·9 g/100 g, with low protein quality according to amino acid composition. Median Na content was 389 mg/100 g, equivalent to 1 g salt. Compared with references, the median serving provided 31% of energy intake based on a 2000 kcal per day and contributed to carbohydrates (17-28%), dietary fibre (42%), protein (40%), total fat (48%), SFA (26%) and Na (54%). One serving provided 15-23% of the reference values for Ca, K and Mg, while higher contributions were found for Zn, Mn, P and Fe (30-67%). The ultra-processed plant-based burgers provide protein, dietary fibre and essential minerals and contain relatively high levels of energy, Na and total fats. The amino acid composition indicated low protein quality. The multifaceted nutritional profile of plant-based burgers highlights the need for manufacturers to implement improvements to better support healthy dietary habits, including reducing energy, Na and total fats.

Hierarchical Zeolites Prepared Using a Surfactant-Mediated Strategy: ZSM-5 vs. Y as Catalysts for Friedel-Crafts Acylation Reaction.

Hierarchical ZSM5 and Y zeolites were prepared through a surfactant-mediated strategy with NH4OH changing the duration of the treatment and the amount of CTAB surfactant and taking as reference multiples of the critical micellar concentration (CMC). The materials were characterized using powder X-ray diffraction, N2 adsorption isotherms at -196 °C, and SEM and TEM microscopy. The catalytic performance was evaluated in Friedel-Crafts acylation of furan with acetic anhydride at 80 °C. The alkaline surfactant-mediated treatment had different effects on the two zeolites. For ZSM5, the CTAB molecular aggregates can hardly diffuse inside the medium-size pores, leading mainly to intercrystalline mesoporosity and increased external surface area, with no positive catalytic impact. On the other hand, for large-pore Y zeolite, the CTAB molecular aggregates can easily diffuse and promote the rearrangement of crystal units around micelles, causing the enlargement of the pores, i.e., intracrystalline porosity. The optimized Y-based sample, treated for 12 h with a CTAB amount 32 times the CMC, shows an increase in product yield and rate constant that was not observed when a higher amount of surfactant was added. The reuse of spent catalysts upon thermal treatment at 400 °C shows a regeneration efficiency around 90%, showing good potentialities for the modified catalysts.

Smell loss associated with SARS-CoV-2 is not clinically different from other viruses: a multicenter cohort study.

BACKGROUND: Although the COVID-19 pandemic has increased the prevalence of cases with olfactory loss, other respiratory viruses can also cause this condition. We aimed to compare the prevalence of acute SARS-CoV-2 infection and other respiratory viruses in patients with sudden smell loss, and to assess the impact of SARS-CoV-2 viral load and co-infection on olfactory symptoms. METHODS: Patients with sudden smell loss were recruited in a multicenter prospective cohort study in 15 hospitals in Brazil. Clinical questionnaire, Connecticut Chemosensory Clinical Research Center (CCCRC) olfactory test and nasopharyngeal swab to perform a PCR-based respiratory viral panel were collected at first visit (day 0) and 30 and 60 days after recruitment. RESULTS: 188 of 213 patients presented positive test result for SARS-CoV-2, among which 65 were co-infected with other respiratory viruses (e.g., rhinovirus, enterovirus, and parainfluenza). 25 had negative test results for SARS-CoV-2. Patients in both SARSCoV-2 and non-SARS-CoV-2 groups had objective anosmia (less than 2 points according to the psychophysical olfactory CCCRC) at day 0, with no significant difference between them. Both groups had significant smell scores improvement after 30 and 60 days, with no difference between them. Co-infection with other respiratory viruses, and SARS-CoV-2 viral load did not impact olfactory scores. CONCLUSION: Patients with sudden smell loss associated with SARS-CoV-2 and other respiratory viruses had similar presentation, with most participants initiating with anosmia, and total or near total recovery after 60 days. SARS-CoV-2 viral load and co-infections with other respiratory viruses were not associated with poorer olfactory outcomes.