Large scale sequence-based screen for recessive variants allows for identification and monitoring of rare deleterious variants in pigs.

Most deleterious variants are recessive and segregate at relatively low frequency. Therefore, high sample sizes are required to identify these variants. In this study we report a large-scale sequence based genome-wide association study (GWAS) in pigs, with a total of 120,000 Large White and 80,000 Synthetic breed animals imputed to sequence using a reference population of approximately 1,100 whole genome sequenced pigs. We imputed over 20 million variants with high accuracies (R2>0.9) even for low frequency variants (1-5% minor allele frequency). This sequence-based analysis revealed a total of 14 additive and 9 non-additive significant quantitative trait loci (QTLs) for growth rate and backfat thickness. With the non-additive (recessive) model, we identified a deleterious missense SNP in the CDHR2 gene reducing growth rate and backfat in homozygous Large White animals. For the Synthetic breed, we revealed a QTL on chromosome 15 with a frameshift variant in the OBSL1 gene. This QTL has a major impact on both growth rate and backfat, resembling human 3M-syndrome 2 which is related to the same gene. With the additive model, we confirmed known QTLs on chromosomes 1 and 5 for both breeds, including variants in the MC4R and CCND2 genes. On chromosome 1, we disentangled a complex QTL region with multiple variants affecting both traits, harboring 4 independent QTLs in the span of 5 Mb. Together we present a large scale sequence-based association study that provides a key resource to scan for novel variants at high resolution for breeding and to further reduce the frequency of deleterious alleles at an early stage in the breeding program.

CD5L is upregulated upon infection with Mycobacterium tuberculosis with no effect on disease progression.

Tuberculosis (TB) alone caused over a billion deaths in the last 200 years, making it one of the deadliest diseases to humankind. Understanding the immune mechanisms underlying protection or pathology in TB is key to uncover the much needed innovative approaches to tackle TB. The scavenger receptor cysteine-rich molecule CD5 antigen-like (CD5L) has been associated with TB, but whether and how CD5L shapes the immune response during the course of disease remains poorly understood. Here, we show an upregulation of CD5L in circulation and at the site of infection in C57BL/6 Mycobacterium tuberculosis-infected mice. To investigate the role of CD5L in TB, we studied the progression of M. tuberculosis aerosol infection in a recently described genetically engineered mouse model lacking CD5L. Despite the increase of CD5L during infection of wild-type mice, absence of CD5L did not impact bacterial burden, histopathology or survival of infected mice. Absence of CD5L associated with a modest increase in the numbers of CD4+ T cells and the expression of IFN-γ in the lungs of infected mice, with no major effect in overall immune cell dynamics. Collectively, this study confirms CD5L as a potential diagnostic biomarker to TB, showing no discernible impact on the outcome of the infection.

Phylogenetic variations in a novel family of hyperstable apple snail egg proteins: insights into structural stability and functional trends.

The relationship between protein stability and functional evolution is little explored in proteins purified from natural sources. Here, we investigated a novel family of egg proteins (Perivitellin-1, PV1) from Pomacea snails. Their remarkable stability and clade-related functions in most derived clades (Canaliculata and Bridgesii) make them excellent candidates for exploring this issue. To that aim, we studied PV1 (PpaPV1) from the most basal lineage, Flagellata. PpaPV1 displays unparalleled structural and kinetic stability, surpassing PV1s from derived clades, ranking among the most hyperstable proteins documented in nature. Its spectral features contribute to a pale egg coloration, exhibiting a milder glycan binding lectin activity with a narrower specificity than PV1s from the closely related Bridgesii clade. These findings provide evidence for substantial structural and functional changes throughout the genus' PV1 evolution. We observed that structural and kinetic stability decreased in a clade-related fashion and was associated with large variations in defensive traits. For instance, pale PpaPV1 lectin turns potent in the Bridgesii clade, adversely affecting gut morphology, while giving rise to brightly colored PV1s providing eggs with a conspicuous, probably warning signal in the Canaliculata clade. This work provides a comprehensive comparative analysis of PV1s from various apple snail species within a phylogenetic framework, offering insights into the interplay among their structural features, stability profiles and functional roles. More broadly, our work provides one of the first examples from natural evolution showing the crucial link among protein structure, stability and evolution of new functions.

The weight, urine colour and thirst Venn diagram is an accurate tool compared with urinary and blood markers for hydration assessment at morning and afternoon timepoints in euhydrated and free-living individuals.

The weight, urine colour and thirst (WUT) Venn diagram is a practical hydration assessment tool; however, it has only been investigated during first-morning. This study investigated accuracy of the WUT Venn diagram at morning and afternoon timepoints compared with blood and urine markers. Twelve men (21 ± 2 years; 81·0 ± 15·9 kg) and twelve women (22 ± 3 years; 68·8 ± 15·2 kg) completed the study. Body mass, urine colour, urine specific gravity (USG), urine osmolality (UOSM), thirst and plasma osmolality (POSM) were collected at first-morning and afternoon for 3 consecutive days in free-living (FL) and euhydrated states. Number of markers indicating dehydration levels were categorised into either 3, 2, 1 or 0 WUT markers. Receiver operating characteristics analysis calculated the sensitivity and specificity of 1, 2 or 3 hydration markers in detecting dehydration or euhydration. Specificity values across morning and afternoon exhibited high diagnostic accuracy for USG (0·890-1·000), UOSM (0·869-1·000) and POSM (0·787-0·990) when 2 and 3 WUT markers were met. Sensitivity values across both timepoints exhibited high diagnostic accuracy for USG (0·826-0·941) and UOSM (0·826-0·941), but not POSM in the afternoon (0·324) when 0 and 1 WUT markers were met. The WUT Venn diagram is accurate in detecting dehydration for WUT2 and WUT3 based off USG, UOSM and POSM during first-morning and afternoon. Applied medical, sport and occupational practitioners can use this tool in field settings for hydration assessment not only at various timepoints throughout the day but also in FL individuals.

Colorimetric enzymatic rapid test for the determination of atropine in baby food using a smartphone.

A method for the enzymatic determination of atropine has been developed, which is based on a sequence of reactions involving (1) the hydrolysis of atropine to give tropine; (2) the enzymatic oxidation of tropine with NAD (catalysed by tropinone reductase); and (3) an indicator reaction, in which the NADH previously formed reduces the dye iodonitrotetrazolium chloride (INT) to a reddish species, the reaction catalysed by diaphorase. The method was first developed in solution (linear response range from 2.4 × 10-6 M to 1.0 × 10-4 M). It was then implemented in cellulose platforms to develop a rapid test where the determination is made by measuring the RGB coordinates of the platforms using a smartphone-based device. The device is based on the integrating sphere concept and contains a light source to avoid external illumination effects. The smartphone is controlled by an app that allows a calibration line to be generated and the atropine concentration to be quantified; moreover, since the app normalizes the CCD response of the smartphone, the results and calibrations obtained with different smartphones are similar and can be shared. Using the G coordinate, the results were shown to have a linear response with the concentration of atropine ranging from 1.2 × 10-5 M to 3.0 × 10-4 M with an RSD of 1.4% (n = 5). The method has been applied to the determination of atropine in baby food and buckwheat samples with good results.

Ectoparasite crustaceans of ten fish species from the upper Araguari River in northern Brazil.

Fish parasites are an important part of aquatic biodiversity and knowing these species and their interactions with their hosts helps in monitoring the aquatic biota. The present study investigated the ectoparasite crustacean fauna of ten fish species from the upper Araguari River, in the state of Amapá, northern Brazil. A total of 508 fish were collected and analyzed from July to November 2014, of which 82.6% (109) were parasitized by one or more crustacean ectoparasite species. In the ten host fish species, a total of 308 ectoparasite specimens were collected, from 12 taxa, such as Argulus multicolor Stekhoven, 1937, Argulus spinulosus Silva, 1980, Argulus sp.1, Argulus sp.2, Argulus sp.3, Dipteropeltis sp., Dipteropeltis hirundo Calman, 1912, Dolops bidentata Bouvier, 1899, Dolops striata Bouvier, 1899 (Argulidae), Braga fluviatilis Richardson, 1911, Braga amapaensis Thatcher, 1996 (Cymothoidae) and Excorallana berbicensis Boone, 1918 (Corallanidae). Higher levels of prevalence and abundance were recorded for Hoplias aimara (Valenciennes, 1847) and Tometes trilobatus Valenciennes, 1850, respectively. These ectoparasites were found in the fins, integument, mouth, and anus of the host fish. Argulus sp.2 and D. bidentata were the most abundant parasites (65.1%), and had the highest species richness. This study registered 36 novel host-parasite interactions, and thus represents a new record for all host species here examined.

Spatial distribution, host specificity, and affinity of Branchiura for surface and macrohabitat types in fish species from the Brazilian Amazon.

This study investigated the spatial distribution, parasite interactions, and affinities of Branchiura parasites according to macrohabitat and surface type on fish from the Araguari River, Amapá State, in the Brazilian Amazon. This study presents novel information on the interactions of branchiuran species with host fish, and how the morphology of their attachment structures is associated with different host surface morphologies, with and without scales. A total of 558 fish specimens of 26 species were collected, of which 109 fish (10 species) were parasitized by at least one branchiuran parasite; these were selected for further study. The parasites were collected from the buccal cavity, gills, fins, and integument of the host fish. Parasites with suction discs (Argulus) were mainly associated to hosts with small scales and no scales, while parasites with hooks (Dolops) were mainly associated to hosts with large scales. Overall, parasites with suction discs were more specialized per site than those with hooks.

Determination of Partial Propagation Velocity and Partial Isentropic Compressibility Coefficient in Water-Ethanol System.

This study introduces an innovative approach to the layered model, emphasizing the physical-chemical characterization of miscible liquid systems through ultrasonic techniques, with a specific focus on the water-ethanol system used in pharmaceutical formulations. Traditional characterization methods, while effective, face challenges due to the complex nature of solutions, such as the need for large pressure variations and strict temperature control. The proposed approach integrates partial molar volumes and partial propagation velocity functions into the layered model, enabling a nuanced understanding of miscibility and interactions. Ultrasonic techniques are used to calculate the isentropic compressibility coefficient for each component of the mixture as well as the total value using an additive mixing rule. Unlike conventional methods, this technique uses tabulated and experimental data to estimate the propagation velocity in the mixture, leading to a more precise computation of the isentropic compressibility coefficient. The results indicate a significant improvement in predicting the behavior of the water-ethanol system compared to the classical layered model. The methodology demonstrates the potential to provide new physicochemical insights that can be applied to other miscible systems beyond water-ethanol. This research has implications for improving the efficiency and accuracy of liquid medication formulations in the pharmaceutical industry.

General Psychiatric Management for Adolescents With Borderline Personality Disorder and Eating Disorders.

Borderline personality disorder and eating disorders frequently co-occur among youths. These disorders emerge in adolescence, during the critical developmental period of building an independent sense of self and the capacity to relate to one's community. Because of core differences in the development and psychopathology of borderline personality disorder and eating disorders, adjustments are required when treating these disorders when they co-occur. Few established treatment approaches can address these disorders simultaneously. Evidence-based psychotherapies for borderline personality disorder, such as dialectical behavior therapy and mentalization-based treatment, have been adapted to accommodate the shared vulnerabilities and features of the two disorders. However, these approaches are specialized, intensive, and lengthy and are therefore poorly suited to implementation in general psychiatric or primary health care, where most frontline mental health care is provided. Generalist approaches can fill this public health gap, guiding nonspecialists in structuring informed clinical management for these impairing and sometimes fatal disorders. In this overview, the authors describe the adjustment of good (or general) psychiatric management (GPM) for adolescents with borderline personality disorder to incorporate the prevailing best practices for eating disorder treatment. The adjusted treatment relies on interventions most clinicians already use (diagnostic disclosure, psychoeducation, focusing on life outside treatment, managing patients' self-destructive behaviors, and conservative psychopharmacology with active management of comorbid conditions). Limitations of the adjusted treatment, as well as guidelines for referring patients to specialized and general medical treatments and for returning them to primary generalist psychiatric care, are discussed.

Immune thrombotic thrombocytopenic purpura in older patients: Results from the Spanish TTP Registry (REPTT).

Immune thrombotic thrombocytopenic purpura (iTTP) is an ultra-rare disease that seldom occurs in the elderly. Few reports have studied the clinical course of iTTP in older patients. In this study, we have analysed the clinical characteristics at presentation and response to therapy in a series of 44 patients with iTTP ≥60 years at diagnosis from the Spanish TTP Registry and compared them with 209 patients with <60 years at diagnosis from the same Registry. Similar symptoms and laboratory results were described in both groups, except for a higher incidence of renal dysfunction among older patients (23% vs. 43.1%; p = 0.008). Front-line treatment in patients ≥60 years was like that administered in younger patients. Also, no evidence of a difference in clinical response and overall survival was seen in both groups. Of note, 14 and 25 patients ≥60 years received treatment with caplacizumab and rituximab, respectively, showing a favourable safety and efficacy profile, like that observed in patients <60 years.

Predicting the impact of genotype-by-genotype interaction on the purebred-crossbred genetic correlation from phenotype and genotype marker data of parental lines.

BACKGROUND: The genetic correlation between purebred (PB) and crossbred (CB) performances ([Formula: see text]) partially determines the response in CB when selection is on PB performance in the parental lines. An earlier study has derived expressions for an upper and lower bound of [Formula: see text], using the variance components of the parental purebred lines, including e.g. the additive genetic variance in the sire line for the trait expressed in one of the dam lines. How to estimate these variance components is not obvious, because animals from one parental line do not have phenotypes for the trait expressed in the other line. Thus, the aim of this study was to propose and compare three methods for approximating the required variance components. The first two methods are based on (co)variances of genomic estimated breeding values (GEBV) in the line of interest, either accounting for shrinkage (VCGEBV-S) or not (VCGEBV). The third method uses restricted maximum likelihood (REML) estimates directly from univariate and bivariate analyses (VCREML) by ignoring that the variance components should refer to the line of interest, rather than to the line in which the trait is expressed. We validated these methods by comparing the resulting predicted bounds of [Formula: see text] with the [Formula: see text] estimated from PB and CB data for five traits in a three-way cross in pigs. RESULTS: With both VCGEBV and VCREML, the estimated [Formula: see text] (plus or minus one standard error) was between the upper and lower bounds in 14 out of 15 cases. However, the range between the bounds was much smaller with VCREML (0.15-0.22) than with VCGEBV (0.44-0.57). With VCGEBV-S, the estimated [Formula: see text] was between the upper and lower bounds in only six out of 15 cases, with the bounds ranging from 0.21 to 0.44. CONCLUSIONS: We conclude that using REML estimates of variance components within and between parental lines to predict the bounds of [Formula: see text] resulted in better predictions than methods based on GEBV. Thus, we recommend that the studies that estimate [Formula: see text] with genotype data also report estimated genetic variance components within and between the parental lines.

Baru (Dipteryx alata Vog.) agro-industrial by-products promote the growth and metabolism of probiotic strains.

AIMS: To evaluate the phytochemical composition and effects of the baru peel and pulp (BPP) and the partially defatted baru nut (DBN) on the growth and metabolism of probiotics. METHODS AND RESULTS: The proximate composition, including dietary fibers, and polyphenol profile were determined in the BPP and DBN, and the prebiotic activity was evaluated on the growth and metabolism of the Lactobacillus and Bifidobacterium strains. BPP and DBN have a high content of insoluble fibers and phenolic compounds, mainly flavonoids and phenolic acids. Moreover, DBN stands out for its high content of proteins and lipids. BPP and DBN stimulated the growth and metabolism of Bifidobacterium animalis subsp. lactis BB-12, Lactobacillus acidophilus LA-05, and Lacticaseibacillus casei L-26. CONCLUSIONS: Baru by-products have potential prebiotic properties to be confirmed in preclinical and clinical studies, and to be explored as an ingredient in new health-promoting foods. IMPACT STATEMENT: Agro-industrial baru wastes, the peel plus pulp and the partially defatted nut, are sources of health-promoting compounds and stimulate the growth and metabolism of probiotics, indicating prebiotic properties.

Global distribution patterns of Caligus Müller, 1785 (Copepoda: Caligidae) associated to teleost fishes, with physiological and histopathological data and description of treatment strategies.

This review surveyed information on Caligus Müller, 1785 to identify global infestation patterns and geographic distribution in teleost fishes, as well as physiological and histopathological data and description of treatment strategies. A total 990 samples of Caligus spp. (N = 212 species) obtained of 233 scientific papers on farmed and wild teleost species from 99 families and 30 orders were used, and the highest number of occurrences was on Carangidae. Caligus spp. was predominantly found in marine environments, and only Caligus lacustris and Caligus epidemicus were found in teleost fish of freshwater environments. There was a high prevalence of Caligus spp. on hosts and infestation occurred predominantly in both the tegument and the gills. Caligus species are distributed across different countries and some particularities were identified and discussed. Caligus elongatus and Caligus bonito bonito had the broadest geographic distribution. Histomorphological and hematological disorders caused by infestation by Caligus spp. were reported and discussed, as well as chemotherapeutic products used for controlling and treating the infestations. Variation in the distribution and geographic patterns of Caligus spp. were little evident in many ecosystems and due to the limited data on the infestation of these sea lice on teleost populations in different regions.

Weed spatial distribution as a function of soil properties in two distinct environments of the Brazilian semi-arid region.

The present study aimed was to evaluate the spatial variability of weed species by means of phytosociological parameters and their correlations with the physical-chemical soil properties, under semiarid climate conditions. Weed phytosociology and soil characterization were carried out in two areas one newly deforested area covering 8.86 ha, and one experimental agricultural area covering 24.7 ha; both in the semi-arid region of Brazil. Weed and soil were sampled by following georeferenced grids in each area. Biomass and the total number of weed individuals, as well as soil properties, were mapped by the ordinary Kriging method. The predominant herbaceous plants in the newly deforested area were Hexasepalum teres and Digitaria insularis. The weed species that predominated in the agricultural area were Cyperus rotundus L., Euphorbia heterophylla L. and Herissantia Crispa (L.) Brizicky; the latter species outstanding for dry biomass (873.5g). Spatial dependence was observed for the predominant species, except for Digitaria insularis. The spatial distribution of these weeds was conditioned by soil K+ contents in both areas, and by sand content for the experimental agricultural area. Therefore, these two soil attributes resulted key factors for weed infestation in this semi-arid region.

Loss of function mutations in essential genes cause embryonic lethality in pigs.

Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size domestic and wild populations, those alleles might be exposed by inbreeding, caused by matings between related parents that inherited the same recessive lethal allele from a common ancestor. In this study we report five relatively common (up to 13.4% carrier frequency) recessive lethal haplotypes in two commercial pig populations. The lethal haplotypes have a large effect on carrier-by-carrier matings, decreasing litter sizes by 15.1 to 21.6%. The causal mutations are of different type including two splice-site variants (affecting POLR1B and TADA2A genes), one frameshift (URB1), and one missense (PNKP) variant, resulting in a complete loss-of-function of these essential genes. The recessive lethal alleles affect up to 2.9% of the litters within a single population and are responsible for the death of 0.52% of the total population of embryos. Moreover, we provide compelling evidence that the identified embryonic lethal alleles contribute to the observed heterosis effect for fertility (i.e. larger litters in crossbred offspring). Together, this work marks specific recessive lethal variation describing its functional consequences at the molecular, phenotypic, and population level, providing a unique model to better understand fertility and heterosis in livestock.

Morphological and functional structure of two Ergasilidae parasites determine their microhabitat affinity on the gills of an Anostomidae fish from the Amazon.

The aim of this study was to investigate the microhabitat affinities of Ergasilus sp. and Therodamas longicollum on the gills of Leporinus fasciatus ("aracu-piau"), an anostomid fish from the Amazon. A total of 143 specimens of L. fasciatus were examined, of which 35% had their gills parasitized by at least one ergasilid species. A total of 159 specimens of Ergasilus sp. and 97 specimens of T. longicollum were recovered. Both ergasilids species exhibited a greater affinity for attachment in arch 1 of the gills of the host. There was a negative correlation between the abundance of Ergasilus sp. and the abundance of T. longicollum within each gill arch. Analysis of distribution along the gill arch showed a higher occurrence of Ergasilus sp. in Section 5, while T. longicollum occurred mainly in Section 3 of the gills. There was a positive correlation between the abundance of these ectoparasites and the size of the gill arch. Ergasilus sp. occurred only on the filament of the gill arch and exhibited affinity for the proximal region, while T. longicollum occurred only in the gill arch itself. The results reveal that these two parasite species compete in the gills of the host without the overlapping of their niches.

Accelerated discovery of functional genomic variation in pigs.

The genotype-phenotype link is a major research topic in the life sciences but remains highly complex to disentangle. Part of the complexity arises from the number of genes contributing to the observed phenotype. Despite the vast increase of molecular data, pinpointing the causal variant underlying a phenotype of interest is still challenging. In this study, we present an approach to map causal variation and molecular pathways underlying important phenotypes in pigs. We prioritize variation by utilizing and integrating predicted variant impact scores (pCADD), functional genomic information, and associated phenotypes in other mammalian species. We demonstrate the efficacy of our approach by reporting known and novel causal variants, of which many affect non-coding sequences. Our approach allows the disentangling of the biology behind important phenotypes by accelerating the discovery of novel causal variants and molecular mechanisms affecting important phenotypes in pigs. This information on molecular mechanisms could be applicable in other mammalian species, including humans.

Underwater Energy Harvesting to Extend Operation Time of Submersible Sensors.

A linear electromagnetic energy harvesting device for underwater applications, fabricated with a simple manufacturing process, was developed to operate with movement frequencies from 0.1 to 0.4 Hz. The generator has two coils, and the effect of the combination of the two coils was investigated. The experimental study has shown that the energy capture system was able to supply energy to several ocean sensors, producing 7.77 mJ per second with wave movements at 0.4 Hz. This study shows that this energy is enough to restore the energy used by the battery or the capacitor and continue supplying energy to the sensors used in the experimental work. For an ocean wave frequency of 0.4 Hz, the generator can supply power to 8 sensors or 48 sensors, depending on the energy consumed and its optimization.

Immobilization and Application of the Recombinant Xylanase GH10 of Malbranchea pulchella in the Production of Xylooligosaccharides from Hydrothermal Liquor of the Eucalyptus (Eucalyptus grandis) Wood Chips.

Xylooligosaccharides (XOS) are widely used in the food industry as prebiotic components. XOS with high purity are required for practical prebiotic function and other biological benefits, such as antioxidant and inflammatory properties. In this work, we immobilized the recombinant endo-1,4-ß-xylanase of Malbranchea pulchella (MpXyn10) in various chemical supports and evaluated its potential to produce xylooligosaccharides (XOS) from hydrothermal liquor of eucalyptus wood chips. Values >90% of immobilization yields were achieved from amino-activated supports for 120 min. The highest recovery values were found on Purolite (142%) and MANAE-MpXyn10 (137%) derivatives, which maintained more than 90% residual activity for 24 h at 70 °C, while the free-MpXyn10 maintained only 11%. In addition, active MpXyn10 derivatives were stable in the range of pH 4.0−6.0 and the presence of the furfural and HMF compounds. MpXyn10 derivatives were tested to produce XOS from xylan of various sources. Maximum values were observed for birchwood xylan at 8.6 mg mL−1 and wheat arabinoxylan at 8.9 mg mL−1, using Purolite-MpXyn10. Its derivative was also successfully applied in the hydrolysis of soluble xylan present in hydrothermal liquor, with 0.9 mg mL−1 of XOS after 3 h at 50 °C. This derivative maintained more than 80% XOS yield after six cycles of the assay. The results obtained provide a basis for the application of immobilized MpXyn10 to produce XOS with high purity and other high-value-added products in the lignocellulosic biorefinery field.

Latex membranes with methylene blue dye for antimicrobial photodynamic therapy.

The search for new materials that can be applied in the treatment of injured human tissues has led to the development of new dressings. Membranes have potential as dressing materials because they can be fitted to and interact with the tissue surface. In this study, we analyze the morphological properties and wettability of latex membranes, along with the incorporation of the photosensitizer methylene blue, in the context of the utility of the membranes in curative applications involving photodynamic therapy (PDT). It was observed that deposition of the photosensitizer into latex membranes increased both the surface roughness and wettability. Antifungal testing indicated that antimicrobial PDT assisted by the latex membranes incorporating methylene blue effectively inactivated Candida albicans.