A whole-body transcriptome assembly of the annelid worm Hediste diversicolor.

The Annelida phylum is composed of a myriad of species exhibiting key phenotypic adaptations. They occupy key ecological niches in a variety of marine, freshwater and terrestrial ecosystems. Importantly, the increment of omic resources is rapidly modifying the taxonomic landscape and knowledge of species belonging to this phylum. Here, we comprehensively characterised and annotated a transcriptome of the common ragworm, Hediste diversicolor (OF Müller). This species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, H. diversicolor plays an important role in benthic food webs. Given its commercial value, H. diversicolor is a promising candidate for aquaculture development and production in farming facilities, under a circular economy framework. We used Illumina next-generation sequencing technology, to produce a total of 105 million (M) paired-end (PE) raw reads and generate the first whole-body transcriptome assembly of H. diversicolor species. This high-quality transcriptome contains 69,335 transcripts with an N50 transcript length of 2313 bp and achieved a BUSCO gene completeness of 97.7% and 96% in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological applications using this species.

Unravelling the main immune repertoire of Paracentrotus lividus following Vibrio anguillarum bath challenge.

Paracentrotus lividus is the most abundant echinoid species in the North East Atlantic Ocean and Mediterranean Sea. Although there is abundant genomic information of the species, there is no deep characterisation of the genes involved in the immune response. Here, a reference transcriptome of male and female coelomocytes was produced. The generated P. lividus transcriptome assembly has 203,511 transcripts, N50 transcript length of 1079 bp, and more than 90% estimated gene completeness in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses showed 54 and 55 up-regulated genes in P. lividus female and male coelomocyte tissues, respectively. These results suggest a similar immune gene repertoire between sexes. To examine the immune response, P. lividus was challenged with Vibrio anguillarum, one of the candidate pathogens for bald disease. Immune parameters were evaluated at cell and humoral levels, as well as the expression analysis of immune related genes at an early response stage. No differences were found at cellular and humoral levels with the exception of the increase of nitric oxide in perivisceral fluid of challenged animals. At the gene expression level, a total of 2721 genes were upregulated in challenged animals, 13.6 times higher expression than control group. Our analysis revealed that four major KEGG pathways were enriched in challenged animals: Autophagy (KEGG:04140), Endocytosis (KEGG:04144), Phagosome (KEGG:04145) and Protein processing in endoplasmic reticulum (KEGG:04141). Several toll-like receptors (TLR), scavenger receptors cysteine-rich (SRCR) or nucleotide-binding oligomerisation domain like receptors (NLR) were identified as major family genes for pathogen recognition and immune defence. This study provides a valuable transcriptomic resource and unfolds the molecular basis of immune response to V. anguillarum exposure. Overall, our findings contribute to the conservation effort of the P. lividus populations, as well as its sustainable exploitation in an aquaculture context.

Case study: Visual barriers reduce pacing in captive tigers.

Captive large felines are prone to abnormal repetitive behaviors like pacing, which are associated with welfare issues. Visual contact without the opportunity to engage in appropriate behavior is known to increase pacing. To better understand the relationship between pacing and conspecific visual contact, we investigated this effect by conducting a barrier experiment on a male-female pair of Sumatran tigers (Panthera tigris sumatrae) in Rotterdam Zoo, the Netherlands. The tigers were exposed to four consecutive housing treatments: (i) housed in the same enclosure (baseline), (ii) housed in separate enclosures with visual contact, (iii) housed in separate enclosures without visual contact, and (iv) housed in the same enclosure after the separation. We used focal and scan sampling to measure pacing and recorded the number of visitors. Moreover, we applied scan sampling to measure activity. Overall, our results indicate that the tigers paced significantly more when housed in separate enclosures with conspecific visual contact. Moreover, our results suggest that limiting visual contact between neighboring tigers can mitigate pacing. Implementing these findings in tiger husbandry and enclosure design has the potential to improve animal welfare zoo populations of large felines.

Dataset of the complete mitogenome of the deep-sea sailfin roughshark, Oxynotus paradoxus Frade, 1929.

Chondrichthyans comprise a diverse group of vertebrate species with extraordinary ecological relevance. Yet, multiple members of this evolutionary lineage are associated with significant extinction risk. The sailfin roughshark Oxynotus paradoxus is a deep-water benthic shark currently listed as vulnerable due to population declines in parts of its range. Here we provide the first complete mitochondrial genome of O. paradoxus, comprising also the first record for the genus and family Oxynotidae. These data can facilitate future monitoring of the genetic diversity in this and related species. Genomic DNA was extracted from O. paradoxus collected in the eastern North Atlantic off western Portugal (37.59°N, 9.51°W) and sent for Illumina Paired-End (2 × 150 bp) library construction and whole genome sequencing on a Novaseq6000 platform. Trimmomatic (version 0.38) was used to remove adapters and MitoZ (version 3.4) to assemble and annotate the mitogenome. This mitogenome with 17 100 bp has a total of 38 genes, 13 of which are protein-coding genes, 23 transfer RNA genes, and 2 ribosomal RNA genes. Eight transfer RNAs and 1 protein-coding gene (NADH dehydrogenase subunit 6, NAD6) are in the complementary strand. In the provided phylogenetic inference, with all available and verified Squalomorphii mitogenomes, the four orders are well separated, and as expected, O. paradoxus is placed in the Squaliformes order. This data reinforces the need for more genomic resources for the Oxynotidae family.

There and back again: when and how the world's richest snake family (Dipsadidae) dispersed and speciated across the Neotropical region

Aim The widespread megadiverse Neotropical snake family Dipsadidae occurs in a large range of diverse habitats. Therefore, it represents an excellent model to study the diversification of Neotropical biota. Herein, by generating a time-calibrated species-level phylogeny, we investigate the origin and historical biogeography of Dipsadidae and test if its two main Neotropical subfamilies, Xenodontinae and Dipsadinae, have different geographical origins. Location Neotropical region. Taxon Dipsadidae (Serpentes). Methods We generated a new Bayesian time-calibrated phylogeny based on published sequences from six genes for 344 species, including 287 species of Dipsadidae. We subsequently estimated ancestral areas of distribution by comparing models in BioGeoBEARS: DEC (subset sympatry, narrow vicariance), DIVALIKE (narrow and wide vicariance), BAYAREALIKE (no vicariance and widespread sympatry), also testing jump dispersal. We also estimated shifts in the diversification of this group using BAMM, exploring possible relationships with its historical biogeography. Results The best models show that Dipsadidae likely originated approximately 50 million years ago (mya) in Asia. Dispersal was a fundamental process in its historical biogeography. The DEC model with jump dispersal indicated that this family underwent a range extension from Asia and posterior vicariance of North and Central America ancestors. Both Xenodontinae and Dipsadinae originated in Central America and dispersed to South America during Middle Eocene, but did so to different regions (cis and trans-Andean South America, respectively). Xenodontinae entered cis-Andean South America around 39 mya and jump dispersed to the West Indies around 33 mya, while Dipsadinae entered trans-Andean South America multiple times 20–38 mya. The diversification rate decreased through time, except for a clade within Dipsadinae composed of the Dipsadini tribe and the Atractus and Geophis genera. Main Conclusions Our results show that Dipsadidae has an Asian origin and that the two main Neotropical subfamilies originated in Central America, later dispersing to South America in different time periods. This difference is also reflected in the higher diversification rate for the ‘goo-eaters’ in the Dipsadinae subfamily. The current biogeographical patterns of the family Dipsadidae, the most species-rich snake family in the world, have likely been shaped by complex evolutionary and geological processes such as Eocene land bridges, Andean uplift and the formation of the Panama isthmus.

An Ancestral Major Histocompatibility Complex Organization in Cartilaginous Fish: Reconstructing MHC Origin and Evolution.

Cartilaginous fish (sharks, rays, and chimeras) comprise the oldest living jawed vertebrates with a mammalian-like adaptive immune system based on immunoglobulins (Ig), T-cell receptors (TCRs), and the major histocompatibility complex (MHC). Here, we show that the cartilaginous fish "adaptive MHC" is highly regimented and compact, containing (i) a classical MHC class Ia (MHC-Ia) region containing antigen processing (antigen peptide transporters and immunoproteasome) and presenting (MHC-Ia) genes, (ii) an MHC class II (MHC-II) region (with alpha and beta genes) with linkage to beta-2-microglobulin (ß2m) and bromodomain-containing 2, (iii) nonclassical MHC class Ib (MHC-Ib) regions with 450 million-year-old lineages, and (iv) a complement C4 associated with the MHC-Ia region. No MHC-Ib genes were found outside of the elasmobranch MHC. Our data suggest that both MHC-I and MHC-II genes arose after the second round of whole-genome duplication (2R) on a human chromosome (huchr) 6 precursor. Further analysis of MHC paralogous regions across early branching taxa from all jawed vertebrate lineages revealed that Ig/TCR genes likely arose on a precursor of the huchr9/12/14 MHC paralog. The ß2m gene is linked to the Ig/TCR genes in some vertebrates suggesting that it was present at 1R, perhaps as the donor of C1 domain to the primordial MHC gene. In sum, extant cartilaginous fish exhibit a conserved and prototypical MHC genomic organization with features found in various vertebrates, reflecting the ancestral arrangement for the jawed vertebrates.

Mitochondrial replication's role in vertebrate mtDNA strand asymmetry.

Mitogenomes are defined as compact and structurally stable over aeons. This perception results from a vertebrate-centric vision, where few types of mtDNA rearrangements are described. Here, we bring a new light to the involvement of mitochondrial replication in the strand asymmetry of the vertebrate mtDNA. Using several species of deep-sea hatchetfish (Sternoptychidae) displaying distinct mtDNA structural arrangements, we unravel the inversion of the coding direction of protein-coding genes (PCGs). This unexpected change is coupled with a strand asymmetry nucleotide composition reversal and is shown to be directly related to the strand location of the Control Region (CR). An analysis of the fourfold redundant sites of the PCGs (greater than 6000 vertebrates), revealed the rarity of this phenomenon, found in nine fish species (five deep-sea hatchetfish). Curiously, in Antarctic notothenioid fishes (Trematominae), where a single PCG inversion (the only other record in fish) is coupled with the inversion of the CR, the standard asymmetry is disrupted for the remaining PCGs but not yet reversed, suggesting a transitory state. Our results hint that a relaxation of the classic vertebrate mitochondrial structural stasis promotes disruption of the natural balance of asymmetry of the mtDNA. These findings support the long-lasting hypothesis that replication is the main molecular mechanism promoting the strand-specific compositional bias of this unique and indispensable molecule.

Extensive gene loss parallels kidney aglomerulism in Syngnathidae.

The eccentric seahorses, seadragons, pipehorses and pipefishes (Syngnathidae) have an aglomerular kidney1. Here, we show that nephron genes2 conserved in Bilateria are secondarily eroded/deleted in Syngnathidae genomes. A transcriptome enrichment analysis suggests the predominance of excretion processes in the Syngnathidae kidney. In a lineage where crypsis and idleness are tightly associated, we propose that aglomerulism evolved as an energy-saving strategy.

Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species.

Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.

Image-guided surgical planning of percutaneous nephrolithotomy with patient-specific CTRs.

PURPOSE: We propose the utilization of patient-specific concentric-tube robots (CTRs) whose designs are optimized to enhance their volumetric reachability of the renal stone, thus reducing the morbidities associated with percutaneous nephrolithotomy procedures. By employing a nested optimization-driven scheme, this work aims to determine a single surgical tract through which the patient-tailored CTR is deployed. We carry out a sensitivity analysis on the combined percutaneous access and optimized CTR design with respect to breathing-induced excursion of the kidneys based on preoperative images. Further, an investigation is also performed of the appropriateness and effectiveness of the percutaneous access provided by the proposed algorithm compared to that of an expert urologist. METHODS: The method is based on an ellipsoidal approximation to the renal calculi and a grid search over candidate skin areas and available renal calyces using an anatomically constrained kinematic mapping of the CTR. Percutaneous access is selected for collision-free CTR deployment to the centroid of the stones with minimal positional error at the renal calyx. Further optimization of the CTR design results in a robot tailored to the therapeutic anatomical features of each clinical case. The study examined 14 sets of clinical data of PCNL patients, analyzing stone reachability using preoperative images and breathing-induced motions of the kidney. An experienced urologist qualitatively assessed the adequacy of percutaneous access generated by the algorithm. RESULTS: An assessment conducted by an expert urologist found that the percutaneous accesses produced by the proposed approach were found to be comparable to those chosen by the expert surgeon in most clinical cases. The simulated results demonstrated a mean volume coverage of [Formula: see text] for static anatomy and [Formula: see text] and [Formula: see text] when considering a 1 cm excursion of the kidney in the craniocaudal directions due to respiration or tool-tissue interaction. CONCLUSION: The optimization-driven scheme for determining a single tract surgical plan, coupled with the use of a patient-specific CTR, shows promising results for improving percutaneous access in PCNL procedures. This approach clearly shows the potential for enhancing the quality and suitability of percutaneous accesses, addressing the challenges posed by staghorn and non-staghorn stones during PCNL procedures. Further research involving clinical validation is necessary to confirm these findings and explore the potential clinical benefits of the approach.

Composition Dependent Instabilities in Mixtures with Many Components.

Understanding the phase behavior of mixtures with many components is important in many contexts, including as a key step toward a physics-based description of intracellular compartmentalization. Here, we study phase ordering instabilities in a paradigmatic model that represents the complexity of-e.g., biological-mixtures via random second virial coefficients. Using tools from free probability theory we obtain the exact spinodal curve and the nature of instabilities for a mixture with an arbitrary composition, thus lifting an important restriction in previous work. We show that, by controlling the concentration of only a few components, one can systematically change the nature of the spinodal instability and achieve demixing for realistic scenarios by a strong composition imbalance amplification. This results from a nontrivial interplay of interaction complexity and entropic effects due to the nonuniform composition. Our approach can be extended to include additional systematic interactions, leading to a competition between different forms of demixing as density is varied.

Reproductive and environmental traits explain the variation in egg size among Medusozoa (Cnidaria).

Medusozoa (Cnidaria) are characterized by diverse life cycles, with different semaphoronts (medusa, medusoid, fixed gonophore, polyp) representing the sexual phase and carrying the gametes. Although egg size is often considered a proxy to understand reproductive and developmental traits of medusozoans, understanding of the processes influencing egg size variation in the group under an evolutionary context is still limited. We carried out a comprehensive review of the variation of egg size in Medusozoa to test whether this variation is related to biological/sexual or environmental traits. Egg size presents a strong phylogenetic signal (λ = 0.79, K = 0.67), explaining why closely related species with different reproductive strategies and different individual sizes have similar egg sizes. However, variation in egg size is influenced by the number of eggs, depth and temperature, with larger eggs frequently present in species with few eggs (1-15), in deep-sea species and in cold-water species. Conversely, the production of small eggs among cold-water species of Staurozoa might be associated with the development of a small benthic larvae in this group. Our study reinforces that egg sizes respond to reproductive and environmental traits, although egg size is highly conserved within medusa classes.

Nonequilibrium mixture dynamics: A model for mobilities and its consequences.

Extending the famous model B for the time evolution of a liquid mixture, we derive an approximate expression for the mobility matrix that couples different mixture components. This approach is based on a single component fluid with particles that are artificially grouped into separate species labeled by "colors." The resulting mobility matrix depends on a single dimensionless parameter, which can be determined efficiently from experimental data or numerical simulations, and includes existing standard forms as special cases. We identify two distinct mobility regimes, corresponding to collective motion and interdiffusion, respectively, and show how they emerge from the microscopic properties of the fluid. As a test scenario, we study the dynamics after a thermal quench, providing a number of general relations and analytical insights from a Gaussian theory. Specifically, for systems with two or three components, analytical results for the time evolution of the equal time correlation function compare well to results of Monte Carlo simulations of a lattice gas. A rich behavior is observed, including the possibility of transient fractionation.

Crohn's disease: review and standardization of nomenclature.

Crohn's disease is an inflammatory bowel disease that can affect any segment of the gastrointestinal tract. It has a variable clinical course, with alternating periods of disease activity and remission. Because the incidence and prevalence of Crohn's disease have been increasing, evaluation by imaging methods has become more important. The most widely used methods are computed tomography enterography, magnetic resonance enterography (as an elective examination), and contrast-enhanced computed tomography (in the context of emergency). Computed tomography enterography and magnetic resonance enterography are useful for diagnosis, follow-up, evaluation of complications, and prognosis. Both can be used in order to evaluate the small bowel loops and the associated mesenteric findings, as well as to evaluate other abdominal organs. They both also can detect signs of disease activity, fibrosis, penetrating disease, and complications. The interpretation of such changes is essential to the multidisciplinary approach, as is the standardization of the nomenclature employed in the reports. In this paper, we review and illustrate the imaging findings of Crohn's disease, using the standardized nomenclature proposed in the multidisciplinary consensus statement issued by the Society of Abdominal Radiology, the Society of Pediatric Radiology, and the American Gastroenterology Association, with recommendations for descriptions, interpretations, and impressions related to those findings.

Doença de Crohn é uma doença inflamatória intestinal que pode acometer qualquer segmento do trato gastrointestinal, com curso clínico variado, alternando períodos de atividade de doença e remissão. Sua incidência e prevalência vêm aumentando, tornando a avaliação por métodos de imagem mais importante. Os métodos mais utilizados são enterotomografia computadorizada, enterorressonância magnética eletivamente e tomografia computadorizada com contraste no contexto da emergência. A enterotomografia computadorizada e a enterorressonância magnética são úteis para diagnóstico, seguimento, avaliação de complicações e para prognóstico. Avaliam as alças intestinais delgadas e os achados mesentéricos associados, além dos demais órgãos abdominais. Detectam sinais de atividade de doença, sinais de cronicidade e doença penetrante e complicações, importantes para a escolha do melhor tratamento. A interpretação dessas alterações é fundamental para que a equipe multidisciplinar trabalhe conjuntamente com compreensão da linguagem utilizada nos relatórios. Neste artigo, apresentamos uma revisão dos achados de imagem da doença de Crohn e ilustramos os possíveis achados dessa doença utilizando a nomenclatura padronizada proposta no consenso multidisciplinar composto pelas Sociedade de Radiologia Abdominal, Sociedade de Radiologia Pediátrica e a Associação Americana de Gastroenterologia, com recomendações de descrição, interpretação dos achados e recomendações de impressão.

Corrigendum: Uncovering a 500 million year old history and evidence of pseudogenization for TLR15.

[This corrects the article DOI: 10.3389/fimmu.2022.1020601.].

Decay of Skin-Specific Gene Modules in Pangolins.

The mammalian skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation, Awat1/2, show patterns of inactivation in the stem pangolin branch, while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function is intact and expressed in the pangolin skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes.

Predictors of cardiac involvement in idiopathic inflammatory myopathies.

Objectives: Idiopathic inflammatory myopathies (IIM) are a group of rare disorders that can affect the heart. This work aimed to find predictors of cardiac involvement in IIM. Methods: Multicenter, open cohort study, including patients registered in the IIM module of the Rheumatic Diseases Portuguese Register (Reuma.pt/Myositis) until January 2022. Patients without cardiac involvement information were excluded. Myo(peri)carditis, dilated cardiomyopathy, conduction abnormalities, and/or premature coronary artery disease were considered. Results: 230 patients were included, 163 (70.9%) of whom were females. Thirteen patients (5.7%) had cardiac involvement. Compared with IIM patients without cardiac involvement, these patients had a lower bilateral manual muscle testing score (MMT) at the peak of muscle weakness [108.0 ± 55.0 vs 147.5 ± 22.0, p=0.008] and more frequently had oesophageal [6/12 (50.0%) vs 33/207 (15.9%), p=0.009] and lung [10/13 (76.9%) vs 68/216 (31.5%), p=0.001] involvements. Anti-SRP antibodies were more commonly identified in patients with cardiac involvement [3/11 (27.3%) vs 9/174 (5.2%), p=0.026]. In the multivariate analysis, positivity for anti-SRP antibodies (OR 104.3, 95% CI: 2.5-4277.8, p=0.014) was a predictor of cardiac involvement, regardless of sex, ethnicity, age at diagnosis, and lung involvement. Sensitivity analysis confirmed these results. Conclusion: Anti-SRP antibodies were predictors of cardiac involvement in our cohort of IIM patients, irrespective of demographical characteristics and lung involvement. We suggest considering frequent screening for heart involvement in anti-SRP-positive IIM patients.

Crohn's disease: review and standardization of nomenclature / Doença de Crohn: revisão e padronização da nomenclatura

Abstract Crohn's disease is an inflammatory bowel disease that can affect any segment of the gastrointestinal tract. It has a variable clinical course, with alternating periods of disease activity and remission. Because the incidence and prevalence of Crohn's disease have been increasing, evaluation by imaging methods has become more important. The most widely used methods are computed tomography enterography, magnetic resonance enterography (as an elective examination), and contrast-enhanced computed tomography (in the context of emergency). Computed tomography enterography and magnetic resonance enterography are useful for diagnosis, follow-up, evaluation of complications, and prognosis. Both can be used in order to evaluate the small bowel loops and the associated mesenteric findings, as well as to evaluate other abdominal organs. They both also can detect signs of disease activity, fibrosis, penetrating disease, and complications. The interpretation of such changes is essential to the multidisciplinary approach, as is the standardization of the nomenclature employed in the reports. In this paper, we review and illustrate the imaging findings of Crohn's disease, using the standardized nomenclature proposed in the multidisciplinary consensus statement issued by the Society of Abdominal Radiology, the Society of Pediatric Radiology, and the American Gastroenterology Association, with recommendations for descriptions, interpretations, and impressions related to those findings.

Resumo Doença de Crohn é uma doença inflamatória intestinal que pode acometer qualquer segmento do trato gastrointestinal, com curso clínico variado, alternando períodos de atividade de doença e remissão. Sua incidência e prevalência vêm aumentando, tornando a avaliação por métodos de imagem mais importante. Os métodos mais utilizados são enterotomografia computadorizada, enterorressonância magnética eletivamente e tomografia computadorizada com contraste no contexto da emergência. A enterotomografia computadorizada e a enterorressonância magnética são úteis para diagnóstico, seguimento, avaliação de complicações e para prognóstico. Avaliam as alças intestinais delgadas e os achados mesentéricos associados, além dos demais órgãos abdominais. Detectam sinais de atividade de doença, sinais de cronicidade e doença penetrante e complicações, importantes para a escolha do melhor tratamento. A interpretação dessas alterações é fundamental para que a equipe multidisciplinar trabalhe conjuntamente com compreensão da linguagem utilizada nos relatórios. Neste artigo, apresentamos uma revisão dos achados de imagem da doença de Crohn e ilustramos os possíveis achados dessa doença utilizando a nomenclatura padronizada proposta no consenso multidisciplinar composto pelas Sociedade de Radiologia Abdominal, Sociedade de Radiologia Pediátrica e a Associação Americana de Gastroenterologia, com recomendações de descrição, interpretação dos achados e recomendações de impressão.

The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus).

BACKGROUND: The loach (Misgurnus anguillicaudatus), the most widely distributed species of the family Cobitidae, displays a mud-dwelling behavior and intestinal air-breathing, inhabiting the muddy bottom of extensive freshwater habitats. However, lack of high-quality reference genome seriously limits the interpretation of the genetic basis of specialized adaptations of the loach to the adverse environments including but not limited to the extreme water temperature, hypoxic and noxious mud environment. RESULTS: This study generated a 1.10-Gb high-quality, chromosome-anchored genome assembly, with a contig N50 of 3.83 Mb. Multiple comparative genomic analyses found that proto-oncogene c-Fos (fos), a regulator of bone development, is positively selected in loach. Knockout of fos (ID: Mis0086400.1) led to severe osteopetrosis and movement difficulties, combined with the comparison results of bone mineral density, supporting the hypothesis that fos is associated with loach mud-dwelling behavior. Based on genomic and transcriptomic analysis, we identified two key elements involved in the intestinal air-breathing of loach: a novel gene (ID: mis0158000.1) and heat shock protein beta-1 (hspb1). The flavin-containing monooxygenase 5 (fmo5) genes, central to xenobiotic metabolism, undergone expansion in loach and were identified as differentially expressed genes in a drug stress trial. A fmo5-/- (ID: Mis0185930.1) loach displayed liver and intestine injury, indicating the importance of this gene to the adaptation of the loach to the noxious mud. CONCLUSIONS: Our work provides valuable insights into the genetic basis of biological adaptation to adverse environments.