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Purpose To assess the efficacy of tasimelteon to improve sleep in Smith–Magenis syndrome (SMS). Methods A 9-week, double-blind, randomized, two-period crossover study was conducted at four US clinical centers. Genetically confirmed patients with SMS, aged 3 to 39, with sleep complaints participated in the study. Patients were assigned to treatment with tasimelteon or placebo in a 4-week crossover study with a 1-week washout between treatments. Eligible patients participated in an open-label study and were followed for >3 months. Results Improvement of sleep quality (DDSQ50) and total sleep time (DDTST50) on the worst 50% of nights were primary endpoints. Secondary measures included actigraphy and behavioral parameters. Over three years, 52 patients were screened, and 25 patients completed the randomized portion of the study. DDSQ50 significantly improved over placebo (0.4, p = 0.0139), and DDTST50 also improved (18.5 minutes, p = 0.0556). Average sleep quality (0.3, p = 0.0155) and actigraphy-based total sleep time (21.1 minutes, p = 0.0134) improved significantly, consistent with the primary outcomes. Patients treated for ≥90 days in the open-label study showed persistent efficacy. Adverse events were similar between placebo and tasimelteon. Conclusion Tasimelteon safely and effectively improved sleep in SMS.

Lissencephaly represents a spectrum of rare malformations of cortical development including agyria, pachygyria and subcortical band heterotopia. The progress in molecular genetics has led to identification of 31 lissencephaly-associated genes with the overall diagnostic yield over 80%. In this review, we focus on clinical and molecular diagnosis of lissencephaly and summarize the current knowledge on histopathological changes and their correlation with the MRI imaging. Additionally we provide the overview of clinical follow-up recommendations and available data on epilepsy management in patients with lissencephaly.

International audience; Background.-Information to kin is one of the major ethical problems of the new genetics. In France, the revised bioethics law in 2011 created the possibility for patients to authorize professionals, under certain conditions, to directly contact their relatives at risk. Beyond this, other actors, such as GPs, could however play a role in this process. Methods.-Our article is based on an ethnographic-type sociological study by observations and semi-structured interviews with patients (n = 59) and genetic professionals (n = 16) that took place from 2014 to 2016 in three genetic hospital wards in France and Canada. It focuses particularly on genetic predispositions to breast and ovarian cancers as well as genetic hemochromatosis. Results.-Because of its position as a primary care specialist, the general practitioner can play a decisive role in the process of informing relatives about genetic disorders. Upstream of the genetic test, the generalist, thanks to his knowledge of the family context of his patients, can play a referral role towards a specialized consultation. Downstream, it can also ensure a more effective follow-up of the information procedures undertaken by its patients thanks to the medical follow-up that it carries out. Conclusion.-The data collected during our study highlight the unprecedented place that could be that of the general practitioner in the field of prevention in genetics. At the articulation between primary care and highly specialized care, it is the figure of the ''family'' doctor who seems to be called here to be renewed by genetics.

International audience; Newborn screening for severe combined immunodeficiency (SCID) is now routinely performed in many countries across Europe and around the world. The number of T-cell receptor excision circles (TRECs) reflects T cell levels. TREC quantification is possible using dried blood spot (DBS) samples already collected from newborns to screen for other conditions. This method is very sensitive and highly specific. Data in the literature show that the survival rate for children with SCID is much higher when the disease is detected through early screening, as opposed to a later diagnosis. Newborns diagnosed with SCID may receive the appropriate care quickly, before the onset of serious infectious complications, which raises survival rates, improves quality of life, and limits side effects and treatment costs. At the request of the French Ministry of Health, France's National Authority for Health (Haute Autorité de Santé) is expected to issue recommendations on this topic soon. The nationwide DEPISTREC study, involving 48 maternity units across France, showed that routine SCID screening is feasible and effective. Such screening offers the additional benefit of also diagnosing non-SCID lymphopenia within the infant population.

Human Phenotype Ontology (HPO)-based analysis has become standard for genomic diagnostics of rare diseases. Current algorithms use a variety of semantic and statistical approaches to prioritize the typically long lists of genes with candidate pathogenic variants. These algorithms do not provide robust estimates of the strength of the predictions beyond the placement in a ranked list, nor do they provide measures of how much any individual phenotypic observation has contributed to the prioritization result. However, given that the overall success rate of genomic diagnostics is only around 25%–50% or less in many cohorts, a good ranking cannot be taken to imply that the gene or disease at rank one is necessarily a good candidate. Here, we present an approach to genomic diagnostics that exploits the likelihood ratio (LR) framework to provide an estimate of (1) the posttest probability of candidate diagnoses, (2) the LR for each observed HPO phenotype, and (3) the predicted pathogenicity of observed genotypes. LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) placed the correct diagnosis within the first three ranks in 92.9% of 384 case reports comprising 262 Mendelian diseases, and the correct diagnosis had a mean posttest probability of 67.3%. Simulations show that LIRICAL is robust to many typically encountered forms of genomic and phenomic noise. In summary, LIRICAL provides accurate, clinically interpretable results for phenotype-driven genomic diagnostics.

Diagnosis of genetic disorders is hampered by large numbers of variants of uncertain significance (VUSs) identified through next-generation sequencing. Many such variants may disrupt normal RNA splicing. We examined effects on splicing of a large cohort of clinically identified variants and compared performance of bioinformatic splicing prediction tools commonly used in diagnostic laboratories. Two hundred fifty-seven variants (coding and noncoding) were referred for analysis across three laboratories. Blood RNA samples underwent targeted reverse transcription polymerase chain reaction (RT-PCR) analysis with Sanger sequencing of PCR products and agarose gel electrophoresis. Seventeen samples also underwent transcriptome-wide RNA sequencing with targeted splicing analysis based on Sashimi plot visualization. Bioinformatic splicing predictions were obtained using Alamut, HSF 3.1, and SpliceAI software. Eighty-five variants (33%) were associated with abnormal splicing. The most frequent abnormality was upstream exon skipping (39/85 variants), which was most often associated with splice donor region variants. SpliceAI had greatest accuracy in predicting splicing abnormalities (0.91) and outperformed other tools in sensitivity and specificity. Splicing analysis of blood RNA identifies diagnostically important splicing abnormalities and clarifies functional effects of a significant proportion of VUSs. Bioinformatic predictions are improving but still make significant errors. RNA analysis should therefore be routinely considered in genetic disease diagnostics.

Puntos para una lectura rapida • La anamnesis de los antecedentes familiares se considera un elemento central en la practica clinica, con finalidad de ayuda al diagnostico y a la prevencion. • Los nuevos conocimientos sobre la heredabilidad de muchas enfermedades cronicas hacen que el medico de familia deba ser capaz de obtener un historial familiar adecuado para el manejo clinico y preventivo de cada paciente. • La anamnesis sobre antecedentes familiares proporciona datos sobre herencia, estilo de vida y ambiente compartidos por toda la familia. • El medico de familia debe integrar estos antecedentes medicos familiares junto a otros datos sociologicos y relacionales que constituyen el genograma del paciente. • En atencion primaria, el grado de registro de los antecedentes familiares en las historias clinicas es bajo. El tiempo disponible y la herramienta de registro son las principales barreras para su implementacion. • Un cuestionario breve, con soporte electronico, que pueda ser cumplimentado por el paciente o el profesional, integrado en la historia clinica electronica, seria una herramienta factible que ayudaria a los profesionales. • Una tendencia internacional creciente es el uso de arboles genealogicos que las personas completan online. Algunas de estas herramientas proporcionan posteriormente consejo a la persona segun su riesgo familiar. Tambien pueden imprimirse para comentarlas en la consulta de atencion primaria. • Son necesarias herramientas breves validadas en atencion primaria para facilitar el aumento de los registros de antecedentes familiares por el medico de familia. • Estas herramientas deben proporcionar asimismo apoyo para calcular el riesgo familiar de cada individuo y para la toma de decisiones clinicas o preventivas. • No existe evidencia suficiente de que la anamnesis rutinaria sobre antecedentes familiares tenga un resultado positivo sobre la salud del paciente y/o su familia.

Purpose Our laboratory has classified patients with methylmalonic aciduria using somatic cell studies for over four decades. We have accumulated 127 fibroblast lines from patients with persistent elevated methylmalonic acid (MMA) levels in which no genetic cause could be identified. Cultured fibroblasts from 26 of these patients had low [14C]propionate incorporation into macromolecules, possibly reflecting decreased methylmalonyl-CoA mutase function. Methods Genome sequencing (GS), copy-number variation (CNV) analysis, and RNA sequencing were performed on genomic DNA and complementary DNA (cDNA) from these 26 patients. Results No patient had two pathogenic variants in any gene associated with cobalamin metabolism. Nine patients had heterozygous variants of unknown significance previously identified by a next-generation sequencing (NGS) panel targeting cobalamin metabolic genes. Three patients had pathogenic changes in genes not associated with cobalamin metabolism (PCCA, EPCAM, and a 17q12 duplication) that explain parts of their phenotypes other than elevated MMA. Conclusion Genome and RNA sequencing did not detect any additional putative causal genetic defects in known cobalamin genes following somatic cell studies and the use of a targeted NGS panel. They did detect pathogenic variants in other genes in three patients that explained some aspects of their clinical presentation.

Purpose: In 2014, our institution launched a randomized control trial (RCT) comparing rapid genome sequencing (GS) to standard clinical evaluations of infants with suspected genetic disorders. This study aimed to understand parental response to the use of GS for their newborn babies. Methods: 23 of 128 parents whose infant had enrolled in the RCT completed a retrospective survey and interview addressing attitudes about GS and responses to receiving diagnostic information. We also collected information about participants’ genetic literacy, genetic knowledge, numeracy, and symptoms of anxiety and depression. Results: The majority reported positive, 13 (56.5%), or neutral, 4 (17.4%), feelings when approached about GS for their infant and 100% felt that GS was generally beneficial. The 12 participants who had received a unifying diagnosis for their child’s symptoms described personal utility of the information. Some reported the diagnosis led to changes in medical care. Participants showed understanding of some of the psychological risks of GS. For example, 21 (91.3%) agreed or strongly agreed that genetic testing could reveal disturbing results. Conclusion: Parents who enrolled their newborn in a RCT of GS demonstrated awareness of a psychological risk, but generally held positive beliefs about GS and perceived the benefits outweighed the risk.

People undergoing diagnostic genome-scale sequencing are expected to have better psychological outcomes when they can incorporate and act on accurate, relevant knowledge that supports informed decision making. This longitudinal study used data from the North Carolina Clinical Genomic Evaluation by NextGen Exome Sequencing Study (NCGENES) of diagnostic exome sequencing to evaluate associations between factual genomic knowledge (measured with the University of North Carolina Genomic Knowledge Scale at three assessments from baseline to after return of results) and sequencing outcomes that reflected participants’ perceived understanding of the study and sequencing, regret for joining the study, and responses to learning sequencing results. It also investigated differences in genomic knowledge associated with subgroups differing in race/ethnicity, income, education, health literacy, English proficiency, and prior genetic testing. Multivariate models revealed higher genomic knowledge at baseline for non-Hispanic Whites and those with higher income, education, and health literacy (p values < 0.001). These subgroup differences persisted across study assessments despite a general increase in knowledge among all groups. Greater baseline genomic knowledge was associated with lower test-related distress (p = 0.047) and greater perceived understanding of diagnostic genomic sequencing (p values 0.04 to

Recommendations are made for the genetic screening of gamete donors. These recommendations are the result of the consensus reached by a work group consisting of representatives from the Spanish Fertility Society, the Spanish Association of Andrology, the Spanish Association of Medical Biopathology and Laboratory Medicine, the Association for the Study of Reproductive Biology and the Spanish Association of Human Genetics and were subsequently reviewed and approved by the executive boards of each of these associations. This document describes 2 types of genetic screening: a basic mandatory screening of all donors and an extended genetic screening for donor-recipient genetic matching. The importance of pre- and post-screening genetic counselling, the management of the occurrence of adverse reactions of a genetic nature and the use of informed consent from donors who accept the management of their DNA samples stored in the centre's bank are emphasized. The role of informed consent to find out patients’ opinions on what type of screening they want to be carried out, their desire to know the results of the screening and aptitude for future genetic data is also highlighted.

This article is based on the address given by the author at the 2020 virtual meeting of the American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website.

Purpose: Where multiple in silico tools are concordant, the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) framework affords supporting evidence toward pathogenicity or benignity, equivalent to a likelihood ratio of ~2. However, limited availability of “clinical truth sets” and prior use in tool training limits their utility for evaluation of tool performance. Methods: We created a truth set of 9,436 missense variants classified as deleterious or tolerated in clinically validated high-throughput functional assays for BRCA1, BRCA2, MSH2, PTEN, and TP53 to evaluate predictive performance for 44 recommended/commonly used in silico tools. Results: Over two-thirds of the tool–threshold combinations examined had specificity of 0.7. For Meta-SNP, the equivalent PLR = 42.9 (14.4–406) and NLR = 19.4 (15.6–24.9). Conclusion: Against these clinically validated “functional truth sets," there was wide variation in the predictive performance of commonly used in silico tools. Overall, REVEL and Meta-SNP had best balanced accuracy and might potentially be used at stronger evidence weighting than current ACMG/AMP prescription, in particular for predictions of benignity.

Purpose: Beckwith-Wiedemann syndrome (BWS) is a developmental disorder caused by dysregulation of the imprinted gene cluster of chromosome 11p15.5 and often associated with loss of methylation (LOM) of the imprinting center 2 (IC2) located in KCNQ1 intron 10. To unravel the etiological mechanisms underlying these epimutations, we searched for genetic variants associated with IC2 LOM.Methods: We looked for cases showing the clinical features of both BWS and long QT syndrome (LQTS), which is often associated with KCNQ1 variants. Pathogenic variants were identified by genomic analysis and targeted sequencing. Functional experiments were performed to link these pathogenic variants to the imprinting defect.Results: We found three rare cases in which complete IC2 LOM is associated with maternal transmission of KCNQ1 variants, two of which were demonstrated to affect KCNQ1 transcription upstream of IC2. As a consequence of KCNQ1 haploinsufficiency, these variants also cause LQTS on both maternal and paternal transmission.Conclusion: These results are consistent with the hypothesis that, similar to what has been demonstrated in mouse, lack of transcription across IC2 results in failure of methylation establishment in the female germline and BWS later in development, and also suggest a new link between LQTS and BWS that is important for genetic counseling.

Polyadenylation plays important roles in gene expression regulation in eukaryotes, which typically involves cleavage and poly(A) tail addition at the polyadenylation site (PAS) of the pre-mature mRNA. Many eukaryotic genes contain more than one PASs, termed as alternative polyadenylation (APA). As a crucial post-transcriptional regulation, polyadenylation affects various aspects of RNA metabolism such as mRNA stability, translocation, and translation. However, polyadenylation has been rarely studied in teleosts. Here we conducted polyadenylation analysis in channel catfish, a commercially important aquaculture species around the world. Using RNA-Seq data, we identified 20,320 PASs which were classified into 14,500 clusters by merging adjacent PASs. Most of the PASs were found in 3' UTRs, followed by intron regions based on the annotation of channel catfish reference genome. No apparent difference in PAS distribution was observed between the sense and antisense strand of the channel catfish genome. The sequence analysis of nucleotide composition and motif around PASs yielded a highly similar profile among various organisms, suggesting the conservation and importance of polyadenylation in evolution. Using APA genes with more than two PASs, gene ontology enrichment revealed genes particularly involved in RNA binding. Reactome pathway analysis showed the enrichment of the innate immune system, especially neutrophil degranulation.

The Trachinotus ovatus (T. ovatus) reach sexual maturity as late as 4–5 years, and there are no obvious morphology differences between males and females, even at maturity, making the selection of male and female parents for selective breeding difficult. To examine the potential regulatory mechanism of sexual differentiation, we conducted a microRNAs (miRNAs) analysis on the ovaries and testes of T. ovatus. A total of 13,423,691 and 11,734,953 raw reads, representing 91,883,908 and 86,879,726 unique sequences of 18–35 nt length obtained from the ovaries and testes, respectively. After mapping to the T. ovatus transcriptome reference sequence (unpublished data), and comparing the miRNA sequences with the miRBase database, 179 known mature miRNAs and 100 novel miRNAs were identified. Expression analysis showed that, 165 miRNAs were differentially expressed between the ovary and testis. To validate the Illumina results, the expression patterns of the nine most differently expressed miRNAs (dre-miR-7a, dre-miR-7b, dre-miR-153a-3p, dre-miR-144-3p, dre-miR-301a, dre-miR-92a-3p, dre-miR-727-5p, Novel 124, and Novel 190, as well as those of five miRNAs that may relate to gonad development (dre-miR-143, dre-miR-101a, dre-miR-202-5p, dre-let-7c-5p, and dre-miR-181a-5p), were assayed with RT-qPCR. The expression trends for all the miRNAs validated with RT-qPCR were consistent with the next-generation sequencing data. The identification and characterization of the miRNAs differentially expressed between the ovary and the testis of the T. ovatus will increase our understanding of the role of miRNAs in gonad differentiation. These data also facilitate studies on miRNA regulation of teleost reproduction.

The glucose transporters (GLUTs) are well known for their essential roles in moving the key metabolites, glucose, galactose, fructose and a number of other important substrates in and out of cells. In this study, we identified a total of 21 glut genes in spotted sea bass (Lateolabrax maculatus) through extensive data mining of existing genomic and transcriptomic databases. Glut genes of spotted sea bass were classified into three subfamilies (Class I, Class II and Class III) according to the phylogenetic analysis. Glut genes of spotted sea bass were distributed in 15 out of 24 chromosomes. Deduced gene structure analysis including the secondary structure and the three-dimensional structures, as well as the syntenic analysis further supported their annotations and orthologies. Expression profile in healthy tissues indicated that 9 of 21 glut genes were expressed in liver of spotted sea bass. During short-term starvation, the mRNA expression levels of 3 glut genes (glut2, glut5, and glut10) were significantly up-regulated in liver (P 0.05), indicating their potential roles in sugar transport and consumption. These findings in our study will facilitate the further evolutionary characterization of glut genes in fish species and provide a theoretical basis for their functional study.

Bioluminescence, the emission of visible light in a living organism, is an intriguing phenomenon observed in different species and environments. In terrestrial organisms, the bioluminescence is observed mainly in beetles of the Elateroidea superfamily (Coleoptera). Several phylogenetic studies have been used different strategies to propose a scenario for the origin and evolution of the bioluminescence within this group, however some of them showed incongruences, mainly about the relationship of the bioluminescent families. In order to increase the number of molecular markers available for Elateroidea species and to propose a more accurate phylogeny, with high supported topology, we employed the Next-Generation Sequencing (NGS) methodology to perform the RNA-Seq analysis of luminescent (Elateridae, Phengodidae, Rhagophthalmidae, and Lampyridae) and non-luminescent (Cantharidae) species of Neotropical beetles. We used the RNA-Seq data to construct a calibrated phylogeny of Elateroidea superfamily using a large number of nuclear molecular markers. The results indicate Lampyridae and Phengodidae/Rhagophthalmidae as sister-groups, suggesting that the bioluminescence evolved later in Elateridae than other families (Lampyridae, Phengodidae, and Rhagophthalmidae), and indicating the Upper Cretaceous as the period for the main diversification of Elateroidea bioluminescent species.

ATP-binding cassette (ABC) transporters belong to a large protein superfamily found in both prokaryotic and eukaryotic organisms. In arthropods, ABC transporters are involved in defense and resistance to insecticides. The Asian citrus psyllid (ACP), Diaphorina citri, is a major vector of the Huanglongbing pathogen (Candidatus Liberibacter asiaticus) worldwide. In this study, the ABC transporter genes were identified based on the transcriptome and genome database of D. citri. A total of 44 DcitABC transporters were identified and grouped into 8 subfamilies (ABCA-ABCH), including 4 DcitABCAs, 4 Bs, 5 Cs, 2 Ds, 1 E, 3 Fs, 15 Gs and 10 Hs, respectively. Phylogenetic analysis of ABC transporters revealed a close relationship between D. citri and Laodelphax striatellus. qPCR analyses showed that several DcitABC transporters were highly expressed in fat body, midgut and the hindgut with Malpighian tubules. In particular, DcitABCG11 and DcitABCG14 were most highly expressed in the hindgut. The transcript abundance of 11 DcitABC genes was significantly upregulated upon exposure to an LC50 concentration of imidacloprid. The expressions of three cytochrome P450 genes and one glutathione S-transferase gene were also significantly elevated. This suggested that DcitABC genes, together with metabolic enzyme genes, are associated with imidacloprid detoxification.

Peptides are known to contribute to central pattern generator (CPG) flexibility throughout the animal kingdom. However, the role played by receptor diversity/complement in determining this functional flexibility is not clear. The stomatogastric ganglion (STG) of the crab, Cancer borealis, contains CPGs that are models for investigating peptidergic control of rhythmic behavior. Although many Cancer peptides have been identified, their peptide receptors are largely unknown. Thus, the extent to which receptor diversity/complement contributes to modulatory flexibility in this system remains unresolved. Here, a Cancer mixed nervous system transcriptome was used to determine the peptide receptor complement for the crab nervous system as a whole. Receptors for 27 peptide families, including multiple receptors for some groups, were identified. To increase confidence in the predicted sequences, receptors for allatostatin-A, allatostatin-B, and allatostatin-C were cloned, sequenced, and expressed in an insect cell line; as expected, all three receptors trafficked to the cell membrane. RT-PCR was used to determine whether each receptor was expressed in the Cancer STG. Transcripts for 36 of the 46 identified receptors were amplified; these included at least one for each peptide family except RYamide. Finally, two peptides untested on the crab STG were assessed for their influence on its motor outputs. Myosuppressin, for which STG receptors were identified, exhibited clear modulatory effects on the motor patterns of the ganglion, while a native RYamide, for which no STG receptors were found, elicited no consistent modulatory effects. These data support receptor diversity/complement as a major contributor to the functional flexibility of CPGs.

Ciliopathies are clinical disorders of the primary cilium with widely recognized phenotypic and genetic heterogeneity. In two Arab consanguineous families, we mapped a ciliopathy phenotype that most closely matches Joubert syndrome (hypotonia, developmental delay, typical facies, oculomotor apraxia, polydactyly, and subtle posterior fossa abnormalities) to a single locus in which a founder homozygous truncating variant in FAM149B1 was identified by exome sequencing. We subsequently identified a third Arab consanguineous multiplex family in which the phenotype of Joubert syndrome/oral-facial-digital syndrome (OFD VI) was found to co-segregate with the same founder variant in FAM149B1. Independently, autozygosity mapping and exome sequencing in a consanguineous Turkish family with Joubert syndrome highlighted a different homozygous truncating variant in the same gene. FAM149B1 encodes a protein of unknown function. Mutant fibroblasts were found to have normal ciliogenesis potential. However, distinct cilia-related abnormalities were observed in these cells: abnormal accumulation IFT complex at the distal tips of the cilia, which assumed bulbous appearance, increased length of the primary cilium, and dysregulated SHH signaling. We conclude that FAM149B1 is required for normal ciliary biology and that its deficiency results in a range of ciliopathy phenotypes in humans along the spectrum of Joubert syndrome.

Cold stress has caused great economic loss in fish culture worldwide. Orange-spotted grouper (Epinephelus coioides) is one of the most serious lost aquatic animals in 2016 cold fronts in South China. However, the molecular mechanism of grouper's cold resistance has remained largely unknown. In the present study, HiSeq™2000 (Illumina) was used to analyze the transcriptomic profiles of the liver from grouper under control temperature (CT, 28 °C) and low temperature (LT, 13 °C). Two normalized liver cDNA libraries of CT and LT groups were created. We obtained 51,944,970 and 51,905,036 clean reads from CT and LT groups, respectively. Comparing the LT group to the CT group, a total of 5905 significantly differentially expressed genes (DEGs) were identified, including 2093 up-regulated unigenes and 3812 down-regulated unigenes. GO annotation and functional enrichment analysis indicated that all of the DEGs were classified into three categories: biological process (23 subclasses), cellular component (18 subclasses) and molecular function (13 subclasses). KEGG analysis of the DEGs showed that 2732 DEGs were annotated to 253 signaling pathways. The most highly enriched pathways were cell adhesion molecules, Staphylococcus aureus infection, PPAR signaling pathway, Vibrio cholerae infection, primary immunodeficiency, fatty acid elongation, and we found cold stress mainly affects immunity, metabolic and signal transduction. Thirteen of the DEGs were further validated by qRT-PCR. Our results provide valuable information for further analysis of the mechanisms of groupers response under cold stress.

We investigated changes in the metabolome in juvenile red drum (Sciaenops ocellatus) induced by increasing amounts of soybean meal (0% to 60%) in extruded, fishmeal-free diets using a nuclear magnetic resonance spectroscopy (NMR)-based metabolomics approach in a 12-week feeding trial. All of the diets were composed of ≈40% total crude protein, ≈11% total crude lipid and were energetically balanced. A fishmeal-containing, commercial extruded diet was used as a control diet throughout the trial. Each week, liver, muscle, intestine and plasma samples were collected and analyzed by NMR to provide a "snapshot" of the metabolome at different time points. Results indicate significant time-dependence of the metabolic profiles in various tissues with stable metabolomic profiles forming after about 9-weeks on the experimental diets. We identify a previously unexploited biomarker of potential dietary stress (N‑formimino‑l‑glutamate (FIGLU)) in the fish that may prove to be useful for optimization of alternative diet formulations.

In juvenile Chinese mitten crabs, ovarian maturation occurring in the first year is known as precocity, and can cause huge economic losses to crab breeding. To discover the molecular mechanisms underlying the regulation of the nervous system of female precocious crabs, eyestalk, brain, and thoracic ganglion transcriptome data were obtained in normal and precocious crabs via high-throughput sequencing technology. A total of 81, 4276, and 22,684 differentially-expressed genes were obtained from the eyestalk, brain, and thoracic ganglion groups, respectively. Functional analysis showed that these genes were significantly enriched in the categories of nutrition metabolism, immunity, endocrine regulation, and circadian rhythm. In precocious eyestalk, the expression of vrille was up-regulated significantly and the ribosome endocrine function decreased, which may result in the decline of gonad-inhibiting hormone secretion. In precocious brains, the expression of period2 with the function of delaying clock phase was down-regulated significantly. In precocious thoracic ganglion, expression changes in circadian rhythm-related genes were very complex, and the precocity of female crabs may be the concrete reflex of integrated actions of many endocrine hormones such as estradiol, ecdysteroid, and juvenile hormone, among others. In addition, we found that the mRNA of vitellogenin was highly expressed in the thoracic ganglion. This study discovered some clock genes and related molecular regulatory mechanisms by the RNA-sequence, which would provide foundational information to further study precocity in female Chinese mitten crabs.

Rising atmospheric carbon dioxide (CO2), primarily from anthropogenic emissions, are resulting in increasing absorption of CO2 by the oceans, leading to a decline in oceanic pH in a process known as ocean acidification (OA). There is a growing body of evidence demonstrating the potential effect of OA on the energetics/physiology and consequently life-history traits of commensally important marine organisms. However, despite this little is known of how fundamental metabolic pathways that underpin changes in organismal physiology are affected by OA. Consequently, a gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) based metabolic profiling approach was applied to examine the metabolic responses of Crassostrea gigas to elevated pCO2 levels, under otherwise natural field conditions. Oysters were exposed natural environmental pCO2 (~625.40 μatm) and elevated pCO2 (~1432.94 μatm) levels for 30 days. Results indicated that 36 differential metabolites were identified. Differential metabolites were mapped in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to search for the related metabolic pathways. Pathway enrichment analysis indicates that alanine, aspartate and glutamate metabolism and glycine, serine and threonine metabolism were the most statistically enriched pathways. Further analysis suggested that elevated pCO2 disturb the TCA cycle via succinate accumulation and C. gigas most likely adjust their energy metabolic via alanine and GABA accumulation accordingly to cope with elevated pCO2. These findings provide an understanding of the molecular mechanisms involved in modulating C. gigas metabolism under elevated pCO2.

A source of premium animal protein, crustaceans are widely distributed and cultivated around the world. Short-term or long-term starvation events occur frequently owing to natural environment changes or manual management strategies in the life cycle of crustaceans. The result induced by starvation is that somatic growth of crustaceans will be retarded, while the immune mechanism is activated in this process. The aim of this study was to investigate whether the immune regulatory pathways are involved in the growth of crustaceans. Twelve muscle tissue transcriptomes of the oriental river prawn Macrobrachium nipponense were sequenced across four fasting stages lasting 0, 7, 14 and 21 d. The results showed that three immune-related pathways were involved in the growth of M. nipponense by regulating actin expression inducing the chemokine signaling pathway, the leukocyte transendothelial migration pathway and the FcR-mediated phagocytosis pathway. Furthermore, we employed RNA interference (RNAi) to further verify the effects that genes involved in the pathways had on regulating growth of M. nipponense. Comparative transcriptional analysis and RNA interference reveal that VASP and WAVE positively regulated the expression of actin; however, WASP negatively regulated the expression of actin. This is the first report that the immune regulatory pathways play key roles in the growth of crustaceans. Our results will not only provide an entirely new understanding of the immune mechanism of crustaceans from a unique angle but also further enrich and develop the theory of growth and developmental biology in crustaceans.

Na+/H+ exchangers (NHEs) are one of the major groups of transmembrane proteins that play crucial roles in pH homeostasis, cell volume regulation and Na+ transport in animals. In our study, twelve NHEs were identified from transcriptomic and genomic databases of Lateolabrax maculatus. The evolutionary footprint of each NHE gene was revealed via the analysis of phylogenetic tree, copy numbers, exon-intron structures and motif compositions. NHEs harbored a high proportion of α-helices (54.7% to 67.0%) and a low proportion of β-sheets (1.3%) and contained 9–13 transmembrane helices (TM). Results of tissue distribution detection revealed that L. maculatus NHE genes exhibited different expression profiles in a tissue-specific manner under normal physiological conditions. In the main osmoregulatory organ, gill, NHE2c and NHE3 showed significant higher expression comparing with other L. maculatus NHE genes. To gain insight into the potential function of L. maculatus NHE genes in response to salinity changes, we evaluated their expression variation after different salinity treatment (0 ppt, 12 ppt, 30 ppt, 45 ppt). During acute salinity stress experiment, L. maculatus NHE genes were regulated in a gene-specific and time-dependent manner. Most NHE genes were upregulated to different extent by low salinity (0 ppt) and exhibited the highest expression value in gills at 6 h, while NHE2c and NHE3 were the most strongly induced genes, suggesting they may play crucial roles in salinity and osmotic regulation. In addition, the expressions of several NHE genes were regulated by isotonic or high salinity treatments, indicating their potential involvements in response to salinity challenge. Our findings in this study provide a foundation for future studies about NHE gene deciphering stress physiology correlated to salinity and osmotic regulation in teleosts.

Publisher Copyright: © 2021 The Authors Background: Atopic dermatitis (AD) is a common chronic inflammatory skin disease with high heritability. Previous genome-wide association studies have identified several loci predisposing to AD. These findings explain approximately 30% of the variance in AD susceptibility, suggesting that further work is required to fully understand the genetic underpinnings. Objective: We sought to gain additional understanding of the genetic contribution to AD risk by using biobank resources. Methods: We completed a genome-wide meta-analysis of AD in 796,661 individuals (Ncases = 22,474) from the FinnGen study, the Estonian Biobank, and the UK Biobank. We further performed downstream in silico analyses to characterize the risk variants at the novel loci. Results: We report 30 loci associating with AD (P < 5 × 10−8), 5 of which are novel. In 2 of the novel loci, we identified missense mutations with deleterious predictions in desmocollin 1 and serpin family B member 7, genes encoding proteins crucial to epidermal strength and integrity. Conclusions: These findings elucidate novel genetic pathways involved in AD pathophysiology. The likely involvement of desmocollin 1 and serpin family B member 7 in AD pathogenesis may offer opportunities for the development of novel treatment strategies for AD in the future.

Nonalcoholic fatty liver disease (NAFLD) is associated with dietary folate deficiency and mutations in genes required for one‑carbon metabolism. However, the mechanism through which this occurs is unclear. To improve our understanding of this link, we investigated liver morphology, metabolism and fuel storage in adult mice with a hypomorphic mutation in the gene methionine synthase reductase (Mtrrgt). MTRR enzyme is a key regulator of the methionine and folate cycles. The Mtrrgt mutation in mice was previously shown to disrupt one‑carbon metabolism and cause a wide-spectrum of developmental phenotypes and late adult-onset macrocytic anaemia. Here, we showed that livers of Mtrrgt/gt female mice were enlarged compared to control C57Bl/6J livers. Histological analysis of these livers revealed eosinophilic hepatocytes with decreased glycogen content, which was associated with down-regulation of genes involved in glycogen synthesis (e.g., Ugp2 and Gsk3a genes). While female Mtrrgt/gt livers showed evidence of reduced β-oxidation of fatty acids, there were no other associated changes in the lipidome in female or male Mtrrgt/gt livers compared with controls. Defects in glycogen storage and lipid metabolism often associate with disruption of mitochondrial electron transfer system activity. However, defects in mitochondrial function were not detected in Mtrrgt/gt livers as determined by high-resolution respirometry analysis. Overall, we demonstrated that adult Mtrrgt/gt female mice showed abnormal liver morphology that differed from the NAFLD phenotype and that was accompanied by subtle changes in their hepatic metabolism and fuel storage., Highlights • Mtrrgt is a knockdown mutation in mice that disrupts one-carbon metabolism • Mtrrgt/gt female livers are enlarged, with eosinophilic hepatocytes • Hepatic glycogen content and lipid metabolism is altered in Mtrrgt/gt mice • Mitochondrial electron transfer system activity was unaffected in Mtrrgt/gt livers • Mtrrgt/gt liver phenotype is weaker than other mutations in one-carbon metabolism

The sharing, circulation, distribution, and use of human tissue samples and related data have become a major political and scientific pre-occupation during the past two decades. In the age of big data, the political, scientific, and economic momentum around the need to increasingly collect and collate massive amounts of data has intensified. At the same time, the control and sharing of samples and data have become increasingly strategic in positioning biobanks within the global biomedical research market. Numerous commentators have identified several reasons why and with whom biobanks choose to share. Despite intensified efforts to encourage sharing within networks, there are still actors who have not embraced the values of sharing. The term 'data hugging' is introduced as a form of data work through which value is generated but sharing as a practice is not exercised according to community expectations. Data hugging is a term used within the biobanking community to describe the practice of withholding samples or data from other network members. While some biobankers consider data hugging to be an impediment to efficient and responsible science, it can also be another way of generating value in an otherwise challenging value creation environment. European biobanking policies, as well as the biobanking community, need a better understanding of these value-generating practices in relation to the life cycle of the biobank.

Large vertebrates are extremely sensitive to anthropogenic pressures, and their populations are declining fast. The white rhinoceros (​Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhino subspecies, the Northern (NWR) and the Southern white rhino (SWR), however, underwent opposite fates: the NWR vanished quickly after the onset of the decline, while the SWR recovered after a severe bottleneck. Such demographic events are predicted to have an erosive effect at the genomic level, linked to increased genetic drift and inbreeding. However, there is little empirical data available with which to reconstruct the subtleties of such processes. We therefore generated a whole-genome, temporal dataset consisting of 52 re-sequenced white rhino genomes, that represents both subspecies at two time windows throughout the past ~ 170 years. Our data not only reveals previously unknown population substructure within both subspecies, but allowed us to quantify the genomic erosion they underwent, with post-bottleneck white rhinos showing significantly lower levels of heterozygosity and higherinbreeding coefficients than pre-bottleneck individuals. Moreover, the effective population size (N​e​) has suffered a decrease of two and three orders of magnitude in the NWR and SWR, respectively. Our data provides empirical support for theoretical predictions about the genomic consequences ofshrinking populations, which is relevant for understanding the process of population extinction. Furthermore, our findings have the potential to inform tailored management approaches for the conservation of the remaining white rhinos.

Newborns with cystic degeneration with or without intractable seizures should be investigated for inborn errors of metabolism, including molybdenum cofactor deficiency (MoCoD). MoCoD may present with non-specific hypoxic ischemic injury in the neonatal period with MRI showing extensive prenatally acquired cystic encephalomalacia involving grey and white matter. Most newborns with MoCoD will present with normal head size and brain appearance at birth and postnatally rapidly develop cystic encephalomalacia. A significant minority will present with signs of prenatal brain injury or malformation. It is important to consider the diagnosis in both scenarios. Low plasma urate and homocysteine may help direct the diagnostic evaluation. Herein, we describe the clinical, radiological and biochemical features of a newborn with MoCoD that was initially suspected of having the condition on biochemical screening and confirmed on rapid whole exome sequencing. Keywords: Molybdenum cofactor deficiency, Cystic, Brain MRI, Inborn errors of metabolism

Bioluminescence in Diptera is found in the Keroplatidae family, within Arachnocampininae and Keroplatinae subfamilies, with reported occurrences in Oceania, Eurasia, and Americas. Larvae of Orfelia fultoni, which inhabit stream banks in the Appalachian Mountains, emit the bluest bioluminescence among insects, using it for prey attraction, similarly to Arachnocampa spp. Although bioluminescence has a similar prey attraction function, the systems of Arachonocampininae and Keroplatinae subfamilies are morphologically/biochemically distinct, indicating different evolutionary origins. To identify the possible coding genes associated with physiological control, ecological adaptations, and origin/evolution of bioluminescence in the Keroplatinae subfamily, we performed the RNA-Seq analysis of O. fultoni larvae during day and night and compared it with the transcriptomes of Arachnocampa luminosa, and reanalyzed the previously published proteomic data of O. fultoni against the RNA-Seq dataset. The abundance of chaperones/heat-shock and hexamerin gene products at night and in luciferase enriched fractions supports their possible association and participation in bioluminescence. The low diversity of copies/families of opsins indicate a simpler visual system in O. fultoni. Noteworthy, gene products associated with silk protein biosynthesis in Orfelia were more similar to Lepidoptera than to the Arachnocampa, indicating that, similarly to the bioluminescent systems, at some point, the biochemical apparatus for web construction may have evolved independently in Orfelia and Arachnocampa.

Type 2 Diabetes mellitus (T2DM) is a multifactorial and polygenic disorder with the molecular bases still idiopathic. Experimental analyses and tests are quite limited upon human samples due to the access, variability of patient's conditions, and the size and complexity of the genome. Therefore, high-sugar diet exposure is commonly used for modeling T2DM in non-human animals, which includes invertebrate organisms like the fruit fly Drosophila melanogaster. Interestingly, high-sugar diet (HSD) induces delayed time for pupation and reduced viability in fruit fly larvae hatched from a 30% sucrose-containing medium (HSD-30%). Here we carried out an mRNA-deep sequencing study to identify differentially transcribed genes in adult fruit fly hatched and reared from an HSD-30%. Seven days after hatching, flies reared on control and HSD-30% were used to glucose and triglyceride level measurements and RNA extraction for sequencing. Remarkably, glucose levels were about 2-fold higher than the control group in fruit flies exposed to HSD-30%, whereas triglycerides levels increased 1.7-fold. After RNA-sequencing, we found that 13.5% of the genes were differentially transcribed in the dyslipidemic and hyperglycaemic insects. HSD-30% up-regulated genes involved in ribosomal biogenesis (e.g. dTOR, ERK and dS6K) and down-regulated genes involved in energetic process (e.g. Pfk, Gapdh1, and Pyk from pyruvate metabolism; kdn, Idh and Mdh2 from the citric acid cycle; ATPsynC and ATPsynẞ from ATP synthesis) and insect development. We found a remarkable down-regulation for Actin (Act88F) that likely impairs muscle development. Moreover, HSD-30% up-regulated both the insulin-like peptides 7 and 8 and down-regulated the insulin receptor substrate p53, isoform A and insulin-like peptide 6 genes, whose functional products are insulin signaling markers. All these features pointed together to a tightly correlation of the T2DM-like phenotype modeled by the D. melanogaster and an intricate array of phenomena, which includes energetic processes, muscle development, and ribosomal synthesis as that observed for the human pathology.

Oxidation Resistance Gene 1 (OXR1) is a conserved gene family involved in protecting various species against oxidative stress. The zebrafish expresses a pair of OXR1 paralogs (i.e., oxr1a and oxr1b). Our previous work has revealed the importance of oxr1a in regulating antioxidant defenses during oxidative stress, but the role of oxr1b is remains unknown. Herein we reported the spatial-temporal expression of oxr1b and revealed its function through reverse genetics. The results showed that, as with oxr1a, oxr1b is a typical maternal-zygotic gene. Its mRNA is mainly distributed in the eye, brain and nervous system (e.g., anterior/posterior lateral line ganglion, neuromasts and spinal cord neuron). Although oxr1a and oxr1b genes have similar expression patterns during embryonic development, the latter have higher levels at the corresponding stages. Subsequently, a viable oxr1b-/- mutant was generated by the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) system. Oxr1b knockout caused multiple antioxidant genes (i.e., gpx4a, gpx4b, sod1 and sod3b) to be downregulated, resulting in hypersensitive to oxidative stress. Furthermore, by comparative transcriptome analysis, we found that oxr1b knockout inhibits multiple signal transduction pathways (e.g., MAPK signaling pathway, calcium signaling pathway, cAMP signaling pathway and ErbB signaling pathway) during oxidative stress, thereby suppressing early stress response and ultimately impairing the anti-apoptosis pathway. In conclusion, our findings demonstrate that the duplicated oxr1b gene has an important role in regulating the antioxidant defenses by modulating signaling transduction and early stress response during oxidative stress.

Background: There is a paucity of real-world epidemiological data on patients with mucopolysaccharidoses (MPS) in Latin America. This real-world study assessed the disease burden, management patterns and multidisciplinary clinical approaches for MPS-IVA and MPS-VI patients in Latin America (Colombia, Ecuador, Mexico, Peru). Methods: Data were collected from physicians/specialists experienced in treating MPS patients between April–June 2020, via an online patient-diary survey. Results: Overall, 29 physicians/specialists participated in this study. Data from 98 patients were analyzed (MPS-IVA, 71 patients and MPS-VI, 27 patients). Mean age for MPS-IVA patients was 17.5 years and for MPS-VI patients was 11.6 years, and the majority were females (52% and 78%, respectively). MPS-IVA and VI patients presented a high absenteeism from school (55% and 37%, respectively; 18 years age), indicating an impact of the disease on some aspects of the patients' quality of life. The onset of the first symptom occurred at the age of 3.1 years for MPS-IVA patients and at 1 year for MPS-VI, with delay in diagnosis (3.5–3.9 years from symptom onset) and enzyme replacement therapy (ERT) initiation (1.1–3.6 years from diagnosis). ERT interruptions were observed for MPS-IVA (48%) and MPS-VI patients (44%), with non-availability of medication recorded as the main reason for non-adherence (46% and 60% patients, respectively). ERT showed noticeable treatment benefits in MPS-IVA/VI patients, with stabilization/reduction in complications or the number of surgeries. A multidisciplinary clinical team approach was used for patient management. Conclusion: The disease burden for MPS-IVA/VI was high in Latin America, with consistent management, treatment and socio-demographic trends throughout the region.

The sea cucumber Apostichopus japonicus is an economically important marine organism, and its aquaculture has rapidly developed in China. The very large market demand puts forward higher requirements for the economically efficient breeding of sea cucumbers. Sex and the associated reproductive processes have been reported to affect the physiological characteristics of sea cucumbers. However, little is known about the metabolism differences that related to sex and the associated reproductive processes and their potential effects on the efficiency of A. japonicus aquaculture. In this study, ultra-performance liquid chromatography was applied to investigate the variations in metabolic profiles in cell-free coelomic fluids (CCFs) of sea cucumbers of different sexes and reproductive states. A total of 4435 metabolites were detected, and the metabolic profiles of A. japonicus were significantly affected by both sexes and reproductive process. The differentially abundant metabolites in CCFs of A. japonicus of different sexes and reproductive states were also screened and analyzed. The findings revealed that unsaturated fatty acid synthesis and phenylalanine metabolism were the most significantly changed pathways. Moreover, the weakest ability to synthesize capsaicin using phenylalanine was found in A. japonicus after spawning. Our study provides new insights into the metabolic response of A. japonicus during the reproductive process, and also provides valuable references for the economically efficient breeding of A. japonicus.

Congenital disorders of glycosylation (CDG) constitute an ever-growing group of genetic diseases affecting the glycosylation of proteins. CDG individuals usually present with severe multisystem disorders. MAN1B1-CDG is a CDG with nonspecific clinical symptoms such as intellectual deficiency and developmental delay. Although up to 40 affected individuals were described so far, its final diagnosis is not straightforward using common biochemical methods due to the trace-level accumulation of defective glycan structures. In this study, we present three unreported MAN1B1-CDG individuals and propose a decision tree to reach diagnosis using a panel of techniques ranging from exome sequencing to gel electrophoresis and mass spectrometry. The occurrence of MAN1B1-CDG in patients showing unexplained intellectual disability and development delay, as well as a particular transferrin glycosylation profile, can be ascertained notably using matrix assisted laser desorption/ionization – time of flight (MALDI-TOF) mass spectrometry analysis of endo-β-acetylglucosaminidase H-released serum N-glycans. In addition to reporting new pathogenic variants and additional clinical signs such as hypersialorrhea, we highlight particular biochemical features of MAN1B1-CDG with potential glycoprotein-specific glycosylation defects.

The diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae) is a holometabolous insect that its cuticles must undergo the significant changes during the larval-pupal metamorphosis development. To elucidate these changes at molecular levels, RNA-seq analysis of cuticles from LLS (later fourth instar larval stage), PPS (prepupal stage) and PS (pupal stage) were performed in P. xylostella. In this paper, a total of 17,710 transcripts were obtained in the larval-pupal transition of P. xylostella, and out of which 2293 (881 up-regulated and 1412 down-regulated) and 2989 transcripts (2062 up-regulated and 927 down-regulated) were identified to be differentially expressed between LLS and PPS, as well as PPS and PS, respectively. The further GO and KEGG analysis of differentially expressed genes (DEGs) revealed that the 'structural constituent of cuticle', 'chitin metabolic process', 'chitin binding', 'tyrosine metabolism' and 'insect hormone biosynthesis' pathways were significantly enriched, indicating these pathways might be involved in the process of larval pupation in P. xylostella. Then, we found some genes that encoded cuticular proteins, chitinolytic enzymes, chitin synthesis enzymes, and cuticle tanning proteins changed their expression levels remarkably, indicating these genes might play important roles in the restruction (degradation and biosynthesis) of insect cuticles during the larval metamorphosis. Additionally, the significant changes in the mRNA levels of 20-hydroxyecdysone (20E) and juvenile hormone (JH) related genes suggested their crucial roles in regulating cuticle remodeling during the larval metamorphosis of P. xylostella. In conclusion, the present study provide us the comprehensive gene expression profiles to explore the molecular mechanisms of cuticle metamorphosis in P. xylostella, which laid a molecular basis to study roles of specific pathways and genes in insect development.

An increasing number of laboratory studies are showing that environmental stressors and diet affect the fish gut microbiome. However, the application of these results to wild populations is uncertain as little is known about how the gut microbiome shifts when fish are transitioned from the field to the laboratory. To assess this, intestinal contents (i.e. digesta) of wild-caught rainbow darter (Etheostoma caeruleum) were sampled in the field and in the lab after 14- and 42-days acclimation. In addition, from days 15–42 some fish were exposed to waterborne triclosan, an antimicrobial found in aquatic ecosystems, or to dilutions of municipal wastewater effluents, to determine how these stressors affect the bacterial communities of gut contents. 16S rRNA gene amplicon sequencing was used to determine microbial community composition, alpha, and beta diversity present in the fish gut contents. In total, there was 8,074,658 reads and 11,853 amplicon sequence variants (ASVs) identified. The gut contents of wild fish were dominant in both Proteobacteria (35%) and Firmicutes (27%), while lab fish were dominant in Firmicutes (37–47%) and had lower alpha diversity. Wild fish had greater ASVs per sample (423-1304) compared to lab fish (19-685). Similarly, the beta-diversity of these bacterial communities differed between field and lab control fish; control fish were distinct from the 10% wastewater effluent and 100 ng/L TCS treatment groups. Results indicate that the gut microbiome of wild fish changes with the transition to laboratory environments; hence, prolonged acclimation to new settings may be required to achieve a stable gut content microbiome in wild-caught fish. Research is required to understand the length of time required to reach a stable fish gut microbiome.

The incidence of hypoxia in water bodies is increasing more rapidly than aquatic life can adapt. This study aimed to determine the effects of hypoxia on fish physiology, as well as protein expression through proteomics. To do this, 40 rainbow trout were divided into normoxic control (11.5 mg/L dissolved oxygen) and hypoxic treatment (5 mg/L dissolved oxygen) tanks for a period of 7 days. Fish were then anesthetized and blood was sampled. Fish were then euthanized and heart and liver samples were taken. Blood glucose, cortisol and lipid, body and liver mass, fork length, hematocrit and, blood cell counts and global heart methylation were measured. Red blood cell counts were significantly lower, while hematocrit and mean corpuscular volume were significantly higher in the hypoxic treatment. Global DNA methylation was significantly decreased in hypoxic heart tissue. Plasma cortisol and 18:1 monoacylglyerol increased, while 15:0-18:1 phosphatidylethanolamine, and 18:1 lysophosphatidylethanolamine decreased in plasma of rainbow trout under hypoxic conditions. Plasma proteomics revealed 70 significantly altered proteins (p 0.05) in the hypoxia treatment (Data are available via ProteomeXchange with identifier PXD026589). Many of these molecular changes appear to be related to the observed increase in red blood cell volume and epigenetic modifications, as well as to angiogenesis, lipid, and glucose metabolism. This study highlights a range of cellular and molecular responses in the blood and plasma of freshwater fish that may be phenotypic adaptions to hypoxia, and that could aid in diagnosing the health status of wild fish populations using several, potential, discovered biomarkers.

Chemosensory proteins (CSPs) are important for insect chemoreception, which bind, solubilize and transport hydrophobic chemical molecules from external environment to dendrite membrane of chemosensory neurons. Moreover, CSPs are also involved in non-sensory physiological activities. The peach fruit borers Carposina sasakii Matsumura (Lepidoptera: Carposinidae) seriously damage fruit trees and their chemoreception mainly occurs in the adult stage. We identified 10 putative CSPs (CsasCSP1 ~ CsasCSP10) from head transcriptomes of C. sasakii adult males and females, all of which are classic CSPs that have 4 conserved cysteines with a spacing pattern C1–X6–C2–X17–18–C3–X2–C4. Their phylogenetic characteristics were also described. An analysis using fluorescence quantitative PCR showed CsasCSP2 has the highest level of expression in the heads, so it is more likely to be involved in C. sasakii chemoreception than the other C. sasakii CSPs. CsasCSP1, CsasCSP3, CsasCSP4, CsasCSP6, CsasCSP7 and CsasCSP8 are expressed dominantly in the wings; CsasCSP5 and CsasCSP10 have the highest expression level in the thoraxes; CsasCSP9 is dominantly and equally expressed in the thoraxes and abdomens. This study contributes to understanding physiological functions of C. sasakii CSPs and chemosensory mechanism at C. sasakii molecular level.

QTc prolongation is reported in patients with hypertrophic cardiomyopathy (HCM). However, the causes of the QTc interval increase remain unclear. The main contribution to QTc prolongation in HCM is attributed to the myocardial hypertrophy and related structural damage. In a 24-year-old male proband, affected by HCM and long QTc, we identified by Next Generation Sequencing a pathogenic variant in gene TNNI3 co-inherited with a damaging variant in KCNQ1 gene. This evidence suggests the possibility that QTc interval prolongation and its dispersion in HCM could be associated not only to the severity of left ventricular hypertrophy but also to the co-inheritance of pathogenic variants related to both long QT Syndrome (LQTS) and HCM. Although the simultaneous presence of pathogenic variants in genes related to different heart diseases is extremely rare, counseling and genetic testing appear crucial for the clinical diagnosis. Screening of LQTS genes should be considered in HCM patients to clarify the origin of long QTc, to provide more information about the clinical presentation and to evaluate the incidence of the co-existence of LQTS/HCM gene variants that could occur more frequently than so far reported.

Mercenaria mercenaria is an economically important clam species and exhibits an outstanding resistance to multiple environmental stressors. However, our understanding of their stress adaptability is limited due to a lack of genomic information, such as transcriptome resources. In this study, single-molecule long-read (SMRT) mRNA sequencing was performed to obtain the full-length gill transcriptome reference sequences of M. mercenaria under air exposure stress. In all, 14.5 G subreads were obtained and assembled into 64,603 unigenes, among which 50,613 were successfully annotated. Additionally, 56,295 SSRs, 1457 transcription factors, and 5924 lncRNAs were identified in M. mercenaria transcriptome. Furthermore, numerous apoptosis-related transcripts were identified according to Swiss-Prot annotation and their numbers were counted. We also found that most apoptosis-related transcripts exhibited typical domains of a certain protein family through conserved domain prediction. Additionally, eight typical sequences related to apoptosis pathway were detected by RT-PCR, with the aim to show the sequential variation of gene expression levels under air exposure. These results implied that the complicated apoptosis system, especially the powerful anti-apoptotic system was critical for M. mercenaria to endure air exposure.

The ark shell, Scapharca subcrenata, is susceptible to high temperature which may lead to mass mortality in hot summers. Herein, we conducted the transcriptomic analyses of haemocytes in ark shells under thermal stress, to reveal the underlying molecular mechanisms of heat resistance in these animals. The results showed that a total of 7773, 11,500 and 13,046 unigenes were expressed differentially at 12, 24 and 48 h post thermal stress, respectively. The expression levels of key DEGs as revealed by RNA-seq were confirmed by quantitative real-time PCR. GO and KEGG enrichment analyses showed that the DEGs were mainly associated with apoptosis, NF-kappa B signaling pathway, TNF signaling pathway and RIG-I-like receptor signaling pathway. Among the DEGs, 40 were candidate heat stress response-related genes and 169 were identified to be involved in antioxidant defense, cell detoxification, protein metabolism and endoplasmic reticulum stress responses. It seemed that ark shells may adapt to short term thermal stress through regulation of protein metabolism, DNA replication and anti-apoptotic system. However, if the stress sustains, it may cause irreparable injury gradually in the animals due to oxygen limitation and metabolic dysregulation. Noteworthily, the expression of DEGs involved in protein biosynthesis and proteolysis was significantly elevated in ark shells under heat stress. These findings may provide preliminary insights into the molecular response of ark shells to acute thermal stress and lay the groundwork for marker-assisted selection of heat-resistant strains in S. subcrenata.

Environmental salinity not only affects the physiological processes such as osmoregulation and hormonal control, but also changes the immune system in fishes. Studies are limited in fish on the roles of the T cell receptor (TCR)-related genes in relation to changes in environmental salinity. A large group of salinity-challenged transcripts was obtained in gills of marbled eel (Anguilla marmorata). Moreover, bioinformatic ways were used to identify the enriched TCR pathway related genes which were significantly different expressed in fresh water (FW), brackish water (BW) and seawater (SW). Meanwhile, the RT-qPCR results were validated and consistent with the RNA-seq results. TCR a, TCR b, CD45, CD28, PI3K, LCK and LAT were up-regulated when the salinity increases in BW and SW, which connected with the related signaling pathways (Ras-MAPK and PKC pathway). CD4 and Zap70 were down-regulated when the salinity increases in BW and SW, which connected with the PLC pathway. The research offers a novel viewpoint to explore the immune pathways including the TCR pathway in fish based on transcriptome.

Introduction Late infantile neuronal ceroid lipofuscinosis is an autosomal recessive disease caused by mutations in the CLN2/TPP1 gene, with secondary enzyme deficiency. In classical phenotypes, initial symptoms include seizures and delayed language development between 2 and 4 years of age. This article describes the presentation of CLN2 disease in a cohort of Colombian patients, as well as the impact of treatment on the course and progression of the disease. Methods Case series report of 8 patients with a confirmed diagnosis of neuronal ceroid lipofuscinosis treated with cerliponase alfa who remained on clinical and paraclinical follow-up for up to 24 months before and after treatment. Results An atypical phenotype, associated with initial symptoms and late diagnosis, was present in 5/8 patients. The most frequent symptoms were seizures and developmental delay, with age of onset at 24 months (classical phenotype) and 48 months (atypical phenotype). A novel mutation (c.1438G > A) was found in two siblings. All of the patients received cerliponase alfa, and there were no serious adverse events. No decline in the clinical status greater than 2 points on Hamburg, Weill Cornell and CNL2 clinical assessment scale was observed during follow-up after treatment initiation. Conclusion This is the first case series reported for neuronal ceroid lipofuscinosis patients in Colombia. In contrast with other reports, the majority of cases reported here displayed an atypical phenotype. Our study highlights the importance of early diagnosis and timely initiation of therapy, which is a feasible therapy, well tolerated by patients and accepted by caregivers in this country, generating a positive impact in the quality of life of CLN2 patients and on disease outcome.

The endangered cold-water fish species taimen (Hucho taimen) suffer acute temperature changes in culture and wild conditions. Understanding the effects of acute temperature changes on physiological processes of this species is essential for aquaculture practices and conservation. Liver transcriptomic profiles of the taimen (n = 24) exposed to acute temperature decrease (from 20 °C to 10 °C) and acute temperature increase (from 10 °C to 20 °C) was evaluated using high-throughput RNA-Sequencing. Samples were collected at day 0, 1, 7 and 35 in both treatments. Compared to day 0, the total numbers of differentially expressed genes (DEGs) in the taimen after acute temperature decrease were 173, 226 and 42 at day 1, 7 and 35, respectively, and the total numbers of DEGs following acute temperature increase were 260, 253 and 282 at day 1, 7 and 35, respectively. Particularly, 14 key regulatory genes were commonly found between both acute temperature treatments. Functional analysis based on the commonly identified DEGs revealed important metabolic pathways related to metabolism and immune function, suggesting a specific response mechanism of taimen against cold and heat shock. The results may assist in developing management strategies for stress mediation caused by acute temperature changes in the taimen and other cold water fish.