SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses.

BACKGROUND: The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained. RESULTS: To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers. CONCLUSIONS: The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature.

DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique.

The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.

Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species.

Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.

An update on COVID-19 for the otorhinolaryngologist - a Brazilian Association of Otolaryngology and Cervicofacial Surgery (ABORL-CCF) Position Statement / Atualização sobre o COVID-19 para o otorrinolaringologista - um documento sobre a posição da Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial (ABORL-CCF)

Abstract Introduction: We are facing a pandemic with a great impact worldwide, as a result of the rapid spread of the novel coronavirus (COVID-19). The medical community is still getting to know behavior of this virus and the consequences from a population point of view. All this knowledge is extremely dynamic, so some behaviors are still not well established. Otorhinolaryngologists have a central role in the management of this situation, in which they must assess the patient, avoid contamination to and by health professionals and other patients. Thus, the recommendations of the Brazilian Association of Otorhinolaryngology and Cervical-Facial Surgery (ABORL-CCF) have the main objective of reducing the spread of the new coronavirus during otorhinolaryngological care and assisting in the management of these patients. Methods: Review of the main recommendations of national and international scientific societies, decisions by government agencies and class councils. The topics will be related to the general aspects of COVID-19, personal protective equipment, care in patient assistance, endoscopic exam routines and the management of sinonasal, otological and pediatric evaluations related to COVID-19. Results: The use of personal protective equipment is considered crucial in routine ENT care. We recommend postponing appointments, exams and elective surgeries to reduce the spread of COVID-19. Similarly, we recommend changing routines in several areas of otolaryngology. Additionally, guidance is provided on the use of telemedicine resources during the pandemic period. Conclusions: We are still at the beginning of the COVID-19 pandemic and scientific evidence is still scarce and incomplete, so these ABORL-CCF recommendations for otorhinolaryngologists may be updated based on new knowledge and the pattern of the new coronavirus spread.

Resumo: Introdução: Estamos diante de uma pandemia de grande impacto mundial como resultado da rápida propagação do novo coronavírus, COVID-19. A comunidade médica está ainda conhecendo o comportamento desse vírus e as repercussões do ponto de vista populacional. Todo esse conhecimento é extremamente dinâmico, por isso algumas condutas ainda não estão bem estabelecidas. O otorrinolaringologista tem um papel central no manejo dessa situação em que deve avaliar o paciente e evitar a contaminação dos profissionais da saúde e dos demais pacientes. Dessa forma, as recomendações da Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial (ABORL-CCF) têm por objetivo principal reduzir a propagação do novo coronavírus durante o atendimento otorrinolaringológico e auxiliar no manejo desses pacientes. Método: Revisão das principais recomendações das sociedades científicas nacionais, internacionais, decisões de órgãos governamentais e de conselhos de classe. Os tópicos serão relativos aos aspectos gerais do COVID-19, equipamentos de proteção individual, cuidados no atendimento ao paciente, as rotinas dos exames endoscópicos e o manejo de aspectos nasossinusais, otológicos e pediátricos relacionados ao COVID-19. Resultados: É considerado crucial o uso de equipamento de proteção individual no atendimento otorrinolaringológico de rotina. Recomendamos postergar atendimentos, exames e cirurgias eletivas para diminuir a propagação do COVID-19. Da mesma forma, recomendamos mudança de rotinas em diversas áreas da otorrinolaringologia. Além disso, orientações sobre o uso do recurso da telemedicina durante o período de vigência da pandemia. Conclusões: Estamos ainda no início da pandemia do COVID-19 e as evidências científicas são ainda escassas, por isso essas recomendações da ABORL-CCF para os otorrinolaringologistas podem sofrer atualizações baseadas nos novos conhecimentos e no padrão de disseminação do novo coronavírus.

An update on COVID-19 for the otorhinolaryngologist - a Brazilian Association of Otolaryngology and Cervicofacial Surgery (ABORL-CCF) Position Statement.

INTRODUCTION: We are facing a pandemic with a great impact worldwide, as a result of the rapid spread of the novel coronavirus (COVID-19). The medical community is still getting to know behavior of this virus and the consequences from a population point of view. All this knowledge is extremely dynamic, so some behaviors are still not well established. Otorhinolaryngologists have a central role in the management of this situation, in which they must assess the patient, avoid contamination to and by health professionals and other patients. Thus, the recommendations of the Brazilian Association of Otorhinolaryngology and Cervical-Facial Surgery (ABORL-CCF) have the main objective of reducing the spread of the new coronavirus during otorhinolaryngological care and assisting in the management of these patients. METHODS: Review of the main recommendations of national and international scientific societies, decisions by government agencies and class councils. The topics will be related to the general aspects of COVID-19, personal protective equipment, care in patient assistance, endoscopic exam routines and the management of sinonasal, otological and pediatric evaluations related to COVID-19. RESULTS: The use of personal protective equipment is considered crucial in routine ENT care. We recommend postponing appointments, exams and elective surgeries to reduce the spread of COVID-19. Similarly, we recommend changing routines in several areas of otolaryngology. Additionally, guidance is provided on the use of telemedicine resources during the pandemic period. CONCLUSIONS: We are still at the beginning of the COVID-19 pandemic and scientific evidence is still scarce and incomplete, so these ABORL-CCF recommendations for otorhinolaryngologists may be updated based on new knowledge and the pattern of the new coronavirus spread.

Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing.

BACKGROUND: The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. RESULTS: The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. CONCLUSION: In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management.

De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish.

BACKGROUND: The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species. RESULTS: Four libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female arapaima, while the levels of expression in the liver are similar between the sexes. CONCLUSION: Transcriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts.

Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing.

Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the "biological processes" domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools.

The past and present of an estuarine-resident fish, the "four-eyed fish" Anableps anableps (Cyprinodontiformes, Anablepidae), revealed by mtDNA sequences.

Historical events, such as changes in sea level during the Pleistocene glacial cycles, had a strong impact on coastal habitats, limiting connectivity and promoting the genetic divergence of various species. In this study, we evaluated the influence of climate oscillations and the possibility of estuary function as a barrier to gene flow among populations of the four-eyed fish, Anableps anableps. This species is fully estuarine-resident, has internal fertilization, is viviparous and does not migrate across long distances. These features make the four-eyed fish an excellent model for the study of evolutionary processes related to genetic differentiation of species and populations in estuaries. The evolutionary history of A. anableps was inferred from phylogeographic and population analyses using sequences of the mitochondrial DNA Control Region of 13 populations distributed in the Amazon and Northeast Coast of Brazil from Calcoene (Amapa) to Parnaiba (Piaui). The 83 retrieved haplotypes show a pattern of four distinct mitochondrial lineages, with up to 3.4% nucleotide divergence among them. The evolutionary reconstruction suggests that these lineages diverged recently in the late Pleistocene/early Holocene after the Atlantic Ocean reaching current levels. Analysis of variability, neutrality and the genetic expansion pattern revealed that the lineages have distinct characteristics, which were shaped by the different geomorphological features of coastal regions combined with sea level oscillations over a very long period of time. Only few neighboring populations show a discreet gene flow. This study may also be helpful for designing new experiments to better understand the geomorphological evolutionary history of the estuaries of the Amazon and the Northeast Coast of Brazil using estuarine-resident species as a model.

The use of a neck brace does not influence visual vertical perception.

UNLABELLED: Subjective visual vertical (SVV) evaluates the individual's capacity to determine the vertical orientation. Using a neck brace (NB) allow volunteers' heads fixation to reduce cephalic tilt during the exam, preventing compensatory ocular torsion and erroneous influence on SVV result. OBJECTIVE: To analyze the influence of somatosensory inputs caused by a NB on the SVV. METHOD: Thirty healthy volunteers performed static and dynamic SVV: six measures with and six without the NB. RESULTS: The mean values for static SVV were -0.075º±1.15º without NB and -0.372º±1.21º with NB. For dynamic SVV in clockwise direction were 1.73º±2.31º without NB and 1.53º±1.80º with NB. For dynamic SVV in counterclockwise direction was -1.50º±2.44º without NB and -1.11º±2.46º with NB. Differences between measurements with and without the NB were not statistically significant. CONCLUSION: Although the neck has many sensory receptors, the use of a NB does not provide sufficient afferent input to change healthy subjects' perception of visual verticality.

The use of a neck brace does not influence visual vertical perception / O uso do colar cervical não influência na percepção de verticalidade visual

Subjective visual vertical (SVV) evaluates the individual's capacity to determine the vertical orientation. Using a neck brace (NB) allow volunteers' heads fixation to reduce cephalic tilt during the exam, preventing compensatory ocular torsion and erroneous influence on SVV result. OBJECTIVE: To analyze the influence of somatosensory inputs caused by a NB on the SVV. METHOD: Thirty healthy volunteers performed static and dynamic SVV: six measures with and six without the NB. RESULTS: The mean values for static SVV were -0.075º±1.15º without NB and -0.372º±1.21º with NB. For dynamic SVV in clockwise direction were 1.73º±2.31º without NB and 1.53º±1.80º with NB. For dynamic SVV in counterclockwise direction was -1.50º±2.44º without NB and -1.11º±2.46º with NB. Differences between measurements with and without the NB were not statistically significant. CONCLUSION: Although the neck has many sensory receptors, the use of a NB does not provide sufficient afferent input to change healthy subjects' perception of visual verticality.

A subjetiva vertical visual (SVV) avalia a capacidade do indivíduo determinar a posição vertical. O uso do colar cervical (CC) fixa a cabeça do voluntário, reduzindo a inclicação cefálica durante o exame e prevenindo a torção ocular compensatória que influencia na SVV. OBJETIVO: Analisar a influência de informações sometossensoriais causadas pelo uso de um CC na SVV. MÉTODO: Trinta voluntários saudáveis realizaram a SVV estática e dinâmica: seis medidas com e seis medidas sem o CC. RESULTADOS: O valor médio da SVV estática foi -0,075º±1,15º sem CC e -0,372º±1,21º com. Na SVV dinâmica no sentido horário foi 1,73º±2,31º sem CC e 1,53º±1,80º com. Na SVV dinâmica no sentido anti-horário foi -1,50º±2,44º sem CC e -1,11º±2,46º com. As diferenças entre as medidas com e sem CC não foram estatisticamente significativas. CONCLUSÃO: Apesar de o pescoço possuir inumeros receptores sensoriais, o uso do CC não fornece aferências suficientes para alterar a percepção de visual de verticalidade de voluntários saudáveis.