Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format.

BACKGROUND: The STRUCTURE software has gained popularity as a tool for population structure and genetic analysis. Nevertheless, formatting data to meet STRUCTURE's specific requirements can be daunting and susceptible to errors, especially when handling multilocus data. This article highlights the creation of a graphical user interface (GUI) application tailored to streamline the process of converting multiple sequence alignments into a single, cohesive file that is compatible with the STRUCTURE software. RESULTS: The application has been developed utilizing Tkinter for the GUI and Biopython for handling FASTA files. This program processes the files, pinpoints variable sites, and converts the sequences into a binary format. Subsequently, the sequences are concatenated and presented within the graphical interface's text area, enabling users to review and confirm the results. Furthermore, the program stores the concatenated results in a file, delivering a ready-to-use input for the STRUCTURE software. CONCLUSION: This application offers an efficient and dependable solution for transforming multiple aligned FASTA files into a concatenated binary format file, which is compatible with the STRUCTURE software. With its user-friendly graphical interface and error-reduction approach, this tool proves invaluable for researchers engaged in population structure and genetic analysis.

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.

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.

First record of mudskipper Boleophthalmus dussumieri (Gobiidae: Oxudercinae) on the coast of Mozambique and evidence of two putative lineages along its known distribution range.

Boleophthalmus dussumieri is one of the most widely distributed mudskippers and is native to the Persian Gulf in Iran down to the northeast of the Arabian Sea and the coast of India. Nonetheless, the present study is the first to confirm the presence of B. dussumieri in the marine areas of the Mozambique coast. In addition, molecular analysis revealed strong evidence for the existence of two lineages with a high level of nucleotide divergence along the sampled area, revealing a still-neglected taxonomic condition for this lineage/species.

Phylogenetic relationships of sleeper gobies (Eleotridae: Gobiiformes: Gobioidei), with comments on the position of the miniature genus Microphilypnus.

Microphilypnus and Leptophilypnion are miniaturized genera within the family Eleotridae. The evolutionary relationships among these taxa are still poorly understood, and molecular analyses are restricted to mitochondrial genes, which have not been conclusive. We compiled both mitochondrial and nuclear genes to study the phylogenetic position of Microphilypnus and the evolutionary history and relationships of eleotrids. We propose that Microphilypnus and Leptophilypnus (a non-miniature genus) are not sister groups as suggested by previous studies, but rather separate lineages that arose in the early Eocene, with Leptophilypnus recovered as a sister group to the other analyzed eleotrids. In fact, Microphilypnus is currently associated with the Neotropical clade Guavina/Dormitator/Gobiomorus. We also identified a well-supported clade that indicated Gobiomorus and Hemieleotris as paraphyletic groups, besides a close relationship among Calumia godeffroyi, Bunaka gyrinoides, Eleotris and Erotelis species. This is the first comprehensive report about the evolutionary relationships in members of the family Eleotridae, including multiloci and multispecies approaches. Therefore, we provided new insights about the phylogenetic position of some taxa absent in previous studies, such as the miniature genus Microphilypnus and a recently described species of Eleotris from South America.

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex.

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt.

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.

Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon.

The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world's most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.

A nurse-run walk-in clinic: cost-effective alternative to non-urgent emergency department use by the uninsured.

Non-urgent healthcare problems are responsible for more than 9 million visits to the emergency department (ED) in US hospitals each year, largely due to patients' lack of access to a primary care physician. To avoid costly and unnecessary ED usage for non-urgent health problems, a walk-in clinic run by nurses (CHEER Clinic) was developed as an extension of the services provided by an existing free clinic in a low-income neighborhood of Providence, RI, with the goal of providing uninsured patients with a convenient, no-cost means of accessing healthcare. An evaluation and cost-effectiveness analysis of the clinic's first 5 months of operation were performed. During this pilot period, 256 patients were seen. When incorporating the quality-adjusted-life-year value of preventive services rendered, an estimated $1.28 million in future healthcare costs was avoided. Dividing these cost-savings by the clinic's operational cost yielded a mean return on investment of $34 per $1 invested. Adding nurse-run walk-in hours at a free clinic significantly expanded access to healthcare for uninsured patients and was cost-effective for both the clinic and the patient. Ultimately, replication of this model in community clinics serving the uninsured could reduce ED burden by treating a substantial number of non-urgent medical concerns at a lower cost than would be incurred for treatment of the same problems in EDs.

Diagnosis of oral manifestations in HIV/AIDS patients who used HAART and developed diabetes mellitus

Aim: To assess the prevalence of oral manifestations in HIV/AIDS patients and a possible correlation of the development of diabetes mellitus due to highly active antiretroviral therapy (HAART) Methods: 56 patients were examined, divided into two groups, Group 1, the HIV group, with 28 patients known to be HIV+, who developed diabetes mellitus due to HAART, and Group 2, the control group, with 28 patients with HIV- diagnosed with diabetes mellitus. Results: In Group 1, normal salivary flow rate and buffering capacity were observed in 18 (64.3%) patients, but the bleeding index high (46.53%) and higher incidence of periodontal disease was found in this group. In Group 2, 11 (39.2%) and 15 (53.5%) patients had low and normal salivary flow rate, respectively. High T-CD4 indices with mean value of 22.46 for each patient, showing xerostomia in 9 (32.1%) patients and dental caries in 11 (39.3%). Conclusions: Regarding the oral and general manifestations, the HIV group showed higher rates of pathologies when compared with the control group. The HIV group and the control group were diagnosed with diabetes, but this condition in the HIV group presented earlier than in the control group, suggesting a possible association with HAART.

Study of emotional and psychological factors that may interfere in the dental treatment / Estudo dos fatores emocionais e psicológicos que podem interferir no tratamento odontológico

Introduction - Submission to dental treatment has been reported by patients as a condition giving rise to stress because they may experience some discomfort causing them to postpone visits to the dental office because of situations that include pain. Identify these conditions is a challenge that dentists should include their care procedures in order to modify this pessimistic view where the main focus (oral health) can be achieved. This work results in the identification of factors that interfere with patient-dentist approximation for the dental treatment. Material and Method - We interviewed 54 patients. Results - The results were significant: 14.85% said they going to the dental office is stressful, 83.3% reported that the dentist managed to deal with fear and anxiety during the dental treatment, 22.0% had requested to stop a consultation because of not keeping the self control. The most common symptoms: palpitations, cold hands, panic, increased sweating. When questioned about what most frightened them: equipment used during the consultations is the main cause of fear. Conclusion - It was concluded that the patient-dentist relationship is a complex and extensive subject, however, it identifies situations that may be related to fear, so that when controlled it facilitates adherence and reduce the dropout to dental treatments, improving clinical and practical care and the patient approach to the dentist.

Introdução - Submeter a tratamento odontológico (TO) tem sido relatado, por pacientes, como condição geradora de estresse, pois acredita-se experimentar algum desconforto levando-os a adiar idas aos consultórios odontológicos a situações limítrofes como a dor. Identificar tais condições é mais um desafio que os cirurgiões-dentistas (CD) devem incluir aos seus atendimentos, com objetivo de modificar esta visão pessimista onde o foco principal (saúde bucal) possa ser atingido. Este trabalho resulta na identificação dos fatores que interferem na aproximação paciente-CD para o TO. Material e Método - Foram entrevistados 54 pacientes. Resultados - Os resultados foram significativos: 14,85% afirmaram que ir ao consultório odontológico é estressante, 83,3% relataram que o CD conseguiu lidar com situações de medo e ansiedade durante o TO; 22,0% já solicitaram interromper a consulta por não conseguir manter o autocontrole. Os sintomas mais frequentes: palpitações, mãos frias, pânico, sudorese aumentada. Quando interrogados sobre o que mais os amedrontam: equipamentos utilizados durante os atendimentos são principais desencadeadores de medo. Conclusão - Conclui-se que a relação paciente-CD é um assunto complexo e extenso, contudo, identifica as situações que devem ser relacionadas ao medo, para que, ao contorná-las possam facilitar aderência e diminuir evasão aos TO, melhorando o atendimento clínico-prático bem como a aproximação dentista-paciente.