Minimal and hybrid hydrogenases are active from archaea.

Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.

Prospective Cohort Study Identifies Medical Predictors of Treatment-Related Oral Toxicities in Oral and Oropharyngeal Cancer Patients.

The dental treatment of patients with oral cavity and oropharyngeal squamous cell carcinoma (OOPSCC) may be challenging for dentists. This study aimed to characterize systemic changes in patients with OOPSCC undergoing dental treatment prior to cancer therapy, with a specific focus on laboratory assessments. The primary objectives included identifying potential adverse events, such as infections or bleeding, resulting from dental procedures. Additionally, the study aimed to correlate baseline patient characteristics with treatment-related toxicities. This was a prospective cohort study that included 110 OOPSCC patients referred to the Dental Oncology Service at São Paulo State Cancer Institute, Brazil, between November/2019 and December/2020. Comorbidities, sociodemographic data, medication in use, cancer treatment-related toxicities, and altered laboratory tests results were correlated. The most common comorbidities and altered laboratory results were hypertension, dyslipidemia, diabetes, as well as elevated levels of C-reactive protein, hemoglobin, and hematocrit. Toxicities exhibited a progressive pattern over time, encompassing oral mucositis (OM), xerostomia, dysphagia, dysgeusia, trismus, and radiodermatitis. No correlation between comorbidities and cancer treatment-related toxicities, a positive correlation between medications in use and OM, and a negative correlation between medications and dysgeusia were found. OM was associated with altered thyroxine (T4) and free thyroxine (FT4), calcium, urea, creatinine, alkaline phosphatase, and syphilis. Family income and housing were OM predictors. Altered T4/FT4/urea/calcium/alkaline phosphatase/creatinine/syphilis may be useful clinical predictors of OM. Despite the elevated prevalence of comorbidities and abnormal laboratory findings, dental treatment prior to cancer treatment yielded no adverse events.

Big jaw, small genome: first description of the mitochondrial genome of Odontomachus (Formicidae, Ponerinae): evolutionary implications for Ponerinae ants.

Mitochondrial DNA is a valuable tool for population genetics and evolutionary studies in a wide range of organisms. With advancements in sequencing techniques, it's now possible to gain deeper insights into this molecule. By understanding how many genes there are, how they're organized within the molecule, identifying the presence of spacers, and analyzing the composition of the D-Loop, we can better grasp the rearrangements that play a crucial role in the evolutionary dynamics of mitochondrial DNA. Additionally, phylogenetic analyses benefit significantly from having access to a larger pool of mtDNA genes. This wealth of genetic information allows for the establishment of evolutionary relationships with greater accuracy than ever before, providing a more robust framework than analyses based on a limited number of genes. Studies on mitogenomes belonging to the family Formicidae have proven promising, enabling the identification of gene rearrangements and enhancing our understanding of the internal relationships within the group. Despite this, the number of mitogenomes available for the subfamily Ponerinae is still limited, and here we present for the first time the complete mitogenome of Odontomachus. Our data reveal a gene duplication event in Formicidae, the first involving trnV, and new gene arrangements involving the trnM-trnI-trnQ and trnW-trnC-trnY clusters, suggesting a possible synapomorphy for the genus. Our phylogenetic analysis using the PCGs available for Formicidae supports the monophyly of the subfamily Ponerinae and sheds light on the relationship between Odontomachus and Pachycondyla.

The impact of radiation caries on morbidity and mortality outcomes of head and neck squamous cell carcinoma patients.

AIMS: Radiation caries (RC) is a highly prevalent and chronic complication of head and neck radiotherapy (HNRT) and presents a challenge for clinicians and patients. The present study aimed to assess the impact of RC on the morbidity and mortality outcomes of head and neck squamous cell carcinoma (HNSCC) patients. METHODS AND RESULTS: Patients were divided into three groups: (1) RC (n = 20), (2) control (n = 20), and (3) edentulous (n = 20). Information regarding the number of appointments, dental procedures, osteoradionecrosis (ORN), prescriptions, and hospital admissions were collected. Mortality outcomes were assessed through disease-free survival (DFS) and overall survival (OS) rates. RC patients required more dental appointments (p < .001), restorations (p < .001), extractions (p = .001), and antibiotic and analgesic prescriptions (p < .001). Kaplan-Meier subgroup analyses showed a significantly increased risk of ORN in RC compared to edentulous patients (p = .015). RC patients presented lower DFS rates (43.2 months) than the control and edentulous groups (55.4 and 56.1 months, respectively). CONCLUSIONS: RC impacts morbidity outcomes among cancer survivors due to increased demand for medication prescriptions, multiple specialized dental appointments, invasive surgical treatments, increased risk of ORN, and increased need for hospital admissions.

Novel resin-based material containing ß-tricalcium phosphate nanoparticles for the reduction of dentin permeability.

OBJECTIVES: To synthesize and characterize a novel dentin adhesive containing Beta-Tricalcium Phosphate (ß-TCP) nanoparticles and test its ability to reduce dentin permeability (dP). METHODS: Experimental adhesives were prepared by mixing Bis-GMA, TEGDMA, HEMA (50/25/25 wt.%), photo-initiators, and inhibitors. The following groups were tested: Experimental adhesives without ß-TCP (Exp.); with 10 wt.% ß-TCP (Exp.10 wt.% ß-TCP); with 15 wt.% ß-TCP (Exp.15 wt.% ß-TCP), Scotchbond Multi-Purpose (SBMP) and Clearfil SE Protect Bond (CFPB). Degree of conversion (DC%, 10 and 20 s); Flexural Strength (FS), Knoop Hardness (KHN), and Cell Viability (OD%) tests were performed. dP was evaluated by hydraulic conductance, using human dentin disks (n=12), at three-time intervals: post-EDTA (T0); post-treatment (T1); and post-erosion/abrasion cycling (T2). Data were statistically analyzed (α=0.05). RESULTS: For all groups, exposure time for 20 s presented a higher DC% than for 10 s. For FS, filled adhesives did not differ from unfilled and from CFPB. Experimental adhesives did not differ among them and showed lower KHN than the commercial products. Cell viability did not differ among adhesives, except Exp. 15 wt.%, which showed lower OD% than Exp., Exp. 10% and, CFPB. For dP, only Exp.10 and 15 wt.% ß-TCP did not present difference between the times T1 and T2. After cycling, Exp.10 wt.% ß-TCP presented lower permeability than Exp. and CFPB. CONCLUSIONS: The incorporation of 10 wt.% ß-TCP nanoparticles into the resin-based dental material did not affect its mechanical properties and biocompatibility, and promoted the greatest reduction in dentin permeability, sustaining this effect under erosive/abrasive challenges. CLINICAL SIGNIFICANCE: A novel resin-based dental material containing ß-TCP nanoparticles was able to reduce dentin permeability, maintaining its efficacy after erosive/abrasive challenges. The synthesized material did not affect dental pulp cell viability and might be promising for other conditions that require dental remineralization, such as tooth wear and dental caries.

Influence of Diabetes Mellitus and Nutritional Parameters on Clinical and Functional Aspects and Quality of Life in Patients Hospitalized Due to Exacerbation of Chronic Obstructive Pulmonary Disease.

Patients with chronic obstructive pulmonary disease (COPD) may experience exacerbations. During severe exacerbations, nutritional and endocrinological comorbidities can play an important role in the clinical and functional aspects of these patients. The aim of this study was to analyse the influence of the presence of diabetes mellitus (DM) and nutritional parameters on the deterioration of symptoms and quality of life during a severe exacerbation in patients with COPD. An observational study was conducted on COPD patients admitted due to an exacerbation. The COPD Assessment Test (CAT) questionnaire was administered, and clinical and functional parameters were compared based on the presence of nutritional and endocrinological alterations. A total of 50 patients were included, of whom 30 (60%) were male. The mean age was 70.5 years (standard deviation (SD) 9.6). The median CAT score during exacerbation was 25 (interquartile range (IQR) 17.5-30), and the baseline score was 13.5 (IQR 7-19), which represented a statistically significant difference (p < 0.001). Patients with iron deficiencies had a lower total CAT score (p = 0.041), specifically for items related to daily activity (p = 0.009) and energy (p = 0.007). Diabetic patients exhibited a greater decline in pulmonary function during exacerbation (p = 0.016), while patients with high thyroid-stimulating hormone (TSH) levels had a shorter hospital stay (p = 0.016). For COPD patients admitted due to an exacerbation, the metabolic assessment is useful and relevant in the clinical set-up, as endocrinological comorbidities negatively affect clinical and functional aspects of these patients.

Systematic review and meta-analysis of the global prevalence of sexually transmitted infections in people living with HIV and associated risk factors.

People living with HIV (PLWH) constitute a vulnerable population for acquiring additional sexually transmitted infections (STIs). This study was conducted to provide a summary of the evidence on the global prevalence of STIs in PLWH with an emphasis on infectious agents, diagnostic methods, and related risk factors. PubMed, Scopus, and Web of Science were systematically searched to include records published from January 01, 1990, to January 31, 2022, and the Google Scholar search engine was used to check the search strategy. In total, 132 eligible studies reporting STIs in PLWH were included, enrolling subjects from 35 countries across five continents. The pooled proportion of STIs was estimated to be 30.23% (95% CI, 26.1-34.45%) in PLWH and 20.01% (95% CI, 17.17-23.01%) in HIV-negative patients. Our meta-analysis indicated that in PLWH, the pooled OR of STIs compared to HIV-negatives was 1.77 (95% CI: 1.58-1.98) (p < 0.0001). The pooled OR of STIs by viral infectious agents was highest in PLWH (52.19% [95% CI: 43.88-60.43]) compared with fungal (22.19% [95% CI: 15.64-29.53]), bacterial (19.07% [95% CI: 13.59-26.63]), and parasitic (14.05% [95% CI: 11.88-16.38]) infections. Our findings show that there is a rather significant frequency of STIs among PLWH. This study highlights the need for new programs for the detection, treatment, and prevention of STIs in this at-risk population.

Prognostic Factors and Markers in Non-Small Cell Lung Cancer: Recent Progress and Future Challenges.

Lung cancer is a highly aggressive neoplasm and, despite the development of recent therapies, tumor progression and recurrence following the initial response remains unsolved. Several questions remain unanswered about non-small cell lung cancer (NSCLC): (1) Which patients will actually benefit from therapy? (2) What are the predictive factors of response to MAbs and TKIs? (3) What are the best combination strategies with conventional treatments or new antineoplastic drugs? To answer these questions, an integrative literature review was carried out, searching articles in PUBMED, NCBI-PMC, Google Academic, and others. Here, we will examine the molecular genetics of lung cancer, emphasizing NSCLC, and delineate the primary categories of inhibitors based on their molecular targets, alongside the main treatment alternatives depending on the type of acquired resistance. We highlighted new therapies based on epigenetic information and a single-cell approach as a potential source of new biomarkers. The current and future of NSCLC management hinges upon genotyping correct prognostic markers, as well as on the evolution of precision medicine, which guarantees a tailored drug combination with precise targeting.

Induction of TLR5, IRAK1, and NF-κB expression by Trichomonas vaginalis in cervical cancer cell (HeLa) and normal human vaginal epithelial cell (HVECs) lines.

INTRODUCTION: Trichomoniasis is the most common non-viral sexually transmitted infection that increases the risk of cervical cancer. Trichomonas vaginalis (T. vaginalis) can regulate the pro-inflammatory cytokine production in the host cells. Toll-like receptors (TLRs) are a family of the pattern recognition receptors (PRRs) of mammalian cells, expressed in various host cells and have an important role in recognizing pathogens, and pro-inflammatory responses. The aim of the present study is to investigate the role of TLR5 in cervical cancer cells (HeLa) and human vaginal epithelial cells (HVECs) exposed to T. vaginalis. METHODOLOGY: First, the cells and parasites were cultured in RPMI and trypticase yeast extract maltose (TYM), respectively. After adaption of parasite and epithelial cells by RPMI-TYM medium co-culture (9:1 vol/vol), HVECs and HeLa cells were stimulated with T. vaginalis trophozoites (24-hour incubation at 37 °C, 5% CO2). Following RNA extraction and cDNA synthesis, the gene expression levels of TLR5, IRAK1, and NF-κB were assessed using real-time PCR. Besides, the protein levels were measured using western blotting. All tests and controls were normalized using ß-actin as a housekeeping control. RESULTS: Real-time PCR results showed an increased gene expression of TLR5, IRAK1, and NF-κB in T. vaginalis exposed HVECs and HeLa cells compared to the control group (p < 0.05). Additionally, western blot analysis showed a statistically significant increase in TLR5, and NF-κB proteins in both groups after exposure to the parasite (p < 0.05). CONCLUSIONS: These findings provide insight into the host-parasite interaction, and the results indicated that T. vaginalis could stimulate TLR5 and activate related pathways.

Phylogeography and karyotypic evolution of some Deuterodon species from southeastern Brazil (Characiformes, Characidae, Stethaprioninae).

Deuterodon is a genus of the subfamily Stethaprioninae, a group of Neotropical fish known as tetras. Deuterodon hastatus represents a species complex, which is supported by cytogenetic and molecular data. In this study, we show the results of comparative evolutionary analyses of the ATP synthase subunit 6 gene in four Deuterodon species, in addition to ribosomal markers (18S rDNA and 5S rDNA), of a new population of the D. hastatus species complex from the Angra dos Reis/RJ region. The study population comprised a new cytotype, which we refer to as cytotype D, in D. hastatus, with 2n = 50 = 6M+8SM+8ST+28A. We obtained three different clades of D. hastatus in our phylogeny, one of them composed only by specimens of cytotype D. By using molecular clock dating, we observed that the radiation of Deuterodon from southeastern Brazil seemed to be associated with neotectonic events that occurred during the Miocene-Pliocene and Pliocene-Pleistocene transitions, marked by the capture of headwater streams and marine transgressions. The results obtained reinforce the idea that D. hastatus is a species complex, and at least three evolutionary significant units were identified in this group.

Microscopic and Molecular Identification of Cyclospora cayetanensis and Cystoisospora belli in HIV-Infected People in Tabriz, Northwest of Iran.

Opportunistic pathogens such as Cryptosporidium, Cystoisospora belli, and Cyclospora cayetanensis cause various gastrointestinal and non-digestive disorders in people with HIV/AIDS. These symptoms are especially severe in HIV-infected people who have a CD4+ count of less than 200 cells/mL. This study aimed to determine the prevalence of C. belli and C. cayetanensis infections among people living with HIV in Tabriz, northwest of Iran. This descriptive study was performed on 137 people with HIV who had been referred to behavioral disease counseling centers in Tabriz. Then, after receiving written consent, fecal samples were collected and evaluated for the detection of parasitic infections using direct methods and modified acid fast staining, as well as polymerase chain reaction (PCR).From the 137 fecal samples collected (98 males and 39 females, between 20 and 40 years old), 1.5% were positive for C. cayetanensis and 2.9% were positive for C. belli. Due to the prevalence of C. cayetanensis and C. belli in people with HIV in Tabriz, essential measures, including personal hygiene training for infection control and prevention, seem necessary.

Podoplanin and CLEC-2 levels in patients with COVID-19.

Introduction: Podoplanin (PDPN gene) and CLEC-2 are involved in inflammatory hemostasis and have also been related with the pathogenesis of thrombosis. Emerging evidence also suggest that podoplanin can exert protective effects in sepsis and in acute lung injury. In lungs, podoplanin is co-expressed with ACE2, which is the main entry receptor for SARS-CoV-2. Aim: To explore the role of podoplanin and CLEC-2 in COVID-19. Methods: Circulating levels of podoplanin and CLEC-2 were measured in 30 consecutive COVID-19 patients admitted due to hypoxia, and in 30 age- and sex-matched healthy individuals. Podoplanin expression in lungs from patients who died of COVID-19 was obtained from two independent public databases of single-cell RNAseq from which data from control lungs were also available. Results: Circulating podoplanin levels were lower in COVID-19, while no difference was observed in CLEC-2 levels. Podoplanin levels were significantly inversely correlated with markers of coagulation, fibrinolysis and innate immunity. scRNAseq data confirmed that PDPN is co-expressed with ACE2 in pneumocytes, and showed that PDPN expression is lower in this cell compartment in lungs from patients with COVID-19. Conclusion: Circulating levels of podoplanin are lower in COVID-19, and the magnitude of this reduction is correlated with hemostasis activation. We also demonstrate the downregulation of PDPN at the transcription level in pneumocytes. Together, our exploratory study questions whether an acquired podoplanin deficiency could be involved in the pathogenesis of acute lung injury in COVID-19, and warrant additional studies to confirm and refine these findings.

Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family.

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

Gastrointestinal Parasites of Domestic Mammalian Hosts in Southeastern Iran.

Gastrointestinal parasites (GIP) are a major cause of disease and production loss in livestock. Some have zoonotic potential, so production animals can be a source of human infections. We describe the prevalence of GIP in domestic mammals in Southeastern Iran. Fresh fecal samples (n = 200) collected from cattle (n = 88), sheep (n = 50), goats (n = 23), camels (n = 30), donkeys (n = 5), horse (n = 1), and dogs (n = 3) were subjected to conventional coprological examination for the detection of protozoan (oo)cysts and helminth ova. Overall, 83% (166/200) of the samples were positive for one or more GIP. Helminths were found in dogs, donkeys, sheep (42%), camels (37%), goats (30%), and cattle (19%), but not in the horse. Protozoa were found in cattle (82%), goats (78%), sheep (60%), and camels (13%), but not in donkeys, dogs, or the horse. Lambs were 3.5 times more likely to be infected by protozoa than sheep (OR = 3.5, 95% CI: 1.05-11.66), whereas sheep were at higher odds of being infected by helminths than lambs (OR = 4.09, 95% CI: 1.06-16.59). This is the first study assessing the prevalence of GIP in domestic mammals in Southeastern Iran.

Type 1 Diabetes Mellitus: A Review on Advances and Challenges in Creating Insulin Producing Devices.

Type 1 diabetes mellitus (T1DM) is the most common autoimmune chronic disease in young patients. It is caused by the destruction of pancreatic endocrine ß-cells that produce insulin in specific areas of the pancreas, known as islets of Langerhans. As a result, the body becomes insulin deficient and hyperglycemic. Complications associated with diabetes are life-threatening and the current standard of care for T1DM consists still of insulin injections. Lifesaving, exogenous insulin replacement is a chronic and costly burden of care for diabetic patients. Alternative therapeutic options have been the focus in these fields. Advances in molecular biology technologies and in microfabrication have enabled promising new therapeutic options. For example, islet transplantation has emerged as an effective treatment to restore the normal regulation of blood glucose in patients with T1DM. However, this technique has been hampered by obstacles, such as limited islet availability, extensive islet apoptosis, and poor islet vascular engraftment. Many of these unsolved issues need to be addressed before a potential cure for T1DM can be a possibility. New technologies like organ-on-a-chip platforms (OoC), multiplexed assessment tools and emergent stem cell approaches promise to enhance therapeutic outcomes. This review will introduce the disorder of type 1 diabetes mellitus, an overview of advances and challenges in the areas of microfluidic devices, monitoring tools, and prominent use of stem cells, and how they can be linked together to create a viable model for the T1DM treatment. Microfluidic devices like OoC platforms can establish a crucial platform for pathophysiological and pharmacological studies as they recreate the pancreatic environment. Stem cell use opens the possibility to hypothetically generate a limitless number of functional pancreatic cells. Additionally, the integration of stem cells into OoC models may allow personalized or patient-specific therapies.

Effect of carbohydrate mouth rinse on muscle strength and muscular endurance: A systematic review with meta-analysis.

The present systematic review with meta-analysis summarized studies that investigated the effect of carbohydrate (CHO) mouth rinse on muscle strength and muscular endurance. The search was performed in six databases. Thirteen randomized clinical trials were selected and the standardized mean difference between CHO mouth rinse and placebo for maximal strength and muscular endurance was determined via a random-effects model using Review Manager 5.4 software. Meta-regression was also performed to explore the influence of load, number of sets, number of exercises, fasting time, CHO concentration, and number of mouth rinses on the main outcomes. There was no significant effect of CHO mouth rinse on maximal strength (mean difference= 0.25 kg, 95%CI - 1.81 to 2.32 kg, z = 0.24, p = 0.810). However, there was a significant positive effect of CHO mouth rinse on muscular endurance (mean difference = 1.24 repetitions, 95%CI 0.70 to 1.77 repetitions, z = 4.55, p < 0.001). Meta-regression identified that CHO mouth rinse has greater benefits on muscular endurance when using high workloads, multiple exercises, and a smaller number of mouth rinses (p = 0.001). In conclusion, CHO mouth rinse has no effect on maximal muscle strength but has a positive effect on muscular endurance and seems to optimize when fewer mouth rinses, high workloads and numbers of exercises are used.Supplemental data for this article is available online at https://doi.org/10.1080/10408398.2022.2057417.

Actin cytoskeleton and complex cell architecture in an Asgard archaeon.

Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell1-3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated4-6, but never visualized. Here we describe a highly enriched culture of 'Candidatus Lokiarchaeum ossiferum', a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7-14 days, reaches cell densities of up to 5 × 107 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain7. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying 'Ca. L. ossiferum' cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin-one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.

Description of eight new mitochondrial genomes for the genus Neoarius and phylogenetic considerations for the family Ariidae (Siluriformes).

The genus Neoarius, known as marine catfish, is a group of the family Ariidae, composed of 10 species found in Oceania. None of the species in this genus have their mitochondrial genome described, which is highly valuable in phylogenetic and molecular evolution studies. For the present work, eight species from the Neoarius genus were selected: Neoarius utarus, Neoarius midgleyi, Neoarius graeffei, Neoarius leptaspis, Neoarius berenyi, Neoarius paucus, Neoarius pectoralis, and Neoarius aff. graeffei. DNA sequences of the eight species were obtained through the NCBI Sequence Read Archive (SRA) database, and the mitochondrial genomes were assembled using the NOVOplasty tool on the Galaxy platform, subsequently annotated with the MitoAnnotator tool. We then utilized the protein-coding genes from the mitogenomes to estimate the phylogenetic relationships within the group, including seven additional mitogenomes available in the NCBI. In all species, the mitochondrial genomes presented 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 D-loop.

The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR / A influência da escolha de iniciadores na filogenia de Archaea em ensaios de PCR para o gene rRNA 16S

Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

A amplificação de genes que codificam o rRNA 16S por reação em cadeia da polimerase (PCR) e o seu sub sequentesequenciamento consistem em uma ferramenta importante na caracterização de comunidades microbianas presentes em amostras ambientais. No entanto, apesar do crescente número de sequências de DNA de Archaea depositadas em bancos de dados, a especificidade e efetividade dos iniciadores de PCR descritos como universais e amplamente utilizados na descrição desse grupo ainda não está clara. Neste estudo foram comparados os perfis filogenéticos de comunidades de arqueias obtidos a partir amostras de DNA de sedimentos lacustres do Cerrado submetidas a ensaios de PCR empregando três pares de iniciadores específicos para Archaea, comumente utilizados neste tipo de estudo. Nossos resultados indicam que as comunidades de arqueias detectadas com cada par de iniciadores apresentaram grande variação filogenética, sugerindo que a escolha de iniciadores dirigidos ao gene de rRNA 16S tem efeito significativo no perfil da comunidade descrita, com diferenças tanto em relação aos táxons detectados, como nas estimativas de unidades taxonômicas operacionais (OTU).

The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

Resumo A amplificação de genes que codificam o rRNA 16S por reação em cadeia da polimerase (PCR) e o seu subsequente sequenciamento consistem em uma ferramenta importante na caracterização de comunidades microbianas presentes em amostras ambientais. No entanto, apesar do crescente número de sequências de DNA de Archaea depositadas em bancos de dados, a especificidade e efetividade dos iniciadores de PCR descritos como universais e amplamente utilizados na descrição desse grupo ainda não está clara. Neste estudo foram comparados os perfis filogenéticos de comunidades de arqueias obtidos a partir amostras de DNA de sedimentos lacustres do Cerrado submetidas a ensaios de PCR empregando três pares de iniciadores específicos para Archaea, comumente utilizados neste tipo de estudo. Nossos resultados indicam que as comunidades de arqueias detectadas com cada par de iniciadores apresentaram grande variação filogenética, sugerindo que a escolha de iniciadores dirigidos ao gene de rRNA 16S tem efeito significativo no perfil da comunidade descrita, com diferenças tanto em relação aos táxons detectados, como nas estimativas de unidades taxonômicas operacionais (OTU).