Genetic variations in immune mediators and prostate cancer risk: A field synopsis with Bayesian calculations.

OBJECTIVE: Our study aimed to revaluate the significant data from meta-analyses on genetic variations in immune mediators and the risk of prostate cancer (PCa) by Bayesian approaches. METHODS: We performed a search on the literature before September 5th, 2023, for meta-analytic studies on polymorphisms in immune mediator genes and the risk of PCa. Two Bayesian approaches were used to assess the level of noteworthiness in the meta-analytic data: the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) with a statistical power of 1.2 and 1.5 of Odds Ratio at a prior probability of 10-3 and 10-6. The quality evaluation of studies was performed with the Venice criteria. Gene-gene and protein-protein networks were designed for the genes and products enrolled in the results. RESULTS: As results, 18 meta-analyses on 17 polymorphisms in several immune mediator genes were included (IL1B rs16944/rs1143627, IL4 rs2243250/rs2227284/rs2070874, IL6 1800795/rs1800796/rs1800797, IL8 rs4073, IL10 rs1800896/rs1800871/rs1800872, IL18 rs1946518, COX2 rs2745557, TNFA rs361525 and PTGS2 rs20417/689470). The Bayesian calculations showed the rs1143627 and the rs1946518 polymorphisms in IL1B and IL18 genes, respectively, were noteworthy. The Venice criteria showed that only four studies received the highest level of evidence. The gene-gene and protein-protein networks reinforced the findings on IL1B and IL18 genes. CONCLUSION: In conclusion, this current Bayesian revaluation showed that the rs1143627 and the rs1946518 polymorphisms in the IL1B and IL18 genes, respectively, were noteworthy biomarker candidates for PCa risk.

Meniscal repair with additive manufacture of bioresorbable polymer: From physicochemical characterization to implantation of 3D printed poly (L-co-D, L lactide-co-trimethylene carbonate) with autologous stem cells in rabbits.

Three-dimensional (3D) structures are actually the state-of-the-art technique to create porous scaffolds for tissue engineering. Since regeneration in cartilage tissue is limited due to intrinsic cellular properties this study aims to develop and characterize three-dimensional porous scaffolds of poly (L-co-D, L lactide-co-trimethylene carbonate), PLDLA-TMC, obtained by 3D fiber deposition technique. The PLDLA-TMC terpolymer scaffolds (70:30), were obtained and characterized by scanning electron microscopy, gel permeation chromatography, differential scanning calorimetry, thermal gravimetric analysis, compression mechanical testing and study on in vitro degradation, which showed its amorphous characteristics, cylindrical geometry, and interconnected pores. The in vitro degradation study showed significant loss of mechanical properties compatible with a decrease in molar mass, accompanied by changes in morphology. The histocompatibility association of mesenchymal stem cells from rabbit's bone marrow, and PLDLA-TMC scaffolds, were evaluated in the meniscus regeneration, proving the potential of cell culture at in vivo tissue regeneration. Nine New Zealand rabbits underwent total medial meniscectomy, yielding three treatments: implantation of the seeded PLDLA-TMC scaffold, implantation of the unseeded PLDLA-TMC and negative control (defect without any implant). After 24 weeks, the results revealed the presence of fibrocartilage in the animals treated with polymer. However, the regeneration obtained with the seeded PLDLA-TMC scaffolds with mesenchymal stem cells had become intimal to mature fibrocartilaginous tissue of normal meniscus both macroscopically and histologically. This study demonstrated the effectiveness of the PLDLA-TMC scaffold in meniscus regeneration and the potential of mesenchymal stem cells in tissue engineering, without the use of growth factors. It is concluded that bioresorbable polymers represent a promising alternative for tissue regeneration.

Daily Formative Assessment in Undergraduate Medical Training: construction and presentation of an instrument / Avaliação diária de atitudes e profissionalismo na Graduação Médica: apresentação de um instrumento

The objective is to present a daily attitudes and professionalism assessment instrument for medical students in theoretical-practical activities. The development of the instrument was based on the manuals of the program for student integration with the community, on the program's pedagogical project, and on the National Curricular Guidelines for Undergraduate Programs in Medicine, and was carried out by professors. These were consulted in weekly 50-minute meetings held between August and November 2016. At the end of the process, a version of the instrument was consolidated with five items and six descriptors to discriminate learning situations that enable competency-based assessment from the simplest to the most complex level. With the use of the instrument, points considered important in medical training in theoretical-practical activities cannot be overlooked (AU).

Objetiva-se apresentar um instrumento de avaliação diária de atitudes e profissionalismo para estudantes de Medicina em atividades teórico-práticas. A elaboração do instrumento foi baseada nos manuais do programa de integração do aluno com a comunidade, projeto pedagógico do curso e nas Diretrizes Curriculares Nacionais da Graduação em Medicina, realizada por docentes. Os docentes foram consultados em reuniões com duração de 50 minutos, com periodicidade semanal, entre agosto e novembro de 2016. Ao final do processo foi consolidada uma versão do instrumento com cinco itens e seis descritores para discriminação de situações de aprendizagem que permitem a avaliação da competência de um nível mais simples até o mais complexo. Com a utilização do instrumento elaborado não se deixa de avaliar pontos considerados importantes para a formação médica em atividades teórico-prática (AU).

Corrigendum to "How, what, and why: housing, water & sanitation and wealth patterns in a cross-sectional study of the Guarani Birth Cohort, the first indigenous birth cohort in Brazil" [The Lancet Regional Health - Americas 2023;21: 100496].

[This corrects the article DOI: 10.1016/j.lana.2023.100496.].

How, what, and why: housing, water & sanitation and wealth patterns in a cross-sectional study of the Guarani Birth Cohort, the first Indigenous birth cohort in Brazil.

Background: Despite the importance of social determinants of health, studies on the effects of socioeconomic, sanitary, and housing conditions on Indigenous child health are scarce worldwide. This study aims to identify patterns in housing, water & sanitation, and wealth (HSW) in the first Indigenous birth cohort in Brazil-The Guarani Birth Cohort. Methods: Cross-sectional study using baseline data from The Guarani Birth Cohort. We used Multiple Correspondence Analysis and Cluster Analysis. The clusters identified were ordered in increasing degrees of access to public policies and wealth, defining the patterns of HSW. Finally, we explored the association between the patterns and one of the health outcomes, hospitalization, in the birth cohort. Findings: Three patterns were identified for housing and water & sanitation, and four for wealth status, resulting in 36 combinations of patterns (3 × 3 × 4). More than 62% of children in the cohort were found with the lowest wealth patterns. The distribution of children across patterns in one dimension was not fully determined by the other two dimensions. Statistically significant associations were found between precarious households and extreme poverty, and hospitalization. Interpretation: We observed substantial heterogeneity in the distribution of children across the 36 combinations. These findings highlight that, should the dimensions of HSW be associated with health outcomes, as seen for hospitalization, they should be considered separately in multivariable models, in order to improve the estimation of their independent effects. Funding: National Council for Scientific and Technological Development, Brazil (CNPq); Oswaldo Cruz Foundation, Brazil (Fiocruz); Research Foundation of the State of Rio de Janeiro, Brazil (FAPERJ).

Zika Virus Infects Human Placental Mast Cells and the HMC-1 Cell Line, and Triggers Degranulation, Cytokine Release and Ultrastructural Changes.

Zika virus (ZIKV) is an emergent arthropod-borne virus whose outbreak in Brazil has brought major public health problems. Infected individuals have different symptoms, including rash and pruritus, which can be relieved by the administration of antiallergics. In the case of pregnant women, ZIKV can cross the placenta and infect the fetus leading to congenital defects. We have identified that mast cells in the placentae of patients who had Zika during pregnancy can be infected. This led to our investigation on the possible role of mast cells during a ZIKV infection, using the HMC-1 cell line. We analyzed their permissiveness to infection, release of mediators and ultrastructural changes. Flow cytometry detection of ZIKV-NS1 expression 24 h post infection in 45.3% of cells showed that HMC-1 cells are permissive to ZIKV infection. Following infection, ß-hexosaminidase was measured in the supernatant of the cells with a notable release at 30 min. In addition, an increase in TNF-α, IL-6, IL-10 and VEGF levels were measured at 6 h and 24 h post infection. Lastly, different intracellular changes were observed in an ultrastructural analysis of infected cells. Our findings suggest that mast cells may represent an important source of mediators that can activate other immune cell types during a ZIKV infection, which has the potential to be a major contributor in the spread of the virus in cases of vertical transmission.

Identification of benzene-degrading Proteobacteria in a constructed wetland by employing in situ microcosms and RNA-stable isotope probing.

Constructed wetlands (CWs) are effective ecological remediation technologies for various contaminated water bodies. Here, we queried for benzene-degrading microbes in a horizontal subsurface flow CW with reducing conditions in the pore water and fed with benzene-contaminated groundwater. For identification of relevant microbes, we employed in situ microcosms (BACTRAPs, which are made from granulated activated carbon) coupled with 13C-stable isotope probing and Illumina sequencing of 16S rRNA amplicons. A significant incorporation of 13C was detected in RNA isolated from BACTRAPs loaded with 13C-benzene and exposed in the CW for 28 days. A shorter incubation time did not result in detectable 13C incorporation. After 28 days, members from four genera, namely Dechloromonas, Hydrogenophaga, and Zoogloea from the Betaproteobacteria and Arcobacter from the Epsilonproteobacteria were significantly labeled with 13C and were abundant in the bacterial community on the BACTRAPs. Sequences affiliated to Geobacter were also numerous on the BACTRAPs but apparently those microbes did not metabolize benzene as no 13C label incorporation was detected. Instead, they may have metabolized plant-derived organic compounds while using the BACTRAPs as electron sink. In representative wetland samples, sequences affiliated with Dechloromonas, Zoogloea, and Hydrogenophaga were present at relative proportions of up to a few percent. Sequences affiliated with Arcobacter were present at < 0.01% in wetland samples. In conclusion, we identified microbes of likely significance for benzene degradation in a CW used for remediation of contaminated water.

Molecular diagnosis of cutaneous leishmaniasis in an endemic area of Acre State in the Amazonian Region of Brazil.

INTRODUCTION: This study proposes to identify the Leishmania species found in the skin lesions of cutaneous leishmaniasis (CL) patients from Brasiléia municipality (Acre). METHODS: Skin biopsy imprints or biopsy fragments were assayed via kDNA-PCR/RFLP and FRET-real-time PCR. RESULTS: Of individuals with suspected CL, 18 were positive for Leishmania kDNA. Leishmania (Viannia) braziliensis (61.1%) and Leishmania (Viannia) guyanensis (5.5%) were identified in the positive samples. CONCLUSIONS: These results are congruent with the previous reports in Acre and Bolivia, revealing L. braziliensis as the most prevalent species. L. guyanensis identification also corroborates with the epidemiology of the disease in the Amazon Basin.

Molecular diagnosis of cutaneous leishmaniasis in an endemic area of Acre State in the Amazonian Region of Brazil

Abstract INTRODUCTION This study proposes to identify the Leishmania species found in the skin lesions of cutaneous leishmaniasis (CL) patients from Brasiléia municipality (Acre). METHODS Skin biopsy imprints or biopsy fragments were assayed via kDNA-PCR/RFLP and FRET-real-time PCR. RESULTS Of individuals with suspected CL, 18 were positive for Leishmania kDNA. Leishmania (Viannia) braziliensis (61.1%) and Leishmania (Viannia) guyanensis (5.5%) were identified in the positive samples. CONCLUSIONS These results are congruent with the previous reports in Acre and Bolivia, revealing L. braziliensis as the most prevalent species. L. guyanensis identification also corroborates with the epidemiology of the disease in the Amazon Basin.

Feasibility of using risk prompts to prevent falls, dehydration and pulmonary aspiration in nursing homes: a clinical study protocol.

BACKGROUND: Evidence has shown a relationship between dehydration, falls, and pulmonary aspiration among older adults in nursing homes, all of which contribute to loss of independence and quality of life. It is believed that improving communication among healthcare professionals in nursing homes (physicians, nurses, rehabilitation team, psychologist, social workers, dieticians and medical assistants) decreases the number of adverse events in institutionalized patients. This study will evaluate the feasibility of using a set of written signs, designed to caution against the risk of falls, dehydration, and pulmonary aspiration, and will enable the proposal of tailored interventions to manage these events in nursing homes. METHODS/DESIGN: All patients from Campus Neurológico Sénior (CNS) nursing home, at risk of falls and/ordysphagia and/or dehydration will be invited to participate in the study. Patients will undertake a screeningrisk assessment and the corresponding risk prompts will be attributed. Study duration will be a minimum ofthree months per participant, including daily record of falls, dehydration and pulmonary aspiration eventsand monthly interview assessments, conducted by a member of the research team. Data of the events that occur will be compared with historical data extracted retrospectively from medical and nursing charts. This study has been approved by the Ethics Committee of the Medical Academic Center of Lisbon, Faculty of Medicine, University of Lisbon (Ref. 176/15). All participants will give their written informed consent before entering the study. DISCUSSION: This study is unique in evaluating the feasibility of a communication system in preventing the three major risks in nursing home. Thoughtful selection and display of proper risk prompts in nursing homes could be an essential step along a path toward efficient communication of risks among healthcare teams. We expect that the displays will be easily applicable given their simplicity, low complexity, and minimal physical requirements. TRIAL REGISTRATION: NCT03123601. March 7, 2017. Retrospectively registered.

Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.

A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422 750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds.

Microbial communities in pyrene amended soil-compost mixture and fertilized soil.

Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of 13C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH. We performed statistical analyses of bacterial genera abundance data based on total DNA and RNA (for comparison) extracted from the soil samples. The results revealed complex pyrene degrading communities with low abundance of individual degraders instead of a limited number of abundant key players. The bacterial degrader communities of the soil-compost mixture and soil fertilized with farmyard manure differed considerably in composition albeit showing similar degradation kinetics. Additional analyses were carried out on enrichment cultures and enabled the reconstruction of several nearly complete genomes, thus allowing to link microcosm and enrichment experiments. However, pyrene mineralizing bacteria enriched from the compost or unfertilized soil-compost samples did not dominate pyrene degradation in the soils. Based on the present findings, evaluations of PAH degrading microorganisms in complex soil mixtures with high organic matter content should not target abundant key degrading species, since the specific degraders may be highly diverse, of low abundance, and masked by high bacterial background.

[The interaction between people with Down syndrome and their siblings: an exploratory study]. / A interação entre as pessoas com síndrome de Down e seus irmãos: um estudo exploratório.

The presence of a disabled person causes transformations in the family that demand a redefinition of the role of each member. Siblings, like all other members, experience frustration, acceptance, guilt and adaptation. In this respect, an attempt was made to; (a) analyze the interaction between a sibling with standard development and a sibling with Down syndrome; (b) identify what information and reaction the siblings with standard development have regarding the diagnosis of Down syndrome; (c) verify whether or not there were changes in the family context and also changes in their own lives after the birth of the sibling with Down syndrome. The survey was conducted through interviews, the participants being seven children with standard development having siblings with Down syndrome. The study showed that the siblings, as well as the other family members, experience processes of acceptance, confusion and other complex emotions related to the disability, albeit they are not as marked as those experienced by their parents. A fact revealed in this study is the importance of support groups for siblings, seeking to handle issues such as prejudice and adverse feelings towards disability. The siblings with standard development must have correct information, as well as support, in order to foster healthy interaction between siblings.

A interação entre as pessoas com síndrome de Down e seus irmãos: um estudo exploratório / The interaction between people with Down syndrome and their siblings: an exploratory study

Resumo A presença de uma pessoa com deficiência provoca transformações na família que exigem, de cada membro, redefinição de papéis. O irmão, como todos os outros membros, passa por processos de frustração, aceitação, culpa e mudanças. Nesse sentido, objetivou-se (a) analisar a interação entre o irmão com desenvolvimento típico e o com síndrome de Down; (b) identificar que informação e reação os irmãos com desenvolvimento típico possuem sobre o diagnóstico da síndrome de Down; (c) verificar se houve ou não modificações no contexto familiar e em suas próprias vidas após o nascimento do irmão com síndrome de Down. A pesquisa, realizada por meio de entrevistas, teve como participantes sete sujeitos com desenvolvimento típico, irmãos de pessoas com síndrome de Down. O estudo demonstrou que os irmãos, assim como os demais agentes familiares, passam por processos de aceitação, confusão e por várias outras complexidades com a qual a deficiência está atrelada, mas que estas não são tão marcantes quanto aos de seus pais. Um indicativo apontado no estudo se refere à importância de grupos de apoio para irmãos, que visem trabalhar questões como preconceito e sentimentos aversivos perante a deficiência. Aqueles com desenvolvimento típico precisam de informações corretas, bem como apoio, visando favorecer a interação entre irmãos.

Abstract The presence of a disabled person causes transformations in the family that demand a redefinition of the role of each member. Siblings, like all other members, experience frustration, acceptance, guilt and adaptation. In this respect, an attempt was made to; (a) analyze the interaction between a sibling with standard development and a sibling with Down syndrome; (b) identify what information and reaction the siblings with standard development have regarding the diagnosis of Down syndrome; (c) verify whether or not there were changes in the family context and also changes in their own lives after the birth of the sibling with Down syndrome. The survey was conducted through interviews, the participants being seven children with standard development having siblings with Down syndrome. The study showed that the siblings, as well as the other family members, experience processes of acceptance, confusion and other complex emotions related to the disability, albeit they are not as marked as those experienced by their parents. A fact revealed in this study is the importance of support groups for siblings, seeking to handle issues such as prejudice and adverse feelings towards disability. The siblings with standard development must have correct information, as well as support, in order to foster healthy interaction between siblings.

In situ†protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model.

In constructed wetlands, organic pollutants are mainly degraded via microbial processes. Helophytes, plants that are commonly used in these systems, provide oxygen and root exudates to the rhizosphere, stimulating microbial degradation. While the treatment performance of constructed wetlands can be remarkable, a mechanistic understanding of microbial degradation processes in the rhizosphere is still limited. We investigated microbial toluene removal in a constructed wetland model system combining 16S rRNA gene sequencing, metaproteomics and (13) C-toluene in situ protein-based stable isotope probing (protein-SIP). The rhizospheric bacterial community was dominated by Burkholderiales and Rhizobiales, each contributing about 20% to total taxon abundance. Protein-SIP data revealed that the members of Burkholderiaceae, the proteins of which showed about 73% of (13) C-incorporation, were the main degraders of toluene in the planted system, while the members of Comamonadaceae were involved to a lesser extent in degradation (about 64% (13) C-incorporation). Among the Burkholderiaceae, one of the key players of toluene degradation could be assigned to Ralstonia pickettii. We observed that the main pathway of toluene degradation occurred via two subsequent monooxygenations of the aromatic ring. Our study provides a suitable approach to assess the key processes and microbes that are involved in the degradation of organic pollutants in complex rhizospheric ecosystems.

Determination of quality attributes in wax jambu fruit using NIRS and PLS.

The aim of this work was to develop an analytical method to predict total anthocyanins content (TAC) and total phenolic compounds (TPC) in intact wax jambu fruit [Syzygium malaccense (L.) Merryl et Perry] using near-infrared spectroscopy (NIRS) and partial least squares (PLS). The estimation accuracy was based on parameters such as root mean square error of prediction (RMSEP), correlation coefficients [calibration (rc) and prediction (rp) set] and ratio of performance to deviation (RPD). TAC, rp = 0.98, RMSEP = 9.0 mg L(-1) and RPD = 5.19 were attained using second derivative pre-treatment. TPC, rp = 0.94, RMSEP = 22.18 (mg gallic acid equivalents (GAE)/100g) and RPD = 3.27 (excellent accuracy) were also obtained using second derivative pre-treatment. These findings suggest that the NIRS and PLS algorithms can be used to determine TCA and TPC in intact wax jambu fruit.

Pharmacobotanical study of Baccharis pentaptera

AbstractBaccharis L. sect. Caulopterae, Asteraceae, comprises thirty species in Brazil that show stems represented by cladodes, which are very similar in morphology. These species are popularly known as “carqueja” in Brazil and Argentina and are used in popular medicine as diuretic and stomachic. The aim of this work was to examine the morpho-anatomical characters of cladodes of Baccharis pentaptera (Less.) DC. for diagnosis purposes. The plant material was prepared by light and scanning electron microscopy. B. pentaptera shows opposite and spread wings in the two-winged cladode axis and irregular arrangement in the three-winged cladode. The wings have a uniseriate epidermis with palisade parenchyma next to both sides of epidermis. The spongy parenchyma crossed by minor collateral vascular bundles is observed in the central region of wings. The glandular trichomes are capitate and biseriate and the non-glandular trichomes are uniseriate and flagelliform with 2–3 cells that extend from the base. In caulinar axis, there are uniseriate epidermis, chlorenchyma alternating with angular collenchyma and perivascular fiber caps adjoining the phloem which is outside the xylem. Prismatic and styloid crystals are verified in the perimedullary zone. These combined characters can assist the diagnosis of Baccharis species sect. Caulopterae.

Structure-guided engineering of molinate hydrolase for the degradation of thiocarbamate pesticides.

Molinate is a recalcitrant thiocarbamate used to control grass weeds in rice fields. The recently described molinate hydrolase, from Gulosibacter molinativorax ON4T, plays a key role in the only known molinate degradation pathway ending in the formation of innocuous compounds. Here we report the crystal structure of recombinant molinate hydrolase at 2.27 Å. The structure reveals a homotetramer with a single mononuclear metal-dependent active site per monomer. The active site architecture shows similarities with other amidohydrolases and enables us to propose a general acid-base catalysis mechanism for molinate hydrolysis. Molinate hydrolase is unable to degrade bulkier thiocarbamate pesticides such as thiobencarb which is used mostly in rice crops. Using a structural-based approach, we were able to generate a mutant (Arg187Ala) that efficiently degrades thiobencarb. The engineered enzyme is suitable for the development of a broader thiocarbamate bioremediation system.

Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers.

Polycyclic aromatic hydrocarbons (PAH) are widespread and persistent environmental contaminants, especially in oxygen-free environments. The occurrence of anaerobic PAH-degrading bacteria and their underlying metabolic pathways are rarely known. In this study, PAH degraders were enriched in laboratory microcosms under sulfate-reducing conditions using groundwater and sediment samples from four PAH-contaminated aquifers. Five enrichment cultures were obtained showing sulfate-dependent naphthalene degradation. Mineralization of naphthalene was demonstrated by the formation of sulfide concomitant with the depletion of naphthalene and the development of (13)C-labeled CO2 from [(13)C6]-naphthalene. 16S rRNA gene and metaproteome analyses revealed that organisms related to Desulfobacterium str. N47 were the main naphthalene degraders in four enrichment cultures. Protein sequences highly similar to enzymes of the naphthalene degradation pathway of N47 were identified, suggesting that naphthalene was activated by a carboxylase, and that the central metabolite 2-naphthoyl-CoA was further reduced by two reductases. The data indicate an importance of members of the family Desulfobacteraceae for naphthalene degradation under sulfate-reducing conditions in freshwater environments.

AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics.

Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL: http://aromadeg.siona.helmholtz-hzi.de