Genomics approaches to exploit the biotechnological potential of marine sponge-derived Streptomyces spp. isolates

Members of the Streptomyces genus are widely known for their capability in producing compounds of pharmacological, clinical, and biotechnological interest, being the source of approximately a third of all the antibiotics that have been identified to date. However, the discovery of natural products with antimicrobial activities has declined following the so-called “Golden Age of Antibiotics” (1940s-1950s), particularly due to the common re-discovery of previously known compounds. Thus, natural products discovery research has shifted towards investigating diverse environmental niches, such as marine ecosystems, mangroves, and symbiotic communities of insects and sponges, resulting in the discovery of a variety of previously unidentified compounds of pharmacological interest; including those isolated from marine-derived Streptomyces species. However, in despite of their relevance as producers of potentially novel bio-active molecules with pharmacological, clinical and biotechnological interest, marine-derived Streptomyces isolates are still rather underexplored and under-characterized, particularly those found in association with marine sponges. In the studies presented in this thesis, various state-of-the-art methodologies related to genome mining and bioinformatics-based pipelines, together with molecular and synthetic biology, were employed and proved to be extremely useful in helping to uncover the biotechnological potential of marine sponge-derived Streptomyces isolates. These studies essentially aimed at a) genetically characterizing marine sponge-derived Streptomyces spp. isolates and their potential to produce novel secondary metabolites, as shown in Chapter 2; b) to in silico identify, isolate, and quantify a secondary metabolite produced by a marine sponge-derived Streptomyces isolate, together with genetically characterizing its genome-encoded biosynthetic gene cluster (BGC), as reported in Chapter 3; and c) to perform an in silico screening of a novel polyesterase from a marine sponge-derived Streptomyces isolate, followed by heterologous protein expression in an E. coli host, as demonstrated in Chapter 4. In Chapter 2, two of the first complete genomes from marine sponge-derived Streptomyces spp. isolates were determined, namely from Streptomyces sp. SM17 and Streptomyces sp. SM18. The high-quality data provided in this study allowed for a reliable prediction of secondary metabolites biosynthetic gene clusters (BGCs) in their genomes, which determined that these isolates possess a variety of BGCs potentially encoding for the production of known compounds, and also potentially new molecules. Differential growth assessment determined that the marine isolates SM17 and SM18 grew and differentiated better in the presence of salts in the culture medium, when compared to their phylogenetically determined closely-related terrestrial relatives, namely S. albidoflavus J1074 (referred to as S. albus J1074 in Chapter 2) and S. pratensis ATCC 33331, respectively. Comparative genomics allowed for the identification of a proposed environmental niche adaptations (ENA) gene pool, which included genes related to osmotic stress defence, transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defence-related features. These results shed new light on some of the genetic traits possessed by these marine sponge-derived isolates, and on how these might be linked to secondary metabolites production, and further highlighted their importance for the discovery of potentially novel natural products. In Chapter 3, the previously unreported capability of the Streptomyces sp. SM17 to produce surugamides has been described. Surugamides are a family of compounds that have been previously reported to possess antitumor and antifungal activities. This was performed employing genome mining, which allowed for the identification of the surugamides BGC (sur BGC) in the SM17 genome, and analytical chemistry techniques for compound isolation and quantification. Phylogenomics analyses provided novel insights with respect to the distribution and conservation of the sur BGC at a genetic level, and provided evidence that the sur BGC might have had a marine origin. Additionally, when comparing the surugamide A production capabilities of a marine isolate (strain SM17) with a terrestrial relative (strain J1074) employing a “One Strain Many Compounds” (OSMAC)-based cultivation approach, the Streptomyces sp. SM17 isolate was shown to produce higher levels of surugamide A in all the conditions tested for. These findings may provide important insights towards a better characterisation, improved production and industrial development of this family of compounds. In Chapter 4, the capability of marine sponge-derived Streptomyces spp. isolates to degrade synthetic polyesters was investigated. This was based on the fact that these microorganisms might have developed mechanisms to assimilate components of micro-plastics, which are now believed to be ubiquitous in marine ecosystems and pose as one of the top environmental problems that society faces today. Using 15 known PET hydrolases (PETases) as references, including the Ideonella sakaiensis 201-F6 PETase, in silico screening was performed to determine the presence of homologs to these reference PETase enzymes in 52 Streptomyces genome sequences (of which 29 were derived from marine ecosystems). The best candidate identified, namely the SM14est protein from the marine sponge-derived Streptomyces sp. SM14, was in silico characterised with respect to its amino acid sequence and predicted three dimensional structure, and was subsequently heterologously expressed in an E. coli host. This allowed for the confirmation of the polyesterase activity possessed by the SM14est enzyme, via a polycaprolactone (PCL) plate-clearing assay. Better characterising, identifying sources, and determining methods for improved protein expression are essential steps towards the development of biotechnological applications and industrial processes employing this family of enzymes, such as new plastic waste processing technologies

Hybrid Maneuver for Gradient Search with Multiple Coordinated AUVs

This work presents a hybrid maneuver for gradient search with multiple AUV's. The mission consists in following a gradient field in order to locate the source of a hydrothermal vent or underwater freshwater source. The formation gradient search exploits the environment structuring by the phenomena to be studied. The ingredients for coordination are the payload data collected by each vehicle and their knowledge of the behaviour of other vehicles and detected formation distortions

Draft genome sequence of the antimycin-producing bacterium Streptomyces sp. strain SM8, isolated from the marine sponge Haliclona simulans

Streptomyces sp. strain SM8, isolated from Haliclona simulans, possesses antifungal and antibacterial activities and inhibits the calcineurin pathway in yeast. The draft genome sequence is 7,145,211 bp, containing 5,929 predicted coding sequences. Several secondary metabolite biosynthetic gene clusters are present, encoding known and novel metabolites, including antimycin

Draft genome sequence of Pseudomonas putida CA-3, a bacterium capable of styrene degradation and medium-chain-length polyhydroxyalkanoate synthesis

Pseudomonas putida strain CA-3 is an industrial bioreactor isolate capable of synthesizing biodegradable polyhydroxyalkanoate polymers via the metabolism of styrene and other unrelated carbon sources. The pathways involved are subject to regulation by global cellular processes. The draft genome sequence is 6,177,154 bp long and contains 5,608 predicted coding sequences

Hospitalization and mortality rates for heart failure in public hospitals in São Paulo

BACKGROUND: Advances in the treatment of heart failure (HF) have resulted in reduced mortality and hospitalization rates. On the other hand, when hospitalized, patients are at high risk of death. OBJECTIVE: As there are few studies in this group of patients in Brazil, we analyzed the numbers of hospitalization and deaths due to HF in the Brazilian Public Health System (SUS) in the city of São Paulo. METHODS: Historical prospective study carried out between 1992 and 2010. The data were obtained from DATASUS. We used Chi-square and t tests for comparison between the periods 1992-1993 and 2008-2009 and logistic regression models when appropriate. The level of significance was set at 5%. RESULTS: There was a 32% decrease in the number of hospitalizations for HF between 1992-1993 and 2008-2009 (p = 0.002). The in-hospital mortality rate for HF was 15%, with a 15% increase in the period (p = 0.004). Between 1992 and 1993, the mean time of hospitalization for HF was 8.8 days. Between 2008 and 2009, it was 11.3 days (p = 0.001). August was the month with the highest incidence of hospitalizations for HF, 20% higher than in February, the month with the lowest incidence (p = 0.041). CONCLUSION: This study showed changes in trends of hospitalization for HF and mortality over the last two decades. We emphasize important implications: 1: 32% decrease in the number of hospitalizations for HF in SUS hospitals in São Paulo; 2: 25% increase in hospitalization time, and 3: seasonal pattern of hospitalization for HF, with a peak in the third quarter.FUNDAMENTO: Os avanços no tratamento da insuficiência cardíaca (IC) resultaram em redução da taxa de mortalidade e de hospitalização. Por outro lado, quando hospitalizados, os pacientes apresentam alto risco de óbito. OBJETIVO: Como são poucos os estudos com esse grupo de pacientes no Brasil, analisamos os números de internação e óbito por IC no SUS do município de São Paulo. MÉTODOS: Estudo prospectivo histórico realizado entre 1992 e 2010. Os dados foram obtidos no DATASUS. Utilizamos os testes qui-quadrado e T para a comparação entre os períodos 1992-1993 e 2008-2009 e modelos de regressão logística quando apropriado. O nível de significância considerado foi de 5%. RESULTADOS: Houve redução de 32% no número de internações por IC entre 1992-1993 e 2008-2009 (p = 0,002). A taxa de mortalidade hospitalar por IC foi de 15%, com aumento de 15% no período (p = 0,004). Entre 1992-1993, o tempo médio de hospitalização por IC foi de 8,8 dias. Entre 2008-2009, 11,3 dias (p = 0,001). Agosto foi o mês com maior incidência de internações por IC, 20% maior do que fevereiro, mês de menor incidência (p = 0,041). CONCLUSÃO: Este estudo apresentou as modificações nas tendências de hospitalização e mortalidade hospitalar por IC ao longo das duas últimas décadas. Ressaltamos importantes implicações: 1º: redução em 32% no número de internações por IC em hospitais do SUS no município de São Paulo; 2º: aumento de 25% no tempo de hospitalização; e 3º: padrão sazonal de internação por IC, com pico no terceiro trimestre.Universidade Federal de São Paulo (UNIFESP)UNIFESPSciEL

Characterization of recycled carbon fibers reinforcing thermoplastic polymers

In recent years, the metallic materials used in the automotive sector have been replaced by plastic materials. Also associated with this, the recycling or reuse of plastics parts is increasingly important. This work appears framed within a project that intends to substitute thermosetting materials for thermoplastics materials, that will be apply in the automotive sector. So, this article compares two thermoplastics materials reinforced by recycled carbon fibers. In the first case, the used materials were layers of recycled carbon fiber prepreg with polypropylene (PP) and in the second case it were used layers of recycling carbon fiber and layers of PP nonwovens. Both materials were processed by compression moulding process, at the same temperature. After processing, the composite materials obtained were evaluated mechanically, physically and thermally. A flammability test was also carried out to verify if it could be used in the automotive sector. After the characterization tests, as a conclusion, the material that offers the better properties is the recycled carbon fiber prepreg with polypropylene, with both materials fulfilling the requirements of the flammability standard.P2020 - Individual Project SI I&DT nº NORTE-01-0247-FEDER-009292 - “Functional_dashboard – Functional components in composite material for vehicle interiors”.info:eu-repo/semantics/publishedVersio

HIPE: HMC Instruction Predication Extension Applied on Database Processing

The recent Hybrid Memory Cube (HMC) is a smart memory which includes functional units inside one logic layer of the 3D stacked memory design. In order to execute instructions inside the Hybrid Memory Cube (HMC), the processor needs to send instructions to be executed near data, keeping most of the pipeline complexity inside the processor. Thus, control-flow and data-flow dependencies are all managed inside the processor, in such way that only update instructions are supported by the HMC. In order to solve data-flow dependencies inside the memory, previous work proposed HMC Instruction Vector Extensions (HIVE), which embeds a high number of functional units with a interlock register bank. In this work we propose HMC Instruction Prediction Extensions (HIPE), that supports predicated execution inside the memory, in order to transform control-flow dependencies into data-flow dependencies. Our mechanism focus on removing the high latency iteration between the processor and the smart memory during the execution of branches that depends on data processed inside the memory. In this paper we evaluate a balanced design of HIVE comparing to x86 and HMC executions. After we show the HIPE mechanism results when executing a database workload, which is a strong candidate to use smart memories. We show interesting trade-offs of performance when comparing our mechanism to previous work

Distance Functions and Normalization Under Stream Scenarios

Data normalization is an essential task when modeling a classification system. When dealing with data streams, data normalization becomes especially challenging since we may not know in advance the properties of the features, such as their minimum/maximum values, and these properties may change over time. We compare the accuracies generated by eight well-known distance functions in data streams without normalization, normalized considering the statistics of the first batch of data received, and considering the previous batch received. We argue that experimental protocols for streams that consider the full stream as normalized are unrealistic and can lead to biased and poor results. Our results indicate that using the original data stream without applying normalization, and the Canberra distance, can be a good combination when no information about the data stream is known beforehand.Comment: Paper accepted to the 2023 International Joint Conference on Neural Network

Obtenção de dados meteorológicos para sistemas de alerta fitossanitário: o caso da duração do período de molhamento foliar

Disease-warning systems are decision support tools designed to help growers determine when to apply control measures to suppress crop diseases. Weather data are nearly ubiquitous inputs to warning systems. This contribution reviews ways in which weather data are gathered for use as inputs to disease-warning systems, and the associated logistical challenges. Grower-operated weather monitoring is contrasted with obtaining data from networks of weather stations, and the advantages and disadvantages of measuring vs. estimating weather data are discussed. Special emphasis is given to leaf wetness duration (LWD), not only because LWD data are inputs to many disease-warning systems but also because accurate data are uniquely challenging to obtain. It is concluded that there is no single best method to acquire weather data for use in disease-warning systems; instead, local, regional, and national circumstances are likely to influence which strategy is most successful.Os sistemas de alerta fitossanitário são ferramentas de suporte à decisão desenvolvidos para ajudar os agricultures a determinar o melhor momento da aplicação das medidas de controle para combater as doenças de plantas. As variáveis meteorológicas são dados de entrada quase que obrigatórios desses sistemas. Este trabalho apresenta uma revisão sobre os meios pelos quais as variáveis meteorológicas são coletadas para serem usadas como dados de entrada em sistemas de alerta fitossanitário e sobre os desafios associados à logística de obtenção desses dados. Essa revisão compara o monitoramento meteorológico ao nível do produtor, nas propriedades agrícolas, com aquele feito ao nível de redes de estações meteorológicas, assim como discute as vantagens e desvantagens entre medir e estimar tais variáveis meteorológicas. Especial ênfase é dada à duração do período de molhamento foliar (DPM), não somente pela sua importância como dado de entrada em diversos sistemas de alerta fitossanitário, mas também pelo desafio de se obter dados acurados dessa variável. Pode-se concluir, após ampla discussão do assunto, que não há um método único e melhor para se obter os dados meteorológicos para uso em sistemas de alerta fitossanitário; por outro lado, as circunstâncias a nível local, regional e nacional provavelmente influenciam a estratégia de maior sucesso