A ciclagem de matéria orgânica (MO) no ambiente marinho é um processo-chave para o ciclo global de carbono. Os sedimentos costeiros são de suma importância para a ciclagem de carbono pois atuam como receptores de grandes quantidades de MO alóctone (i.e. terrestre) e autóctone (i.e. marinho). A miríade dos componentes orgânicos e suas diferentes características dificultam o entendimento das fontes de MO em ambientes costeiros. Este trabalho visou entender a origem e a composição da MO (através de biomarcadores lipídicos) e a dinâmica da comunidade microbiana (método ATP) em sedimentos superficiais de diferentes ecossistemas marinhos da costa sudeste do Brasil: (i) margem continental de Cabo Frio; (ii) sistema lagunar de Saquarema; (iii) áreas costeiras e a plataforma continental de Ubatuba; (iv) e a plataforma adjacente ao estuário de Santos. Os resultados apontaram uma origem predominantemente autóctone para a MO nestes sistemas, com contribuição terrestre reduzida e limitada à áreas próximas à costa. Processos oceanográficos e forçantes ambientais são cruciais para a composição da MO sedimentar e são discutidas para cada um dos ecossistemas estudados. / The cycling of the organic matter (OM) in the marine environment is a key process in the global carbon cycle. Coastal sediments are important to the global carbon cycle, since they receive large inputs from both marine and terrestrial OM. The myriad of organic compounds and their spectrum of reactivity complicate the understanding of OM sources in coastal environments. In this work, we aimed to access the origin and composition of the OM (through lipid biomarkers) and the microbial dynamics (ATP method) in surface sediments of diverse marine ecosystems from the SE Brazilian coast: (i) the continental margin off Cabo Frio; (ii) the lagoonal system of Saquarema; (iii) coastal and shelf areas from Ubatuba; and (iv) the continental shelf adjacent to Santos estuary. The results showed a dominance of autochthonous OM, with a minor fraction of the OM derived from terrestrial sources and restricted to areas close to the coast. Oceanographic processes and environmental forces are crucial to the composition of sedimentary OM and are discussed for each of those ecosystems.

A ciclagem de matéria orgânica (MO) no ambiente marinho é um processo-chave para o ciclo global de carbono. Os sedimentos costeiros são de suma importância para a ciclagem de carbono pois atuam como receptores de grandes quantidades de MO alóctone (i.e. terrestre) e autóctone (i.e. marinho). A miríade dos componentes orgânicos e suas diferentes características dificultam o entendimento das fontes de MO em ambientes costeiros. Este trabalho visou entender a origem e a composição da MO (através de biomarcadores lipídicos) e a dinâmica da comunidade microbiana (método ATP) em sedimentos superficiais de diferentes ecossistemas marinhos da costa sudeste do Brasil: (i) margem continental de Cabo Frio; (ii) sistema lagunar de Saquarema; (iii) áreas costeiras e a plataforma continental de Ubatuba; (iv) e a plataforma adjacente ao estuário de Santos. Os resultados apontaram uma origem predominantemente autóctone para a MO nestes sistemas, com contribuição terrestre reduzida e limitada à áreas próximas à costa. Processos oceanográficos e forçantes ambientais são cruciais para a composição da MO sedimentar e são discutidas para cada um dos ecossistemas estudados. / The cycling of the organic matter (OM) in the marine environment is a key process in the global carbon cycle. Coastal sediments are important to the global carbon cycle, since they receive large inputs from both marine and terrestrial OM. The myriad of organic compounds and their spectrum of reactivity complicate the understanding of OM sources in coastal environments. In this work, we aimed to access the origin and composition of the OM (through lipid biomarkers) and the microbial dynamics (ATP method) in surface sediments of diverse marine ecosystems from the SE Brazilian coast: (i) the continental margin off Cabo Frio; (ii) the lagoonal system of Saquarema; (iii) coastal and shelf areas from Ubatuba; and (iv) the continental shelf adjacent to Santos estuary. The results showed a dominance of autochthonous OM, with a minor fraction of the OM derived from terrestrial sources and restricted to areas close to the coast. Oceanographic processes and environmental forces are crucial to the composition of sedimentary OM and are discussed for each of those ecosystems.

[pt] A matéria orgânica (MO) sedimentar de origem natural na Ria de Aveiro e no estuário Mondego foi caracterizada usando a composição elementar (C e N) e lipídios biomarcadores (esteróis, n-álcoois e triterpenoides). A contribuição por esgotos foi avaliada através de coprostanol e outros esteróis fecais. Amostras de sedimento superficial foram coletadas em 22 estações ao longo das regiões. Os lipídios biomarcadores foram extraídos, purificação com sílica-gel e analisados por cromatografia em fase gasosa acoplada a espectrometria de massas. O carbono orgânico total (9,94 e 43,00 mg g(-1)) teve uma correlação com o nitrogênio total (r(2) = 0,86). A razão C/N molar (14,34 mais ou menos 1,75) foi um valor típico de MO continental. Existe uma contribuição maior de MO terrestre nas amostras, como mostra as evidencias: a predominância de n-álcoois de cadeia longa (maior ou igual à C22), maior abundancia no somatório de sitosterol, estigmasterol e campesterol sobre outros fitoesterois, como o colesterol e o brassicasterol; e a alta concentração de triterpenoides de plantas superiores, como Beta-amirina e a Alfa amirina. A concentração de coprostanol (0,05 a 16,6 microgramas g(-1)) indicou a presença de esgotos em sete estações localizadas no largo do Laranjo (S4, S5, S6, S7, S10), porto de Aveiro (S14) e no canal de Ílhavo (S16). Os aportes mais significativos foram no largo do Laranjo (S8 e S9) e no porto do Mondego (S19). / [en] The sedimentary organic matter (OM) of natural origin in the Ria de Aveiro and the estuary of Mondego River was characterized using elemental composition (C and N) and lipid biomarkers (sterols, alcohols and triterpenoids). In addition, the contribution by sewage was evaluated by coprostanol and other fecal sterols. Surface sediment samples were collected at 22 stations along the two regions. The lipid biomarkers was extracted, separated with silica-gel and analyzed by gas chromatography coupled to mass spectrometry. Concentrations of total organic carbon (9.94 and 43.00 mg g(-1)) was highly correlated with total nitrogen (r(2) = 0.86). The C/N molar ratio: 14,34 plus-minus 1,75 are typical values of OM of continental origin. There is a major contribution of terrestrially OM to the sediments, as suggested by proxies, including: predominance of long-chain (greater-than or equal to C22) alcohols, higher abundance of sitosterol, estigmasterol and campesterol over other phytosterols, like cholesterol and brassicasterol, and elevated concentrations of triterpenoids from higher plants, as Beta-amyrin and Alpha-amyrin. The concentrations of coprostanol (0.05 to 16.6 micrograms g(-1)) indicated the presence of sewage in seven stations located in the Largo do Laranjo (S4, S5, S6, S7, S10), Port of Aveiro (S14) and in Ílhavo Channel (S16). The more significant contribution of sewage was identified in the Largo do Laranjo (S8 and S9) and the Port of Mondego (S19).

O presente estudo compreende a análise de distribuição dos foraminíferos bentônicos vivos no talude continental da Bacia de Campos e Platô de São Paulo (entre 400 e 3000 m de profundidade), buscando entender os processos condicionantes dessa distribuição. Dados sedimentológicos, geoquímicos e microfaunísticos permitiram identificar três grupos na área de estudo. O grupo I inclui amostras do talude superior, médio e inferior (400-1300 m de profundidade), e é caracterizado por valores maiores de densidade de foraminíferos bentônicos, carbono orgânico total, concentração de fitopigmentos, biomassa de bactérias, menores valores de sortable silt e de conteúdo de carbonato de cálcio, e pela presença de espécies como Globocassidulina subglobosa, Reophax scorpiurus, Reophax subfusiformis, Reophax spiculotestus e Epistominella exigua. O grupo II, constituído de amostras do talude inferior e Platô de São Paulo (1900-3000 m de profundidade), é caracterizado por menores densidades de foraminíferos bentônicos, carbono orgânico total, concentração de fitopigmentos, biomassa de bactérias, maiores valores de sortable silt e de conteúdo de carbonato de cálcio, e pela presença de espécies como Saccorhiza ramosa, Rhizammina algaeformis, Karrerulina sp2. e Hyperammina rugosa. O grupo III (1900-3000 m de profundidade) diferencia-se do grupo II pela presença da Glomospira gordialis, Pyrgoella irregularis e Reophax helenae. Constatou-se que os processos hidrossedimentares (p.e. ação da Corrente do Brasil e Corrente de Contorno Intermediária junto ao fundo), o fluxo vertical de matéria orgânica particulada e concentração de fitopigmentos no sedimento são fatores controladores das condições tróficas no ambiente e estão relacionados às feições de mesoescala (meandros e vórtices de Cabo Frio, Cabo de São Tomé e Vitória), determinando, assim, variações na microfauna de foraminíferos bentônicos vivos na Bacia de Campos. / The present study comprises the analysis of the distribution of living benthic foraminifera on the continental slope of Campos Basin and Plateau of São Paulo (400-3000 m water depth) in order to understand the environmental processes determining this distribution. Sedimentological, geochemical and microfaunal data indicated the existence of three groups in the study area. Group I includes samples from the upper and middle slope (400-1300 m water depth) and is characterized by high values of benthic foraminifera density, total organic carbon, phytopigment concentration, biomass of bacteria, lower values of sortable silt and calcium carbonate content, and the presence of species such as Globocassidulina subglobosa, Reophax scorpiurus, Reophax subfusiformis, Reophax spiculotestus and Epistominella exigua. Group II, consisting of samples of the lower slope and Plateau of São Paulo (1900-3000 m water depth), is characterized by lower densities of benthic foraminifera, total organic carbon, phytopigment concentration, biomass of bacteria, higher values of sortable silt and calcium carbonate content, and the presence of species such as Saccorhiza ramosa, Rhizammina algaeformis, Karrerulina sp2. and Hyperammina rugosa. Group III (1900-3000 m water depth) differs from group II due to the presence of Glomospira gordialis, Pyrgoella irregularis and Reophax helenae. Hydro-sedimentary processes (e.g. action of the Brazil Current and Intermediate Western Boundary Current), the particulate organic matter flux and phytopigment concentration in the sediment are factors controlling the trophic conditions in the environment, and are related to features of mesoscale (meanders and Cabo Frio, Cabo de São Tomé and Vitória eddies), thereby determining changes in living benthic foraminifera in Campos Basin.

O presente estudo compreende a análise de distribuição dos foraminíferos bentônicos vivos no talude continental da Bacia de Campos e Platô de São Paulo (entre 400 e 3000 m de profundidade), buscando entender os processos condicionantes dessa distribuição. Dados sedimentológicos, geoquímicos e microfaunísticos permitiram identificar três grupos na área de estudo. O grupo I inclui amostras do talude superior, médio e inferior (400-1300 m de profundidade), e é caracterizado por valores maiores de densidade de foraminíferos bentônicos, carbono orgânico total, concentração de fitopigmentos, biomassa de bactérias, menores valores de sortable silt e de conteúdo de carbonato de cálcio, e pela presença de espécies como Globocassidulina subglobosa, Reophax scorpiurus, Reophax subfusiformis, Reophax spiculotestus e Epistominella exigua. O grupo II, constituído de amostras do talude inferior e Platô de São Paulo (1900-3000 m de profundidade), é caracterizado por menores densidades de foraminíferos bentônicos, carbono orgânico total, concentração de fitopigmentos, biomassa de bactérias, maiores valores de sortable silt e de conteúdo de carbonato de cálcio, e pela presença de espécies como Saccorhiza ramosa, Rhizammina algaeformis, Karrerulina sp2. e Hyperammina rugosa. O grupo III (1900-3000 m de profundidade) diferencia-se do grupo II pela presença da Glomospira gordialis, Pyrgoella irregularis e Reophax helenae. Constatou-se que os processos hidrossedimentares (p.e. ação da Corrente do Brasil e Corrente de Contorno Intermediária junto ao fundo), o fluxo vertical de matéria orgânica particulada e concentração de fitopigmentos no sedimento são fatores controladores das condições tróficas no ambiente e estão relacionados às feições de mesoescala (meandros e vórtices de Cabo Frio, Cabo de São Tomé e Vitória), determinando, assim, variações na microfauna de foraminíferos bentônicos vivos na Bacia de Campos. / The present study comprises the analysis of the distribution of living benthic foraminifera on the continental slope of Campos Basin and Plateau of São Paulo (400-3000 m water depth) in order to understand the environmental processes determining this distribution. Sedimentological, geochemical and microfaunal data indicated the existence of three groups in the study area. Group I includes samples from the upper and middle slope (400-1300 m water depth) and is characterized by high values of benthic foraminifera density, total organic carbon, phytopigment concentration, biomass of bacteria, lower values of sortable silt and calcium carbonate content, and the presence of species such as Globocassidulina subglobosa, Reophax scorpiurus, Reophax subfusiformis, Reophax spiculotestus and Epistominella exigua. Group II, consisting of samples of the lower slope and Plateau of São Paulo (1900-3000 m water depth), is characterized by lower densities of benthic foraminifera, total organic carbon, phytopigment concentration, biomass of bacteria, higher values of sortable silt and calcium carbonate content, and the presence of species such as Saccorhiza ramosa, Rhizammina algaeformis, Karrerulina sp2. and Hyperammina rugosa. Group III (1900-3000 m water depth) differs from group II due to the presence of Glomospira gordialis, Pyrgoella irregularis and Reophax helenae. Hydro-sedimentary processes (e.g. action of the Brazil Current and Intermediate Western Boundary Current), the particulate organic matter flux and phytopigment concentration in the sediment are factors controlling the trophic conditions in the environment, and are related to features of mesoscale (meanders and Cabo Frio, Cabo de São Tomé and Vitória eddies), thereby determining changes in living benthic foraminifera in Campos Basin.

<div> Advancements in cancer treatments have increased rapidly in recent years, but cures remain elusive. Surgical tumor resection is a central treatment for many solid malignancies. Residual tumor at surgical margins leads to tumor recurrence. Novel tools for assessing residual tumor at surgical margins could improve surgical outcomes by helping to maximize the extent of resection. Ambient ionization-mass spectrometry (MS) methods generate and analyze ions from minimally prepared samples in near-real-time (e.g. seconds to minutes). These methods leverage the high sensitivity and specificity of mass spectrometry for analyzing gas phase ions and generating those ions quickly and with minimal sample preparation. Recent work has shown that differential profiles of ions, corresponding to phospholipids and small metabolites, are detected from cancerous and their respective normal tissue with ambient ionization-MS methods. When properly implemented, ambient ionization-MS could be used to assess for tumor at surgical margins and provide a molecular diagnosis during surgery. </div><div><br></div><div>The research herein reports efforts in developing rapid intraoperative ambient ionization-MS methods for the molecular assessment of cancerous tissues. Touch spray (TS) ionization and desorption electrospray ionization (DESI) were utilized to analyze kidney cancer and brain cancer.</div><div><br></div><div> As a demonstration of the applicability of TS-MS to provide diagnostic information from fresh surgical tissues, TS-MS was used to rapidly analyze renal cell carcinoma and healthy renal tissue biopsies obtained from human subjects undergoing nephrectomy surgery. Differential phospholipid profiles were identified using principal component analysis (PCA), and the significant ions were characterized using multiple stages of mass spectrometry and high resolution/exact mass MS. The same TS-MS analyzed renal tissues were subsequently analyzed with DESI-MS imaging to corroborate the TS-MS results, and the significant DESI-MS ions were also characterized with MS.</div><div><br></div><div>Significant efforts were made in developing and evaluating a standalone intraoperative DESI-MS system for analyzing brain tissue biopsies during brain tumor surgery. The intraoperative DESI-MS system consists of a linear trap quadrupole mass spectrometer placed on a custom-machined cart that contains all hardware for operating the mass spectrometer. This instrument was operated in the neurosurgical suites at Indiana University School of Medicine to rapidly analyze brain tissue biopsies obtained from glioma resection surgeries. A DESI-MS library of normal brain tissue and glioma was used to statistically classify the brain tissue biopsies collected in the operating room. Multivariate statistical methodologies were employed to predict the disease state and tumor cell percentage of the samples. A DESI-MS assay for detecting 2-hydroxyglutarate (2HG), the oncometabolic product of the isocitrate dehydrogenase (IDH) mutation (a key glioma prognostic marker), was developed and applied to determine the IDH mutation status during the surgical resection. The strengths, weaknesses, and areas of future work in this field are discussed. </div><div><br></div>

<p>My research has focused on the development and translation of ambient ionization mass spectrometry (MS)-based platforms in clinical and surgical settings, specifically in the area of brain cancer diagnostics and surgical decision making. Ambient ionization MS methods, such as those described herein, generate and analyze gas phase ions with high sensitivity and specificity from minimally prepared samples in near-real-time, on the order of seconds to minutes, rendering them well suited to point-of-care applications. We used ambient ionization MS methods, specifically desorption electrospray ionization mass spectrometry (DESI-MS) and extraction nanoelectrospray ionization mass spectrometry (nESI-MS) to molecularly characterize brain cancer biopsies. The characterization was made using diagnostic compounds identified as markers of disease state, tissue composition, tumor type, and genotype in human brain tissue. Methods were developed and validated offline in the laboratory and translated to clinical and surgical settings, thereby generating chemical information on prognostic features intraoperatively and providing valuable information that would be otherwise unavailable. We believe that, with approval, the methodologies described can assist physicians and improve patient outcomes by providing analytical tools and molecular information that can inform surgical decision making and adjuvant treatment strategies, complementing and not interfering with standard of care protocols.</p> <p><br></p> <p>We have successfully demonstrated the use of desorption electrospray ionization mass spectrometry (DESI-MS) for the expedient molecular assessment of human glioma tissue biopsies based on lipid profiles and prognostic metabolites, both at the tumor core and near surgical margins, in two small-scale, clinical studies. Maximal surgical resection of gliomas that avoids non-infiltrated tissue is associated with survival benefit in patients with glioma. The infiltrative nature of gliomas, as well as their morphological and genetic diversity, renders treatment difficult and demands an integrated imaging and diagnostic approach during surgery to guide clinicians in achieving maximal tumor resection. Further, the estimation of tumor cell percentage (TCP), a measure of tumor infiltration at surgical margins, is not routinely assessed intraoperatively. </p> <p>We have previously shown that rapid, offline molecular assessment of tumor infiltration in tissue biopsies is possible and believe that the same assessment performed intraoperatively in biopsied tissue near surgical margins could improve resection and better inform patient management strategies, including postoperative radiotherapy. Using a DESI-MS spectral library of normal brain tissue and glioma biopsies to generate a statistical model to classify brain tissue biopsies intraoperatively, multivariate statistical approaches were used to predict the disease state and tumor cell percentage (TCP) of each biopsy, thereby providing an measure of tumor infiltration at surgical margins via molecular indicators. In addition to assessment of tumor infiltration, we have developed DESI-MS assays for detecting the oncometabolite 2-Hydroxyglutarate (2HG) to detect isocitrate dehydrogenase (IDH) mutations in gliomas intraoperatively. Knowledge of IDH genotypes at the time of surgical resection could improve patient outcomes, as more aggressive tumor resection of IDH-mutated gliomas is associated with increased survival. While assessments of IDH genotype are typically not available until days after surgery, we have demonstrated the ability to provide this information is less than five minutes. An intraoperative DESI-MS system has successfully been used in a proof-of-concept clinical study and intraoperative performance validation of this platform is ongoing. The findings of these two studies as well as strengths, weaknesses, and areas of improvement for upcoming future iterations of the research are discussed.</p> <p><br></p> <p>Point-of-care applications necessitate the adaptation of MS methodologies to smaller devices. Miniature mass spectrometers (Mini MS) boast small footprints, simple operation, and low power consumption, noise levels, and cost, making them attractive candidates for point-of-care use. In a small-scale clinical study, we demonstrated the first application of a Mini MS for determination of IDH mutation status in gliomas intraoperatively. This study paves a path forward for the application of Mini MS in the OR. With its small footprint and low power consumption and noise level, this application of miniature mass spectrometers represents a simple and cost-effective platform for an important intraoperative measurement. </p> <p><br></p> <p>While MS-based methods of tissue analysis can detect molecular features of interest and rapidly produce large quantities of data, their inherent speed is rarely utilized because they are traditionally coupled with time-consuming separation techniques (e.g., chromatography). Ambient ionization MS, specifically DESI-MS, is well suited for high-throughput applications due to its lack of sample preparation and purification techniques. In an attempt to rapidly characterize microarrays of tissue biopsies, we developed a high-throughput DESI-MS (HT-DESI-MS) method for the rapid characterization of disease state, human brain tumor type, glioma classification, and detection of IDH mutations in tissue microarrays (TMA) of banked and fresh human brain tissue biopsies. We anticipate that HT-DESI-MS analysis of TMAs could become a standard tool for the generation of spectral libraries for sample classification, the identification of biomarkers through large-scale studies, the correlation of molecular features with anatomical features when coupled to digital pathology, and the assessment of drug efficacy. </p>