Evaluation of exposure biomarkers in offshore workers exposed to low benzene and toluene concentrations.

Characterize ethylbenzene and xylene air concentrations, and explore the biological exposure markers (urinary t,t-muconic acid (t,t-MA) and unmetabolized toluene) among petroleum workers offshore. Offshore workers have increased health risks due to simultaneous exposures to several hydrocarbons present in crude oil. We discuss the pooled benzene exposure results from our previous and current studies and possible co-exposure interactions. BTEX air concentrations were measured during three consecutive 12-h work shifts among 10 tank workers, 15 process operators, and 18 controls. Biological samples were collected pre-shift on the first day of study and post-shift on the third day of the study. The geometric mean exposure over the three work shifts were 0.02 ppm benzene, 0.05 ppm toluene, 0.03 ppm ethylbenzene, and 0.06 ppm xylene. Benzene in air was significantly correlated with unmetabolized benzene in blood (r = 0.69, p < 0.001) and urine (r = 0.64, p < 0.001), but not with urinary t,t-MA (r = 0.27, p = 0.20). Toluene in air was highly correlated with the internal dose of toluene in both blood (r = 0.70, p < 0.001) and urine (r = 0.73, p < 0.001). Co-exposures were present; however, an interaction of metabolism was not likely at these low benzene and toluene exposures. Urinary benzene, but not t,t-MA, was a reliable biomarker for benzene at low exposure levels. Urinary toluene was a useful biomarker for toluene exposure. Xylene and ethylbenzene air levels were low. Dermal exposure assessment needs to be performed in future studies among these workers.

An exploratory study for the discovery of non-invasive hepatocellular carcinoma biomarkers among high-risk hepatitis C virus infected patients

Hepatocellular Carcinoma (HCC) is a major healthcare problem, representing the third most common cause of cancer-related mortality worldwide. Chronic infections with Hepatitis B virus (HBV) and/or Hepatitis C virus (HCV) are the major risk factors for the development of HCC. The incidence of HBV -associated HCC is in decline as a result of an effective HBV vaccine; however, since an equally effective HCV vaccine has not yet been developed, there are 130 million HCV infected patients worldwide who are at a high-risk for developing HCC. Because reliable parameters and/or tools for the early detection of HCC among high-risk individuals are severely lacking, HCC patients are always diagnosed at a late stage where surgical solutions or effective treatment are not possible. Using urine as a non-invasive sample source, two different approaches (proteomic-based and genomic-based approaches) were pursued with the common goal of discovering potential biomarker candidates for the early detection of HCC among high-risk chronic HCV infected patients. Urine was collected from 106 HCV infected Egyptian patients, 32 of whom had already developed HCC and 74 patients who were diagnosed as HCC-free at the time of initial sample collection. In addition to these patients, urine samples were also collected from 12 healthy control individuals. Total urinary proteins, Trans-renal nucleic acid (Tr-NA) and microRNA (miRNA) were isolated from urine using novel methodologies and silicon carbide-loaded spin columns. In the first, "proteomic-based", approach, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to identify potential candidates from pooled urine samples. This was followed by validating relative expression levels of proteins present in urine among all the patients using quantitative real time-PCR (qRT-PCR). This approach revealed that significant over-expression of three proteins: DJ-1, Chromatin Assembly Factor-1 (CAF-1) and 11 Moemen Abdalla HCC Biomarkers Heat Shock Protein 60 (HSP60), were characteristic events among HCC-post HCV infected patients. As a single-based HCC biomarker, CAF-1 over-expression identified HCC among HCV infected patients with a specificity of 90%, sensitivity of 66% and with an overall diagnostic accuracy of 78%. Moreover, the CAF-lIHSP60 tandem identified HCC among HCV infected patients with a specificity of 92%, sensitivity of 61 % and with an overall diagnostic accuracy of 77%. In the second genomic-based approach, two different approaches were processed. The first approach was the miRNA-based approach. The expression levels of miRNAs isolated from urine were studied using the Illumina MicroRNA Expression Profiling Assay. This was followed by qRT-PCR-based validation of deregulated expression of identified miRNA candidates among all the patients. This approach shed the light on the deregulated expression of a number of miRNAs, which may have a role in either the development of HCC among HCV infected patients (i.e. miR-640, miR-765, miR-200a, miR-521 and miR-520) or may allow for a better understanding of the viral-host interaction (miR-152, miR-486, miR-219, miR452, miR-425, miR-154 and miR-31). Moreover, the deregulated expression of both miR-618 and miR-650 appeared to be a common event among HCC-post HCV infected patients. The results of the search for putative targets of these two miRNA suggested that miR-618 may be a potent oncogene, as it targets the tumor-suppressor gene Low density lipoprotein-related protein 12 (LPR12), while miR-650 may be a potent tumor-suppressor gene, as it is supposed to downregulate the TNF receptor-associated factor-4 (TRAF4) oncogene. The specificity of miR-618 and miR-650 deregulated expression patterns for the early detection of HCC among HCV infected patients was 68% and 58%, respectively, whereas the sensitivity was 64% and 72%, respectively. When the deregulated expression of both miRNAs was combined as a tandem biomarker, the specificity and the sensitivity were 75% and 58% respectively. 111 Moemen Abdalla HCC Biomarkers In the second, "Trans-renal nucleic acid-based", approach, the urinary apoptotic nucleic acid (uaNA) levels of 70ng/mL or more were found to be a good predictor of HCC among chronic HCV infected patients. The specificity and the sensitivity of this diagnostic approach were 76% and 86%, respectively, with an overall diagnostic value of 81 %. The uaNA levels positively correlated to HCC disease progression as monitored by epigenetic changes of a panel of eight tumor-suppressor genes (TSGs) using methylation-sensitive PCR. Moreover, the pairing of high uaNA levels (:::: 70 ng/mL) and CAF-1 over-expreSSIOn produced a highly specific (l 00%) multiple-based HCC biomarker with an acceptable sensitivity of 64%, and with a diagnostic accuracy of 82%. In comparison to the previous pairing, the uaNA levels (:::: 70 ng/mL) in tandem with HSP60 over-expression was less specific (89%) but highly sensitive (72%), resulting in a diagnostic accuracy of 64%. The specificities of miR-650 deregulated expression in combination with either high uaNA content or HSP 60 over-expression were 82% and 79%, respectively, whereas, the sensitivities of these combinations were 64% and 58%, respectively. The potential biomarkers identified in this study compare favorably with the diagnostic accuracy of the a-fetoprotein levels test, which has a specificity of 75%, sensitivity of 68% and an overall diagnostic accuracy of 70%. Here we present an intriguing study which shows the significance of using urine as a noninvasive sample source for the identification of promising HCC biomarkers. We have also introduced new techniques for the isolation of different urinary macromolecules, especially miRNA, from urine. Furthermore, we strongly recommend the potential biomarkers indentified in this study as focal points of any future research on HCC diagnosis. A larger testing pool will determine if their use is practical for mass population screening. This explorative study identified potential targets that merit further investigation for the development of diagnostically accurate biomarkers isolated from 1-2 mL urine samples that were acquired in a non-invasive manner.

Prostate Cancer and the Search for Novel Biomarkers

The primary objective of this research project was to identify prostate cancer (PCa) -specific biomarkers from urine. This was done using a multi-faceted approach that targeted (1) the genome (DNA); (2) the transcriptome (mRNA and miRNA); and (3) the proteome. Toward this end, urine samples were collected from ten healthy individuals, eight men with PCa and twelve men with enlarged, non-cancerous prostates or with Benign Prostatic Hyperplasia (BPH). Urine samples were also collected from the same patients (PCa and BPH) as part of a two-year follow-up. Initially urinary nucleic acids and proteins were assessed both qualitatively and quantitatively for characteristics either unique or common among the groups. Subsequently macromolecules were pooled within each group and assessed for either protein composition via LC-MS/MS or microRNA (miRNA) expression by microarray. A number of potential candidates including miRNAs were identified as being deregulated in either pooled PCa or BPH with respect to the healthy control group. Candidate biomarkers were then assessed among individual samples to validate their utility in diagnosing PCa and/or differentiating PCa from BPH. A number of potential targets including deregulation of miRNAs 1825 and 484, and mRNAs for Fibronectin and Tumor Protein 53 Inducible Nuclear Protein 2 (TP53INP2) appeared to be indicative of PCa. Furthermore, deregulation of miR-498 appeared to be indicative of BPH. The sensitivities and specificities associated with using deregulation in many of these targets to subsequently predict PCa or BPH were also determined. This research project has identified a number of potential targets, detectable in urine, which merit further investigation towards the accurate identification of PCa and its discrimination from BPH. The significance of this work is amplified by the non-invasive nature of the sample source from which these candidates were derived, urine. Many cancer biomarker discovery studies have tended to focus primarily on blood (plasma or serum) and/or tissue samples. This is one of the first PCa biomarker studies to focus exclusively on urine as a sample source.

STUDYING ABERRANT METHYLATION AND miRNA PROFILING FOR THE DETECTION OF LUNG CANCER BIOMARKERS

Lung cancer is a major chronic disease responsible for the highest mortality rate, among other types of cancer, and represents 29% of all deaths in Canada. The clinical diagnosis of lung carcinoma still requires a standard diagnostic approach, as there are no symptoms in its early stage. Therefore, it is usually diagnosed at a later stage, when the survival rate is low. With the recent advancement in molecular biology and biotechnology, a molecular biomarker approach for the diagnosis of early lung cancer seems to be a potential option. In this study, we aimed to investigate and standardize a promising Lung ,Cancer Biomarker by studying the aberrant methylation of two tumour suppressor genes, namely RASSFIA and RAR-B, and the miRNA profiling of four . commonly deregulated miRNA (miR-199a-3p, miR-182, miR-lOO and miR-221). Four lung cancer cell lines were used (two SCLC and two NSCLC), with comparisons being made with normal lung cell lines. Our results, we found that none of these genes were methylated. We then evaluated TP53, and found the promoter of this gene to be methylated in the cancer cell lines, as compared to the normal cell lines, indicating gene inactivation. We carried out miRNA profiling of the cancer cell lines and reported that 80 miRNAs are deregulated in lung cancer cell lines as compared to the normal cell lines. Our study was the first of its kind to indicate that hsa-mir-4301, hsa-mir-4707-5p and hsa-mir-4497 (newly discovered miRNAs) are deregulated in lung cancer cell lines. We also investigated miR-199a-3p, mir-lOO and miR-182, and found that miR-199a -3p and mir-l00 were down-regulated in cancer lines, whereas miR-182 was up-regulated in the cancer cell lines. In the final part of the study we observed that mir-221 could be a putative biomarker to distinguish between the two types of lung cancer because it was down-regulated in SCLC, and up-regulated in the NSCLC cell lines. In conclusion, we found four miRNA molecular biomarkers that possibly could be used in the early diagnosis of the lung cancer. More studies are still required with larger numbers of samples to effectively establish these as molecular biomarkers for the diagnosis of lung cancer

Prediction of hypertensive disorders in pregnancy by combined uterine artery Doppler, serum biomarkers and maternal characteristics

Objectif: Évaluer l'efficacité du dépistage de l’hypertension gestationnelle par les caractéristiques démographiques maternelles, les biomarqueurs sériques et le Doppler de l'artère utérine au premier et au deuxième trimestre de grossesse. Élaborer des modèles prédictifs de l’hypertension gestationnelle fondées sur ces paramètres. Methods: Il s'agit d'une étude prospective de cohorte incluant 598 femmes nullipares. Le Doppler utérin a été étudié par échographie transabdominale entre 11 +0 à 13 +6 semaines (1er trimestre) et entre 17 +0 à 21 +6 semaines (2e trimestre). Tous les échantillons de sérum pour la mesure de plusieurs biomarqueurs placentaires ont été recueillis au 1er trimestre. Les caractéristiques démographiques maternelles ont été enregistrées en même temps. Des courbes ROC et les valeurs prédictives ont été utilisés pour analyser la puissance prédictive des paramètres ci-dessus. Différentes combinaisons et leurs modèles de régression logistique ont été également analysés. Résultats: Parmi 598 femmes, on a observé 20 pré-éclampsies (3,3%), 7 pré-éclampsies précoces (1,2%), 52 cas d’hypertension gestationnelle (8,7%) , 10 cas d’hypertension gestationnelle avant 37 semaines (1,7%). L’index de pulsatilité des artères utérines au 2e trimestre est le meilleur prédicteur. En analyse de régression logistique multivariée, la meilleure valeur prédictive au 1er et au 2e trimestre a été obtenue pour la prévision de la pré-éclampsie précoce. Le dépistage combiné a montré des résultats nettement meilleurs comparés avec les paramètres maternels ou Doppler seuls. Conclusion: Comme seul marqueur, le Doppler utérin du deuxième trimestre a la meilleure prédictive pour l'hypertension, la naissance prématurée et la restriction de croissance. La combinaison des caractéristiques démographiques maternelles, des biomarqueurs sériques maternels et du Doppler utérin améliore l'efficacité du dépistage, en particulier pour la pré-éclampsie nécessitant un accouchement prématuré.

Prevention of Cardiometabolic Disease in Familial Hypercholesterolemia

L’hypercholestérolémie familiale (FH) est un désordre lipidique associé aux maladies cardiovasculaires les plus fréquentes. La FH est causée par des mutations dans les gènes LDLR, APOB et PCSK9. Toutefois, chez 20% des patients souffrant de FH, aucune mutation dans ces gènes n'a été détectée et ceci suggère que d’autres gènes seraient à l’origine de la FH. Actuellement, le seul traitement de la FH est une thérapie aux statines. En général les statines sont bien tolérées, cependant, une monothérapie ne permet pas d’atteindre des niveaux thérapeutiques acceptables et dans bien des cas, une thérapie combinée devient nécessaire. De plus, l’intolérance aux statines est présente dans environ 12% des patients. Dans les trois dernières décennies, la survie des patients avec la FH a augmentée de façon notoire mais on observe aussi l’apparition d’une calcification vasculaire sévère chez certains d’entre eux. Il est donc primordial de développer des nouvelles approches thérapeutiques afin de prévenir ces complications tardives. Dans cette thèse doctorat, nous présentons l’étude d’une famille avec un phénotype de FH sévère non causé par des mutations dans les gènes LDLR, APOB et PCSK9. Par des études biochimiques et par séquençage d’ADN utilisant les technologies de nouvelle génération (NextGenSeq), nous avons découvert une mutation dans le gène de l’APOE (Leu167del). Ceci nous permet de proposer le gène codant pour l’APOE comme le 4e locus responsable de la FH (FH4). Par la suite, nous avons effectué deux études de cohortes chez les patients atteints de FH. Premièrement, dans l’étude JUPITER, nous avons démontré que la rosuvastatin augmente les niveaux sanguins de la protéine PCSK9 et ceci limiterait l’efficacité du traitement aux statines. Nous avons aussi étudié l’influence du mutant naturel R46L (perte de fonction de la PCSK9) dans la réponse aux statines. Deuxièmement, nous avons examiné les effets de la perte de fonction de la PCSK9 sur le profil cardiométabolique au sein d’une population pédiatrique. Nous avons déterminé que le génotype de l’APOE est déterminant dans ce profil cardiométabolique. Enfin, nous avons étudié la calcification vasculaire chez les patients atteints de FH. Cette calcification vasculaire progresse de façon indépendante des niveaux de cholestérol sérique et n’est pas associée aux anomalies de l’homéostasie du calcium. En utilisant des modèles murins, nous avons démontré que les souris Ldlr-/- et Tg(Pcsk9) développent des calcifications vasculaires semblables à celles observées chez l’homme. De plus, nous avons confirmé l’implication de la voie de signalisation LRP5/Wnt dans la pathophysiologie de la calcification artérielle. Avec une étude interventionnelle, nous avons trouvé que l’inhibition de l’interleukine 1β (IL-1β) diminue fortement l’apparition de calcifications vasculaire dans notre modèle murin. En conclusion, nos études ont permis l’identification d’un nouveau gène impliqué dans la FH, ont démontré aussi que les statines augmentent les niveaux sériques de PCSK9 et que la perte de fonction de la PCSK9 altère le profil cardiométabolique. Enfin, nous avons établi que la calcification vasculaire représente une complication tardive chez les patients atteints de FH et que, dans notre modèle murin, la calcification vasculaire peut être retardée par l’inhibition d’IL-1β. Ces découvertes peuvent avoir d’importantes répercussions cliniques chez l’humain.

Detecting uterine cervical cancer cells using molecular biomarkers

Arrière-plan: les cellules tumorales circulantes (CTC) sont détectables dans de nombreux cancers et peuvent être utiles cliniquement pour le pronostic de la maladie, pour mesurer la récidive et pour prédire la sensibilité aux medicaments chimiothérapeutiques. Au cours des dernières années, l’études des CTC dans de nombreux cancers tels que le cancer du sein, du poumon, du côlon et de la prostate a grandement évolué. Alternativement, il y peu d'études à ce sujet concernant le cancer du col de l’utérus (CCU). Objectifs: Notre objectif est d’optimiser le processus d'enrichissement des CTC dans le CCU et la détection moléculaire des biomarqueurs E6 et E7. Matériel et Méthodes: Dans l’optique de mimer la présence de CTC dans le sang, nous avons dilué des cellules cancéreuses CaSki VPH16-positif provenant d’un CCU dans du sang humain prélevé sur des volontaires sains. Les CaSki ont été collectées suite à une centrifugation par densité avec le Ficoll, la lyse des globules rouges (RBC) et la lyse des RBC combinée avec un enrichissement positif et négatif à l’aide de marqueurs de surface cellulaire. Les CTC ont été détectées par la mesure d’expression des oncogènes E6 et E7 du virus du papillome humain (VPH), de la cytokératine 19 (CK19) et de la cycline p16INK4 en utilisant la technique quantitative en temps réel de Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR). Pour valider notre méthode de détection des CTC in vivo, nous avons recruté dix patientes atteintes d’un CCU VPH16 positif et six contrôles sains. Résultats: Dans le modèle de dilutions de cellules CaSki, la lyse des RBC seule ou combinée avec l'enrichissement négatif ou positif suggèrent des limites de détection de 1 CTC par mL de sang pour tous les biomarqueurs moléculaires utilisés. La sensibilité de détection est accrue lors de l'utilisation de l’enrichissement positif et négatif en réduisant le bruit de fond causé par les monocytes sanguins. Contrairement aux oncogènes E6 et E7, les marqueurs CK19 et p16INK4A ont été détectés chez des individus sains, les niveaux d'expression de base appropriés doivent donc être déterminés avec précision par rapport aux patientes CCU. Le gradient de densité par Ficoll a une limite de détection de seulement environ 1000 cellules par mL de sang. Enfin, les CTC ont été détectées dans 2/10 patientes en utilisant le marqueur CK19. Cependant, ces patientes étaient négatives pour les oncogènes E6/E7. Le marqueur p16INK4A était exprimé au même niveau dans tous les échantillons (CCU et normaux). Conclusion: Notre étude suggère que les oncogènes E6 et E7 du VPH16 sont les marqueurs biologiques les plus sensibles et spécifiques en qRT-PCR pour détecter les CTC dans le modèle de dilution de cellules de CCU dans le sang. Chez les patientes atteintes d’un CCU de stade précoce, seulement CK19 a révélé la présence potentielle de CTC, ce qui suggère que ces cellules sont rares à ce stade de la maladie. Mots clés: cancer du col de l’utérus, cellules tumorales circulantes, RT-qPCR, E6 et E7, CK19, p16INK4A, enrichissement immunomagnétique, détection moléculaire.

Identification and characterization of new biomarkers in aggressive subtypes of breast cancer

En 2015, la récidive tumorale et les métastases du cancer du sein demeurent une cause importante de décès à travers le monde. Toutefois, ces cancers sont souvent hétérogènes car en dépit d’un phénotype similaire, l’évolution clinique et la réponse au traitement peuvent varier considérablement. Il y a donc un intérêt évident à identifier et à caractériser de nouveaux biomarqueurs pour permettre classer les tumeurs mammaires dans des sous-groupes plus homogènes. Notre hypothèse est que chaque cancer mammaire possède des caractéristiques distinctes au plan des altérations du génome et des profils d’expression géniques et que ces changements se traduisent cliniquement par une prédisposition à former des métastases ou à répondre ou non à la chimiothérapie et aux thérapies ciblées. Dans le cadre de nos travaux, nous nous sommes intéressés aux sous-types agressifs de tumeurs mammaires et notamment les cancers de type triple négatif. Nous avons aussi tenté d’identifier des marqueurs capables de distinguer l’une de l’autre les tumeurs de type luminal A et luminal B. Pour ce faire, nous avons d’abord utilisé une stratégie in silico à partir de données publiques (micro-puces d’ADN et séquençage de l’ARN). Nous avons ensuite construit sept micro-matrices tissulaires (TMA) provenant de tissus mammaires normaux et tumoraux fixés à la formaline et enrobés en paraffine. Ces outils nous ont permis d’évaluer par immunohistochimie les niveaux d’expression différentielle des marqueurs suivants : ANXA1, MMP-9, DP103 et MCM2. Ceux-ci ont été comparés aux marqueurs usuels du cancer du sein (ER, PR, HER2, CK5/6 et FOXA1) et corrélés aux données cliniques (survie globale et métastase). Nos résultats indiquent que ces nouveaux marqueurs jouent un rôle important dans l’évolution clinique défavorable des tumeurs de haut grade. Dans un premier article nous avons montré que l’expression d’ANXA1 est dérégulée dans les cancers de type triple-négatif et aussi, dans une certaine mesure, dans les tumeurs HER2+. Nous croyons qu’ANXA1 permet de mieux comprendre le processus d’hétérogénéité tumorale et facilite l’identification des tumeurs de haut grade. Nous proposons également qu’ d’ANXA1 stimule la transition épithélio-mésenchymateuse (EMT) et la formation des métastases. Dans un second temps, nous avons montré que les niveaux d’expression de MMP-9 reflètent la différenciation cellulaire et corrèlent avec les sous-types de cancers mammaires ayant un mauvais pronostic. Nous estimons que MMP-9 permet de mieux comprendre et d’identifier les tumeurs mammaires à haut risque. De fait, la surexpression de MMP-9 est associée à une augmentation des métastases, une récidive précoce et une diminution de la survie globale. Dans le cadre d’un troisième article, nous avons montré que la surexpression du marqueur de prolifération MCM2 s’observe dans les cancers triple-négatifs, HER2+ et Luminal B par comparaison aux cancers luminal A (p< 0.0001). Nos résultats suggèrent qu’en utilisant un seuil de 40% de noyaux marqués, nous pourrions distinguer l’une de l’autre les tumeurs de type luminal A et luminal B. Cela dit, avant de pouvoir envisager l’utilisation de ce marqueur en clinique, une étude de validation sur une nouvelle cohorte de patientes s’impose. En somme, les résultats de nos travaux suggèrent qu’ANXA1, MMP-9 et MCM2 sont des marqueurs intéressants pour mieux comprendre les mécanismes physiopathologiques impliqués dans la progression tumorale et le développement des métastases. À terme, ces nouveaux marqueurs pourraient être utilisés seuls ou en combinaison avec d’autres gènes candidats pour permettre le développement de trousses « multigènes » ou d’essais protéomiques multiplex pour prédire l’évolution clinique des cancers mammaires.

Assessment of meat authenticity using bioinformatics, targeted peptide biomarkers and high-resolution mass spectrometry

In recent years, we observed a significant increase of food fraud ranging from false label claims to the use of additives and fillers to increase profitability. Recently in 2013, horse and pig DNA were detected in beef products sold from several retailers. Mass spectrometry has become the workhorse in protein research and the detection of marker proteins could serve for both animal species and tissue authentication. Meat species authenticity will be performed using a well defined proteogenomic annotation, carefully chosen surrogate tryptic peptides and analysis using a hybrid quadrupole-Orbitrap mass spectrometer. Selected mammalian meat samples were homogenized, proteins were extracted and digested with trypsin. The samples were analyzed using a high-resolution mass spectrometer. The chromatography was achieved using a 30 minutes linear gradient along with a BioBasic C8 100 × 1 mm column at a flow rate of 75 µL/min. The mass spectrometer was operated in full-scan high resolution and accurate mass. MS/MS spectra were collected for selected proteotypic peptides. Muscular proteins were methodically analyzed in silico in order to generate tryptic peptide mass lists and theoretical MS/MS spectra. Following a comprehensive bottom-up proteomic analysis, we were able to detect and identify a proteotypic myoglobin tryptic peptide [120-134] for each species with observed m/z below 1.3 ppm compared to theoretical values. Moreover, proteotypic peptides from myosin-1, myosin-2 and -hemoglobin were also identified. This targeted method allowed a comprehensive meat speciation down to 1% (w/w) of undesired product.

Fatty acids as Biomarkers in the Mangrove sediments of Cochin

The biogeochemistry of mangroves are the least understood ecological properties because of their sediment complexicity due to the tidal influx of allochthonous organic matter and the autochthonous inputs.In order to understand the relative importance of biogeochemical processes,it is necessary not only to characterise and qualify the organic matter but also to identify its major sources .The present study is a preliminary investigation to identify the sources of organic matter in three mangrove systems of Cochin Estuary using fatty acid biomarkers,δ13 C of total organic matter,elemental composition and biochemical composition.

Triterpenoids as Biomarkers of Mangrove Organic Matter in Cochin Estuarine System

This thesis entitled triterpenoids as biomarkers of mangrove organic matter in cochin estuarine system.Mangrove forests, known as rainforests of the sea are one of the most important coastal ecosystems in the world in terms of primary production and coastal protection.Estuaries, the important areas of world’s coastal zones link the carbon cycle of the oceans to the continents.Three mangrove ecosystems and three estuarine stations around Cochin region, southwest coast of India were selected for the present study. The thesis is divided into five chapters. Chapter 1 is the Introduction and it deals with the aim and scope of the present study. Chapter 2 is Materials and Methods. This chapter deals with the nature and general geographical features of the study area. It also contains the details of the sampling and analytical methodology.the present study. Chapter 3 is Geochemistry and it includes the seasonal and spatial variations of the geochemical parameters in the surface sediments.Chapter 4 is Biochemical Composition. It covers the biochemical composition of organic matter in the surface sediments to examine the quality and quantity of organic matter.Chapter 5, Triterpenoid Biomarkers in Sediments, characterize the organic matter in the sediments of the mangrove and estuarine ecosystems under study, to assess the possible sources with the help of triterpenoid biomarkers along with other lipid biomarkers.

Bioactive Metabolites and Biomarkers from Rhizophoraceae mangroves- A Chemotaxonomic Approach

Mangroves are specialised ecosystems developed along estuarine sea coasts and river mouths in tropical and subtropical regions of the world, mainly in the intertidal zone. Hence, the ecosystem and its biological components is under the influence of both marine and freshwater conditions and has developed a set of physiological adaptations to overcome problems of anoxia, salinity and frequent tidal inundations. This has led to the assemblage of a wide variety of plant and animal species of special adaptations suited to the ecosystem. The path of photosynthesis in mangroves is different from other glycophytes. There are modifications or alterations in other physiological processes such as carbohydrate metabolism or polyphenol synthesis. As they survive under extreme conditions of salinity, temperature, tides and anoxic soil conditions they may have chemical compounds, which protect them from these destructive elements. Mangroves are necessarily tolerant of high salt levels and have mechanisms to take up water despite strong osmotic potentials. Some also take up salts, but excrete them through specialised glands in the leaves. Others transfer salts into senescent leaves or store them in the bark or the wood. Still others simply become increasingly conservative in their water use as water salinity increases. A usual transportation or biosynthetic path as other plants cannot be expected in mangrove plants. In India, the states like West Bengal, Orissa, Andhra Pradesh, Tamil Nadu, Andaman and Nicobar Islands, Kerala, Goa, Maharashtra, and Gujarat occupy vast area of mangroves. Kerala has only 6 km2 total mangrove area with Rhizophora apiculata, Rhizophora mucronata, Bruguiera gymnorrhiza, Bruguiera cylindrica, Avicennia officinalis, Sonneratia caseolaris, Sonneratia apetala and Kandelia candal, as the important species present, most of which belong to the family Rhizophoraceae.Rhizophoraceae mangroves are ranked as “major elements of mangroves” as they give the real shape of this unique and interesting ecosystem and these mangrove species most productive and typical characteristic ecosystem of World renowned. It was found that the Rhizophoraceae mangrove extracts exhibit several bioactive properties. Various parts of these mangroves are used in ethnomedicinal practices. Even though extracts from these mangroves possess therapeutic activity against humans, animal and plant pathogens, the specific metabolites responsible for these bioactivities remains to be elucidated. Various parts of these mangroves are used in ethnomedicinal practices. There is a gap of information towards the chemistry of Rhizophoraceae mangroves from Kerala. Thorough phytochemical investigation can achieve the validity of ethnomedicines as well as apply the use of mangrove plants in the development of new drugs. Such studies can pave a firm base for their use in biomarker and chemotaxonomic studies as well as for the better management of the existing mangrove ecosystem. In this study, the various chemical parameters including minerals, biochemical components, bioactive and biomarker molecules were used to classify and assess the possible potentials of the mangrove plants of the true mangrove family Rhizophoraceae from Kochi.

Peptides generated ex vivo from serum proteins by tumor-specific exopeptidases are not useful biomarkers in ovarian cancer

BACKGROUND: The serum peptidome may be a valuable source of diagnostic cancer biomarkers. Previous mass spectrometry (MS) studies have suggested that groups of related peptides discriminatory for different cancer types are generated ex vivo from abundant serum proteins by tumor-specific exopeptidases. We tested 2 complementary serum profiling strategies to see if similar peptides could be found that discriminate ovarian cancer from benign cases and healthy controls. METHODS: We subjected identically collected and processed serum samples from healthy volunteers and patients to automated polypeptide extraction on octadecylsilane-coated magnetic beads and separately on ZipTips before MALDI-TOF MS profiling at 2 centers. The 2 platforms were compared and case control profiling data analyzed to find altered MS peak intensities. We tested models built from training datasets for both methods for their ability to classify a blinded test set. RESULTS: Both profiling platforms had CVs of approximately 15% and could be applied for high-throughput analysis of clinical samples. The 2 methods generated overlapping peptide profiles, with some differences in peak intensity in different mass regions. In cross-validation, models from training data gave diagnostic accuracies up to 87% for discriminating malignant ovarian cancer from healthy controls and up to 81% for discriminating malignant from benign samples. Diagnostic accuracies up to 71% (malignant vs healthy) and up to 65% (malignant vs benign) were obtained when the models were validated on the blinded test set. CONCLUSIONS: For ovarian cancer, altered MALDI-TOF MS peptide profiles alone cannot be used for accurate diagnoses.

Variation in the ovarian reserve Is linked to alterations in intrafollicular estradiol production and ovarian biomarkers of follicular differentiation and oocyte quality in cattle

The mechanisms whereby the high variation in numbers of morphologically healthy oocytes and follicles in ovaries (ovarian reserve) may have an impact onovarian function, oocyte quality, and fertility are poorly understood. The objective was to determine whether previously validated biomarkers for follicular differentiation and function, as well as oocyte quality differed between cattle with low versus a high antral follicle count (AFC). Ovaries were removed (n = 5 per group) near the beginning of the nonovulatory follicular wave, before follicles could be identified via ultrasonography as being dominant, from heifers with high versus a low AFC. The F1, F2, and F3 follicles were dissected and diameters determined. Follicular fluid and thecal, granulosal, and cumulus cells and the oocyte were isolated and subjected to biomarker analyses. Although the size and numerous biomarkers of differentiation, such as mRNAs for the gonadotropin receptors, were similar, intrafollicular concentrations of estradiol and the abundance of mRNAs for CYP19A1 in granulosal cells and ESR1, ESR2, and CTSB in cumulus cells were greater, whereas mRNAs for AMH in granulosal cells and TBC1D1 in thecal cells were lower for animals with low versus a high AFC during follicle waves. Hence, variation in the ovarian reserve may have an impact on follicular function and oocyte quality via alterations in intrafollicular estradiol production and expression of key genes involved in follicle-stimulating hormone action (AMH) and estradiol (CYP19A1) production by granulosal cells, function and survival of thecal cells (TBC1D1), responsiveness of cumulus cells to estradiol (ESR1, ESR2), and cumulus cell determinants of oocyte quality (CTSB).