Search results for: biomarker
208 Estimating the Receiver Operating Characteristic Curve from Clustered Data and Case-Control Studies
Authors: Yalda Zarnegarnia, Shari Messinger
Abstract:Receiver operating characteristic (ROC) curves have been widely used in medical research to illustrate the performance of the biomarker in correctly distinguishing the diseased and non-diseased groups. Correlated biomarker data arises in study designs that include subjects that contain same genetic or environmental factors. The information about correlation might help to identify family members at increased risk of disease development, and may lead to initiating treatment to slow or stop the progression to disease. Approaches appropriate to a case-control design matched by family identification, must be able to accommodate both the correlation inherent in the design in correctly estimating the biomarker’s ability to differentiate between cases and controls, as well as to handle estimation from a matched case control design. This talk will review some developed methods for ROC curve estimation in settings with correlated data from case control design and will discuss the limitations of current methods for analyzing correlated familial paired data. An alternative approach using Conditional ROC curves will be demonstrated, to provide appropriate ROC curves for correlated paired data. The proposed approach will use the information about the correlation among biomarker values, producing conditional ROC curves that evaluate the ability of a biomarker to discriminate between diseased and non-diseased subjects in a familial paired design.
Keywords: biomarker, correlation, familial paired design, ROC curveProcedia PDF Downloads 156
207 The Identification of Combined Genomic Expressions as a Diagnostic Factor for Oral Squamous Cell Carcinoma
Authors: Ki-Yeo Kim
Abstract:Trends in genetics are transforming in order to identify differential coexpressions of correlated gene expression rather than the significant individual gene. Moreover, it is known that a combined biomarker pattern improves the discrimination of a specific cancer. The identification of the combined biomarker is also necessary for the early detection of invasive oral squamous cell carcinoma (OSCC). To identify the combined biomarker that could improve the discrimination of OSCC, we explored an appropriate number of genes in a combined gene set in order to attain the highest level of accuracy. After detecting a significant gene set, including the pre-defined number of genes, a combined expression was identified using the weights of genes in a gene set. We used the Principal Component Analysis (PCA) for the weight calculation. In this process, we used three public microarray datasets. One dataset was used for identifying the combined biomarker, and the other two datasets were used for validation. The discrimination accuracy was measured by the out-of-bag (OOB) error. There was no relation between the significance and the discrimination accuracy in each individual gene. The identified gene set included both significant and insignificant genes. One of the most significant gene sets in the classification of normal and OSCC included MMP1, SOCS3 and ACOX1. Furthermore, in the case of oral dysplasia and OSCC discrimination, two combined biomarkers were identified. The combined genomic expression achieved better performance in the discrimination of different conditions than in a single significant gene. Therefore, it could be expected that accurate diagnosis for cancer could be possible with a combined biomarker.
Keywords: oral squamous cell carcinoma, combined biomarker, microarray dataset, correlated genesProcedia PDF Downloads 365
206 The Predictive Significance of Metastasis Associated in Colon Cancer-1 (MACC1) in Primary Breast Cancer
Authors: Jasminka Mujic, Karin Milde-Langosch, Volkmar Mueller, Mirza Suljagic, Tea Becirevic, Jozo Coric, Daria Ler
Abstract:MACC1 (metastasis associated in colon cancer-1) is a prognostic biomarker for tumor progression, metastasis, and survival of a variety of solid cancers. MACC1 also causes tumor growth in xenograft models and acts as a master regulator of the HGF/MET signaling pathway. In breast cancer, the expression of MACC1 determined by immunohistochemistry was significantly associated with positive lymph node status and advanced clinical stage. The aim of the present study was to further investigate the prognostic or predictive value of MACC1 expression in breast cancer using western blot analysis and immunohistochemistry. The results of our study have shown that high MACC1 expression in breast cancer is associated with shorter disease-free survival, especially in node-negative tumors. The MACC1 might be a suitable biomarker to select patients with a higher probability of recurrence which might benefit from adjuvant chemotherapy. Our results support a biologic role and potentially open the perspective for the use of MACC1 as predictive biomarker for treatment decision in breast cancer patients.
Keywords: breast cancer, biomarker, HGF/MET, MACC1Procedia PDF Downloads 154
205 Detection of Telomerase Activity as Cancer Biomarker Using Nanogap-Rich Au Nanowire SERS Sensor
Authors: G. Eom, H. Kim, A. Hwang, T. Kang, B. Kim
Abstract:Telomerase activity is overexpressed in over 85% of human cancers while suppressed in normal somatic cells. Telomerase has been attracted as a universal cancer biomarker. Therefore, the development of effective telomerase activity detection methods is urgently demanded in cancer diagnosis and therapy. Herein, we report a nanogap-rich Au nanowire (NW) surface-enhanced Raman scattering (SERS) sensor for detection of human telomerase activity. The nanogap-rich Au NW SERS sensors were prepared simply by uniformly depositing nanoparticles (NPs) on single-crystalline Au NWs. We measured SERS spectra of methylene blue (MB) from 60 different nanogap-rich Au NWs and obtained the relative standard deviation (RSD) of 4.80%, confirming the superb reproducibility of nanogap-rich Au NW SERS sensors. The nanogap-rich Au NW SERS sensors enable us to detect telomerase activity in 0.2 cancer cells/mL. Furthermore, telomerase activity is detectable in 7 different cancer cell lines whereas undetectable in normal cell lines, which suggest the potential applicability of nanogap-rich Au NW SERS sensor in cancer diagnosis. We expect that the present nanogap-rich Au NW SERS sensor can be useful in biomedical applications including a diverse biomarker sensing.
Keywords: cancer biomarker, nanowires, surface-enhanced Raman scattering, telomeraseProcedia PDF Downloads 264
204 An Initial Evaluation of Newly Proposed Biomarker of Zinc Status in Humans: The Erythrocyte Linoleic Acid: Dihomo-γ-Linolenic Acid (LA:DGLA) Ratio
Authors: Marija Knez, James C.R. Stangoulis, Manja Zec, Zoran Pavlovic, Jasmina D. Martacic, Mirjana Gurinovic, Maria Glibetic
Abstract:Background: Zinc is an essential micronutrient for humans with important physiological functions. A sensitive and specific biomarker for assessing Zn status is still needed. Objective: The major aim of this study was to examine if the changes in the content of plasma phospholipid LA, DGLA and LA: DGLA ratio can be used to efficiently predict the dietary Zn intake and plasma Zn status of humans. Methods: The study was performed on apparently healthy human volunteers. The dietary Zn intake was assessed using 24h recall questionnaires. Plasma phospholipid fatty acid analysis was done by gas chromatography and plasma analysis of minerals by atomic absorption spectrometry. Biochemical, anthropometrical and hematological parameters were assessed. Results: No significant relationship was found between the dietary and plasma zinc status (r=0.07; p=0.6). There is a statistically significant correlation between DGLA and plasma Zn (r=0.39, p=0.00). No relationship was observed between the linoleic acid and plasma Zn, while there was a significant negative correlation between LA: DGLA ratio and plasma Zn status (r=-0.35, p=0.01). Similarly, there were statistically significant difference in DGLA status (p=0.004) and LA: DGLA ratio (p=0.042) between the Zn formed groups. Conclusions: This study is an initial step in evaluating LA: DGLA ratio as a biomarker of Zn status in humans. The results are encouraging as they show that concentration of DGLA is decreased and LA: DGLA ratio increased in people with lower dietary Zn intake. However, additional studies are needed to fully examine the sensitivity of this biomarker.
Keywords: dietary Zn intake Zinc, fatty acid composition, LA: DGLA, healthy population, plasma Zn status, Zn biomarkerProcedia PDF Downloads 210
203 Evaluation of Longitudinal Relaxation Time (T1) of Bone Marrow in Lumbar Vertebrae of Leukaemia Patients Undergoing Magnetic Resonance Imaging
Authors: M. G. R. S. Perera, B. S. Weerakoon, L. P. G. Sherminie, M. L. Jayatilake, R. D. Jayasinghe, W. Huang
Abstract:The aim of this study was to measure and evaluate the Longitudinal Relaxation Times (T1) in bone marrow of an Acute Myeloid Leukaemia (AML) patient in order to explore the potential for a prognostic biomarker using Magnetic Resonance Imaging (MRI) which will be a non-invasive prognostic approach to AML. MR image data were collected in the DICOM format and MATLAB Simulink software was used in the image processing and data analysis. For quantitative MRI data analysis, Region of Interests (ROI) on multiple image slices were drawn encompassing vertebral bodies of L3, L4, and L5. T1 was evaluated using the T1 maps obtained. The estimated bone marrow mean value of T1 was 790.1 (ms) at 3T. However, the reported T1 value of healthy subjects is significantly (946.0 ms) higher than the present finding. This suggests that the T1 for bone marrow can be considered as a potential prognostic biomarker for AML patients.
Keywords: acute myeloid leukaemia, longitudinal relaxation time, magnetic resonance imaging, prognostic biomarker.Procedia PDF Downloads 457
202 The Exploration Targets of the Nanpu Sag: Insight from Organic Geochemical Characteristics of Source Rocks and Oils
Authors: Lixin Pei, Zhilong Huang, Wenzhe Gang
Abstract:Organic geochemistry of source rocks and oils in the Nanpu Sag, Bohai Bay basin was studied on the basis of the results of Rock-Eval and biomarker. The possible source rocks consist of the third member (Es₃) and the first member (Es₁) of Shahejie formation and the third member of Dongying Formation (Ed₃) in the Nanpu Sag. The Es₃, Es₁, and Ed₃ source rock intervals in the Nanpu Sag all have high organic-matter richness and are at hydrocarbon generating stage, which are regarded as effective source rocks. The three possible source rock intervals have different biomarker associations and can be differentiated by gammacerane/αβ C₃₀ hopane, ETR ([C₂₈+C₂₉]/ [C₂₈+C₂₉+Ts]), C₂₇ diasterane/sterane and C₂₇/C₂₉ steranes, which suggests they deposited in different environments. Based on the oil-source rock correlation, the shallow oils mainly originated from the Es₃ and Es₁ source rocks in the Nanpu Sag. Through hydrocarbon generation and expulsion history of the source rocks, trap development history and accumulation history, the shallow oils mainly originated from paleo-reservoirs in the Es₃ and Es₁ during the period of Neotectonism, and the residual paleo-reservoirs in the Es₃ and Es₁ would be the focus targets in the Nanpu Sag; Bohai Bay Basin.
Keywords: source rock, biomarker association, Nanpu Sag, Bohai Bay BasinProcedia PDF Downloads 314
201 Using Speech Emotion Recognition as a Longitudinal Biomarker for Alzheimer’s Diseases
Authors: Yishu Gong, Liangliang Yang, Jianyu Zhang, Zhengyu Chen, Sihong He, Xusheng Zhang, Wei Zhang
Abstract:Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that affects millions of people worldwide and is characterized by cognitive decline and behavioral changes. People living with Alzheimer’s disease often find it hard to complete routine tasks. However, there are limited objective assessments that aim to quantify the difficulty of certain tasks for AD patients compared to non-AD people. In this study, we propose to use speech emotion recognition (SER), especially the frustration level, as a potential biomarker for quantifying the difficulty patients experience when describing a picture. We build an SER model using data from the IEMOCAP dataset and apply the model to the DementiaBank data to detect the AD/non-AD group difference and perform longitudinal analysis to track the AD disease progression. Our results show that the frustration level detected from the SER model can possibly be used as a cost-effective tool for objective tracking of AD progression in addition to the Mini-Mental State Examination (MMSE) score.
Keywords: Alzheimer’s disease, speech emotion recognition, longitudinal biomarker, machine learningProcedia PDF Downloads 24
200 Evaluation of the Role of Circulating Long Non-Coding RNA H19 as a Promising Biomarker in Plasma of Patients with Gastric Cancer
Authors: Doaa Hashad, Amany Elbanna, Abeer Ibrahim, Gihan Khedr
Abstract:Background: H19 is one of the long non coding RNAs (LncRNA) that is related to the progression of many diseases including cancers. This work was carried out to study the level of the long non-coding RNA; H119, in plasma of patients with gastric cancer (GC) and to assess its significance in their clinical management. Methods: A total of sixty-two participants were enrolled in the present study. The first group included thirty-two GC patients, while the second group was formed of thirty age and sex matched healthy volunteers serving as a control group. Plasma samples were used to assess H19 gene expression using real time quantitative PCR technique. Results: H19 expression was up-regulated in GC patients with positive correlation to TNM cancer stages. Conclusions: Up-regulation of H19 is closely associated with gastric cancer and correlates well with tumor staging. Convenient, efficient quantification of H19 in plasma using real time PCR technique implements its role as a potential noninvasive prognostic biomarker in gastric cancer, that predicts patient’s outcome and most importantly as a novel target in gastric cancer treatment with better performance achieved on using both CEA and H19 simultaneously.
Keywords: biomarker, gastric, cancer, LncRNAProcedia PDF Downloads 238
199 Thyroid-Stimulating Hormone as a Stress Biomarker in Thyroidectomy Patients: A Cohort Study
Authors: Jeonghun Lee
Abstract:In this study, we investigated the relationship between stress and thyroid dysfunction in such patients who underwent thyroidectomy. This study included 101 patients who underwent thyroidectomy from January 2015 to June 2020 and experienced hypothyroidism. The included patients had good drug compliance with the same dosage of levothyroxine (LT4). The male-to-female ratio was 1:4.6, and the mean age was 45.4 years at surgery and 50.2 years at stressful events. Eighteen patients underwent lobectomies and, of these, 12 did not take LT4. The mean follow-up period was 49(8-93) months. Statistical analyses were performed using the paired t-test, Wilcoxon signed-rank test, and McNemer test using PROC MIXED with SAS 9.4. Forty-five patients (44.6%) had hypothyroidism with thyroid-stimulating hormone (TSH) >10 μIU/mL. There was distress in 81 patients and eustress in 10 patients. TSH levels increased during a mean 5.8 months (min 1, max 12) in 24 patients who specified the date of their life events. Even though each patient took the same dose of LT4, when the patients were under stress, both the free T4 and T3 decreased and TSH increased, regardless of whether the patient experienced distress or eustress (P <0.001). While adjusting for the effect of the free T4 and T3, TSH increased significantly in the patients after stress (P <0.001). For patients with thyroid cancer who are simultaneously experiencing life events, TSH may be used as a stress biomarker to enable the implementation of appropriate treatment and counseling strategies.
Keywords: endocrine, thyroid, thyroid function, biomarker, stressProcedia PDF Downloads 16
198 Proteomic Analysis of Excretory Secretory Antigen (ESA) from Entamoeba histolytica HM1: IMSS
Authors: N. Othman, J. Ujang, M. N. Ismail, R. Noordin, B. H. Lim
Abstract:Amoebiasis is caused by the Entamoeba histolytica and still endemic in many parts of the tropical region, worldwide. Currently, there is no available vaccine against amoebiasis. Hence, there is an urgent need to develop a vaccine. The excretory secretory antigen (ESA) of E. histolytica is a suitable biomarker for the vaccine candidate since it can modulate the host immune response. Hence, the objective of this study is to identify the proteome of the ESA towards finding suitable biomarker for the vaccine candidate. The non-gel based and gel-based proteomics analyses were performed to identify proteins. Two kinds of mass spectrometry with different ionization systems were utilized i.e. LC-MS/MS (ESI) and MALDI-TOF/TOF. Then, the functional proteins classification analysis was performed using PANTHER software. Combination of the LC -MS/MS for the non-gel based and MALDI-TOF/TOF for the gel-based approaches identified a total of 273 proteins from the ESA. Both systems identified 29 similar proteins whereby 239 and 5 more proteins were identified by LC-MS/MS and MALDI-TOF/TOF, respectively. Functional classification analysis showed the majority of proteins involved in the metabolic process (24%), primary metabolic process (19%) and protein metabolic process (10%). Thus, this study has revealed the proteome the E. histolytica ESA and the identified proteins merit further investigations as a vaccine candidate.
Keywords: E. histolytica, ESA, proteomics, biomarkerProcedia PDF Downloads 274
197 Role of Surfactant Protein D (SP-D) as a Biomarker of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection
Authors: Lucia Salvioni, Pietro Giorgio Lovaglio, Valerio Leoni, Miriam Colombo, Luisa Fiandra
Abstract:The involvement of plasmatic surfactant protein-D (SP-D) in pulmonary diseases has been long investigated, and over the last two years, more interest has been directed to determine its role as a marker of COVID-19. In this direction, several studies aimed to correlate pulmonary surfactant proteins with the clinical manifestations of the virus indicated SP-D as a prognostic biomarker of COVID-19 pneumonia severity. The present work has performed a retrospective study on a relatively large cohort of patients of Hospital Pio XI of Desio (Lombardia, Italy) with the aim to assess differences in the hematic SP-D concentrations among COVID-19 patients and healthy donors and the role of SP-D as a prognostic marker of severity and/or of mortality risk. The obtained results showed a significant difference in the mean of log SP-D levels between COVID-19 patients and healthy donors, so as between dead and survived patients. SP-D values were significantly higher for both hospitalized COVID-19 and dead patients, with threshold values of 150 and 250 ng/mL, respectively. SP-D levels at admission and increasing differences among follow-up and admission values resulted in the strongest significant risk factors of mortality. Therefore, this study demonstrated the role of SP-D as a predictive marker of SARS-CoV-2 infection and its outcome. A significant correlation of SP-D with patient mortality indicated that it is also a prognostic factor in terms of mortality, and its early detection should be considered to design adequate preventive treatments for COVID-19 patients.
Keywords: SARS-CoV-2 infection, COVID-19, surfactant protein-D (SP-D), mortality, biomarkerProcedia PDF Downloads 11
196 Specific Biomarker Level and Function Outcome Changes in Treatment of Patients with Frozen Shoulder Using Dextrose Prolotherapy Injection
Authors: Nuralam Sam, Irawan Yusuf, Irfan Idris, Endi Adnan
Abstract:The most case in the shoulder in the the adult is the frozen shoulder. It make an uncomfortable sensation which disturbance daily activity. The studies of frozen shoulder are still limited. This study used a true experimental pre and post test design with a group design. The participant underwent dextrose prolotherapy injection in the rotator cuff, intraarticular glenohumeral joint, long head tendon biceps, and acromioclavicular joint injections with 15% dextrose, respectively, at week 2, week 4, and week 6. Participants were followed for 12 weeks. The specific biomarker MMP and TIMP, ROM, DASH score were measured at baseline, at week 6, and week 12. The data were analyzed by multivariate analysis (repeated measurement ANOVA, Paired T-Test, and Wilcoxon) to determine the effect of the intervention. The result showed a significant decrease in The Disability of the Arm, Shoulder, and Hand (DASH) score in prolo injection patients in each measurement week (p < 0.05). While the measurement of Range of Motion (ROM), each direction of shoulder motion showed a significant difference in average each week, from week 0 to week 6 (p <0.05).Dextrose prolotherapy injection results give a significant improvement in functional outcome of the shoulder joint, and ROMand did not show significant results in assessing the specific biomarker, MMP-1, and TIMP-1 in tissue repair. This study suggestion an alternative to the use of injection prolotherapy in Frozen shoulder patients, which has fewer side effects and better effectiveness than the use of corticosteroid injections.
Keywords: frozen shoulder, ROM, DASH score, prolotherapy, MMP-1, TIMP-1Procedia PDF Downloads 45
195 Micro-Ribonucleic Acid-21 as High Potential Prostate Cancer Biomarker
Authors: Regina R. Gunawan, Indwiani Astuti, H. Raden Danarto
Abstract:Cancer is the leading cause of death worldwide. Cancer is caused by mutations that alter the function of normal human genes and give rise to cancer genes. MicroRNA (miRNA) is a small non-coding RNA that regulates the gen through complementary bond towards mRNA target and cause mRNA degradation. miRNA works by either promoting or suppressing cell proliferation. miRNA level expression in cancer may offer another value of miRNA as a biomarker in cancer diagnostic. miRNA-21 is believed to have a role in carcinogenesis by enhancing proliferation, anti-apoptosis, cell cycle progression and invasion of tumor cells. Hsa-miR-21-5p marker has been identified in Prostate Cancer (PCa) and Benign Prostatic Hyperplasia (BPH) patient’s urine. This research planned to explore the diagnostic performance of miR-21 to differentiate PCa and BPH patients. In this study, urine samples were collected from 20 PCa patients and 20 BPH patients. miR-21 relative expression against the reference gene was analyzed and compared between the two. miRNA expression was analyzed using the comparative quantification method to find the fold change. miR-21 validity in identifying PCa patients was performed by quantifying the sensitivity and specificity with the contingency table. miR-21 relative expression against miR-16 in PCa patient and in BPH patient has 12,98 differences in fold change. From a contingency table of Cq expression of miR-21 in identifying PCa patients from BPH patient, Cq miR-21 has 100% sensitivity and 75% specificity. miR-21 relative expression can be used in discriminating PCa from BPH by using a urine sample. Furthermore, the expression of miR-21 has higher sensitivity compared to PSA (Prostate specific antigen), therefore miR-21 has a high potential to be analyzed and developed more.
Keywords: benign prostate hyperplasia, biomarker, miRNA-21, prostate cancerProcedia PDF Downloads 71
194 Experimental Measurements for the Effect of Dilution Procedure in Blood Esterases as Animals Biomarker for Exposure to Organophosphate Compounds
Authors: Kasim Sakran Abass
Abstract:This main aim of this study was to confirm and extend our current knowledge about the effects of dilutions on esterases activities in the blood for birds with respect to protecting the enzyme from organophosphate inhibition. There were significantly higher esterases activities in dilution 1:10 in all blood samples from quail, duck, and chick compared to other dilutions (1:5, 1:15, 1:20, and 1:25). Furthermore, our results also pointed to the importance of estimating different dilutions effects prior to using in birds as biomarker tools of environmental exposure. Concentration–inhibition curves were determined for the inhibitor in the presence of dilutions 1:5, 1:10 plus 1:15 (to stimulate carboxylesterase). Point estimates (concentrations calculated to produce 20, 50, and 80% inhibition) were compared across conditions and served as a measure of esterase-mediated detoxification. Among the thiol esters (dilution 1:5) was observed to have the highest specificity constant (kcat/Km), and the Km and kcat values were 176 μM and 16,765 s−1, respectively for S-phenyl thioacetate ester, while detected in (dilution 1:15) the lowest specificity constant (kcat/Km), and the Km and kcat values were 943 μM and 1154 s−1, respectively for acetylthiocholine iodide ester.
Keywords: esterase, animal, dilution, pesticidesProcedia PDF Downloads 467
193 Hepatoxicity induced Glyphosate-Based Herbicide Baron in albino rats
Authors: Manal E. A Elhalwagy, Nadia Amin Abdulmajeed, Hanan S. Alnahdi, Enas N. Danial
Abstract:Baron is herbicide includes (48% glyphosate) widely used in Egypt. The present study assesses the cytotoxic and genotoxic effect of baron on rats liver. Two groups of rats were treated orally with 1/10 LD 50, (275.49 mg kg -1) and 1/40 LD 50, (68.86 mg kg-1) glyphosate for 28 days compared with control group. Serum and liver tissues were taken at 14 and 28 days of treatment. An inhibition in Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities were recorded at both treatment periods and reduction in total serum protein (TP) and albumin (ALB). However, non-significant changes in serum acetylcholinesterase (AChE). Elevation in oxidative stress biomarker malondyaldehyde (MDA) and the decline in detoxification biomarker total reduced glutathione (GSH), Glutathione S-transferase (GST) and superoxide dismutase (SOD) in liver tissues led to increase in percentage of DNA damage. Destruction in liver tissue architecture was observed . Although, Baron was classified in the safe category pesticides repeated exposure to small doses has great danger effect.
Keywords: glyphosate, liver toxicity, oxidative stress, DNA damage, commet assayProcedia PDF Downloads 312
192 Oil-Oil Correlation Using Polar and Non-Polar Fractions of Crude Oil: A Case Study in Iranian Oil Fields
Authors: Morteza Taherinezhad, Ahmad Reza Rabbani, Morteza Asemani, Rudy Swennen
Abstract:Oil-oil correlation is one of the most important issues in geochemical studies that enables to classify oils genetically. Oil-oil correlation is generally estimated based on non-polar fractions of crude oil (e.g., saturate and aromatic compounds). Despite several advantages, the drawback of using these compounds is their susceptibility of being affected by secondary processes. The polar fraction of crude oil (e.g., asphaltenes) has similar characteristics to kerogen, and this structural similarity is preserved during migration, thermal maturation, biodegradation, and water washing. Therefore, these structural characteristics can be considered as a useful correlation parameter, and it can be concluded that asphaltenes from different reservoirs with the same genetic signatures have a similar origin. Hence in this contribution, an integrated study by using both non-polar and polar fractions of oil was performed to use the merits of both fractions. Therefore, five oil samples from oil fields in the Persian Gulf were studied. Structural characteristics of extracted asphaltenes were investigated by Fourier transform infrared (FTIR) spectroscopy. Graphs based on aliphatic and aromatic compounds (predominant compounds in asphaltenes structure) and sulphoxide and carbonyl functional groups (which are representatives of sulphur and oxygen abundance in asphaltenes) were used for comparison of asphaltenes structures in different samples. Non-polar fractions were analyzed by GC-MS. The study of asphaltenes showed the studied oil samples comprise two oil families with distinct genetic characteristics. The first oil family consists of Salman and Reshadat oil samples, and the second oil family consists of Resalat, Siri E, and Siri D oil samples. To validate our results, biomarker parameters were employed, and this approach completely confirmed previous results. Based on biomarker analyses, both oil families have a marine source rock, whereby marl and carbonate source rocks are the source rock for the first and the second oil family, respectively.
Keywords: biomarker, non-polar fraction, oil-oil correlation, petroleum geochemistry, polar fractionProcedia PDF Downloads 70
191 Urinary Exosome miR-30c-5p as a Biomarker for Early-Stage Clear Cell Renal Cell Carcinoma
Authors: Shangqing Song, Bin Xu, Yajun Cheng, Zhong Wang
Abstract:miRNAs derived from exosomes exist in a body fluid such as urine were regarded as potential biomarkers for various human cancers diagnosis and prognosis, as mature miRNAs can be steadily preserved by exosomes. However, its potential value in clear cell renal cell carcinoma (ccRCC) diagnosis and prognosis remains unclear. In the present study, differentially expressed miRNAs from urinal exosomes were identified by next-generation sequencing (NGS) technology. The 16 differentially expressed miRNAs were identified between ccRCC patients and healthy donors. To explore the specific diagnosis biomarker of ccRCC, we validated these urinary exosomes from 70 early-stage renal cancer patients, 30 healthy people and other urinary system cancers, including 30 early-stage prostate cancer patients and 30 early-stage bladder cancer patients by qRT-PCR. The results showed that urinary exosome miR-30c-5p could be stably amplified and meanwhile the expression of miR-30c-5p has no significant difference between other urinary system cancers and healthy control, however, expression level of miR-30c-5p in urinary exosomal of ccRCC patients was lower than healthy people and receiver operation characterization (ROC) curve showed that the area under the curve (AUC) values was 0.8192 (95% confidence interval was 0.7388-0.8996, P= 0.0000). In addition, up-regulating miR-30c-5p expression could inhibit renal cell carcinoma cells growth. Lastly, HSP5A was found as a direct target gene of miR-30c-5p. HSP5A depletion reversed the promoting effect of ccRCC growth casued by miR-30c-5p inhibitor, respectively. In conclusion, this study demonstrated that urinary exosomal miR-30c-5p is readily accessible as diagnosis biomarker of early-stage ccRCC, and miR-30c-5p might modulate the expression of HSPA5, which correlated with the progression of ccRCC.
Keywords: clear cell renal cell carcinoma, exosome, HSP5A, miR-30c-5pProcedia PDF Downloads 197
190 Effect of Oxidative Stress from Smoking on Erythrocyte Phosphatidylserine Externalization
Authors: Ratchaneewan Maneemaroj, Paveena Noisuwan, Chonlada Lakhonphon
Abstract:The smoking is one of the major risk factors in Non-Communicable Disease. Free radicals from cigarette smoke can cause oxidative stress. The oxidative insults can lead to red blood cell (RBC) senescence and are involved in the clearance of red blood cells. The objective of the present study is to assess the association between smoke, oxidative stress evaluated with serum Malondialdehyde (MDA) level and phosphatidylserine (PS) externalization (biomarker of RBC senescence) evaluated with annexin V binding. A total of sixty-four male volunteers aged 25-60 years old were recruited in this study. MDA was measured by colorimetric method. Annexin V binding was detected by flow cytometry. Our results show that there was a significant increase in MDA levels in cigarette smokers as compared to non-smokers (p < 0.001). However, there was no significant different between annexin V binding (% gate) in cigarette smokers and non-smokers (p = 0.978). These results provide evidence of free radical from smoking is associated with oxidative damage to erythrocytes. However, our results suggest that PS externalization is unlikely to have a role in RBC senescence pathway of stressed erythrocytes from cigarette smoke. The other biomarker of RBC senescence should be determined on cigarette smoker erythrocytes.
Keywords: malondialdehyde, phosphatidylserine, RBC senescence, annexin VProcedia PDF Downloads 373
189 Target and Biomarker Identification Platform to Design New Drugs against Aging and Age-Related Diseases
Authors: Peter Fedichev
Abstract:We studied fundamental aspects of aging to develop a mathematical model of gene regulatory network. We show that aging manifests itself as an inherent instability of gene network leading to exponential accumulation of regulatory errors with age. To validate our approach we studied age-dependent omic data such as transcriptomes, metabolomes etc. of different model organisms and humans. We build a computational platform based on our model to identify the targets and biomarkers of aging to design new drugs against aging and age-related diseases. As biomarkers of aging, we choose the rate of aging and the biological age since they completely determine the state of the organism. Since rate of aging rapidly changes in response to an external stress, this kind of biomarker can be useful as a tool for quantitative efficacy assessment of drugs, their combinations, dose optimization, chronic toxicity estimate, personalized therapies selection, clinical endpoints achievement (within clinical research), and death risk assessments. According to our model, we propose a method for targets identification for further interventions against aging and age-related diseases. Being a biotech company, we offer a complete pipeline to develop an anti-aging drug-candidate.
Keywords: aging, longevity, biomarkers, senescenceProcedia PDF Downloads 212
188 The Potential of Differential-Related Gene-1 (DRG1) as a Biomarker for Metastasis of Estrogen Receptor-Positive Breast Cancer
Authors: Hillary Bor, Esther N. Maina, Benson Nyambga, Kirtika Tushar Patel, Chales Ochieng Olwal, Walter Nalyanya, Yahaya Gavmukulya
Abstract:Introduction: Breast cancer is a major burden worldwide and the majority of breast cancers express estrogen receptors (ER), suggesting a high dependence on estrogen hormone. Age is among the major determinants of breast cancer development. However, although Western Kenya is one of the areas with high breast cancer cases, the age distribution of ER-positive breast cancer in the sub-region remains largely undocumented. Differentiation-related gene-1 (DRG1) is a metastasis suppressor and, thus, a potential biomarker for predicting the level of metastasis, but its potential application in assessing the extent of metastasis of ER-positive breast cancer has not been fully explored. This study, therefore, investigated the age distribution and the potential expression of DRG1 in assessing metastasis of ER-positive breast cancer. Materials and Methods: Breast cancer tumor blocks archived in safe cabins in the histology laboratory section, Moi Teaching and Referral Hospital, Eldoret, Kenya, were used. Clinico- pathological parameters such as histology grade and tumor size, which are associated with metastatic cancer, were assessed using the archived clinicopathological reports and/or histological analysis of the tumor blocks. The expression of DRG1 and Ki-67 proteins was determined using immunohistochemistry. Results: ER-positive breast cancer was predominant among women aged 40 and 50 years. No association was observed between the immunohistochemical expression of DRG1 and parameters such as histology grade, tumor size, or expression of Ki-67 protein expressed DRG1 (p > 0.05).Conclusion: The findings suggest that expression of DRG1 protein is not associated with parameters that indicate breast cancer metastasis. Thus, DRG1 expression is not a potential biomarker candidate for ER-positive breast cancer metastasis. However, since the small sample size was used, further research using a larger prospective study is necessary to support the present findings.
Keywords: differential-related gene-1 (DRG1), Estrogen receptor-positive breast cancer, Western Kenya, ageProcedia PDF Downloads 12
187 Histological Characteristics of the Organs of Adult Zebrafish as a Biomarker for the Study of New Drugs with Effect on the Snake Venom of Bothrops alternatus
Authors: Jose Carlos Tavares Carvalho, Hady Keita, Giovanna Rocha Santana, Igor Victor Ferreira Dos Santos, Jesus Rafael Rodriguez Amado, Ariadna Lafourcade Prada, Adriana Maciel Ferreira, Helison Oliveira
Abstract:Summary: As animal model, zebrafish can be a good opportunity to establish a profile of tissue alteration caused by Bothrops alternatus venom and to screen new anti-venom drugs. Objective: To establish tissue biomarkers from zebrafish injected by snake venom and elucidate the use of glucocorticoids in ophidic accidents. Materials and Methods: The Danio rerio fish were randomly divided into four groups: control group, venom group, Dexamethasone1h before venom injected group and Dexamethasone 1 h after venom injected group. The concentration of Bothrops alternatus venom was 0.13 mg/ml and the fish received 20µl/Fish. The Body weight measurement and histological characteristics of gills, kidneys, liver, and intestine were determinate. Results: Physical analysis shows necrosis accompanied by inflammation in animals receiving the Bothrops alternatus venom. Significant difference was observed in the variation of weight between the control group, and the groups received the venom (t student test, p < 0.05). The average histological alterations index of gill, liver, kidney or intestine was statistically higher in animals received the venom (t Student test, p < 0.05). The alterations were lower in the groups that received Dexamethasone 1h before and after venom injected compared to the group that received only the venom. Dexamethasone 1h before venom injected group had minor histopathological alterations. Conclusion: The organs of zebrafish may be a tissue biomarker of alterations from Bothrops alternatus venom and dexamethasone reduced the damage caused by this venom in the organs studied, which may suggest the use of zebrafish as animal model for research related to screening new drug against snake venom.
Keywords: zebrafish, snake venom, biomarker, drugsProcedia PDF Downloads 261
186 ADAM10 as a Potential Blood Biomarker of Cognitive Frailty
Authors: Izabela P. Vatanabe, Rafaela Peron, Patricia Manzine, Marcia R. Cominetti
Abstract:Introduction: Considering the increase in life expectancy of world population, there is an emerging concern in health services to allocate better care and care to elderly, through promotion, prevention and treatment of health. It has been observed that frailty syndrome is prevalent in elderly people worldwide and this complex and heterogeneous clinical syndrome consist of the presence of physical frailty associated with cognitive dysfunction, though in absence of dementia. This can be characterized by exhaustion, unintentional weight loss, decreased walking speed, weakness and low level of physical activity, in addition, each of these symptoms may be a predictor of adverse outcomes such as hospitalization, falls, functional decline, institutionalization, and death. Cognitive frailty is a recent concept in literature, which is defined as the presence of physical frailty associated with mild cognitive impairment (MCI) however in absence of dementia. This new concept has been considered as a subtype of frailty, which along with aging process and its interaction with physical frailty, accelerates functional declines and can result in poor quality of life of the elderly. MCI represents a risk factor for Alzheimer's disease (AD) in view of high conversion rate for this disease. Comorbidities and physical frailty are frequently found in AD patients and are closely related to heterogeneity and clinical manifestations of the disease. The decreased platelets ADAM10 levels in AD patients, compared to cognitively healthy subjects, matched by sex, age and education. Objective: Based on these previous results, this study aims to evaluate whether ADAM10 platelet levels of could act as a biomarker of cognitive frailty. Methods: The study was approved by Ethics Committee of Federal University of São Carlos (UFSCar) and conducted in the municipality of São Carlos, headquarters of Federal University of São Carlos (UFSCar). Biological samples of subjects were collected, analyzed and then stored in a biorepository. ADAM10 platelet levels were analyzed by western blotting technique in subjects with MCI and compared to subjects without cognitive impairment, both with and without presence of frailty. Statistical tests of association, regression and diagnostic accuracy were performed. Results: The results have shown that ADAM10/β-actin ratio is decreased in elderly individuals with cognitive frailty compared to non-frail and cognitively healthy controls. Previous studies performed by this research group, already mentioned above, demonstrated that this reduction is still higher in AD patients. Therefore, the ADAM10/β-actin ratio appears to be a potential biomarker for cognitive frailty. The results bring important contributions to an accurate diagnosis of cognitive frailty from the perspective of ADAM10 as a biomarker for this condition, however, more experiments are being conducted, using a high number of subjects, and will help to understand the role of ADAM10 as biomarker of cognitive frailty and contribute to the implementation of tools that work in the diagnosis of cognitive frailty. Such tools can be used in public policies for the diagnosis of cognitive frailty in the elderly, resulting in a more adequate planning for health teams and better quality of life for the elderly.
Keywords: ADAM10, biomarkers, cognitive frailty, elderlyProcedia PDF Downloads 154
185 Urinary Neutrophil Gelatinase Associated Lipocalin as Diagnostic Biomarkers for Lupus Nephritis
Authors: Lorena GóMez Escorcia, Gustavo Aroca MartíNez, Jose Luiz Villarreal, Elkin Navarro Quiroz
Abstract:Lupus nephritis (LN) is a high-cost disease, occurring in about half of patients with Systemic Lupus Erythematosus (SLE). Renal biopsy constitutes the only protocol that, to date, allows a correct diagnosis of the level of renal involvement in these patients. However, this procedure can have various adverse effects such as kidney bleeding, muscle bleeding, infection, pain, among others. Therefore, the development of new diagnostic alternatives is required. The neutrophil gelatinase-associated lipocalin (NGAL) has been emerging as a novel biomarker of acute kidney injury. The aim of this study was to assess urinary NGAL levels as a marker for disease activity in patients with lupus nephritis. For this work included 50 systemic lupus erythematosus (SLE) patients, 50 with active lupus nephritis (LN), and 50 without autoimmune and renal disease as controls. TNGAL in urine samples was measured by enzyme-linked immunosorbent assay (ELISA). The results revealed that patients with kidney damage had an elevated urinary NGAL as compared to patients with lupus without kidney damage and controls (p <0.005), and the mean of uNGAL was (28.72 ± 4.53), (19.51 ± 4.72), (8.91 ± 3.37) respectively. Measurement of urinary NGAL levels showed a very good diagnostic performance for discriminating patients with Lupus nephritis from SLE without renal damage and of control individuals.
Keywords: lupus nephritis, biomarker, NGAL, urine samplesProcedia PDF Downloads 142
184 Effect of Pulmonary Rehabilitation towards Length of Stay and IL-6 Level on Community-Acquired Pneumonia Patients
Authors: Santony Santony, Teguh Rahayu Sartono, Iin Noor Chozin
Abstract:Introduction: Pneumonia is acute inflammation on lung parenchyma which is caused by bacteria, virus, fungi, or parasite. In Indonesia, Pneumonia is among the ten inpatient cases. Length of stay is related to the increased morbidity rate, nosocomial infection, and costs. The aim of this study is to assess the effect of pulmonary rehabilitation on the difference in length of stay and the level of Interleukin 6 (IL-6) as an inflammation biomarker for community-acquired pneumonia (CAP) patients in non-intensive rooms. Therefore, pulmonary rehabilitation as adjunctive therapy can be routinely exercised in order to shorten the length of stay, along with the decrease in IL-6 level. Methods: This study was conducted from May to October 2019 at Saiful Anwar General Hospital, Malang. 40 community-acquired pneumonia patients in non-intensive rooms were divided into two groups. 20 patients in the treatment group and 20 patients in the control group, all of them were selected through both inclusion and exclusion criteria. This study used simple consecutive random sampling. In the treatment group, pulmonary rehabilitation performed was composed of breathing exercise, effective coughing technique, clapping (percussion), postural drainage, as well as respiratory muscle training using incentive spirometry device. Pulmonary rehabilitation was conducted twice over five days with a minimum duration of 15 minutes. Blood samples were taken both on the first and the fifth day of the treatment to measure IL-6 level as an inflammation biomarker. Result: For the treatment group, the length of stay was 5.35 days whereas the control group 7.6 days. It can be seen that the treatment group had a shorter length of stay by 2.25 days (P<0,001). The IL-6 level on the first day for the treatment group was 36.27 pg/ml, whereas on the fifth day was 34.36 pg/ml. There was a decrease in IL-6 level on the fifth day of treatment even though it was not statistically significant (P=0.628). IL-6 level on the control group for the first day was 67.76 pg/ml, and after the fifth day, the level decreased to 54.43 pg/ml. There seemed to be a decrease in the IL-6, but it was not statistically significant (P=0.502). On the fifth day, the treatment group showed an average IL-6 level of 34.36 pg/ml. This value was lower than that of the control group which did not receive pulmonary rehabilitation having an IL-6 level of 54.43 pg/ml, even though it was not statistically significant (p=0.221). Conclusion: This study concluded that pulmonary rehabilitation as an adjunctive therapy shortened length of stay by 2.25 days for community-acquired pneumonia patients in a non-intensive room. Both groups experienced a decrease in IL-6 level on the fifth day in comparison with the first day even though it was not statistically significant P>0,05. IL-6 level as an inflammation biomarker decreased on the fifth day of treatment which was in accordance with improvement on pneumonia patients.
Keywords: community-acquired pneumonia, interleukin-6, length of stay, pulmonary rehabilitationProcedia PDF Downloads 44
183 The Administration of Infection Diseases During the Pandemic COVID-19 and the Role of the Differential Diagnosis with Biomarkers VB10
Authors: Sofia Papadimitriou
Abstract:INTRODUCTION: The differential diagnosis between acute viral and bacterial infections is an important cost-effectiveness parameter at the stage of the treatment process in order to achieve the maximum benefits in therapeutic intervention by combining the minimum cost to ensure the proper use of antibiotics.The discovery of sensitive and robust molecular diagnostic tests in response to the role of the host in infections has enhanced the accurate diagnosis and differentiation of infections. METHOD: The study used a sample of six independent blood samples (total=756) which are associated with human proteins-proteins, each of which at the transcription stage expresses a different response in the host network between viral and bacterial infections.Τhe individual blood samples are subjected to a sequence of computer filters that identify a gene panel corresponding to an autonomous diagnostic score. The data set and the correspondence of the gene panel to the diagnostic patents a new Bangalore -Viral Bacterial (BL-VB). FINDING: We use a biomarker based on the blood of 10 genes(Panel-VB) that are an important prognostic value for the detection of viruses from bacterial infections with a weighted average AUROC of 0.97(95% CL:0.96-0.99) in eleven independent samples (sets n=898). We discovered a base with a patient score (VB 10 ) according to the table, which is a significant diagnostic value with a weighted average of AUROC 0.94(95% CL: 0.91-0.98) in 2996 patient samples from 56 public sets of data from 19 different countries. We also studied VB 10 in a new cohort of South India (BL-VB,n=56) and found 97% accuracy in confirmed cases of viral and bacterial infections. We found that VB 10 (a)accurately identifies the type of infection even in unspecified cases negative to the culture (b) shows its clinical condition recovery and (c) applies to all age groups, covering a wide range of acute bacterial and viral infectious, including non-specific pathogens. We applied our VB 10 rating to publicly available COVID 19 data and found that our rating diagnosed viral infection in patient samples. RESULTS: Τhe results of the study showed the diagnostic power of the biomarker VB 10 as a diagnostic test for the accurate diagnosis of acute infections in recovery conditions. We look forward to helping you make clinical decisions about prescribing antibiotics and integrating them into your policies management of antibiotic stewardship efforts. CONCLUSIONS: Overall, we are developing a new property of the RNA-based biomarker and a new blood test to differentiate between viral and bacterial infections to assist a physician in designing the optimal treatment regimen to contribute to the proper use of antibiotics and reduce the burden on antimicrobial resistance, AMR.
Keywords: acute infections, antimicrobial resistance, biomarker, blood transcriptome, systems biology, classifier diagnostic scoreProcedia PDF Downloads 77
182 Optical Coherence Tomography in Parkinson’s Disease: A Potential in-vivo Retinal α-Synuclein Biomarker in Parkinson’s Disease
Authors: Jessica Chorostecki, Aashka Shah, Fen Bao, Ginny Bao, Edwin George, Navid Seraji-Bozorgzad, Veronica Gorden, Christina Caon, Elliot Frohman
Abstract:Background: Parkinson’s Disease (PD) is a neuro degenerative disorder associated with the loss of dopaminergic cells and the presence α-synuclein (AS) aggregation in of Lewy bodies. Both dopaminergic cells and AS are found in the retina. Optical coherence tomography (OCT) allows high-resolution in-vivo examination of retinal structure injury in neuro degenerative disorders including PD. Methods: We performed a cross-section OCT study in patients with definite PD and healthy controls (HC) using Spectral Domain SD-OCT platform to measure the peripapillary retinal nerve fiber layer (pRNFL) thickness and total macular volume (TMV). We performed intra-retinal segmentation with fully automated segmentation software to measure the volume of the RNFL, ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL), and the outer nuclear layer (ONL). Segmentation was performed blinded to the clinical status of the study participants. Results: 101 eyes from 52 PD patients (mean age 65.8 years) and 46 eyes from 24 HC subjects (mean age 64.1 years) were included in the study. The mean pRNFL thickness was not significantly different (96.95 μm vs 94.42 μm, p=0.07) but the TMV was significantly lower in PD compared to HC (8.33 mm3 vs 8.58 mm3 p=0.0002). Intra-retinal segmentation showed no significant difference in the RNFL volume between the PD and HC groups (0.95 mm3 vs 0.92 mm3 p=0.454). However, GCL, IPL, INL, and ONL volumes were significantly reduced in PD compared to HC. In contrast, the volume of OPL was significantly increased in PD compared to HC. Conclusions: Our finding of the enlarged OPL corresponds with mRNA expression studies showing localization of AS in the OPL across vertebrate species and autopsy studies demonstrating AS aggregation in the deeper layers of retina in PD. We propose that the enlargement of the OPL may represent a potential biomarker of AS aggregation in PD. Longitudinal studies in larger cohorts are warranted to confirm our observations that may have significant implications in disease monitoring and therapeutic development.
Keywords: Optical Coherence Tomography, biomarker, Parkinson's disease, alpha-synuclein, retinaProcedia PDF Downloads 359
181 Update on Epithelial Ovarian Cancer (EOC), Types, Origin, Molecular Pathogenesis, and Biomarkers
Authors: Salina Yahya Saddick
Abstract:Ovarian cancer remains the most lethal gynecological malignancy due to the lack of highly sensitive and specific screening tools for detection of early-stage disease. The OSE provides the progenitor cells for 90% of human ovarian cancers. Recent morphologic, immunohistochemical and molecular genetic studies have led to the development of a new paradigm for the pathogenesis and origin of epithelial ovarian cancer (EOC) based on a ualistic model of carcinogenesis that divides EOC into two broad categories designated Types I and II which are characterized by specific mutations, including KRAS, BRAF, ERBB2, CTNNB1, PTEN PIK3CA, ARID1A, and PPPR1A, which target specific cell signaling pathways. Type 1 tumors rarely harbor TP53. type I tumors are relatively genetically stable and typically display a variety of somatic sequence mutations that include KRAS, BRAF, PTEN, PIK3CA CTNNB1 (the gene encoding beta catenin), ARID1A and PPP2R1A but very rarely TP53 . The cancer stem cell (CSC) hypothesis postulates that the tumorigenic potential of CSCs is confined to a very small subset of tumor cells and is defined by their ability to self-renew and differentiate leading to the formation of a tumor mass. Potential protein biomarker miRNA, are promising biomarkers as they are remarkably stable to allow isolation and analysis from tissues and from blood in which they can be found as free circulating nucleic acids and in mononuclear cells. Recently, genomic anaylsis have identified biomarkers and potential therapeutic targets for ovarian cancer namely, FGF18 which plays an active role in controlling migration, invasion, and tumorigenicity of ovarian cancer cells through NF-κB activation, which increased the production of oncogenic cytokines and chemokines. This review summarizes update information on epithelial ovarian cancers and point out to the most recent ongoing research.
Keywords: epithelial ovarian cancers, somatic sequence mutations, cancer stem cell (CSC), potential protein, biomarker, genomic analysis, FGF18 biomarkerProcedia PDF Downloads 319
180 Potential Serological Biomarker for Early Detection of Pregnancy in Cows
Authors: Shveta Bathla, Preeti Rawat, Sudarshan Kumar, Rubina Baithalu, Jogender Singh Rana, Tushar Kumar Mohanty, Ashok Kumar Mohanty
Abstract:Pregnancy is a complex process which includes series of events such as fertilization, formation of blastocyst, implantation of embryo, placental formation and development of fetus. The success of these events depends on various interactions which are synchronized by endocrine interaction between a receptive dam and competent embryo. These interactions lead to change in expression of hormones and proteins. But till date no protein biomarker is available which can be used to detect successful completion of these events. We employed quantitative proteomics approach to develop putative serological biomarker which has diagnostic applicability for early detection of pregnancy in cows. For this study, sera were collected from control (non-pregnant, n=6) and pregnant animals on successive days of pregnancy (7, 19, 45, n=6). The sera were subjected to depletion for removal of albumin using Norgen depletion kit. The tryptic peptides were labeled with iTRAQ. The peptides were pooled and fractionated using bRPLC over 80 min gradient. Then 12 fractions were injected to nLC for identification and quantitation in DDA mode using ESI. Identification using Mascot search revealed 2056 proteins out of which 352 proteins were differentially expressed. Twenty proteins were upregulated and twelve proteins were down-regulated with fold change > 1.5 and < 0.6 respectively (p < 0.05). The gene ontology studies of DEPs using Panther software revealed that majority of proteins are actively involved in catalytic activities, binding and enzyme regulatory activities. The DEP'S such as NF2, MAPK, GRIPI, UGT1A1, PARP, CD68 were further subjected to pathway analysis using KEGG and Cytoscape plugin Cluego that showed involvement of proteins in successful implantation, maintenance of pluripotency, regulation of luteal function, differentiation of endometrial macrophages, protection from oxidative stress and developmental pathways such as Hippo. Further efforts are continuing for targeted proteomics, western blot to validate potential biomarkers and development of diagnostic kit for early pregnancy diagnosis in cows.
Keywords: bRPLC, Cluego, ESI, iTRAQ, KEGG, PantherProcedia PDF Downloads 402
179 Comparison of Quality Indices for Sediment Assessment in Ireland
Authors: Tayyaba Bibi, Jenny Ronan, Robert Hernan, Kathleen O’Rourke, Brendan McHugh, Evin McGovern, Michelle Giltrap, Gordon Chambers, James Wilson
Abstract:Sediment contamination is a major source of ecosystem stress and has received significant attention from the scientific community. Both the Water Framework Directive (WFD) and Marine Strategy Framework Directive (MSFD) require a robust set of tools for biological and chemical monitoring. For the MSFD in particular, causal links between contaminant and effects need to be assessed. Appropriate assessment tools are required in order to make an accurate evaluation. In this study, a range of recommended sediment bioassays and chemical measurements are assessed in a number of potentially impacted and lowly impacted locations around Ireland. Previously, assessment indices have been developed on individual compartments, i.e. contaminant levels or biomarker/bioassay responses. A number of assessment indices are applied to chemical and ecotoxicological data from the Seachange project (Project code) and compared including the metal pollution index (MPI), pollution load index (PLI) and Chapman index for chemistry as well as integrated biomarker response (IBR). The benefits and drawbacks of the use of indices and aggregation techniques are discussed. In addition to this, modelling of raw data is investigated to analyse links between contaminant and effects.
Keywords: bioassays, contamination indices, ecotoxicity, marine environment, sedimentsProcedia PDF Downloads 163