ProteomicsDB.

Science.gov (United States)

Schmidt, Tobias; Samaras, Patroklos; Frejno, Martin; Gessulat, Siegfried; Barnert, Maximilian; Kienegger, Harald; Krcmar, Helmut; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias

2018-01-04

ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines. We recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e.g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of 10 Candidate Biomarkers Distinguishing Tuberculous and Malignant Pleural Fluid by Proteomic Methods

OpenAIRE

Lee, Chang Youl; Hong, Ji Young; Lee, Myung-Goo; Suh, In-Bum

2017-01-01

Purpose Pleural effusion, an accumulation of fluid in the pleural space, usually occurs in patients when the rate of fluid formation exceeds the rate of fluid removal. The differential diagnosis of tuberculous pleurisy and malignant pleural effusion is a difficult task in high tuberculous prevalence areas. The aim of the present study was to identify novel biomarkers for the diagnosis of pleural fluid using proteomics technology. Materials and Methods We used samples from five patients with t...

Proteomic analysis of chinook salmon (Oncorhynchus tshawytscha ovarian fluid.

Directory of Open Access Journals (Sweden)

Sheri L Johnson

Full Text Available The ovarian, or coelomic, fluid that is released with the egg mass of many fishes is increasingly found to play an important role in several biological processes crucial for reproductive success. These include maintenance of oocyte fertility and developmental competence, prolonging of sperm motility, and enhancing sperm swimming speed. Here we examined if and how the proteome of chinook salmon (Oncorhynchus tshawytscha ovarian fluid varied among females and then sought to examine the composition of this fluid. Ovarian fluid in chinook salmon was analyzed using 1D SDS PAGE and LC-MS/MS tryptic digest screened against Mascot and Sequest databases. We found marked differences in the number and concentrations of proteins in salmon ovarian fluid across different females. A total of 174 proteins were identified in ovarian fluid, 47 of which were represented by six or more peptides, belonging to one of six Gene Ontology pathways. The response to chemical stimulus and response to hypoxia pathways were best represented, accounting for 26 of the 174 proteins. The current data set provides a resource that furthers our understanding of those factors that influence successful egg production and fertilisation in salmonids and other species.

Comprehensive proteomic analysis of human pancreatic juice

DEFF Research Database (Denmark)

Grønborg, Mads; Bunkenborg, Jakob; Kristiansen, Troels Zakarias

2004-01-01

Proteomic technologies provide an excellent means for analysis of body fluids for cataloging protein constituents and identifying biomarkers for early detection of cancers. The biomarkers currently available for pancreatic cancer, such as CA19-9, lack adequate sensitivity and specificity...... contributing to late diagnosis of this deadly disease. In this study, we carried out a comprehensive characterization of the "pancreatic juice proteome" in patients with pancreatic adenocarcinoma. Pancreatic juice was first fractionated by 1-dimensional gel electrophoresis and subsequently analyzed by liquid...... in this study could be directly assessed for their potential as biomarkers for pancreatic cancer by quantitative proteomics methods or immunoassays....

One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.

Science.gov (United States)

Megger, Dominik A; Padden, Juliet; Rosowski, Kristin; Uszkoreit, Julian; Bracht, Thilo; Eisenacher, Martin; Gerges, Christian; Neuhaus, Horst; Schumacher, Brigitte; Schlaak, Jörg F; Sitek, Barbara

2017-02-10

The proteome analysis of bile fluid represents a promising strategy to identify biomarker candidates for various diseases of the hepatobiliary system. However, to obtain substantive results in biomarker discovery studies large patient cohorts necessarily need to be analyzed. Consequently, this would lead to an unmanageable number of samples to be analyzed if sample preparation protocols with extensive fractionation methods are applied. Hence, the performance of simple workflows allowing for "one sample, one shot" experiments have been evaluated in this study. In detail, sixteen different protocols implying modifications at the stages of desalting, delipidation, deglycosylation and tryptic digestion have been examined. Each method has been individually evaluated regarding various performance criteria and comparative analyses have been conducted to uncover possible complementarities. Here, the best performance in terms of proteome coverage has been assessed for a combination of acetone precipitation with in-gel digestion. Finally, a mapping of all obtained protein identifications with putative biomarkers for hepatocellular carcinoma (HCC) and cholangiocellular carcinoma (CCC) revealed several proteins easily detectable in bile fluid. These results can build the basis for future studies with large and well-defined patient cohorts in a more disease-related context. Human bile fluid is a proximal body fluid and supposed to be a potential source of disease markers. However, due to its biochemical composition, the proteome analysis of bile fluid still represents a challenging task and is therefore mostly conducted using extensive fractionation procedures. This in turn leads to a high number of mass spectrometric measurements for one biological sample. Considering the fact that in order to overcome the biological variability a high number of biological samples needs to be analyzed in biomarker discovery studies, this leads to the dilemma of an unmanageable number of

Decoding the Proteome of In-Vitro Fertilization Ovarian Follicular Fluid for Women Over 35 Years

Directory of Open Access Journals (Sweden)

Mohamed Sabry

2014-12-01

Full Text Available Aim: The study of follicular fluid using proteomic techniques could provide a useful tool for understanding follicular fluid components and their effect on pregnancy outcome. The aim of the study is to identify and catalog follicular fluid proteins in women 35 years of age or older. Material and Method: Follicular fluid was collected from 21 couples, of which 11 couples achieved successful pregnancy and 10 couples failed to get pregnant. Samples were analyzed by multidimensional chromatography coupled with in-line nano-spray ionization mass spectrometry on an LTQ XL ion trap mass spectrometer. We used the Biomarker Analysis Program from PDQuest software to identify protein constituents in pregnant and non-pregnant groups. Results: In total, 1024 protein specimens were identified. The proteins identified were consistent throughout the experiment and within each of the analyzed specimens. Discussion: A compiled listing of follicular fluid proteins could be a potential starting point for the identification and evaluation of important proteins involved in the development of oocytes; the results of our study may fill a noticeable knowledge-gap in the understanding of follicular fluid proteome.

Comparative proteomic analysis of human malignant ascitic fluids for the development of gastric cancer biomarkers.

Science.gov (United States)

Jin, Jonghwa; Son, Minsoo; Kim, Hyeyoon; Kim, Hyeyeon; Kong, Seong-Ho; Kim, Hark Kyun; Kim, Youngsoo; Han, Dohyun

2018-04-11

Malignant ascites is a sign of peritoneal seeding, which is one of the most frequent forms of incurable distant metastasis. Because the development of malignant ascites is associated with an extremely poor prognosis, determining whether it resulted from peritoneal seeding has critical clinical implications in diagnosis, choice of treatment, and active surveillance. At present, the molecular characterizations of malignant ascites are especially limited in case of gastric cancer. We aimed to identify malignant ascites-specific proteins that may contribute to the development of alternative methods for diagnosis and therapeutic monitoring and also increase our understanding of the pathophysiology of peritoneal seeding. First, comprehensive proteomic strategies were employed to construct an in-depth proteome of ascitic fluids. Label-free quantitative proteomic analysis was subsequently performed to identify candidates that can differentiate between malignant ascitic fluilds of gastric cancer patients from benign ascitic fluids. Finally, two candidate proteins were verified by ELISA in 84 samples with gastric cancer or liver cirrhosis. Comprehensive proteome profiling resulted in the identification of 5347 ascites proteins. Using label-free quantification, we identified 299 proteins that were differentially expressed in ascitic fluids between liver cirrhosis and stage IV gastric cancer patients. In addition, we identified 645 proteins that were significantly expressed in ascitic fluids between liver cirrhosis and gastric cancer patients with peritoneal seeding. Finally, Gastriscin and Periostin that can distinguish malignant ascites from benign ascites were verified by ELISA. This study identified and verified protein markers that can distinguish malignant ascites with or without peritoneal seeding from benign ascites. Consequently, our results could be a significant resource for gastric cancer research and biomarker discovery in the diagnosis of malignant ascites

Identification of azurocidin as a potential periodontitis biomarker by a proteomic analysis of gingival crevicular fluid

Directory of Open Access Journals (Sweden)

Lee Jae-Mok

2011-07-01

Full Text Available Abstract Background The inflammatory disease periodontitis results in tooth loss and can even lead to diseases of the whole body if not treated. Gingival crevicular fluid (GCF reflects the condition of the gingiva and contains proteins transuded from serum or cells at inflamed sites. In this study, we aimed to discover potential protein biomarkers for periodontitis in GCF proteome using LC-MS/MS. Results We identified 305 proteins from GCF of healthy individuals and periodontitis patients collected using a sterile gel loading tip by ESI-MS/MS coupled to nano-LC. Among these proteins, about 45 proteins were differentially expressed in the GCF proteome of moderate periodontitis patients when compared to the healthy individuals. We first identified azurocidin in the GCF, but not the saliva, as an upregulated protein in the periodontitis patients and verified its increased expression during periodontitis by ELISA using the GCF of the classified periodontitis patients compared to the healthy individuals. In addition, we found that azurocidin inhibited the differentiation of bone marrow-derived macrophages to osteoclasts. Conclusions Our results show that GCF collection using a gel loading tip and subsequent LC-MS/MS analysis following 1D-PAGE proteomic separation are effective for the analysis of the GCF proteome. Our current results also suggest that azurocidin could be a potential biomarker candidate for the early detection of inflammatory periodontal destruction by gingivitis and some chronic periodontitis. Our data also suggest that azurocidin may have an inhibitory role in osteoclast differentiation and, thus, a protective role in alveolar bone loss during the early stages of periodontitis.

Proteomic Assessment of Fluid Shifts and Association with Visual Impairment and Intracranial Pressure in Twin Astronauts

Science.gov (United States)

Rana, Brinda K.; Stenger, Michael B.; Lee, Stuart M. C.; Macias, Brandon R.; Siamwala, Jamila; Piening, Brian Donald; Hook, Vivian; Ebert, Doug; Patel, Hemal; Smith, Scott;

309 proteomic analysis of the blastocoel fluid and remaining cells of bovine blastocysts

DEFF Research Database (Denmark)

Jensen, P L; Groendahl, M L; Beck, Helle

2012-01-01

Human embryonic stem cells (hESC) are derived from the human blastocyst and possess the potential to differentiate into any cell type present in the adult human body. Human ESC are considered to have great potential in regenerative medicine for the future treatment of severe diseases and conditions...... such as Parkinson's disease, diabetes, and spinal cord injury. One of today's challenges in regenerative medicine is to define proper culture conditions for hESC. The natural milieu in the blastocyst may provide clues on how to improve culture conditions, and the aim of the present study was to determine...... the proteome of the blastocoel fluid and the remaining cells of bovine blastocysts. Bovine blastocysts were produced by in vitro fertilization of oocytes retrieved from slaughterhouse ovaries. The blastocoel from 195 blastocysts (1-8nL per blastocyst) were isolated by micromanipulation and analysed by nano...

Proteomic Analysis of Early Mid-Trimester Amniotic Fluid Does Not Predict Spontaneous Preterm Delivery

Science.gov (United States)

Lenco, Juraj; Vajrychova, Marie; Link, Marek; Tambor, Vojtech; Liman, Victor; Bullarbo, Maria; Nilsson, Staffan; Tsiartas, Panagiotis; Cobo, Teresa; Kacerovsky, Marian; Jacobsson, Bo

2016-01-01

Objective The aim of this study was to identify early proteomic biomarkers of spontaneous preterm delivery (PTD) in mid-trimester amniotic fluid from asymptomatic women. Methods This is a case-cohort study. Amniotic fluid from mid-trimester genetic amniocentesis (14–19 weeks of gestation) was collected from 2008 to 2011. The analysis was conducted in 24 healthy women with subsequent spontaneous PTD (cases) and 40 randomly selected healthy women delivering at term (controls). An exploratory phase with proteomics analysis of pooled samples was followed by a verification phase with ELISA of individual case and control samples. Results The median (interquartile range (IQR: 25th; 75th percentiles) gestational age at delivery was 35+5 (33+6–36+6) weeks in women with spontaneous PTD and 40+0 (39+1–40+5) weeks in women who delivered at term. In the exploratory phase, the most pronounced differences were found in C-reactive protein (CRP) levels, that were approximately two-fold higher in the pooled case samples than in the pooled control samples. However, we could not verify these differences with ELISA. The median (25th; 75th IQR) CRP level was 95.2 ng/mL (64.3; 163.5) in women with spontaneous PTD and 86.0 ng/mL (51.2; 145.8) in women delivering at term (p = 0.37; t-test). Conclusions Proteomic analysis with mass spectrometry of mid-trimester amniotic fluid suggests CRP as a potential marker of spontaneous preterm delivery, but this prognostic potential was not verified with ELISA. PMID:27214132

Establishing the proteome of normal human cerebrospinal fluid.

Directory of Open Access Journals (Sweden)

Steven E Schutzer

2010-06-01

Full Text Available Knowledge of the entire protein content, the proteome, of normal human cerebrospinal fluid (CSF would enable insights into neurologic and psychiatric disorders. Until now technologic hurdles and access to true normal samples hindered attaining this goal.We applied immunoaffinity separation and high sensitivity and resolution liquid chromatography-mass spectrometry to examine CSF from healthy normal individuals. 2630 proteins in CSF from normal subjects were identified, of which 56% were CSF-specific, not found in the much larger set of 3654 proteins we have identified in plasma. We also examined CSF from groups of subjects previously examined by others as surrogates for normals where neurologic symptoms warranted a lumbar puncture but where clinical laboratory were reported as normal. We found statistically significant differences between their CSF proteins and our non-neurological normals. We also examined CSF from 10 volunteer subjects who had lumbar punctures at least 4 weeks apart and found that there was little variability in CSF proteins in an individual as compared to subject to subject.Our results represent the most comprehensive characterization of true normal CSF to date. This normal CSF proteome establishes a comparative standard and basis for investigations into a variety of diseases with neurological and psychiatric features.

Combining RNA-seq and proteomic profiling to identify seminal fluid proteins in the migratory grasshopper Melanoplus sanguinipes (F).

Science.gov (United States)

Bonilla, Martha L; Todd, Christopher; Erlandson, Martin; Andres, Jose

2015-12-22

Seminal fluid proteins control many aspects of fertilization and in turn, they play a key role in post-mating sexual selection and possibly reproductive isolation. Because effective proteome profiling relies on the availability of high-quality DNA reference databases, our knowledge of these proteins is still largely limited to model organisms with ample genetic resources. New advances in sequencing technology allow for the rapid characterization of transcriptomes at low cost. By combining high throughput RNA-seq and shotgun proteomic profiling, we have characterized the seminal fluid proteins secreted by the primary male accessory gland of the migratory grasshopper (Melanoplus sanguinipes), one of the main agricultural pests in central North America. Using RNA sequencing, we characterized the transcripts of ~ 8,100 genes expressed in the long hyaline tubules (LHT) of the accessory glands. Proteomic profiling identified 353 proteins expressed in the long hyaline tubules (LHT). Of special interest are seminal fluid proteins (SFPs), such as EJAC-SP, ACE and prostaglandin synthetases, which are known to regulate female oviposition in insects. Our study provides new insights into the proteomic components of male ejaculate in Orthopterans, and highlights several important patterns. First, the presence of proteins that lack predicted classical secretory tags in accessory gland proteomes is common in male accessory glands. Second, the products of a few highly expressed genes dominate the accessory gland secretions. Third, accessory gland transcriptomes are enriched for novel transcripts. Fourth, there is conservation of SFPs' functional classes across distantly related taxonomic groups with very different life histories, mating systems and sperm transferring mechanisms. The identified SFPs may serve as targets of future efforts to develop species- specific genetic control strategies.

The Escherichia coli O157:H7 bovine rumen fluid proteome reflects adaptive bacterial responses

OpenAIRE

Kudva, Indira T; Stanton, Thaddeus B; Lippolis, John D

2014-01-01

Background To obtain insights into Escherichia coli O157:H7 (O157) survival mechanisms in the bovine rumen, we defined the growth characteristics and proteome of O157 cultured in rumen fluid (RF; pH 6.0-7.2 and low volatile fatty acid content) obtained from rumen-fistulated cattle fed low protein content “maintenance diet” under diverse in vitro conditions. Results Bottom-up proteomics (LC-MS/MS) of whole cell-lysates of O157 cultured under anaerobic conditions in filter-sterilized RF (fRF; d...

Altered Proteomic Polymorphisms in the Caterpillar Body and Stroma of Natural Cordyceps sinensis during Maturation

Science.gov (United States)

Wu, Zi-Mei; Gao, Ling; Yao, Yi-Sang; Tan, Ning-Zhi; Wu, Jian-Yong; Ni, Luqun; Zhu, Jia-Shi

2014-01-01

Objective To examine the maturational changes in proteomic polymorphisms resulting from differential expression by multiple intrinsic fungi in the caterpillar body and stroma of natural Cordyceps sinensis (Cs), an integrated micro-ecosystem. Methods The surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) biochip technique was used to profile the altered protein compositions in the caterpillar body and stroma of Cs during its maturation. The MS chromatograms were analyzed using density-weighted algorithms to examine the similarities and cluster relationships among the proteomic polymorphisms of the Cs compartments and the mycelial products Hirsutella sinensis (Hs) and Paecilomyces hepiali (Ph). Results: SELDI-TOF MS chromatograms displayed dynamic proteomic polymorphism alterations among samples from the different Cs compartments during maturation. More than 1,900 protein bands were analyzed using density-weighted ZUNIX similarity equations and clustering methods, revealing integral polymorphism similarities of 57.4% between the premature and mature stromata and 42.8% between the premature and mature caterpillar bodies. The across-compartment similarity was low, ranging from 10.0% to 18.4%. Consequently, each Cs compartment (i.e., the stroma and caterpillar body) formed a clustering clade, and the 2 clades formed a Cs cluster. The polymorphic similarities ranged from 0.51% to 1.04% between Hs and the Cs compartments and were 2.8- to 4.8-fold higher (1.92%–4.34%) between Ph and the Cs compartments. The Hs and Ph mycelial samples formed isolated clades outside of the Cs cluster. Conclusion Proteomic polymorphisms in the caterpillar body and stroma of Cs change dynamically during maturation. The proteomic polymorphisms in Hs and Ph differ from those in Cs, suggesting the presence of multiple Cs-associated fungi and multiple Ophiocordyceps sinensis genotypes with altered differential protein expression in the Cs compartments

Non-invasively collected amniotic fluid as a source of possible biomarkers for premature rupture of membranes investigated by proteomic approach.

Science.gov (United States)

Consonni, Sara; Mainini, Veronica; Pizzardi, Agnese; Gianazza, Erica; Chinello, Clizia; Locatelli, Anna; Magni, Fulvio

2014-02-01

Preterm delivery is one of the main causes of perinatal morbidity and mortality and it accounts for 75 % of perinatal mortality and more than half of the long-term morbidity. We applied a proteomic approach based on mass spectrometry (MS) for biomarkers discovery of preterm premature rupture of membranes (pPROM) by investigating amniotic fluid (AF) invasively and non-invasively collected. Amniotic fluid was obtained from vagina of women with pPROM (group 1), PROM at term (group 2) and by genetic amniocentesis (group 3). Pre-fractionated AF proteome was analyzed through matrix assisted laser desorption ionization-time of flight (MALDI-TOF) MS. The characterization of proteins/peptides of interest was obtained by high performance liquid chromatography-electrospray tandem MS. Three peptides overexpressed in pPROM and able to discriminate the groups 1 and 2 were detected. One peptide was identified as the fragment Gly452LAVPDGPLGLPPKPro466 of the protein KIAA1522, expressed by fetal brain and liver. This peptide was overexpressed in a patient of the group 3, completely asymptomatic at the time of the amniocentesis, who later developed pPROM. Amniotic fluid invasively and non-invasively collected can be analyzed by MALDI-TOF MS to obtain proteomic profiles. Proteomic analysis identified a peptide with promising diagnostic capability for pPROM.

Neural Control Mechanisms and Body Fluid Homeostasis

Science.gov (United States)

Johnson, Alan Kim

1998-01-01

The goal of the proposed research was to study the nature of afferent signals to the brain that reflect the status of body fluid balance and to investigate the central neural mechanisms that process this information for the activation of response systems which restore body fluid homeostasis. That is, in the face of loss of fluids from intracellular or extracellular fluid compartments, animals seek and ingest water and ionic solutions (particularly Na(+) solutions) to restore the intracellular and extracellular spaces. Over recent years, our laboratory has generated a substantial body of information indicating that: (1) a fall in systemic arterial pressure facilitates the ingestion of rehydrating solutions and (2) that the actions of brain amine systems (e.g., norepinephrine; serotonin) are critical for precise correction of fluid losses. Because both acute and chronic dehydration are associated with physiological stresses, such as exercise and sustained exposure to microgravity, the present research will aid in achieving a better understanding of how vital information is handled by the nervous system for maintenance of the body's fluid matrix which is critical for health and well-being.

Data for a comprehensive map and functional annotation of the human cerebrospinal fluid proteome

Directory of Open Access Journals (Sweden)

Yang Zhang

2015-06-01

Full Text Available Knowledge about the normal human cerebrospinal fluid (CSF proteome serves as a baseline reference for CSF biomarker discovery and provides insight into CSF physiology. In this study, high-pH reverse-phase liquid chromatography (hp-RPLC was first integrated with a TripleTOF 5600 mass spectrometer to comprehensively profile the normal CSF proteome. A total of 49,836 unique peptides and 3256 non-redundant proteins were identified. To obtain high-confidence results, 2513 proteins with at least 2 unique peptides were further selected as bona fide CSF proteins. Nearly 30% of the identified CSF proteins have not been previously reported in the normal CSF proteome. More than 25% of the CSF proteins were components of CNS cell microenvironments, and network analyses indicated their roles in the pathogenesis of neurological diseases. The top canonical pathway in which the CSF proteins participated was axon guidance signaling. More than one-third of the CSF proteins (788 proteins were related to neurological diseases, and these proteins constitute potential CSF biomarker candidates. The mapping results can be freely downloaded at http://122.70.220.102:8088/csf/, which can be used to navigate the CSF proteome. For more information about the data, please refer to the related original article [1], which has been recently accepted by Journal of Proteomics.

Advances of Proteomic Sciences in Dentistry.

Science.gov (United States)

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-05-13

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

Quantification of interstitial fluid on whole body CT: comparison with whole body autopsy.

Science.gov (United States)

Lo Gullo, Roberto; Mishra, Shelly; Lira, Diego A; Padole, Atul; Otrakji, Alexi; Khawaja, Ranish Deedar Ali; Pourjabbar, Sarvenaz; Singh, Sarabjeet; Shepard, Jo-Anne O; Digumarthy, Subba R; Kalra, Mannudeep K; Stone, James R

2015-12-01

Interstitial fluid accumulation can occur in pleural, pericardial, and peritoneal spaces, and subcutaneous tissue planes. The purpose of the study was to assess if whole body CT examination in a postmortem setting could help determine the presence and severity of third space fluid accumulation in the body. Our study included 41 human cadavers (mean age 61 years, 25 males and 16 females) who had whole-body postmortem CT prior to autopsy. All bodies were maintained in the morgue in the time interval between death and autopsy. Two radiologists reviewed the whole-body CT examinations independently to grade third space fluid in the pleura, pericardium, peritoneum, and subcutaneous space using a 5-point grading system. Qualitative CT grading for third space fluid was correlated with the amount of fluid found on autopsy and the quantitative CT fluid volume, estimated using a dedicated software program (Volume, Syngo Explorer, Siemens Healthcare). Moderate and severe peripheral edema was seen in 16/41 and 7/41 cadavers respectively. It is not possible to quantify anasarca at autopsy. Correlation between imaging data for third space fluid and the quantity of fluid found during autopsy was 0.83 for pleural effusion, 0.4 for pericardial effusion and 0.9 for ascites. The degree of anasarca was significantly correlated with the severity of ascites (p < 0.0001) but not with pleural or pericardial effusion. There was strong correlation between volumetric estimation and qualitative grading for anasarca (p < 0.0001) and pleural effusion (p < 0.0001). Postmortem CT can help in accurate detection and quantification of third space fluid accumulation. The quantity of ascitic fluid on postmortem CT can predict the extent of anasarca.

Steroid hormones content and proteomic analysis of canine follicular fluid during the preovulatory period

Directory of Open Access Journals (Sweden)

Reynaud Karine

2010-11-01

Full Text Available Abstract Background Follicular fluid contains substances involved in follicle activity, cell differentiation and oocyte maturation. Studies of its components may contribute to better understanding of the mechanisms underlying follicular development and oocyte quality. The canine species is characterized by several ovarian activity features that are not extensively described such as preovulatory luteinization, oocyte ovulated at the GV stage (prophase 1 and poly-oocytic follicles. In this study, we examined the hypothesis that the preovulatory LH surge is associated with changes in steroid and protein content of canine follicular fluid prior to ovulation. Methods Follicular fluid samples were collected from canine ovaries during the preovulatory phase, before (pre-LH; n = 16 bitches and after (post-LH; n = 16 the LH surge. Blood was simultaneously collected. Steroids were assayed by radioimmunoassay and proteomic analyses were carried out by 2D-PAGE and mass spectrometry. Results The concentrations of 17beta-estradiol and progesterone at the pre-LH stage were 737.2 +/- 43.5 ng/ml and 2630.1 +/- 287.2 ng/ml in follicular fluid vs. 53 +/- 4.1 pg/ml and 3.9 +/- 0.3 ng/ml in plasma, respectively. At that stage, significant positive correlations between follicular size and intra-follicular steroid concentrations were recorded. After the LH peak, the intrafollicular concentration of 17beta-estradiol decreased significantly (48.3 +/- 4.4 ng/ml; p Proteomic analysis of canine follicular fluid identified 38 protein spots, corresponding to 21 proteins, some of which are known to play roles in the ovarian physiology. The comparison of 2D-PAGE patterns of follicular fluids from the pre- and post-LH stages demonstrated 3 differentially stained single spot or groups of spots. One of them was identified as complement factor B. A comparison of follicular fluid and plasma protein patterns demonstrated a group of 4 spots that were more concentrated in plasma than

Comparative proteomics of cerebrospinal fluid reveals a predictive model for differential diagnosis of pneumococcal, meningococcal, and enteroviral meningitis, and novel putative therapeutic targets

Science.gov (United States)

2015-01-01

Background Meningitis is the inflammation of the meninges in response to infection or chemical agents. While aseptic meningitis, most frequently caused by enteroviruses, is usually benign with a self-limiting course, bacterial meningitis remains associated with high morbidity and mortality rates, despite advances in antimicrobial therapy and intensive care. Fast and accurate differential diagnosis is crucial for assertive choice of the appropriate therapeutic approach for each form of meningitis. Methods We used 2D-PAGE and mass spectrometry to identify the cerebrospinal fluid proteome specifically related to the host response to pneumococcal, meningococcal, and enteroviral meningitis. The disease-specific proteome signatures were inspected by pathway analysis. Results Unique cerebrospinal fluid proteome signatures were found to the three aetiological forms of meningitis investigated, and a qualitative predictive model with four protein markers was developed for the differential diagnosis of these diseases. Nevertheless, pathway analysis of the disease-specific proteomes unveiled that Kallikrein-kinin system may play a crucial role in the pathophysiological mechanisms leading to brain damage in bacterial meningitis. Proteins taking part in this cellular process are proposed as putative targets to novel adjunctive therapies. Conclusions Comparative proteomics of cerebrospinal fluid disclosed candidate biomarkers, which were combined in a qualitative and sequential predictive model with potential to improve the differential diagnosis of pneumococcal, meningococcal and enteroviral meningitis. Moreover, we present the first evidence of the possible implication of Kallikrein-kinin system in the pathophysiology of bacterial meningitis. PMID:26040285

Role of proteomics in the discovery of autism biomarkers

Energy Technology Data Exchange (ETDEWEB)

Ayadhi, L. A.; Halepoto, D. M. [King Saud Univ., Riyadh (Saudi Arabia). Dept. of Physiology

2013-02-15

The epidemiology of autism is continuously increasing all over the world with social, behavioural and economical burdens. Autism is considered as a multi-factorial disorder, influenced by genetic, neurological, environmental and immunological aspects. Autism is still believed to be incurable disorder with little information about the role of proteins patterns in the diagnosis of the disease. Knowing the applications of proteomic tools, it is possible to identify quantitative and qualitative protein patterns in a wide variety of tissues and body fluids such as blood, urine, saliva and cerebrospinal fluid in order to establish specific diagnostic and prognostic biomarkers. The aim of this review is to provide an overview of the various protocols available for proteomics by using mass spectrometry analysis, discuss reports in which these techniques have been previously applied in biomarker discovery for the diagnosis of autism, and consider the future development of this area of research. (author)

Role of proteomics in the discovery of autism biomarkers

International Nuclear Information System (INIS)

Ayadhi, L.A.; Halepoto, D.M.

2013-01-01

The epidemiology of autism is continuously increasing all over the world with social, behavioural and economical burdens. Autism is considered as a multi-factorial disorder, influenced by genetic, neurological, environmental and immunological aspects. Autism is still believed to be incurable disorder with little information about the role of proteins patterns in the diagnosis of the disease. Knowing the applications of proteomic tools, it is possible to identify quantitative and qualitative protein patterns in a wide variety of tissues and body fluids such as blood, urine, saliva and cerebrospinal fluid in order to establish specific diagnostic and prognostic biomarkers. The aim of this review is to provide an overview of the various protocols available for proteomics by using mass spectrometry analysis, discuss reports in which these techniques have been previously applied in biomarker discovery for the diagnosis of autism, and consider the future development of this area of research. (author)

Raman spectroscopic signature of vaginal fluid and its potential application in forensic body fluid identification.

Science.gov (United States)

Sikirzhytskaya, Aliaksandra; Sikirzhytski, Vitali; Lednev, Igor K

2012-03-10

Traces of human body fluids, such as blood, saliva, sweat, semen and vaginal fluid, play an increasingly important role in forensic investigations. However, a nondestructive, easy and rapid identification of body fluid traces at the scene of a crime has not yet been developed. The obstacles have recently been addressed in our studies, which demonstrated the considerable potential of Raman spectroscopy. In this study, we continued to build a full library of body fluid spectroscopic signatures. The problems concerning vaginal fluid stain identification were addressed using Raman spectroscopy coupled with advanced statistical analysis. Calculated characteristic Raman and fluorescent spectral components were used to build a multidimensional spectroscopic signature of vaginal fluid, which demonstrated good specificity and was able to handle heterogeneous samples from different donors. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Gravitational equilibrium of a multi-body fluid system

International Nuclear Information System (INIS)

Eriguchi, Yoshiharu; Hachisu, Izumi.

1983-01-01

We have computed gravitational equilibrium sequences for systems consisting of N incompressible fluid bodies (N = 3, 4, 5). The component fluids are assumed congruent. The system seems to become a lobe-like shape for N = 3 case and a ring-like shape for N>=4 cases according as the fluid bodies come nearer to each other. For every sequence there is a critical equilibrium whose dimensionless angular momentum has the minimum value of the sequence. As the final outcome is nearly in equilibrium in the computation of a collapsing gas cloud, we can apply the present results to the interpretation of these dynamical calculations. For instance, the gas cloud can never fissure into any N-body equilibrium when its dimensionless angular momentum is below the critical value of the N-body sequence. (author)

Lunar Fluid Core and Solid-Body Tides

Science.gov (United States)

Williams, J. G.; Boggs, D. H.; Ratcliff, J. T.

2005-01-01

Variations in rotation and orientation of the Moon are sensitive to solid-body tidal dissipation, dissipation due to relative motion at the fluid-core/solid-mantle boundary, and tidal Love number k2 [1,2]. There is weaker sensitivity to flattening of the core-mantle boundary (CMB) [2-5] and fluid core moment of inertia [1]. Accurate Lunar Laser Ranging (LLR) measurements of the distance from observatories on the Earth to four retroreflector arrays on the Moon are sensitive to lunar rotation and orientation variations and tidal displacements. Past solutions using the LLR data have given results for dissipation due to solid-body tides and fluid core [1] plus Love number [1-5]. Detection of CMB flattening has been improving [3,5] and now seems significant. This strengthens the case for a fluid lunar core.

Body fluid matrix evaluation on a Roche cobas 8000 system.

Science.gov (United States)

Owen, William E; Thatcher, Mindy L; Crabtree, Karolyn J; Greer, Ryan W; Strathmann, Frederick G; Straseski, Joely A; Genzen, Jonathan R

2015-09-01

Chemical analysis of body fluids is commonly requested by physicians. Because most commercial FDA-cleared clinical laboratory assays are not validated by diagnostic manufacturers for "non-serum" and "non-plasma" specimens, laboratories may need to complete additional validation studies to comply with regulatory requirements regarding body fluid testing. The objective of this report is to perform recovery studies to evaluate potential body fluid matrix interferences for commonly requested chemistry analytes. Using an IRB-approved protocol, previously collected clinical body fluid specimens (biliary/hepatic, cerebrospinal, dialysate, drain, pancreatic, pericardial, peritoneal, pleural, synovial, and vitreous) were de-identified and frozen (-20°C) until experiments were performed. Recovery studies (spiking with high concentration serum, control, and/or calibrator) were conducted using 10% spiking solution by volume; n=5 specimens per analyte/body fluid investigated. Specimens were tested on a Roche cobas 8000 system (c502, c702, e602, and ISE modules). In all 80 analyte/body fluid combinations investigated (including amylase, total bilirubin, urea nitrogen, carbohydrate antigen 19-9, carcinoembryonic antigen, cholesterol, chloride, creatinine, glucose, potassium, lactate dehydrogenase, lipase, rheumatoid factor, sodium, total protein, triglycerides, and uric acid), the average percent recovery was within predefined acceptable limits (less than ±10% from the calculated ideal recovery). The present study provides evidence against the presence of any systematic matrix interference in the analyte/body fluid combinations investigated on the Roche cobas 8000 system. Such findings support the utility of ongoing body fluid validation initiatives conducted to maintain compliance with regulatory requirements. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives.

Science.gov (United States)

Zhou, Li; Wang, Kui; Li, Qifu; Nice, Edouard C; Zhang, Haiyuan; Huang, Canhua

2016-01-01

Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.

Proteomic analysis of Taenia hydatigena cyst fluid reveals unique internal microenvironment.

Science.gov (United States)

Zheng, Yadong

2017-12-01

Taenia hydatigena is a parasitic flatworm that is widely distributed around the world. Using MS/MS, the proteome of T. hydatigena cyst fluid (CF) was profiled and a total of 520 proteins were identified, 430 of which were of sheep origin. T. hydatigena shared 37 parasite-origin and 109 host-origin CF proteins with Echinococcus granulosus. Compared with E. granulosus, T. hydatigena had much more CF proteins associated with amino acid synthesis and complement cascades. In addition, glutamate metabolism and anti-oxidative reactions were identified as relatively more important events. These results suggest that T. hydatigena metacestodes have internal microenvironment with special immune and oxidative conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

DNA Methylation as a Biomarker for Body Fluid Identification

Directory of Open Access Journals (Sweden)

Rania Gomaa

2017-12-01

Full Text Available Currently, available identification techniques for forensic samples are either enzyme or protein based, which can be subjected to degradation, thus limiting its storage potentials. Epigenetic changes arising due to DNA methylation and histone acetylation can be used for body fluid identification. Markers DACT1, USP49, ZC3H12D, FGF7, cg23521140, cg17610929, chromosome 4 (25287119–25287254, chromosome 11 (72085678–72085798, 57171095–57171236, 1493401–1493538, and chromosome 19 (47395505–47395651 are currently being used for semen identification. Markers cg26107890, cg20691722, cg01774894 and cg14991487 are used to differentiate saliva and vaginal secretions from other body fluids. However, such markers show overlapping methylation pattern. This review article aimed to highlight the feasibility of using DNA methylation of certain genetic markers in body fluid identification and its implications for forensic investigations. The reviewed articles have employed molecular genetics techniques such as Bisulfite sequencing PCR (BSP, methylation specific PCR (MSP, Pyrosequencing, Combined Bisulfite Restriction Analysis (COBRA, Methylation-sensitive Single Nucleotide Primer Extension (SNuPE, and Multiplex SNaPshot Microarray. Bioinformatics software such as MATLAB and BiQ Analyzer has been used. Biological fluids have different methylation patterns and thus, this difference can be used to identify the nature of the biological fluid found at the crime scene. Using DNA methylation to identify the body fluids gives accurate results without consumption of the trace evidence and requires a minute amount of DNA for analysis. Recent studies have incorporated next-generation sequencing aiming to find out more reliable markers that can differentiate between different body fluids. Nonetheless, new DNA methylation markers are yet to be discovered to accurately differentiate between saliva and vaginal secretions with high confidence. Epigenetic changes are

Many-Body Effects on the Thermodynamics of Fluids, Mixtures, and Nanoconfined Fluids.

Science.gov (United States)

Desgranges, Caroline; Delhommelle, Jerome

2015-11-10

Using expanded Wang-Landau simulations, we show that taking into account the many-body interactions results in sharp changes in the grand-canonical partition functions of single-component systems, binary mixtures, and nanoconfined fluids. The many-body contribution, modeled with a 3-body Axilrod-Teller-Muto term, results in shifts toward higher chemical potentials of the phase transitions from low-density phases to high-density phases and accounts for deviations of more than, e.g., 20% of the value of the partition function for a single-component liquid. Using the statistical mechanics formalism, we analyze how this contribution has a strong impact on some properties (e.g., pressure, coexisting densities, and enthalpy) and a moderate impact on others (e.g., Gibbs or Helmholtz free energies). We also characterize the effect of the 3-body terms on adsorption isotherms and adsorption thermodynamic properties, thereby providing a full picture of the effect of the 3-body contribution on the thermodynamics of nanoconfined fluids.

Body drop into a fluid tank and dynamic loads calculation

Directory of Open Access Journals (Sweden)

Komarov Aleksandr Andreevich

2014-05-01

Full Text Available The theory of a body striking a fluid began intensively developing due to the tasks of hydroplanes landing. For the recent years the study of a stroke and submersion of bodies into fluid became even more current. We face them in the process of strength calculation of ship hulls and other structures in modern technology. These tasks solution represents great mathematical difficulty even in case of the mentioned simplifications. These difficulties emerge due to the unsteady character of fluid motion in case of body submersion, and also jet and spray phenomena, which lead to discontinuous motions. On the basis of G.V. Logvinovich’s concept the problem of loads determination with consideration for air gap is solved for both a body and reservoir enclosing structures when a body falls into a fluid. Numerical method is based on the decay of an arbitrary discontinuity.

Proteomic analysis of human blastocoel fluid and blastocyst cells

DEFF Research Database (Denmark)

Jensen, Pernille; Beck, Hans Christian; Petersen, Jørgen

2013-01-01

Human embryonic stem cells (hESCs) are derived from the inner cell mass (ICM) of the blastocyst and can differentiate into any cell type in the human body. These cells hold a great potential for regenerative medicine, but to obtain enough cells needed for medical treatment, culture is required......, the blastocoel fluid, which is in contact with all the cells in the blastocyst, including hESCs. Fifty-three surplus human blastocysts were donated after informed consent, and blastocoel fluid was isolated by micromanipulation. Using highly sensitive nano-high-pressure liquid chromatography-tandem mass...... from the ICM of the human blastocyst are exposed to via the blastocoel fluid. These results can be an inspiration for the development of improved culture conditions for hESCs....

Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken.

Science.gov (United States)

Atikuzzaman, Mohammad; Sanz, Libia; Pla, Davinia; Alvarez-Rodriguez, Manuel; Rubér, Marie; Wright, Dominic; Calvete, Juan J; Rodriguez-Martinez, Heriberto

2017-03-01

The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n=4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds. The PCA clearly highlighted a clear intra-group similarity among individual roosters as well as a clear inter-group variability (e.g. between RJF, WL and AIL) validating the use of pools to minimize confounding individual variation. Protein expression varied considerably for processes related to sperm motility, nutrition, transport and survival in the female, including signaling towards immunomodulation. The major conserved SF-proteins were serum albumin and ovotransferrin. Aspartate aminotransferase, annexin A5, arginosuccinate synthase, glutathione S-transferase 2 and l-lactate dehydrogenase-A were RJF-specific. Glyceraldehyde-3-phosphate dehydrogenase appeared specific to the WL-SF while angiotensin-converting enzyme, γ-enolase, coagulation factor IX, fibrinogen α-chain, hemoglobin subunit α-D, lysozyme C, phosphoglycerate kinase, Src-substrate protein p85, tubulins and thioredoxin were AIL-specific. The RJF-SF contained fewer immune system process proteins and lower amounts of the anti-inflammatory/immunomodulatory TGF-β2 compared to WL and AIL, which had low levels- or lacked pro-inflammatory CXCL10 compared to RJF. The seminal

The Escherichia coli O157:H7 bovine rumen fluid proteome reflects adaptive bacterial responses.

Science.gov (United States)

Kudva, Indira T; Stanton, Thaddeus B; Lippolis, John D

2014-02-21

To obtain insights into Escherichia coli O157:H7 (O157) survival mechanisms in the bovine rumen, we defined the growth characteristics and proteome of O157 cultured in rumen fluid (RF; pH 6.0-7.2 and low volatile fatty acid content) obtained from rumen-fistulated cattle fed low protein content "maintenance diet" under diverse in vitro conditions. Bottom-up proteomics (LC-MS/MS) of whole cell-lysates of O157 cultured under anaerobic conditions in filter-sterilized RF (fRF; devoid of normal ruminal microbiota) and nutrient-depleted and filtered RF (dRF) resulted in an anaerobic O157 fRF-and dRF-proteome comprising 35 proteins functionally associated with cell structure, motility, transport, metabolism and regulation, but interestingly, not with O157 virulence. Shotgun proteomics-based analysis using isobaric tags for relative and absolute quantitation used to further study differential protein expression in unfiltered RF (uRF; RF containing normal rumen microbial flora) complemented these results. Our results indicate that in the rumen, the first anatomical compartment encountered by this human pathogen within the cattle gastrointestinal tract (GIT), O157 initiates a program of specific gene expression that enables it to adapt to the in vivo environment, and successfully transit to its colonization sites in the bovine GIT. Further experiments in vitro using uRF from animals fed different diets and with additional O157 strains, and in vivo using rumen-fistulated cattle will provide a comprehensive understanding of the adaptive mechanisms involved, and help direct evolution of novel modalities for blocking O157 infection of cattle.

Normotension, hypertension and body fluid regulation

DEFF Research Database (Denmark)

Bie, Peter; Evans, R G

2017-01-01

The fraction of hypertensive patients with essential hypertension (EH) is decreasing as the knowledge of mechanisms of secondary hypertension increases, but in most new cases of hypertension the pathophysiology remains unknown. Separate neurocentric and renocentric concepts of aetiology have...... activity are elevated in about 50% of cases; (iii) in EH as in normal conditions, mediators other than arterial blood pressure are the major determinants of renal sodium excretion; (iv) chronic hypertension is always associated with a shift in the pressure-natriuresis curve, but this may...... prevailed without much interaction. In this regard, several questions regarding the relationships between body fluid and blood pressure regulation are pertinent. Are all forms of EH associated with sympathetic overdrive or a shift in the pressure-natriuresis curve? Is body fluid homoeostasis normally driven...

The Motion Of A Deformable Body In - Bounded Fluid

International Nuclear Information System (INIS)

Galpert, A.R.; Miloh, T.

1998-01-01

The Hamiltonian formalism for the motion of a deformable body in an inviscid irrotational fluid is generalized for the case of the motion in a bounded fluid. We found that the presence of the boundaries in a liquid leads to the chaotization of the body's motion. The ('memory' effect connected with a free surface boundary condition is also accounted for

Prey handling using whole-body fluid dynamics in batoids.

Science.gov (United States)

Wilga, Cheryl D; Maia, Anabela; Nauwelaerts, Sandra; Lauder, George V

2012-02-01

Fluid flow generated by body movements is a foraging tactic that has been exploited by many benthic species. In this study, the kinematics and hydrodynamics of prey handling behavior in little skates, Leucoraja erinacea, and round stingrays, Urobatis halleri, are compared using kinematics and particle image velocimetry. Both species use the body to form a tent to constrain the prey with the pectoral fin edges pressed against the substrate. Stingrays then elevate the head, which increases the volume between the body and the substrate to generate suction, while maintaining pectoral fin contact with the substrate. Meanwhile, the tip of the rostrum is curled upwards to create an opening where fluid is drawn under the body, functionally analogous to suction-feeding fishes. Skates also rotate the rostrum upwards although with the open rostral sides and the smaller fin area weaker fluid flow is generated. However, skates also use a rostral strike behavior in which the rostrum is rapidly rotated downwards pushing fluid towards the substrate to potentially stun or uncover prey. Thus, both species use the anterior portion of the body to direct fluid flow to handle prey albeit in different ways, which may be explained by differences in morphology. Rostral stiffness and pectoral fin insertion onto the rostrum differ between skates and rays and this corresponds to behavioral differences in prey handling resulting in distinct fluid flow patterns. The flexible muscular rostrum and greater fin area of stingrays allow more extensive use of suction to handle prey while the stiff cartilaginous rostrum of skates lacking extensive fin insertion is used as a paddle to strike prey as well as to clear away sand cover. Copyright © 2011 Elsevier GmbH. All rights reserved.

Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients

Energy Technology Data Exchange (ETDEWEB)

Mu, Jun [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Yang, Yongtao [Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing (China); Chen, Jin; Cheng, Ke; Li, Qi; Wei, Yongdong; Zhu, Dan; Shao, Weihua; Zheng, Peng [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Xie, Peng, E-mail: xiepeng@cqmu.edu.cn [Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing (China); Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing (China); Chongqing Key Laboratory of Neurobiology, Chongqing (China); Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing (China)

2015-10-30

Purpose: Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). Methods: CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology and proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Results: Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. Conclusions: CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. - Highlights: • The first proteomic study on the cerebrospinal fluid of tuberculous meningitis patients using iTRAQ. • Identify 4 differential proteins invloved in the lipid metabolism. • Elevated expression of ApoB gives

Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients

International Nuclear Information System (INIS)

Mu, Jun; Yang, Yongtao; Chen, Jin; Cheng, Ke; Li, Qi; Wei, Yongdong; Zhu, Dan; Shao, Weihua; Zheng, Peng; Xie, Peng

2015-01-01

Purpose: Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). Methods: CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology and proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Results: Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. Conclusions: CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. - Highlights: • The first proteomic study on the cerebrospinal fluid of tuberculous meningitis patients using iTRAQ. • Identify 4 differential proteins invloved in the lipid metabolism. • Elevated expression of ApoB gives

Quantitative proteomics of delirium cerebrospinal fluid

Science.gov (United States)

Poljak, A; Hill, M; Hall, R J; MacLullich, A M; Raftery, M J; Tai, J; Yan, S; Caplan, G A

2014-01-01

Delirium is a common cause and complication of hospitalization in older people, being associated with higher risk of future dementia and progression of existing dementia. However relatively little data are available on which biochemical pathways are dysregulated in the brain during delirium episodes, whether there are protein expression changes common among delirium subjects and whether there are any changes which correlate with the severity of delirium. We now present the first proteomic analysis of delirium cerebrospinal fluid (CSF), and one of few studies exploring protein expression changes in delirium. More than 270 proteins were identified in two delirium cohorts, 16 of which were dysregulated in at least 8 of 17 delirium subjects compared with a mild Alzheimer's disease neurological control group, and 31 proteins were significantly correlated with cognitive scores (mini-mental state exam and acute physiology and chronic health evaluation III). Bioinformatics analyses revealed expression changes in several protein family groups, including apolipoproteins, secretogranins/chromogranins, clotting/fibrinolysis factors, serine protease inhibitors and acute-phase response elements. These data not only provide confirmatory evidence that the inflammatory response is a component of delirium, but also reveal dysregulation of protein expression in a number of novel and unexpected clusters of proteins, in particular the granins. Another surprising outcome of this work is the level of similarity of CSF protein profiles in delirium patients, given the diversity of causes of this syndrome. These data provide additional elements for consideration in the pathophysiology of delirium as well as potential biomarker candidates for delirium diagnosis. PMID:25369144

Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease

Energy Technology Data Exchange (ETDEWEB)

Angel, Thomas E.; Jacobs, Jon M.; Smith, Robert P.; Pasternack, Mark S.; Elias, Susan; Gritsenko, Marina A.; Shukla, Anil K.; Gilmore, Edward C.; McCarthy, Carol; Camp, David G.; Smith, Richard D.

2012-10-05

Acute Lyme disease results from transmission of and infection by the bacterium Borrelia burgdorferi following a tick bite. During acute infection, bacteria can disseminate to the central nervous system (CNS) leading to the development of Lyme meningitis. Here we have analyzed pooled cerebrospinal fluid (CSF) allowing for a deep view into the proteome for a cohort of patients with early-disseminated Lyme disease and CSF inflammation leading to the identification of proteins that reflect host responses, which are distinct for subjects with acute Lyme disease. Additionally, we analyzed individual patient samples and quantified changes in protein abundance employing label-free quantitative mass spectrometry based methods. The measured changes in protein abundances reflect the impact of acute Lyme disease on the CNS as presented in CSF. We have identified 89 proteins that differ significantly in abundance in patients with acute Lyme disease. A number of the differentially abundant proteins have been found to be localized to brain synapse and thus constitute important leads for better understanding of the neurological consequence of disseminated Lyme disease.

One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation

NARCIS (Netherlands)

Megger, D.A.; Padden, J.; Rosowski, K.; Uszkoreit, J.; Bracht, T.; Eisenacher, M.; Gerges, C.; Neuhaus, H.; Schumacher, B.; Schlaak, J.F.; Sitek, B.

2017-01-01

The proteome analysis of bile fluid represents a promising strategy to identify biomarker candidates for various diseases of the hepatobiliary system. However, to obtain substantive results in biomarker discovery studies large patient cohorts necessarily need to be analyzed. Consequently, this would

Assaying of drugs in body fluids

International Nuclear Information System (INIS)

Braestrup, C.; Squires, R.F.

1981-01-01

The invention provides, in general terms, a process for determining the concentration of a psychotropically active benzodiazepine drug in blood or other body fluid or urine, including bringing a sample of the fluid or urine into contact with brain tissue and with tritium labelled molecules of a benzodiazepine which can bind reversibly to receptors of the brain tissue to induce binding of molecules of the unlabelled drug and of the tritium labelled benzodiazepine to the receptors, and determining the radioactivity of the brain tissue, preferably by scintillation counting. (author)

Rigid Body Sampling and Individual Time Stepping for Rigid-Fluid Coupling of Fluid Simulation

Directory of Open Access Journals (Sweden)

Xiaokun Wang

2017-01-01

Full Text Available In this paper, we propose an efficient and simple rigid-fluid coupling scheme with scientific programming algorithms for particle-based fluid simulation and three-dimensional visualization. Our approach samples the surface of rigid bodies with boundary particles that interact with fluids. It contains two procedures, that is, surface sampling and sampling relaxation, which insures uniform distribution of particles with less iterations. Furthermore, we present a rigid-fluid coupling scheme integrating individual time stepping to rigid-fluid coupling, which gains an obvious speedup compared to previous method. The experimental results demonstrate the effectiveness of our approach.

THE URINE PROTEOME FOR RADIATION BIODOSIMETRY: EFFECT OF TOTAL BODY VERSUS LOCAL KIDNEY IRRADIATION

Science.gov (United States)

Sharma, Mukut; Halligan, Brian D.; Wakim, Bassam T.; Savin, Virginia J.; Cohen, Eric P.; Moulder, John E.

2009-01-01

Victims of nuclear accidents or radiological terrorism are likely to receive varying doses of ionizing radiation inhomogeneously distributed over the body. Early biomarkers may be useful in determining organ-specific doses due to total body irradiation (TBI) or partial body irradiation. We used liquid chromatography and mass spectrometry to compare the effect of TBI and local kidney irradiation (LKI) on the rat urine proteome using a single 10 Gy dose of X-rays. Both TBI and LKI altered the urinary protein profile within 24 hours with noticeable differences in Gene Ontology categories. Some proteins including fetuin-B, tissue kallikrein, beta-glucuronidase, vitamin D-dependent calcium binding protein and chondroitin sulfate proteoglycan NG2 were detected only in the TBI group. Some other proteins including major urinary protein-1, RNA binding protein 19, neuron navigator, Dapper homolog 3, WD repeat and FYVE domain containing protein 3, sorting nexin-8, ankycorbin and aquaporin were detected only in the LKI group. Protease inhibitors and kidney proteins were more abundant (fraction of total scans) in the LKI group. Up/Uc ratio and urinary albumin abundance decreased in both TBI and LKI groups. Several markers of acute kidney injury were not detectable in either irradiated group. Present data indicate that abundance and number of proteins may follow opposite trends. These novel findings demonstrate intriguing differences between TBI and LKI, and suggest that urine proteome may be useful in determining organ-specific changes caused by partial body irradiation. PMID:20065682

Identification of 10 Candidate Biomarkers Distinguishing Tuberculous and Malignant Pleural Fluid by Proteomic Methods.

Science.gov (United States)

Lee, Chang Youl; Hong, Ji Young; Lee, Myung Goo; Suh, In Bum

2017-11-01

Pleural effusion, an accumulation of fluid in the pleural space, usually occurs in patients when the rate of fluid formation exceeds the rate of fluid removal. The differential diagnosis of tuberculous pleurisy and malignant pleural effusion is a difficult task in high tuberculous prevalence areas. The aim of the present study was to identify novel biomarkers for the diagnosis of pleural fluid using proteomics technology. We used samples from five patients with transudative pleural effusions for internal standard, five patients with tuberculous pleurisy, and the same numbers of patients having malignant effusions were enrolled in the study. We analyzed the proteins in pleural fluid from patients using a technique that combined two-dimensional liquid-phase electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry. We identified a total of 10 proteins with statistical significance. Among 10 proteins, trasthyretin, haptoglobin, metastasis-associated protein 1, t-complex protein 1, and fibroblast growth factor-binding protein 1 were related with malignant pleural effusions and human ceruloplasmin, lysozyme precursor, gelsolin, clusterin C complement lysis inhibitor, and peroxirexdoxin 3 were expressed several times or more in tuberculous pleural effusions. Highly expressed proteins in malignant pleural effusion were associated with carcinogenesis and cell growth, and proteins associated with tuberculous pleural effusion played a role in the response to inflammation and fibrosis. These findings will aid in the development of novel diagnostic tools for tuberculous pleurisy and malignant pleural effusion of lung cancer. © Copyright: Yonsei University College of Medicine 2017

Identification of body fluid-specific DNA methylation markers for use in forensic science.

Science.gov (United States)

Park, Jong-Lyul; Kwon, Oh-Hyung; Kim, Jong Hwan; Yoo, Hyang-Sook; Lee, Han-Chul; Woo, Kwang-Man; Kim, Seon-Young; Lee, Seung-Hwan; Kim, Yong Sung

2014-11-01

DNA methylation, which occurs at the 5'-position of the cytosine in CpG dinucleotides, has great potential for forensic identification of body fluids, because tissue-specific patterns of DNA methylation have been demonstrated, and DNA is less prone to degradation than proteins or RNA. Previous studies have reported several body fluid-specific DNA methylation markers, but DNA methylation differences are sometimes low in saliva and vaginal secretions. Moreover, specific DNA methylation markers in four types of body fluids (blood, saliva, semen, and vaginal secretions) have not been investigated with genome-wide profiling. Here, we investigated novel DNA methylation markers for identification of body fluids for use in forensic science using the Illumina HumanMethylation 450K bead array, which contains over 450,000 CpG sites. Using methylome data from 16 samples of blood, saliva, semen, and vaginal secretions, we first selected 2986 hypermethylated or hypomethylated regions that were specific for each type of body fluid. We then selected eight CpG sites as novel, forensically relevant DNA methylation markers: cg06379435 and cg08792630 for blood, cg26107890 and cg20691722 for saliva, cg23521140 and cg17610929 for semen, and cg01774894 and cg14991487 for vaginal secretions. These eight selected markers were evaluated in 80 body fluid samples using pyrosequencing, and all showed high sensitivity and specificity for identification of the target body fluid. We suggest that these eight DNA methylation markers may be good candidates for developing an effective molecular assay for identification of body fluids in forensic science. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

DEFF Research Database (Denmark)

Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

2016-01-01

Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed...... by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly...

Proteomic Changes in Cerebrospinal Fluid of Presymptomatic and Affected Persons Carrying Familial Alzheimer Disease Mutations

Science.gov (United States)

Ringman, John M.; Schulman, Howard; Becker, Chris; Jones, Ted; Bai, Yuchen; Immermann, Fred; Cole, Gregory; Sokolow, Sophie; Gylys, Karen; Geschwind, Daniel H.; Cummings, Jeffrey L.; Wan, Hong I.

2013-01-01

Objective To identify cerebrospinal fluid (CSF) protein changes in persons who will develop familial Alzheimer disease (FAD) due to PSEN1 and APP mutations, using unbiased proteomics. Design We compared proteomic profiles of CSF from individuals with FAD who were mutation carriers (MCs) and related noncarriers (NCs). Abundant proteins were depleted and samples were analyzed using liquid chromatography– electrospray ionization–mass spectrometry on a high-resolution time-of-flight instrument. Tryptic peptides were identified by tandem mass spectrometry. Proteins differing in concentration between the MCs and NCs were identified. Setting A tertiary dementia referral center and a proteomic biomarker discovery laboratory. Participants Fourteen FAD MCs (mean age, 34.2 years; 10 are asymptomatic, 12 have presenilin-1 [PSEN1] gene mutations, and 2 have amyloid precursor protein [APP] gene mutations) and 5 related NCs (mean age, 37.6 years). Results Fifty-six proteins were identified, represented by multiple tryptic peptides showing significant differences between MCs and NCs (46 upregulated and 10 downregulated); 40 of these proteins differed when the analysis was restricted to asymptomatic individuals. Fourteen proteins have been reported in prior proteomic studies in late-onset AD, including amyloid precursor protein, transferrin, α1β-glycoprotein, complement components, afamin precursor, spondin 1, plasminogen, hemopexin, and neuronal pentraxin receptor. Many other proteins were unique to our study, including calsyntenin 3, AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) 4 glutamate receptor, CD99 antigen, di-N-acetyl-chitobiase, and secreted phosphoprotein 1. Conclusions We found much overlap in CSF protein changes between individuals with presymptomatic and symptomatic FAD and those with late-onset AD. Our results are consistent with inflammation and synaptic loss early in FAD and suggest new presymptomatic biomarkers of potential usefulness in drug

Time- and radiation-dose dependent changes in the plasma proteome after total body irradiation of non-human primates: Implications for biomarker selection.

Directory of Open Access Journals (Sweden)

Stephanie D Byrum

Full Text Available Acute radiation syndrome (ARS is a complex multi-organ disease resulting from total body exposure to high doses of radiation. Individuals can be exposed to total body irradiation (TBI in a number of ways, including terrorist radiological weapons or nuclear accidents. In order to determine whether an individual has been exposed to high doses of radiation and needs countermeasure treatment, robust biomarkers are needed to estimate radiation exposure from biospecimens such as blood or urine. In order to identity such candidate biomarkers of radiation exposure, high-resolution proteomics was used to analyze plasma from non-human primates following whole body irradiation (Co-60 at 6.7 Gy and 7.4 Gy with a twelve day observation period. A total of 663 proteins were evaluated from the plasma proteome analysis. A panel of plasma proteins with characteristic time- and dose-dependent changes was identified. In addition to the plasma proteomics study reported here, we recently identified candidate biomarkers using urine from these same non-human primates. From the proteomic analysis of both plasma and urine, we identified ten overlapping proteins that significantly differentiate both time and dose variables. These shared plasma and urine proteins represent optimal candidate biomarkers of radiation exposure.

Longitudinal quantification of the gingival crevicular fluid proteome during progression from gingivitis to periodontitis in a canine model.

Science.gov (United States)

Davis, Ian J; Jones, Andrew W; Creese, Andrew J; Staunton, Ruth; Atwal, Jujhar; Chapple, Iain L C; Harris, Stephen; Grant, Melissa M

2016-07-01

Inflammatory periodontal disease is widespread in dogs. This study evaluated site-specific changes in the canine gingival crevicular fluid (GCF) proteome during longitudinal progression from very mild gingivitis to mild periodontitis. Periodontitis diagnosis in dogs requires general anaesthesia with associated risks and costs; our ultimate aim was to develop a periodontitis diagnostic for application in conscious dogs. The objective of this work was to identify potential biomarkers of periodontal disease progression in dogs. Gingival crevicular fluid was sampled from a total of 10 teeth in eight dogs at three different stages of health/disease and samples prepared for quantitative mass spectrometry (data available via ProteomeXchange; identifier PXD003337). A univariate mixed model analysis determined significantly altered proteins between health states and six were evaluated by ELISA. Four hundred and six proteins were identified with 84 present in all samples. The prevalence of 40 proteins was found to be significantly changed in periodontitis relative to gingivitis. ELISA measurements confirmed that haptoglobin was significantly increased. This study demonstrates for the first time that proteins detected by mass spectrometry have potential to identify novel biomarkers for canine periodontal disease. Further work is required to validate additional biomarkers for a periodontitis diagnostic. © 2016 The Authors. Journal of Clinical Periodontology Published by John Wiley & Sons Ltd.

Proteomic profiles reveal age-related changes in coelomic fluid of sea urchin species with different life spans.

Science.gov (United States)

Bodnar, Andrea

2013-05-01

Sea urchins have a different life history from humans and traditional model organisms used to study the process of aging. Sea urchins grow indeterminately, reproduce throughout their life span and some species have been shown to exhibit negligible senescence with no increase in mortality rate at advanced ages. Despite these properties, different species of sea urchins are reported to have very different natural life spans providing a unique model to investigate cellular mechanisms underlying life span determination and negligible senescence. To gain insight into the biological changes that accompany aging in these animals, proteomic profiles were examined in coelomic fluid from young and old sea urchins of three species with different life spans: short-lived Lytechinus variegatus, long-lived Strongylocentrotus franciscanus and Strongylocentrotus purpuratus which has an intermediate life span. The proteomic profiles of cell-free coelomic fluid were complex with many proteins exhibiting different forms and extensive post-translational modifications. Approximately 20% of the protein spots on 2-D gels showed more than two-fold change with age in each of the species. Changes that are consistent with age in all three species may prove to be useful biomarkers for age-determination for these commercially fished marine invertebrates and also may provide clues to mechanisms of negligible senescence. Among the proteins that change with age, the ectodomain of low-density lipoprotein receptor-related protein 4 (LRP4) was significantly increased in the coelomic fluid of all three sea urchin species suggesting that the Wnt signaling pathway should be further investigated for its role in negligible senescence. Copyright © 2012 Elsevier Inc. All rights reserved.

The urine proteome for radiation biodosimetry: effect of total body vs. local kidney irradiation.

Science.gov (United States)

Sharma, Mukut; Halligan, Brian D; Wakim, Bassam T; Savin, Virginia J; Cohen, Eric P; Moulder, John E

2010-02-01

Victims of nuclear accidents or radiological terrorism are likely to receive varying doses of ionizing radiation inhomogeneously distributed over the body. Early biomarkers may be useful in determining organ-specific doses due to total body irradiation (TBI) or partial body irradiation. The authors used liquid chromatography and mass spectrometry to compare the effect of TBI and local kidney irradiation (LKI) on the rat urine proteome using a single 10-Gy dose of x-rays. Both TBI and LKI altered the urinary protein profile within 24 h with noticeable differences in gene ontology categories. Some proteins, including fetuin-B, tissue kallikrein, beta-glucuronidase, vitamin D-dependent calcium binding protein and chondroitin sulfate proteoglycan NG2, were detected only in the TBI group. Some other proteins, including major urinary protein-1, RNA binding protein 19, neuron navigator, Dapper homolog 3, WD repeat and FYVE domain containing protein 3, sorting nexin-8, ankycorbin and aquaporin were detected only in the LKI group. Protease inhibitors and kidney proteins were more abundant (fraction of total scans) in the LKI group. Urine protein (Up) and creatinine (Uc) (Up/Uc) ratios and urinary albumin abundance decreased in both TBI and LKI groups. Several markers of acute kidney injury were not detectable in either irradiated group. Present data indicate that abundance and number of proteins may follow opposite trends. These novel findings demonstrate intriguing differences between TBI and LKI, and suggest that urine proteome may be useful in determining organ-specific changes caused by partial body irradiation.

The Seminal fluid proteome of the polyandrous Red junglefowl offers insights into the molecular basis of fertility, reproductive ageing and domestication.

Science.gov (United States)

Borziak, Kirill; Álvarez-Fernández, Aitor; L Karr, Timothy; Pizzari, Tommaso; Dorus, Steve

2016-11-02

Seminal fluid proteins (SFPs) are emerging as fundamental contributors to sexual selection given their role in post-mating reproductive events, particularly in polyandrous species where the ejaculates of different males compete for fertilisation. SFP identification however remains taxonomically limited and little is known about avian SFPs, despite extensive work on sexual selection in birds. We characterize the SF proteome of the polyandrous Red junglefowl, Gallus gallus, the wild species that gave rise to the domestic chicken. We identify 1,141 SFPs, including proteins involved in immunity and antimicrobial defences, sperm maturation, and fertilisation, revealing a functionally complex SF proteome. This includes a predominant contribution of blood plasma proteins that is conserved with human SF. By comparing the proteome of young and old males with fast or slow sperm velocity in a balanced design, we identify proteins associated with ageing and sperm velocity, and show that old males that retain high sperm velocity have distinct proteome characteristics. SFP comparisons with domestic chickens revealed both qualitative and quantitative differences likely associated with domestication and artificial selection. Collectively, these results shed light onto the functional complexity of avian SF, and provide a platform for molecular studies of fertility, reproductive ageing, and domestication.

A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples

Directory of Open Access Journals (Sweden)

Rígel Licier

2016-10-01

Full Text Available The proper handling of samples to be analyzed by mass spectrometry (MS can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.

A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples.

Science.gov (United States)

Licier, Rígel; Miranda, Eric; Serrano, Horacio

2016-10-17

The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.

Xylem sap proteomics.

Science.gov (United States)

de Bernonville, Thomas Dugé; Albenne, Cécile; Arlat, Matthieu; Hoffmann, Laurent; Lauber, Emmanuelle; Jamet, Elisabeth

2014-01-01

Proteomic analysis of xylem sap has recently become a major field of interest to understand several biological questions related to plant development and responses to environmental clues. The xylem sap appears as a dynamic fluid undergoing changes in its proteome upon abiotic and biotic stresses. Unlike cell compartments which are amenable to purification in sufficient amount prior to proteomic analysis, the xylem sap has to be collected in particular conditions to avoid contamination by intracellular proteins and to obtain enough material. A model plant like Arabidopsis thaliana is not suitable for such an analysis because efficient harvesting of xylem sap is difficult. The analysis of the xylem sap proteome also requires specific procedures to concentrate proteins and to focus on proteins predicted to be secreted. Indeed, xylem sap proteins appear to be synthesized and secreted in the root stele or to originate from dying differentiated xylem cells. This chapter describes protocols to collect xylem sap from Brassica species and to prepare total and N-glycoprotein extracts for identification of proteins by mass spectrometry analyses and bioinformatics.

Alanyl-glutamine dipeptide restores the cytoprotective stress proteome of mesothelial cells exposed to peritoneal dialysis fluids.

Science.gov (United States)

Kratochwill, Klaus; Boehm, Michael; Herzog, Rebecca; Lichtenauer, Anton Michael; Salzer, Elisabeth; Lechner, Michael; Kuster, Lilian; Bergmeister, Konstantin; Rizzi, Andreas; Mayer, Bernd; Aufricht, Christoph

2012-03-01

Exposure of mesothelial cells to peritoneal dialysis fluids (PDF) results in cytoprotective cellular stress responses (CSR) that counteract PDF-induced damage. In this study, we tested the hypothesis that the CSR may be inadequate in relevant models of peritoneal dialysis (PD) due to insufficient levels of glutamine, resulting in increased vulnerability against PDF cytotoxicity. We particularly investigated the role of alanyl-glutamine (Ala-Gln) dipeptide on the cytoprotective PDF stress proteome. Adequacy of CSR was investigated in two human in vitro models (immortalized cell line MeT-5A and mesothelial cells derived from peritoneal effluent of uraemic patients) following exposure to heat-sterilized glucose-based PDF (PD4-Dianeal, Baxter) diluted with medium and, in a comparative proteomics approach, at different levels of glutamine ranging from depletion (0 mM) via physiological (0.7 mM) to pharmacological levels (8 mM administered as Ala-Gln). Despite severe cellular injury, expression of cytoprotective proteins was dampened upon PDF exposure at physiological glutamine levels, indicating an inadequate CSR. Depletion of glutamine aggravated cell injury and further reduced the CSR, whereas addition of Ala-Gln at pharmacological level restored an adequate CSR, decreasing cellular damage in both PDF exposure systems. Ala-Gln specifically stimulated chaperoning activity, and cytoprotective processes were markedly enhanced in the PDF stress proteome. Taken together, this study demonstrates an inadequate CSR of mesothelial cells following PDF exposure associated with low and physiological levels of glutamine, indicating a new and potentially relevant pathomechanism. Supplementation of PDF with pharmacological doses of Ala-Gln restored the cytoprotective stress proteome, resulting in improved resistance of mesothelial cells to exposure to PDF. Future work will study the clinical relevance of CSR-mediated cytoprotection.

Effect of bicarbonate on biodegradation behaviour of pure magnesium in a simulated body fluid

International Nuclear Information System (INIS)

Li, Zaichun; Song, Guang-Ling; Song, Shizhe

2014-01-01

The effect of bicarbonate on biodegradation of pure magnesium in a simulated body fluid is investigated by means of X-ray diffraction, X-ray photoelectron spectroscopy, polarization curve and electrochemical impedance spectroscopy. The results show that magnesium biodegrades rapidly and non-uniformly during 27 h of immersion in four simulated body fluid solutions containing different concentrations of bicarbonate. The biodegradation rate first decreases and then increases with time. A small amount of bicarbonate in simulated body fluid has an inhibition effect on the Mg dissolution, while an overdose of bicarbonate addition activates the magnesium surface in the simulated body fluid. The interesting phenomena can be interpreted by a surface film model involving precipitation of calcium carbonate and further ionization of bicarbonate in the simulated body fluids, incorporation of calcium, carbonate and phosphate compounds in the surface film, and development of chloride-induced pitting corrosion damage on the magnesium with time

MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates.

Science.gov (United States)

Berger, Sebastian T; Ahmed, Saima; Muntel, Jan; Cuevas Polo, Nerea; Bachur, Richard; Kentsis, Alex; Steen, Judith; Steen, Hanno

2015-10-01

We describe a 96-well plate compatible membrane-based proteomic sample processing method, which enables the complete processing of 96 samples (or multiples thereof) within a single workday. This method uses a large-pore hydrophobic PVDF membrane that efficiently adsorbs proteins, resulting in fast liquid transfer through the membrane and significantly reduced sample processing times. Low liquid transfer speeds have prevented the useful 96-well plate implementation of FASP as a widely used membrane-based proteomic sample processing method. We validated our approach on whole-cell lysate and urine and cerebrospinal fluid as clinically relevant body fluids. Without compromising peptide and protein identification, our method uses a vacuum manifold and circumvents the need for digest desalting, making our processing method compatible with standard liquid handling robots. In summary, our new method maintains the strengths of FASP and simultaneously overcomes one of the major limitations of FASP without compromising protein identification and quantification. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Protein profiling reveals inter-individual protein homogeneity of arachnoid cyst fluid and high qualitative similarity to cerebrospinal fluid

Directory of Open Access Journals (Sweden)

Berle Magnus

2011-05-01

Full Text Available Abstract Background The mechanisms behind formation and filling of intracranial arachnoid cysts (AC are poorly understood. The aim of this study was to evaluate AC fluid by proteomics to gain further knowledge about ACs. Two goals were set: 1 Comparison of AC fluid from individual patients to determine whether or not temporal AC is a homogenous condition; and 2 Evaluate the protein content of a pool of AC fluid from several patients and qualitatively compare this with published protein lists of cerebrospinal fluid (CSF and plasma. Methods AC fluid from 15 patients with temporal AC was included in this study. In the AC protein comparison experiment, AC fluid from 14 patients was digested, analyzed by LC-MS/MS using a semi-quantitative label-free approach and the data were compared by principal component analysis (PCA to gain knowledge of protein homogeneity of AC. In the AC proteome evaluation experiment, AC fluid from 11 patients was pooled, digested, and fractionated by SCX chromatography prior to analysis by LC-MS/MS. Proteins identified were compared to published databases of proteins identified from CSF and plasma. AC fluid proteins not found in these two databases were experimentally searched for in lumbar CSF taken from neurologically-normal patients, by a targeted protein identification approach called MIDAS (Multiple Reaction Monitoring (MRM initiated detection and sequence analysis. Results We did not identify systematic trends or grouping of data in the AC protein comparison experiment, implying low variability between individual proteomic profiles of AC. In the AC proteome evaluation experiment, we identified 199 proteins. When compared to previously published lists of proteins identified from CSF and plasma, 15 of the AC proteins had not been reported in either of these datasets. By a targeted protein identification approach, we identified 11 of these 15 proteins in pooled CSF from neurologically-normal patients, demonstrating that

Label-Free LC-MS/MS Proteomic Analysis of Cerebrospinal Fluid Identifies Protein/Pathway Alterations and Candidate Biomarkers for Amyotrophic Lateral Sclerosis.

Science.gov (United States)

Collins, Mahlon A; An, Jiyan; Hood, Brian L; Conrads, Thomas P; Bowser, Robert P

2015-11-06

Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control (HC), and other neurological disease (OND) subjects using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 1712 CSF proteins were detected and relatively quantified by spectral counting. Levels of several proteins with diverse biological functions were significantly altered in sALS samples. Enrichment analysis was used to link these alterations to biological pathways, which were predominantly related to inflammation, neuronal activity, and extracellular matrix regulation. We then used our CSF proteomic profiles to create a support vector machines classifier capable of discriminating training set ALS from non-ALS (HC and OND) samples. Four classifier proteins, WD repeat-containing protein 63, amyloid-like protein 1, SPARC-like protein 1, and cell adhesion molecule 3, were identified by feature selection and externally validated. The resultant classifier distinguished ALS from non-ALS samples with 83% sensitivity and 100% specificity in an independent test set. Collectively, our results illustrate the utility of CSF proteomic profiling for identifying ALS protein/pathway alterations and candidate disease biomarkers.

Fluid sign in the treated bodies after percutaneous vertebroplasty

International Nuclear Information System (INIS)

Lin, Chao-Chun; Yen, Pao-Sheng; Wen, Shu-Hui

2008-01-01

The aims of this study are to describe non-healing in the treated vertebral body after percutaneous vertebroplasty and analyze the influence of vacuum cleft, location, and severity of collapse on the development of nonunion cement. Of 208 patients (266 treated vertebral bodies) who were treated with percutaneous vertebroplasty from September 2002 to May 2006, 23 patients (41 treated levels) with residual or recurrent pain underwent follow-up magnetic resonance imaging (MRI) study. Retrospective chart review with analysis of preoperative and postoperative MRIs were performed in these 23 patients. In the 41 treated vertebral bodies, 22 of 41 bodies had vacuum cleft found in the preoperative MRI study. Eight of the 22 treated vertebral bodies with preoperative vacuum clefts were found to have fluid between the interface of cement and the residual bone in the collapsed vertebral bodies on follow-up MRI. The adjacent discs of these treated vertebral bodies were upward/downward displaced. The endplate of the adjacent vertebral body exhibited fibrotic change. Treated bodies with vacuum clefts and level A location (T9, T11, T12, and L1) had higher probability of developing nonunion of the cement with statistical significance. The probability of nonunion cement in severe collapsed bodies might be higher than that of union cement in mild collapsed ones, but was not statistically significant. Fluid sign in the treated body represents unhealed bone-cement interface. The location of the treated vertebral body and existence of vacuum cleft in the treated bodies may be important factors influencing the nonunion of cement. (orig.)

Current Applications of Chromatographic Methods in the Study of Human Body Fluids for Diagnosing Disorders.

Science.gov (United States)

Jóźwik, Jagoda; Kałużna-Czaplińska, Joanna

2016-01-01

Currently, analysis of various human body fluids is one of the most essential and promising approaches to enable the discovery of biomarkers or pathophysiological mechanisms for disorders and diseases. Analysis of these fluids is challenging due to their complex composition and unique characteristics. Development of new analytical methods in this field has made it possible to analyze body fluids with higher selectivity, sensitivity, and precision. The composition and concentration of analytes in body fluids are most often determined by chromatography-based techniques. There is no doubt that proper use of knowledge that comes from a better understanding of the role of body fluids requires the cooperation of scientists of diverse specializations, including analytical chemists, biologists, and physicians. This article summarizes current knowledge about the application of different chromatographic methods in analyses of a wide range of compounds in human body fluids in order to diagnose certain diseases and disorders.

Ultra-sensitive high performance liquid chromatography-laser-induced fluorescence based proteomics for clinical applications.

Science.gov (United States)

Patil, Ajeetkumar; Bhat, Sujatha; Pai, Keerthilatha M; Rai, Lavanya; Kartha, V B; Chidangil, Santhosh

2015-09-08

An ultra-sensitive high performance liquid chromatography-laser induced fluorescence (HPLC-LIF) based technique has been developed by our group at Manipal, for screening, early detection, and staging for various cancers, using protein profiling of clinical samples like, body fluids, cellular specimens, and biopsy-tissue. More than 300 protein profiles of different clinical samples (serum, saliva, cellular samples and tissue homogenates) from volunteers (normal, and different pre-malignant/malignant conditions) were recorded using this set-up. The protein profiles were analyzed using principal component analysis (PCA) to achieve objective detection and classification of malignant, premalignant and healthy conditions with high sensitivity and specificity. The HPLC-LIF protein profiling combined with PCA, as a routine method for screening, diagnosis, and staging of cervical cancer and oral cancer, is discussed in this paper. In recent years, proteomics techniques have advanced tremendously in life sciences and medical sciences for the detection and identification of proteins in body fluids, tissue homogenates and cellular samples to understand biochemical mechanisms leading to different diseases. Some of the methods include techniques like high performance liquid chromatography, 2D-gel electrophoresis, MALDI-TOF-MS, SELDI-TOF-MS, CE-MS and LC-MS techniques. We have developed an ultra-sensitive high performance liquid chromatography-laser induced fluorescence (HPLC-LIF) based technique, for screening, early detection, and staging for various cancers, using protein profiling of clinical samples like, body fluids, cellular specimens, and biopsy-tissue. More than 300 protein profiles of different clinical samples (serum, saliva, cellular samples and tissue homogenates) from healthy and volunteers with different malignant conditions were recorded by using this set-up. The protein profile data were analyzed using principal component analysis (PCA) for objective

Partitioning of body fluids in the Lake Nicaragua shark and three marine sharks.

Science.gov (United States)

THORSON, T B

1962-11-09

The relative volumes of major body fluids of freshwater and marine sharks are remarkably similar in spite of the differences in external medium and in osmotic pressure of body fluids. The small differences detected are in agreement with differences reported in comparisons of freshwater and marine teleosts: a slightly higher total water content and a smiller ratio of extracellular to intracellular fluids in freshwater forms.

The cerebrospinal fluid proteome in HIV infection: change associated with disease severity.

Energy Technology Data Exchange (ETDEWEB)

Angel, Thomas E.; Jacobs, Jon M.; Spudich, Serena S.; Gritsenko, Marina A.; Fuchs, Dietmar; Liegler, Teri; Zetterberg, Henrik; Camp, David G.; Price, Richard W.; Smith, Richard D.

2012-03-20

Central nervous system (CNS) infection is a constant feature of systemic HIV infection with a clinical spectrum that ranges from chronic asymptomatic infection to severe cognitive and motor dysfunction. Analysis of cerebrospinal fluid (CSF) has played an important part in defining the character of this evolving infection and response to treatment. To further characterize CNS HIV infection and its effects, we applied advanced high-throughput proteomic methods to CSF to identify novel proteins and their changes with disease progression and treatment. After establishing an accurate mass and time (AMT) tag database containing 23,141 AMT tags for CSF peptides, we analyzed 91 CSF samples by LC-MS from 12 HIV-uninfected and 14 HIV-infected subjects studied in the context of initiation of antiretroviral and correlated abundances of identified proteins (a) within and between subjects, (b) with all other proteins across the entire sample set, and (c) with 'external' CSF biomarkers of infection (HIV RNA), immune activation (neopterin) and neural injury (neurofilament light chain protein, NFL). We identified a mean of 2,333 +/- 328 (SD) peptides covering 307 +/-16 proteins in the 91 CSF sample set. Protein abundances differed both between and within subjects sampled at different time points and readily separated those with and without HIV infection. Proteins also showed inter-correlations across the sample set that were associated with biologically relevant dynamic processes. One-hundred and fifty proteins showed correlations with the external biomarkers. For example, using a threshold of cross correlation coefficient (Pearson's) {le}0.3 and {ge}0.3 for potentially meaningful relationships, a total of 99 proteins correlated with CSF neopterin (43 negative and 56 positive correlations) and related principally to neuronal plasticity and survival and to innate immunity. Pathway analysis defined several networks connecting the identified proteins, including one with

A refractometry-based glucose analysis of body fluids.

Science.gov (United States)

Zirk, Kai; Poetzschke, Harald

2007-05-01

In principle, refractometry appears to be a suitable method for the measurement of glucose concentrations in body fluids (such as blood and the intercellular fluid), even though the refractive index of the measured samples, as an additive property, is not specific. But, if certain conditions are fulfilled, the glucose content can be calculated using the refractive index in combination with values from a further measurement. This study describes the determination of the glucose content using refractometry in human blood serum derivates, which were selected - due to their ready availability - to be used as a model for interstitial fluid. Refractometry of body fluids requires the elimination of disturbing components from the measurement sample. First of all, a homogenous fluid (i.e. consisting of one phase) is required, so that all cells and components in suspension need to be separated out. Furthermore, certain dissolved macromolecular components which are known to disturb the measurement process must also be removed. In human serum samples which had been ultrafiltrated with a range of ultrafilters of different pore sizes, a comparative evaluation showed that only ultrafiltration through a filter with a separation limit of between 3 and 30kDa resulted in maximal reduction of the refractive index (compared to native serum), whereas ultrafilters with greater separation limits did not. The total content of osmotically active solutes (the tonicity) also exerts a clear influence. However, exemplary measurements in blood plasma fluid from one volunteer showed that the electrical conductivity is (without an additive component) directly proportional to the osmolality: physiological changes in the state of body hydration (hyperhydration and dehydration) do not lead to any considerable changes in the relation between ionised and uncharged solute particles, but instead result in a sufficiently clear dilution or concentration of the blood fluid's low molecular components. This

Occurrence of tetrodotoxin-binding high molecular weight substances in the body fluid of shore crab (Hemigrapsus sanguineus).

Science.gov (United States)

Shiomi, K; Yamaguchi, S; Kikuchi, T; Yamamori, K; Matsui, T

1992-12-01

The shore crab (Hemigrapsus sanguineus) is highly resistant to tetrodotoxin (TTX) although it contains no detectable amount of TTX (less than 5 MU/g, where 1 MU is defined as the amount of TTX killing a 20 g mouse in 30 min). Its body fluid was examined for neutralizing effects against the lethal activity of TTX. When the mixture of the body fluid and TTX was injected i.p. into mice, the lethal activity of TTX was significantly reduced; 1 ml of the body fluid was evaluated to neutralize 3.6-4.0 MU of TTX. Higher neutralizing activity (7.2-12.5 MU/ml of the body fluid) was exhibited by i.v. administration of the body fluid into mice before or after i.p. challenge of TTX. The lethal effect of paralytic shellfish poisons was not counteracted by the body fluid. Analysis by gel filtration on Sepharose 6B revealed that the body fluid contained TTX-binding high mol. wt substances (> 2,000,000) responsible for the neutralizing activity of the body fluid against TTX, which accounts for the high resistibility of the crab to TTX. When the crude toxin extracted from the liver of puffer (Takifugu niphobles) was mixed with the body fluid and chromatographed on Sepharose 6B, almost pure TTX was obtained from the fractions containing the TTX-binding high mol. wt substances, suggesting that the TTX-binding high mol. wt substances could be useful in purification of TTX from biological samples.

Advances in proteomics of digestive juices for the diagnosis of digestive system malignancies%消化液蛋白质组学在消化系肿瘤诊断中的作用

Institute of Scientific and Technical Information of China (English)

万勤思; 张焜和

2012-01-01

体液蛋白组学分析为疾病诊疗研究提供了新的技术与策略.血液是临床蛋白分析最常用的标本,但其作为一种系统性体液有其不足之处:成分复杂,与疾病相关的蛋白丰度很低,而局部性体液接近病变部位,其蛋白质组学分析能更好地反映疾病相关信息.消化系统产生胃液等多种局部体液,当相关器官发生病变时,相应消化液的蛋白质组成和数量将发生改变,因而消化液被认为是消化疾病标志物库.近年来关于唾液、胃液、胆汁和胰液的蛋白组学研究有不少报道,发现了一些消化系肿瘤相关蛋白,其中有的显示出良好的诊断应用前景,而结果的重复性、标本处理的标准化等是消化液蛋白组学分析需解决的技术问题.%Body fluid proteomic analysis is a new technology and strategy for disease diagnosis and treatment. Blood is the most commonly used specimen in body fluid proteomics, but as a systemic fluid, it has limitations because of complex composition and low abundance of disease-related proteins. In contrast, local body fluids are closest to the lesions, contain more pathological information, and therefore are more valuable in clinical proteomics. In the digestive system, there are a variety of body fluids which are considered potential reservoirs of biomarkers for their quality and quantity of proteins will alter during lesions occurring in corresponding organs. In recent years, more and more clinical proteomic analyses of saliva, gastric juice, bile and pancreatic juice has been reported and the proteins related to digestive cancers have been found, and some proteins show application potentials in cancer diagnosis. However, the proteomic analyses of digestive juices are facing technical challenges in terms of the reproducibility of results and standardization of specimen handling.

Messenger RNA biomarker signatures for forensic body fluid identification revealed by targeted RNA sequencing.

Science.gov (United States)

Hanson, E; Ingold, S; Haas, C; Ballantyne, J

2018-05-01

The recovery of a DNA profile from the perpetrator or victim in criminal investigations can provide valuable 'source level' information for investigators. However, a DNA profile does not reveal the circumstances by which biological material was transferred. Some contextual information can be obtained by a determination of the tissue or fluid source of origin of the biological material as it is potentially indicative of some behavioral activity on behalf of the individual that resulted in its transfer from the body. Here, we sought to improve upon established RNA based methods for body fluid identification by developing a targeted multiplexed next generation mRNA sequencing assay comprising a panel of approximately equal sized gene amplicons. The multiplexed biomarker panel includes several highly specific gene targets with the necessary specificity to definitively identify most forensically relevant biological fluids and tissues (blood, semen, saliva, vaginal secretions, menstrual blood and skin). In developing the biomarker panel we evaluated 66 gene targets, with a progressive iteration of testing target combinations that exhibited optimal sensitivity and specificity using a training set of forensically relevant body fluid samples. The current assay comprises 33 targets: 6 blood, 6 semen, 6 saliva, 4 vaginal secretions, 5 menstrual blood and 6 skin markers. We demonstrate the sensitivity and specificity of the assay and the ability to identify body fluids in single source and admixed stains. A 16 sample blind test was carried out by one lab with samples provided by the other participating lab. The blinded lab correctly identified the body fluids present in 15 of the samples with the major component identified in the 16th. Various classification methods are being investigated to permit inference of the body fluid/tissue in dried physiological stains. These include the percentage of reads in a sample that are due to each of the 6 tissues/body fluids tested and

Monitoring Change of Body Fluid during Physical Exercise using Bioimpedance Spectroscopy and Finite Element Simulations

Directory of Open Access Journals (Sweden)

Lisa Röthlingshöfer

2011-12-01

Full Text Available Athletes need a balanced body composition in order to achieve maximum performance. Especially dehydration reduces power and endurance during physical exercise. Monitoring the body composition, with a focus on body fluid, may help to avoid reduction in performance and other health problems.For this, a potential measurement method is bioimpedance spectroscopy (BIS. BIS is a simple, non-invasive measurement method that allows to determine different body compartments (body fluid, fat, fat-free mass. However, because many physiological changes occur during physical exercise that can influence impedance measurements and distort results, it cannot be assumed that the BIS data are related to body fluid loss alone.To confirm that BIS can detect body fluid loss due to physical exercise, finite element (FE simulations were done. Besides impedance, also the current density contribution during a BIS measurement was modeled to evaluate the influence of certain tissues on BIS measurements.Simulations were done using CST EM Studio (Computer Simulation Technology, Germany and the Visible Human Data Set (National Library of Medicine, USA. In addition to the simulations, BIS measurements were also made on athletes. Comparison between the measured bioimpedance data and simulation data, as well as body weight loss during sport, indicates that BIS measurements are sensitive enough to monitor body fluid loss during physical exercise.doi:10.5617/jeb.178 J Electr Bioimp, vol. 2, pp. 79-85, 2011

Adapting mass spectrometry-based platforms for clinical proteomics applications: The capillary electrophoresis coupled mass spectrometry paradigm

Science.gov (United States)

Metzger, Jochen; Luppa, Peter B.; Good, David M.; Mischak, Harald

2018-01-01

Single biomarker detection is common in clinical laboratories due to the currently available method spectrum. For various diseases, however, no specific single biomarker could be identified. A strategy to overcome this diagnostic void is to shift from single analyte detection to multiplexed biomarker profiling. Mass spectrometric methods were employed for biomarker discovery in body fluids. The enormous complexity of biofluidic proteome compartments implies upstream fractionation. For this reason, mass spectrometry (MS) was coupled to two-dimensional gel electrophoresis, liquid chromatography, surface-enhanced laser desorption/ionization, or capillary electrophoresis (CE). Differences in performance and operating characteristics make them differentially suited for routine laboratory applications. Progress in the field of clinical proteomics relies not only on the use of an adequate technological platform, but also on a fast and efficient proteomic workflow including standardized sample preparation, proteomic data processing, statistical validation of biomarker selection, and sample classification. Based on CE-MS analysis, we describe how proteomic technology can be implemented in a clinical laboratory environment. In the last part of this review, we give an overview of CE-MS-based clinical studies and present information on identity and biological significance of the identified peptide biomarkers providing evidence of disease-induced changes in proteolytic processing and posttranslational modification. PMID:19404829

Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers

LENUS (Irish Health Repository)

Dakna, Mohammed

2010-12-10

Abstract Background The purpose of this manuscript is to provide, based on an extensive analysis of a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of clinically relevant biomarkers. As tractable example we define the measurable proteomic differences between apparently healthy adult males and females. We choose urine as body-fluid of interest and CE-MS, a thoroughly validated platform technology, allowing for routine analysis of a large number of samples. The second urine of the morning was collected from apparently healthy male and female volunteers (aged 21-40) in the course of the routine medical check-up before recruitment at the Hannover Medical School. Results We found that the Wilcoxon-test is best suited for the definition of potential biomarkers. Adjustment for multiple testing is necessary. Sample size estimation can be performed based on a small number of observations via resampling from pilot data. Machine learning algorithms appear ideally suited to generate classifiers. Assessment of any results in an independent test-set is essential. Conclusions Valid proteomic biomarkers for diagnosis and prognosis only can be defined by applying proper statistical data mining procedures. In particular, a justification of the sample size should be part of the study design.

Multidimensional Raman spectroscopic signatures as a tool for forensic identification of body fluid traces: a review.

Science.gov (United States)

Sikirzhytski, Vitali; Sikirzhytskaya, Aliaksandra; Lednev, Igor K

2011-11-01

The analysis of body fluid traces during forensic investigations is a critical step in determining the key details of a crime. Several confirmatory and presumptive biochemical tests are currently utilized. However, these tests are all destructive, and no single method can be used to analyze all body fluids. This review outlines recent progress in the development of a novel universal approach for the nondestructive, confirmatory identification of body fluid traces using Raman spectroscopy. The method is based on the use of multidimensional spectroscopic signatures of body fluids and accounts for the intrinsic heterogeneity of dry traces and donor variation. The results presented here demonstrate that Raman spectroscopy has potential for identifying traces of semen, blood, saliva, sweat, and vaginal fluid with high confidence.

Discriminant Analysis of Raman Spectra for Body Fluid Identification for Forensic Purposes

OpenAIRE

Sikirzhytski, Vitali; Virkler, Kelly; Lednev, Igor K.

2010-01-01

Detection and identification of blood, semen and saliva stains, the most common body fluids encountered at a crime scene, are very important aspects of forensic science today. This study targets the development of a nondestructive, confirmatory method for body fluid identification based on Raman spectroscopy coupled with advanced statistical analysis. Dry traces of blood, semen and saliva obtained from multiple donors were probed using a confocal Raman microscope with a 785-nm excitation wave...

On fluid flow driven by topography in a librating body

Science.gov (United States)

Wu, C.; Roberts, P. H.

2009-12-01

Currently considerable effort and resources are being devoted to studies of Mercury, the Moon and Europa. Measuring the libration of these bodies can provide significant knowledge about their internal structures and physical properties; see Williams et al., 2001, Peale et al., 2002, Wu et al., 2007. To interpret such observations, it is important to understand better how libration affects the motion of the fluid in their interiors. To this end, Noir et al. (2009) investigated, via laboratory experiments and numerical simulations, the flow in a fluid filling a rotating spherical cavity driven by an axial oscillation of the container about a diameter. More realistically, the cavity is better represented by a triaxial ellipsoid. We may then distinguish between topographic and axisymmetricli libration. The latter refers to libration about a symmetry axis of the container which is therefore only viscously coupled to the fluid. In topographic libration, pressure forces on the boundary also affect the fluid motions in the cavity. We describe results from preliminary studies of topographic libration obtained through numerical simulation of incompressible fluid motion in an oblate spheroidal cavity with a libration axis perpendicular to the symmetry axis of the container. The computer code is a modification of one recently developed to study precessionally-driven flows in a spheroidal body of fluid (Wu and Roberts, 2009). It advances the flow in time using finite differences on overlapping grids; in this way the numerical difficulty known as the pole problem, is completely avoided.

Tear film proteome in age-related macular degeneration.

Science.gov (United States)

Winiarczyk, Mateusz; Kaarniranta, Kai; Winiarczyk, Stanisław; Adaszek, Łukasz; Winiarczyk, Dagmara; Mackiewicz, Jerzy

2018-06-01

Age-related macular degeneration (AMD) is the main reason for blindness in elderly people in the developed countries. Current screening protocols have limitations in detecting the early signs of retinal degeneration. Therefore, it would be desirable to find novel biomarkers for early detection of AMD. Development of novel biomarkers would help in the prevention, diagnostics, and treatment of AMD. Proteomic analysis of tear film has shown promise in this research area. If an optimal set of biomarkers could be obtained from accessible body fluids, it would represent a reliable way to monitor disease progression and response to novel therapies. Tear films were collected on Schirmer strips from a total of 22 patients (8 with wet AMD, 6 with dry AMD, and 8 control individuals). 2D electrophoresis was used to separate tear film proteins prior to their identification with matrix-assisted laser desorption/ionization time of flight spectrometer (MALDI-TOF/TOF) and matching with functional databases. A total of 342 proteins were identified. Most of them were previously described in various proteomic studies concerning AMD. Shootin-1, histatin-3, fidgetin-like protein 1, SRC kinase signaling inhibitor, Graves disease carrier protein, actin cytoplasmic 1, prolactin-inducible protein 1, and protein S100-A7A were upregulated in the tear film samples isolated from AMD patients and were not previously linked with this disease in any proteomic analysis. The upregulated proteins supplement our current knowledge of AMD pathogenesis, providing evidence that certain specific proteins are expressed into the tear film in AMD. As far we are aware, this is the first study to have undertaken a comprehensive in-depth analysis of the human tear film proteome in AMD patients.

Proteomic Analysis of Human Blastocoel Fluid and Blastocyst Cells

DEFF Research Database (Denmark)

Linnert Jensen, Pernille; Beck, Hans Christian; Petersen, Jørgen

The human blastocyst consists of 100-200 cells that are organized in an outer layer of differentiated trophectoderm (TE) cells lining the blastocyst cavity into which the undifferentiated inner cell mass (ICM) protrudes. The cavity of the blastocyst is filled with blastocoel fluid to which all...... the cells of the blastocyst are exposed. The ICM is the starting point for the development of undifferentiated human embryonic stem cells (hESCs), which posses the potential to develop into any cell type present in the adult human body [1,2]. This ability makes hESCs a potential source of cells...

Inactivation of human immunodeficiency virus (HIV) by ionizing radiation in body fluids and serological evidence

International Nuclear Information System (INIS)

Bigbee, P.D.; Sarin, P.S.; Humphreys, J.C.; Eubanks, W.G.; Sun, D.; Hocken, D.G.; Thornton, A.; Adams, D.E.; Simic, M.G.

1989-01-01

A method to use ionizing radiation to inactivate HIV (Human Immunodeficiency Virus) in human body fluids was studied in an effort to reduce the risk of accidental infection to forensic science laboratory workers. Experiments conducted indicate that an X-ray absorbed dose of 25 krad was required to completely inactivate HIV. This does not alter forensically important constituents such as enzymes and proteins in body fluids. This method of inactivation of HIV cannot be used on body fluids which will be subjected to deoxyribonucleic acid (DNA) typing

Survey of 800+ datasets from human tissue and body fluid reveals XenomiRs are likely artifacts

DEFF Research Database (Denmark)

Kang, Wenjing; Bang-Berthelsen, Claus Heiner; Holm, Anja

2017-01-01

the main bloodstream (such as brain and cerebro-spinal fluids). Interestingly, the majority (81%) of body fluid xenomiRs stem from rodents, which are rare human dietary contributions, but common laboratory animals. Body fluid samples from the same studies tend to group together when clustered by xenomi...

Tissue-based map of the human proteome

DEFF Research Database (Denmark)

Uhlén, Mathias; Fagerberg, Linn; Hallström, Björn M.

2015-01-01

Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transc...

Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification.

Science.gov (United States)

Donfack, Joseph; Wiley, Anissa

2015-05-01

Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework. Published by Elsevier Ireland Ltd.

Bioimpedance identifies body fluid loss after exercise in the heat: a pilot study with body cooling.

Directory of Open Access Journals (Sweden)

Hannes Gatterer

Full Text Available Assessment of post-exercise changes in hydration with bioimpedance (BI is complicated by physiological adaptations that affect resistance (R and reactance (Xc values. This study investigated exercise-induced changes in R and Xc, independently and in bioelectrical impedance vector analysis, when factors such as increased skin temperature and blood flow and surface electrolyte accumulation are eliminated with a cold shower.Healthy males (n = 14, 24.1±1.7 yr; height (H: 182.4±5.6 cm, body mass: 72.3±6.3 kg exercised for 1 hr at a self-rated intensity (15 BORG in an environmental chamber (33°C and 50% relative humidity, then had a cold shower (15 min. Before the run BI, body mass, hematocrit and Posm were measured. After the shower body mass was measured; BI measurements were performed continuously every 20 minutes until R reached a stable level, then hematocrit and Posm were measured again.Compared to pre-trial measurements body mass decreased after the run and Posm, Hct, R/H and Xc/H increased (p<0.05 with a corresponding lengthening of the impedance vector along the major axis of the tolerance ellipse (p<0.001. Changes in Posm were negatively related to changes in body mass (r = -0.564, p = 0.036 and changes in Xc/H (r = -0.577, p = 0.041.Present findings showed that after a bout of exercise-induced dehydration followed by cold shower the impedance vector lengthened that indicates fluid loss. Additionally, BI values might be useful to evaluate fluid shifts between compartments as lower intracellular fluid loss (changed Xc/R indicated greater Posm increase.

Renal renin secretion as regulator of body fluid homeostasis

DEFF Research Database (Denmark)

Damkjær, Mads; Isaksson, Gustaf L; Stubbe, Jane

2013-01-01

The renin-angiotensin system is essential for body fluid homeostasis and blood pressure regulation. This review focuses on the homeostatic regulation of the secretion of active renin in the kidney, primarily in humans. Under physiological conditions, renin secretion is determined mainly by sodium...

Development of Swimming Human Simulation Model Considering Rigid Body Dynamics and Unsteady Fluid Force for Whole Body

Science.gov (United States)

Nakashima, Motomu; Satou, Ken; Miura, Yasufumi

The purpose of this study is to develop a swimming human simulation model considering rigid body dynamics and unsteady fluid force for the whole body, which will be utilized to analyze various dynamical problems in human swimming. First, the modeling methods and their formulations for the human body and the fluid force are respectively described. Second, experiments to identify the coefficients of the normal drag and the added mass are conducted by use of an experimental setup, in which a limb model rotates in the water, and its rotating angle and the bending moment at the root are measured. As the result of the identification, the present model for the fluid force was found to have satisfactory performance in order to represent the unsteady fluctuations of the experimental data, although it has 10% error. Third, a simulation for the gliding position is conducted in order to identify the tangential drag coefficient. Finally, a simulation example of standard six beat front crawl swimming is shown. The swimming speed of the simulation became a reasonable value, indicating the validity of the present simulation model, although it is 7.5% lower than the actual swimming.

Analysis of selenium in body fluids: A review

International Nuclear Information System (INIS)

Alaejos, M.S.; Romero, C.D.

1995-01-01

This article reviews numerous analytical techniques for determining trace amounts of selenium in body fluids. In addition, sampling storage and treatment procedures are evaluated. The analytical techniques reviewed include the following: spectrofluorometry and spectrophotometry; atomic absorption spectrometry; fluorescence and atomic emission spectroscopy; mass spectroscopy; X-ray spectrometric analysis; neutron activation analysis; chromatographic methods; and electrochemical methods. 469 refs

Elevated host lipid metabolism revealed by iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid of tuberculous meningitis patients.

Science.gov (United States)

Mu, Jun; Yang, Yongtao; Chen, Jin; Cheng, Ke; Li, Qi; Wei, Yongdong; Zhu, Dan; Shao, Weihua; Zheng, Peng; Xie, Peng

2015-10-30

Tuberculous meningitis (TBM) remains to be one of the most deadly infectious diseases. The pathogen interacts with the host immune system, the process of which is largely unknown. Various cellular processes of Mycobacterium tuberculosis (MTB) centers around lipid metabolism. To determine the lipid metabolism related proteins, a quantitative proteomic study was performed here to identify differential proteins in the cerebrospinal fluid (CSF) obtained from TBM patients (n = 12) and healthy controls (n = 12). CSF samples were desalted, concentrated, labelled with isobaric tags for relative and absolute quantitation (iTRAQ™), and analyzed by multi-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene ontology and proteomic phenotyping analysis of the differential proteins were conducted using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. ApoE and ApoB were selected for validation by ELISA. Proteomic phenotyping of the 4 differential proteins was invloved in the lipid metabolism. ELISA showed significantly increased ApoB levels in TBM subjects compared to healthy controls. Area under the receiver operating characteristic curve analysis demonstrated ApoB levels could distinguish TBM subjects from healthy controls and viral meningitis subjects with 89.3% sensitivity and 92% specificity. CSF lipid metabolism disregulation, especially elevated expression of ApoB, gives insights into the pathogenesis of TBM. Further evaluation of these findings in larger studies including anti-tuberculosis medicated and unmedicated patient cohorts with other center nervous system infectious diseases is required for successful clinical translation. Copyright © 2015 Elsevier Inc. All rights reserved.

Strongly Coupled Fluid-Body Dynamics in the Immersed Boundary Projection Method

Science.gov (United States)

Wang, Chengjie; Eldredge, Jeff D.

2014-11-01

A computational algorithm is developed to simulate dynamically coupled interaction between fluid and rigid bodies. The basic computational framework is built upon a multi-domain immersed boundary method library, whirl, developed in previous work. In this library, the Navier-Stokes equations for incompressible flow are solved on a uniform Cartesian grid by the vorticity-based immersed boundary projection method of Colonius and Taira. A solver for the dynamics of rigid-body systems is also included. The fluid and rigid-body solvers are strongly coupled with an iterative approach based on the block Gauss-Seidel method. Interfacial force, with its intimate connection with the Lagrange multipliers used in the fluid solver, is used as the primary iteration variable. Relaxation, developed from a stability analysis of the iterative scheme, is used to achieve convergence in only 2-4 iterations per time step. Several two- and three-dimensional numerical tests are conducted to validate and demonstrate the method, including flapping of flexible wings, self-excited oscillations of a system of linked plates and three-dimensional propulsion of flexible fluked tail. This work has been supported by AFOSR, under Award FA9550-11-1-0098.

Growth hormone treatment improves body fluid distribution in patients undergoing elective abdominal surgery

DEFF Research Database (Denmark)

Møller, J; Jensen, M B; Frandsen, E

1998-01-01

OBJECTIVE: To investigate the possible beneficial effects of growth hormone (GH) in catabolic patients we examined the impact of GH on body fluid distribution in patients with ulcerative colitis undergoing elective abdominal surgery. DESIGN AND MEASUREMENTS: Twenty-four patients (14 female, 10 male...... at day -2 and at day 7, and body composition was estimated by dual X-ray absorptiometry and bioimpedance. Changes in body weight and fluid balance were recorded and hence intracellular volume was assessed. RESULTS: During placebo treatment body weight decreased 4.3 +/- 0.6 kg; during GH treatment body.......05). Plasma renin and aldosterone remained unchanged in both study groups. CONCLUSION: Body weight, plasma volume and intracellular volume is preserved during GH treatment in catabolic patients and ECV is increased. From a therapeutic point of view these effects may be desirable under conditions of surgical...

Development of mRNA-based body fluid identification using reverse transcription loop-mediated isothermal amplification.

Science.gov (United States)

Satoh, Tetsuya; Kouroki, Seiya; Ogawa, Keita; Tanaka, Yorika; Matsumura, Kazutoshi; Iwase, Susumu

2018-04-25

Identifying body fluids from forensic samples can provide valuable evidence for criminal investigations. Messenger RNA (mRNA)-based body fluid identification was recently developed, and highly sensitive parallel identification using reverse transcription polymerase chain reaction (RT-PCR) has been described. In this study, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a simple, rapid assay for identifying three common forensic body fluids, namely blood, semen, and saliva, and evaluated its specificity and sensitivity. Hemoglobin beta (HBB), transglutaminase 4 (TGM4), and statherin (STATH) were selected as marker genes for blood, semen, and saliva, respectively. RT-LAMP could be performed in a single step including both reverse transcription and DNA amplification under an isothermal condition within 60 min, and detection could be conveniently performed via visual fluorescence. Marker-specific amplification was performed in each assay, and no cross-reaction was observed among five representative forensically relevant body fluids. The detection limits of the assays were 0.3 nL, 30 nL, and 0.3 μL for blood, semen, and saliva, respectively, and their sensitivities were comparable with those of RT-PCR. Furthermore, RT-LAMP assays were applicable to forensic casework samples. It is considered that RT-LAMP is useful for body fluid identification.

Position feedback control of a nonmagnetic body levitated in magnetic fluid

International Nuclear Information System (INIS)

Lee, J H; Nam, Y J; Park, M K; Yamane, R

2009-01-01

This paper is concerned with the position feedback control of a magnetic fluid actuator which is characterized by the passive levitation of a nonmagnetic body immersed in a magnetic fluid under magnetic fields. First of all, the magnetic fluid actuator is designed based on the ferrohydrostatic relation. After manufacturing the actuator, its static and dynamic characteristics are investigated experimentally. With the aid of the dynamic governing relation obtained experimentally and the proportional-derivative controller, the position tracking control of the actuator is carried out both theoretically and experimentally. As a result, the applicability of the proposed magnetic fluid actuator to various engineering devices is verified.

Flutter Instability of a Fluid-Conveying Fluid-Immersed Pipe Affixed to a Rigid Body

Science.gov (United States)

2011-01-01

rigid body, denoted by y in Fig. 4, is small. This is in addition to the Euler– Bernoulli beam assumption that the slope of the tail is small everywhere...here. These include the efficiency with which the prime mover can generate fluid momentum , pipe losses, and external drag acting on both the hull and the

Corrosion behavior of coated and uncoated bio implants in SBF(simulated body fluid)

International Nuclear Information System (INIS)

Iqbal, W.; Zahra, N.; Alam, S.; Habib, F.; Irfan, M.

2013-01-01

Surgical implants used in medical applications are basically the specific type of stainless steel materials. Stainless steel has been used widely and successfully for various types of trauma and orthopedic reconstructions. If an uncoated (bare) stainless steel metal piece is implanted in any part of the body, it will get corrode in Simulated Body Fluid (SBF) present inside the human body (a mixture of different salts). To overcome this problem a coating of Titanium Nitride (TiN) was developed on stainless steel bio-implants using physical vapor deposition (PVD) method. Both coated and uncoated implants were kept dipped in Simulated Body Fluid for five months. The samples were removed and tested for corrosion life assessment after every fifteen days using weight loss method. (author)

Enrichment methodology to increase the positivity of cultures from body fluids

Directory of Open Access Journals (Sweden)

Alessandra Valle Daur

Full Text Available Isolation and identification of etiological agents found in body fluids can be of critical importance for the recovery of patients suffering from potentially-severe infections, which are often followed by serious sequels. Eighty-two samples of different body fluids were analyzed using two different methods: (1 the conventional culture method (agar plating and (2 the enrichment culture technique, using the Bact/Alert® blood culture bottle. The number of positive cultures increased on average from 9.7% to 23.1% with the enrichment culture technique. Pseudomonas aeruginosa, Escherichia coli and Staphylococcus aureus were the most frequently isolated bacteria. The enrichment method could provide a more accurate means the identifying etiological agents.

Autoantibody profiling on human proteome microarray for biomarker discovery in cerebrospinal fluid and sera of neuropsychiatric lupus.

Directory of Open Access Journals (Sweden)

Chaojun Hu

Full Text Available Autoantibodies in cerebrospinal fluid (CSF from patients with neuropsychiatric systemic lupus erythematosus (NPSLE may be potential biomarkers for prediction, diagnosis, or prognosis of NPSLE. We used a human proteome microarray with~17,000 unique full-length human proteins to investigate autoantibodies associated with NPSLE. Twenty-nine CSF specimens from 12 NPSLE, 7 non-NPSLE, and 10 control (non-systemic lupus erythematosuspatients were screened for NPSLE-associated autoantibodies with proteome microarrays. A focused autoantigen microarray of candidate NPSLE autoantigens was applied to profile a larger cohort of CSF with patient-matched sera. We identified 137 autoantigens associated with NPSLE. Ingenuity Pathway Analysis revealed that these autoantigens were enriched for functions involved in neurological diseases (score = 43.Anti-proliferating cell nuclear antigen (PCNA was found in the CSF of NPSLE and non-NPSLE patients. The positive rates of 4 autoantibodies in CSF specimens were significantly different between the SLE (i.e., NPSLE and non-NPSLE and control groups: anti-ribosomal protein RPLP0, anti-RPLP1, anti-RPLP2, and anti-TROVE2 (also known as anti-Ro/SS-A. The positive rate for anti-SS-A associated with NPSLE was higher than that for non-NPSLE (31.11% cf. 10.71%; P = 0.045.Further analysis showed that anti-SS-A in CSF specimens was related to neuropsychiatric syndromes of the central nervous system in SLE (P = 0.009. Analysis with Spearman's rank correlation coefficient indicated that the titers of anti-RPLP2 and anti-SS-A in paired CSF and serum specimens significantly correlated. Human proteome microarrays offer a powerful platform to discover novel autoantibodies in CSF samples. Anti-SS-A autoantibodies may be potential CSF markers for NPSLE.

Fluid electrolyte excretion during different hypokinetic body positions of trained subjects

Science.gov (United States)

Zorbas, Yan G.; Naexu, Konstantin A.; Federenko, Youri F.

The aim of this study was to evaluate the effect of different body positions on renal excretion of fluid and electrolytes after exposure to 364 days of decreased number of steps per day (hypokinesia, HK). The studies were performed on 18 endurance trained male volunteers aged 19-24 years who had an average of VO 2max 67 ml/kg body/min. All volunteers were divided into three equal groups: the 1st group subjected to 12 h orthostatic position (OP) and 12 h clinostatic position (CP)/day, the 2nd group exposed to 8 h orthostatic position and 14 h clinostatic position/day, and the 3rd group submitted to 10 h orthostatic position and 16 h clinostatic position/day for 364 days. For the simulation of the hypokinetic effect all volunteers were kept under an average of 3000 steps/day for 364 days. Diuresis and the concentrations of sodium, potassium, chloride, calcium and magnesium as well as excretion of creatine were determined in 24-h urine samples. By the end of the hypokinetic period all volunteers, regardless of their body position during HK, manifested a significant increase in renal excretion of fluid and electrolytes as compared to prehypokinetic period values. It was concluded that prolonged restriction of motor activity induced a significant increase in renal excretion of fluid and electrolytes in endurance trained subjects regardless to their body position and duration thereof per day.

Proteomics of Skeletal Muscle: Focus on Insulin Resistance and Exercise Biology

Directory of Open Access Journals (Sweden)

Atul S. Deshmukh

2016-02-01

Full Text Available Skeletal muscle is the largest tissue in the human body and plays an important role in locomotion and whole body metabolism. It accounts for ~80% of insulin stimulated glucose disposal. Skeletal muscle insulin resistance, a primary feature of Type 2 diabetes, is caused by a decreased ability of muscle to respond to circulating insulin. Physical exercise improves insulin sensitivity and whole body metabolism and remains one of the most promising interventions for the prevention of Type 2 diabetes. Insulin resistance and exercise adaptations in skeletal muscle might be a cause, or consequence, of altered protein expressions profiles and/or their posttranslational modifications (PTMs. Mass spectrometry (MS-based proteomics offer enormous promise for investigating the molecular mechanisms underlying skeletal muscle insulin resistance and exercise-induced adaptation; however, skeletal muscle proteomics are challenging. This review describes the technical limitations of skeletal muscle proteomics as well as emerging developments in proteomics workflow with respect to samples preparation, liquid chromatography (LC, MS and computational analysis. These technologies have not yet been fully exploited in the field of skeletal muscle proteomics. Future studies that involve state-of-the-art proteomics technology will broaden our understanding of exercise-induced adaptations as well as molecular pathogenesis of insulin resistance. This could lead to the identification of new therapeutic targets.

Discriminant analysis of Raman spectra for body fluid identification for forensic purposes.

Science.gov (United States)

Sikirzhytski, Vitali; Virkler, Kelly; Lednev, Igor K

2010-01-01

Detection and identification of blood, semen and saliva stains, the most common body fluids encountered at a crime scene, are very important aspects of forensic science today. This study targets the development of a nondestructive, confirmatory method for body fluid identification based on Raman spectroscopy coupled with advanced statistical analysis. Dry traces of blood, semen and saliva obtained from multiple donors were probed using a confocal Raman microscope with a 785-nm excitation wavelength under controlled laboratory conditions. Results demonstrated the capability of Raman spectroscopy to identify an unknown substance to be semen, blood or saliva with high confidence.

Discriminant Analysis of Raman Spectra for Body Fluid Identification for Forensic Purposes

Directory of Open Access Journals (Sweden)

Vitali Sikirzhytski

2010-03-01

Full Text Available Detection and identification of blood, semen and saliva stains, the most common body fluids encountered at a crime scene, are very important aspects of forensic science today. This study targets the development of a nondestructive, confirmatory method for body fluid identification based on Raman spectroscopy coupled with advanced statistical analysis. Dry traces of blood, semen and saliva obtained from multiple donors were probed using a confocal Raman microscope with a 785-nm excitation wavelength under controlled laboratory conditions. Results demonstrated the capability of Raman spectroscopy to identify an unknown substance to be semen, blood or saliva with high confidence.

Interactions between internal forces, body stiffness, and fluid environment in a neuromechanical model of lamprey swimming.

Science.gov (United States)

Tytell, Eric D; Hsu, Chia-Yu; Williams, Thelma L; Cohen, Avis H; Fauci, Lisa J

2010-11-16

Animal movements result from a complex balance of many different forces. Muscles produce force to move the body; the body has inertial, elastic, and damping properties that may aid or oppose the muscle force; and the environment produces reaction forces back on the body. The actual motion is an emergent property of these interactions. To examine the roles of body stiffness, muscle activation, and fluid environment for swimming animals, a computational model of a lamprey was developed. The model uses an immersed boundary framework that fully couples the Navier-Stokes equations of fluid dynamics with an actuated, elastic body model. This is the first model at a Reynolds number appropriate for a swimming fish that captures the complete fluid-structure interaction, in which the body deforms according to both internal muscular forces and external fluid forces. Results indicate that identical muscle activation patterns can produce different kinematics depending on body stiffness, and the optimal value of stiffness for maximum acceleration is different from that for maximum steady swimming speed. Additionally, negative muscle work, observed in many fishes, emerges at higher tail beat frequencies without sensory input and may contribute to energy efficiency. Swimming fishes that can tune their body stiffness by appropriately timed muscle contractions may therefore be able to optimize the passive dynamics of their bodies to maximize peak acceleration or swimming speed.

Examining hemodialyzer membrane performance using proteomic technologies.

Science.gov (United States)

Bonomini, Mario; Pieroni, Luisa; Di Liberato, Lorenzo; Sirolli, Vittorio; Urbani, Andrea

2018-01-01

The success and the quality of hemodialysis therapy are mainly related to both clearance and biocompatibility properties of the artificial membrane packed in the hemodialyzer. Performance of a membrane is strongly influenced by its interaction with the plasma protein repertoire during the extracorporeal procedure. Recognition that a number of medium-high molecular weight solutes, including proteins and protein-bound molecules, are potentially toxic has prompted the development of more permeable membranes. Such membrane engineering, however, may cause loss of vital proteins, with membrane removal being nonspecific. In addition, plasma proteins can be adsorbed onto the membrane surface upon blood contact during dialysis. Adsorption can contribute to the removal of toxic compounds and governs the biocompatibility of a membrane, since surface-adsorbed proteins may trigger a variety of biologic blood pathways with pathophysiologic consequences. Over the last years, use of proteomic approaches has allowed polypeptide spectrum involved in the process of hemodialysis, a key issue previously hampered by lack of suitable technology, to be assessed in an unbiased manner and in its full complexity. Proteomics has been successfully applied to identify and quantify proteins in complex mixtures such as dialysis outflow fluid and fluid desorbed from dialysis membrane containing adsorbed proteins. The identified proteins can also be characterized by their involvement in metabolic and signaling pathways, molecular networks, and biologic processes through application of bioinformatics tools. Proteomics may thus provide an actual functional definition as to the effect of a membrane material on plasma proteins during hemodialysis. Here, we review the results of proteomic studies on the performance of hemodialysis membranes, as evaluated in terms of solute removal efficiency and blood-membrane interactions. The evidence collected indicates that the information provided by proteomic

Minimally-invasive, microneedle-array extraction of interstitial fluid for comprehensive biomedical applications: transcriptomics, proteomics, metabolomics, exosome research, and biomarker identification.

Science.gov (United States)

Taylor, Robert M; Miller, Philip R; Ebrahimi, Parwana; Polsky, Ronen; Baca, Justin T

2018-01-01

Interstitial fluid (ISF) has recently garnered interest as a biological fluid that could be used as an alternate to blood for biomedical applications, diagnosis, and therapy. ISF extraction techniques are promising because they are less invasive and less painful than venipuncture. ISF is an alternative, incompletely characterized source of physiological data. Here, we describe a novel method of ISF extraction in rats, using microneedle arrays, which provides volumes of ISF that are sufficient for downstream analysis techniques such as proteomics, genomics, and extracellular vesicle purification and analysis. This method is potentially less invasive than previously reported techniques. The limited invasiveness and larger volumes of extracted ISF afforded by this microneedle-assisted ISF extraction method provide a technique that is less stressful and more humane to laboratory animals, while also allowing for a reduction in the numbers of animals needed to acquire sufficient volumes of ISF for biomedical analysis and application.

Metabolic stability of new anticonvulsants in body fluids and organ homogenates.

Science.gov (United States)

Marszałek, Dorota; Goldnik, Anna; Pluciński, Franciszek; Mazurek, Aleksander P; Jakubiak, Anna; Lis, Ewa; Tazbir, Piotr; Koziorowska, Agnieszka

2012-01-01

The stability as a function of time of compounds with established anticonvulsant activity: picolinic acid benzylamide (Pic-BZA), picolinic acid 2-fluorobenzylamide (Pic-2-F-BZA), picolinic acid 3-fluorobenzylamide (Pic-3-F-BZA), picolinic acid 4-fluorobenzylamide (Pic-4-F-BZA) and picolinic acid 2-methylbenzylamide (Pic-2-Me-BZA) in body fluids and homogenates of body organs were determined after incubation. It was found that they decompose relatively rapidly in liver and kidney and are stable against enzymes present in body fluids and some organs. These results are consistent with the bond strength expressed as total energy of amide bonds (calculated by quantum chemical methods) in the studied anticonvulsants. The calculated values of the amide bond energy are: 199.4 kcal/mol, 200.2 kcal/mol, 207.5 kcal/mol, 208.4 kcal/mol and 198.2 kcal/mol, respectively. The strength of the amide bonds in the studied anticonvulsants correctly reflects their stability in liver or kidney.

Power of Proteomics in Linking Oxidative Stress and Female Infertility

Science.gov (United States)

Gupta, Sajal; Sharma, Rakesh; Agarwal, Ashok

2014-01-01

Endometriosis, PCOS, and unexplained infertility are currently the most common diseases rendering large numbers of women infertile worldwide. Oxidative stress, due to its deleterious effects on proteins and nucleic acids, is postulated to be the one of the important mechanistic pathways in differential expression of proteins and in these diseases. The emerging field of proteomics has allowed identification of proteins involved in cell cycle, as antioxidants, extracellular matrix (ECM), cytoskeleton, and their linkage to oxidative stress in female infertility related diseases. The aim of this paper is to assess the association of oxidative stress and protein expression in the reproductive microenvironments such as endometrial fluid, peritoneal fluid, and follicular fluid, as well as reproductive tissues and serum. The review also highlights the literature that proposes the use of the fertility related proteins as potential biomarkers for noninvasive and early diagnosis of the aforementioned diseases rather than utilizing the more invasive methods used currently. The review will highlight the power of proteomic profiles identified in infertility related disease conditions and their linkage with underlying oxidative stress. The power of proteomics will be reviewed with regard to eliciting molecular mechanisms for early detection and management of these infertility related conditions. PMID:24900998

Power of Proteomics in Linking Oxidative Stress and Female Infertility

Directory of Open Access Journals (Sweden)

Sajal Gupta

2014-01-01

Full Text Available Endometriosis, PCOS, and unexplained infertility are currently the most common diseases rendering large numbers of women infertile worldwide. Oxidative stress, due to its deleterious effects on proteins and nucleic acids, is postulated to be the one of the important mechanistic pathways in differential expression of proteins and in these diseases. The emerging field of proteomics has allowed identification of proteins involved in cell cycle, as antioxidants, extracellular matrix (ECM, cytoskeleton, and their linkage to oxidative stress in female infertility related diseases. The aim of this paper is to assess the association of oxidative stress and protein expression in the reproductive microenvironments such as endometrial fluid, peritoneal fluid, and follicular fluid, as well as reproductive tissues and serum. The review also highlights the literature that proposes the use of the fertility related proteins as potential biomarkers for noninvasive and early diagnosis of the aforementioned diseases rather than utilizing the more invasive methods used currently. The review will highlight the power of proteomic profiles identified in infertility related disease conditions and their linkage with underlying oxidative stress. The power of proteomics will be reviewed with regard to eliciting molecular mechanisms for early detection and management of these infertility related conditions.

Evaluation of nuclear magnetic resonance spectroscopy for determination of deuterium abundance in body fluids: application to measurement of total-body water in human infants

International Nuclear Information System (INIS)

Rebouche, C.J.; Pearson, G.A.; Serfass, R.E.; Roth, C.W.; Finley, J.W.

1987-01-01

Nuclear magnetic resonance (NMR) spectroscopy was used to quantitate abundance of 2H in body water of human infants. This method provides precise measurement of total-body water without the extensive sample preparation requirements of previously described methods for determination of 2H content in body fluids. 2H2O (1 g/kg body weight) was administered to infants and saliva and urine were collected for up to 5 h. An internal standard was added directly to the fluid specimen and 2H enrichment in water was measured by NMR spectroscopy. Working range of deuterium abundance was 0.04-0.32 atom %. Coefficients of variation for saliva samples at 0.20 atom % 2H was 1.97%. 2H content in urine and saliva water reached a plateau by 4 h after administration, and amounts in the two fluids were virtually identical. Mean total-body water determination for six infants was 58.3 +/- 5.8% of body weight (range 53-66%)

Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders

Directory of Open Access Journals (Sweden)

Venugopal Abhilash

2009-01-01

Full Text Available Mass spectrometry-based quantitative proteomics has emerged as a powerful approach that has the potential to accelerate biomarker discovery, both for diagnostic as well as therapeutic purposes. Proteomics has traditionally been synonymous with 2D gels but is increasingly shifting to the use of gel-free systems and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS. Quantitative proteomic approaches have already been applied to investigate various neurological disorders, especially in the context of identifying biomarkers from cerebrospinal fluid and serum. This review highlights the scope of different applications of quantitative proteomics in understanding neurological disorders with special emphasis on biomarker discovery.

Quantitative analysis of lamellar bodies in amniotic fluid as fetal pulmonary maturity indicator

Directory of Open Access Journals (Sweden)

Ljubić Vesna

2009-01-01

Full Text Available Background/Aim. Although lamellar bodies have been the center of interest over the last years, the published results of fetal pulmonary maturity determination according to their concentration in amniotic fluid are controversial. The aim of this study was to determine the significance of lamellar bodies, as well as the ratio lecithin/sphingomyelin (L/S in amniotic fluid for the assessment of fetal pulmonary maturity. Methods. This prospective 2-year study included 102 female examinees, ranging from 17 to 44 years of age, in whom lamellar bodies concentrations in amniotic fluid were determined to check the efficacy of the applied therapy for obtaining arteficial fetal pulmonary maturity. The shake test was applied as a comparative test for determining a quantitative L/S ratio. To determine a fetus maturity and development stage we followed up biparietal diameter, abdominal circumference, femure length, ponderal index at birth and body mass. Results. Out of a total of 102 amniocenteses within a period from 26th to 40th gestation week only 70 results were considered due to 32 unknown neonatal outcomes. Biparietal diameter was 224-362 mm, femur length 56 - 78 mm, ponderal index 1.22-2.84, fetus body mass 1300- 4 350 g. There was found a significant relation between gestation age and lamellar bodies concentration (R = 0.396398, p < 0.01, as well as between gestation age and the ratio L/S (R = 0.691297, p < 0.01. Also, there was a significant correlation of lamellar bodies concentration to the ratio L/S determined (R = 0.493609, p < 0.01. Conclusion. Determination of lamellar bodies concentration values is a reliable method to confirm fetal pulmonary maturity.

Two-body perturbation theory versus first order perturbation theory: A comparison based on the square-well fluid.

Science.gov (United States)

Mercier Franco, Luís Fernando; Castier, Marcelo; Economou, Ioannis G

2017-12-07

We show that the Zwanzig first-order perturbation theory can be obtained directly from a truncated Taylor series expansion of a two-body perturbation theory and that such truncation provides a more accurate prediction of thermodynamic properties than the full two-body perturbation theory. This unexpected result is explained by the quality of the resulting approximation for the fluid radial distribution function. We prove that the first-order and the two-body perturbation theories are based on different approximations for the fluid radial distribution function. To illustrate the calculations, the square-well fluid is adopted. We develop an analytical expression for the two-body perturbed Helmholtz free energy for the square-well fluid. The equation of state obtained using such an expression is compared to the equation of state obtained from the first-order approximation. The vapor-liquid coexistence curve and the supercritical compressibility factor of a square-well fluid are calculated using both equations of state and compared to Monte Carlo simulation data. Finally, we show that the approximation for the fluid radial distribution function given by the first-order perturbation theory provides closer values to the ones calculated via Monte Carlo simulations. This explains why such theory gives a better description of the fluid thermodynamic behavior.

Determination of toxic trace elements in body fluid reference samples

International Nuclear Information System (INIS)

Gills, T.E.; McClendon, L.T.; Maienthal, E.J.; Becker, D.A.; Durst, R.A.; LaFleur, P.D.

1974-01-01

The measurement of elemental concentration in body fluids has been widely used to give indication of exposures to certain toxic materials and/or a measure of body burden. To understand fully the toxicological effect of these trace elements on our physiological system, meaningful analytical data are required along with accurate standards or reference samples. The National Bureau of Standards has prepared for the National Institute for Occupational Safety and Health (NIOSH) a number of reference samples containing selected toxic trace elements in body fluids. The reference samples produced include mercury in urine at three concentration levels, five elements (Se, Cu, As, Ni and Cr) in freeze-dried urine at two levels, fluorine in freeze-dried urine at two levels and lead in blood at two concentration levels. These reference samples have been found to be extremely useful for the evaluation of field and laboratory analytical methods for the analysis of toxic trace elements. In particular the use of at least two calibration points (i.e., ''normal'' and ''elevated'' levels) for a given matrix provides a more positive calibration for most analytical techniques over the range of interest for occupational toxicological levels of exposure. (U.S.)

Impact of color blindness on recognition of blood in body fluids.

Science.gov (United States)

Reiss, M J; Labowitz, D A; Forman, S; Wormser, G P

2001-02-12

Color blindness is a common hereditary X-linked disorder. To investigate whether color blindness affects the ability to detect the presence of blood in body fluids. Ten color-blind subjects and 20 sex- and age-matched control subjects were shown 94 photographs of stool, urine, or sputum. Frank blood was present in 57 (61%) of the photographs. Surveys were done to determine if board-certified internists had ever considered whether color blindness would affect detection of blood and whether an inquiry on color blindness was included in their standard medical interview. Color-blind subjects were significantly less able to identify correctly whether pictures of body fluids showed blood compared with non-color-blind controls (P =.001); the lowest rate of correct identifications occurred with pictures of stool (median of 26 [70%] of 37 for color-blind subjects vs 36.5 [99%] of 37 for controls; Pcolor-blind subjects were significantly less accurate than those with less severe color deficiency (P =.009). Only 2 (10%) of the 21 physicians had ever considered the possibility that color blindness might affect the ability of patients to detect blood, and none routinely asked their patients about color blindness. Color blindness impairs recognition of blood in body fluids. Color-blind individuals and their health care providers need to be made aware of this limitation.

Effect of irrigation fluid temperature on body temperature during arthroscopic elbow surgery in dogs.

Science.gov (United States)

Thompson, K R; MacFarlane, P D

2013-01-01

This prospective randomised clinical trial evaluated the effect of warmed irrigation fluid on body temperature in anaesthetised dogs undergoing arthroscopic elbow surgery. Nineteen dogs undergoing elbow arthroscopy were included in the study and were randomly allocated to one of two groups. Group RT received irrigation fluid at room temperature (RT) while dogs in group W received warmed (W) irrigation fluid (36°C). A standardised patient management and anaesthetic protocol was used and body temperature was measured at four time points; (T1) pre-anaesthetic examination, (T2) arrival into theatre, (T3) end of surgery and (T4) arrival into recovery. There was no significant difference in body temperature at any time point between the groups. The mean overall decrease in body temperature between pre-anaesthetic examination (T1) and return to the recovery suite (T4) was significant in both groups, with a fall of 1.06±0.58°C (pdogs were hypothermic (temperature management protocol in dogs undergoing elbow arthroscopy during general anaesthesia did not lead to decreased temperature losses.

Analysis of body fluids for forensic purposes: from laboratory testing to non-destructive rapid confirmatory identification at a crime scene.

Science.gov (United States)

Virkler, Kelly; Lednev, Igor K

2009-07-01

Body fluid traces recovered at crime scenes are among the most important types of evidence to forensic investigators. They contain valuable DNA evidence which can identify a suspect or victim as well as exonerate an innocent individual. The first step of identifying a particular body fluid is highly important since the nature of the fluid is itself very informative to the investigation, and the destructive nature of a screening test must be considered when only a small amount of material is available. The ability to characterize an unknown stain at the scene of the crime without having to wait for results from a laboratory is another very critical step in the development of forensic body fluid analysis. Driven by the importance for forensic applications, body fluid identification methods have been extensively developed in recent years. The systematic analysis of these new developments is vital for forensic investigators to be continuously educated on possible superior techniques. Significant advances in laser technology and the development of novel light detectors have dramatically improved spectroscopic methods for molecular characterization over the last decade. The application of this novel biospectroscopy for forensic purposes opens new and exciting opportunities for the development of on-field, non-destructive, confirmatory methods for body fluid identification at a crime scene. In addition, the biospectroscopy methods are universally applicable to all body fluids unlike the majority of current techniques which are valid for individual fluids only. This article analyzes the current methods being used to identify body fluid stains including blood, semen, saliva, vaginal fluid, urine, and sweat, and also focuses on new techniques that have been developed in the last 5-6 years. In addition, the potential of new biospectroscopic techniques based on Raman and fluorescence spectroscopy is evaluated for rapid, confirmatory, non-destructive identification of a body

Proteomic analysis of oil bodies in mature Jatropha curcas seeds with different lipid content.

Science.gov (United States)

Liu, Hui; Wang, Cuiping; Chen, Fan; Shen, Shihua

2015-01-15

To reveal the difference among three mature Jatropha curcas seeds (JcVH, variant with high lipid content; JcW, wild type and JcVL, variant with low lipid content) with different lipid content, comparative proteomics was employed to profile the changes of oil body (OB) associated protein species by using gels-based proteomic technique. Eighty-three protein species were successfully identified through LTQ-ES-MS/MS from mature JcW seeds purified OBs. Two-dimensional electrophoresis analysis of J. curcas OB associated protein species revealed they had essential interactions with other organelles and demonstrated that oleosin and caleosin were the most abundant OB structural protein species. Twenty-eight OB associated protein species showed significant difference among JcVH, JcW and JcVL according to statistical analysis. Complementary transient expression analysis revealed that calcium ion binding protein (CalBP) and glycine-rich RNA binding protein (GRP) were well targeted in OBs apart from the oleosins. This study demonstrated that ratio of lipid content to caleosins abundance was involved in the regulation of OB size, and the mutant induced by ethylmethylsulfone treatment might be related to the caleosin like protein species. These findings are important for biotechnological improvement with the aim to alter the lipid content in J. curcas seeds. The economic value of Jatropha curcas largely depends on the lipid content in seeds which are mainly stored in the special organelle called oil bodies (OBs). In consideration of the biological importance and applications of J. curcas OB in seeds, it is necessary to further explore the components and functions of J. curcas OBs. Although a previous study concerning the J. curcas OB proteome revealed oleosins were the major OB protein component and additional protein species were similar to those in other oil seed plants, these identified OB associated protein species were corresponding to the protein bands instead of protein

The Proteomics Big Challenge for Biomarkers and New Drug-Targets Discovery

Science.gov (United States)

Savino, Rocco; Paduano, Sergio; Preianò, Mariaimmacolata; Terracciano, Rosa

2012-01-01

In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets. PMID:23203042

Role of passive body dynamics in micro-organism swimming in complex fluids

Science.gov (United States)

Thomases, Becca; Guy, Robert

2016-11-01

We investigate the role of passive body dynamics in the kinematics of swimming micro-organisms in complex fluids. Asymptotic analysis and linear theory are used to predict shape changes that result as body elasticity and fluid elasticity are varied. The analysis is compared with a computational model of a finite length swimmer in a Stokes-Oldroyd-B fluid. Simulations and theory agree quantitatively for small amplitude motions with low fluid elasticity (Deborah number). This may not be surprising as the theory is expected hold in these two regimes. What is more remarkable is that the predicted shape changes match the computational shape changes quantitatively for large amplitudes, even for large Deborah numbers. Shape changes only tell part of the story. Swimming speed depends on other effects as well. We see that shape changes can predict swimming speed well when either the amplitude is small (including large Deborah number) or when the Deborah number is small (including large amplitudes). It is only in the large De AND large amplitude regime where the theory breaks down and swimming speed can no longer be inferred from shape changes alone.

Proteomic characterisation of endoplasmic reticulum-derived protein bodies in tobacco leaves

Directory of Open Access Journals (Sweden)

Joseph Minu

2012-03-01

Full Text Available Abstract Background The N-terminal proline-rich domain (Zera of the maize storage protein γ-zein, is able to induce the formation of endoplasmic reticulum (ER-derived protein bodies (PBs when fused to proteins of interest. This encapsulation enables a recombinant fused protein to escape from degradation and facilitates its recovery from plant biomass by gradient purification. The aim of the present work was to evaluate if induced PBs encapsulate additional proteins jointly with the recombinant protein. The exhaustive analysis of protein composition of PBs is expected to facilitate a better understanding of PB formation and the optimization of recombinant protein purification approaches from these organelles. Results We analysed the proteome of PBs induced in Nicotiana benthamiana leaves by transient transformation with Zera fused to a fluorescent marker protein (DsRed. Intact PBs with their surrounding ER-membrane were isolated on iodixanol based density gradients and their integrity verified by confocal and electron microscopy. SDS-PAGE analysis of isolated PBs showed that Zera-DsRed accounted for around 85% of PB proteins in term of abundance. Differential extraction of PBs was performed for in-depth analysis of their proteome and structure. Besides Zera-DsRed, 195 additional proteins were identified including a broad range of proteins resident or trafficking through the ER and recruited within the Zera-DsRed polymer. Conclusions This study indicates that Zera-protein fusion is still the major protein component of the new formed organelle in tobacco leaves. The analysis also reveals the presence of an unexpected diversity of proteins in PBs derived from both the insoluble Zera-DsRed polymer formation, including ER-resident and secretory proteins, and a secretory stress response induced most likely by the recombinant protein overloading. Knowledge of PBs protein composition is likely to be useful to optimize downstream purification of

Elimination of cotinine from body fluids: implications for noninvasive measurement of tobacco smoke exposure.

Science.gov (United States)

Jarvis, M J; Russell, M A; Benowitz, N L; Feyerabend, C

1988-01-01

Cotinine elimination from plasma, saliva, and urine was studied over 11 days in five subjects (three nonsmokers and two occasional smokers). Half-lives for cotinine averaged 16-19 hours in the different body fluids (range 10 to 27 hours between subjects). There was no tendency for the half-life in saliva to be longer than in plasma or urine. We conclude that choice of body fluid for cotinine assay in smoking studies should depend on practical rather than pharmacokinetic considerations. PMID:3369603

Cold-water acclimation does not modify whole-body fluid regulation during subsequent cold-water immersion.

Science.gov (United States)

Stocks, J M; Patterson, M J; Hyde, D E; Jenkins, A B; Mittleman, K D; Taylor, N A S

2004-06-01

We investigated the impact of cold-water acclimation on whole-body fluid regulation using tracer-dilution methods to differentiate between the intracellular and extracellular fluid compartments. Seven euhydrated males [age 24.7 (8.7) years, mass 74.4 (6.4) kg, height 176.8 (7.8) cm, sum of eight skinfolds 107.4 (20.4) mm; mean (SD)] participated in a 14-day cold-water acclimation protocol, with 60-min resting cold-water stress tests [CWST; 18.1 (0.1) degrees C] on days 1, 8 and 15, and 90-min resting cold-water immersions [18.4 (0.4) degrees C] on intervening days. Subjects were immersed to the 4th intercostal space. Intracellular and extracellular fluid compartments, and plasma protein, electrolyte and hormone concentrations were investigated. During the first CWST, the intracellular fluid (5.5%) and plasma volumes were reduced (6.1%), while the interstitial fluid volume was simultaneously expanded (5.4%). This pattern was replicated on days 8 and 15, but did not differ significantly among test days. Acclimation did not produce significant changes in the pre-immersion distribution of total body water, or changes in plasma osmolality, total protein, electrolyte, atrial natriuretic peptide or aldosterone concentrations. Furthermore, a 14-day cold-water acclimation regimen did not elicit significant changes in body-fluid distribution, urine production, or the concentrations of plasma protein, electrolytes or the fluid-regulatory hormones. While acclimation trends were not evident, we have confirmed that fluid from extravascular cells is displaced into the interstitium during acute cold-water immersion, both before and after cold acclimation.

Variations in the cerebrospinal fluid proteome following traumatic brain injury and subarachnoid hemorrhage.

Science.gov (United States)

Connor, David E; Chaitanya, Ganta V; Chittiboina, Prashant; McCarthy, Paul; Scott, L Keith; Schrott, Lisa; Minagar, Alireza; Nanda, Anil; Alexander, J Steven

2017-09-01

Proteomic analysis of cerebrospinal fluid (CSF) has shown great promise in identifying potential markers of injury in neurodegenerative diseases [1-13]. Here we compared CSF proteomes in healthy individuals, with patients diagnosed with traumatic brain injury (TBI) and subarachnoid hemorrhage (SAH) in order to characterize molecular biomarkers which might identify these different clinical states and describe different molecular mechanisms active in each disease state. Patients presenting to the Neurosurgery service at the Louisiana State University Hospital-Shreveport with an admitting diagnosis of TBI or SAH were prospectively enrolled. Patients undergoing CSF sampling for diagnostic procedures were also enrolled as controls. CSF aliquots were subjected to 2-dimensional gel electrophoresis (2D GE) and spot percentage densities analyzed. Increased or decreased spot expression (compared to controls) was defined in terms of in spot percentages, with spots showing consistent expression change across TBI or SAH specimens being followed up by Matrix-Assisted Laser Desorption/Ionization mass spectrometry (MALDI-MS). Polypeptide masses generated were matched to known standards using a search of the NCBI and/or GenPept databases for protein matches. Eight hundred fifteen separately identifiable polypeptide migration spots were identified on 2D GE gels. MALDI-MS successfully identified 13 of 22 selected 2D GE spots as recognizable polypeptides. Statistically significant changes were noted in the expression of fibrinogen, carbonic anhydrase-I (CA-I), peroxiredoxin-2 (Prx-2), both α and β chains of hemoglobin, serotransferrin (Tf) and N-terminal haptoglobin (Hp) in TBI and SAH specimens, as compared to controls. The greatest mean fold change among all specimens was seen in CA-I and Hp at 30.7 and -25.7, respectively. TBI specimens trended toward greater mean increases in CA-I and Prx-2 and greater mean decreases in Hp and Tf. Consistent CSF elevation of CA-I and Prx-2 with

Comparative study of the biodegradability of porous silicon films in simulated body fluid.

Science.gov (United States)

Peckham, J; Andrews, G T

2015-01-01

The biodegradability of oxidized microporous, mesoporous and macroporous silicon films in a simulated body fluid with ion concentrations similar to those found in human blood plasma were studied using gravimetry. Film dissolution rates were determined by periodically weighing the samples after removal from the fluid. The dissolution rates for microporous silicon were found to be higher than those for mesoporous silicon of comparable porosity. The dissolution rate of macroporous silicon was much lower than that for either microporous or mesoporous silicon. This is attributed to the fact that its specific surface area is much lower than that of microporous and mesoporous silicon. Using an equation adapted from [Surf. Sci. Lett. 306 (1994), L550-L554], the dissolution rate of porous silicon in simulated body fluid can be estimated if the film thickness and specific surface area are known.

Difference gel electrophoresis (DiGE) identifies differentially expressed proteins in endoscopically-collected pancreatic fluid

Science.gov (United States)

Paulo, Joao A.; Lee, Linda S.; Banks, Peter A.; Steen, Hanno; Conwell, Darwin L.

2012-01-01

Alterations in the pancreatic fluid proteome of individuals with chronic pancreatitis may offer insights into the development and progression of the disease. The endoscopic pancreas function test (ePFT) can safely collect large volumes of pancreatic fluid that are potentially amenable to proteomic analyses using difference gel electrophoresis (DiGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Pancreatic fluid was collected endoscopically using the ePFT method following secretin stimulation from three individuals with severe chronic pancreatitis and three chronic abdominal pain controls. The fluid was processed to minimize protein degradation and the protein profiles of each cohort, as determined by DiGE and LC-MS/MS, were compared. This DiGE-LC-MS/MS analysis reveals proteins that are differentially expressed in chronic pancreatitis compared to chronic abdominal pain controls. Proteins with higher abundance in pancreatic fluid from chronic pancreatitis individuals include: actin, desmoplankin, alpha-1-antitrypsin, SNC73, and serotransferrin. Those of relatively lower abundance include carboxypeptidase B, lipase, alpha-1-antichymotrypsin, alpha-2-macroglobulin, Arp2/3 subunit 4, glyceraldehyde-3-phosphate dehydrogenase, and protein disulfide isomerase. Endoscopic collection (ePFT) in tandem with DiGE-LC-MS/MS is a suitable approach for pancreatic fluid proteome analysis, however, further optimization of our protocol, as outlined herein, may improve proteome coverage in future analyses. PMID:21792986

Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth

Directory of Open Access Journals (Sweden)

Kai P. Law

2015-05-01

Full Text Available Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered.

Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth

Science.gov (United States)

Law, Kai P.; Han, Ting-Li; Tong, Chao; Baker, Philip N.

2015-01-01

Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered. PMID:26006232

Exosome levels in human body fluids: A tumor marker by themselves?

Science.gov (United States)

Cappello, Francesco; Logozzi, Mariantonia; Campanella, Claudia; Bavisotto, Celeste Caruso; Marcilla, Antonio; Properzi, Francesca; Fais, Stefano

2017-01-01

Despite considerable research efforts, the finding of reliable tumor biomarkers remains challenging and unresolved. In recent years a novel diagnostic biomedical tool with high potential has been identified in extracellular nanovesicles or exosomes. They are released by the majority of the cells and contain detailed molecular information on the cell of origin including tumor hallmarks. Exosomes can be isolated from easy accessible body fluids, and most importantly, they can provide several biomarkers, with different levels of specificity. Recent clinical evidence shows that the levels of exosomes released into body fluids may themselves represent a predictive/diagnostic of tumors, discriminating cancer patients from healthy subjects. The aim of this review is to highlight these latest challenging findings to provide novel and groundbreaking ideas for successful tumor early diagnosis and follow-up. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of exercise on fluid exchange and body composition in man during 14-day bed rest

Science.gov (United States)

Greenleaf, J. E.; Bernauer, E. M.; Juhos, L. T.; Young, H. L.; Morse, J. T.; Staley, R. W.

1977-01-01

A description is presented of an investigation in which body composition, fluid intake, and fluid and electrolyte losses were measured in seven normal, healthy men during three 2-wk bed-rest periods, separated by two 3-wk recovery periods. During bed rest the subjects remained in the horizontal position continuously. During the dietary control periods, body mass decreased significantly with all three regimens, including no exercise, isometric exercise, and isotonic excercise. During bed rest, body mass was essentially unchanged with no exercise, but decreased significantly with isotonic and isometric exercise. With one exception, there were no statistically significant changes in body density, lean body mass, or body fat content by the end of each of the three bed-rest periods.

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

DEFF Research Database (Denmark)

Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

2016-01-01

Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed ...

Body fluid derived exosomes as a novel template for clinical diagnostics

Directory of Open Access Journals (Sweden)

Janssen Johannes WG

2011-06-01

Full Text Available Abstract Background Exosomes are small membrane vesicles with a size of 40-100 nm that are released by different cell types from a late endosomal cellular compartment. They can be found in various body fluids including plasma, malignant ascites, urine, amniotic fluid and saliva. Exosomes contain proteins, miRNAs and mRNAs (exosome shuttle RNA, esRNA that could serve as novel platform for diagnosis. Method We isolated exosomes from amniotic fluid, saliva and urine by differential centrifugation on sucrose gradients. Marker proteins were identified by Western blot and FACS analysis after adsorption of exosomes to latex beads. We extracted esRNA from exosomes, carried out RT-PCR, and analyzed amplified products by restriction length polymorphism. Results Exosomes were positive for the marker proteins CD24, CD9, Annexin-1 and Hsp70 and displayed the correct buoyant density and orientation of antigens. In sucrose gradients the exosomal fractions contained esRNA that could be isolated with sufficient quantity for further analysis. EsRNAs were protected in exosomes from enzymatic degradation. Amniotic fluid esRNA served as template for the typing of the CD24 single nucleotide polymorphism (rs52812045. It also allowed sex determination of the fetus based on the detection of the male specific ZFY gene product. Conclusions Our data demonstrate that exosomes from body fluids carry esRNAs which can be analyzed and offers access to the transcriptome of the host organism. The exosomal lipid bilayer protects the genetic information from degradation. As the isolation of exosomes is a minimally invasive procedure, this technique opens new possibilities for diagnostics.

Is cupping blister harmful?-A proteomical analysis of blister fluid induced by cupping therapy and scald.

Science.gov (United States)

Liu, Zhidan; Chen, Chunlan; Li, Xiaoyan; Zhao, Chuang; Li, Zunyuan; Liang, Wei; Lin, Yufang

2018-02-01

Cupping therapy has a long history in traditional medicine especially in Asian countries. It was controversial whether cupping induced blisters are beneficial to healing effects, and the formation and content in the blisters remain unexplored. We aimed to identify and compare the molecular components of the blister fluid from the cupping therapy and the scalds to explore the necessary of inducing cupping induced blisters. Fluid sample of blisters from fifteen patients receiving cupping therapy (Cupping group) and scald burns (Scald group) were collected in this study. Proteins from the blisters were separated by two-dimensional electrophoresis (2D-gel) and further analyzed by mass spectrometry. In addition, the changes in particular proteins were confirmed by Western blotting. The protein components are significantly different between blister from cupping therapy and scalds. The immune responses, oxidative stress and metabolic related proteins (Ig lambda-2 chain C regions, Ig gamma-1 chain C region, hemopexin, prdx2, calmodulin, succinyl-CoA ligase and tetranectin) were increased, whereas the hemoglobin subunit beta was decreased in the Cupping group compared with the Scald group. Cupping induced blisters contain several proteins which relate to the activation of certain immune pathways including anti-oxidation, anti-apoptosis, tissue repairing and metabolic regulation. This proteomic analysis may indicate a significant clue to the mechanism study of cupping. Copyright © 2017 Elsevier Ltd. All rights reserved.

Steady fall of a rigid body in viscous fluid

Czech Academy of Sciences Publication Activity Database

Nečasová, Šárka

2005-01-01

Roč. 63, Sp. Is. (2005), s. 2113-2119 ISSN 0362-546X. [Invited Talks from the Fourth World Congress of Nonlinear Analysts (WCNA 2004). Orlando , 30.7.2004-7.8.2004] R&D Projects: GA ČR(CZ) GA201/02/0684 Institutional research plan: CEZ:AV0Z1019905 Keywords : steady fall * rigid body * viscous fluid Subject RIV: BA - General Mathematics Impact factor: 0.519, year: 2005

Proteomic Analysis of Cerebrospinal Fluid in a Fulminant Case of Multiple Sclerosis

Directory of Open Access Journals (Sweden)

Jonas Bergquist

2012-06-01

Full Text Available Multiple Sclerosis (MS is a chronic disease, but in rare fulminant cases rapid progression may lead to death shortly after diagnosis. Currently there is no diagnostic test to predict disease course. The aim of this study was to identify potential biomarkers/proteins related to rapid progression. We present the case history of a 15-year-old male MS patient. Cerebrospinal fluid (CSF was taken at diagnosis and at the time of rapid progression leading to the patient’s death. Using isobaric tag labeling and nanoflow liquid chromatography in conjunction with matrix assisted laser desorption/ionization time of flight tandem mass spectrometry we quantitatively analyzed the protein content of two CSF samples from the patient with fulminant MS as well as one relapsing-remitting (RR MS patient and one control headache patient, whose CSF analysis was normal. Seventy-eight proteins were identified and seven proteins were found to be more abundant in both fulminant MS samples but not in the RR MS sample compared to the control. These proteins are involved in the immune response, blood coagulation, cell proliferation and cell adhesion. In conclusion, in this pilot study we were able to show differences in the CSF proteome of a rapidly progressing MS patient compared to a more typical clinical form of MS and a control subject.

Proteomic Analysis of Cerebrospinal Fluid in a Fulminant Case of Multiple Sclerosis

Science.gov (United States)

Füvesi, Judit; Hanrieder, Jörg; Bencsik, Krisztina; Rajda, Cecilia; Kovács, S. Krisztián; Kaizer, László; Beniczky, Sándor; Vécsei, László; Bergquist, Jonas

2012-01-01

Multiple Sclerosis (MS) is a chronic disease, but in rare fulminant cases rapid progression may lead to death shortly after diagnosis. Currently there is no diagnostic test to predict disease course. The aim of this study was to identify potential biomarkers/proteins related to rapid progression. We present the case history of a 15-year-old male MS patient. Cerebrospinal fluid (CSF) was taken at diagnosis and at the time of rapid progression leading to the patient’s death. Using isobaric tag labeling and nanoflow liquid chromatography in conjunction with matrix assisted laser desorption/ionization time of flight tandem mass spectrometry we quantitatively analyzed the protein content of two CSF samples from the patient with fulminant MS as well as one relapsing-remitting (RR) MS patient and one control headache patient, whose CSF analysis was normal. Seventy-eight proteins were identified and seven proteins were found to be more abundant in both fulminant MS samples but not in the RR MS sample compared to the control. These proteins are involved in the immune response, blood coagulation, cell proliferation and cell adhesion. In conclusion, in this pilot study we were able to show differences in the CSF proteome of a rapidly progressing MS patient compared to a more typical clinical form of MS and a control subject. PMID:22837721

Guidelines for uniform reporting of body fluid biomarker studies in neurologic disorders

DEFF Research Database (Denmark)

Gnanapavan, Sharmilee; Hegen, Harald; Khalil, Michael

2014-01-01

, there are concerns over the high attrition rate of promising candidate biomarkers at later phases of development. METHODS: BioMS-eu consortium, a collaborative network working toward improving the quality of biomarker research in neurologic disorders, discussed the merits of standardizing the reporting of body fluid...... biomarker research. A checklist of items integrating the results of other published guidances, literature, conferences, regulatory opinion, and personal expertise was created to ultimately form a structured summary guidance incorporating the key features. RESULTS: The summary guidance is comprised of a 10......-point uniform reporting format ranging from introduction, materials and methods, through to results and discussion. Each item is discussed in detail in the guidance report. CONCLUSIONS: To enhance the future development of body fluid biomarkers, it will be important to standardize the reporting...

Diffuse interface immersed boundary method for multi-fluid flows with arbitrarily moving rigid bodies

Science.gov (United States)

Patel, Jitendra Kumar; Natarajan, Ganesh

2018-05-01

We present an interpolation-free diffuse interface immersed boundary method for multiphase flows with moving bodies. A single fluid formalism using the volume-of-fluid approach is adopted to handle multiple immiscible fluids which are distinguished using the volume fractions, while the rigid bodies are tracked using an analogous volume-of-solid approach that solves for the solid fractions. The solution to the fluid flow equations are carried out using a finite volume-immersed boundary method, with the latter based on a diffuse interface philosophy. In the present work, we assume that the solids are filled with a "virtual" fluid with density and viscosity equal to the largest among all fluids in the domain. The solids are assumed to be rigid and their motion is solved using Newton's second law of motion. The immersed boundary methodology constructs a modified momentum equation that reduces to the Navier-Stokes equations in the fully fluid region and recovers the no-slip boundary condition inside the solids. An implicit incremental fractional-step methodology in conjunction with a novel hybrid staggered/non-staggered approach is employed, wherein a single equation for normal momentum at the cell faces is solved everywhere in the domain, independent of the number of spatial dimensions. The scalars are all solved for at the cell centres, with the transport equations for solid and fluid volume fractions solved using a high-resolution scheme. The pressure is determined everywhere in the domain (including inside the solids) using a variable coefficient Poisson equation. The solution to momentum, pressure, solid and fluid volume fraction equations everywhere in the domain circumvents the issue of pressure and velocity interpolation, which is a source of spurious oscillations in sharp interface immersed boundary methods. A well-balanced algorithm with consistent mass/momentum transport ensures robust simulations of high density ratio flows with strong body forces. The

Maillard Proteomics: Opening New Pages

Directory of Open Access Journals (Sweden)

Alena Soboleva

2017-12-01

Full Text Available Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer’s disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus, proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.

Effects of growth hormone (GH) treatment on body fluid distribution in patients undergoing elective abdominal surgery

DEFF Research Database (Denmark)

Møller, Jacob; Jensen, Martin Bach; Frandsen, E.

1998-01-01

OBJECTIVE: To investigate the possible beneficial effects of growth hormone (GH) in catabolic patients we examined the impact of GH on body fluid distribution in patients with ulcerative colitis undergoing elective abdominal surgery. DESIGN AND MEASUREMENTS: Twenty-four patients (14 female, 10 male...... at day -2 and at day 7, and body composition was estimated by dual X-ray absorptiometry and bioimpedance. Changes in body weight and fluid balance were recorded and hence intracellular volume was assessed. RESULTS: During placebo treatment body weight decreased 4.3 +/- 0.6 kg; during GH treatment body.......05). Plasma renin and aldosterone remained unchanged in both study groups. CONCLUSION: Body weight, plasma volume and intracellular volume is preserved during GH treatment in catabolic patients and ECV is increased. From a therapeutic point of view these effects may be desirable under conditions of surgical...

Multivariate proteomic analysis of the cerebrospinal fluid of patients with peripheral neuropathic pain and healthy controls – a hypothesis-generating pilot study

Directory of Open Access Journals (Sweden)

Bäckryd E

2015-07-01

Full Text Available Emmanuel Bäckryd,1,2 Bijar Ghafouri,1,2 Anders K Carlsson,1,2 Patrik Olausson,1,2 Björn Gerdle1,2 1Division of Community Medicine, Department of Medical and Health Sciences, Faculty of Health Sciences, Linköping University, Linköping, Sweden; 2Pain and Rehabilitation Centre, Anaesthetics, Operations and Specialty Surgery Centre, Region Östergötland, Linköping, SwedenAbstract: Pain medicine lacks objective biomarkers to guide diagnosis and treatment. Combining two-dimensional gel proteomics with multivariate data analysis by projection, we exploratively analyzed the cerebrospinal fluid of eleven patients with severe peripheral neuropathic pain due to trauma and/or surgery refractory to conventional treatment and eleven healthy controls. Using orthogonal partial least squares discriminant analysis, we identified a panel of 36 proteins highly discriminating between the two groups. Due to a possible confounding effect of age, a new model with age as outcome variable was computed for patients (n=11, and four out of 36 protein spots were excluded due to a probable influence of age. Of the 32 remaining proteins, the following seven had the highest discriminatory power between the two groups: an isoform of angiotensinogen (upregulated in patients, two isoforms of alpha-1-antitrypsin (downregulated in patients, three isoforms of haptoglobin (upregulated in patients, and one isoform of pigment epithelium-derived factor (downregulated in patients. It has recently been hypothesized that the renin–angiotensin system may play a role in the pathophysiology of neuropathic pain, and a clinical trial of an angiotensin II receptor antagonist was recently published. It is noteworthy that when searching for neuropathic pain biomarkers with a purely explorative methodology, it was indeed a renin–angiotensin system protein that had the highest discriminatory power between patients and controls in the present study. The results from this hypothesis

Examining hemodialyzer membrane performance using proteomic technologies

Directory of Open Access Journals (Sweden)

Bonomini M

2017-12-01

Full Text Available Mario Bonomini,1 Luisa Pieroni,2 Lorenzo Di Liberato,1 Vittorio Sirolli,1 Andrea Urbani2,3 1Department of Medicine, G. d’Annunzio University, Chieti, 2Proteomic and Metabonomic Units, IRCCS S. Lucia Foundation, Rome, 3Faculty of Medicine, Biochemistry and Clinical Biochemistry Institute, Catholic University of the “Sacred Heart”, Rome, Italy Abstract: The success and the quality of hemodialysis therapy are mainly related to both clearance and biocompatibility properties of the artificial membrane packed in the hemodialyzer. Performance of a membrane is strongly influenced by its interaction with the plasma protein repertoire during the extracorporeal procedure. Recognition that a number of medium–high molecular weight solutes, including proteins and protein-bound molecules, are potentially toxic has prompted the development of more permeable membranes. Such membrane engineering, however, may cause loss of vital proteins, with membrane removal being nonspecific. In addition, plasma proteins can be adsorbed onto the membrane surface upon blood contact during dialysis. Adsorption can contribute to the removal of toxic compounds and governs the biocompatibility of a membrane, since surface-adsorbed proteins may trigger a variety of biologic blood pathways with pathophysiologic consequences. Over the last years, use of proteomic approaches has allowed polypeptide spectrum involved in the process of hemodialysis, a key issue previously hampered by lack of suitable technology, to be assessed in an unbiased manner and in its full complexity. Proteomics has been successfully applied to identify and quantify proteins in complex mixtures such as dialysis outflow fluid and fluid desorbed from dialysis membrane containing adsorbed proteins. The identified proteins can also be characterized by their involvement in metabolic and signaling pathways, molecular networks, and biologic processes through application of bioinformatics tools. Proteomics may

Proteogenomics Dashboard for the Human Proteome Project.

Science.gov (United States)

Tabas-Madrid, Daniel; Alves-Cruzeiro, Joao; Segura, Victor; Guruceaga, Elizabeth; Vialas, Vital; Prieto, Gorka; García, Carlos; Corrales, Fernando J; Albar, Juan Pablo; Pascual-Montano, Alberto

2015-09-04

dasHPPboard is a novel proteomics-based dashboard that collects and reports the experiments produced by the Spanish Human Proteome Project consortium (SpHPP) and aims to help HPP to map the entire human proteome. We have followed the strategy of analog genomics projects like the Encyclopedia of DNA Elements (ENCODE), which provides a vast amount of data on human cell lines experiments. The dashboard includes results of shotgun and selected reaction monitoring proteomics experiments, post-translational modifications information, as well as proteogenomics studies. We have also processed the transcriptomics data from the ENCODE and Human Body Map (HBM) projects for the identification of specific gene expression patterns in different cell lines and tissues, taking special interest in those genes having little proteomic evidence available (missing proteins). Peptide databases have been built using single nucleotide variants and novel junctions derived from RNA-Seq data that can be used in search engines for sample-specific protein identifications on the same cell lines or tissues. The dasHPPboard has been designed as a tool that can be used to share and visualize a combination of proteomic and transcriptomic data, providing at the same time easy access to resources for proteogenomics analyses. The dasHPPboard can be freely accessed at: http://sphppdashboard.cnb.csic.es.

Estimation of body fluids with bioimpedance spectroscopy: state of the art methods and proposal of novel methods

International Nuclear Information System (INIS)

Buendia, R; Seoane, F; Lindecrantz, K; Bosaeus, I; Gil-Pita, R; Johannsson, G; Ellegård, L; Ward, L C

2015-01-01

Determination of body fluids is a useful common practice in determination of disease mechanisms and treatments. Bioimpedance spectroscopy (BIS) methods are non-invasive, inexpensive and rapid alternatives to reference methods such as tracer dilution. However, they are indirect and their robustness and validity are unclear. In this article, state of the art methods are reviewed, their drawbacks identified and new methods are proposed. All methods were tested on a clinical database of patients receiving growth hormone replacement therapy. Results indicated that most BIS methods are similarly accurate (e.g.  <  0.5   ±   3.0% mean percentage difference for total body water) for estimation of body fluids. A new model for calculation is proposed that performs equally well for all fluid compartments (total body water, extra- and intracellular water). It is suggested that the main source of error in extracellular water estimation is due to anisotropy, in total body water estimation to the uncertainty associated with intracellular resistivity and in determination of intracellular water a combination of both. (paper)

Regulation of body fluid and salt homeostasis--from observations in space to new concepts on Earth.

Science.gov (United States)

Gerzer, R; Heer, M

2005-08-01

The present manuscript summarizes recent discoveries that were made by studying salt and fluid homeostasis in weightlessness. These data indicate that 1. atrial natriuretic peptide appears not to play an important role in natriuresis in physiology, 2. the distribution of body fluids appears to be tightly coupled with hunger and thirst regulation, 3. intrathoracic pressure may be an important co-regulator of body fluid homeostasis, 4. a so far unknown low-affinity, high capacity osmotically inactive sodium storage mechanism appears to be present in humans that is acting through sodium/hydrogen exchange on glycosaminoglycans and might explain the pathophysiology, e.g., of salt sensitive hypertension. The surprising and unexpected data underline that weightlessness is an excellent tool to investigate the physiology of our human body: If we knew it, we should be able to predict changes that occur when gravity is absent. But, as data from space demonstrate, we do not.

Comparative proteome and peptidome analysis of the cephalic fluid secreted by Arapaima gigas (Teleostei: Osteoglossidae) during and outside parental care.

Science.gov (United States)

Torati, Lucas S; Migaud, Hervé; Doherty, Mary K; Siwy, Justyna; Mullen, Willian; Mesquita, Pedro E C; Albalat, Amaya

2017-01-01

Parental investment in Arapaima gigas includes nest building and guarding, followed by a care provision when a cephalic fluid is released from the parents' head to the offspring. This fluid has presumably important functions for the offspring but so far its composition has not been characterised. In this study the proteome and peptidome of the cephalic secretion was studied in parental and non-parental fish using capillary electrophoresis coupled to mass spectrometry (CE-MS) and GeLC-MS/MS analyses. Multiple comparisons revealed 28 peptides were significantly different between males and parental males (PC-males), 126 between females and parental females (PC-females), 51 between males and females and 9 between PC-males and PC-females. Identification revealed peptides were produced in the inner ear (pcdh15b), eyes (tetraspanin and ppp2r3a), central nervous system (otud4, ribeye a, tjp1b and syn1) among others. A total of 422 proteins were also identified and gene ontology analysis revealed 28 secreted extracellular proteins. From these, 2 hormones (prolactin and stanniocalcin) and 12 proteins associated to immunological processes (serotransferrin, α-1-antitrypsin homolog, apolipoprotein A-I, and others) were identified. This study provides novel biochemical data on the lateral line fluid which will enable future hypotheses-driven experiments to better understand the physiological roles of the lateral line in chemical communication.

Comparative proteome and peptidome analysis of the cephalic fluid secreted by Arapaima gigas (Teleostei: Osteoglossidae during and outside parental care.

Directory of Open Access Journals (Sweden)

Lucas S Torati

Full Text Available Parental investment in Arapaima gigas includes nest building and guarding, followed by a care provision when a cephalic fluid is released from the parents' head to the offspring. This fluid has presumably important functions for the offspring but so far its composition has not been characterised. In this study the proteome and peptidome of the cephalic secretion was studied in parental and non-parental fish using capillary electrophoresis coupled to mass spectrometry (CE-MS and GeLC-MS/MS analyses. Multiple comparisons revealed 28 peptides were significantly different between males and parental males (PC-males, 126 between females and parental females (PC-females, 51 between males and females and 9 between PC-males and PC-females. Identification revealed peptides were produced in the inner ear (pcdh15b, eyes (tetraspanin and ppp2r3a, central nervous system (otud4, ribeye a, tjp1b and syn1 among others. A total of 422 proteins were also identified and gene ontology analysis revealed 28 secreted extracellular proteins. From these, 2 hormones (prolactin and stanniocalcin and 12 proteins associated to immunological processes (serotransferrin, α-1-antitrypsin homolog, apolipoprotein A-I, and others were identified. This study provides novel biochemical data on the lateral line fluid which will enable future hypotheses-driven experiments to better understand the physiological roles of the lateral line in chemical communication.

Wing-Body Aeroelasticity Using Finite-Difference Fluid/Finite-Element Structural Equations on Parallel Computers

Science.gov (United States)

Byun, Chansup; Guruswamy, Guru P.; Kutler, Paul (Technical Monitor)

1994-01-01

In recent years significant advances have been made for parallel computers in both hardware and software. Now parallel computers have become viable tools in computational mechanics. Many application codes developed on conventional computers have been modified to benefit from parallel computers. Significant speedups in some areas have been achieved by parallel computations. For single-discipline use of both fluid dynamics and structural dynamics, computations have been made on wing-body configurations using parallel computers. However, only a limited amount of work has been completed in combining these two disciplines for multidisciplinary applications. The prime reason is the increased level of complication associated with a multidisciplinary approach. In this work, procedures to compute aeroelasticity on parallel computers using direct coupling of fluid and structural equations will be investigated for wing-body configurations. The parallel computer selected for computations is an Intel iPSC/860 computer which is a distributed-memory, multiple-instruction, multiple data (MIMD) computer with 128 processors. In this study, the computational efficiency issues of parallel integration of both fluid and structural equations will be investigated in detail. The fluid and structural domains will be modeled using finite-difference and finite-element approaches, respectively. Results from the parallel computer will be compared with those from the conventional computers using a single processor. This study will provide an efficient computational tool for the aeroelastic analysis of wing-body structures on MIMD type parallel computers.

Handling and storage of human body fluids for analysis of extracellular vesicles

NARCIS (Netherlands)

Yuana, Yuana; Böing, Anita N.; Grootemaat, Anita E.; van der Pol, Edwin; Hau, Chi M.; Cizmar, Petr; Buhr, Egbert; Sturk, Auguste; Nieuwland, Rienk

2015-01-01

Because procedures of handling and storage of body fluids affect numbers and composition of extracellular vesicles (EVs), standardization is important to ensure reliable and comparable measurements of EVs in a clinical environment. We aimed to develop standard protocols for handling and storage of

Proteomic Investigations into Hemodialysis Therapy

Directory of Open Access Journals (Sweden)

Mario Bonomini

2015-12-01

Full Text Available The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(incompatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research.

Proteomic Investigations into Hemodialysis Therapy

Science.gov (United States)

Bonomini, Mario; Sirolli, Vittorio; Pieroni, Luisa; Felaco, Paolo; Amoroso, Luigi; Urbani, Andrea

2015-01-01

The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(in)compatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research. PMID:26690416

A collaborative European exercise on mRNA-based body fluid/skin typing and interpretation of DNA and RNA results

DEFF Research Database (Denmark)

van den Berge, M; Carracedo, A; Gomes, I

2014-01-01

The European Forensic Genetics Network of Excellence (EUROFORGEN-NoE) undertook a collaborative project on mRNA-based body fluid/skin typing and the interpretation of the resulting RNA and DNA data. Although both body fluids and skin are composed of a variety of cell types with different function...

Unmasking a sustained negative effect of SGLT2 inhibition on body fluid volume in the rat.

Science.gov (United States)

Masuda, Takahiro; Watanabe, Yuko; Fukuda, Keiko; Watanabe, Minami; Onishi, Akira; Ohara, Ken; Imai, Toshimi; Koepsell, Hermann; Muto, Shigeaki; Vallon, Volker; Nagata, Daisuke

2018-05-23

The chronic intrinsic diuretic and natriuretic tone of sodium-glucose cotransporter 2 (SGLT2) inhibitors is incompletely understood, because their effect on body fluid volume (BFV) has not been fully evaluated and because they often increase food and fluid intake at the same time. Here we first compared the effect of the SGLT2 inhibitor ipragliflozin (Ipra, 0.01% in diet for 8 weeks) and vehicle (Veh) in Spontaneously Diabetic Torii rat, a non-obese type 2 diabetic model, and non-diabetic Sprague-Dawley rats. In non-diabetic rats, Ipra increased urinary excretion of Na+ (UNaV) and fluid (UV) associated with increased food and fluid intake. Diabetes increased these 4 parameters, but Ipra had no further effect; probably due to its antihyperglycemic effect, such that glucosuria and as a consequence food and fluid intake were unchanged. Fluid balance and BFV, determined by bioimpedance spectroscopy, were similar among the 4 groups. To study the impact of food and fluid intake, non-diabetic rats were treated for 7 days with Veh, Ipra or Ipra+pair-feeding+pair-drinking (Pair-Ipra). Pair-Ipra maintained a small increase in UV and UNaV versus Veh despite similar food and fluid intake. Pair-Ipra induced a negative fluid balance and decreased BFV, while Ipra or Veh had no significant effect compared with basal values. In conclusion, SGLT2 inhibition induces a sustained diuretic and natriuretic tone. Homeostatic mechanisms are activated to stabilize body fluid volume, including compensatory increases in fluid and food intake.

Birth of plant proteomics in India: a new horizon.

Science.gov (United States)

Narula, Kanika; Pandey, Aarti; Gayali, Saurabh; Chakraborty, Niranjan; Chakraborty, Subhra

2015-09-08

In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Body fluid markers to monitor multiple sclerosis: The assays and the challenges

NARCIS (Netherlands)

Laman, J.D.; Thompson, E.J.; Kappos, L.

1998-01-01

The need for reliable markers of disease activity in multiple sclerosis (MS) to better guide basic research, diagnosis, treatment, and monitoring of therapy is well-recognized. A recent European Charcot Foundation Symposium (Body fluid markers for course and activity of disease in multiple sclerosis

Bions: a family of biomimetic mineralo-organic complexes derived from biological fluids.

Directory of Open Access Journals (Sweden)

Cheng-Yeu Wu

Full Text Available Mineralo-organic nanoparticles form spontaneously in human body fluids when the concentrations of calcium and phosphate ions exceed saturation. We have shown previously that these mineralo-organic nanoparticles possess biomimetic properties and can reproduce the whole phenomenology of the so-called nanobacteria-mineralized entities initially described as the smallest microorganisms on earth. Here, we examine the possibility that various charged elements and ions may form mineral nanoparticles with similar properties in biological fluids. Remarkably, all the elements tested, including sodium, magnesium, aluminum, calcium, manganese, iron, cobalt, nickel, copper, zinc, strontium, and barium form mineralo-organic particles with bacteria-like morphologies and other complex shapes following precipitation with phosphate in body fluids. Upon formation, these mineralo-organic particles, which we term bions, invariably accumulate carbonate apatite during incubation in biological fluids; yet, the particles also incorporate additional elements and thus reflect the ionic milieu in which they form. Bions initially harbor an amorphous mineral phase that gradually converts to crystals in culture. Our results show that serum produces a dual inhibition-seeding effect on bion formation. Using a comprehensive proteomic analysis, we identify a wide range of proteins that bind to these mineral particles during incubation in medium containing serum. The two main binding proteins identified, albumin and fetuin-A, act as both inhibitors and seeders of bions in culture. Notably, bions possess several biomimetic properties, including the possibility to increase in size and number and to be sub-cultured in fresh culture medium. Based on these results, we propose that bions represent biological, mineralo-organic particles that may form in the body under both physiological and pathological homeostasis conditions. These mineralo-organic particles may be part of a

Proteomic analysis of apoplastic fluid of Coffea arabica leaves highlights novel biomarkers for resistance against Hemileia vastatrix

Directory of Open Access Journals (Sweden)

Leonor eGuerra-Guimarães

2015-06-01

Full Text Available A proteomic analysis of the apoplastic fluid (APF of coffee leaves was conducted to investigate the cellular processes associated with incompatible (resistant and compatible (susceptible Coffea arabica-Hemileia vastatrix interactions, during the 24-96 hai period. The APF proteins were extracted by leaf vacuum infiltration and protein profiles were obtained by 2-DE. The comparative analysis of the gels revealed 210 polypeptide spots whose volume changed in abundance between samples (control, resistant and susceptible during the 24-96 hai period. The proteins identified were involved mainly in protein degradation, cell wall metabolism and stress/defense responses, most of them being hydrolases (around 70%, particularly sugar hydrolases and peptidases/proteases. The changes in the APF proteome along the infection process revealed two distinct phases of defense responses, an initial/basal one (24-48 hai and a late/specific one (72-96 hai. Compared to susceptibility, resistance was associated with a higher number of proteins, which was more evident in the late/specific phase. Proteins involved in the resistance response were mainly, glycohydrolases of the cell wall, serine proteases and pathogen related-like proteins (PR-proteins, suggesting that some of these proteins could be putative candidates for resistant markers of coffee to H. vastatrix. Antibodies were produced against chitinase, pectin methylesterase, serine carboxypeptidase, reticuline oxidase and subtilase and by an immunodetection assay it was observed an increase of these proteins in the resistant sample. With this methodology we have identified proteins that are candidate markers of resistance and that will be useful in coffee breeding programs to assist in the selection of cultivars with resistance to H. vastatrix.

Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome.

Directory of Open Access Journals (Sweden)

Steven E Schutzer

2011-02-01

Full Text Available Neurologic Post Treatment Lyme disease (nPTLS and Chronic Fatigue (CFS are syndromes of unknown etiology. They share features of fatigue and cognitive dysfunction, making it difficult to differentiate them. Unresolved is whether nPTLS is a subset of CFS.Pooled cerebrospinal fluid (CSF samples from nPTLS patients, CFS patients, and healthy volunteers were comprehensively analyzed using high-resolution mass spectrometry (MS, coupled with immunoaffinity depletion methods to reduce protein-masking by abundant proteins. Individual patient and healthy control CSF samples were analyzed directly employing a MS-based label-free quantitative proteomics approach. We found that both groups, and individuals within the groups, could be distinguished from each other and normals based on their specific CSF proteins (p<0.01. CFS (n = 43 had 2,783 non-redundant proteins, nPTLS (n = 25 contained 2,768 proteins, and healthy normals had 2,630 proteins. Preliminary pathway analysis demonstrated that the data could be useful for hypothesis generation on the pathogenetic mechanisms underlying these two related syndromes.nPTLS and CFS have distinguishing CSF protein complements. Each condition has a number of CSF proteins that can be useful in providing candidates for future validation studies and insights on the respective mechanisms of pathogenesis. Distinguishing nPTLS and CFS permits more focused study of each condition, and can lead to novel diagnostics and therapeutic interventions.

Advanced statistical analysis of Raman spectroscopic data for the identification of body fluid traces: semen and blood mixtures.

Science.gov (United States)

Sikirzhytski, Vitali; Sikirzhytskaya, Aliaksandra; Lednev, Igor K

2012-10-10

Conventional confirmatory biochemical tests used in the forensic analysis of body fluid traces found at a crime scene are destructive and not universal. Recently, we reported on the application of near-infrared (NIR) Raman microspectroscopy for non-destructive confirmatory identification of pure blood, saliva, semen, vaginal fluid and sweat. Here we expand the method to include dry mixtures of semen and blood. A classification algorithm was developed for differentiating pure body fluids and their mixtures. The classification methodology is based on an effective combination of Support Vector Machine (SVM) regression (data selection) and SVM Discriminant Analysis of preprocessed experimental Raman spectra collected using an automatic mapping of the sample. This extensive cross-validation of the obtained results demonstrated that the detection limit of the minor contributor is as low as a few percent. The developed methodology can be further expanded to any binary mixture of complex solutions, including but not limited to mixtures of other body fluids. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Simulated body-fluid tests and electrochemical investigations on biocompatibility of metallic glasses

International Nuclear Information System (INIS)

Lin, C.H.; Huang, C.H.; Chuang, J.F.; Lee, H.C.; Liu, M.C.; Du, X.H.; Huang, J.C.; Jang, J.S.C.; Chen, C.H.

2012-01-01

This paper presents the in-vitro and electrochemical investigations of four metallic glasses (MGs) for finding potential MG-based bio-materials. The simulation body-fluid Hanks solution is utilized for testing the corrosion resistance of MGs, and microorganisms of Escherichia coli are used in testing the bio-toxicity. In addition, a simple cyclic voltammetry method is used for rapid verification of the potential electrochemical responses. It is found that the Zr-based MG can sustain in the body-fluid, exhibiting the best corrosion resistance and electrochemical stability. The microbiologic test shows that E. coli can grow on the surface of the Zr-based metallic glass, confirming the low cell toxicity of this Zr-based MG. Highlights: ► Vanadium is added in Cu–Zr–Al alloy to induce B2-CuZr formation. ► The more induced B2-CuZr phase can improve compressive plasticity. ► The plasticity improvement might be caused by B2 phase dynamic coarsening.

First proteome of the egg perivitelline fluid of a freshwater gastropod with aerial oviposition

KAUST Repository

Sun, Jin

2012-08-03

Pomacea canaliculata is a freshwater snail that deposits eggs on solid substrates above the water surface. Previous studies have emphasized the nutritional and protective functions of the three most abundant perivitelline fluid (PVF) protein complexes (ovorubin, PV2, and PV3) during its embryonic development, but little is known about the structure and function of other less abundant proteins. Using 2-DE, SDS-PAGE, MALDI TOF/TOF, and LC-MS/MS, we identified 59 proteins from the PVF of P. canaliculata, among which 19 are novel. KEGG analysis showed that the functions of the majority of these proteins are "unknown" (n = 34), "environmental information processing" (10), 9 of which are related to innate immunity, and "metabolism" (7). Suppressive subtractive hybridization revealed 21 PVF genes to be specific to the albumen gland, indicating this organ is the origin of many of the PVF proteins. Further, the 3 ovorubin subunits were identified with 30.2-35.0% identity among them, indicating their common origin but ancient duplications. Characterization of the PVF proteome has opened the gate for further studies aiming to understand the evolution of the novel proteins and their contribution to the switch to aerial oviposition. © 2012 American Chemical Society.

Computer modelling of the chemical speciation of Americium (III) in human body fluids

International Nuclear Information System (INIS)

Jiang, Shu-bin; Lei, Jia-rong; Wang, He-yi; Zhong, Zhi-jing; Yang, Yong; Du, Yang

2008-01-01

A multi-phase equilibrium model consisted of multi-metal ion and low molecular mass ligands in human body fluid has been constructed to discuss the speciation of Am 3+ in gastric juice, sweat, interstitial fluid, intracellular fluid and urine of human body, respectively. Computer simulations indicated that the major Am(III)P Species were Am 3+ , [Am Cl] 2+ and [AmH 2 PO 4 ] 2+ at pH 4 became dominant with higher pH value when [Am] = 1 x 10 -7 mol/L in gastric juice model and percentage of AmPO 4 increased with [Am]. in sweat system, Am(III) existed with soluble species at pH 4.2∼pH 7.5 when [Am] = 1 x 10 -7 mol/L and Am(III) existed with Am 3+ and [Am OH] 2+ at pH 6.5 when [Am] -10 mol/L or [Am] > 5 x 10 -8 mol/L . With addition of EDTA, the Am(III) existed with soluble [Am EDTA] - whereas the Am(III) existed with insoluble AmPO 4 when [Am] > 1 x 10 -12 mol/L at interstitial fluid. The major Am(III) species was AmPO 4 at pH 7.0 and [Am]=4 x 10 -12 mol/L in intracellular fluid, which implied Am(III) represented strong cell toxicity. The percentage of Am(III) soluble species increased at lower pH hinted that the Am(III), in the form of aerosol, ingested by macrophage, could released into interstitial fluid and bring strong toxicity to skeleton system. The soluble Am(III) species was dominant when pH 4 when pH > 4.5 when [Am] = 1 x 10 -10 Pmol/L in human urine, so it was favorable to excrete Am(III) from kidney by taking acid materials. (author)

Application of Proteomics and Peptidomics to COPD

Directory of Open Access Journals (Sweden)

Girolamo Pelaia

2014-01-01

Full Text Available Chronic obstructive pulmonary disease (COPD is a complex disorder involving both airways and lung parenchyma, usually associated with progressive and poorly reversible airflow limitation. In order to better characterize the phenotypic heterogeneity and the prognosis of patients with COPD, there is currently an urgent need for discovery and validation of reliable disease biomarkers. Within this context, proteomic and peptidomic techniques are emerging as very valuable tools that can be applied to both systemic and pulmonary samples, including peripheral blood, induced sputum, exhaled breath condensate, bronchoalveolar lavage fluid, and lung tissues. Identification of COPD biomarkers by means of proteomic and peptidomic approaches can thus also lead to discovery of new molecular targets potentially useful to improve and personalize the therapeutic management of this widespread respiratory disease.

[Study of work accidents related to human body fluids exposure among health workers at a university hospital].

Science.gov (United States)

Balsamo, Ana Cristina; Felli, Vanda Elisa Andres

2006-01-01

This descriptive and exploratory study from a quantitative approach aimed to characterize workers who were victims of work accidents related to human body fluids exposure and to evaluate the accident victim care protocol. The population consisted of 48 workers who were victims of work accidents involving exposure to human body fluids, from July 2000 to June 2001. Data were collected through a form and interviews. Results showed that nursing workers presented higher accident risk levels and that 87.50% involved piercing and cutting material, such as needles and butterflies (70%). As to the accident-related situation/activity, the workers indicated that 25% were due to an "inadequate act during the procedure"; 19.64% mentioned that "it happened" and 29.17% answered that they did not have any suggestion. This study provided important tools to review and elaborate strategies to prevent accidents involving exposure to human body fluids.

Reprint of "EXOSOME LEVELS IN HUMAN BODY FLUIDS: A TUMOR MARKER BY THEMSELVES?"

Science.gov (United States)

Cappello, Francesco; Logozzi, Mariantonia; Campanella, Claudia; Bavisotto, Celeste Caruso; Marcilla, Antonio; Properzi, Francesca; Fais, Stefano

2017-02-15

Despite considerable research efforts, the finding of reliable tumor biomarkers remains challenging and unresolved. In recent years a novel diagnostic biomedical tool with high potential has been identified in extracellular nanovesicles or exosomes. They are released by the majority of the cells and contain detailed molecular information on the cell of origin including tumor hallmarks. Exosomes can be isolated from easy accessible body fluids, and most importantly, they can at once provide with several biomarkers, with different levels of specificity. Recent clinical evidence shows that the levels of exosomes released into body fluids may by themselves represent a predictive/diagnostic of tumors, discriminating cancer patients from healthy subjects. The aim of this review is to highlight these latest challenging findings to provide novel and groundbreaking ideas for successful tumor early diagnosis and follow-up. Copyright © 2016 Elsevier B.V. All rights reserved.

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis.

Science.gov (United States)

Hanson, Erin K; Ballantyne, Jack

2013-01-01

Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive

Non-Darcy Free Convection of Power-Law Fluids Over a Two-Dimensional Body Embedded in a Porous Medium

KAUST Repository

El-Amin, Mohamed

2010-11-27

A boundary layer analysis was presented to study the non-Darcy-free convection of a power-law fluid over a non-isothermal two-dimensional body embedded in a porous medium. The Ostwald-de Waele power-law model was used to characterize the non-Newtonian fluid behavior. Similarity solutions were obtained with variations in surface temperature or surface heat flux. In view of the fact that most of the non-Newtonian fluids have large Prandtl numbers, this study was directed toward such fluids. The effects of the porous medium parameters, k1 and k2, body shape parameter, m, and surface thermal variations parameter, p, as well as the power-law index, n, were examined. © 2010 Springer Science+Business Media B.V.

Non-Darcy Free Convection of Power-Law Fluids Over a Two-Dimensional Body Embedded in a Porous Medium

KAUST Repository

El-Amin, Mohamed; Sun, Shuyu; El-Ameen, M. A.; Jaha, Y. A.; Gorla, Rama Subba Reddy

2010-01-01

A boundary layer analysis was presented to study the non-Darcy-free convection of a power-law fluid over a non-isothermal two-dimensional body embedded in a porous medium. The Ostwald-de Waele power-law model was used to characterize the non-Newtonian fluid behavior. Similarity solutions were obtained with variations in surface temperature or surface heat flux. In view of the fact that most of the non-Newtonian fluids have large Prandtl numbers, this study was directed toward such fluids. The effects of the porous medium parameters, k1 and k2, body shape parameter, m, and surface thermal variations parameter, p, as well as the power-law index, n, were examined. © 2010 Springer Science+Business Media B.V.

The relationship between nocturnal polyuria and the distribution of body fluid: assessment by bioelectric impedance analysis.

Science.gov (United States)

Torimoto, Kazumasa; Hirayama, Akihide; Samma, Shoji; Yoshida, Katsunori; Fujimoto, Kiyohide; Hirao, Yoshihiko

2009-01-01

Increased nocturnal urinary volume is closely associated with nocturia. We investigated the relationship between nocturnal polyuria and the variation of body fluid distribution during the daytime using bioelectric impedance analysis. A total of 34 men older than 60 years were enrolled in this study. A frequency volume chart was recorded. Nocturnal polyuria was defined as a nocturnal urine volume per 24-hour production of greater than 0.35 (the nocturnal polyuria index). Bioelectric impedance analysis was performed 4 times daily at 8 and 11 a.m., and 5 and 9 p.m. using an InBody S20 body composition analyzer (BioSpace, Seoul, Korea). A significant difference was found in mean +/- SEM 24-hour urine production per fat-free mass between the groups with and without nocturnal polyuria (17.8 +/- 1.4 vs 7.7 +/- 0.9 ml/kg). The increase in fluid in the legs compared with the volume at 8 a.m. was significantly larger at 5 p.m., while there was no difference in the arms or trunk. Nocturnal urine volume significantly correlated with the difference in fluid volume in the legs (r = 0.527, p = 0.0019) and extracellular fluid volume (r = 0.3844, p = 0.0248) between the volumes at 8 a.m. and 9 p.m. Overproduction of urine per fat-free mass leads to nocturnal polyuria. Extracellular fluid accumulates as edema in the legs during the day in patients with nocturnal polyuria. The volume of accumulated extracellular fluid correlates with nocturnal urine volume. We suggest that leg edema is the source of nocturnal urine volume and decreasing edema may cure nocturnal polyuria.

Proteome Analysis of the Hemolymph, Mushroom Body, and Antenna Provides Novel Insight into Honeybee Resistance against Varroa Infestation.

Science.gov (United States)

Hu, Han; Bienefeld, Kaspar; Wegener, Jakob; Zautke, Fred; Hao, Yue; Feng, Mao; Han, Bin; Fang, Yu; Wubie, Abebe Jenberie; Li, Jianke

2016-08-05

Varroa destructor has been identified as a major culprit responsible for the losses of millions of honeybee colonies. Varroa sensitive hygiene (VSH) is a suite of behaviors from adult bees to suppress mite reproduction by uncapping and/or removing mite infested pupae from a sealed brood. Despite the efforts to elucidate the molecular underpinnings of VSH, they remain largely unknown. We investigated the proteome of mushroom bodies (MBs) and antennae of adult bees with and without VSH from a stock selected for VSH based on their response to artificially Varroa-infected brood cells by near-infrared camera observation. The pupal hemolymph proteome was also compared between the VSH-line and the line that was not selected for VSH. The identified 8609 proteins in the hemolymph, MBs, and antennae represent the most depth coverage of the honeybee proteome (>55%) to date. In the hemolymph, the VSH-line adapts a unique strategy to boost the social immunity and drive pupal organogenesis by enhancing energy metabolism and protein biosynthesis. In MBs, the up-regulated proteins implicated in neuronal sensitivity suggest their roles to promote the execution of VSH by activation of synaptic vesicles and calcium channel activities. In antennae, the highly expressed proteins associated with sensitivity of olfactory senses and signal transmissions signify their roles by inputting a strong signal to the MBs for initiating VSH. These observations illustrate that the enhanced social immunities and olfactory and neuronal sensitivity play key roles in the combat against Varroa infestation. The identified candidate markers may be useful for accelerating marker-associated selection for VSH to aid in resistance to a parasite responsible for decline in honeybee health.

Proteomic analyses of host and pathogen responses during bovine mastitis.

Science.gov (United States)

Boehmer, Jamie L

2011-12-01

The pursuit of biomarkers for use as clinical screening tools, measures for early detection, disease monitoring, and as a means for assessing therapeutic responses has steadily evolved in human and veterinary medicine over the past two decades. Concurrently, advances in mass spectrometry have markedly expanded proteomic capabilities for biomarker discovery. While initial mass spectrometric biomarker discovery endeavors focused primarily on the detection of modulated proteins in human tissues and fluids, recent efforts have shifted to include proteomic analyses of biological samples from food animal species. Mastitis continues to garner attention in veterinary research due mainly to affiliated financial losses and food safety concerns over antimicrobial use, but also because there are only a limited number of efficacious mastitis treatment options. Accordingly, comparative proteomic analyses of bovine milk have emerged in recent years. Efforts to prevent agricultural-related food-borne illness have likewise fueled an interest in the proteomic evaluation of several prominent strains of bacteria, including common mastitis pathogens. The interest in establishing biomarkers of the host and pathogen responses during bovine mastitis stems largely from the need to better characterize mechanisms of the disease, to identify reliable biomarkers for use as measures of early detection and drug efficacy, and to uncover potentially novel targets for the development of alternative therapeutics. The following review focuses primarily on comparative proteomic analyses conducted on healthy versus mastitic bovine milk. However, a comparison of the host defense proteome of human and bovine milk and the proteomic analysis of common veterinary pathogens are likewise introduced.

Quantitative Clinical Chemistry Proteomics (qCCP) using mass spectrometry: general characteristics and application.

Science.gov (United States)

Lehmann, Sylvain; Hoofnagle, Andrew; Hochstrasser, Denis; Brede, Cato; Glueckmann, Matthias; Cocho, José A; Ceglarek, Uta; Lenz, Christof; Vialaret, Jérôme; Scherl, Alexander; Hirtz, Christophe

2013-05-01

Proteomics studies typically aim to exhaustively detect peptides/proteins in a given biological sample. Over the past decade, the number of publications using proteomics methodologies has exploded. This was made possible due to the availability of high-quality genomic data and many technological advances in the fields of microfluidics and mass spectrometry. Proteomics in biomedical research was initially used in 'functional' studies for the identification of proteins involved in pathophysiological processes, complexes and networks. Improved sensitivity of instrumentation facilitated the analysis of even more complex sample types, including human biological fluids. It is at that point the field of clinical proteomics was born, and its fundamental aim was the discovery and (ideally) validation of biomarkers for the diagnosis, prognosis, or therapeutic monitoring of disease. Eventually, it was recognized that the technologies used in clinical proteomics studies [particularly liquid chromatography-tandem mass spectrometry (LC-MS/MS)] could represent an alternative to classical immunochemical assays. Prior to deploying MS in the measurement of peptides/proteins in the clinical laboratory, it seems likely that traditional proteomics workflows and data management systems will need to adapt to the clinical environment and meet in vitro diagnostic (IVD) regulatory constraints. This defines a new field, as reviewed in this article, that we have termed quantitative Clinical Chemistry Proteomics (qCCP).

Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library.

Directory of Open Access Journals (Sweden)

Jenny Rivers

Full Text Available Immobilized combinatorial peptide libraries have been advocated as a strategy for equalization of the dynamic range of a typical proteome. The technology has been applied predominantly to blood plasma and other biological fluids such as urine, but has not been used extensively to address the issue of dynamic range in tissue samples. Here, we have applied the combinatorial library approach to the equalization of a tissue where there is also a dramatic asymmetry in the range of abundances of proteins; namely, the soluble fraction of skeletal muscle. We have applied QconCAT and label-free methodology to the quantification of the proteins that bind to the beads as the loading is progressively increased. Although some equalization is achieved, and the most abundant proteins no longer dominate the proteome analysis, at high protein loadings a new asymmetry of protein expression is reached, consistent with the formation of complex assembles of heat shock proteins, cytoskeletal elements and other proteins on the beads. Loading at different ionic strength values leads to capture of different subpopulations of proteins, but does not completely eliminate the bias in protein accumulation. These assemblies may impair the broader utility of combinatorial library approaches to the equalization of tissue proteomes. However, the asymmetry in equalization is manifest at either low and high ionic strength values but manipulation of the solvent conditions may extend the capacity of the method.

Review of application of mass spectrometry for analyses of anterior eye proteome

Institute of Scientific and Technical Information of China (English)

Sherif; Elsobky; Ashley; M; Crane; Michael; Margolis; Teresia; A; Carreon; Sanjoy; K; Bhattacharya

2014-01-01

Proteins have important functional roles in the body, which can be altered in disease states. The eye is a complex organ rich in proteins; in particular, the anterior eye is very sophisticated in function and is most commonly involved in ophthalmic diseases. Proteomics, the large scale study of proteins, has greatly impacted our knowledge and understanding of gene function in the post-genomic period. The most significant breakthrough in proteomics has been mass spectrometric identification of proteins, which extends analysis far beyond the mere display of proteins that classical techniques provide. Mass spectrometry functions as a "mass analyzer" which simplifies the identification and quantification of proteins extracted from biological tissue. Mass spectrometric analysis of the anterior eye proteome provides a differential display for protein comparison of normal and diseased tissue. In this article wepresent the key proteomic findings in the recent literature related to the cornea, aqueous humor, trabecular meshwork, iris, ciliary body and lens. Through this we identified unique proteins specific to diseases related to the anterior eye.

Proteomics Core

Data.gov (United States)

Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

Application of FTA technology to extraction of sperm DNA from mixed body fluids containing semen.

Science.gov (United States)

Fujita, Yoshihiko; Kubo, Shin-ichi

2006-01-01

FTA technology is a novel method designed to simplify the collection, shipment, archiving and purification of nucleic acids from a wide variety of biological sources. In this study, we report a rapid and simple method of extracting DNA from sperm when body fluids mixed with semen were collected using FTA cards. After proteinase K digestion of the sperm and body fluid mixture, the washed pellet suspension as the sperm fraction and the concentrated supernatant as the epithelial cell fraction were respectively applied to FTA cards containing DTT. The FTA cards were dried, then directly added to a polymerase chain reaction (PCR) mix and processed by PCR. The time required from separation of the mixed fluid into sperm and epithelial origin DNA extractions was only about 2.5-3h. Furthermore, the procedure was extremely simple. It is considered that our designed DNA extraction procedure using an FTA card is available for application to routine work.

The "chloride theory", a unifying hypothesis for renal handling and body fluid distribution in heart failure pathophysiology.

Science.gov (United States)

Kataoka, Hajime

2017-07-01

Body fluid volume regulation is a complex process involving the interaction of various afferent (sensory) and neurohumoral efferent (effector) mechanisms. Historically, most studies focused on the body fluid dynamics in heart failure (HF) status through control of the balance of sodium, potassium, and water in the body, and maintaining arterial circulatory integrity is central to a unifying hypothesis of body fluid regulation in HF pathophysiology. The pathophysiologic background of the biochemical determinants of vascular volume in HF status, however, has not been known. I recently demonstrated that changes in vascular and red blood cell volumes are independently associated with the serum chloride concentration, but not the serum sodium concentration, during worsening HF and its recovery. Based on these observations and the established central role of chloride in the renin-angiotensin-aldosterone system, I propose a unifying hypothesis of the "chloride theory" for HF pathophysiology, which states that changes in the serum chloride concentration are the primary determinant of changes in plasma volume and the renin-angiotensin-aldosterone system under worsening HF and therapeutic resolution of worsening HF. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spinal Cord Stimulation Alters Protein Levels in the Cerebrospinal Fluid of Neuropathic Pain Patients: A Proteomic Mass Spectrometric Analysis.

Science.gov (United States)

Lind, Anne-Li; Emami Khoonsari, Payam; Sjödin, Marcus; Katila, Lenka; Wetterhall, Magnus; Gordh, Torsten; Kultima, Kim

2016-08-01

Electrical neuromodulation by spinal cord stimulation (SCS) is a well-established method for treatment of neuropathic pain. However, the mechanism behind the pain relieving effect in patients remains largely unknown. In this study, we target the human cerebrospinal fluid (CSF) proteome, a little investigated aspect of SCS mechanism of action. Two different proteomic mass spectrometry protocols were used to analyze the CSF of 14 SCS responsive neuropathic pain patients. Each patient acted as his or her own control and protein content was compared when the stimulator was turned off for 48 hours, and after the stimulator had been used as normal for three weeks. Eighty-six proteins were statistically significantly altered in the CSF of neuropathic pain patients using SCS, when comparing the stimulator off condition to the stimulator on condition. The top 12 of the altered proteins are involved in neuroprotection (clusterin, gelsolin, mimecan, angiotensinogen, secretogranin-1, amyloid beta A4 protein), synaptic plasticity/learning/memory (gelsolin, apolipoprotein C1, apolipoprotein E, contactin-1, neural cell adhesion molecule L1-like protein), nociceptive signaling (neurosecretory protein VGF), and immune regulation (dickkopf-related protein 3). Previously unknown effects of SCS on levels of proteins involved in neuroprotection, nociceptive signaling, immune regulation, and synaptic plasticity are demonstrated. These findings, in the CSF of neuropathic pain patients, expand the picture of SCS effects on the neurochemical environment of the human spinal cord. An improved understanding of SCS mechanism may lead to new tracks of investigation and improved treatment strategies for neuropathic pain. © 2016 International Neuromodulation Society.

Quantitative targeted proteomics for understanding the blood-brain barrier: towards pharmacoproteomics.

Science.gov (United States)

Ohtsuki, Sumio; Hirayama, Mio; Ito, Shingo; Uchida, Yasuo; Tachikawa, Masanori; Terasaki, Tetsuya

2014-06-01

The blood-brain barrier (BBB) is formed by brain capillary endothelial cells linked together via complex tight junctions, and serves to prevent entry of drugs into the brain. Multiple transporters are expressed at the BBB, where they control exchange of materials between the circulating blood and brain interstitial fluid, thereby supporting and protecting the CNS. An understanding of the BBB is necessary for efficient development of CNS-acting drugs and to identify potential drug targets for treatment of CNS diseases. Quantitative targeted proteomics can provide detailed information on protein expression levels at the BBB. The present review highlights the latest applications of quantitative targeted proteomics in BBB research, specifically to evaluate species and in vivo-in vitro differences, and to reconstruct in vivo transport activity. Such a BBB quantitative proteomics approach can be considered as pharmacoproteomics.

Normotension, hypertension and body fluid regulation: brain and kidney.

Science.gov (United States)

Bie, P; Evans, R G

2017-01-01

The fraction of hypertensive patients with essential hypertension (EH) is decreasing as the knowledge of mechanisms of secondary hypertension increases, but in most new cases of hypertension the pathophysiology remains unknown. Separate neurocentric and renocentric concepts of aetiology have prevailed without much interaction. In this regard, several questions regarding the relationships between body fluid and blood pressure regulation are pertinent. Are all forms of EH associated with sympathetic overdrive or a shift in the pressure-natriuresis curve? Is body fluid homoeostasis normally driven by the influence of arterial blood pressure directly on the kidney? Does plasma renin activity, driven by renal nerve activity and renal arterial pressure, provide a key to stratification of EH? Our review indicates that (i) a narrow definition of EH is useful; (ii) in EH, indices of cardiovascular sympathetic activity are elevated in about 50% of cases; (iii) in EH as in normal conditions, mediators other than arterial blood pressure are the major determinants of renal sodium excretion; (iv) chronic hypertension is always associated with a shift in the pressure-natriuresis curve, but this may be an epiphenomenon; (v) plasma renin levels are useful in the analysis of EH only after metabolic standardization and then determination of the renin function line (plasma renin as a function of sodium intake); and (vi) angiotensin II-mediated hypertension is not a model of EH. Recent studies of baroreceptors and renal nerves as well as sodium intake and renin secretion help bridge the gap between the neurocentric and renocentric concepts. © 2016 Scandinavian Physiological Society. Published by John Wiley & Sons Ltd.

Differentiation of Body Fluid Stains on Fabrics Using External Reflection Fourier Transform Infrared Spectroscopy (FT-IR) and Chemometrics.

Science.gov (United States)

Zapata, Félix; de la Ossa, Ma Ángeles Fernández; García-Ruiz, Carmen

2016-04-01

Body fluids are evidence of great forensic interest due to the DNA extracted from them, which allows genetic identification of people. This study focuses on the discrimination among semen, vaginal fluid, and urine stains (main fluids in sexual crimes) placed on different colored cotton fabrics by external reflection Fourier transform infrared spectroscopy (FT-IR) combined with chemometrics. Semen-vaginal fluid mixtures and potential false positive substances commonly found in daily life such as soaps, milk, juices, and lotions were also studied. Results demonstrated that the IR spectral signature obtained for each body fluid allowed its identification and the correct classification of unknown stains by means of principal component analysis (PCA) and soft independent modeling of class analogy (SIMCA). Interestingly, results proved that these IR spectra did not show any bands due to the color of the fabric and no substance of those present in daily life which were analyzed, provided a false positive. © The Author(s) 2016.

Proteomic approach to nanotoxicity.

Science.gov (United States)

Matysiak, Magdalena; Kapka-Skrzypczak, Lucyna; Brzóska, Kamil; Gutleb, Arno C; Kruszewski, Marcin

2016-03-30

In recent years a large number of engineered nanomaterials (NMs) have been developed with promising technical benefits for consumers and medical appliances. In addition to already known potentially advantageous biological properties (antibiotic, antifungal and antiviral activity) of NMs, many new medical applications of NMs are foreseen, such as drug carriers, contrast agents, radiopharmaceuticals and many others. However, there is increasing concern about potential environmental and health effects due to NMs exposure. An increasing body of evidence suggests that NMs may trigger undesirable hazardous interactions with biological systems with potential to generate harmful effects. In this review we summarized a current state of knowledge on the proteomics approaches to nanotoxicity, including protein corona formation, in vitro and in vivo effects of exposure to NMs on proteome of different classes of organisms, from bacteria and plants to mammals. The effects of NMs on the proteome of environmentally relevant organisms are also described. Despite the benefit that development of nanotechnology may bring to the society, there are still major gaps of knowledge on the influence of nanomaterials on human health and the environment. Thus, it seems necessary to conduct further interdisciplinary research to fill the knowledge gaps in NM toxicity, using more holistic approaches than offered by conventional biological techniques. “OMICS” techniques will certainly help researchers in this field. In this paper we summarized the current stage of knowledge of the effects of nanoparticles on the proteome of different organisms, including those commonly used as an environmentally relevant indicator organisms.

The landscape of viral proteomics and its potential to impact human health

Energy Technology Data Exchange (ETDEWEB)

Oxford, Kristie L.; Wendler, Jason P.; McDermott, Jason E.; White III, Richard A.; Powell, Joshua D.; Jacobs, Jon M.; Adkins, Joshua N.; Waters, Katrina M.

2016-05-06

Translating the intimate discourse between viruses and their host cells during infection is a challenging but critical task for development of antiviral interventions and diagnostics. Viruses commandeer cellular processes at every step of their life cycle, altering expression of genes and proteins. Advances in mass spectrometry-based proteomic technologies are enhancing studies of viral pathogenesis by identifying virus-induced changes in the protein repertoire of infected cells or extracellular fluids. Interpretation of proteomics results using knowledge of cellular pathways and networks leads to identification of proteins that influence a range of infection processes, thereby focusing efforts for clinical diagnoses and therapeutics development. Herein we discuss applications of global proteomic studies of viral infections with the goal of providing a basis for improved studies that will benefit community-wide data integration and interpretation.

Clarke's Isolation and identification of drugs in pharmaceuticals, body fluids, and post-mortem material

National Research Council Canada - National Science Library

Clarke, E. G. C; Moffat, A. C; Jackson, J. V

1986-01-01

This book is intended for scientists faced with the difficult problem of identifying an unknown drug in a pharmaceutical product, in a sample of tissue or body fluid from a living patient, or in post-mortem material...

A finite volume procedure for fluid flow, heat transfer and solid-body stress analysis

KAUST Repository

Jagad, P. I.; Puranik, B. P.; Date, A. W.

2018-01-01

A unified cell-centered unstructured mesh finite volume procedure is presented for fluid flow, heat transfer and solid-body stress analysis. An in-house procedure (A. W. Date, Solution of Transport Equations on Unstructured Meshes with Cell

Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp novicida

Energy Technology Data Exchange (ETDEWEB)

Varnum, Susan M.; Webb-Robertson, Bobbie-Jo M.; Pounds, Joel G.; Moore, Ronald J.; Smith, Richard D.; Frevert, Charles; Skerret, Shawn J.; Wunschel, David S.

2012-07-06

Francisella tularensis causes the zoonosis tularemia in humans and is one of the most virulent bacterial pathogens. We utilized a global proteomic approach to characterize protein changes in bronchoalveolar lavage fluid from mice exposed to one of three organisms, F. tularensis ssp. novicida, an avirulent mutant of F. tularensis ssp. novicida (F.t. novicida-ΔmglA); and Pseudomonas aeruginosa. The composition of BALF proteins was altered following infection, including proteins involved in neutrophil activation, oxidative stress and inflammatory responses. Components of the innate immune response were induced including the acute phase response and the complement system, however the timing of their induction varied. Francisella tularensis ssp. novicida infected mice do not appear to have an effective innate immune response in the first hours of infection, however within 24 hours they show an upregulation of innate immune response proteins. This delayed response is in contrast to P. aeruginosa infected animals which show an early innate immune response. Likewise, F.t. novicida-ΔmglA infection initiates an early innate immune response, however this response is dimished by 24 hours. Finally, this study identifies several candidate biomarkers, including Chitinase 3-like-1 (CHI3L1 or YKL-40) and peroxiredoxin 1, that are associated with F. tularensis ssp. novicida but not P. aeruginosa infection.

Proteomics of Skeletal Muscle

DEFF Research Database (Denmark)

Deshmukh, Atul

2016-01-01

, of altered protein expressions profiles and/or their posttranslational modifications (PTMs). Mass spectrometry (MS)-based proteomics offer enormous promise for investigating the molecular mechanisms underlying skeletal muscle insulin resistance and exercise-induced adaptation; however, skeletal muscle......Skeletal muscle is the largest tissue in the human body and plays an important role in locomotion and whole body metabolism. It accounts for ~80% of insulin stimulated glucose disposal. Skeletal muscle insulin resistance, a primary feature of Type 2 diabetes, is caused by a decreased ability...... of muscle to respond to circulating insulin. Physical exercise improves insulin sensitivity and whole body metabolism and remains one of the most promising interventions for the prevention of Type 2 diabetes. Insulin resistance and exercise adaptations in skeletal muscle might be a cause, or consequence...

Changes of body fluid and hematology in toad and their rehabilitation following intermittent exposure to simulated high altitude

Science.gov (United States)

Biswas, H. M.; Boral, M. C.

1986-06-01

Three groups of adult male toads were exposed intermittently in a decompression chamber for a daily period of 4 and 8 hours at a time for 6 consecutive days to an “altitude” of 12,000; 18,000 and 24,000 feet (3658; 5486; 7315 m) respectively. Most of the exposed animals were sacrificed immediately after the last exposure, but only a few animals experiencing 8 hours of exposure were sacrificed after a further 16 hours of exposure at normal atmospheric pressure. Eight hours of daily exposure for 6 days causes a decrease of body fluids and an increase of hematological parameters in all the altitude exposed animals compared with to the changes noted in the animals having 4 hours of daily exposure for 6 days at the same altitude levels. The animals that were exposed to pressures equivalent to altitudes of 12,000 and 18,000 feet daily for 8 hours were found to return nearly to their normal body fluids and hematological balance after 16 hours of exposure to normal atmospheric pressure, whereas the animals exposed for a similar period at an equivalent 24,000 feet failed to get back their normal balance of body fluids and hematology after 16 hours of exposure at normal atmospheric pressure. The present experiment shows that the body weight loss and changes of body fluid and hematological parameters in the toad after exposure to simulated high altitude are due not only to dehydration, but suggest that hypoxia may also have a role.

Clinical proteomics

DEFF Research Database (Denmark)

Albrethsen, Jakob; Frederiksen, Hanne; Johannsen, Trine Holm

2018-01-01

Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS)-platforms...... standards and calibrants. The present challenge is to examine if targeted proteomics of IGF-I can truly measure up to the routine performance that must be expected from a clinical testing platform.......Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS......)-platforms already implemented in many clinical laboratories for routine quantitation of small molecules (i.e. uHPLC coupled to triple-quadrupole MS). Progress in targeted proteomics of circulating insulin-like growth factor 1 (IGF-I) have provided valuable insights about tryptic peptides, transitions, internal...

Partial-Body Irradiation in Patients with Prostate Cancer Treated with IMRT Has Little Effect on the Composition of Serum Proteome.

Science.gov (United States)

Pietrowska, Monika; Jelonek, Karol; Polanska, Joanna; Wojakowska, Anna; Marczak, Lukasz; Chawinska, Ewa; Chmura, Aleksanda; Majewski, Wojciech; Miszczyk, Leszek; Widlak, Piotr

2015-06-30

Partial body irradiation during cancer radiotherapy (RT) induces a response of irradiated tissues that could be observed at the level of serum proteome. Here we aimed to characterize the response to RT in group of patients treated because of prostate cancer. Five consecutive blood samples were collected before, during, and after the end of RT in a group of 126 patients who received definitive treatment with a maximum dose of 76 Gy. Serum peptidome, which was profiled in the 2000-16,000 Da range using MALDI-MS. Serum proteins were identified and quantified using the shotgun LC-MS/MS approach. The majority of changes in serum peptidome were detected between pre-treatment samples and samples collected after 3-4 weeks of RT (~25% of registered peptides changed their abundances significantly), yet the intensity of observed changes was not correlated significantly with the degree of acute radiation toxicity or the volume of irradiated tissues. Furthermore, there were a few serum proteins identified, the abundances of which were different in pre-RT and post-RT samples, including immunity and inflammation-related factors. Observed effects were apparently weaker than in comparable groups of head and neck cancer patients in spite of similar radiation doses and volumes of irradiated tissues in both groups. We concluded that changes observed at the level of serum proteome were low for this cohort of prostate cancer patients, although the specific components involved are associated with immunity and inflammation, and reflect the characteristic acute response of the human body to radiation.

Partial-Body Irradiation in Patients with Prostate Cancer Treated with IMRT Has Little Effect on the Composition of Serum Proteome

Directory of Open Access Journals (Sweden)

Monika Pietrowska

2015-06-01

Full Text Available Partial body irradiation during cancer radiotherapy (RT induces a response of irradiated tissues that could be observed at the level of serum proteome. Here we aimed to characterize the response to RT in group of patients treated because of prostate cancer. Five consecutive blood samples were collected before, during, and after the end of RT in a group of 126 patients who received definitive treatment with a maximum dose of 76 Gy. Serum peptidome, which was profiled in the 2000–16,000 Da range using MALDI-MS. Serum proteins were identified and quantified using the shotgun LC-MS/MS approach. The majority of changes in serum peptidome were detected between pre-treatment samples and samples collected after 3–4 weeks of RT (~25% of registered peptides changed their abundances significantly, yet the intensity of observed changes was not correlated significantly with the degree of acute radiation toxicity or the volume of irradiated tissues. Furthermore, there were a few serum proteins identified, the abundances of which were different in pre-RT and post-RT samples, including immunity and inflammation-related factors. Observed effects were apparently weaker than in comparable groups of head and neck cancer patients in spite of similar radiation doses and volumes of irradiated tissues in both groups. We concluded that changes observed at the level of serum proteome were low for this cohort of prostate cancer patients, although the specific components involved are associated with immunity and inflammation, and reflect the characteristic acute response of the human body to radiation.

The Spanish biology/disease initiative within the human proteome project: Application to rheumatic diseases.

Science.gov (United States)

Ruiz-Romero, Cristina; Calamia, Valentina; Albar, Juan Pablo; Casal, José Ignacio; Corrales, Fernando J; Fernández-Puente, Patricia; Gil, Concha; Mateos, Jesús; Vivanco, Fernando; Blanco, Francisco J

2015-09-08

The Spanish Chromosome 16 consortium is integrated in the global initiative Human Proteome Project, which aims to develop an entire map of the proteins encoded following a gene-centric strategy (C-HPP) in order to make progress in the understanding of human biology in health and disease (B/D-HPP). Chromosome 16 contains many genes encoding proteins involved in the development of a broad range of diseases, which have a significant impact on the health care system. The Spanish HPP consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. Proteomics strategies have enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. In this manuscript we describe how the Spanish HPP-16 consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. We show how the Proteomic strategy has enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. This article is part of a Special Issue entitled: HUPO 2014. Copyright © 2015 Elsevier B.V. All rights reserved.

Urine, peritoneal fluid and omental fat proteomes of reproductive age women: Endometriosis-related changes and associations with endocrine disrupting chemicals.

Science.gov (United States)

Williams, Katherine E; Miroshnychenko, Olga; Johansen, Eric B; Niles, Richard K; Sundaram, Rajeshwari; Kannan, Kurunthachalam; Albertolle, Matthew; Zhou, Yan; Prasad, Namrata; Drake, Penelope M; Giudice, Linda C; Hall, Steven C; Witkowska, H Ewa; Buck Louis, Germaine M; Fisher, Susan J

2015-01-15

Endometriosis, ectopic growth of the uterine lining (endometrium), which affects 6-11% of reproductive age women, is associated with pelvic pain and infertility. We investigated the peritoneal fluid (PF), urine and omental fat (OF) proteomes of women with endometriosis vs. individuals with no surgically visualized endometriosis. All participants were enrolled in the NICHD-funded ENDO Study. A two-step proteomic study was performed. The first, a broad survey, employed a semi-quantitative gel LC-mass spectrometry (MS) workflow: SDS PAGE fractionation, trypsin digestion and LC-MS/MS. The results showed sample integrity but failed to detect any differences between women with and without endometriosis. The second step was a quantitative analysis of OF samples. We employed another sample set (n=30) from women ± disease and isobaric mass-tag (iTRAQ) chemistry to label peptides and 2D LC-MS/MS for protein identification and quantification. Three proteins-matrix metalloproteinase-9, neutrophil elastase, and FAM49B-were significantly lower in abundance in samples from women with endometriosis. Interestingly, neutrophil elastase and FAM49B levels were associated with higher levels of a subset of endocrine disrupting chemicals (EDCs) that were previously measured in the same samples. The results of these experiments showed the feasibility of associating endometriosis with changes in the OF protein repertoire and EDC levels. Endometriosis, pathological growth of the uterine lining, is associated with significant morbidities, including pain and infertility. However, the causes of this common condition are poorly understood. This study determined whether endometriosis was associated with changes in the protein composition of peritoneal fluid, urine and/or omental fat. A protein of unknown function (FAM49B) and two proteinases (metalloproteinase-9, neutrophil elastase) were down regulated in OF samples from women with versus without endometriosis. These findings suggested

A Hybrid Feature Subset Selection Algorithm for Analysis of High Correlation Proteomic Data

Science.gov (United States)

Kordy, Hussain Montazery; Baygi, Mohammad Hossein Miran; Moradi, Mohammad Hassan

2012-01-01

Pathological changes within an organ can be reflected as proteomic patterns in biological fluids such as plasma, serum, and urine. The surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS) has been used to generate proteomic profiles from biological fluids. Mass spectrometry yields redundant noisy data that the most data points are irrelevant features for differentiating between cancer and normal cases. In this paper, we have proposed a hybrid feature subset selection algorithm based on maximum-discrimination and minimum-correlation coupled with peak scoring criteria. Our algorithm has been applied to two independent SELDI-TOF MS datasets of ovarian cancer obtained from the NCI-FDA clinical proteomics databank. The proposed algorithm has used to extract a set of proteins as potential biomarkers in each dataset. We applied the linear discriminate analysis to identify the important biomarkers. The selected biomarkers have been able to successfully diagnose the ovarian cancer patients from the noncancer control group with an accuracy of 100%, a sensitivity of 100%, and a specificity of 100% in the two datasets. The hybrid algorithm has the advantage that increases reproducibility of selected biomarkers and able to find a small set of proteins with high discrimination power. PMID:23717808

Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform.

Science.gov (United States)

Pan, Sheng; Rush, John; Peskind, Elaine R; Galasko, Douglas; Chung, Kathryn; Quinn, Joseph; Jankovic, Joseph; Leverenz, James B; Zabetian, Cyrus; Pan, Catherine; Wang, Yan; Oh, Jung Hun; Gao, Jean; Zhang, Jianpeng; Montine, Thomas; Zhang, Jing

2008-02-01

Targeted quantitative proteomics by mass spectrometry aims to selectively detect one or a panel of peptides/proteins in a complex sample and is particularly appealing for novel biomarker verification/validation because it does not require specific antibodies. Here, we demonstrated the application of targeted quantitative proteomics in searching, identifying, and quantifying selected peptides in human cerebrospinal spinal fluid (CSF) using a matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF)-based platform. The approach involved two major components: the use of isotopic-labeled synthetic peptides as references for targeted identification and quantification and a highly selective mass spectrometric analysis based on the unique characteristics of the MALDI instrument. The platform provides high confidence for targeted peptide detection in a complex system and can potentially be developed into a high-throughput system. Using the liquid chromatography (LC) MALDI TOF/TOF platform and the complementary identification strategy, we were able to selectively identify and quantify a panel of targeted peptides in the whole proteome of CSF without prior depletion of abundant proteins. The effectiveness and robustness of the approach associated with different sample complexity, sample preparation strategies, as well as mass spectrometric quantification were evaluated. Other issues related to chromatography separation and the feasibility for high-throughput analysis were also discussed. Finally, we applied targeted quantitative proteomics to analyze a subset of previously identified candidate markers in CSF samples of patients with Parkinson's disease (PD) at different stages and Alzheimer's disease (AD) along with normal controls.

Effects of immersion water temperature on whole-body fluid distribution in humans.

Science.gov (United States)

Stocks, J M; Patterson, M J; Hyde, D E; Jenkins, A B; Mittleman, K D; Taylor, N A S

2004-09-01

In this study, we quantified acute changes in the intracellular and extracellular fluid compartments during upright neutral- and cold-water immersion. We hypothesized that, during short-term cold immersion, fluid shifts would be wholly restricted to the extracellular space. Seven males were immersed 30 days apart: control (33.3 degrees SD 0.6 degrees C); and cold (18.1 degrees SD 0.3 degrees C). Posture was controlled for 4 h prior to a 60-min seated immersion. Significant reductions in terminal oesophageal (36.9 degrees +/- 0.1 degrees -36.3 degrees +/- 0.1 degrees C) and mean skin temperatures (30.3 degrees +/- 0.3 degrees -23.0 degrees +/- 0.3 degrees C) were observed during the cold, but not the control immersion. Both immersions elicited a reduction in intracellular fluid [20.17 +/- 6.02 mL kg(-1) (control) vs. 22.72 +/- 9.90 mL kg(-1)], while total body water (TBW) remained stable. However, significant plasma volume (PV) divergence was apparent between the trials at 60 min [12.5 +/- 1.0% (control) vs. 6.1 +/- 3.1%; P cold immersion, consistent with its role in PV regulation. We observed that, regardless of the direction of the PV change, both upright immersions elicited reductions in intracellular fluid. These observations have two implications. First, one cannot assume that PV changes reflect those of the entire extracellular compartment. Second, since immersion also increases interstitial fluid pressure, fluid leaving the interstitium must have been rapidly replaced by intracellular water.

Measurement of glycosaminoglycans in canine synovial fluid and its correlation with the cause of secondary osteoarthritis, age and body weight

Directory of Open Access Journals (Sweden)

Radka Andrysíková

2012-01-01

Full Text Available Glycosaminoglycans are natural components of healthy joint cartilage and they also appear in healthy synovial fluid. An increased amount of glycosaminoglycans in synovial fluid is believed to be a marker of secondary osteoarthritis, regardless of its primary cause. The aim of our study was to define the relationship between glycosaminoglycans in the synovial fluid and joint disorders, age, and body weight. The samples of synovial fluid were obtained from dogs suffering from secondary secondary osteoarthritis (n = 35 and from control dogs (n = 18; control dogs had normal body weight. The results were compared among joints of dogs with secondary osteoarthritis divided into groups according to the criteria mentioned above and control dogs. Glycosaminoglycan concentrations in synovial fluid were measured using dimethylmethylene blue assay. The lowest mean value of glycosaminoglycans in synovial fluid was measured in the control group. Significantly higher glycosaminoglycan content (P < 0.05 was found in synovial fluid isolated from obese dogs compared to control dogs. Furthermore, we observed an age-related trend, in which the highest mean values were reached either in old dogs or pups. Despite the absence of significant differences in glycosaminoglycan values among dogs suffering from various types of secondary secondary osteoarthritis, the highest mean values were measured in fragmented coronoid processus group. Our data suggest that abnormally increased body weight has an impact on glycosaminoglycan concentration in synovial fluid which may imply faster degradation and turnover of joint cartilage. Such observation has not yet been published in veterinary medicine.

Optical detection and virotherapy of live metastatic tumor cells in body fluids with vaccinia strains.

Directory of Open Access Journals (Sweden)

Huiqiang Wang

Full Text Available Metastatic tumor cells in body fluids are important targets for treatment, and critical surrogate markers for evaluating cancer prognosis and therapeutic response. Here we report, for the first time, that live metastatic tumor cells in blood samples from mice bearing human tumor xenografts and in blood and cerebrospinal fluid samples from patients with cancer were successfully detected using a tumor cell-specific recombinant vaccinia virus (VACV. In contrast to the FDA-approved CellSearch system, VACV detects circulating tumor cells (CTCs in a cancer biomarker-independent manner, thus, free of any bias related to the use of antibodies, and can be potentially a universal system for detection of live CTCs of any tumor type, not limited to CTCs of epithelial origin. Furthermore, we demonstrate for the first time that VACV was effective in preventing and reducing circulating tumor cells in mice bearing human tumor xenografts. Importantly, a single intra-peritoneal delivery of VACV resulted in a dramatic decline in the number of tumor cells in the ascitic fluid from a patient with gastric cancer. Taken together, these results suggest VACV to be a useful tool for quantitative detection of live tumor cells in liquid biopsies as well as a potentially effective treatment for reducing or eliminating live tumor cells in body fluids of patients with metastatic disease.

[Diet and exercise influence on the proteomic profile of an athlete population].

Science.gov (United States)

Toro, Rocio; Mangas, Alipio; Quezada, Maribel; Rodriguez-Rosety, Manuel; Fournielles, Gabriel; Rodriguez-Rosety, Ignacio; Rodriguez Rosety, Miguel Angel; Alonso, Jose Angel; Garcia-Cozar, Francisco Jose; Duran, Maria Del Carmen

2014-11-01

Nutrition has emerged as a fundamental tool included in the training program of athletes. Body composition seeks different objectives depending on type of sport, position, or time of the season. Furthermore, analysis proteomics allows us to know the structure and function of proteins. To study, using proteomics, the influence of two different diets on the anthropometric profile in a rugby players group. It is a prospective and interventionist study. Thirty-two rugby players were included. Two groups were defined, one followed proteic diet (PD) and, the other group subscribed the Mediterranean diet (MD). All participants were evaluated anthropometrically at the beginning and after six months. A blood sample was taken to twenty -two players, half of each group, used for the proteomic analysis. MD highlight more benefit for these athletes. Two groups were defined based on their anthropometric behavior, G1 and G2. The proteomic analysis related significantly some TGF-family mediators with these groups. MD improves the muscular mass without increasing the total body weight, so this data could be determinant to define profiles for athletes. Some TGF-members could be implicated in the adipose tissue and muscular mass balance. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

In vitro studies evaluating leaching of mercury from mine waste calcine using simulated human body fluids

Science.gov (United States)

Gray, John E.; Plumlee, Geoffrey S.; Morman, Suzette A.; Higueras, Pablo L.; Crock, James G.; Lowers, Heather A.; Witten, Mark L.

2010-01-01

In vitro bioaccessibility (IVBA) studies were carried out on samples of mercury (Hg) mine-waste calcine (roasted Hg ore) by leaching with simulated human body fluids. The objective was to estimate potential human exposure to Hg due to inhalation of airborne calcine particulates and hand-to-mouth ingestion of Hg-bearing calcines. Mine waste calcines collected from Hg mines at Almadén, Spain, and Terlingua, Texas, contain Hg sulfide, elemental Hg, and soluble Hg compounds, which constitute primary ore or compounds formed during Hg retorting. Elevated leachate Hg concentrations were found during calcine leaching using a simulated gastric fluid (as much as 6200 μg of Hg leached/g sample). Elevated Hg concentrations were also found in calcine leachates using a simulated lung fluid (as much as 9200 μg of Hg leached/g), serum-based fluid (as much as 1600 μg of Hg leached/g), and water of pH 5 (as much as 880 μg of Hg leached/g). The leaching capacity of Hg is controlled by calcine mineralogy; thus, calcines containing soluble Hg compounds contain higher leachate Hg concentrations. Results indicate that ingestion or inhalation of Hg mine-waste calcine may lead to increased Hg concentrations in the human body, especially through the ingestion pathway.

Self-powered implantable electronic-skin for in situ analysis of urea/uric-acid in body fluids and the potential applications in real-time kidney-disease diagnosis.

Science.gov (United States)

Yang, Wenyan; Han, Wuxiao; Gao, Huiling; Zhang, Linlin; Wang, Shuai; Xing, Lili; Zhang, Yan; Xue, Xinyu

2018-01-25

As the concentration of different biomarkers in human body fluids are an important parameter of chronic disease, wearable biosensors for in situ analysis of body fluids with high sensitivity, real-time detection, flexibility and biocompatibility have significant potential therapeutic applications. In this paper, a flexible self-powered implantable electronic-skin (e-skin) for in situ body fluids analysis (urea/uric-acid) as a real-time kidney-disease diagnoser has been proposed based on the piezo-enzymatic-reaction coupling process of ZnO nanowire arrays. It can convert the mechanical energy of body movements into a piezoelectric impulse, and the outputting piezoelectric signal contains the urea/uric-acid concentration information in body fluids. This piezoelectric-biosensing process does not need an external electricity supply or battery. The e-skin was implanted under the abdominal skin of a mouse and provided in situ analysis of the kidney-disease parameters. These results provide a new approach for developing a self-powered in situ body fluids-analysis technique for chronic-disease diagnosis.

Effectiveness of protocols for preventing occupational exposure to blood and body fluids in Dutch hospitals

NARCIS (Netherlands)

van Gemert-Pijnen, Julia E.W.C.; Hendrix, M.G.R.; van der Palen, Jacobus Adrianus Maria; Schellens, P.J.

2006-01-01

Compliance of different healthcare workers (HCWs) (nurses, physicians, laboratory technicians and cleaners) with protocols to prevent exposure to blood and body fluids (BBF) was studied. Questionnaires were used to assess perception of risks, familiarity with protocols, motivation and actual

Building ProteomeTools based on a complete synthetic human proteome

Science.gov (United States)

Zolg, Daniel P.; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J.; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

2018-01-01

The ProteomeTools project builds molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we report the generation and multimodal LC-MS/MS analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products and exemplify the utility of this data. The resource will be extended to >1 million peptides and all data will be shared with the community via ProteomicsDB and proteomeXchange. PMID:28135259

Manual versus automated streaking system in clinical microbiology laboratory: Performance evaluation of Previ Isola for blood culture and body fluid samples.

Science.gov (United States)

Choi, Qute; Kim, Hyun Jin; Kim, Jong Wan; Kwon, Gye Cheol; Koo, Sun Hoe

2018-01-04

The process of plate streaking has been automated to improve routine workflow of clinical microbiology laboratories. Although there were many evaluation reports about the inoculation of various body fluid samples, few evaluations have been reported for blood. In this study, we evaluated the performance of automated inoculating system, Previ Isola for various routine clinical samples including blood. Blood culture, body fluid, and urine samples were collected. All samples were inoculated on both sheep blood agar plate (BAP) and MacConkey agar plate (MCK) using Previ Isola and manual method. We compared two methods in aspect of quality and quantity of cultures, and sample processing time. To ensure objective colony counting, an enumeration reading reference was made through a preliminary experiment. A total of 377 nonduplicate samples (102 blood culture, 203 urine, 72 body fluid) were collected and inoculated. The concordance rate of quality was 100%, 97.0%, and 98.6% in blood, urine, and other body fluids, respectively. In quantitative aspect, it was 98.0%, 97.0%, and 95.8%, respectively. The Previ Isola took a little longer to inoculate the specimen than manual method, but the hands-on time decreased dramatically. The shortened hands-on time using Previ Isola was about 6 minutes per 10 samples. We demonstrated that the Previ Isola showed high concordance with the manual method in the inoculation of various body fluids, especially in blood culture sample. The use of Previ Isola in clinical microbiology laboratories is expected to save considerable time and human resources. © 2018 Wiley Periodicals, Inc.

Isolation and proteomic analysis of Chlamydomonas centrioles.

Science.gov (United States)

Keller, Lani C; Marshall, Wallace F

2008-01-01

Centrioles are barrel-shaped cytoskeletal organelles composed of nine triplet microtubules blades arranged in a pinwheel-shaped array. Centrioles are required for recruitment of pericentriolar material (PCM) during centrosome formation, and they act as basal bodies, which are necessary for the outgrowth of cilia and flagella. Despite being described over a hundred years ago, centrioles are still among the most enigmatic organelles in all of cell biology. To gain molecular insights into the function and assembly of centrioles, we sought to determine the composition of the centriole proteome. Here, we describe a method that allows for the isolation of virtually "naked" centrioles, with little to no obscuring PCM, from the green alga, Chlamydomonas. Proteomic analysis of this material provided evidence that multiple human disease gene products encode protein components of the centriole, including genes involved in Meckel syndrome and Oral-Facial-Digital syndrome. Isolated centrioles can be used in combination with a wide variety of biochemical assays in addition to being utilized as a source for proteomic analysis.

Modeling the time evolution of the nanoparticle-protein corona in a body fluid.

Directory of Open Access Journals (Sweden)

Daniele Dell'Orco

Full Text Available BACKGROUND: Nanoparticles in contact with biological fluids interact with proteins and other biomolecules, thus forming a dynamic corona whose composition varies over time due to continuous protein association and dissociation events. Eventually equilibrium is reached, at which point the continued exchange will not affect the composition of the corona. RESULTS: We developed a simple and effective dynamic model of the nanoparticle protein corona in a body fluid, namely human plasma. The model predicts the time evolution and equilibrium composition of the corona based on affinities, stoichiometries and rate constants. An application to the interaction of human serum albumin, high density lipoprotein (HDL and fibrinogen with 70 nm N-iso-propylacrylamide/N-tert-butylacrylamide copolymer nanoparticles is presented, including novel experimental data for HDL. CONCLUSIONS: The simple model presented here can easily be modified to mimic the interaction of the nanoparticle protein corona with a novel biological fluid or compartment once new data will be available, thus opening novel applications in nanotoxicity and nanomedicine.

Proteomic analysis of isolated chlamydomonas centrioles reveals orthologs of ciliary-disease genes.

Science.gov (United States)

Keller, Lani C; Romijn, Edwin P; Zamora, Ivan; Yates, John R; Marshall, Wallace F

2005-06-21

The centriole is one of the most enigmatic organelles in the cell. Centrioles are cylindrical, microtubule-based barrels found in the core of the centrosome. Centrioles also act as basal bodies during interphase to nucleate the assembly of cilia and flagella. There are currently only a handful of known centriole proteins. We used mass-spectrometry-based MudPIT (multidimensional protein identification technology) to identify the protein composition of basal bodies (centrioles) isolated from the green alga Chlamydomonas reinhardtii. This analysis detected the majority of known centriole proteins, including centrin, epsilon tubulin, and the cartwheel protein BLD10p. By combining proteomic data with information about gene expression and comparative genomics, we identified 45 cross-validated centriole candidate proteins in two classes. Members of the first class of proteins (BUG1-BUG27) are encoded by genes whose expression correlates with flagellar assembly and which therefore may play a role in ciliogenesis-related functions of basal bodies. Members of the second class (POC1-POC18) are implicated by comparative-genomics and -proteomics studies to be conserved components of the centriole. We confirmed centriolar localization for the human homologs of four candidate proteins. Three of the cross-validated centriole candidate proteins are encoded by orthologs of genes (OFD1, NPHP-4, and PACRG) implicated in mammalian ciliary function and disease, suggesting that oral-facial-digital syndrome and nephronophthisis may involve a dysfunction of centrioles and/or basal bodies. By analyzing isolated Chlamydomonas basal bodies, we have been able to obtain the first reported proteomic analysis of the centriole.

Potential Exposure to Ebola Virus from Body Fluids due to Ambulance Compartment Permeability in Sierra Leone.

Science.gov (United States)

Casey, Megan L; Nguyen, Duong T; Idriss, Barrie; Bennett, Sarah; Dunn, Angela; Martin, Stephen

2015-12-01

Prehospital care, including patient transport, is integral in the patient care process during the Ebola response. Transporting ill persons from the community to Ebola care facilities can stop community spread. Vehicles used for patient transport in infectious disease outbreaks should be evaluated for adequate infection prevention and control. An ambulance driver in Sierra Leone attributed his Ebola infection to exposure to body fluids that leaked from the patient compartment to the driver cabin of the ambulance. A convenience sample of 14 vehicles used to transport patients with suspected or confirmed Ebola in Sierra Leone were assessed. The walls separating the patient compartment and driver cabin in these vehicles were evaluated for structural integrity and potential pathways for body fluid leakage. Ambulance drivers and other staff were asked to describe their cleaning and decontamination practices. Ambulance construction and design standards from the National Fire Protection Association, US General Services Administration, and European Committee on Standardization (CEN) were reviewed. Many vehicles used by ambulance staff in Sierra Leone were not traditional ambulances, but were pick-up trucks or sport-utility vehicles that had been assembled or modified for patient transport. The wall separating the patient compartment and driver cabin in many vehicles did not have a waterproof seal around the edges. Staff responsible for cleaning and disinfection did not thoroughly clean bulk body fluids with disposable towels before disinfection of the patient compartment. Pressure from chlorine sprayers used in the decontamination process may have pushed body fluids from the patient compartment into the driver cabin through gaps around the wall. Ambulance design standards do not require a waterproof seal between the patient compartment and driver cabin. Sealing the wall by tightening or replacing existing bolts is recommended, followed by caulking of all seams with a

Clinical veterinary proteomics: Techniques and approaches to decipher the animal plasma proteome.

Science.gov (United States)

Ghodasara, P; Sadowski, P; Satake, N; Kopp, S; Mills, P C

2017-12-01

Over the last two decades, technological advancements in the field of proteomics have advanced our understanding of the complex biological systems of living organisms. Techniques based on mass spectrometry (MS) have emerged as powerful tools to contextualise existing genomic information and to create quantitative protein profiles from plasma, tissues or cell lines of various species. Proteomic approaches have been used increasingly in veterinary science to investigate biological processes responsible for growth, reproduction and pathological events. However, the adoption of proteomic approaches by veterinary investigators lags behind that of researchers in the human medical field. Furthermore, in contrast to human proteomics studies, interpretation of veterinary proteomic data is difficult due to the limited protein databases available for many animal species. This review article examines the current use of advanced proteomics techniques for evaluation of animal health and welfare and covers the current status of clinical veterinary proteomics research, including successful protein identification and data interpretation studies. It includes a description of an emerging tool, sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS), available on selected mass spectrometry instruments. This newly developed data acquisition technique combines advantages of discovery and targeted proteomics approaches, and thus has the potential to advance the veterinary proteomics field by enhancing identification and reproducibility of proteomics data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mass Spectrometry–based Proteomic Profiling of Lung Cancer

Science.gov (United States)

Ocak, Sebahat; Chaurand, Pierre; Massion, Pierre P.

2009-01-01

In an effort to further our understanding of lung cancer biology and to identify new candidate biomarkers to be used in the management of lung cancer, we need to probe these tissues and biological fluids with tools that address the biology of lung cancer directly at the protein level. Proteins are responsible of the function and phenotype of cells. Cancer cells express proteins that distinguish them from normal cells. Proteomics is defined as the study of the proteome, the complete set of proteins produced by a species, using the technologies of large-scale protein separation and identification. As a result, new technologies are being developed to allow the rapid and systematic analysis of thousands of proteins. The analytical advantages of mass spectrometry (MS), including sensitivity and high-throughput, promise to make it a mainstay of novel biomarker discovery to differentiate cancer from normal cells and to predict individuals likely to develop or recur with lung cancer. In this review, we summarize the progress made in clinical proteomics as it applies to the management of lung cancer. We will focus our discussion on how MS approaches may advance the areas of early detection, response to therapy, and prognostic evaluation. PMID:19349484

Alterations in body fluid content can be detected by bioelectrical impedance analysis.

Science.gov (United States)

Scheltinga, M R; Jacobs, D O; Kimbrough, T D; Wilmore, D W

1991-05-01

The electrical resistance across the whole body and its segments to the conduction of a weak alternating current was determined in human subjects under three different conditions: (1) during bed rest, (2) during infusion of 1 liter of saline, and (3) during donation of 1 unit of blood. During bed rest, extracellular and total body water were measured by dilution of bromide and heavy water, respectively. Electrical resistance obtained from electrodes placed on proximal portions of extremities ("proximal resistance") accounted for less than 50% of that determined by electrodes positioned on routinely used portions of a hand and foot ("whole body resistance"). Following saline infusion, resistance determined from the whole body and all its segments fell (P less than 0.001); the magnitude of the drop in both proximal and whole body resistance was inversely related to the volume of total body water (TBW) (r = -0.82, P less than 0.002, and r = -0.73, P less than 0.01, respectively). In contrast, blood donation was associated with significantly increased resistance at both measurement sites. TBW predicted from anthropometrics was inversely related to both proximal (r = -0.90, P less than 0.001) and whole body resistance (r = -0.75, P less than 0.001). Bioelectrical impedance analysis is a simple technique which may be useful in monitoring minimal alterations in TBW. Furthermore, altered fluid status may be predicted more accurately by changes in proximal resistance compared to changes in traditionally used whole body resistance.

Exposure to and precautions for blood and body fluids among workers in the funeral home franchises of Fort Worth, Texas.

Science.gov (United States)

Nwanyanwu, O C; Tabasuri, T H; Harris, G R

1989-08-01

In 1982 the Centers for Disease Control published a set of recommendations and measures to protect persons working in health care settings or performing mortician services from possible exposure to the human immunodeficiency virus. This study of a number of funeral homes in the Fort Worth area was designed to determine the level of exposure of funeral home workers to blood and other body fluids and also to assess existing protective measures and practices in the industry. Workers in 22 funeral home franchises were surveyed with a predesigned questionnaire. Eighty-five responses from 20 of the 22 establishments were received. All 85 respondents admitted exposure of varying degrees to blood and body fluids. Sixty persons (70%) admitted heavy exposure, that is, frequent splashes. Analysis of the responses showed that 81 of 85 (95.3%) persons consistently wore gloves while performing tasks that might expose them to blood or other body fluids. Of the 60 persons who were heavily exposed, 43 wore long-sleeved gowns, 27 wore waterproof aprons, 17 surgical masks, and 15 goggles. The study further revealed that 52.9% (45/85) of the respondents had sustained accidental cuts or puncture wounds on the job. In light of these findings it is important to target educational efforts to persons in this industry to help them minimize their risks of infection with blood and body fluid borne infections.

Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex

Directory of Open Access Journals (Sweden)

Joaquín eFernández-Irigoyen

2014-03-01

Full Text Available The amygdaloid complex is a key brain structure involved in the expression of behaviours and emotions such as learning, fear, and anxiety. Brain diseases including depression, epilepsy, autism, schizophrenia, and Alzheimer`s disease, have been associated with amygdala dysfunction. For several decades, neuroanatomical, neurophysiological, volumetric, and cognitive approaches have been the gold standard techniques employed to characterize the amygdala functionality. However, little attention has been focused specifically on the molecular composition of the human amygdala from the perspective of proteomics. We have performed a global proteome analysis employing protein and peptide fractionation methods followed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS, detecting expression of at least 1820 protein species in human amygdala, corresponding to 1814 proteins which represent a 9-fold increase in proteome coverage with respect to previous proteomic profiling of the rat amygdala. Gene ontology analysis were used to determine biological process represented in human amygdala highlighting molecule transport, nucleotide binding, and oxidoreductase and GTPase activities. Bioinformatic analyses have revealed that nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, and 26% of amygdaloid proteins were also found to be present in cerebrospinal fluid (CSF. In particular, a subset of amygdaloid proteins was mainly involved in axon guidance, synaptic vesicle release, L1CAM interactome, and signaling pathways transduced by NGF and NCAM1. Taken together, our data contributes to the repertoire of the human brain proteome, serving as a reference library to provide basic information for understanding the neurobiology of the human amygdala.

A wireless pH sensor using magnetoelasticity for measurement of body fluid acidity.

Science.gov (United States)

Pang, Pengfei; Gao, Xianjuan; Xiao, Xilin; Yang, Wenyue; Cai, Qingyun; Yao, Shouzhuo

2007-04-01

The determination of body fluid acidity using a wireless magnetoelastic pH-sensitive sensor is described. The sensor was fabricated by casting a layer of pH-sensitive polymer on a magnetoelastic ribbon. In response to an externally applied time-varying magnetic field, the magnetoelastic sensor mechanically vibrates at a characteristic frequency that is inversely dependent upon the mass of the pH polymer film, which varies as the film swells and shrinks in response to pH. As the magnetoelastic sensor is magnetostrictive, the mechanical vibrations of the sensor launch magnetic flux that can be detected remotely using a pickup coil. The sensor can be used for direct measurements of body fluid acidity without a pretreatment of the sample by using a filtration membrane. A reversible and linear response was obtained between pH 5.0 and 8.0 with a measurement resolution of pH 0.1 and a slope of 0.2 kHz pH(-1). Since there are no physical connections between the sensor and the instrument, the sensor can be applied to in vivo and in situ monitoring of the physiological pH and its fluctuations.

Lecture notes on: Electrical theory behind the measurement of body fluids with bioimpedance spectroscopy (BIS)

DEFF Research Database (Denmark)

Jødal, Lars

The lecture notes describe how body fluid volumes can be measured/estimated using the technique bio-impedance spectroscopy (BIS). The opening chapters assume little or none technical/mathematical knowledge and can hopefully be read by anyone interested in the techneque. Later chapters become more...

Proteomic approach in human health and disease: Preventive and cure studies

Directory of Open Access Journals (Sweden)

Khaled MM Koriem

2018-01-01

Full Text Available Proteomic is a branch of science that deals with various numbers of proteins where proteins are essential human constituents. Proteomic has a lot of functions inside the human and animal living organisms. This review helps to make a thought on the importance of proteomic application in human health and disease with special reference to preventive and cure studies. The human health can be divided into physical and mental health. The physical health relates to keeping human body state in a good health and to nutritional type and environmental factors. The mental health correlates to human psychological state. The main factors that affect the status of human health are human diet, exercise and sleep. The healthy diet is very important and needs to maintain the human health. The training program exercise improves human fitness and overall health and wellness. The sleep is a vital factor to sustain the human health. The human disease indicates abnormal human condition which influences the specific human part or the whole human body. There are external and internal factors which induce human disease. The external factors include pathogens while internal factors include allergies and autoimmunity. There are 4 principle types of human diseases: (1 infectious disease, (2 deficiency disease, (3 genetic disease and (4 physiological disease. There are many and various external microbes' factors that induce human infectious disease and these agents include viruses, bacteria, fungi and protozoa. The lack of necessary and vital dietary rudiments such as vitamins and minerals is the main cause of human deficiency disease. The genetic disease is initiated by hereditary disturbances that occur in the human genetic map. The physiological disease occurs when the normal human function body is affected due to human organs become malfunction. In conclusion, proteomic plays a vital and significant role in human health and disease.

Proteomics dataset

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

2017-01-01

The datasets presented in this article are related to the research articles entitled “Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies” (Bennike et al., 2015 [1]), and “Proteome Analysis of Rheumatoid Arthritis Gut Mucosa” (Bennike et al., 2017 [2])...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

On the linear problem arising from motion of a fluid around a moving rigid body

Czech Academy of Sciences Publication Activity Database

Nečasová, Šárka; Wolf, J.

2015-01-01

Roč. 140, č. 2 (2015), s. 241-259 ISSN 0862-7959 R&D Projects: GA ČR(CZ) GAP201/11/1304 Institutional support: RVO:67985840 Keywords : incompressible fluid * rotating rigid body * strong solution Subject RIV: BA - General Mathematics http://hdl.handle.net/10338.dmlcz/144329

Effects of Three Commonly-used Diuretics on the Urinary Proteome

Directory of Open Access Journals (Sweden)

Xundou Li

2014-06-01

Full Text Available Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. Here, we evaluated the effects of three commonly-used diuretics (furosemide, F; hydrochlorothiazide, H; and spirolactone, S on the urinary proteome in rats. Urine samples were collected before and after intragastric administration of diuretics at therapeutic doses and the proteomes were analyzed using label-free liquid chromatography–tandem mass spectrometry (LC–MS/MS. Based on the criteria of P ⩽ 0.05, a fold change ⩾2, a spectral count ⩾5, and false positive rate (FDR ⩽1%, 14 proteins (seven for F, five for H, and two for S were identified by Progenesis LC–MS. The human orthologs of most of these 14 proteins are stable in the healthy human urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics.

Effects of three commonly-used diuretics on the urinary proteome.

Science.gov (United States)

Li, Xundou; Zhao, Mindi; Li, Menglin; Jia, Lulu; Gao, Youhe

2014-06-01

Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. Here, we evaluated the effects of three commonly-used diuretics (furosemide, F; hydrochlorothiazide, H; and spirolactone, S) on the urinary proteome in rats. Urine samples were collected before and after intragastric administration of diuretics at therapeutic doses and the proteomes were analyzed using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). Based on the criteria of P≤0.05, a fold change ≥2, a spectral count ≥5, and false positive rate (FDR) ≤1%, 14 proteins (seven for F, five for H, and two for S) were identified by Progenesis LC-MS. The human orthologs of most of these 14 proteins are stable in the healthy human urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics. Copyright © 2014. Production and hosting by Elsevier Ltd.

Biomineralization of hydroxyapatite in silver ion-exchanged nanocrystalline ZSM-5 zeolite using simulated body fluid.

Science.gov (United States)

Kaur, Balwinder; Srivastava, Rajendra; Satpati, Biswarup; Kondepudi, Kanthi Kiran; Bishnoi, Mahendra

2015-11-01

Silver ion-exchanged nanocrystalline zeolite (Ag-Nano-ZSM-5) and silver ion-exchanged conventional zeolite (Ag-ZSM-5) were synthesized. Zeolites were incubated in simulated body fluid at 310K for different time periods to grow hydroxyapatite in their matrixes. Significant large amount of hydroxyapatite was grown in Ag-Nano-ZSM-5 matrix after incubation in simulated body fluid when compared to Ag-ZSM-5. The resultant material was characterized using X-ray diffraction, N2-adsorption, scanning/transmission electron microscopy, energy dispersive X-ray, and inductively coupled plasma analysis. Mechanical properties such as compressive modulus, compressive strength, and strain at failure of the parent materials were evaluated. Biocompatibility assays suggested that Ag-Nano-ZSM-5 and hydroxyapatite grown in Ag-Nano-ZSM-5 were compatible and did not impose any toxicity to RAW 264.7 cells macrophase and Caco2 cells suggesting considerable potential for biomedical applications such as bone implants. Copyright © 2015 Elsevier B.V. All rights reserved.

On the motion of rigid bodies in an incompressible or compressible viscous fluid under the action of gravitational forces

Czech Academy of Sciences Publication Activity Database

Ducomet, B.; Nečasová, Šárka

2013-01-01

Roč. 6, č. 5 (2013), s. 1193-1213 ISSN 1937-1632 R&D Projects: GA ČR(CZ) GAP201/11/1304 Institutional support: RVO:67985840 Keywords : motion of rigid bodies * incompressible fluid * compressible fluid Subject RIV: BA - General Mathematics https://www.aimsciences.org/journals/displayArticlesnew.jsp?paperID=8331

Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.

Science.gov (United States)

Hempel, Kristina; Herbst, Florian-Alexander; Moche, Martin; Hecker, Michael; Becher, Dörte

2011-04-01

Staphylococcus aureus is capable of colonizing and infecting humans by its arsenal of surface-exposed and secreted proteins. Iron-limited conditions in mammalian body fluids serve as a major environmental signal to bacteria to express virulence determinants. Here we present a comprehensive, gel-free, and GeLC-MS/MS-based quantitative proteome profiling of S. aureus under this infection-relevant situation. (14)N(15)N metabolic labeling and three complementing approaches were combined for relative quantitative analyses of surface-associated proteins. The surface-exposed and secreted proteome profiling approaches comprise trypsin shaving, biotinylation, and precipitation of the supernatant. By analysis of the outer subproteomic and cytoplasmic protein fraction, 1210 proteins could be identified including 221 surface-associated proteins. Thus, access was enabled to 70% of the predicted cell wall-associated proteins, 80% of the predicted sortase substrates, two/thirds of lipoproteins and more than 50% of secreted and cytoplasmic proteins. For iron-deficiency, 158 surface-associated proteins were quantified. Twenty-nine proteins were found in altered amounts showing particularly surface-exposed proteins strongly induced, such as the iron-regulated surface determinant proteins IsdA, IsdB, IsdC and IsdD as well as lipid-anchored iron compound-binding proteins. The work presents a crucial subject for understanding S. aureus pathophysiology by the use of methods that allow quantitative surface proteome profiling.

Fluid Redistribution and Heart Rate in Humans During Whole-Body Tilting, G(z) Centrifugation, and Lower Body Negative Pressure

Science.gov (United States)

Watenpaugh, D. E.; Breit, G. A.; Ballard, R. E.; Murthy, G.; Hargens, A. R.

1994-01-01

Gravity creates blood pressure gradients which redistribute body fluids towards the feet. Positive G(z) centrifugation and lower body negative pressure (LBNP) have been proposed to simulate these and other effects of gravity during long-term existence in microgravity. We hypothesized that the magnitude of upper-to-lower body fluid redistribution would increase according to the following order: short-arm centrifugation (SAC), long-arm centrifugation (LAC), head-up tilt (HUT), and LBNP. To test this hypothesis, we employed strain gauge plethysmography of the neck, thigh and calf during HUT and supine SAC and LAC up to lG(z) at the feet, and during supine LBNP to 100 mm Hg. Supine 100 mm Hg LBNP generates footward force and produces transmural blood pressures in the foot approximately equal to 1 G(z) (90 deg) HUT. Heart rate was measured via cardiotachometry. Control measurements were made while supine. SAC and LAC elicited similar increases in thigh volume at 1 G(z) (2.3 +/- 0.4 and 2.1 +/- 0.1%, respectively; mean +/- se, n greater than or equal to 7). At 100 mm Hg LBNP, thigh volume increased (3.4 +/- 0.3%) significantly more than during l G(z) centrifugation (p less than 0.05). Surprisingly, due to a paradoxical 0.6% reduction of thigh volume between 0.8 and 1.0 G(z) HUT, thigh volume was increased only 0.6 +/- 0.3% at 1 G(z) HUT. The calf demonstrated similar, although less definitive, responses to the various gravitational stimuli. Neck volume tended to decrease less during HUT than during the other stimuli. Heart rate increased similarly during HUT (18 +/- 2 beats/min) and LAC (12 +/- 2 beats/min), and exhibited still greater elevation during LBNP (29 +/- 4 beats/min), yet did not increase during SAC. These results suggest upright posture activates mechanisms that counteract footward fluid redistribution which are not activated during supine applications of simulated gravity. LAC more closely approximated effects of normal gravity (HUT) than LBNP. Therefore

Proteomics research in India: an update.

Science.gov (United States)

Reddy, Panga Jaipal; Atak, Apurva; Ghantasala, Saicharan; Kumar, Saurabh; Gupta, Shabarni; Prasad, T S Keshava; Zingde, Surekha M; Srivastava, Sanjeeva

2015-09-08

After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Protein corona as a proteome fingerprint: The example of hidden biomarkers for cow mastitis.

Science.gov (United States)

Miotto, Giovanni; Magro, Massimiliano; Terzo, Milo; Zaccarin, Mattia; Da Dalt, Laura; Bonaiuto, Emanuela; Baratella, Davide; Gabai, Gianfranco; Vianello, Fabio

2016-04-01

Proteome modifications in a biological fluid can potentially indicate the occurrence of pathologies, even if the identification of a proteome fingerprint correlated to a specific disease represents a very difficult task. When a nanomaterial is introduced into a biological fluid, macromolecules compete to form a protein corona on the nanoparticle surface, and depending on the specific proteome, different patterns of proteins will form the final protein corona shell depending on their affinity for the nanoparticle surface. Novel surface active maghemite nanoparticles (SAMNs) display a remarkable selectivity toward protein corona formation, and they are able to concentrate proteins and peptides presenting high affinities for their surface even if they are present in very low amounts. Thus, SAMNs may confer visibility to hidden biomarkers correlated to the occurrence of a pathology. In the present report, SAMNs were introduced into milk samples from healthy cows and from animals affected by mastitis, and the selectively bound protein corona shell was easily analyzed and quantified by gel electrophoresis and characterized by mass spectrometry. Upon incubation in mastitic milk, SAMNs were able to selectively bind αs2-casein fragments containing the FALPQYLK sequence, as part of the larger casocidin-1 peptide with strong antibacterial activity, which were not present in healthy samples. Thus, SAMNs can be used as a future candidate for the rapid diagnosis of mastitis in bovine milk. The present report proposes protein competition for SAMN protein corona formation as a means of mirroring proteome modifications. Thus, the selected protein shell on the nanoparticles results in a fingerprint of the specific pathology. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of a standardized procedure for [corrected] microscopic cell counts [corrected] in body fluids.

Science.gov (United States)

Emerson, Jane F; Emerson, Scott S

2005-01-01

A standardized urinalysis and manual microscopic cell counting system was evaluated for its potential to reduce intra- and interoperator variability in urine and cerebrospinal fluid (CSF) cell counts. Replicate aliquots of pooled specimens were submitted blindly to technologists who were instructed to use either the Kova system with the disposable Glasstic slide (Hycor Biomedical, Inc., Garden Grove, CA) or the standard operating procedure of the University of California-Irvine (UCI), which uses plain glass slides for urine sediments and hemacytometers for CSF. The Hycor system provides a mechanical means of obtaining a fixed volume of fluid in which to resuspend the sediment, and fixes the volume of specimen to be microscopically examined by using capillary filling of a chamber containing in-plane counting grids. Ninety aliquots of pooled specimens of each type of body fluid were used to assess the inter- and intraoperator reproducibility of the measurements. The variability of replicate Hycor measurements made on a single specimen by the same or different observers was compared with that predicted by a Poisson distribution. The Hycor methods generally resulted in test statistics that were slightly lower than those obtained with the laboratory standard methods, indicating a trend toward decreasing the effects of various sources of variability. For 15 paired aliquots of each body fluid, tests for systematically higher or lower measurements with the Hycor methods were performed using the Wilcoxon signed-rank test. Also examined was the average difference between the Hycor and current laboratory standard measurements, along with a 95% confidence interval (CI) for the true average difference. Without increasing labor or the requirement for attention to detail, the Hycor method provides slightly better interrater comparisons than the current method used at UCI. Copyright 2005 Wiley-Liss, Inc.

The energy supplied to a body in the theory of relativity and the impulse-energy tensor of a compressible fluid

International Nuclear Information System (INIS)

Ricard, J.

1979-01-01

In the relativity theory, the variation of a certain amount of energy supplied to a body, according to its speed, has been a matter of controversy. We study this variation either for a fluid that is submitted by a compression, or for a gas receiving heat from outward. It is shown that the problem is solved by a simple matter of definition of the energy received in the system of coordinate where the body is moving. Besides, we establish the impulse-energy tensor for a compressible fluid [fr

The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

Directory of Open Access Journals (Sweden)

Li Zhang

Full Text Available Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

Proteomic profiling of human pleural effusion using two-dimensional nano liquid chromatography tandem mass spectrometry.

Science.gov (United States)

Tyan, Yu-Chang; Wu, Hsin-Yi; Lai, Wu-Wei; Su, Wu-Chou; Liao, Pao-Chi

2005-01-01

Pleural effusion, an accumulation of pleural fluid, contains proteins originated from plasma filtrate and, especially when tissues are damaged, parenchyma interstitial spaces of lungs and/or other organs. This study details protein profiles in human pleural effusion from 43 lung adenocarcinoma patients by a two-dimensional nano-high performance liquid chromatography electrospray ionization tandem mass spectrometry (2D nano-HPLC-ESI-MS/MS) system. The experimental results revealed the identification of 1415 unique proteins from human pleural effusion. Among these 124 proteins identified with higher confidence levels, some proteins have not been reported in plasma and may represent proteins specifically present in pleural effusion. These proteins are valuable for mass identification of differentially expressed proteins involved in proteomics database and screening biomarker to further study in human lung adenocarcinoma. The significance of the use of proteomics analysis of human pleural fluid for the search of new lung cancer marker proteins, and for their simultaneous display and analysis in patients suffering from lung disorders has been examined.

Proteomics and the Inner Ear

Directory of Open Access Journals (Sweden)

Isolde Thalmann

2001-01-01

Full Text Available The inner ear, one of the most complex organs, contains within its bony shell three sensory systems, the evolutionary oldest gravity receptor system, the three semicircular canals for the detection of angular acceleration, and the auditory system - unrivaled in sensitivity and frequency discrimination. All three systems are susceptible to a host of afflictions affecting the quality of life for all of us. In the first part of this review we present an introduction to the milestones of inner ear research to pave the way for understanding the complexities of a proteomics approach to the ear. Minute sensory structures, surrounded by large fluid spaces and a hard bony shell, pose extreme challenges to the ear researcher. In spite of these obstacles, a powerful preparatory technique was developed, whereby precisely defined microscopic tissue elements can be isolated and analyzed, while maintaining the biochemical state representative of the in vivo conditions. The second part consists of a discussion of proteomics as a tool in the elucidation of basic and pathologic mechanisms, diagnosis of disease, as well as treatment. Examples are the organ of Corti proteins OCP1 and OCP2, oncomodulin, a highly specific calcium-binding protein, and several disease entities, Meniere's disease, benign paroxysmal positional vertigo, and perilymphatic fistula.

Distribution of polybrominated diphenyl ethers in Japanese autopsy tissue and body fluid samples.

Science.gov (United States)

Hirai, Tetsuya; Fujimine, Yoshinori; Watanabe, Shaw; Nakano, Takeshi

2012-09-01

Brominated flame retardants are components of many plastics and are used in products such as cars, textiles, televisions, and personal computers. Human exposure to polybrominated diphenyl ether (PBDE) flame retardants has increased exponentially during the last three decades. Our objective was to measure the body burden and distribution of PBDEs and to determine the concentrations of the predominant PBDE congeners in samples of liver, bile, adipose tissue, and blood obtained from Japanese autopsy cases. Tissues and body fluids obtained from 20 autopsy cases were analyzed. The levels of 25 PBDE congeners, ranging from tri- to hexa-BDEs, were assessed. The geometric means of the sum of the concentrations of PBDE congeners having detection frequencies >50 % (ΣPBDE) in the blood, liver, bile, and adipose tissue were 2.4, 2.6, 1.4, and 4.3 ng/g lipid, respectively. The most abundant congeners were BDE-47 and BDE-153, followed by BDE-100, BDE-99, and BDE-28+33. These concentrations of PBDE congeners were similar to other reports of human exposure in Japan but were notably lower than concentrations than those reported in the USA. Significant positive correlations were observed between the concentrations of predominant congeners and ΣPBDE among the samples analyzed. The ΣPBDE concentration was highest in the adipose tissue, but PBDEs were distributed widely among the tissues and body fluids analyzed. The PBDE levels observed in the present study are similar to those reported in previous studies in Japan and significantly lower than those reported in the USA.

Body fluid identification of blood, saliva and semen using second generation sequencing of micro-RNA

DEFF Research Database (Denmark)

Petersen, Christel H.; Hjort, Benjamin Benn; Tvedebrink, Torben

2013-01-01

We report a new second generation sequencing method for identification micro-RNA (miRNA) that can be used to identify body fluids and tissues. Principal component analysis of 10 miRNAs with high expression in 16 samples of blood, saliva and semen showed clear differences in the expression of mi...

Transport of fluid and solutes in the body I. Formulation of a mathematical model.

Science.gov (United States)

Gyenge, C C; Bowen, B D; Reed, R K; Bert, J L

1999-09-01

A compartmental model of short-term whole body fluid, protein, and ion distribution and transport is formulated. The model comprises four compartments: a vascular and an interstitial compartment, each with an embedded cellular compartment. The present paper discusses the assumptions on which the model is based and describes the equations that make up the model. Fluid and protein transport parameters from a previously validated model as well as ionic exchange parameters from the literature or from statistical estimation [see companion paper: C. C. Gyenge, B. D. Bowen, R. K. Reed, and J. L. Bert. Am. J. Physiol. 277 (Heart Circ. Physiol. 46): H1228-H1240, 1999] are used in formulating the model. The dynamic model has the ability to simulate 1) transport across the capillary membrane of fluid, proteins, and small ions and their distribution between the vascular and interstitial compartments; 2) the changes in extracellular osmolarity; 3) the distribution and transport of water and ions associated with each of the cellular compartments; 4) the cellular transmembrane potential; and 5) the changes of volume in the four fluid compartments. The validation and testing of the proposed model against available experimental data are presented in the companion paper.

Fluid-thermal analysis of aerodynamic heating over spiked blunt body configurations

Science.gov (United States)

Qin, Qihao; Xu, Jinglei; Guo, Shuai

2017-03-01

When flying at hypersonic speeds, the spiked blunt body is constantly subjected to severe aerodynamic heating. To illustrate the thermal response of different configurations and the relevant flow field variation, a loosely-coupled fluid-thermal analysis is performed in this paper. The Mesh-based parallel Code Coupling Interface (MpCCI) is adopted to implement the data exchange between the fluid solver and the thermal solver. The results indicate that increases in spike diameter and length will result in a sharp decline of the wall temperature along the spike, and the overall heat flux is remarkably reduced to less than 300 W/cm2 with the aerodome mounted at the spike tip. Moreover, the presence and evolution of small vortices within the recirculation zone are observed and proved to be induced by the stagnation effect of reattachment points on the spike. In addition, the drag coefficient of the configuration with a doubled spike length presents a maximum drop of 4.59% due to the elevated wall temperature. And the growing difference of the drag coefficient is further increased during the accelerating process.

Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data.

Science.gov (United States)

Kustatscher, Georg; Grabowski, Piotr; Rappsilber, Juri

2016-02-01

Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically, we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about ⅓ of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by multiclassifier combinatorial proteomics to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available. © 2015 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomics approaches shed new light on hibernation physiology.

Science.gov (United States)

Grabek, Katharine R; Martin, Sandra L; Hindle, Allyson G

2015-08-01

The broad phylogenetic distribution and rapid phenotypic transitions of mammalian hibernators imply that hibernation is accomplished by differential expression of common genes. Traditional candidate gene approaches have thus far explained little of the molecular mechanisms underlying hibernation, likely due to (1) incomplete and imprecise sampling of a complex phenotype, and (2) the forming of hypotheses about which genes might be important based on studies of model organisms incapable of such dynamic physiology. Unbiased screening approaches, such as proteomics, offer an alternative means to discover the cellular underpinnings that permit successful hibernation and may reveal previously overlooked, important pathways. Here, we review the findings that have emerged from proteomics studies of hibernation. One striking feature is the stability of the proteome, especially across the extreme physiological shifts of torpor-arousal cycles during hibernation. This has led to subsequent investigations of the role of post-translational protein modifications in altering protein activity without energetically wasteful removal and rebuilding of protein pools. Another unexpected finding is the paucity of universal proteomic adjustments across organ systems in response to the extreme metabolic fluctuations despite the universality of their physiological challenges; rather each organ appears to respond in a unique, tissue-specific manner. Additional research is needed to extend and synthesize these results before it will be possible to address the whole body physiology of hibernation.

[Proteomics and transfusion medicine].

Science.gov (United States)

Lion, N; Prudent, M; Crettaz, D; Tissot, J-D

2011-04-01

The term "proteomics" covers tools and techniques that are used to analyze and characterize complex mixtures of proteins from various biological samples. In this short review, a typical proteomic approach, related to the study of particular and illustrative situation related to transfusion medicine is reported. This "case report" will allow the reader to be familiar with a practical proteomic approach of a real situation, and will permit to describe the tools that are usually used in proteomic labs, and, in a second part, to present various proteomic applications in transfusion medicine. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply

Directory of Open Access Journals (Sweden)

Laura eCeballos-Laita

2015-03-01

Full Text Available The fluid collected by direct leaf centrifugation has been used to study the proteome of the sugar beet apoplastic fluid as well as the changes induced by Fe deficiency and Fe resupply to Fe-deficient plants in the protein profile. Plants were grown in Fe-sufficient and Fe-deficient conditions, and Fe resupply was carried out with 45 μM Fe(III-EDTA for 24 h. Protein extracts of leaf apoplastic fluid were analyzed by two-dimensional isoelectric focusing-SDS-PAGE electrophoresis. Gel image analysis revealed 203 consistent spots, and proteins in 81% of them (164 were identified by nLC-MS/MS using a custom made reference repository of beet protein sequences. When redundant UniProt entries were deleted, a non-redundant leaf apoplastic proteome consisting of 109 proteins was obtained. TargetP and SecretomeP algorithms predicted that 63% of them were secretory proteins. Functional classification of the non-redundant proteins indicated that stress and defense, protein metabolism, cell wall and C metabolism accounted for approximately 75% of the identified proteome. The effects of Fe-deficiency on the leaf apoplast proteome were limited, with only five spots (2.5% changing in relative abundance, thus suggesting that protein homeostasis in the leaf apoplast fluid is well maintained upon Fe shortage. The identification of three chitinase isoforms among proteins increasing in relative abundance with Fe-deficiency suggests that one of the few effects of Fe deficiency in the leaf apoplast proteome includes cell wall modifications. Iron resupply to Fe deficient plants changed the relative abundance of 16 spots when compared to either Fe-sufficient or Fe-deficient samples. Proteins identified in these spots can be broadly classified as those responding to Fe-resupply, which included defense and cell wall related proteins, and non-responsive, which are mainly protein metabolism related proteins and whose changes in relative abundance followed the same trend as

Proteomic profiling of white muscle from freshwater catfish Rita rita.

Science.gov (United States)

Mohanty, Bimal Prasanna; Mitra, Tandrima; Banerjee, Sudeshna; Bhattacharjee, Soma; Mahanty, Arabinda; Ganguly, Satabdi; Purohit, Gopal Krishna; Karunakaran, Dhanasekar; Mohanty, Sasmita

2015-06-01

Muscle tissues contribute 34-48 % of the total body mass in fish. Proteomic analysis enables better understanding of the skeletal muscle physiology and metabolism. A proteome map reflects the general fingerprinting of the fish species and has the potential to identify novel proteins which could serve as biomarkers for many aspects of aquaculture including fish physiology and growth, flesh quality, food safety and aquatic environmental monitoring. The freshwater catfish Rita rita of the family Bagridae inhabiting the tropical rivers and estuaries is an important food fish with high nutritive value and is also considered a species of choice in riverine pollution monitoring. Omics information that could enhance utility of this species in molecular research is meager. Therefore, in the present study, proteomic analysis of Rita rita muscle has been carried out and functional genomics data have been generated. A reference muscle proteome has been developed, and 23 protein spots, representing 18 proteins, have been identified by MALDI-TOF/TOF-MS and LC-MS/MS. Besides, transcript information on a battery of heat shock proteins (Hsps) has been generated. The functional genomics information generated could act as the baseline data for further molecular research on this species.

Pre-analytical factors influencing the stability of cerebrospinal fluid proteins

DEFF Research Database (Denmark)

Simonsen, Anja H; Bahl, Justyna M C; Danborg, Pia B

2013-01-01

Cerebrospinal fluid (CSF) is a potential source for new biomarkers due to its proximity to the brain. This study aimed to clarify the stability of the CSF proteome when undergoing pre-analytical factors. We investigated the effects of repeated freeze/thaw cycles, protease inhibitors and delayed s...

Fetal Alcohol Syndrome (FAS) in C57BL/6 Mice Detected through Proteomics Screening of the Amniotic Fluid

Science.gov (United States)

Datta, Susmita; Turner, Delano; Singh, Reetu; Ruest, L. Bruno; Pierce, William M.; Knudsen, Thomas B.

2009-01-01

BACKGROUND Fetal Alcohol Syndrome (FAS), a severe consequence of the Fetal Alcohol Spectrum Disorders, is associated with craniofacial defects, mental retardation, and stunted growth. Previous studies in C57BL/6J and C57BL/6N mice provide evidence that alcohol-induced pathogenesis follows early changes in gene expression within specific molecular pathways in the embryonic headfold. Whereas the former (B6J) pregnancies carry a high-risk for dysmorphogenesis following maternal exposure to 2.9 g/kg alcohol (two injections spaced 4.0 h apart on gestation day 8), the latter (B6N) pregnancies carry a low-risk for malformations. The present study used this murine model to screen amniotic fluid for biomarkers that could potentially discriminate between FAS-positive and FAS-negative pregnancies. METHODS B6J and B6N litters were treated with alcohol (exposed) or saline (control) on day 8 of gestation. Amniotic fluid aspirated on day 17 (n = 6 replicate litters per group) was subjected to trypsin digestion for analysis by matrix-assisted laser desorption–time of flight mass spectrometry with the aid of denoising algorithms, statistical testing, and classification methods. RESULTS We identified several peaks in the proteomics screen that were reduced consistently and specifically in exposed B6J litters. Preliminary characterization by liquid chromatography tandem mass spectrometry and multidimensional protein identification mapped the reduced peaks to alpha fetoprotein (AFP). The predictive strength of AFP deficiency as a biomarker for FAS-positive litters was confirmed by area under the receiver operating characteristic curve. CONCLUSIONS These findings in genetically susceptible mice support clinical observations in maternal serum that implicate a decrease in AFP levels following prenatal alcohol damage. PMID:18240165

Principles of proteome allocation are revealed using proteomic data and genome-scale models

DEFF Research Database (Denmark)

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.

2016-01-01

to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the "generalist" (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions......Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked...... of these sectors for the general stress response sigma factor sigma(S). Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally...

Changes in body fluid and energy compartments during prolonged hunger strike.

Science.gov (United States)

Faintuch, J; Soriano, F G; Ladeira, J P; Janiszewski, M; Velasco, I T; Gama-Rodrigues, J J

2000-01-01

Prolonged total food deprivation in non-obese adults is rare, and few studies have documented body composition changes in this setting. In a group of eight hunger strikers who refused alimentation for 43 days, water and energy compartments were estimated, aiming to assess the impact of progressive starvation. Measurements included body mass index (BMI), triceps skinfold (TSF), arm muscle circumference (AMC), and bioimpedance (BIA) determinations of water, fat, lean body mass (LBM), and total resistance. Indirect calorimetry was also performed in one occasion. The age of the group was 43.3+/-6.2 years (seven males, one female). Only water, intermittent vitamins and electrolytes were ingested, and average weight loss reached 17.9%. On the last two days of the fast (43rd-44th day) rapid intravenous fluid, electrolyte, and vitamin replenishment were provided before proceeding with realimentation. Body fat decreased approximately 60% (BIA and TSF), whereas BMI reduced only 18%. Initial fat was estimated by BIA as 52.2+/-5.4% of body weight, and even on the 43rd day it was still measured as 19.7+/-3.8% of weight. TSF findings were much lower and commensurate with other anthropometric results. Water was comparatively low with high total resistance, and these findings rapidly reversed upon the intravenous rapid hydration. At the end of the starvation period, BMI (21.5+/-2.6 kg/m2) and most anthropometric determinations were still acceptable, suggesting efficient energy and muscle conservation. 1) All compartments diminished during fasting, but body fat was by far the most affected; 2) Total water was low and total body resistance comparatively elevated, but these findings rapidly reversed upon rehydration; 3) Exaggerated fat percentage estimates from BIA tests and simultaneous increase in lean body mass estimates suggested that this method was inappropriate for assessing energy compartments in the studied population; 4) Patients were not morphologically malnourished after

Changes in body fluid and energy compartments during prolonged hunger strike

Directory of Open Access Journals (Sweden)

Faintuch Joel

2000-01-01

Full Text Available Prolonged total food deprivation in non-obese adults is rare, and few studies have documented body composition changes in this setting. In a group of eight hunger strikers who refused alimentation for 43 days, water and energy compartments were estimated, aiming to assess the impact of progressive starvation. Measurements included body mass index (BMI, triceps skinfold (TSF, arm muscle circumference (AMC, and bioimpedance (BIA determinations of water, fat, lean body mass (LBM, and total resistance. Indirect calorimetry was also performed in one occasion. The age of the group was 43.3±6.2 years (seven males, one female. Only water, intermittent vitamins and electrolytes were ingested, and average weight loss reached 17.9%. On the last two days of the fast (43rd-44th day rapid intravenous fluid, electrolyte, and vitamin replenishment were provided before proceeding with realimentation. Body fat decreased approximately 60% (BIA and TSF, whereas BMI reduced only 18%. Initial fat was estimated by BIA as 52.2±5.4% of body weight, and even on the 43rd day it was still measured as 19.7±3.8% of weight. TSF findings were much lower and commensurate with other anthropometric results. Water was comparatively low with high total resistance, and these findings rapidly reversed upon the intravenous rapid hydration. At the end of the starvation period, BMI (21.5±2.6 kg/m² and most anthropometric determinations were still acceptable, suggesting efficient energy and muscle conservation. Conclusions: 1 All compartments diminished during fasting, but body fat was by far the most affected; 2 Total water was low and total body resistance comparatively elevated, but these findings rapidly reversed upon rehydration; 3 Exaggerated fat percentage estimates from BIA tests and simultaneous increase in lean body mass estimates suggested that this method was inappropriate for assessing energy compartments in the studied population; 4 Patients were not morphologically

Verification of protein biomarker specificity for the identification of biological stains by quadrupole time-of-flight mass spectrometry.

Science.gov (United States)

Legg, Kevin M; Powell, Roger; Reisdorph, Nichole; Reisdorph, Rick; Danielson, Phillip B

2017-03-01

Advances in proteomics technology over the past decade offer forensic serologists a greatly improved opportunity to accurately characterize the tissue source from which a DNA profile has been developed. Such information can provide critical context to evidence and can help to prioritize downstream DNA analyses. Previous proteome studies compiled panels of "candidate biomarkers" specific to each of five body fluids (i.e., peripheral blood, vaginal/menstrual fluid, seminal fluid, urine, and saliva). Here, a multiplex quadrupole time-of-flight mass spectrometry assay has been developed in order to verify the tissue/body fluid specificity the 23 protein biomarkers that comprise these panels and the consistency with which they can be detected across a sample population of 50 humans. Single-source samples of these human body fluids were accurately identified by the detection of one or more high-specificity biomarkers. Recovery of body fluid samples from a variety of substrates did not impede accurate characterization and, of the potential inhibitors assayed, only chewing tobacco juice appeared to preclude the identification of a target body fluid. Using a series of 2-component mixtures of human body fluids, the multiplex assay accurately identified both components in a single-pass. Only in the case of saliva and peripheral blood did matrix effects appear to impede the detection of salivary proteins. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

Directory of Open Access Journals (Sweden)

Lindo Micheal

2003-08-01

Full Text Available Abstract Proteomics experiments typically involve protein or peptide separation steps coupled to the identification of many hundreds to thousands of peptides by mass spectrometry. Development of methodology and instrumentation in this field is proceeding rapidly, and effective software is needed to link the different stages of proteomic analysis. We have developed an application, proteogest, written in Perl that generates descriptive and statistical analyses of the biophysical properties of multiple (e.g. thousands protein sequences submitted by the user, for instance protein sequences inferred from the complete genome sequence of a model organism. The application also carries out in silico proteolytic digestion of the submitted proteomes, or subsets thereof, and the distribution of biophysical properties of the resulting peptides is presented. proteogest is customizable, the user being able to select many options, for instance the cleavage pattern of the digestion treatment or the presence of modifications to specific amino acid residues. We show how proteogest can be used to compare the proteomes and digested proteome products of model organisms, to examine the added complexity generated by modification of residues, and to facilitate the design of proteomics experiments for optimal representation of component proteins.

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

Science.gov (United States)

Hermjakob, Henning

2006-09-01

Proteomics is a key field of modern biomolecular research, with many small and large scale efforts producing a wealth of proteomics data. However, the vast majority of this data is never exploited to its full potential. Even in publicly funded projects, often the raw data generated in a specific context is analysed, conclusions are drawn and published, but little attention is paid to systematic documentation, archiving, and public access to the data supporting the scientific results. It is often difficult to validate the results stated in a particular publication, and even simple global questions like "In which cellular contexts has my protein of interest been observed?" can currently not be answered with realistic effort, due to a lack of standardised reporting and collection of proteomics data. The Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organisation (HUPO), defines community standards for data representation in proteomics to facilitate systematic data capture, comparison, exchange and verification. In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process.

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

Science.gov (United States)

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-03-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transport of fluid and solutes in the body II. Model validation and implications.

Science.gov (United States)

Gyenge, C C; Bowen, B D; Reed, R K; Bert, J L

1999-09-01

A mathematical model of short-term whole body fluid, protein, and ion distribution and transport developed earlier [see companion paper: C. C. Gyenge, B. D. Bowen, R. K. Reed, and J. L. Bert. Am. J. Physiol. 277 (Heart Circ. Physiol. 46): H1215-H1227, 1999] is validated using experimental data available in the literature. The model was tested against data measured for the following three types of experimental infusions: 1) hyperosmolar saline solutions with an osmolarity in the range of 2,000-2,400 mosmol/l, 2) saline solutions with an osmolarity of approximately 270 mosmol/l and composition comparable with Ringer solution, and 3) an isosmotic NaCl solution with an osmolarity of approximately 300 mosmol/l. Good agreement between the model predictions and the experimental data was obtained with respect to the trends and magnitudes of fluid shifts between the intra- and extracellular compartments, extracellular ion and protein contents, and hematocrit values. The model is also able to yield information about inaccessible or difficult-to-measure system variables such as intracellular ion contents, cellular volumes, and fluid fluxes across the vascular capillary membrane, data that can be used to help interpret the behavior of the system.

Smart fast blood counting of trace volumes of body fluids from various mammalian species using a compact custom-built microscope cytometer (Conference Presentation)

Science.gov (United States)

Smith, Zachary J.; Gao, Tingjuan; Lin, Tzu-Yin; Carrade-Holt, Danielle; Lane, Stephen M.; Matthews, Dennis L.; Dwyre, Denis M.; Wachsmann-Hogiu, Sebastian

2016-03-01

Cell counting in human body fluids such as blood, urine, and CSF is a critical step in the diagnostic process for many diseases. Current automated methods for cell counting are based on flow cytometry systems. However, these automated methods are bulky, costly, require significant user expertise, and are not well suited to counting cells in fluids other than blood. Therefore, their use is limited to large central laboratories that process enough volume of blood to recoup the significant capital investment these instruments require. We present in this talk a combination of a (1) low-cost microscope system, (2) simple sample preparation method, and (3) fully automated analysis designed for providing cell counts in blood and body fluids. We show results on both humans and companion and farm animals, showing that accurate red cell, white cell, and platelet counts, as well as hemoglobin concentration, can be accurately obtained in blood, as well as a 3-part white cell differential in human samples. We can also accurately count red and white cells in body fluids with a limit of detection ~3 orders of magnitude smaller than current automated instruments. This method uses less than 1 microliter of blood, and less than 5 microliters of body fluids to make its measurements, making it highly compatible with finger-stick style collections, as well as appropriate for small animals such as laboratory mice where larger volume blood collections are dangerous to the animal's health.

Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

Science.gov (United States)

Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

2017-01-01

No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as

Proteomics in medical microbiology.

Science.gov (United States)

Cash, P

2000-04-01

The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

Development of Highly Sensitive and Specific mRNA Multiplex System (XCYR1) for Forensic Human Body Fluids and Tissues Identification

Science.gov (United States)

Xu, Yan; Xie, Jianhui; Cao, Yu; Zhou, Huaigu; Ping, Yuan; Chen, Liankang; Gu, Lihua; Hu, Wei; Bi, Gang; Ge, Jianye; Chen, Xin; Zhao, Ziqin

2014-01-01

The identification of human body fluids or tissues through mRNA-based profiling is very useful for forensic investigations. Previous studies have shown mRNA biomarkers are effective to identify the origin of biological samples. In this study, we selected 16 tissue specific biomarkers to evaluate their specificities and sensitivities for human body fluids and tissues identification, including porphobilinogen deaminase (PBGD), hemoglobin beta (HBB) and Glycophorin A (GLY) for circulatory blood, protamine 2 (PRM2) and transglutaminase 4 (TGM4) for semen, mucin 4 (MUC4) and human beta defensin 1(HBD1) for vaginal secretion, matrix metalloproteinases 7 and 11 (MMP7 and MMP11) for menstrual blood, keratin 4(KRT4) for oral mucosa, loricrin (LOR) and cystatin 6 (CST6) for skin, histatin 3(HTN3) for saliva, statherin (STATH) for nasal secretion, dermcidin (DCD) for sweat and uromodulin (UMOD) for urine. The above mentioned ten common forensic body fluids or tissues were used in the evaluation. Based on the evaluation, a reverse transcription (RT) PCR multiplex assay, XCYR1, which includes 12 biomarkers (i.e., HBB, GLY, HTN3, PRM2, KRT4, MMP11, MUC4, DCD, UMOD, MMP7, TGM4, and STATH) and 2 housekeeping genes [i.e., glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and 18SrRNA], was developed. This assay was further validated with real casework samples and mock samples (with both single source and mixture) and it was approved that XCYR1 is effective to identify common body fluids or tissues (i.e., circulatory blood, saliva, semen, vaginal secretion, menstrual blood, oral mucosa, nasal secretion, sweat and urine) in forensic casework samples. PMID:24991806

A finite volume procedure for fluid flow, heat transfer and solid-body stress analysis

KAUST Repository

Jagad, P. I.

2018-04-12

A unified cell-centered unstructured mesh finite volume procedure is presented for fluid flow, heat transfer and solid-body stress analysis. An in-house procedure (A. W. Date, Solution of Transport Equations on Unstructured Meshes with Cell-Centered Colocated Variables. Part I: Discretization, International Journal of Heat and Mass Transfer, vol. 48 (6), 1117-1127, 2005) is extended to include the solid-body stress analysis. The transport terms for a cell-face are evaluated in a structured grid-like manner. The Cartesian gradients at the center of each cell-face are evaluated using the coordinate transformation relations. The accuracy of the procedure is demonstrated by solving several benchmark problems involving different boundary conditions, source terms, and types of loading.

Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways and transcription factors

DEFF Research Database (Denmark)

Deshmukh, Atul S; Murgia, Marta; Nagaraja, Nagarjuna

2015-01-01

Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is challenging due to highly abundant contractile proteins that interfere with detection of regulatory proteins. Using a state-of-the art mass...

Data from proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis

Directory of Open Access Journals (Sweden)

Yongxin Yang

2015-06-01

Full Text Available Milk fat globules memebrane (MFGM-enriched proteomes from Holstein, Jersey, yak, buffalo, goat, camel, horse, and human were extracted and identified by an iTRAQ quantification proteomic approach. Proteomes data were analyzed by bioinformatic and multivariate statistical analysis and used to present the characteristic traits of the MFGM proteins among the studied mammals. The data of this study are also related to the research article “Proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis” in the Journal of Proteomics [1].

The proteome of neurofilament-containing protein aggregates in blood

Directory of Open Access Journals (Sweden)

Rocco Adiutori

2018-07-01

Full Text Available Protein aggregation in biofluids is a poorly understood phenomenon. Under normal physiological conditions, fluid-borne aggregates may contain plasma or cell proteins prone to aggregation. Recent observations suggest that neurofilaments (Nf, the building blocks of neurons and a biomarker of neurodegeneration, are included in high molecular weight complexes in circulation. The composition of these Nf-containing hetero-aggregates (NCH may change in systemic or organ-specific pathologies, providing the basis to develop novel disease biomarkers. We have tested ultracentrifugation (UC and a commercially available protein aggregate binder, Seprion PAD-Beads (SEP, for the enrichment of NCH from plasma of healthy individuals, and then characterised the Nf content of the aggregate fractions using gel electrophoresis and their proteome by mass spectrometry (MS. Western blot analysis of fractions obtained by UC showed that among Nf isoforms, neurofilament heavy chain (NfH was found within SDS-stable high molecular weight aggregates. Shotgun proteomics of aggregates obtained with both extraction techniques identified mostly cell structural and to a lesser extent extra-cellular matrix proteins, while functional analysis revealed pathways involved in inflammatory response, phagosome and prion-like protein behaviour. UC aggregates were specifically enriched with proteins involved in endocrine, metabolic and cell-signalling regulation. We describe the proteome of neurofilament-containing aggregates isolated from healthy individuals biofluids using different extraction methods.

Bacterial membrane proteomics.

Science.gov (United States)

Poetsch, Ansgar; Wolters, Dirk

2008-10-01

About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

The Urine Proteome as a Biomarker of Radiation Injury: Submitted to Proteomics- Clinical Applications Special Issue: "Renal and Urinary Proteomics (Thongboonkerd)"

Science.gov (United States)

Sharma, Mukut; Halligan, Brian D; Wakim, Bassam T; Savin, Virginia J; Cohen, Eric P; Moulder, John E

2008-06-18

Terrorist attacks or nuclear accidents could expose large numbers of people to ionizing radiation, and early biomarkers of radiation injury would be critical for triage, treatment and follow-up of such individuals. However, no such biomarkers have yet been proven to exist. We tested the potential of high throughput proteomics to identify protein biomarkers of radiation injury after total body X-ray irradiation in a rat model. Subtle functional changes in the kidney are suggested by an increased glomerular permeability for macromolecules measured within 24 hours after TBI. Ultrastructural changes in glomerular podocytes include partial loss of the interdigitating organization of foot processes. Analysis of urine by LC-MS/MS and 2D-GE showed significant changes in the urine proteome within 24 hours after TBI. Tissue kallikrein 1-related peptidase, cysteine proteinase inhibitor cystatin C and oxidized histidine were found to be increased while a number of proteinase inhibitors including kallikrein-binding protein and albumin were found to be decreased post-irradiation. Thus, TBI causes immediately detectable changes in renal structure and function and in the urinary protein profile. This suggests that both systemic and renal changes are induced by radiation and it may be possible to identify a set of biomarkers unique to radiation injury.

Animal board invited review: advances in proteomics for animal and food sciences.

Science.gov (United States)

Almeida, A M; Bassols, A; Bendixen, E; Bhide, M; Ceciliani, F; Cristobal, S; Eckersall, P D; Hollung, K; Lisacek, F; Mazzucchelli, G; McLaughlin, M; Miller, I; Nally, J E; Plowman, J; Renaut, J; Rodrigues, P; Roncada, P; Staric, J; Turk, R

2015-01-01

Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps

Translational plant proteomics: a perspective.

Science.gov (United States)

Agrawal, Ganesh Kumar; Pedreschi, Romina; Barkla, Bronwyn J; Bindschedler, Laurence Veronique; Cramer, Rainer; Sarkar, Abhijit; Renaut, Jenny; Job, Dominique; Rakwal, Randeep

2012-08-03

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics. Copyright © 2012 Elsevier B.V. All rights reserved.

Numerical investigation of incompressible fluid flow and heat transfer across a bluff body in a channel flow

Directory of Open Access Journals (Sweden)

Taymaz Imdat

2015-01-01

Full Text Available The Lattice Boltzmann Method is applied to computationally investigate the laminar flow and heat transfer of an incompressible fluid with constant material properties in a two-dimensional channel with a built-in bluff body. In this study, a triangular prism is taken as the bluff body. Not only the momentum transport, but also the energy transport is modeled by the Lattice Boltzmann Method. A uniform lattice structure with a single time relaxation rule is used. For obtaining a higher flexibility on the computational grid, interpolation methods are applied, where the information is transferred from the lattice structure to the computational grid by Lagrange interpolation. The flow is investigated for different Reynolds numbers, while keeping the Prandtl number at the constant value of 0.7. The results show how the presence of a triangular prism effects the flow and heat transfer patterns for the steady-state and unsteady-periodic flow regimes. As an assessment of the accuracy of the developed Lattice Boltzmann code, the results are compared with those obtained by a commercial Computational Fluid Dynamics code. It is observed that the present Lattice Boltzmann code delivers results that are of similar accuracy to the well-established Computational Fluid Dynamics code, with much smaller computational time for the prediction of the unsteady phenomena.

Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

Science.gov (United States)

Fadda, Silvina; Almeida, André M

2015-11-01

Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomic Characterization of Middle Ear Fluid Confirms Neutrophil Extracellular Traps as a Predominant Innate Immune Response in Chronic Otitis Media.

Directory of Open Access Journals (Sweden)

Stephanie Val

Full Text Available Chronic Otitis Media (COM is characterized by middle ear effusion (MEE and conductive hearing loss. MEE reflect mucus hypersecretion, but global proteomic profiling of the mucosal components are limited.This study aimed at characterizing the proteome of MEEs from children with COM with the goal of elucidating important innate immune responses.MEEs were collected from children (n = 49 with COM undergoing myringotomy. Mass spectrometry was employed for proteomic profiling in nine samples. Independent samples were further analyzed by cytokine multiplex assay, immunoblotting, neutrophil elastase activity, next generation DNA sequencing, and/or immunofluorescence analysis.109 unique and common proteins were identified by MS. A majority were innate immune molecules, along with typically intracellular proteins such as histones and actin. 19.5% percent of all mapped peptide counts were from proteins known to be released by neutrophils. Immunofluorescence and immunoblotting demonstrated the presence of neutrophil extracellular traps (NETs in every MEE, along with MUC5B colocalization. DNA found in effusions revealed unfragmented DNA of human origin.Proteomic analysis of MEEs revealed a predominantly neutrophilic innate mucosal response in which MUC5B is associated with NET DNA. NETs are a primary macromolecular constituent of human COM middle ear effusions.

Cerebrospinal fluid culture

Science.gov (United States)

... Alternative Names Culture - CSF; Spinal fluid culture; CSF culture Images Pneumococci organism References Karcher DS, McPherson RA. Cerebrospinal, synovial, serous body fluids, and alternative specimens. In: McPherson RA, Pincus ...

Prolonged whole-body cold water immersion: fluid and ion shifts.

Science.gov (United States)

Deuster, P A; Smith, D J; Smoak, B L; Montgomery, L C; Singh, A; Doubt, T J

1989-01-01

To characterize fluid and ion shifts during prolonged whole-body immersion, 16 divers wearing dry suits completed four whole-body immersions in 5 degrees C water during each of two 5-day air saturation dives at 6.1 msw. One immersion was conducted at 1000 (AM) and one at 2200 (PM) so that diurnal variations could be evaluated. Fifty-four hours separated the immersions, which lasted up to 6 h; 9 days separated each air saturation dive. Blood was collected before and after immersion; urine was collected for 12 h before, during, and after immersion for a total of 24 h. Plasma volume decreased significantly and to the same extent (approximately 17%) during both AM and PM immersions. Urine flow increased by 236.1 +/- 38.7 and 296.3 +/- 52.0%, urinary excretion of Na increased by 290.4 +/- 89.0 and 329.5 +/- 77.0%, K by 245.0 +/- 73.4 and 215.5 +/- 44.6%, Ca by 211.0 +/- 31.4 and 241.1 +/- 50.4%, Mg by 201.4 +/- 45.9 and 165.3 +/- 287%, and Zn by 427.8 +/- 93.7 and 301.9 +/- 75.4% during AM and PM immersions, respectively, compared with preimmersion. Urine flow and K excretion were significantly higher during the AM than PM. In summary, when subjects are immersed in cold water for prolonged periods, combined with a slow rate of body cooling afforded by thermal protection and enforced intermittent exercise, there is diuresis, decreased plasma volume, and increased excretions of Na, K, Ca, Mg, and Zn.

Internal air flow analysis of a bladeless micro aerial vehicle hemisphere body using computational fluid dynamic

Science.gov (United States)

Othman, M. N. K.; Zuradzman, M. Razlan; Hazry, D.; Khairunizam, Wan; Shahriman, A. B.; Yaacob, S.; Ahmed, S. Faiz; Hussain, Abadalsalam T.

2014-12-01

This paper explain the analysis of internal air flow velocity of a bladeless vertical takeoff and landing (VTOL) Micro Aerial Vehicle (MAV) hemisphere body. In mechanical design, before produce a prototype model, several analyses should be done to ensure the product's effectiveness and efficiency. There are two types of analysis method can be done in mechanical design; mathematical modeling and computational fluid dynamic. In this analysis, I used computational fluid dynamic (CFD) by using SolidWorks Flow Simulation software. The idea came through to overcome the problem of ordinary quadrotor UAV which has larger size due to using four rotors and the propellers are exposed to environment. The bladeless MAV body is designed to protect all electronic parts, which means it can be used in rainy condition. It also has been made to increase the thrust produced by the ducted propeller compare to exposed propeller. From the analysis result, the air flow velocity at the ducted area increased to twice the inlet air. This means that the duct contribute to the increasing of air velocity.

Internal air flow analysis of a bladeless micro aerial vehicle hemisphere body using computational fluid dynamic

International Nuclear Information System (INIS)

Othman, M. N. K.; Zuradzman, M. Razlan; Hazry, D.; Khairunizam, Wan; Shahriman, A. B.; Yaacob, S.; Ahmed, S. Faiz

2014-01-01

This paper explain the analysis of internal air flow velocity of a bladeless vertical takeoff and landing (VTOL) Micro Aerial Vehicle (MAV) hemisphere body. In mechanical design, before produce a prototype model, several analyses should be done to ensure the product's effectiveness and efficiency. There are two types of analysis method can be done in mechanical design; mathematical modeling and computational fluid dynamic. In this analysis, I used computational fluid dynamic (CFD) by using SolidWorks Flow Simulation software. The idea came through to overcome the problem of ordinary quadrotor UAV which has larger size due to using four rotors and the propellers are exposed to environment. The bladeless MAV body is designed to protect all electronic parts, which means it can be used in rainy condition. It also has been made to increase the thrust produced by the ducted propeller compare to exposed propeller. From the analysis result, the air flow velocity at the ducted area increased to twice the inlet air. This means that the duct contribute to the increasing of air velocity

Internal air flow analysis of a bladeless micro aerial vehicle hemisphere body using computational fluid dynamic

Energy Technology Data Exchange (ETDEWEB)

Othman, M. N. K., E-mail: najibkhir86@gmail.com, E-mail: zuradzman@unimap.edu.my, E-mail: hazry@unimap.edu.my, E-mail: khairunizam@unimap.edu.my, E-mail: shahriman@unimap.edu.my, E-mail: s.yaacob@unimap.edu.my, E-mail: syedfaiz@unimap.edu.my, E-mail: abadal@unimap.edu.my; Zuradzman, M. Razlan, E-mail: najibkhir86@gmail.com, E-mail: zuradzman@unimap.edu.my, E-mail: hazry@unimap.edu.my, E-mail: khairunizam@unimap.edu.my, E-mail: shahriman@unimap.edu.my, E-mail: s.yaacob@unimap.edu.my, E-mail: syedfaiz@unimap.edu.my, E-mail: abadal@unimap.edu.my; Hazry, D., E-mail: najibkhir86@gmail.com, E-mail: zuradzman@unimap.edu.my, E-mail: hazry@unimap.edu.my, E-mail: khairunizam@unimap.edu.my, E-mail: shahriman@unimap.edu.my, E-mail: s.yaacob@unimap.edu.my, E-mail: syedfaiz@unimap.edu.my, E-mail: abadal@unimap.edu.my; Khairunizam, Wan, E-mail: najibkhir86@gmail.com, E-mail: zuradzman@unimap.edu.my, E-mail: hazry@unimap.edu.my, E-mail: khairunizam@unimap.edu.my, E-mail: shahriman@unimap.edu.my, E-mail: s.yaacob@unimap.edu.my, E-mail: syedfaiz@unimap.edu.my, E-mail: abadal@unimap.edu.my; Shahriman, A. B., E-mail: najibkhir86@gmail.com, E-mail: zuradzman@unimap.edu.my, E-mail: hazry@unimap.edu.my, E-mail: khairunizam@unimap.edu.my, E-mail: shahriman@unimap.edu.my, E-mail: s.yaacob@unimap.edu.my, E-mail: syedfaiz@unimap.edu.my, E-mail: abadal@unimap.edu.my; Yaacob, S., E-mail: najibkhir86@gmail.com, E-mail: zuradzman@unimap.edu.my, E-mail: hazry@unimap.edu.my, E-mail: khairunizam@unimap.edu.my, E-mail: shahriman@unimap.edu.my, E-mail: s.yaacob@unimap.edu.my, E-mail: syedfaiz@unimap.edu.my, E-mail: abadal@unimap.edu.my; Ahmed, S. Faiz, E-mail: najibkhir86@gmail.com, E-mail: zuradzman@unimap.edu.my, E-mail: hazry@unimap.edu.my, E-mail: khairunizam@unimap.edu.my, E-mail: shahriman@unimap.edu.my, E-mail: s.yaacob@unimap.edu.my, E-mail: syedfaiz@unimap.edu.my, E-mail: abadal@unimap.edu.my [Centre of Excellence for Unmanned Aerial Systems, Universiti Malaysia Perlis, 01000 Kangar, Perlis (Malaysia); and others

2014-12-04

This paper explain the analysis of internal air flow velocity of a bladeless vertical takeoff and landing (VTOL) Micro Aerial Vehicle (MAV) hemisphere body. In mechanical design, before produce a prototype model, several analyses should be done to ensure the product's effectiveness and efficiency. There are two types of analysis method can be done in mechanical design; mathematical modeling and computational fluid dynamic. In this analysis, I used computational fluid dynamic (CFD) by using SolidWorks Flow Simulation software. The idea came through to overcome the problem of ordinary quadrotor UAV which has larger size due to using four rotors and the propellers are exposed to environment. The bladeless MAV body is designed to protect all electronic parts, which means it can be used in rainy condition. It also has been made to increase the thrust produced by the ducted propeller compare to exposed propeller. From the analysis result, the air flow velocity at the ducted area increased to twice the inlet air. This means that the duct contribute to the increasing of air velocity.

Development of a highly sensitive MIP based-QCM nanosensor for selective determination of cholic acid level in body fluids

International Nuclear Information System (INIS)

Gültekin, Aytaç; Karanfil, Gamze; Sönmezoğlu, Savaş; Say, Rıdvan

2014-01-01

Determination of cholic acid is very important and necessary in body fluids due to its both pharmaceutical and clinical significance. In this study, a quartz crystal microbalance (QCM) nanosensor, which is imprinted cholic acid, has been developed for the assignation of cholic acid. The cholic acid selective memories have been generated on QCM electrode surface by using molecularly imprinted polymer (MIP) based on methacryloylamidohistidine-copper (II) (MAH-Cu(II)) pre-organized monomer. The cholic acid imprinted nanosensor was characterized by atomic force microscopy (AFM) and then analytical performance of the cholic acid imprinted QCM nanosensor was studied. The detection limit was found to be 0.0065 μM with linear range of 0.01–1000 μM. Moreover, the high value of Langmuir constant (b) (7.3 * 10 5 ) obtained by Langmuir graph showed that the cholic acid imprinted nanosensor had quite strong binding sites affinity. At the last step of this procedure, cholic acid levels in body fluids were determined by the prepared imprinted QCM nanosensor. - Graphical abstract: QCM responses of the cholic acid imprinted and non-imprinted nanosensors (C CA = 0.1 μM). - Highlights: • The purpose is to synthesize a new cholic acid imprinted QCM nanosensor by MIP. • Analytical applications of QCM nanosensor were investigated. • The cholic acid levels in body fluids were determined by prepared QCM nanosensor

Shotgun proteomic analytical approach for studying proteins adsorbed onto liposome surface

KAUST Repository

Capriotti, Anna Laura

2011-07-02

The knowledge about the interaction between plasma proteins and nanocarriers employed for in vivo delivery is fundamental to understand their biodistribution. Protein adsorption onto nanoparticle surface (protein corona) is strongly affected by vector surface characteristics. In general, the primary interaction is thought to be electrostatic, thus surface charge of carrier is supposed to play a central role in protein adsorption. Because protein corona composition can be critical in modifying the interactive surface that is recognized by cells, characterizing its formation onto lipid particles may serve as a fundamental predictive model for the in vivo efficiency of a lipidic vector. In the present work, protein coronas adsorbed onto three differently charged cationic liposome formulations were compared by a shotgun proteomic approach based on nano-liquid chromatography-high-resolution mass spectrometry. About 130 proteins were identified in each corona, with only small differences between the different cationic liposome formulations. However, this study could be useful for the future controlled design of colloidal drug carriers and possibly in the controlled creation of biocompatible surfaces of other devices that come into contact with proteins into body fluids. © 2011 Springer-Verlag.

Comparative proteome analysis of Chlamydia trachomatis serovar A, D and L2

DEFF Research Database (Denmark)

Shaw, Allan C; Gevaert, Kris; Demol, Hans

2002-01-01

chlamydial diseases, was investigated using a proteomics approach. Based on silver stained two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), gels with purified elementary bodies (EB) and auto-radiography of gels with 35S-labeled C. trachomatis proteins up to 700 protein spots were detectable...

Curvilinear immersed boundary method for simulating fluid structure interaction with complex 3D rigid bodies

Science.gov (United States)

Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

2008-08-01

The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A numerical method for solving the 3D unsteady incompressible Navier-Stokes equations in curvilinear domains with complex immersed boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions the FSI algorithm is unconditionally unstable even when strong coupling FSI is employed. For such cases, however, combining the strong coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI

Molecular and phenotypic adaptation in social insect reproductive fluids

DEFF Research Database (Denmark)

Liberti, Joanito

of sperm competition. The seminal fluid of ants and bees with multiply mated queens are known to have evolved proteins that are able to kill the sperm of rival males, but the identity of the proteins involved has remained poorly understood. I sequenced the seminal fluid proteomes of four fungus-growing ant...... species that span the evolutionary transition from single to multiple queen-mating in the fungus-growing ant phylogeny. I then reconstructed the evolutionary histories of these proteins and identified a number of their functions related to energy production, control of oxidative stress, and proteolysis...

Alteration of cystatin C in cerebrospinal fluid of patients with sciatica revealed by a proteomical approach

International Nuclear Information System (INIS)

Liu, X; Zeng, B.; Xu, J.

2005-01-01

To better understand the pathophysiological mechanisms underlying sciatica induced by lumbar intervertebral disk herniation and to ascertain the protein that presents with the most observable changes in the cerebrospinal fluid (CSF) of patients with sciatica. We conducted the study in the Key Laboratory of Shanghai 6th People's Hospital, Shanghai Jiaotong University, Shanghai, Peoples Republic of China, during the period June 2004 to March 2005. In 2 separate experiments, we carried out the study involving the CSF of sciatica patients (the case group) and the CSF of otherwise, healthy volunteers (the control group). We utilized a proteomical analysis to compare the samples of 10 patients with sciatica with 10 volunteers in the control group. We individually separated each of the groups' CSF by 2-dimensional gel electrophoresis. We analyzed the harvested gel images with PD Quest 2D-gel software (Bio-Rad) to ascertain the differential proteins between the 2 groups. We based the enzyme linked immuno- absorbent assay (ELISA) experiment, which followed, on the results of the first experiment. We found 15 of the protein spots in the CSF differed appreciably in varying degrees between the 2 groups, and identification made by LC-MS/MS revealed that the most significant disparity was with cystatin C. The result of ELISA experiment confirmed a considerable decrease in the level of cystatin C (p<0.01) in the patients with sciatica. In the CSF of patients with sciatica, the volume of cystatin C increased markedly indicating that it may play an important role in the pathophysiological processes of sciatica. (author)

Proteomic analysis of bronchoalveolar lavage fluid (BALF) from lung cancer patients using label-free mass spectrometry.

Science.gov (United States)

Hmmier, Abduladim; O'Brien, Michael Emmet; Lynch, Vincent; Clynes, Martin; Morgan, Ross; Dowling, Paul

2017-06-01

Lung cancer is the leading cause of cancer-related mortality in both men and women throughout the world. The need to detect lung cancer at an early, potentially curable stage, is essential and may reduce mortality by 20%. The aim of this study was to identify distinct proteomic profiles in bronchoalveolar fluid (BALF) and plasma that are able to discriminate individuals with benign disease from those with non-small cell lung cancer (NSCLC). Using label-free mass spectrometry analysis of BALF during discovery-phase analysis, a significant number of proteins were found to have different abundance levels when comparing control to adenocarcinoma (AD) or squamous cell lung carcinoma (SqCC). Validation of candidate biomarkers identified in BALF was performed in a larger cohort of plasma samples by detection with enzyme-linked immunoassay. Four proteins (Cystatin-C, TIMP-1, Lipocalin-2 and HSP70/HSPA1A) were selected as a representative group from discovery phase mass spectrometry BALF analysis. Plasma levels of TIMP-1, Lipocalin-2 and Cystatin-C were found to be significantly elevated in AD and SqCC compared to control. The results presented in this study indicate that BALF is an important proximal biofluid for the discovery and identification of candidate lung cancer biomarkers. There is good correlation between the trend of protein abundance levels in BALF and that of plasma which validates this approach to develop a blood biomarker to aid lung cancer diagnosis, particularly in the era of lung cancer screening. The protein signatures identified also provide insight into the molecular mechanisms associated with lung malignancy.

Synovial Fluid Analysis

Science.gov (United States)

... Plasma Free Metanephrines Platelet Count Platelet Function Tests Pleural Fluid Analysis PML-RARA Porphyrin Tests Potassium Prealbumin ... is being tested? Synovial fluid is a thick liquid that acts as a lubricant for the body's ...

[Methods of quantitative proteomics].

Science.gov (United States)

Kopylov, A T; Zgoda, V G

2007-01-01

In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and functional homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

Studying Different Clinical Syndromes Of Paediatric Severe Malaria Using Plasma Proteomics

KAUST Repository

Ramaprasad, Abhinay

2012-08-01

Background- Severe Plasmodium falciparum malaria remains one of the major causes of childhood morbidity and mortality in Africa. Severe malaria manifests itself as three main clinical syndromes-impaired consciousness (cerebral malaria), respiratory distress and severe malarial anaemia. Cerebral malaria and respiratory distress are major contributors to malaria mortality but their pathophysiology remains unclear. Motivation/Objectives- Most children with severe malaria die within the first 24 hours of admission to a hospital because of their pathophysiological conditions. Thus, along with anti-malarial drugs, various adjuvant therapies such as fluid bolus (for hypovolaemia) and anticonvulsants (for seizures) are given to alleviate the sick child’s condition. But these therapies can sometimes have adverse effects. Hence, a clear understanding of severe malaria pathophysiology is essential for making an informed decision regarding adjuvant therapies. Methodology- We used mass spectrometry-based shotgun proteomics to study plasma samples from Gambian children with severe malaria. We compared the proteomic profiles of different severe malaria syndromes and generated hypotheses regarding the underlying disease mechanisms. Results/Conclusions- The main challenges of studying the severe malaria syndromes using proteomics were the high complexity and variability among the samples. We hypothesized that hepatic injury and nitric oxide play roles in the pathophysiology of cerebral malaria and respiratory distress.

Proteomes of the Female Genital Tract During the Oestrous Cycle.

Science.gov (United States)

Soleilhavoup, Clement; Riou, Cindy; Tsikis, Guillaume; Labas, Valerie; Harichaux, Gregoire; Kohnke, Philippa; Reynaud, Karine; de Graaf, Simon P; Gerard, Nadine; Druart, Xavier

2016-01-01

The female genital tract includes several anatomical regions whose luminal fluids successively interact with gametes and embryos and are involved in the fertilisation and development processes. The luminal fluids from the inner cervix, the uterus and the oviduct were collected along the oestrous cycle at oestrus (Day 0 of the cycle) and during the luteal phase (Day 10) from adult cyclic ewes. The proteomes were assessed by GeLC-MS/MS and quantified by spectral counting. A set of 940 proteins were identified including 291 proteins differentially present along the cycle in one or several regions. The global analysis of the fluid proteomes revealed a general pattern of endocrine regulation of the tract, with the cervix and the oviduct showing an increased differential proteins abundance mainly at oestrus while the uterus showed an increased abundance mainly during the luteal phase. The proteins more abundant at oestrus included several families such as the heat shock proteins (HSP), the mucins, the complement cascade proteins and several redox enzymes. Other proteins known for their interaction with gametes such as oviductin (OVGP), osteopontin, HSPA8, and the spermadhesin AWN were also overexpressed at oestrus. The proteins more abundant during the luteal phase were associated with the immune system such as ceruloplasmin, lactoferrin, DMBT1, or PIGR, and also with tissue remodeling such as galectin 3 binding protein, alkaline phosphatase, CD9, or fibulin. Several proteins differentially abundant between estrus and the luteal phase, such as myosin 9 and fibronectin, were also validated by immunohistochemistry. The potential roles in sperm transit and uterine receptivity of the proteins differentially regulated along the cycle in the female genital tract are discussed. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Proteomic Analysis of Mouse Oocytes Reveals 28 Candidate Factors of the "Reprogrammome"

NARCIS (Netherlands)

Pfeiffer, M.J.; Siatkowski, M.; Paudel, Y.; Balbach, S.T.; Baeumer, N.; Crosetto, N.; Drexler, H.C.A.; Fuellen, G.; Boiani, M.

2011-01-01

The oocyte is the only cell of the body that can reprogram transplanted somatic nuclei and sets the gold standard for all reprogramming methods. Therefore, an in-depth characterization of its proteome holds promise to advance our understanding of reprogramming and germ cell biology. To date,

Drug research methodology. Volume 3, The detection and quantitation of drugs of interest in body fluids from drivers

Science.gov (United States)

1980-03-01

This report presents the findings of a workshop on the chemical analysis of human body fluids for drugs of interest in highway safety. A cross-disciplinary panel of experts reviewed the list of drugs of interest developed in a previous workshop and d...

Effect of greenhouse conditions on the leaf apoplastic proteome of Coffea arabica plants.

Science.gov (United States)

Guerra-Guimarães, Leonor; Vieira, Ana; Chaves, Inês; Pinheiro, Carla; Queiroz, Vagner; Renaut, Jenny; Ricardo, Cândido P

2014-06-02

This work describes the coffee leaf apoplastic proteome and its modulation by the greenhouse conditions. The apoplastic fluid (APF) was obtained by leaf vacuum infiltration, and the recovered proteins were separated by 2-DE and subsequently identified by matrix assisted laser desorption/ionization time of flight-mass spectrometry, followed by homology search in EST coffee databases. Prediction tools revealed that the majority of the 195 identified proteins are involved in cell wall metabolism and in stress/defense responses. Although most of the proteins follow the classical secretory mechanism, a low percentage of them seem to result from unconventional secretion (leaderless secreted proteins). Principal components analysis revealed that the APF samples formed two distinct groups, with the temperature amplitude mostly contributing for this separation (higher or lower than 10°C, respectively). Sixty one polypeptide spots allowed defining these two groups and 28 proteins were identified, belonging to carbohydrate metabolism, cell wall modification and proteolysis. Interestingly stress/defense proteins appeared as more abundant in Group I which is associated with a higher temperature amplitude. It seems that the proteins in the coffee leaf APF might be implicated in structural modifications in the extracellular space that are crucial for plant development/adaptation to the conditions of the prevailing environment. This is the first detailed proteomic study of the coffee leaf apoplastic fluid (APF) and of its modulation by the greenhouse conditions. The comprehensive overview of the most abundant proteins present in the extra-cellular compartment is particularly important for the understanding of coffee responses to abiotic/biotic stress. This article is part of a Special Issue entitled: Environmental and structural proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

Translational plant proteomics: A perspective

NARCIS (Netherlands)

Agrawal, G.K.; Pedreschi, R.; Barkla, B.J.; Bindschedler, L.V.; Cramer, R.; Sarkar, A.; Renaut, J.; Job, D.; Rakwal, R.

2012-01-01

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic

Evolution of Clinical Proteomics and its Role in Medicine | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

NCI's Office of Cancer Clinical Proteomics Research authored a review of the current state of clinical proteomics in the peer-reviewed Journal of Proteome Research. The review highlights outcomes from the CPTC program and also provides a thorough overview of the different technologies that have pushed the field forward. Additionally, the review provides a vision for moving the field forward through linking advances in genomic and proteomic analysis to develop new, molecularly targeted interventions.

Biomarkers in Alzheimer’s Disease Analysis by Mass Spectrometry-Based Proteomics

Directory of Open Access Journals (Sweden)

Yahui Liu

2014-05-01

Full Text Available Alzheimer’s disease (AD is a common chronic and destructive disease. The early diagnosis of AD is difficult, thus the need for clinically applicable biomarkers development is growing rapidly. There are many methods to biomarker discovery and identification. In this review, we aim to summarize Mass spectrometry (MS-based proteomics studies on AD and discuss thoroughly the methods to identify candidate biomarkers in cerebrospinal fluid (CSF and blood. This review will also discuss the potential research areas on biomarkers.

Osmotic relations of the coelomic fluid and body wall tissues in Arenicola marina subjected to salinity change

DEFF Research Database (Denmark)

Weber, Roy E.; Spaargaren, D.H.

1979-01-01

nitrogenous organic molecules (ninhydrin-positive substances, NPS) in the body wall tissues and in the coelomic fluid of specimens of Arenicola in response to sudden changes in salinity. The coelomic solutes consist almost entirely of electrolytes and the osmotic contribution of NPS is essentially negligible....... In the body wall extracts, however, NPS accounts for at least one third of the osmotic concentration and for most of the substantial non-electrolyte fraction. There is no evidence from coelomic NPS measurements for extrusion of cellular amino acids during adaptation to lowered salinity. In diluted sea water...

Proteomics of Maize Root Development.

Science.gov (United States)

Hochholdinger, Frank; Marcon, Caroline; Baldauf, Jutta A; Yu, Peng; Frey, Felix P

2018-01-01

Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Proteomics of Maize Root Development

Directory of Open Access Journals (Sweden)

Frank Hochholdinger

2018-03-01

Full Text Available Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Boosting the globalization of plant proteomics through INPPO: current developments and future prospects.

Science.gov (United States)

Agrawal, Ganesh Kumar; Sarkar, Abhijit; Agrawal, Raj; Ndimba, Bongani Kaiser; Tanou, Georgia; Dunn, Michael J; Kieselbach, Thomas; Cramer, Rainer; Wienkoop, Stefanie; Chen, Sixue; Rafudeen, Mohammed Suhail; Deswal, Renu; Barkla, Bronwyn J; Weckwerth, Wolfram; Heazlewood, Joshua L; Renaut, Jenny; Job, Dominique; Chakraborty, Niranjan; Rakwal, Randeep

2012-02-01

The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities

Newton's Investigation of the Resistance to Moving Bodies in Continuous Fluids and the Nature of "Frontier Science"

Science.gov (United States)

Gauld, Colin F.

2010-01-01

Newton's experiments into the resistance which fluids offer to moving bodies provide some insight into the way he related theory and experiment. His theory demonstrates a way of thought typical of 17th century physics and his experiments are simple enough to be replicated by present day students. Newton's investigations using pendulums were…

Integrating cell biology and proteomic approaches in plants.

Science.gov (United States)

Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

2017-10-03

Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

A DIGE proteomic analysis for high-intensity exercise-trained rat skeletal muscle.

Science.gov (United States)

Yamaguchi, Wataru; Fujimoto, Eri; Higuchi, Mitsuru; Tabata, Izumi

2010-09-01

Exercise training induces various adaptations in skeletal muscles. However, the mechanisms remain unclear. In this study, we conducted 2D-DIGE proteomic analysis, which has not yet been used for elucidating adaptations of skeletal muscle after high-intensity exercise training (HIT). For 5 days, rats performed HIT, which consisted of 14 20-s swimming exercise bouts carrying a weight (14% of the body weight), and 10-s pause between bouts. The 2D-DIGE analysis was conducted on epitrochlearis muscles excised 18 h after the final training exercise. Proteomic profiling revealed that out of 800 detected and matched spots, 13 proteins exhibited changed expression by HIT compared with sedentary rats. All proteins were identified by MALDI-TOF/MS. Furthermore, using western immunoblot analyses, significantly changed expressions of NDUFS1 and parvalbumin (PV) were validated in relation to HIT. In conclusion, the proteomic 2D-DIGE analysis following HIT-identified expressions of NDUFS1 and PV, previously unknown to have functions related to exercise-training adaptations.

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-03-01

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

Accumulation of deuterium oxide in body fluids after ingestion of D2O-labeled beverages

International Nuclear Information System (INIS)

Davis, J.M.; Lamb, D.R.; Burgess, W.A.; Bartoli, W.P.

1987-01-01

A simple low-cost procedure was developed to compare the temporal profiles of deuterium oxide (D 2 O) accumulation in body fluids after ingestion of D 2 O-labeled solutions. D 2 O concentration was measured in plasma and saliva samples taken at various intervals after ingestion of 20 ml of D 2 O mixed with five solutions differing in carbohydrate and electrolyte concentrations. An infrared spectrometer was used to measure D 2 O in purified samples obtained after a 48-h incubation period during which the water (D 2 O and H 2 O) in the sample was equilibrated with an equal volume of distilled water in a sealed diffusion dish. The procedure yields 100% recoveries of 60-500 ppm D 2 O with an average precision of 5%. When compared with values for distilled water, D 2 O accumulation in serial samples of plasma and saliva was slower for ingested solutions containing 40 and 15% glucose and faster for hypotonic saline and a 6% carbohydrate-electrolyte solution. These differences appear to reflect known differences in gastric emptying and intestinal absorption of these beverages. Therefore, this technique may provide a useful index of the rate of water uptake from ingested beverages into the body fluids

Fluid Statics and Archimedes

Indian Academy of Sciences (India)

librium of a vertical slice fluid (Figure Id) of height H and again using the fact .... same fluid having the same shape and same volume as the body. This fluid volume .... example, can be caused by the heating of air near the ground by the sun ...

Proteomic explorations of autism spectrum disorder.

Science.gov (United States)

Szoko, Nicholas; McShane, Adam J; Natowicz, Marvin R

2017-09-01

Proteomics, the large-scale study of protein expression in cells and tissues, is a powerful tool to study the biology of clinical conditions and has provided significant insights in many experimental systems. Herein, we review the basics of proteomic methodology and discuss challenges in using proteomic approaches to study autism. Unlike other experimental approaches, such as genomic approaches, there have been few large-scale studies of proteins in tissues from persons with autism. Most of the proteomic studies on autism used blood or other peripheral tissues; few studies used brain tissue. Some studies found dysregulation of aspects of the immune system or of aspects of lipid metabolism, but no consistent findings were noted. Based on the challenges in using proteomics to study autism, we discuss considerations for future studies. Apart from the complex technical considerations implicit in any proteomic analysis, key nontechnical matters include attention to subject and specimen inclusion/exclusion criteria, having adequate sample size to ensure appropriate powering of the study, attention to the state of specimens prior to proteomic analysis, and the use of a replicate set of specimens, when possible. We conclude by discussing some potentially productive uses of proteomics, potentially coupled with other approaches, for future autism research including: (1) proteomic analysis of banked human brain specimens; (2) proteomic analysis of tissues from animal models of autism; and (3) proteomic analysis of induced pluripotent stem cells that are differentiated into various types of brain cells and neural organoids. Autism Res 2017, 10: 1460-1469. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.

Proteomics dataset

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

2017-01-01

patients (Morgan et al., 2012; Abraham and Medzhitov, 2011; Bennike, 2014) [8–10. Therefore, we characterized the proteome of colon mucosa biopsies from 10 inflammatory bowel disease ulcerative colitis (UC) patients, 11 gastrointestinal healthy rheumatoid arthritis (RA) patients, and 10 controls. We...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

Salivary proteomics: A new adjuvant approach to the early diagnosis of familial juvenile systemic lupus erythematosus.

Science.gov (United States)

Abrão, Aline Lauria P; Falcao, Denise Pinheiro; de Amorim, Rivadávio Fernandes Batista; Bezerra, Ana Cristina B; Pombeiro, Gilson Augusto N M; Guimarães, Luciano Junqueira; Fregni, Felipe; Silva, Luciano Paulino; da Mota, Licia Maria Henrique

2016-04-01

Systemic lupus erythematosus (SLE) is a chronic multisystemic disease characterized by autoimmune inflammatory disturbance. Pleomorphic manifestations are present and a potentially progressive and debilitating course can be detected. SLE rarely manifests before age 5, and its onset peaks is around puberty. Although clinical manifestations, immunological alterations and treatment do not differ between juvenile and adult SLE, children tend to present with a more aggressive disease course than adults. Hence, autoimmune rheumatic diseases are the most common cause of morbidity and mortality in pediatric populations. Blood serum analysis plays an especially important role in the detection and monitoring of autoantibodies in SLE. However, since blood sampling is an uncomfortable procedure, especially in children, novel less invasive techniques and approaches are of utmost importance to evaluate pediatric subjects. In this regard, saliva samples have several advantages, such as: easy access, fast collection, painless and riskless procedure. Saliva has antimicrobial, immunomodulatory and anti-inflammatory properties, as well as several other relevant features. The whole saliva is a complex mixture of major and minor salivary gland secretion, gingival crevicular fluid, transudates plasma protein, keratinocyte products and oral microbiota. This biological fluid reflects the physiological state of the body, including the emotional condition, and endocrine, nutritional and metabolic changes. Therefore, salivary proteomics is becoming increasingly used for the early diagnosis of several diseases such as breast cancer, oral cancer, Sjögren's syndrome, diffuse systemic sclerosis, rheumatoid arthritis, among others. Considering the detection of some potential markers related to SLE in serum and urine, this study aims to conduct an initial evaluation of the possible presence of such biomarkers in saliva. Furthermore, it is expected to track down new salivary proteins that could be

In-vitro biodegradation and corrosion-assisted cracking of a coated magnesium alloy in modified-simulated body fluid.

Science.gov (United States)

Jafari, Sajjad; Singh Raman, R K

2017-09-01

A calcium phosphate coating was directly synthesized on AZ91D magnesium (Mg) alloy. Resistance of this coating to corrosion in a modified-simulated body fluid (m-SBF) was investigated by potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). Mechanical properties of the bare and coated alloy were investigated using slow strain rate tensile (SSRT) and fatigue testing in air and m-SBF. Very little is reported in the literature on human-body-fluid-assisted cracking of Mg alloys, viz., resistance to corrosion fatigue (CF) and stress corrosion cracking (SCC). This study has a particular emphasis on the effect of bio-compatible coatings on mechanical and electrochemical degradations of Mg alloys for their applications as implants. The results suggest the coating to improve the general as well as pitting corrosion resistance of the alloy. The coating also provides visible improvement in resistance to SCC, but little improvement in CF resistance. This is explained on the basis of pitting behaviour in the presence and absence of the coating. Copyright © 2017 Elsevier B.V. All rights reserved.

Influence of successive badminton matches on muscle strength, power, and body-fluid balance in elite players.

Science.gov (United States)

Abian-Vicen, Javier; Castanedo, Adrián; Abian, Pablo; Gonzalez-Millan, Cristina; Salinero, Juan José; Del Coso, Juan

2014-07-01

The aim was to analyze the influence of competitive round on muscle strength, body-fluid balance, and renal function in elite badminton players during a real competition. Body mass, jump height during a countermovement jump, handgrip force, and urine samples were obtained from 13 elite badminton players (6 men and 7 women) before and after the 2nd-round and quarterfinal matches of the national Spanish badminton championship. Sweat rate was determined by using prematch-to-postmatch body-mass change and by weighing individually labeled fluid bottles. Sweat rates were 1.04 ± 0.62 and 0.98 ± 0.43 L/h, while rehydration rate was 0.69 ± 0.26 and 0.91 ± 0.52 L/h for the 2nd round and quarterfinals, respectively. Thus, dehydration was 0.47% ± 1.03% after the 2nd round and 0.23% ± 0.43% after the quarterfinals. There were no differences in prematch-to-postmatch jump height, but jump height was reduced from 37.51 ± 8.83 cm after the 2nd-round game to 34.82 ± 7.37 cm after the quarterfinals (P badminton competition were effective to prevent dehydration. A badminton match did not affect jump height or handgrip force, but jump height was progressively reduced by the competitive round. Badminton players' renal responses reflected diminished renal flux due to the high-intensity nature of this racket sport.

Comparative proteomics in alkaptonuria provides insights into inflammation and oxidative stress.

Science.gov (United States)

Braconi, Daniela; Bernardini, Giulia; Paffetti, Alessandro; Millucci, Lia; Geminiani, Michela; Laschi, Marcella; Frediani, Bruno; Marzocchi, Barbara; Santucci, Annalisa

2016-12-01

Alkaptonuria (AKU) is an ultra-rare inborn error of metabolism associated with a defective catabolism of phenylalanine and tyrosine leading to increased systemic levels of homogentisic acid (HGA). Excess HGA is partly excreted in the urine, partly accumulated within the body and deposited onto connective tissues under the form of an ochronotic pigment, leading to a range of clinical manifestations. No clear genotype/phenotype correlation was found in AKU, and today there is the urgent need to identify biomarkers able to monitor AKU progression and evaluate response to treatment. With this aim, we provided the first proteomic study on serum and plasma samples from alkaptonuric individuals showing pathological SAA, CRP and Advanced Oxidation Protein Products (AOPP) levels. Interesting similarities with proteomic studies on other rheumatic diseases were highlighted together with proteome alterations supporting the existence of oxidative stress and inflammation in AKU. Potential candidate biomarkers to assess disease severity, monitor disease progression and evaluate response to treatment were identified as well. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biodegradable behaviors of AZ31 magnesium alloy in simulated body fluid

International Nuclear Information System (INIS)

Song Yingwei; Shan Dayong; Chen Rongshi; Zhang Fan; Han Enhou

2009-01-01

Magnesium alloys have unique advantages to act as biodegradable implants for clinical application. The biodegradable behaviors of AZ31 in simulated body fluid (SBF) for various immersion time intervals were investigated by electrochemical impedance spectroscopy (EIS) tests and scanning electron microscope (SEM) observation, and then the biodegradable mechanisms were discussed. It was found that a protective film layer was formed on the surface of AZ31 in SBF. With increasing of immersion time, the film layer became more compact. If the immersion time was more than 24 h, the film layer began to degenerate and emerge corrosion pits. In the meantime, there was hydroxyapatite particles deposited on the film layer. The hydroxyapatite is the essential component of human bone, which indicates the perfect biocompatibility of AZ31 magnesium alloy.

[Forensic medical evaluation of a burn injury from combustion of flammable fluids on the human body based on morphological changes in internal organs].

Science.gov (United States)

Khushkadamov, Z K

2009-01-01

The author describes morphological features of splanchnic organs in the patients that suffered an injury from combustion of flammable fluids at the body surface. The burn injury is a specific form of trauma originating from a combination of several injurious factors including thermoinhalation and intoxication with combustion products in the absence of oxygen in the centre of the hot spot. A rather specific combination of morphological changes in internal organs along with results of laboratory studies provides the most reliable criterion for forensic medical diagnosis of burn injuries from combustion of flammable fluids on the human body.

The Genomic and Proteomic Content of Cancer Cell-Derived Exosomes

International Nuclear Information System (INIS)

Henderson, Meredith C.; Azorsa, David O.

2012-01-01

Exosomes are secreted membrane vesicles that have been proposed as an effective means to detect a variety of disease states, including cancer. The properties of exosomes, including stability in biological fluids, allow for their efficient isolation and make them an ideal vehicle for studies on early disease detection and evaluation. Much data has been collected over recent years regarding the messenger RNA, microRNA, and protein contents of exosomes. In addition, many studies have described the functional role that exosomes play in disease initiation and progression. Tumor cells have been shown to secrete exosomes, often in increased amounts compared to normal cells, and these exosomes can carry the genomic and proteomic signatures characteristic of the tumor cells from which they were derived. While these unique signatures make exosomes ideal for cancer detection, exosomes derived from cancer cells have also been shown to play a functional role in cancer progression. Here, we review the unique genomic and proteomic contents of exosomes originating from cancer cells as well as their functional effects to promote tumor progression.

INTERACTION OF BIOMATERIALS CONTAINING CALCIUM HYDROXYAPATITE/ POLY-L-LACTIDE WITH THE SIMULATED BODY FLUID

Directory of Open Access Journals (Sweden)

Marija Petković

2011-12-01

Full Text Available The purpose of biomaterials is to replace a part or a function of the body in a safe, physiologically and economically acceptable way. The process of the reconstruction of bone defects has always been a big problem in orthopedics and maxillofacial surgery. Since hydroxyapatite (HAp was detected as a component, the predominant constituent and the integral element of Mammalian bones, the development of the phospate ceramics as potential materials for implantation was enabled. This study investigated whether and in which way biomaterial calcium hydroxyapatite/poly-L-lactide (HAp/PLLA interacts with the ionic composition of the human plasma. The simulated body fluid (SBF is an artificial fluid that has the ionic composition and ionic concentration similar to the human blood plasma. HAp/PLLA was incubated for 1, 2, 3 and 5 weeks in SBF. The surfaces of both treated and untreated materials were analyzed on a scanning electron microscopy (SEM, and were also exposed to the energy dispersive X-ray spectroscopy (EDS, while SBF was submitted to the measuring of pH and electrical conductivity. However, our results indicate that the degradational changes of the material HAp/PLLA in SBF start from the surface of the treated material and that observed changes are the consequence of dissolution of its polymer component and the precipitation of the material similar to hydroxyapatite on its surface. This material shows good characteristics that place it among good candidates for the application in orthopedics and maxillofacial surgery.

The “Dark Side” of Food Stuff Proteomics: The CPLL-Marshals Investigate

Directory of Open Access Journals (Sweden)

Pier Giorgio Righetti

2014-04-01

Full Text Available The present review deals with analysis of the proteome of animal and plant-derived food stuff, as well as of non-alcoholic and alcoholic beverages. The survey is limited to those systems investigated with the help of combinatorial peptide ligand libraries, a most powerful technique allowing access to low- to very-low-abundance proteins, i.e., to those proteins that might characterize univocally a given biological system and, in the case of commercial food preparations, attest their genuineness or adulteration. Among animal foods the analysis of cow’s and donkey’s milk is reported, together with the proteomic composition of egg white and yolk, as well as of honey, considered as a hybrid between floral and animal origin. In terms of plant and fruits, a survey is offered of spinach, artichoke, banana, avocado, mango and lemon proteomics, considered as recalcitrant tissues in that small amounts of proteins are dispersed into a large body of plant polymers and metabolites. As examples of non-alcoholic beverages, ginger ale, coconut milk, a cola drink, almond milk and orgeat syrup are analyzed. Finally, the trace proteome of white and red wines, beer and aperitifs is reported, with the aim of tracing the industrial manipulations and herbal usage prior to their commercialization.

1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.

Science.gov (United States)

Joshi, Hiren J; Christiansen, Katy M; Fitz, Joffrey; Cao, Jun; Lipzen, Anna; Martin, Joel; Smith-Moritz, A Michelle; Pennacchio, Len A; Schackwitz, Wendy S; Weigel, Detlef; Heazlewood, Joshua L

2012-05-15

The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/

Fundamental trends in fluid-structure interaction

CERN Document Server

Galdi, Giovanni P

2010-01-01

The interaction of a fluid with a solid body is a widespread phenomenon in nature, occurring at different scales and different applied disciplines. Interestingly enough, even though the mathematical theory of the motion of bodies in a liquid is one of the oldest and most classical problems in fluid mechanics, mathematicians have, only very recently, become interested in a systematic study of the basic problems related to fluid-structure interaction, from both analytical and numerical viewpoints. ""Fundamental Trends in Fluid-Structure Interaction"" is a unique collection of important papers wr

Farm animal proteomics - A review

DEFF Research Database (Denmark)

Bendixen, Emøke; Danielsen, Marianne; Hollung, Kristin

2011-01-01

In agricultural sciences as in all other areas of life science, the implementation of proteomics and other post-genomic tools is an important step towards more detailed understanding of the complex biological systems that control physiology and pathology of living beings. Farm animals are raised...... and cattle are relevant not only for farm animal sciences, but also for adding to our understanding of complex biological mechanisms of health and disease in humans. The aim of this review is to present an overview of the specific topics of interest within farm animal proteomics, and to highlight some...... of the areas where synergy between classic model organism proteomics and farm animal proteomics is rapidly emerging. Focus will be on introducing the special biological traits that play an important role in food production, and on how proteomics may help optimize farm animal production...

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.

Science.gov (United States)

Welker, F

2018-02-20

The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized

Proteomic analysis of human tooth pulp: proteomics of human tooth.

Science.gov (United States)

Eckhardt, Adam; Jágr, Michal; Pataridis, Statis; Mikšík, Ivan

2014-12-01

The unique pulp-dentin complex demonstrates strong regenerative potential, which enables it to respond to disease and traumatic injury. Identifying the proteins of the pulp-dentin complex is crucial to understanding the mechanisms of regeneration, tissue calcification, defense processes, and the reparation of dentin by dental pulp. The lack of knowledge of these proteins limits the development of more efficient therapies. The proteomic profile of human tooth pulp was investigated and compared with the proteome of human dentin and blood. The samples of tooth pulp were obtained from 5 sound permanent human third molars of 5 adults (n = 5). The extracted proteins were separated by 2-dimensional gel electrophoresis, analyzed by nano-liquid chromatography tandem mass spectrometry, and identified by correlating mass spectra to the proteomic databases. A total of 342 proteins were identified with high confidence, and 2 proteins were detected for the first time in an actual human sample. The identified tooth pulp proteins have a variety of functions: structural, catalytic, transporter, protease activity, immune response, and many others. In a comparison with dentin and blood plasma, 140 (pulp/dentin) shared proteins were identified, 37 of which were not observed in plasma. It can be suggested that they might participate in the unique pulp-dentin complex. This proteomic investigation of human tooth pulp, together with the previously published study of human dentin, is one of the most comprehensive proteome lists of human teeth to date. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Getting Students Familiar with the Use of Computers: Study of the Falling of a Body in a Fluid.

Science.gov (United States)

Guisasola, J.; Barragues, J. I.; Valdes, P.; Pedroso, F.

1999-01-01

Describes changes in scientific research methods that have been brought about by the use of computers. Presents an example of the falling of a body in a fluid to show students how computers can be used to experiment with mathematical models and to automate experiments. Contains 11 references. (Author/WRM)

Mining the granule proteome

DEFF Research Database (Denmark)

Albrethsen, Jakob; Goetze, Jens P; Johnsen, Anders H

2015-01-01

Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of g...

Proteomics - new analytical approaches

International Nuclear Information System (INIS)

Hancock, W.S.

2001-01-01

Full text: Recent developments in the sequencing of the human genome have indicated that the number of coding gene sequences may be as few as 30,000. It is clear, however, that the complexity of the human species is dependent on the much greater diversity of the corresponding protein complement. Estimates of the diversity (discrete protein species) of the human proteome range from 200,000 to 300,000 at the lower end to 2,000,000 to 3,000,000 at the high end. In addition, proteomics (the study of the protein complement to the genome) has been subdivided into two main approaches. Global proteomics refers to a high throughput examination of the full protein set present in a cell under a given environmental condition. Focused proteomics refers to a more detailed study of a restricted set of proteins that are related to a specified biochemical pathway or subcellular structure. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity (glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components) will be required in disease studies. To characterize these modifications it is necessary to digest the protein mixture with an enzyme to produce the corresponding mixture of peptides. In a process analogous to sequencing of the genome, shot-gun sequencing of the proteome is based on the characterization of the key fragments produced by such a digest. Thus, a glycopeptide and hence a specific glycosylation motif will be identified by a unique mass and then a diagnostic MS/MS spectrum. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. In addition, highly efficient separation processes are an absolute requirement for advanced proteomic studies. For example, a combination of the orthogonal approaches, HPLC and HPCE, can be very powerful

Proteome Exploration to Provide a Resource for the Investigation of Ganoderma lucidum

Science.gov (United States)

Yu, Guo-Jun; Yin, Ya-Lin; Yu, Wen-Hui; Liu, Wei; Jin, Yan-Xia; Shrestha, Alok; Yang, Qing; Ye, Xiang-Dong; Sun, Hui

2015-01-01

Ganoderma lucidum is a basidiomycete white rot fungus that has been used for medicinal purposes worldwide. Although information concerning its genome and transcriptome has recently been reported, relatively little information is available for G. lucidum at the proteomic level. In this study, protein fractions from G. lucidum at three developmental stages (16-day mycelia, and fruiting bodies at 60 and 90 days) were prepared and subjected to LC-MS/MS analysis. A search against the G. lucidum genome database identified 803 proteins. Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies. Fourteen TCA-cycle related proteins, 17 peptidases, two argonaute-like proteins, and two immunomodulatory proteins were also detected. A majority (470) of the 803 proteins had GO annotations and were classified into 36 GO terms, with “binding”, “catalytic activity”, and “hydrolase activity” having high percentages. Additionally, 357 out of the 803 proteins were assigned to at least one COG functional category and grouped into 22 COG classifications. Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity. In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits. PMID:25756518

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko

2017-05-10

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

Science.gov (United States)

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-06-23

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-01-01

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

The proteome of human saliva

Science.gov (United States)

Griffin, Timothy J.

2013-05-01

Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

DEFF Research Database (Denmark)

Welker, F.

2018-01-01

Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identificati......Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein...... not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against......), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations...

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius; Wong, Aloysius Tze; Groen, Arnoud; Serano, Natalia Lorena Gorron; Jankovic, Boris R.; Lilley, Kathryn; Gehring, Christoph A; Thomas, Ludivine

2014-01-01

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

Directory of Open Access Journals (Sweden)

Claudius Marondedze

2014-12-01

Full Text Available The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius

2014-12-31

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Proteomic analysis of bovine blastocoel fluid and blastocyst cells

DEFF Research Database (Denmark)

Jensen, Pernille Linnert; Grøndahl, Marie Louise; Beck, Hans Christian

2014-01-01

by micromanipulation. From two independent replicates, 23 proteins were identified in the blastocoel fluid while 803 proteins were identified in the remaining cell material. The proteins were grouped into categories according to their gene ontology (GO) terms by which proteins involved in cell differentiation, cell...... proliferation, development, and reproduction could be derived. Proteins classified in these categories could be candidates for further functional studies to understand pluripotency and early mammalian development....

Characterization of human neural differentiation from pluripotent stem cells using proteomics/PTMomics

DEFF Research Database (Denmark)

Braga, Marcella Nunes de Melo; Meyer, Morten; Zeng, Xianmin

2015-01-01

Stem cells are unspecialized cells capable of self-renewal and to differentiate into the large variety of cells in the body. The possibility to differentiate these cells into neural precursors and neural cells in vitro provides the opportunity to study neural development, nerve cell biology, neur...... differentiation from pluripotent stem cells. Moreover, some of the challenges in stem cell biology, differentiation, and proteomics/PTMomics that are not exclusive to neural development will be discussed.......Stem cells are unspecialized cells capable of self-renewal and to differentiate into the large variety of cells in the body. The possibility to differentiate these cells into neural precursors and neural cells in vitro provides the opportunity to study neural development, nerve cell biology...... the understanding of molecular processes in cells. Substantial advances in PTM enrichment methods and mass spectrometry has allowed the characterization of a subset of PTMs in large-scale studies. This review focuses on the current state-of-the-art of proteomic, as well as PTMomic studies related to human neural...

The influence of body position on cerebrospinal fluid pressure gradient and movement in cats with normal and impaired craniospinal communication.

Science.gov (United States)

Klarica, Marijan; Radoš, Milan; Erceg, Gorislav; Petošić, Antonio; Jurjević, Ivana; Orešković, Darko

2014-01-01

Intracranial hypertension is a severe therapeutic problem, as there is insufficient knowledge about the physiology of cerebrospinal fluid (CSF) pressure. In this paper a new CSF pressure regulation hypothesis is proposed. According to this hypothesis, the CSF pressure depends on the laws of fluid mechanics and on the anatomical characteristics inside the cranial and spinal space, and not, as is today generally believed, on CSF secretion, circulation and absorption. The volume and pressure changes in the newly developed CSF model, which by its anatomical dimensions and basic biophysical features imitates the craniospinal system in cats, are compared to those obtained on cats with and without the blockade of craniospinal communication in different body positions. During verticalization, a long-lasting occurrence of negative CSF pressure inside the cranium in animals with normal cranio-spinal communication was observed. CSF pressure gradients change depending on the body position, but those gradients do not enable unidirectional CSF circulation from the hypothetical site of secretion to the site of absorption in any of them. Thus, our results indicate the existence of new physiological/pathophysiological correlations between intracranial fluids, which opens up the possibility of new therapeutic approaches to intracranial hypertension.

The influence of body position on cerebrospinal fluid pressure gradient and movement in cats with normal and impaired craniospinal communication.

Directory of Open Access Journals (Sweden)

Marijan Klarica

Full Text Available Intracranial hypertension is a severe therapeutic problem, as there is insufficient knowledge about the physiology of cerebrospinal fluid (CSF pressure. In this paper a new CSF pressure regulation hypothesis is proposed. According to this hypothesis, the CSF pressure depends on the laws of fluid mechanics and on the anatomical characteristics inside the cranial and spinal space, and not, as is today generally believed, on CSF secretion, circulation and absorption. The volume and pressure changes in the newly developed CSF model, which by its anatomical dimensions and basic biophysical features imitates the craniospinal system in cats, are compared to those obtained on cats with and without the blockade of craniospinal communication in different body positions. During verticalization, a long-lasting occurrence of negative CSF pressure inside the cranium in animals with normal cranio-spinal communication was observed. CSF pressure gradients change depending on the body position, but those gradients do not enable unidirectional CSF circulation from the hypothetical site of secretion to the site of absorption in any of them. Thus, our results indicate the existence of new physiological/pathophysiological correlations between intracranial fluids, which opens up the possibility of new therapeutic approaches to intracranial hypertension.

Self-propulsion of a body with rigid surface and variable coefficient of lift in a perfect fluid

Science.gov (United States)

Ramodanov, Sergey M.; Tenenev, Valentin A.; Treschev, Dmitry V.

2012-11-01

We study the system of a 2D rigid body moving in an unbounded volume of incompressible, vortex-free perfect fluid which is at rest at infinity. The body is equipped with a gyrostat and a so-called Flettner rotor. Due to the latter the body is subject to a lifting force (Magnus effect). The rotational velocities of the gyrostat and the rotor are assumed to be known functions of time (control inputs). The equations of motion are presented in the form of the Kirchhoff equations. The integrals of motion are given in the case of piecewise continuous control. Using these integrals we obtain a (reduced) system of first-order differential equations on the configuration space. Then an optimal control problem for several types of the inputs is solved using genetic algorithms.

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Science.gov (United States)

Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

2008-09-01

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Proteomic Analysis of the Follicular Fluid of Tianzhu White Yak during Diestrus

Directory of Open Access Journals (Sweden)

Jinzhong Tao

2014-03-01

Full Text Available The aim of this study was to identify differentially expressed proteins in the follicular fluid of Tianzhu white yak during diestrus. Follicles obtained from female yak were divided into four groups according to their diameter: 0–2, 2–4, 4–6 mm, and greater than 6 mm. The follicular fluid was directly aspirated from the follicles and mixed according to follicular size, and two-dimensional gel electrophoresis was carried out on the crude follicular fluid samples. Thirty-four differentially expressed spots were generated from these four sizes of follicles. Fourteen of these spots were analyzed by MALDI-TOF/TOF-MS and identified as: AS3MT, VDP, ANKRD6, C10orf107 protein, MRP4, MAPKAP1, AGO3, profilin-β-actin, SPT2 homolog, AGP, AR, RNF20, obscurin-like-1, and one unnamed protein. These proteins were first reported in follicular fluid, in addition to VDP and AGP. Based on existing knowledge of their function and patterns of expression, we hypothesize that most of these differentially expressed proteins play a role in ovarian follicular growth and development, dominant follicle selection, or follicular atresia and development of oocytes; however, the function of the other differentially expressed proteins in reproduction remains ambiguous.

Human Saliva Collection Devices for Proteomics: An Update

Directory of Open Access Journals (Sweden)

Zohaib Khurshid

2016-06-01

Full Text Available There has been a rapid growth in the interest and adaptation of saliva as a diagnostic specimen over the last decade, and in the last few years in particular, there have been major developments involving the application of saliva as a clinically relevant specimen. Saliva provides a “window” into the oral and systemic health of an individual, and like other bodily fluids, saliva can be analyzed and studied to diagnose diseases. With the advent of new, more sensitive technologies to detect smaller concentrations of analytes in saliva relative to blood levels, there have been a number of critical developments in the field that we will describe. In particular, recent advances in standardized saliva collection devices that were not available three to four years ago, have made it easy for safe, simple, and non-invasive collection of samples to be carried out from patients. With the availability of these new technologies, we believe that in the next decade salivary proteomics will make it possible to predict and diagnose oral as well as systemic diseases, cancer, and infectious diseases, among others. The aim of this article is to review recent developments and advances in the area of saliva specimen collection devices and applications that will advance the field of proteomics.

Network-based analysis of proteomic profiles

KAUST Repository

Wong, Limsoon

2016-01-26

Mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes. It can be applied for various purposes, e.g. biomarker discovery in diseases and study of drug responses. Although RNA-based high-throughput methods have been useful in providing glimpses into the underlying molecular processes, the evidences they provide are indirect. Furthermore, RNA and corresponding protein levels have been known to have poor correlation. On the other hand, MS-based proteomics tend to have consistency issues (poor reproducibility and inter-sample agreement) and coverage issues (inability to detect the entire proteome) that need to be urgently addressed. In this talk, I will discuss how these issues can be addressed by proteomic profile analysis techniques that use biological networks (especially protein complexes) as the biological context. In particular, I will describe several techniques that we have been developing for network-based analysis of proteomics profile. And I will present evidence that these techniques are useful in identifying proteomics-profile analysis results that are more consistent, more reproducible, and more biologically coherent, and that these techniques allow expansion of the detected proteome to uncover and/or discover novel proteins.

Arabidopsis peroxisome proteomics

Directory of Open Access Journals (Sweden)

John D. Bussell

2013-04-01

Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

Digestion proteomics: tracking lactoferrin truncation and peptide release during simulated gastric digestion.

Science.gov (United States)

Grosvenor, Anita J; Haigh, Brendan J; Dyer, Jolon M

2014-11-01

The extent to which nutritional and functional benefit is derived from proteins in food is related to its breakdown and digestion in the body after consumption. Further, detailed information about food protein truncation during digestion is critical to understanding and optimising the availability of bioactives, in controlling and limiting allergen release, and in minimising or monitoring the effects of processing and food preparation. However, tracking the complex array of products formed during the digestion of proteins is not easily accomplished using classical proteomics. We here present and develop a novel proteomic approach using isobaric labelling to mapping and tracking protein truncation and peptide release during simulated gastric digestion, using bovine lactoferrin as a model food protein. The relative abundance of related peptides was tracked throughout a digestion time course, and the effect of pasteurisation on peptide release assessed. The new approach to food digestion proteomics developed here therefore appears to be highly suitable not only for tracking the truncation and relative abundance of released peptides during gastric digestion, but also for determining the effects of protein modification on digestibility and potential bioavailability.

Finite element approach to study the behavior of fluid distribution in the dermal regions of human body due to thermal stress

Directory of Open Access Journals (Sweden)

M.A. Khanday

2015-10-01

Full Text Available The human body is a complex structure where the balance of mass and heat transport in all tissues is necessary for its normal functioning. The stabilities of intracellular and extracellular fluids are important physiological factors responsible for homoeostasis. To estimate the effects of thermal stress on the behavior of extracellular fluid concentration in human dermal regions, a mathematical model based on diffusion equation along with appropriate boundary conditions has been formulated. Atmospheric temperature, evaporation rate, moisture concentration and other factors affecting the fluid concentration were taken into account. The variational finite element approach has been employed to solve the model and the results were interpreted graphically.

Optimizing human synovial fluid preparation for two-dimensional gel electrophoresis.

Science.gov (United States)

Chen, Carl Pc; Hsu, Chih-Chin; Yeh, Wen-Lin; Lin, Hsiu-Chu; Hsieh, Sen-Yung; Lin, Shih-Cherng; Chen, Tai-Tzung; Chen, Max Jl; Tang, Simon Ft

2011-10-11

Proteome analysis is frequently applied in identifying the proteins or biomarkers in knee synovial fluids (SF) that are associated with osteoarthritis and other arthritic disorders. The 2-dimensional gel electrophoresis (2-DE) is the technique of choice in these studies. Disease biomarkers usually appear in low concentrations and may be masked by high abundant proteins. Therefore, the main aim of this study was to find the most suitable sample preparation method that can optimize the expression of proteins on 2-DE gels that can be used to develop a reference proteome picture for non-osteoarthritic knee synovial fluid samples. Proteome pictures obtained from osteoarthritic knee synovial fluids can then be compared with the reference proteome pictures obtained in this study to assist us in identifying the disease biomarkers more correctly. The proteomic tool of 2-DE with immobilized pH gradients was applied in this study. A total of 12 2-DE gel images were constructed from SF samples that were free of osteoarthritis. In these samples, 3 were not treated with any sample preparation methods, 3 were treated with acetone, 3 were treated with 2-DE Clean-Up Kit, and 3 were treated with the combination of acetone and 2-D Clean-Up Kit prior to 2-DE analysis. Gel images were analyzed using the PDQuest Basic 8.0.1 Analytical software. Protein spots that were of interest were excised from the gels and sent for identification by mass spectrometry. Total SF total protein concentration was calculated to be 21.98 ± 0.86 mg/mL. The untreated SF samples were detected to have 456 ± 33 protein spots on 2-DE gel images. Acetone treated SF samples were detected to have 320 ± 28 protein spots, 2-D Clean-Up Kit treated SF samples were detected to have 413 ± 31 protein spots, and the combined treatment method of acetone and 2-D Clean-Up Kit was detected to have 278 ± 26 protein spots 2-DE gel images. SF samples treated with 2-D Clean-Up Kit revealed clearer presentation of the isoforms

Optimizing Human Synovial Fluid Preparation for Two-Dimensional Gel Electrophoresis

Directory of Open Access Journals (Sweden)

Chen Max JL

2011-10-01

Full Text Available Abstract Background Proteome analysis is frequently applied in identifying the proteins or biomarkers in knee synovial fluids (SF that are associated with osteoarthritis and other arthritic disorders. The 2-dimensional gel electrophoresis (2-DE is the technique of choice in these studies. Disease biomarkers usually appear in low concentrations and may be masked by high abundant proteins. Therefore, the main aim of this study was to find the most suitable sample preparation method that can optimize the expression of proteins on 2-DE gels that can be used to develop a reference proteome picture for non-osteoarthritic knee synovial fluid samples. Proteome pictures obtained from osteoarthritic knee synovial fluids can then be compared with the reference proteome pictures obtained in this study to assist us in identifying the disease biomarkers more correctly. Results The proteomic tool of 2-DE with immobilized pH gradients was applied in this study. A total of 12 2-DE gel images were constructed from SF samples that were free of osteoarthritis. In these samples, 3 were not treated with any sample preparation methods, 3 were treated with acetone, 3 were treated with 2-DE Clean-Up Kit, and 3 were treated with the combination of acetone and 2-D Clean-Up Kit prior to 2-DE analysis. Gel images were analyzed using the PDQuest Basic 8.0.1 Analytical software. Protein spots that were of interest were excised from the gels and sent for identification by mass spectrometry. Total SF total protein concentration was calculated to be 21.98 ± 0.86 mg/mL. The untreated SF samples were detected to have 456 ± 33 protein spots on 2-DE gel images. Acetone treated SF samples were detected to have 320 ± 28 protein spots, 2-D Clean-Up Kit treated SF samples were detected to have 413 ± 31 protein spots, and the combined treatment method of acetone and 2-D Clean-Up Kit was detected to have 278 ± 26 protein spots 2-DE gel images. SF samples treated with 2-D Clean-Up Kit

Proteomics Insights into Autophagy.

Science.gov (United States)

Cudjoe, Emmanuel K; Saleh, Tareq; Hawkridge, Adam M; Gewirtz, David A

2017-10-01

Autophagy, a conserved cellular process by which cells recycle their contents either to maintain basal homeostasis or in response to external stimuli, has for the past two decades become one of the most studied physiological processes in cell biology. The 2016 Nobel Prize in Medicine and Biology awarded to Dr. Ohsumi Yoshinori, one of the first scientists to characterize this cellular mechanism, attests to its importance. The induction and consequent completion of the process of autophagy results in wide ranging changes to the cellular proteome as well as the secretome. MS-based proteomics affords the ability to measure, in an unbiased manner, the ubiquitous changes that occur when autophagy is initiated and progresses in the cell. The continuous improvements and advances in mass spectrometers, especially relating to ionization sources and detectors, coupled with advances in proteomics experimental design, has made it possible to study autophagy, among other process, in great detail. Innovative labeling strategies and protein separation techniques as well as complementary methods including immuno-capture/blotting/staining have been used in proteomics studies to provide more specific protein identification. In this review, we will discuss recent advances in proteomics studies focused on autophagy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Body fluid identification using a targeted mRNA massively parallel sequencing approach - results of a EUROFORGEN/EDNAP collaborative exercise

DEFF Research Database (Denmark)

Ingold, S; Dørum, G; Hanson, E

2018-01-01

to specified protocols. The provided primer pools for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms included 33 and 29 body fluid specific targets, respectively, to identify blood, saliva, semen, vaginal secretion, menstrual blood and skin. The results demonstrated moderate to high count values...

Comparison of the antimicrobial adhesion potential of human body fluid glycoconjugates using fucose-binding lectin (PA-IIL) of Pseudomonas aeruginosa and Ulex europaeus lectin (UEA-I).

Science.gov (United States)

Lerrer, Batia; Lesman-Movshovich, Efrat; Gilboa-Garber, Nechama

2005-09-01

Pseudomonas aeruginosa produces a fucose-binding lectin (PA-IIL) which strongly binds to human cells. This lectin was shown to be highly sensitive to inhibition by fucose-bearing human milk glycoproteins. Since the glycans of these glycoproteins mimic human cell receptors, they may function as decoys in blocking lectin-dependent pathogen adhesion to the host cells. Human saliva and seminal fluid also contain such compounds, and body fluids of individuals who are "secretors" express additional fucosylated (alpha 1,2) residues. The latter are selectively detected by Ulex europaeus lectin UEA-I. The aim of the present research was to compare the PA-IIL and UEA-I interactions with human salivas and seminal fluids of "secretors" and "nonsecretors" with those obtained with the respective milks. Using hemagglutination inhibition and Western blot analyses, we showed that PA-IIL interactions with the saliva and seminal fluid glycoproteins were somewhat weaker than those obtained with the milk and that "nonsecretor" body fluids were not less efficient than those of "secretors" in PA-IIL blocking. UEA-I, which interacted only with the "secretors" glycoproteins, was most sensitive to those of the seminal fluids.

[Progress in stable isotope labeled quantitative proteomics methods].

Science.gov (United States)

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

Fluid Shifts

Science.gov (United States)

Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.;

Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context.

Science.gov (United States)

Marco-Ramell, A; de Almeida, A M; Cristobal, S; Rodrigues, P; Roncada, P; Bassols, A

2016-06-21

Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public. In a context in which animal and human health are intertwined aspects of the one-health concept it is of utmost importance to define the markers of stress and welfare. These are important tools for producers, retailers, regulatory agents and ultimately consumers to effectively monitor and assess the welfare state of production animals. Proteomics is the science that studies the proteins existing in a given tissue or fluid. In this review we address this topic by showing clear examples where proteomics has been used to study stress-induced changes at various levels. We adopt a multi-species (cattle, swine, small ruminants, poultry, fish and shellfish) approach under the effect of various stress inducers (handling, transport, management, nutritional, thermal and exposure to pollutants) clearly demonstrating how proteomics and systems biology are key elements to the study of stress and welfare in farm animals and powerful tools for animal welfare, health and productivity.

Fluid Status in Peritoneal Dialysis Patients: The European Body Composition Monitoring (EuroBCM) Study Cohort

Science.gov (United States)

Van Biesen, Wim; Williams, John D.; Covic, Adrian C.; Fan, Stanley; Claes, Kathleen; Lichodziejewska-Niemierko, Monika; Verger, Christian; Steiger, Jurg; Schoder, Volker; Wabel, Peter; Gauly, Adelheid; Himmele, Rainer

2011-01-01

Background Euvolemia is an important adequacy parameter in peritoneal dialysis (PD) patients. However, accurate tools to evaluate volume status in clinical practice and data on volume status in PD patients as compared to healthy population, and the associated factors, have not been available so far. Methods We used a bio-impedance spectroscopy device, the Body Composition Monitor (BCM) to assess volume status in a cross-sectional cohort of prevalent PD patients in different European countries. The results were compared to an age and gender matched healthy population. Results Only 40% out of 639 patients from 28 centres in 6 countries were normovolemic. Severe fluid overload was present in 25.2%. There was a wide scatter in the relation between blood pressure and volume status. In a multivariate analysis in the subgroup of patients from countries with unrestricted availability of all PD modalities and fluid types, older age, male gender, lower serum albumin, lower BMI, diabetes, higher systolic blood pressure, and use of at least one exchange per day with the highest hypertonic glucose were associated with higher relative tissue hydration. Neither urinary output nor ultrafiltration, PD fluid type or PD modality were retained in the model (total R2 of the model = 0.57). Conclusions The EuroBCM study demonstrates some interesting issues regarding volume status in PD. As in HD patients, hypervolemia is a frequent condition in PD patients and blood pressure can be a misleading clinical tool to evaluate volume status. To monitor fluid balance, not only fluid output but also dietary input should be considered. Close monitoring of volume status, a correct dialysis prescription adapted to the needs of the patient and dietary measures seem to be warranted to avoid hypervolemia. PMID:21390320

NIH Common Fund - Disruptive Proteomics Technologies - Challenges and Opportunities | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

This Request for Information (RFI) is directed toward determining how best to accelerate research in disruptive proteomics technologies. The Disruptive Proteomics Technologies (DPT) Working Group of the NIH Common Fund wishes to identify gaps and opportunities in current technologies and methodologies related to proteome-wide measurements.  For the purposes of this RFI, “disruptive” is defined as very rapid, very significant gains, similar to the "disruptive" technology development that occurred in DNA sequencing technology.

Utility of Cytospin and Cell block Technology in Evaluation of Body Fluids and Urine Samples: A Comparative Study.

Science.gov (United States)

Qamar, Irmeen; Rehman, Suhailur; Mehdi, Ghazala; Maheshwari, Veena; Ansari, Hena A; Chauhan, Sunanda

2018-01-01

Cytologic examination of body fluids commonly involves the use of direct or sediment smears, cytocentrifuge preparations, membrane filter preparations, or cell block sections. Cytospin and cell block techniques are extremely useful in improving cell yield of thin serous effusions and urine samples, and ensure high diagnostic efficacy. We studied cytospin preparations and cell block sections prepared from 180 samples of body fluids and urine samples to compare the relative efficiency of cell retrieval, preservation of cell morphology, ease of application of special stains, and diagnostic efficacy. Samples were collected and processed to prepare cytospin smears and cell block sections. We observed that overall, cell yield and preservation of individual cell morphology were better in cytospin preparations as compared to cell blocks, while preservation of architectural pattern was better in cell block sections. The number of suspicious cases also decreased on cell block sections, with increased detection of malignancy. It was difficult to prepare cell blocks from urine samples due to low cellularity. Cytospin technology is a quick, efficient, and cost-effective method of increasing cell yield in hypocellular samples, with better preservation of cell morphology. Cell blocks are better prepared from high cellularity fluids; however, tissue architecture is better studied, with improved rate of diagnosis and decrease in ambiguous results. Numerous sections can be prepared from a small amount of material. Special stains and immunochemical stains can be easily applied to cell blocks. It also provides a source of archival material.

Elevated levels of protein AMBP in cerebrospinal fluid of women with preeclampsia compared to normotensive pregnant women

NARCIS (Netherlands)

C. Van Den Berg (Caroline); J.J. Duvekot (Hans); C. Güzel (Coşkun); Hansson, S.R. (Stefan R.); T.G. de Leeuw (Tom); E.A.P. Steegers (Eric); Versendaal, J. (Johannes); T.M. Luider (Theo); M.P. Stoop (Marcel)

2017-01-01

textabstractPurpose: To investigate the cerebrospinal fluid (CSF) proteome of patients with preeclampsia (PE) and normotensive pregnant women, in order to provide a better understanding of brain involvement in PE. Experimental design: Ninety-eight CSF samples (43 women with PE and 55 normotensive

Roles of interstitial fluid pH in diabetes mellitus: Glycolysis and mitochondrial function

Science.gov (United States)

Marunaka, Yoshinori

2015-01-01

The pH of body fluids is one the most important key factors regulating various cell function such as enzyme activity and protein-protein interaction via modification of its binding affinity. Therefore, to keep cell function normal, the pH of body fluids is maintained constant by various systems. Insulin resistance is one of the most important, serious factors making the body condition worse in diabetes mellitus. I have recently found that the pH of body (interstitial) fluids is lower in diabetes mellitus than that in non-diabetic control, and that the lowered pH is one of the causes producing insulin resistance. In this review article, I introduce importance of body (interstitial) fluid pH in regulation of body function, evidence on abnormal regulation of body fluid pH in diabetes mellitus, and relationship between the body fluid pH and insulin resistance. Further, this review proposes perspective therapies on the basis of regulation of body fluid pH including propolis (honeybee product) diet. PMID:25685283

A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

Science.gov (United States)

Gadher, Suresh Jivan; Drahos, László; Vékey, Károly; Kovarova, Hana

2017-07-01

The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.

Proteome changes in rat plasma in response to sibutramine.

Science.gov (United States)

Choi, Jung-Won; Joo, Jeong In; Kim, Dong Hyun; Wang, Xia; Oh, Tae Seok; Choi, Duk Kwon; Yun, Jong Won

2011-04-01

Sibutramine is an anti-obesity agent that induces weight loss by selective inhibition of neuronal reuptake of serotonin and norepinephrine; however, it is associated with the risk of cardiovascular diseases (CVD), including heart attack and stroke. Here, we analyzed global protein expression patterns in plasma of control and sibutramine-treated rats using proteomic analysis for a better understanding of the two conflicting functions of this drug, appetite regulation, and cardiovascular risk. The control (n=6) and sibutramine-treated groups (n=6) were injected by vehicle and sibutramine, respectively, and 2-DE combined with MALDI-TOF/MS were performed. Compared to control rats, sibutramine-administered rats gained approximately 18% less body weight and consumed about 13% less food. Plasma leptin and insulin levels also showed a significant decrease in sibutramine-treated rats. As a result of proteomic analysis, 23 differentially regulated proteins were discovered and were reconfirmed by immunoblot analysis. Changed proteins were classified into appetite regulation and cardiovascular risk, according to their regulation pattern. Because the differential levels of proteins that have been well recognized as predictors of CVD risk were not well matched with the results of our proteomic analysis, this study does not conclusively prove that sibutramine has an effect on CVD risk. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Uniting ripple-formation theory under water and winds: A universal scaling relation for the wavelength of fluid-drag ripples across fluids and planetary bodies

Science.gov (United States)

Lapotre, M. G. A.; Lamb, M. P.; Ewing, R. C.; McElroy, B. J.

2016-12-01

Current ripples form on riverbeds and on the seafloor from viscous drag exerted by water flow over sand and are thought to be absent in subaerial systems, where ripple formation is dominated by a mechanism involving the impacting and splashing of sand grains. A fluid-drag mechanism, however, is not precluded in subaerial conditions and was originally hypothesized by R. A. Bagnold. Despite decades of observations in the field and in the laboratory, no universal scaling relation exists to predict the size of fluid-drag ripples. We combine dimensional analysis and a new extensive data compilation to develop a relationship and predict the equilibrium wavelength of current ripples. Our analysis shows that ripples are spaced farther apart when formed by more viscous fluids, smaller bed shear velocities, in coarser grains, or for smaller sediment specific gravity. Our scaling relation also highlights the abrupt transition between current ripples and subaqueous dunes, and thus allows for a process-based segregation of ripples from dunes. When adjusting for subaerial conditions, we predict the formation of decimeter-scale wind-drag ripples on Earth and meter-scale wind-drag ripples on Mars. The latter are ubiquitous on the Red Planet, and are found to co-exist with smaller decimeter-scale ripples, which we interpret as impact ripples. Because the predicted scale of terrestrial wind-drag ripples overlaps with that of impact ripples, it is possible that wind-drag ripples exist on Earth too, but are not recognized as such. When preserved in rocks, fluid-drag ripple stratification records flow directions and fluid properties that are crucial to constrain paleo-environments. Our new theory allows for predictions of ripple size, perhaps in both fluvial and eolian settings, and thus potentially represents a powerful tool for paleo-environmental reconstructions on different planetary bodies.

Fecal electrolyte testing for evaluation of unexplained diarrhea: Validation of body fluid test accuracy in the absence of a reference method.

Science.gov (United States)

Voskoboev, Nikolay V; Cambern, Sarah J; Hanley, Matthew M; Giesen, Callen D; Schilling, Jason J; Jannetto, Paul J; Lieske, John C; Block, Darci R

2015-11-01

Validation of tests performed on body fluids other than blood or urine can be challenging due to the lack of a reference method to confirm accuracy. The aim of this study was to evaluate alternate assessments of accuracy that laboratories can rely on to validate body fluid tests in the absence of a reference method using the example of sodium (Na(+)), potassium (K(+)), and magnesium (Mg(2+)) testing in stool fluid. Validations of fecal Na(+), K(+), and Mg(2+) were performed on the Roche cobas 6000 c501 (Roche Diagnostics) using residual stool specimens submitted for clinical testing. Spiked recovery, mixing studies, and serial dilutions were performed and % recovery of each analyte was calculated to assess accuracy. Results were confirmed by comparison to a reference method (ICP-OES, PerkinElmer). Mean recoveries for fecal electrolytes were Na(+) upon spiking=92%, mixing=104%, and dilution=105%; K(+) upon spiking=94%, mixing=96%, and dilution=100%; and Mg(2+) upon spiking=93%, mixing=98%, and dilution=100%. When autoanalyzer results were compared to reference ICP-OES results, Na(+) had a slope=0.94, intercept=4.1, and R(2)=0.99; K(+) had a slope=0.99, intercept=0.7, and R(2)=0.99; and Mg(2+) had a slope=0.91, intercept=-4.6, and R(2)=0.91. Calculated osmotic gap using both methods were highly correlated with slope=0.95, intercept=4.5, and R(2)=0.97. Acid pretreatment increased magnesium recovery from a subset of clinical specimens. A combination of mixing, spiking, and dilution recovery experiments are an acceptable surrogate for assessing accuracy in body fluid validations in the absence of a reference method. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Proteome reference map of Drosophila melanogaster head.

Science.gov (United States)

Lee, Tian-Ren; Huang, Shun-Hong; Lee, Chi-Ching; Lee, Hsiao-Yun; Chan, Hsin-Tzu; Lin, Kuo-Sen; Chan, Hong-Lin; Lyu, Ping-Chiang

2012-06-01

Drosophila melanogaster has been used as a genetic model organism to understand the fundamental molecular mechanisms in human biology including memory formation that has been reported involving protein synthesis and/or post-translational modification. In this study, we employed a proteomic platform based on fluorescent 2DE and MALDI-TOF MS to build a standard D. melanogaster head proteome map for proteome-proteome comparison. In order to facilitate the comparison, an interactive database has been constructed for systematically integrating and analyzing the proteomes from different conditions and further implicated to study human diseases related to D. melanogaster model. In summary, the fundamental head proteomic database and bioinformatic analysis will be useful for further elucidating the biological mechanisms such as memory formation and neurodegenerative diseases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In Vitro Studies Evaluating Leaching of Mercury from Mine Waste Calcine Using Simulated Human Body Fluids

OpenAIRE

Gray, John E.; Plumlee, Geoffrey S.; Morman, Suzette A.; Higueras, Pablo L.; Crock, James G.; Lowers, Heather A.; Witten, Mark L.

2010-01-01

In vitro bioaccessibility (IVBA) studies were carried out on samples of mercury (Hg) mine-waste calcine (roasted Hg ore) by leaching with simulated human body fluids. The objective was to estimate potential human exposure to Hg due to inhalation of airborne calcine particulates and hand-to-mouth ingestion of Hg-bearing calcines. Mine waste calcines collected from Hg mines at Almad?n, Spain, and Terlingua, Texas, contain Hg sulfide, elemental Hg, and soluble Hg compounds, which constitute prim...

A 3D, fully Eulerian, VOF-based solver to study the interaction between two fluids and moving rigid bodies using the fictitious domain method

Science.gov (United States)

Pathak, Ashish; Raessi, Mehdi

2016-04-01

We present a three-dimensional (3D) and fully Eulerian approach to capturing the interaction between two fluids and moving rigid structures by using the fictitious domain and volume-of-fluid (VOF) methods. The solid bodies can have arbitrarily complex geometry and can pierce the fluid-fluid interface, forming contact lines. The three-phase interfaces are resolved and reconstructed by using a VOF-based methodology. Then, a consistent scheme is employed for transporting mass and momentum, allowing for simulations of three-phase flows of large density ratios. The Eulerian approach significantly simplifies numerical resolution of the kinematics of rigid bodies of complex geometry and with six degrees of freedom. The fluid-structure interaction (FSI) is computed using the fictitious domain method. The methodology was developed in a message passing interface (MPI) parallel framework accelerated with graphics processing units (GPUs). The computationally intensive solution of the pressure Poisson equation is ported to GPUs, while the remaining calculations are performed on CPUs. The performance and accuracy of the methodology are assessed using an array of test cases, focusing individually on the flow solver and the FSI in surface-piercing configurations. Finally, an application of the proposed methodology in simulations of the ocean wave energy converters is presented.

Two-Dimensional Self-Propelled Fish Motion in Medium: An Integrated Method for Deforming Body Dynamics and Unsteady Fluid Dynamics

International Nuclear Information System (INIS)

Yan, Yang; Yong-Liang, Yu; Bing-Gang, Tong; Guan-Hao, Wu

2008-01-01

We present (1) the dynamical equations of deforming body and (2) an integrated method for deforming body dynamics and unsteady fluid dynamics, to investigate a modelled freely self-propelled fish. The theoretical model and practical method is applicable for studies on the general mechanics of animal locomotion such as flying in air and swimming in water, particularly of free self-propulsion. The present results behave more credibly than the previous numerical studies and are close to the experimental results, and the aligned vortices pattern is discovered in cruising swimming

Proteomics in pulmonary research: selected methodical aspects

Directory of Open Access Journals (Sweden)

Martin Petrek

2007-10-01

Full Text Available Recent years witness rapid expansion of applications of proteomics to clinical research including non-malignant lung disorders. These developments bring along the need for standardisation of proteomic experiments. This paper briefly reviews basic methodical aspects of appliedproteomic studies using SELDI-TOF mass spectrometry platform as example but also emphasizes general aspects of quality assurance in proteomics. Key-words: lung proteome, quality assurance, SELDI-TOF MS

The potato tuber mitochondrial proteome

DEFF Research Database (Denmark)

Salvato, Fernanda; Havelund, Jesper Foged; Chen, Mingjie

2014-01-01

Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins...... manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome...

Body fat indices and biomarkers of inflammation: a cross-sectional study with implications for obesity and peri-implant oral health.

Science.gov (United States)

Elangovan, Satheesh; Brogden, Kim A; Dawson, Deborah V; Blanchette, Derek; Pagan-Rivera, Keyla; Stanford, Clark M; Johnson, Georgia K; Recker, Erica; Bowers, Rob; Haynes, William G; Avila-Ortiz, Gustavo

2014-01-01

To examine the relationships between three measures of body fat-body mass index (BMI), waist circumference (WC), and total body fat percent-and markers of inflammation around dental implants in stable periodontal maintenance patients. Seventy-three subjects were enrolled in this cross-sectional assessment. The study visit consisted of a physical examination that included anthropologic measurements of body composition (BMI, WC, body fat %); intraoral assessments were performed (full-mouth plaque index, periodontal and peri-implant comprehensive examinations) and peri-implant sulcular fluid (PISF) was collected on the study implants. Levels of interleukin (IL)-1α, IL-1β, IL-6, IL-8, IL-10, IL-12, IL-17, tumor necrosis factor-α, C-reactive protein, osteoprotegerin, leptin, and adiponectin in the PISF were measured using multiplex proteomic immunoassays. Correlation analysis with body fat measures was then performed using appropriate statistical methods. After adjustments for covariates, regression analyses revealed statistically significant correlation between IL-1β in PISF and WC (R = 0.33; P = .0047). In this study in stable periodontal maintenance patients, a modest but statistically significant positive correlation was observed between the levels of IL-1β, a major proinflammatory cytokine in PISF, and WC, a reliable measure of central obesity.

A comparative proteomic characterization and nutritional assessment of naturally- and artificially-cultivated Cordyceps sinensis.

Science.gov (United States)

Zhang, Xu; Liu, Qun; Zhou, Wei; Li, Ping; Alolga, Raphael N; Qi, Lian-Wen; Yin, Xiaojian

2018-03-30

Cordyceps sinensis has gained increasing attention due to its nutritional and medicinal properties. Herein, we employed label-free quantitative mass spectrometry to explore the proteome differences between naturally- and artificially-cultivated C. sinensis. A total of 22,829 peptides with confidence ≥95%, corresponding to 2541 protein groups were identified from the caterpillar bodies/stromata of 12 naturally- and artificially-cultivated samples of C. sinensis. Among them, 165 proteins showed significant differences between the samples of natural and artificial cultivation. These proteins were mainly involved in energy production/conversion, amino acid transport/metabolism, and transcription regulation. The proteomic results were confirmed by the identification of 4 significantly changed metabolites, thus, lysine, threonine, serine, and arginine via untargeted metabolomics. The change tendencies of these metabolites were partly in accordance with changes in abundance of the proteins, which was upstream of their synthetic pathways. In addition, the nutritional value in terms of the levels of nucleosides, nucleotides, and adenosine between the artificially- and naturally-cultivated samples was virtually same. These proteomic data will be useful for understanding the medicinal value of C. sinensis and serve as reference for its artificial cultivation. C. sinensis is a precious and valued medicinal product, the current basic proteome dataset would provide useful information to understand its development/infection processes as well as help to artificially cultivate it. This work would also provide basic proteome profile for further study of C. sinensis. Copyright © 2018. Published by Elsevier B.V.

Proteomic profiling of the rat hypothalamus

Directory of Open Access Journals (Sweden)

Pedroso Amanda P

2012-04-01

Full Text Available Abstract Background The hypothalamus plays a pivotal role in numerous mechanisms highly relevant to the maintenance of body homeostasis, such as the control of food intake and energy expenditure. Impairment of these mechanisms has been associated with the metabolic disturbances involved in the pathogenesis of obesity. Since rodent species constitute important models for metabolism studies and the rat hypothalamus is poorly characterized by proteomic strategies, we performed experiments aimed at constructing a two-dimensional gel electrophoresis (2-DE profile of rat hypothalamus proteins. Results As a first step, we established the best conditions for tissue collection and protein extraction, quantification and separation. The extraction buffer composition selected for proteome characterization of rat hypothalamus was urea 7 M, thiourea 2 M, CHAPS 4%, Triton X-100 0.5%, followed by a precipitation step with chloroform/methanol. Two-dimensional (2-D gels of hypothalamic extracts from four-month-old rats were analyzed; the protein spots were digested and identified by using tandem mass spectrometry and database query using the protein search engine MASCOT. Eighty-six hypothalamic proteins were identified, the majority of which were classified as participating in metabolic processes, consistent with the finding of a large number of proteins with catalytic activity. Genes encoding proteins identified in this study have been related to obesity development. Conclusion The present results indicate that the 2-DE technique will be useful for nutritional studies focusing on hypothalamic proteins. The data presented herein will serve as a reference database for studies testing the effects of dietary manipulations on hypothalamic proteome. We trust that these experiments will lead to important knowledge on protein targets of nutritional variables potentially able to affect the complex central nervous system control of energy homeostasis.

Anthropometric changes and fluid shifts

Science.gov (United States)

Thornton, W. E.; Hoffler, G. W.; Rummel, J. A.

1974-01-01

Several observations of body size, shape, posture, and configuration were made to document changes resulting from direct effects of weightlessness during the Skylab 4 mission. After the crewmen were placed in orbit, a number of anatomical and anthropometric changes occurred including a straightening of the thoracolumbar spine, a general decrease in truncal girth, and an increase in height. By the time of the earliest in-flight measurement on mission day 3, all crewmen had lost more than two liters of extravascular fluid from the calf and thigh. The puffy facies, the bird legs effect, the engorgement of upper body veins, and the reduced volume of lower body veins were all documented with photographs. Center-of-mass measurements confirmed a fluid shift cephalad. This shift remained throughout the mission until recovery, when a sharp reversal occurred; a major portion of the reversal was completed in a few hours. The anatomical changes are of considerable scientific interest and of import to the human factors design engineer, but the shifts of blood and extravascular fluid are of more consequence. It is hypothesized that the driving force for the fluid shift is the intrinsic and unopposed lower limb elasticity that forces venous blood and then other fluid cephalad.

Contact with hospital syringes containing body fluids: implications for medical waste management regulation Jeringas en contacto con sangre y fluidos corporales utilizadas en el hospital: implicaciones para el manejo de desechos hospitalarios

OpenAIRE

Patricia Volkow; Bénédicte Jacquemin; Diana Vilar-Compte; José Ramón Castillo

2003-01-01

OBJECTIVE: To determine amount of syringes used in the hospital and extent of contact with blood and body fluids of these syringes. MATERIAL AND METHODS: Syringe use was surveyed at a tertiary care center for one week; syringes were classified into the following four categories according to use: a) contained blood; b) contained other body fluids (urine, gastric secretion, cerebrospinal fluid, wound drainage); c) used exclusively for drug dilution and application in plastic intravenous (IV) tu...

Laboratory testing of extravascular body fluids in Croatia: a survey of the Working group for extravascular body fluids of the Croatian Society of Medical Biochemistry and Laboratory Medicine.

Science.gov (United States)

Kopcinovic, Lara Milevoj; Vogrinc, Zeljka; Kocijan, Irena; Culej, Jelena; Aralica, Merica; Jokic, Anja; Antoncic, Dragana; Bozovic, Marija

2016-10-15

We hypothesized that extravascular body fluid (EBF) analysis in Croatia is not harmonized and aimed to investigate preanalytical, analytical and postanalytical procedures used in EBF analysis in order to identify key aspects that should be addressed in future harmonization attempts. An anonymous online survey created to explore laboratory testing of EBF was sent to secondary, tertiary and private health care Medical Biochemistry Laboratories (MBLs) in Croatia. Statements were designed to address preanalytical, analytical and postanalytical procedures of cerebrospinal, pleural, peritoneal (ascites), pericardial, seminal, synovial, amniotic fluid and sweat. Participants were asked to declare the strength of agreement with proposed statements using a Likert scale. Mean scores for corresponding separate statements divided according to health care setting were calculated and compared. The survey response rate was 0.64 (58 / 90). None of the participating private MBLs declared to analyse EBF. We report a mean score of 3.45 obtained for all statements evaluated. Deviations from desirable procedures were demonstrated in all EBF testing phases. Minor differences in procedures used for EBF analysis comparing secondary and tertiary health care MBLs were found. The lowest scores were obtained for statements regarding quality control procedures in EBF analysis, participation in proficiency testing programmes and provision of interpretative comments on EBF's test reports. Although good laboratory EBF practice is present in Croatia, procedures for EBF analysis should be further harmonized to improve the quality of EBF testing and patient safety.

Red blood cell (RBC) membrane proteomics--Part I: Proteomics and RBC physiology.

Science.gov (United States)

Pasini, Erica M; Lutz, Hans U; Mann, Matthias; Thomas, Alan W

2010-01-03

Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of nucleus and organelles in mammalian species other than camelids, and constantly in motion in the blood stream, red blood cells (RBCs) are the sole mammalian oxygen transporter. The fact that mature mammalian RBCs have no internal membrane-bound organelles, somewhat simplifies proteomics analysis of the plasma membrane and the fact that it has no nucleus disqualifies microarray based methods. Proteomics has the potential to provide a better understanding of this critical interface, and thereby assist in identifying new approaches to diseases. (c) 2009 Elsevier B.V. All rights reserved.

Proteomic Analysis of Chinese Hamster Ovary Cells

DEFF Research Database (Denmark)

Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama

2012-01-01

To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimens......To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis...

Modeling meniscus rise in capillary tubes using fluid in rigid-body motion approach

Science.gov (United States)

Hamdan, Mohammad O.; Abu-Nabah, Bassam A.

2018-04-01

In this study, a new term representing net flux rate of linear momentum is introduced to Lucas-Washburn equation. Following a fluid in rigid-body motion in modeling the meniscus rise in vertical capillary tubes transforms the nonlinear Lucas-Washburn equation to a linear mass-spring-damper system. The linear nature of mass-spring-damper system with constant coefficients offers a nondimensional analytical solution where meniscus dynamics are dictated by two parameters, namely the system damping ratio and its natural frequency. This connects the numerous fluid-surface interaction physical and geometrical properties to rather two nondimensional parameters, which capture the underlying physics of meniscus dynamics in three distinct cases, namely overdamped, critically damped, and underdamped systems. Based on experimental data available in the literature and the understanding meniscus dynamics, the proposed model brings a new approach of understanding the system initial conditions. Accordingly, a closed form relation is produced for the imbibition velocity, which equals half of the Bosanquet velocity divided by the damping ratio. The proposed general analytical model is ideal for overdamped and critically damped systems. While for underdamped systems, the solution shows fair agreement with experimental measurements once the effective viscosity is determined. Moreover, the presented model shows meniscus oscillations around equilibrium height occur if the damping ratio is less than one.

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

Science.gov (United States)

Omenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Overall, Christopher M; Deutsch, Eric W

2017-12-01

The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

In-vitro evaluation of corrosion resistance of nitrogen ion implanted titanium simulated body fluid

International Nuclear Information System (INIS)

Subbaiyan, M.; Sundararajian, T.; Rajeswari, S.; Kamachi Mudali, U.; Nair, K.G.M.; Thampi, N.S.

1997-01-01

Titanium and its alloy Ti6Al4V enjoy widespread use in various biomedical applications because of favourable local tissue response, higher corrosion resistance and fatigue strength than the stainless steels and cobalt-chromium alloy previously used. The study reported in this paper aims to optimize the conditions of nitrogen ion implantation on commercially pure titanium and to correlate the implantation parameters to the corrosion resistance. X-ray photoelectron spectroscopy was used to analyse surface concentration and the implantation processes. An improvement in the electrochemical behaviour of the passive film was shown to occur with nitrogen ion implantation on titanium, in simulated body fluids. (UK)

Accurate fluid force measurement based on control surface integration

Science.gov (United States)

Lentink, David

2018-01-01

Nonintrusive 3D fluid force measurements are still challenging to conduct accurately for freely moving animals, vehicles, and deforming objects. Two techniques, 3D particle image velocimetry (PIV) and a new technique, the aerodynamic force platform (AFP), address this. Both rely on the control volume integral for momentum; whereas PIV requires numerical integration of flow fields, the AFP performs the integration mechanically based on rigid walls that form the control surface. The accuracy of both PIV and AFP measurements based on the control surface integration is thought to hinge on determining the unsteady body force associated with the acceleration of the volume of displaced fluid. Here, I introduce a set of non-dimensional error ratios to show which fluid and body parameters make the error negligible. The unsteady body force is insignificant in all conditions where the average density of the body is much greater than the density of the fluid, e.g., in gas. Whenever a strongly deforming body experiences significant buoyancy and acceleration, the error is significant. Remarkably, this error can be entirely corrected for with an exact factor provided that the body has a sufficiently homogenous density or acceleration distribution, which is common in liquids. The correction factor for omitting the unsteady body force, {{{ {ρ f}} {1 - {ρ f} ( {{ρ b}+{ρ f}} )}.{( {{{{ρ }}b}+{ρ f}} )}}} , depends only on the fluid, {ρ f}, and body, {{ρ }}b, density. Whereas these straightforward solutions work even at the liquid-gas interface in a significant number of cases, they do not work for generalized bodies undergoing buoyancy in combination with appreciable body density inhomogeneity, volume change (PIV), or volume rate-of-change (PIV and AFP). In these less common cases, the 3D body shape needs to be measured and resolved in time and space to estimate the unsteady body force. The analysis shows that accounting for the unsteady body force is straightforward to non

Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks (Gasterosteus aculeatus).

Science.gov (United States)

Kültz, Dietmar; Li, Johnathon; Zhang, Xuezhen; Villarreal, Fernando; Pham, Tuan; Paguio, Darlene

2015-12-01

Molecular phenotypes that distinguish resident marine (Bodega Harbor) from landlocked freshwater (FW, Lake Solano) three-spined sticklebacks were revealed by label-free quantitative proteomics. Secreted plasma proteins involved in lipid transport, blood coagulation, proteolysis, plasminogen-activating cascades, extracellular stimulus responses, and immunity are most abundant in this species. Globulins and albumins are much less abundant than in mammalian plasma. Unbiased quantitative proteome profiling identified 45 highly population-specific plasma proteins. Population-specific abundance differences were validated by targeted proteomics based on data-independent acquisition. Gene ontology enrichment analyses and known functions of population-specific plasma proteins indicate enrichment of processes controlling cell adhesion, tissue remodeling, proteolytic processing, and defense signaling in marine sticklebacks. Moreover, fetuin B and leukocyte cell derived chemotaxin 2 are much more abundant in marine fish. These proteins promote bone morphogenesis and likely contribute to population-specific body armor differences. Plasma proteins enriched in FW fish promote translation, heme biosynthesis, and lipid transport, suggesting a greater presence of plasma microparticles. Many prominent population-specific plasma proteins (e.g. apoptosis-associated speck-like protein containing a CARD) lack any homolog of known function or adequate functional characterization. Their functional characterization and the identification of population-specific environmental contexts and selective pressures that cause plasma proteome diversification are future directions emerging from this study. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unraveling incompatibility between wheat and the fungal pathogen Zymoseptoria tritici through apoplastic proteomics.

Science.gov (United States)

Yang, Fen; Li, Wanshun; Derbyshire, Mark; Larsen, Martin R; Rudd, Jason J; Palmisano, Giuseppe

2015-05-08

Hemibiotrophic fungal pathogen Zymoseptoria tritici causes severe foliar disease in wheat. However, current knowledge of molecular mechanisms involved in plant resistance to Z. tritici and Z. tritici virulence factors is far from being complete. The present work investigated the proteome of leaf apoplastic fluid with emphasis on both host wheat and Z. tritici during the compatible and incompatible interactions. The proteomics analysis revealed rapid host responses to the biotrophic growth, including enhanced carbohydrate metabolism, apoplastic defenses and stress, and cell wall reinforcement, might contribute to resistance. Compatibility between the host and the pathogen was associated with inactivated plant apoplastic responses as well as fungal defenses to oxidative stress and perturbation of plant cell wall during the initial biotrophic stage, followed by the strong induction of plant defenses during the necrotrophic stage. To study the role of anti-oxidative stress in Z. tritici pathogenicity in depth, a YAP1 transcription factor regulating antioxidant expression was deleted and showed the contribution to anti-oxidative stress in Z. tritici, but was not required for pathogenicity. This result suggests the functional redundancy of antioxidants in the fungus. The data demonstrate that incompatibility is probably resulted from the proteome-level activation of host apoplastic defenses as well as fungal incapability to adapt to stress and interfere with host cell at the biotrophic stage of the interaction.

Analysis of 3-MCPD- and 3-MCPD dipalmitate-induced proteomic changes in rat liver.

Science.gov (United States)

Braeuning, Albert; Sawada, Stefanie; Oberemm, Axel; Lampen, Alfonso

2015-12-01

3-Monochloropropane-1,2-diol (3-MCPD) and 3-MCPD fatty acid esters are process contaminants in foodstuff which are generated during thermal treatment. Long-term exposure to 3-MCPD or 3-MCPD esters causes toxicity especially in kidney and testis. 3-MCPD esters are efficiently hydrolyzed in the gastrointestinal tract, suggesting that their toxicity is mediated by free 3-MCPD. Combined exposure to free 3-MCPD and 3-MCPD released from 3-MCPD esters might lead to dietary consumption above the tolerable daily intake of 2 μg/kg body weight/day. Suspected mechanisms of 3-MCPD toxicity include the inhibition of glycolysis and oxidative stress. Here, a comparative proteomic approach was followed to analyze the effects of 3-MCPD or 3-MCPD dipalmitate in livers from rats exposed to 10 mg/kg body weight 3-MCPD, an equimolar dose of 3-MCPD dipalmitate, or a 4-fold lower dose of the ester during a 28-day repeated-dose feeding study. Early cellular changes were monitored in the absence of overt toxicity. A comprehensive view of 3-MCPD- or 3-MCPD dipalmitate-triggered proteomic changes in rat liver links to previously proposed mechanisms of toxicity and substantially extends our knowledge on molecular hepatic effects of 3-MCPD. Organ-independent marker proteins altered upon 3-MCPD exposure, for example DJ-1/PARK7, were identified by comparison of the proteomic patterns of kidney, testis and liver. Copyright © 2015 Elsevier Ltd. All rights reserved.

Proteomic approaches in brain research and neuropharmacology.

Science.gov (United States)

Vercauteren, Freya G G; Bergeron, John J M; Vandesande, Frans; Arckens, Lut; Quirion, Rémi

2004-10-01

Numerous applications of genomic technologies have enabled the assembly of unprecedented inventories of genes, expressed in cells under specific physiological and pathophysiological conditions. Complementing the valuable information generated through functional genomics with the integrative knowledge of protein expression and function should enable the development of more efficient diagnostic tools and therapeutic agents. Proteomic analyses are particularly suitable to elucidate posttranslational modifications, expression levels and protein-protein interactions of thousands of proteins at a time. In this review, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) investigations of brain tissues in neurodegenerative diseases such as Alzheimer's disease, Down syndrome and schizophrenia, and the construction of 2D-PAGE proteome maps of the brain are discussed. The role of the Human Proteome Organization (HUPO) as an international coordinating organization for proteomic efforts, as well as challenges for proteomic technologies and data analysis are also addressed. It is expected that the use of proteomic strategies will have significant impact in neuropharmacology over the coming decade.

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznan, Poland

Czech Academy of Sciences Publication Activity Database

Gadher, S. J.; Marczak, L.; Luczak, M.; Stobiecki, M.; Widlak, P.; Kovářová, Hana

2016-01-01

Roč. 13, č. 1 (2016), s. 5-7 ISSN 1478-9450. [Central and Eastern European Proteomic Conference (CEEPC) /9./. Poznaň, 15.06.2015-18.06.2015] Institutional support: RVO:67985904 Keywords : Central and Eastern Proteomic Conference * proteomics * mass spectrometry imaging Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.849, year: 2016

Proteomic Biomarker Discovery in 1000 Human Plasma Samples with Mass Spectrometry.

Science.gov (United States)

Cominetti, Ornella; Núñez Galindo, Antonio; Corthésy, John; Oller Moreno, Sergio; Irincheeva, Irina; Valsesia, Armand; Astrup, Arne; Saris, Wim H M; Hager, Jörg; Kussmann, Martin; Dayon, Loïc

2016-02-05

The overall impact of proteomics on clinical research and its translation has lagged behind expectations. One recognized caveat is the limited size (subject numbers) of (pre)clinical studies performed at the discovery stage, the findings of which fail to be replicated in larger verification/validation trials. Compromised study designs and insufficient statistical power are consequences of the to-date still limited capacity of mass spectrometry (MS)-based workflows to handle large numbers of samples in a realistic time frame, while delivering comprehensive proteome coverages. We developed a highly automated proteomic biomarker discovery workflow. Herein, we have applied this approach to analyze 1000 plasma samples from the multicentered human dietary intervention study "DiOGenes". Study design, sample randomization, tracking, and logistics were the foundations of our large-scale study. We checked the quality of the MS data and provided descriptive statistics. The data set was interrogated for proteins with most stable expression levels in that set of plasma samples. We evaluated standard clinical variables that typically impact forthcoming results and assessed body mass index-associated and gender-specific proteins at two time points. We demonstrate that analyzing a large number of human plasma samples for biomarker discovery with MS using isobaric tagging is feasible, providing robust and consistent biological results.

Establishing Substantial Equivalence: Proteomics

Science.gov (United States)

Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

Proteome identification of the silkworm middle silk gland

Directory of Open Access Journals (Sweden)

Jian-ying Li

2016-03-01

Full Text Available To investigate the functional differentiation among the anterior (A, middle (M, and posterior (P regions of silkworm middle silk gland (MSG, their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014 [1] via the PRIDE partner repository (Vizcaino, 2013 [2] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015 [3]. Keywords: Bombyx mori, Middle silk gland, Silk protein synthesis, Shotgun proteomics, Label-free

A comprehensive proteomics study on platelet concentrates: Platelet proteome, storage time and Mirasol pathogen reduction technology.

Science.gov (United States)

Salunkhe, Vishal; De Cuyper, Iris M; Papadopoulos, Petros; van der Meer, Pieter F; Daal, Brunette B; Villa-Fajardo, María; de Korte, Dirk; van den Berg, Timo K; Gutiérrez, Laura

2018-03-19

Platelet concentrates (PCs) represent a blood transfusion product with a major concern for safety as their storage temperature (20-24°C) allows bacterial growth, and their maximum storage time period (less than a week) precludes complete microbiological testing. Pathogen inactivation technologies (PITs) provide an additional layer of safety to the blood transfusion products from known and unknown pathogens such as bacteria, viruses, and parasites. In this context, PITs, such as Mirasol Pathogen Reduction Technology (PRT), have been developed and are implemented in many countries. However, several studies have shown in vitro that Mirasol PRT induces a certain level of platelet shape change, hyperactivation, basal degranulation, and increased oxidative damage during storage. It has been suggested that Mirasol PRT might accelerate what has been described as the platelet storage lesion (PSL), but supportive molecular signatures have not been obtained. We aimed at dissecting the influence of both variables, that is, Mirasol PRT and storage time, at the proteome level. We present comprehensive proteomics data analysis of Control PCs and PCs treated with Mirasol PRT at storage days 1, 2, 6, and 8. Our workflow was set to perform proteomics analysis using a gel-free and label-free quantification (LFQ) approach. Semi-quantification was based on LFQ signal intensities of identified proteins using MaxQuant/Perseus software platform. Data are available via ProteomeXchange with identifier PXD008119. We identified marginal differences between Mirasol PRT and Control PCs during storage. However, those significant changes at the proteome level were specifically related to the functional aspects previously described to affect platelets upon Mirasol PRT. In addition, the effect of Mirasol PRT on the platelet proteome appeared not to be exclusively due to an accelerated or enhanced PSL. In summary, semi-quantitative proteomics allows to discern between proteome changes due to

Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005.

Directory of Open Access Journals (Sweden)

Sabine Matallana-Surget

Full Text Available The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionation procedures were used and combined with LC-MS/MS analysis, enabling the overall identification of 1306 proteins, which represents 21% coverage of the theoretical proteome. A total of 30 proteins were found to be significantly differentially regulated under light/dark growth transition. Interestingly, most of the proteins showing differential abundance were related to photosynthesis, the Calvin cycle and translation processes. A novel aspect and major achievement of this work is the successful improvement of the cyanobacterial proteome coverage using a 3D LC-MS/MS approach, based on an immobilized metal affinity chromatography, a suitable tool that enabled us to eliminate the most abundant protein, the allophycocyanin. We also demonstrated that cell growth follows a light/dark cycle in A. platensis. This preliminary proteomic study has highlighted new characteristics of the Arthrospira platensis proteome in terms of diurnal regulation.

Comparison of protein extraction methods suitable for proteomics ...

African Journals Online (AJOL)

Jane

2011-07-27

Jul 27, 2011 ... An efficient protein extraction method is a prerequisite for successful implementation of proteomics. ... research, it is noteworthy to discover a proteome ..... Proteomic analysis of rice (Oryza sativa) seeds during germination.

Evaluation of single and stack membraneless enzymatic fuel cells based on ethanol in simulated body fluids.

Science.gov (United States)

Galindo-de-la-Rosa, J; Arjona, N; Moreno-Zuria, A; Ortiz-Ortega, E; Guerra-Balcázar, M; Ledesma-García, J; Arriaga, L G

2017-06-15

The purpose of this work is to evaluate single and double-cell membraneless microfluidic fuel cells (MMFCs) that operate in the presence of simulated body fluids SBF, human serum and blood enriched with ethanol as fuels. The study was performed using the alcohol dehydrogenase enzyme immobilised by covalent binding through an array composed of carbon Toray paper as support and a layer of poly(methylene blue)/tetrabutylammonium bromide/Nafion and glutaraldehyde (3D bioanode electrode). The single MMFC was tested in a hybrid microfluidic fuel cell using Pt/C as the cathode. A cell voltage of 1.035V and power density of 3.154mWcm -2 were observed, which is the highest performance reported to date. The stability and durability were tested through chronoamperometry and polarisation/performance curves obtained at different days, which demonstrated a slow decrease in the power density on day 10 (14%) and day 20 (26%). Additionally, the cell was tested for ethanol oxidation in simulated body fluid (SBF) with ionic composition similar to human blood plasma. Those tests resulted in 0.93V of cell voltage and a power density close to 1.237mWcm -2 . The double cell MMFC (Stack) was tested using serum and human blood enriched with ethanol. The stack operated with blood in a serial connection showed an excellent cell performance (0.716mWcm -2 ), demonstrating the feasibility of employing human blood as energy source. Copyright © 2017 Elsevier B.V. All rights reserved.

Urine Proteomics in the Era of Mass Spectrometry

Directory of Open Access Journals (Sweden)

Ashley Beasley-Green

2016-11-01

Full Text Available With the technological advances of mass spectrometry (MS-based platforms, clinical proteomics is one of the most rapidly growing areas in biomedical research. Urine proteomics has become a popular subdiscipline of clinical proteomics because it is an ideal source for the discovery of noninvasive disease biomarkers. The urine proteome offers a comprehensive view of the local and systemic physiology since the proteome is primarily composed of proteins/peptides from the kidneys and plasma. The emergence of MS-based proteomic platforms as prominent bioanalytical tools in clinical applications has enhanced the identification of protein-based urinary biomarkers. This review highlights the characteristics of urine that make it an attractive biofluid for biomarker discovery and the impact of MS-based technologies on the clinical assessment of urinary protein biomarkers.

Proteomics of Plant Pathogenic Fungi

Directory of Open Access Journals (Sweden)

Raquel González-Fernández

2010-01-01

Full Text Available Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.

'Gate effect' in templated polyacrylamide membranes influences the electrotransport of proteins and finds applications in proteome analysis.

Science.gov (United States)

Bossi, Alessandra; Andreoli, Matteo; Bonini, Francesca; Piletsky, Sergey

2007-09-01

Templating is an effective way for the structural modifications of a material and hence for altering its functional properties. Here protein imprinting was exploited to alter polymeric polyacrylamide (PAA) membranes. The sieving properties and selection abilities of the material formed were evaluated by studying the electrically driven transport of various proteins across templated PAA membranes. The sieving properties correlated with the templating process and depended on the quantity of template used during the polymerisation. For 1 mg/mL protein-templated membranes a 'gate effect' was shown, which induced a preferential migration of the template and of similar-size proteins. Such template preferential electrotransport was exploited for the selective removal of certain proteins in biological fluids prior to proteome analysis (depletion of albumin from human serum); the efficiency of the removal was demonstrated by analysing the serum proteome by two-dimensional electrophoresis experiments.

The Redox Proteome*

Science.gov (United States)

Go, Young-Mi; Jones, Dean P.

2013-01-01

The redox proteome consists of reversible and irreversible covalent modifications that link redox metabolism to biologic structure and function. These modifications, especially of Cys, function at the molecular level in protein folding and maturation, catalytic activity, signaling, and macromolecular interactions and at the macroscopic level in control of secretion and cell shape. Interaction of the redox proteome with redox-active chemicals is central to macromolecular structure, regulation, and signaling during the life cycle and has a central role in the tolerance and adaptability to diet and environmental challenges. PMID:23861437

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznań, Poland.

Science.gov (United States)

Gadher, Suresh Jivan; Marczak, Łukasz; Łuczak, Magdalena; Stobiecki, Maciej; Widlak, Piotr; Kovarova, Hana

2016-01-01

Every year since 2007, the Central and Eastern European Proteomic Conference (CEEPC) has excelled in representing state-of-the-art proteomics in and around Central and Eastern Europe, and linking it to international institutions worldwide. Its mission remains to contribute to all approaches of proteomics including traditional and often-revisited methodologies as well as the latest technological achievements in clinical, quantitative and structural proteomics with a view to systems biology of a variety of processes. The 9th CEEPC was held from June 15th to 18th, 2015, at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznań, Poland. The scientific program stimulated exchange of proteomic knowledge whilst the spectacular venue of the conference allowed participants to enjoy the cobblestoned historical city of Poznań.

Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation.

Science.gov (United States)

Woo, Jongmin; Han, Dohyun; Wang, Joseph Injae; Park, Joonho; Kim, Hyunsoo; Kim, Youngsoo

2017-09-01

The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this technique to an activated microglia cell system to examine changes in the intracellular and extracellular proteomes. Microglia become activated when their homeostatic microenvironment is disrupted. There are varying degrees of microglial activation, and we chose to focus on the proinflammatory reactive state that is induced by exposure to such stimuli as lipopolysaccharide (LPS) and interferon-gamma (IFN-γ). Using an improved shotgun proteomics approach, we identified 5497 proteins in the whole-cell proteome and 4938 proteins in the secretome that were associated with the activation of BV2 mouse microglia by LPS or IFN-γ. Of the differentially expressed proteins in stimulated microglia, we classified pathways that were related to immune-inflammatory responses and metabolism. Our label-free parallel reaction monitoring (PRM) approach made it possible to comprehensively measure the hyper-multiplex quantitative value of each protein by high-resolution mass spectrometry. Over 450 peptides that corresponded to pathway proteins and direct or indirect interactors via the STRING database were quantified by label-free PRM in a single run. Moreover, we performed a longitudinal quantification of secreted proteins during microglial activation, in which neurotoxic molecules that mediate neuronal cell loss in the brain are released. These data suggest that latent pathways that are associated with neurodegenerative diseases can be discovered by constructing and analyzing a pathway network model of proteins. Furthermore, this systematic quantification platform has tremendous potential for applications in large-scale targeted analyses. The proteomics data for

Application of proteomics to ecology and population biology.

Science.gov (United States)

Karr, T L

2008-02-01

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

Virtual Labs in proteomics: new E-learning tools.

Science.gov (United States)

Ray, Sandipan; Koshy, Nicole Rachel; Reddy, Panga Jaipal; Srivastava, Sanjeeva

2012-05-17

Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis of mass spectrometry data in proteomics

DEFF Research Database (Denmark)

Matthiesen, Rune; Jensen, Ole N

2008-01-01

The systematic study of proteins and protein networks, that is, proteomics, calls for qualitative and quantitative analysis of proteins and peptides. Mass spectrometry (MS) is a key analytical technology in current proteomics and modern mass spectrometers generate large amounts of high-quality data...... that in turn allow protein identification, annotation of secondary modifications, and determination of the absolute or relative abundance of individual proteins. Advances in mass spectrometry-driven proteomics rely on robust bioinformatics tools that enable large-scale data analysis. This chapter describes...... some of the basic concepts and current approaches to the analysis of MS and MS/MS data in proteomics....

Overlap of proteomics biomarkers between women with pre-eclampsia and PCOS: a systematic review and biomarker database integration.

Science.gov (United States)

Khan, Gulafshana Hafeez; Galazis, Nicolas; Docheva, Nikolina; Layfield, Robert; Atiomo, William

2015-01-01

Do any proteomic biomarkers previously identified for pre-eclampsia (PE) overlap with those identified in women with polycystic ovary syndrome (PCOS). Five previously identified proteomic biomarkers were found to be common in women with PE and PCOS when compared with controls. Various studies have indicated an association between PCOS and PE; however, the pathophysiological mechanisms supporting this association are not known. A systematic review and update of our PCOS proteomic biomarker database was performed, along with a parallel review of PE biomarkers. The study included papers from 1980 to December 2013. In all the studies analysed, there were a total of 1423 patients and controls. The number of proteomic biomarkers that were catalogued for PE was 192. Five proteomic biomarkers were shown to be differentially expressed in women with PE and PCOS when compared with controls: transferrin, fibrinogen α, β and γ chain variants, kininogen-1, annexin 2 and peroxiredoxin 2. In PE, the biomarkers were identified in serum, plasma and placenta and in PCOS, the biomarkers were identified in serum, follicular fluid, and ovarian and omental biopsies. The techniques employed to detect proteomics have limited ability in identifying proteins that are of low abundance, some of which may have a diagnostic potential. The sample sizes and number of biomarkers identified from these studies do not exclude the risk of false positives, a limitation of all biomarker studies. The biomarkers common to PE and PCOS were identified from proteomic analyses of different tissues. This data amalgamation of the proteomic studies in PE and in PCOS, for the first time, discovered a panel of five biomarkers for PE which are common to women with PCOS, including transferrin, fibrinogen α, β and γ chain variants, kininogen-1, annexin 2 and peroxiredoxin 2. If validated, these biomarkers could provide a useful framework for the knowledge infrastructure in this area. To accomplish this goal, a

Crystallization from a milk-based revised simulated body fluid

International Nuclear Information System (INIS)

Dorozhkin, Sergey V; Dorozhkina, Elena I

2007-01-01

A milk-based revised simulated body fluid (milk-rSBF) was prepared by a conventional route but instead of deionized water, all necessary chemicals were dissolved in whole cow's milk (3.2% fat). In order to accelerate crystallization and increase the amount of precipitates, the influence of milk was studied from condensed solutions equal to four times the ionic concentrations of rSBF (4rSBF). The experiments were performed under physiological conditions (solution pH = 7.35-7.40, temperature 37.0 ± 0.2 deg. C, duration 7 days) in a constant-composition double-diffusion device, which provided a slow crystallization under strictly controlled conditions. Similar experiments with 4rSBF but dissolved in deionized water were used as a control. An extra set of experiments with 4rSBF dissolved in deionized water but with an addition of 40 g l -1 bovine serum albumin (BSA) was used as another control. The influence of milk appeared to be similar to that of dissolved BSA: some components of milk (presumably albumins and proteins) were found to co-precipitate with calcium phosphates, which had a strong negative influence on both the crystallinity and the crystal sizes of the precipitates. In addition, both milk and BSA strongly inhibited crystallization of calcium phosphates: the precipitates turned out to contain a minor amount of calcium phosphates and a substantial amount of organic phase

Simultaneous determination of cucurbitacin B, E, I and E-glucoside in plant material and body fluids by HPLC-MS.

Science.gov (United States)

Bajcsik, Nicole; Pfab, Rudolf; Pietsch, Jörg

2017-05-01

A selective and sensitive analytical method for the simultaneous determination of cucurbitacin B, E, I and E-glucoside in plant material and body fluids by HPLC-MS was developed. After liquid-liquid extraction with dichlormethane, separation was achieved on a Phenomenex Luna Pentafluorophenyl Column (150mm×2mm, 5μm) using acetonitrile-water (90:10, v/v) as mobile phase system. Detection was performed using a 3200 Q Trap mass spectrometer (AB Sciex). For analysis Q1 Scans with negative ionisation were chosen. The method was validated for serum as the matrix of choice. Limits of detection are in the picogram range, limits of quantification are between 0.05 and 0.42ng/mL, recoveries are above 50%. The assay was linear in the calibration range from 1.0 to 50ng/mL for cucurbitacin E and from 0.10 to 50ng/mL for the cucurbitacins B, I and E-glucoside. The applicability of the method was demonstrated by the determination of cucurbitacins in zucchini plant material and body fluids from intoxication cases. Copyright © 2017 Elsevier B.V. All rights reserved.

Flehmen response in bull: role of vaginal mucus and other body fluids of bovine with special reference to estrus.

Science.gov (United States)

Sankar, R; Archunan, G

2004-07-30

The present investigation was carried out with a view to evaluate the frequency of Flehmen behaviour in bull in response to body fluids of cows in various stages of the estrous cycle, in the context of estrus detection. The study was performed on free moving bulls under natural conditions. Samples of vaginal mucus, saliva, faeces and milk of pro-estrus, estrus and di-estrus stages collected from donor cows were rubbed individually onto the genital regions of non-estrus animals (dummy cows) and the bulls were observed for 30 min for assessment of Flehmen behaviour. The duration of Flehmen behaviour shown by bulls was maximum towards the dummy cows receiving estrus sample. Such Flehmen behaviour, however, did not occur in bulls in response to the cows receiving samples of other stages. The statistical significance was higher (P mucus may act as an additional/secondary source along with urine in eliciting copulatary behaviour and executing coitus in bulls during estrus. The results further suggest that in addition to vaginal mucus, other body fluids like saliva, faeces and milk have estrus-related odours and are probably involved in bovine bio-communication.

Intraoperative Fluids and Fluid Management for Ambulatory Dental Sedation and General Anesthesia.

Science.gov (United States)

Saraghi, Mana

2015-01-01

Intravenous fluids are administered in virtually every parenteral sedation and general anesthetic. The purpose of this article is to review the physiology of body-water distribution and fluid dynamics at the vascular endothelium, evaluation of fluid status, calculation of fluid requirements, and the clinical rationale for the use of various crystalloid and colloid solutions. In the setting of elective dental outpatient procedures with minor blood loss, isotonic balanced crystalloid solutions are the fluids of choice. Colloids, on the other hand, have no use in outpatient sedation or general anesthesia for dental or minor oral surgery procedures but may have several desirable properties in long and invasive maxillofacial surgical procedures where advanced hemodynamic monitoring may assess the adequacy of intravascular volume.

Numerical study of magnetohydrodynamic pulsatile flow of Sutterby fluid through an inclined overlapping arterial stenosis in the presence of periodic body acceleration

Science.gov (United States)

Abbas, Z.; Shabbir, M. S.; Ali, N.

2018-06-01

In the present theoretical investigation, we have numerically simulated the problem of blood flow through an overlapping stenosed arterial blood vessel under the action of externally applied body acceleration and the periodic pressure gradient. The rheology of blood is characterized by the Sutterby fluid model. The blood is considered as an electrically conducting fluid. A steady uniform magnetic field is applied in the radial direction of the blood vessel. The governing nonlinear partial differential equations of the present flow together with prescribed boundary conditions are solved by employing explicit finite difference scheme. Results concerning the temporal distribution of velocity, flow rate, shear stress and resistance to the flow are displayed through graphs. The effects of various emerging parameters on the flow variables are analyzed and discussed in detail. The analysis reveals that the applied magnetic field and periodic body acceleration have considerable effects on the flow field.

Whole-body fluid distribution in humans during dehydration and recovery, before and after humid-heat acclimation induced using controlled hyperthermia.

Science.gov (United States)

Patterson, M J; Stocks, J M; Taylor, N A S

2014-04-01

This experiment was designed to test the hypothesis that the plasma volume is not selectively defended during exercise- and heat-induced dehydration following humid-heat acclimation. Eight physically active males were heat acclimated (39.8 °C, relative humidity 59.2%) using 17 days of controlled hyperthermia (core temperature: 38.5 °C). Inter-compartmental fluid losses and movements were tracked (radioisotopes and Evans blue dye) during progressive dehydration (cycling) in these same conditions and also during a resting recovery without fluid replacement (28 °C), before (day 1), during (day 8) and after heat acclimation (day 22). On days 8 and 22, there were significant increases in total body water, interstitial fluid and plasma volume (P 0.05). The baseline plasma volume remained expanded throughout: 43.4 [±2.6 (day 1)], 49.1 [±2.4 (day 8); P recovery, plasma volume restoration commenced, with the intracellular fluid contribution becoming more pronounced as acclimation progressed. It is concluded that the plasma volume was not defended more vigorously following humid-heat acclimation. Indeed, a greater fluid loss may well underlie the mechanisms for enhancing plasma volume recovery when heat acclimation is induced using the controlled-hyperthermia technique. © 2013 Scandinavian Physiological Society. Published by John Wiley & Sons Ltd.

Simulation of the deformation of a fluid domain in motion in another fluid by the boundary element method

International Nuclear Information System (INIS)

Rocchi-Tavares, Miriam

1992-01-01

The objective of this research thesis is to model the sustentation (or aerodynamic levitation) of a drop by a fluid flowing through a porous plate. More precisely, the author developed a general calculation tool to solve the Stokes problem by using the boundary element method. The author reports the calculation of stresses at the surface of a solid body moving in an infinite medium, in order to validate the calculation tool before its extension to more complex problems. Then, the model is developed to describe the deformation of a fluid mass moving in another fluid. The surrounding environment is either infinite or limited by a plane wall which can be impervious or crossed by an ambient fluid. Then, the author addresses the study of the evolution of the surface of a drop moving in an infinite medium, analyses the behaviour of a fluid mass at the vicinity of a plane, infinite and impervious wall. The last part addresses the sustentation of a deformable fluid body above a porous plane wall crossed by another fluid [fr

Silica enhanced formation of hydroxyapatite nanocrystals in simulated body fluid (SBF) at 37 deg. C

Energy Technology Data Exchange (ETDEWEB)

Sadjadi, M.S., E-mail: m.s.sadjad@gmail.com [Department of Chemistry, Sciences and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Ebrahimi, H.R. [Department of Chemistry, Sciences and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Meskinfam, M. [Department of Chemistry, Tonekabon Branch, Islamic Azad University, Tonekabon (Iran, Islamic Republic of); Zare, K. [Department of Chemistry, University of Shahid Beheshti, Eveen Tehran (Iran, Islamic Republic of)

2011-10-17

Highlights: {yields} We report on fast formation of hexagonal nanocrystals of calcium hydroxyapatite (HA) in silica-containing simulated body fluid solution at 37 deg. C. {yields} Bioactivity and biodegradability of TCP precursor have been confirmed by the dissolution of TCP and formation of a bone like layer of new HA nanoparticles outside of the precursor after 24 h soaking in SBF solution. {yields} Successive nucleation and formation of tiny hexagonal HA nanoplates and nanorods have been confirmed by TEM results after 24 h soaking of TCP in silica-containing BSF solution. - Abstract: The chemical modification of implant (prosthesis) surfaces is being investigated worldwide for improving the fixation of orthopaedic and dental implants. The main goal in this surface modification approach is to achieve a faster bone growth and chemical bonding of the implant to the newly generated and/or remodeled bone. In this work, we report fast formation of hexagonal nanocrystals of calcium hydroxyapatite (HA) in simulated body fluid (SBF, inorganic components of human blood plasma) solutions at 37 deg. C, using calcium phosphate (TCP) and sodium silicate as precursors. Characterization and chemical analysis of the synthesized powders were performed by Fourier transform infrared spectroscopy (FT-IR), X-ray powder diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The results indicated enhanced nucleation and formation of bone like layer of HA nanocrystals at the surface of TCP nanoparticles and occurrence of HA nanocrystals during 24 h soaking of TCP in SBF solution containing silica ions. The average size of a nanoparticle, using Scherrer formula, was found to be 18.2 nm.

Silica enhanced formation of hydroxyapatite nanocrystals in simulated body fluid (SBF) at 37 deg. C

International Nuclear Information System (INIS)

Sadjadi, M.S.; Ebrahimi, H.R.; Meskinfam, M.; Zare, K.

2011-01-01

Highlights: → We report on fast formation of hexagonal nanocrystals of calcium hydroxyapatite (HA) in silica-containing simulated body fluid solution at 37 deg. C. → Bioactivity and biodegradability of TCP precursor have been confirmed by the dissolution of TCP and formation of a bone like layer of new HA nanoparticles outside of the precursor after 24 h soaking in SBF solution. → Successive nucleation and formation of tiny hexagonal HA nanoplates and nanorods have been confirmed by TEM results after 24 h soaking of TCP in silica-containing BSF solution. - Abstract: The chemical modification of implant (prosthesis) surfaces is being investigated worldwide for improving the fixation of orthopaedic and dental implants. The main goal in this surface modification approach is to achieve a faster bone growth and chemical bonding of the implant to the newly generated and/or remodeled bone. In this work, we report fast formation of hexagonal nanocrystals of calcium hydroxyapatite (HA) in simulated body fluid (SBF, inorganic components of human blood plasma) solutions at 37 deg. C, using calcium phosphate (TCP) and sodium silicate as precursors. Characterization and chemical analysis of the synthesized powders were performed by Fourier transform infrared spectroscopy (FT-IR), X-ray powder diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The results indicated enhanced nucleation and formation of bone like layer of HA nanocrystals at the surface of TCP nanoparticles and occurrence of HA nanocrystals during 24 h soaking of TCP in SBF solution containing silica ions. The average size of a nanoparticle, using Scherrer formula, was found to be 18.2 nm.

Knowledge Translation: Moving Proteomics Science to Innovation in Society.

Science.gov (United States)

Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

2016-06-01

Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community.

Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas.

Science.gov (United States)

Timmins-Schiffman, Emma; Coffey, William D; Hua, Wilber; Nunn, Brook L; Dickinson, Gary H; Roberts, Steven B

2014-11-03

Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end-of-century open ocean pH reductions. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different p CO2 levels for four weeks: 400 μatm (pH 8.0), 800 μatm (pH 7.7), 1000 μatm (pH 7.6), or 2800 μatm (pH 7.3). At the end of the four week exposure period, oysters in all four p CO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated p CO2. Elevated p CO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with p CO2, with numerous processes significantly affected by mechanical stimulation at high versus low p CO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835). Oyster physiology is significantly altered by exposure to elevated p CO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of p CO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.

Comparison of local and imported osteosynthetic mandibular bone plates in terms of micro hardness in modified simulated body fluid at periodic intervals

International Nuclear Information System (INIS)

Anwar, R.; Kaleem, M.; Baig, AM.; Jamal, M.

2015-01-01

To determine the micro hardness of novel Pakistani manufactured osteosynthetic titanium bone mini plates (MPP) and imported osteosynthetic titanium bone mini plates (MPG) in body like conditions. Study Design: Descriptive study. Place and Duration of Study: This study was carried out at School of Chemical and Material Engineering, NUST from March to May 2013. Material and Methods: Microvicker hardness tester was used for assessment of micro hardness of two types of plates. The hardness was checked before conditioning and after conditioning at (six different places) on interval of 1, 7,14,21,28 and 40 days in modified simulated body fluid with ph 7.4 and temperature 37 degree C. Results: Result showed that hardness of MPG was higher than MPP and after conditioning in simulated body fluid at all time periods, hardness of both types of plates was increased. Conclusion: It can be concluded from this study that micro hardness of imported plates is more than local plates so recommendations should be sent to manufacturers of local industry of Pakistan to improve the hardness of local plates so that they can meet international standards. (author)

Milk bottom-up proteomics: method optimisation.

Directory of Open Access Journals (Sweden)

Delphine eVincent

2016-01-01

Full Text Available Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such as caseins and medium to low abundance whey proteins such as ß-lactoglobulin, lactoferrin, immunoglobulins, glycoproteins, peptide hormones and enzymes. A sample preparation method that enables high reproducibility and throughput is key in reliably identifying proteins present or proteins responding to conditions such as a diet, health or genetics. Using skim milk samples from Jersey and Holstein-Friesian cows, we compared three extraction procedures which have not previously been applied to samples of cows’ milk. Method A (urea involved a simple dilution of the milk in a urea-based buffer, method B (TCA/acetone involved a trichloroacetic acid (TCA/acetone precipitation and method C (methanol/chloroform involved a tri-phasic partition method in chloroform/methanol solution. Protein assays, SDS-PAGE profiling, and trypsin digestion followed by nanoHPLC-electrospray ionisation-tandem mass spectrometry (nLC-ESI-MS/MS analyses were performed to assess their efficiency. Replicates were used at each analytical step (extraction, digestion, injection to assess reproducibility. Mass spectrometry (MS data are available via ProteomeXchange with identifier PXD002529. Overall 186 unique accessions, major and minor proteins, were identified with a combination of methods. Method C (methanol/chloroform yielded the best resolved SDS-patterns and highest protein recovery rates, method A (urea yielded the greatest number of accessions, and, of the three procedures, method B (TCA/acetone was the least compatible of all with a wide range of downstream analytical procedures. Our results also highlighted breed differences between the proteins in milk of Jersey and Holstein-Friesian cows.

First systematic plant proteomics workshop in Botany Department, University of Delhi: transferring proteomics knowledge to next-generation researchers and students.

Science.gov (United States)

Deswal, Renu; Abat, Jasmeet Kaur; Sehrawat, Ankita; Gupta, Ravi; Kashyap, Prakriti; Sharma, Shruti; Sharma, Bhavana; Chaurasia, Satya Prakash; Chanu, Sougrakpam Yaiphabi; Masi, Antonio; Agrawal, Ganesh Kumar; Sarkar, Abhijit; Agrawal, Raj; Dunn, Michael J; Renaut, Jenny; Rakwal, Randeep

2014-07-01

International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to "organize workshops at national and international levels to train manpower and exchange information". This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26-30, 2013 titled - "1(st) Plant Proteomics Workshop / Training Program" under the umbrella of INPPO India-Nepal chapter. Selected 20 participants received on-hand training mainly on gel-based proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel-based and gel-free proteomics. Importance of gel-free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next-generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dietary cation and anion difference: Effects on milk production and body fluid distribution in lactating dairy goats under tropical conditions.

Science.gov (United States)

Nguyen, Thiet; Chaiyabutr, Narongsak; Chanpongsang, Somchai; Thammacharoen, Sumpun

2018-01-01

This study aimed to determine the effect of dietary cation and anion difference (DCAD) on milk production and body fluid distribution in lactating dairy goats. Ten dairy goats were selected and divided into two groups, five animals each. Animals received either control DCAD (control, 22.81 mEq/100 g dry matter (DM)) or high DCAD (DCAD, 39.08 mEq/100 g DM). The results indicated that rectal temperature (Tr), respiration rate, milk yield and compositions did not differ between groups. But the percentage change of Tr from the DCAD group was lower than the control group between 09.00 and 13.00 hours. DM intake tended to increase in the DCAD group. Dairy goats in the DCAD group drank more water, but urinary excretion and plasma antidiuretic hormone concentration remained unchanged. Apparent water balance was higher from the DCAD group over 24 h. There was no effect of DCAD on plasma and blood volumes, but tended to increase in extracellular fluid and thereby increased total body water. The present results indicate that animals supplemented with high DCAD increase their total body water and apparent water balance. These results have contributed to the process of adaptation for evaporative cooling and would be useful in slowing down the elevation in Tr. © 2017 Japanese Society of Animal Science.

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM analysis [v1; ref status: indexed, http://f1000r.es/2hj

Directory of Open Access Journals (Sweden)

Erin K. Hanson