A Summary of the Biological Basis of Frailty.

Science.gov (United States)

Fielding, Roger A

2015-01-01

Frailty has been defined as a geriatric syndrome that is characterized by a reduction in the physiological reserve required for an individual to respond to endogenous and exogenous stressors. Using a discrete definition of frailty that includes sedentariness, involuntary weight loss, fatigue, poor muscle strength, and slow gait speed, 'frailty' has been associated with increased disability, postsurgical complications, and increased mortality. Despite the strong associations between frailty and subsequent poor outcomes, limited attention to this common geriatric condition has been paid in clinical settings. A more fundamental basic understanding of the biological factors that contribute to the frailty phenotype has begun to emerge. Multiple underlying biological factors such as dysregulation of inflammatory processes, genomic instability, oxidative stress, mitochondrial dysfunction, and cellular senescence appear to contribute to the clinical presentation of frailty. This chapter summarizes the papers presented on the biological basis of frailty from the 83rd Nestlé Nutrition Institute Workshop on 'Frailty, Pathophysiology, Phenotype and Patient Care' held in Barcelona, Spain, in March 2014. © 2015 Nestec Ltd., Vevey/S. Karger AG, Basel.

Quality control of X-ray irradiator by biological markers

International Nuclear Information System (INIS)

Miura, Miwa; Lukmanul Hakkim, F.; Yoshida, Masahiro; Matsuda, Naoki; Morita, Naoko

2011-01-01

The exposure of animals or cultured cells to radiation is the essential and common step in experimental researches to elucidate biological effects of radiation. When an X-ray generator is used as a radiation source, physical parameters including dose, dose rate, and the energy spectrum of X-ray play crucial roles in biological outcome. Therefore, those parameters are the important points to be checked in quality control and to be carefully considered in advance to the irradiation to obtain the accurate and reproductive results. Here we measured radiation dose emitted from the X-ray irradiator for research purposes by using clonogenic survival of cultured mammalian cells as a biological marker in parallel with physical dosimetry. The results drawn from both methods exhibited good consistency in the dose distribution on the irradiation stage. Furthermore, the close relationship was observed between cell survival and the photon energy spectrum by using different filter components. These results suggest that biological dosimetry is applicable to quality control of X-ray irradiator in adjunct to physical dosimetry and that it possibly helps better understanding of the optimal irradiating condition by X-ray users in life-science field. (author)

Exploration of Disease Markers under Translational Medicine Model

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Rajagopal Krishnamoorthy

2015-06-01

Full Text Available Disease markers are defined as the biomarkers with specific characteristics during the general physical, pathological or therapeutic process, the detection of which can inform the progression of present biological process of organisms. However, the exploration of disease markers is complicated and difficult, and only a few markers can be used in clinical practice and there is no significant difference in the mortality of cancers before and after biomarker exploration. Translational medicine focuses on breaking the blockage between basic medicine and clinical practice. In addition, it also establishes an effective association between researchers engaged on basic scientific discovery and clinical physicians well informed of patients' requirements, and gives particular attentions on how to translate the basic molecular biological research to the most effective and appropriate methods for the diagnosis, treatment and prevention of diseases, hoping to translate basic research into the new therapeutic methods in clinic. Therefore, this study mainly summarized the exploration of disease markers under translational medicine model so as to provide a basis for the translation of basic research results into clinical application.

Physical Activity, Physical Performance, and Biological Markers of Health among Sedentary Older Latinos

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Gerardo Moreno

2014-01-01

Full Text Available Background. Physical activity is associated with better physical health, possibly by changing biological markers of health such as waist circumference and inflammation, but these relationships are unclear and even less understood among older Latinos—a group with high rates of sedentary lifestyle. Methods. Participants were 120 sedentary older Latino adults from senior centers. Community-partnered research methods were used to recruit participants. Inflammatory (C-reactive protein and metabolic markers of health (waist circumference, HDL-cholesterol, triglycerides, insulin, and glucose, physical activity (Yale physical activity survey, and physical performance (short physical performance NIA battery were measured at baseline and 6-month followup. Results. Eighty percent of the sample was female. In final adjusted cross-sectional models, better physical activity indices were associated with faster gait speed (P<0.05. In adjusted longitudinal analyses, change in self-reported physical activity level correlated inversely with change in CRP (β=-0.05; P=0.03 and change in waist circumference (β=-0.16; P=0.02. Biological markers of health did not mediate the relationship between physical activity and physical performance. Conclusion. In this community-partnered study, higher physical activity was associated with better physical performance in cross-sectional analyses. In longitudinal analysis, increased physical activity was associated with improvements in some metabolic and inflammatory markers of health.

Markers for nutrition studies: review of criteria for the evaluation of markers.

Science.gov (United States)

de Vries, Jan; Antoine, Jean-Michel; Burzykowski, Tomasz; Chiodini, Alessandro; Gibney, Mike; Kuhnle, Gunter; Méheust, Agnès; Pijls, Loek; Rowland, Ian

2013-10-01

Markers are important tools to assess the nutrition status and effects of nutrition interventions. There is currently insufficient consensus in nutrition sciences on how to evaluate markers, despite the need for properly evaluating them. To identify the criteria for the evaluation of markers related to nutrition, health and disease and to propose generic criteria for evaluation. The report on "Evaluation of Biomarker and Surrogate Endpoints in Chronic Disease" from the Institute of Medicine was the starting point for the literature search. Additionally, specific search strategies were developed for Pubmed. In nutrition, no set of criteria or systematic approach to evaluate markers is currently available. There is a reliance on the medical area where statistical methods have been developed to quantify the evaluation of markers. Even here, a systematic approach is lacking-markers are still evaluated on a case-by-case basis. The review of publications from the literature search resulted in a database with definitions, criteria for validity and the rationale behind the criteria. It was recognized that, in nutrition, a number of methodological aspects differ from medical research. The following criteria were identified as essential elements in the evaluation of markers: (1) the marker has a causal biological link with the endpoint, (2) there is a significant association between marker and endpoint in the target population, (3) marker changes consistently with the endpoint, e.g., in response to an intervention, and (4) change in the marker explains a substantial proportion of the change in the endpoint in response to the intervention.

Emotional management and biological markers of dietetic regimen in chronic kidney disease patients.

Science.gov (United States)

Lai, Carlo; Aceto, Paola; Luciani, Massimiliano; Fazzari, Erika; Cesari, Valerio; Luciano, Stella; Fortini, Antonio; Berloco, Desiderata; Canulla, Francesco; Bruzzese, Vincenzo; Lai, Silvia

2017-11-01

The aim of the study was to investigate the association between psychological characteristics and biological markers of adherence in chronic kidney disease patients receiving conservative therapy, hemodialysis, peritoneal dialysis (PD), or kidney transplantation. Seventy-nine adult patients were asked to complete the following questionnaires: Toronto Alexithymia scale, Snaith-Hamilton Pleasure Scale, and Short Form Health Survey. Biological markers of adherence to treatment were measured. Peritoneal dialysis patients showed a lower capacity to feel pleasure from sensorial experience (p = .011) and a higher values of phosphorus compared to the other patients' groups (p = .0001). The inability to communicate emotions was negatively correlated with hemoglobin levels (r = -(0).69; p = .001) and positively correlated with phosphorus values in the PD patients (r = .45; p = .050). Findings showed higher psychological impairments and a lower adherence to the treatment in PD patients and suggest the implication of emotional competence in adherence to treatment.

Biological basis of detoxication

National Research Council Canada - National Science Library

Caldwell, John; Jakoby, William B

1983-01-01

This volume considers that premise that most of the major patterns of biological conversion of foreign compounds are known and may have predictive value in assessing the biological course for novel compounds...

The prognostic value of biological markers in paediatric Hodgkin lymphoma.

Science.gov (United States)

Farruggia, Piero; Puccio, Giuseppe; Sala, Alessandra; Todesco, Alessandra; Buffardi, Salvatore; Garaventa, Alberto; Bottigliero, Gaetano; Bianchi, Maurizio; Zecca, Marco; Locatelli, Franco; Pession, Andrea; Pillon, Marta; Favre, Claudio; D'Amico, Salvatore; Provenzi, Massimo; Trizzino, Angela; Zanazzo, Giulio Andrea; Sau, Antonella; Santoro, Nicola; Murgia, Giulio; Casini, Tommaso; Mascarin, Maurizio; Burnelli, Roberta

2016-01-01

Many biological and inflammatory markers have been proposed as having a prognostic value at diagnosis of Hodgkin lymphoma (HL), but very few have been validated in paediatric patients. We explored the significance of these markers in a large population of 769 affected children. By using the database of patients enrolled in A.I.E.O.P. (Associazione Italiana di Emato-Oncologia Pediatrica) trial LH2004 for paediatric HL, we identified 769 consecutive patients treated with curative intent from 1st June 2004 to 1st April 2014 with ABVD (doxorubicin, bleomycin, vinblastine, and dacarbazine), or hybrid COPP/ABV (cyclophosphamide, vincristine, prednisone, procarbazine, doxorubicin, bleomycin and vinblastine) regimens. On multivariate analysis with categorical forms, the 5-year freedom from progression survival was significantly lower in patients with stage IV or elevated value of platelets, eosinophils and ferritin at diagnosis. Furthermore, stage IV and eosinophils seem to maintain their predictive value independently of interim (after IV cycles of chemotherapy) positron emission tomography. Using the combination of four simple markers such as stage IV and elevated levels of platelets, ferritin and eosinophils, it is possible to classify the patients into subgroups with very different outcomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Entendendo o papel de marcadores biológicos no câncer de pulmão Understanding the role of biological markers in lung cancer

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VERA LUIZA CAPELOZZI

2001-11-01

ógicos intermediários.Biological markers are cellular, structural and biochemical components that can define cellular as well as molecular changes in both normal and neoplastic cells. There are two types of biological markers: 1 intermediate markers that evaluate cellular and molecular alterations before malignancy occurs; and 2 diagnostic markers, present in association with malignancy. The identification and validation of biological markers for clinical use are performed in stages: ¨ initial identification in cell cultures of the tumor; ¨ testing of the marker in tissues obtained in biopsies of patients with an established diagnosis of the tumor; ¨ testing of biopsies of normal tissues and tissues with an inflammatory process; ¨ sputum, blood or urine tests for validation as a non-invasive test that can be used in high-risk populations. Sorologic and histopathologic biological markers are cellular, structural and biochemical components found in both normal and neoplastic cells that can be quantitatively assessed by biochemical, immunological and molecular methods in the body fluids or tissues, respectively, and may be associated with malignancies and, possibly, with the neoplastic organ. Biological markers are studied in diverse primary neoplasms. However, few of them proved to be clinically valuable. The role of biological markers in lung cancer patients remains unclear because only a small number of markers has been properly assessed. The aim of this paper is to understand the role of sorologic and histologic biological markers in the prognosis and survival of lung cancer patients based on our previous works. Furthermore, we present a future perspective of the early detection of lung cancer on the basis of the role of intermediate biological markers.

Oligothiophenes as Fluorescent Markers for Biological Applications

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Antonio Manetto

2012-01-01

Full Text Available This paper summarizes some of our results on the application of oligothiophenes as fluorescent markers for biological studies. The oligomers of thiophene, widely known for their semiconductor properties in organic electronics, are also fluorescent compounds characterized by chemical and optical stability, high absorbance and quantum yield. Their fluorescent emission can be easily modulated via organic synthesis by changing the number of thiophene rings and the nature of side-chains. This review shows how oligothiophenes can be derivatized with active groups such as phosphoramidite, N-hydroxysuccinimidyl and 4-sulfotetrafluorophenyl esters, isothiocyanate and azide by which the (biomolecules of interest can be covalently bound. This paper also describes how molecules such as oligonucleotides, proteins and even nanoparticles, tagged with oligothiophenes, can be used in experiments ranging from hybridization studies to imaging of fixed and living cells. Finally, a few multilabeling experiments are described.

Circulating VEGF as a biological marker in patients with rheumatoid arthritis? Preanalytical and biological variability in healthy persons and in patients

DEFF Research Database (Denmark)

Hetland, Merete Lund; Christensen, Ib Jarle; Lottenburger, Tine

2008-01-01

/ml (range: non-detectable to 352); serum: 328 pg/ml (53-1791)) were independent of gender and age. Short- and long-term biologic variability included diurnal variation (sampling should take place after 7 AM) and impact of exercise (increased VEGF immediately after bicycling normalised within 1 hour......BACKGROUND: Soluble vascular endothelial growth factor (VEGF) is a promising biomarker in monitoring rheumatoid arthritis (RA), but studies of pre-analytical and biologic variability are few. METHODS: VEGF was measured by ELISA methods in serum and plasma from healthy persons and RA patients. Pre......). CONCLUSIONS: Pre-analytical factors and biologic variability including diurnal variation and impact of exercise should be accounted for in future studies that include circulating VEGF as a biological marker....

Biological Prognostic Markers in Chronic Lymphocytic Leukemia

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Vladimíra Vroblová

2009-01-01

Full Text Available Chronic lymphocytic leukemia (CLL is the most frequent leukemic disease of adults in the Western world. It is remarkable by an extraordinary heterogeneity of clinical course with overall survival ranging from several months to more than 15 years. Classical staging sytems by Rai and Binet, while readily available and useful for initial assessment of prognosis, are not able to determine individual patient’s ongoing clinical course of CLL at the time of diagnosis, especially in early stages. Therefore, newer biological prognostic parameters are currently being clinically evaluated. Mutational status of variable region of immunoglobulin heavy chain genes (IgVH, cytogenetic aberrations, and both intracellular ZAP- 70 and surface CD38 expression are recognized as parameters with established prognostic value. Molecules regulating the process of angiogenesis are also considered as promising markers. The purpose of this review is to summarize in detail the specific role of these prognostic factors in chronic lymphocytic leukemia.

Interpretation of results for tumor markers on the basis of analytical imprecision and biological variation

DEFF Research Database (Denmark)

Sölétormos, G; Schiøler, V; Nielsen, D

1993-01-01

Interpretation of results for CA 15.3, carcinoembryonic antigen (CEA), and tissue polypeptide antigen (TPA) during breast cancer monitoring requires data on intra- (CVP) and inter- (CVG) individual biological variation, analytical imprecision (CVA), and indices of individuality. The average CVP...

Does age difference really matter? Facial markers of biological quality and age difference between husband and wife.

Science.gov (United States)

Danel, D P; Dziedzic-Danel, A; Kleisner, K

2016-08-01

Information conveyed by facial attractiveness markers such as averageness, bilateral symmetry, and secondary sexual characteristics may play an important adaptive role in human sexual selection. Nonetheless, mate choice also relies on other non-physical characteristics such as, for instance, an individual's age. Women prefer and enter in relationships with older partners, whereas in men the inverse relation is observed. Surprisingly, the link between facial morphological markers of biological quality on the one hand and age disparity between partners on the other hand has been as yet subject of very little research. This study aims to fill this gap. We had used facial photographs and demographic data of heterosexual marriages. Facial cues of biological quality, such as averageness, bilateral symmetry, and sexual dimorphism, were digitally measured using geometric morphometric methods and then associated with spouses' age difference. It turned out that a greater age disparity between spouses correlates, in both partners, with higher scores in facial measures which indicate partners' biological quality. One exception is female facial masculinity - generally regarded as an unattractive marker of a low biological quality - which, too, is associated with higher spouse age disparity. In general, our results show that facial symmetry, averageness, and secondary sexual characteristics may play a role in age-dependent mate choice. We suggest that in marriages where the wife is considerably younger than the husband, wife's greater facial masculinity may increase her perceived age and with it, her perceived maturity. Copyright © 2016 Elsevier GmbH. All rights reserved.

A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

Science.gov (United States)

Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

2017-11-01

The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach

Cellular resistance in radio- and chemotherapy: biological basis and strategies for circumvention

International Nuclear Information System (INIS)

Twentyman, P.R.

1991-01-01

In this review the author points out that resistance to cytotoxic drugs is a complex, multifactorial phenomenon involving a range of mechanisms. There is accumulating evidence that these are of relevance to both inherent and acquired resistance in the clinic. Demonstration that mechanisms of drug and radiation resistance are closely linked provides a basis for the related patterns of responsiveness observed in clinical practice. Strategies for circumvention of resistance mechanisms will depend for success upon finding ways of improving therapeutic ratio. Optimal clinical trial of resistance circumvention strategies will require the use of quantitative markers of resistance mechanisms in tumour and normal tissues. (author)

Biological and psychological markers of stress in humans: focus on the Trier Social Stress Test.

Science.gov (United States)

Allen, Andrew P; Kennedy, Paul J; Cryan, John F; Dinan, Timothy G; Clarke, Gerard

2014-01-01

Validated biological and psychological markers of acute stress in humans are an important tool in translational research. The Trier Social Stress Test (TSST), involving public interview and mental arithmetic performance, is among the most popular methods of inducing acute stress in experimental settings, and reliably increases hypothalamic-pituitary-adrenal axis activation. However, although much research has focused on HPA axis activity, the TSST also affects the sympathetic-adrenal-medullary system, the immune system, cardiovascular outputs, gastric function and cognition. We critically assess the utility of different biological and psychological markers, with guidance for future research, and discuss factors which can moderate TSST effects. We outline the effects of the TSST in stress-related disorders, and if these responses can be abrogated by pharmacological and psychological treatments. Modified TSST protocols are discussed, and the TSST is compared to alternative methods of inducing acute stress. Our analysis suggests that multiple readouts are necessary to derive maximum information; this strategy will enhance our understanding of the psychobiology of stress and provide the means to assess novel therapeutic agents. Copyright © 2013 Elsevier Ltd. All rights reserved.

Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes.

Science.gov (United States)

Rohde, Palle Duun; Demontis, Ditte; Cuyabano, Beatriz Castro Dias; Børglum, Anders D; Sørensen, Peter

2016-08-01

Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited power to detect genetic markers with small effects. Instead, aggregating genetic markers based on biological information might increase the power to identify sets of genetic markers of etiological significance. Several set test methods have been proposed: Here we propose a new set test derived from genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT was among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case-control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism and immunological responses, which previously have been implicated with schizophrenia based on experimental and observational studies. Copyright © 2016 by the Genetics Society of America.

Social and Behavioral Risk Marker Clustering Associated with Biological Risk Factors for Coronary Heart Disease: NHANES 2001–2004

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Nicholas J. Everage

2014-01-01

Full Text Available Background. Social and behavioral risk markers (e.g., physical activity, diet, smoking, and socioeconomic position cluster; however, little is known whether clustering is associated with coronary heart disease (CHD risk. Objectives were to determine if sociobehavioral clustering is associated with biological CHD risk factors (total cholesterol, HDL cholesterol, systolic blood pressure, body mass index, waist circumference, and diabetes and whether associations are independent of individual clustering components. Methods. Participants included 4,305 males and 4,673 females aged ≥20 years from NHANES 2001–2004. Sociobehavioral Risk Marker Index (SRI included a summary score of physical activity, fruit/vegetable consumption, smoking, and educational attainment. Regression analyses evaluated associations of SRI with aforementioned biological CHD risk factors. Receiver operator curve analyses assessed independent predictive ability of SRI. Results. Healthful clustering (SRI = 0 was associated with improved biological CHD risk factor levels in 5 of 6 risk factors in females and 2 of 6 risk factors in males. Adding SRI to models containing age, race, and individual SRI components did not improve C-statistics. Conclusions. Findings suggest that healthful sociobehavioral risk marker clustering is associated with favorable CHD risk factor levels, particularly in females. These findings should inform social ecological interventions that consider health impacts of addressing social and behavioral risk factors.

Validation of Alzheimer's disease CSF and plasma biological markers: the multicentre reliability study of the pilot European Alzheimer's Disease Neuroimaging Initiative (E-ADNI)

DEFF Research Database (Denmark)

Buerger, Katharina; Frisoni, Giovanni; Uspenskaya, Olga

2009-01-01

BACKGROUND: Alzheimer's Disease Neuroimaging Initiatives ("ADNI") aim to validate neuroimaging and biochemical markers of Alzheimer's disease (AD). Data of the pilot European-ADNI (E-ADNI) biological marker programme of cerebrospinal fluid (CSF) and plasma candidate biomarkers are reported. METHO...

Biological monitoring and assessment of rivers as a basis for identifying and prioritising river management options

CSIR Research Space (South Africa)

Roux, DJ

1999-01-01

Full Text Available management objectives. This paper demonstrates how the results obtained with biological indices and system-specific knowledge, are combined to derive semi quantitative assessments of ecosystem condition. These assessments provide the basis for responding...

Health effects of low-level ionising radiation: biological basis for risk assessment

International Nuclear Information System (INIS)

Upton, A.C.

1987-01-01

The biological basis for risk assessment is discussed. The risks of carcinogenic effects, teratogenic effects, and genetic (heritable) effects are estimated to vary in proportion with the dose of radiation in the low-dose domain; however, the risks also appear to vary with the LET of the radiation, age at the time of irradiation, and other variables. Although the data suffice to place the risks in perspective with other hazards of modern life, further research to refine the reliability of the risk assessment is called for. (author)

Biological markers as predictors of radiosensitivity in syngeneic murine tumors

International Nuclear Information System (INIS)

Chang, Sei Kyung; Shin, Hyun Soo; Seong, Jin Sil; Kim, Sung Hee

2006-01-01

We investigated whether a relationship exists between tumor control dose 50 (TCD 50 ) or tumor growth delay (TGD) and radiation induced apoptosis (RIA) in syngeneic murine tumors. Also we investigated the biological markers that can predict radiosensitivity in murine tumor system through analysis of relationship between TCD 50 , TGD, RIA and constitutive expression levels of the genetic products regulating RIA. Syngeneic murine tumors such as ovarian adenocarcinoma, mammary carcinoma, squamous cell carcinoma, fibrosarcoma, hepatocarcinoma were used in this study. C3H/HeJ mice were bred and maintained in our specific pathogen free mouse colony and were 8 ∼ 12 weeks old when used for the experiments. The tumors, growing in the right hind legs of mice, were analyzed for TCD 50 , TGD, and RIA at 8 mm in diameter. The tumors were also analyzed for the constitutive expression levels of p53, p21 WAF1/CIP1 , BAX, Bcl-2, Bcl-x L , Bcl-x S , and p34. Correlation analysis was performed whether the level of RIA were correlated with TCD 50 or TGD, and the constitutive expression levels of genetic products regulating RIA were correlated with TCD 50 , TGD, RIA. The level of RIA showed a significant positive correlation (R = 0.922, ρ = 0.026) with TGD, and showed a trend to correlation (R = -0.848), marginally significant correlation with TCD 50 (ρ = 0.070). It indicates that tumors that respond to radiation with high percentage of apoptosis were more radiosensitive. The constitutive expression levels of p21 WAF1/CIP1 and p34 showed a significant correlation either with TCD 50 (R = 0.893, ρ = 0.041 and R = 0.904, ρ = 0.035) or with TGD (R = -0.922, ρ 0.026 and R = -0.890, ρ = 0.043). The tumors with high constitutive expression levels of p21 WAF1/CIP1 or p34 were less radiosensitive than those with low expression. Radiosensitivity may be predicted with the level of RIA in murine tumors. The constitutive expression levels of p21 WAF1/CIP1 or p34 can be used as biological

Biological markers as predictors of radiosensitivity in syngeneic murine tumors

Energy Technology Data Exchange (ETDEWEB)

Chang, Sei Kyung; Shin, Hyun Soo [Bundang CHA General Hospital, Seongnam (Korea, Republic of); Seong, Jin Sil; Kim, Sung Hee [Yonsei Cancer Center, Yonsei University College of Medicine, Seoul (Korea, Republic of)

2006-06-15

We investigated whether a relationship exists between tumor control dose 50 (TCD{sub 50}) or tumor growth delay (TGD) and radiation induced apoptosis (RIA) in syngeneic murine tumors. Also we investigated the biological markers that can predict radiosensitivity in murine tumor system through analysis of relationship between TCD{sub 50}, TGD, RIA and constitutive expression levels of the genetic products regulating RIA. Syngeneic murine tumors such as ovarian adenocarcinoma, mammary carcinoma, squamous cell carcinoma, fibrosarcoma, hepatocarcinoma were used in this study. C3H/HeJ mice were bred and maintained in our specific pathogen free mouse colony and were 8 {approx} 12 weeks old when used for the experiments. The tumors, growing in the right hind legs of mice, were analyzed for TCD{sub 50}, TGD, and RIA at 8 mm in diameter. The tumors were also analyzed for the constitutive expression levels of p53, p21{sup WAF1/CIP1}, BAX, Bcl-2, Bcl-x{sub L}, Bcl-x{sub S}, and p34. Correlation analysis was performed whether the level of RIA were correlated with TCD{sub 50} or TGD, and the constitutive expression levels of genetic products regulating RIA were correlated with TCD{sub 50}, TGD, RIA. The level of RIA showed a significant positive correlation (R = 0.922, {rho} = 0.026) with TGD, and showed a trend to correlation (R = -0.848), marginally significant correlation with TCD{sub 50} ({rho} = 0.070). It indicates that tumors that respond to radiation with high percentage of apoptosis were more radiosensitive. The constitutive expression levels of p21{sup WAF1/CIP1} and p34 showed a significant correlation either with TCD{sub 50} (R = 0.893, {rho} = 0.041 and R = 0.904, {rho} = 0.035) or with TGD (R = -0.922, {rho} 0.026 and R = -0.890, {rho} = 0.043). The tumors with high constitutive expression levels of p21{sup WAF1/CIP1} or p34 were less radiosensitive than those with low expression. Radiosensitivity may be predicted with the level of RIA in murine tumors. The

Changes in biological markers, particularly hormone receptors, due to pre-operative chemotherapy (epirubicin/docetaxel in operable breast cancer

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Rumiko Tashima

2011-12-01

Full Text Available We investigated the correlation between biological markers prior to pre-operative chemotherapy with epirubicin and docetaxel (ET therapy and the effect of treatment as well as the clinically significant changes in biological markers before and after chemotherapy. Since April 2002, 52 patients with tumors ≥3 cm in diameter or lymph node metastases have received pre-operative ET chemotherapy. The items investigated were ER/PgR, proliferative activity (MIB-1, etc. The correlation of changes in these factors between pre- and post-treatment status and the clinical and pathological responses was investigated. Clinical response was 82%, BCS rate was 67%. Pathological response was 31.4%. The ER/PgR positive cell rate significantly decreased from 48%/32% to 37%/14%. The MIB-1 decreased from 48% to 27%. The pathological response was significantly high in patients with low ER/PgR-positive rates and those with high MIB-1 values.

Biological basis of combination therapy with radiation and bleomycin

International Nuclear Information System (INIS)

Fukuda, Hiroshi; Matsuzawa, Taiju; Yokoyama, Kumiko; Okuyama, Shinichi; Yamaura, Hiroshi

1976-01-01

The biological basis for combination therapy with radiation and bleomycin (BLM) was studied on C 2 W cells growing in vitro. When BLM was added to the medium before or after irradiation, a potentiating effect was observed. The potentiation remained for 4-6 hours after irradiation. To make clear the mechanism, both type of repair from radiation damage (Elkind type and PLD) by BLM were examined. BLM didn't inhibit the Elkind type recovery but it did inhibit the repair of potentially lethal damage (PLD repair). Plateau phase C 2 W cells were irradiated, incubated at 37 0 C for a various number of hours, then trypsinized for colony formation. PLD repair was inhibited when BLM was added immediately after irradiation. Based on such experimental results, we treated lung cancer with combination of radiation and BLM. BLM was injected intravenously within 30 minutes after irradiation. Although it seems too early to discuss the result of the combination therapy, it is very promising. (J.P.N.)

Biological basis of combination therapy with radiation and bleomycin

Energy Technology Data Exchange (ETDEWEB)

Fukuda, H; Matsuzawa, T; Yokoyama, K; Okuyama, S; Yamaura, H [Tohoku Univ., Sendai (Japan). Research Inst. for Tuberculosis, Leprosy and Cancer

1976-01-01

The biological basis for combination therapy with radiation and bleomycin (BLM) was studied on C/sub 2/W cells growing in vitro. When BLM was added to the medium before or after irradiation, a potentiating effect was observed. The potentiation remained for 4-6 hours after irradiation. To make clear the mechanism, both type of repair from radiation damage (Elkind type and PLD) by BLM were examined. BLM didn't inhibit the Elkind type recovery but it did inhibit the repair of potentially lethal damage (PLD repair). Plateau phase C/sub 2/W cells were irradiated, incubated at 37/sup 0/C for a various number of hours, then trypsinized for colony formation. PLD repair was inhibited when BLM was added immediately after irradiation. Based on such experimental results, we treated lung cancer with combination of radiation and BLM. BLM was injected intravenously within 30 minutes after irradiation. Although it seems too early to discuss the result of the combination therapy, it is very promising.

Biological basis of chemo-radiation

International Nuclear Information System (INIS)

Mornex, F.; Van Houtte, P.; Cosset, J.M.

1997-01-01

Radiation therapy has been for years treatment of choice of locally advanced non small cell lung cancer. Improvement due to the combination of radiation and chemotherapy has been shown recently through several randomized trials and a recent meta-analysis. These results may be explained by biological mechanisms, yet un-completely explored, which are detailed in this review and applied to lung cancer. The optimal combination scheme is not yet defined, even trough the concurrent approach is promising, at the expense of an increased toxicity which is the limiting factor of treatment escalation doses. Biological findings and future results of randomized trials will hopefully open new avenues in the therapeutic strategy of this poor prognosis disease. (authors)

Biological markers in animals can provide information on exposure and bioavailability of environmental contaminants

International Nuclear Information System (INIS)

Shugart, L.R.; Adams, S.M.; Jimenez, B.D.; Talmage, S.S.; McCarthy, J.F.

1987-01-01

Epidemiologic studies of agents present in the environment seek to identify the extent to which they contribute to the causation of a specific toxic, clinical, or pathological endpoint. The multifactorial nature of disease etiology, long latency periods and the complexity of exposure, all contribute to the difficulty of establishing associations and casual relationships between a specific exposure and an adverse outcome. These barriers to studies of exposures and subsequent risk assessment cannot generally be changed. However, the appropriate use of biological markers in animal species living in a contaminated habitat can provide a measure of potential damage from that exposure and, in some instances, act as a surrogate for human environmental exposures. Quantitative predictivity of the effect of exposure to environmental pollutants is being approached by employing an appropriate array of biological end points. 34 refs., 1 fig., 6 tabs

Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

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Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

1984-08-01

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

Pimonidazole: a novel hypoxia marker for complementary study of tumor hypoxia and tumor biology

International Nuclear Information System (INIS)

Varia, Mahesh A.; Kennedy, Andrew S.; Calkins-Adams, Dennise P.; Rinker, Lillian; Novotny, Debra; Fowler, Wesley C.; Raleigh, James A.

1997-01-01

Purpose/Objectives: Tumor hypoxia appears to be associated with treatment resistance and with gene expression that may lead to hypoxia-mediated selection of tumor cells as a source for cell growth and metastases. The objective of this study was to develop complementary techniques of hypoxia detection with molecular markers of cell proliferation and metastases in order to investigate the role of tumor hypoxia in tumor biology. Materials and Methods: Pimonidazole is a 2-nitroimidazole which is reductively-activated and becomes covalently bound to thiol-containing proteins only in hypoxic cells. These adducts can be detected using immunohistochemistry, enzyme linked immunosorbent assay or flow cytometry as a measure of hypoxia in tumors. Quantitative immunohistochemical analysis has been completed for five patients with squamous cell carcinoma of the cervix who were given pimonidazole hydrochloride (0.5 g/m 2 intravenously) followed by cervical biopsies 24 hours later. Informed consent was obtained according to a protocol approved by the Institutional Review Board. A minimum of 3 random biopsies were obtained from the tumors and at least four sections examined from each biopsy site. Formalin fixed, paraffin embedded tissue sections were immunostained for pimonidazole binding using a mouse monoclonal antibody. Commercially available monoclonal antibodies were used to detect cell proliferation markers MIB-1 (Ki-67) and to detect vascular endothelial growth factor (VEGF) in tumor cells in contiguous sections. The extent of immunostaining was expressed as the percent of immunostained to total tumor cells as determined by Chalkley point counting. Results: No clinical toxicities were associated with pimonidazole infusion. Immunostaining with pimonidazole antibody was observed in all patients indicating the presence of tumor hypoxia. Qualitatively there is little or no overlap between the areas of hypoxia and proliferation. Quantitative data tabulated below show the

[Use of the 2D:4D digit ratio as a biological marker of specific language disorders].

Science.gov (United States)

Font-Jordà, Antònia; Gamundí, Antoni; Nicolau Llobera, María Cristina; Aguilar-Mediavilla, Eva

2018-04-03

The finding of biological markers of specific language impairment would facilitate their detection and early intervention. In this sense, the 2D:4D finger ratio is considered an indirect indicator of prenatal exposure to testosterone. Previous studies have related it to linguistic competence and aggressive behaviour, and could be a candidate for a biological marker of language impairment. The aim was to compare the value of the 2D:4D ratio in children with Specific Language Impairment (SLI) with those of children with typical language development, as well as to establish to what extent this biological index correlates with the behaviour (linguistic, cognitive, social,...) in both groups. 2D:4D ratio, language, cognition and social behaviour were compared in a group of children with SLI (n=15), with a group of children without language difficulties (n=16) of the same age (between 5-8 years), gender (male), and socio-cultural level. Children with SLI showed significantly higher values of 2D:4D ratio of the right hand, and a negative correlation between this ratio and their linguistic competence. Although the children with SLI showed impaired adaptive abilities, but not more aggressive behaviour, these measurements did not correlate with the 2D:4D index. Nevertheless, social behaviour correlated with language and cognition competence. A higher value of the biological 2D:4D ration (lower intrauterine exposure to testosterone) seems to be associated with language difficulties in boys with SLI, but not with their behavioural difficulties. Their behavioural difficulties seem to be a consequence of their linguistic difficulties and their level of cognition. Copyright © 2018. Publicado por Elsevier España, S.L.U.

Biological markers of Alzheimer?s disease

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Leonardo Cruz de Souza

2014-03-01

Full Text Available The challenges for establishing an early diagnosis of Alzheimer’s disease (AD have created a need for biomarkers that reflect the core pathology of the disease. The cerebrospinal fluid (CSF levels of total Tau (T-tau, phosphorylated Tau (P-Tau and beta-amyloid peptide (Aβ42 reflect, respectively, neurofibrillary tangle and amyloid pathologies and are considered as surrogate markers of AD pathophysiology. The combination of low Aβ42 and high levels of T-tau and P-Tau can accurately identify patients with AD at early stages, even before the development of dementia. The combined analysis of the CSF biomarkers is also helpful for the differential diagnosis between AD and other degenerative dementias. The development of these CSF biomarkers has evolved to a novel diagnostic definition of the disease. The identification of a specific clinical phenotype combined with the in vivo evidence of pathophysiological markers offers the possibility to make a diagnosis of AD before the dementia stage with high specificity.

Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research

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Saks, Valdur; Monge, Claire; Guzun, Rita

2009-01-01

We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed. PMID:19399243

Validation of systems biology derived molecular markers of renal donor organ status associated with long term allograft function.

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Perco, Paul; Heinzel, Andreas; Leierer, Johannes; Schneeberger, Stefan; Bösmüller, Claudia; Oberhuber, Rupert; Wagner, Silvia; Engler, Franziska; Mayer, Gert

2018-05-03

Donor organ quality affects long term outcome after renal transplantation. A variety of prognostic molecular markers is available, yet their validity often remains undetermined. A network-based molecular model reflecting donor kidney status based on transcriptomics data and molecular features reported in scientific literature to be associated with chronic allograft nephropathy was created. Significantly enriched biological processes were identified and representative markers were selected. An independent kidney pre-implantation transcriptomics dataset of 76 organs was used to predict estimated glomerular filtration rate (eGFR) values twelve months after transplantation using available clinical data and marker expression values. The best-performing regression model solely based on the clinical parameters donor age, donor gender, and recipient gender explained 17% of variance in post-transplant eGFR values. The five molecular markers EGF, CD2BP2, RALBP1, SF3B1, and DDX19B representing key molecular processes of the constructed renal donor organ status molecular model in addition to the clinical parameters significantly improved model performance (p-value = 0.0007) explaining around 33% of the variability of eGFR values twelve months after transplantation. Collectively, molecular markers reflecting donor organ status significantly add to prediction of post-transplant renal function when added to the clinical parameters donor age and gender.

Social stratification in the Sikh population of Punjab (India) has a genetic basis: evidence from serological and biochemical markers.

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Chahal, Sukh Mohinder Singh; Virk, Rupinder Kaur; Kaur, Sukhvir; Bansal, Rupinder

2011-01-01

The present study was planned to assess whether social stratification in the Sikh population inhabiting the northwest border Indian state of Punjab has any genetic basis. Blood samples were collected randomly from a total of 2851 unrelated subjects belonging to 21 groups of two low-ranking Sikh scheduled caste populations, viz. Mazhabi and Ramdasi, and a high-ranking Jat Sikh caste population of Punjab. The genetic profile of Sikh groups was investigated using a total of nine serobiochemical genetic markers, comprising two blood groups (ABO, RH(D)) and a battery of seven red cell enzyme polymorphisms (ADA, AK1, ESD, PGM1, GLO1, ACP1, GPI), following standard serological and biochemical laboratory protocols. Genetic structure was studied using original allele frequency data and statistical measures of heterozygosity, genic differentiation, genetic distance, and genetic admixture. Great heterogeneity was observed between Sikh scheduled caste and Jat Sikh populations, especially in the RH(D) blood group system, and distribution of ESD, ACP1, and PGM1 enzyme markers was also found to be significantly different between many of their groups. Genetic distance trees demonstrated little or no genetic affinities between Sikh scheduled caste and Jat Sikh populations; the Mazhabi and Ramdasi also showed little genetic relationship. Genetic admixture analysis suggested a higher element of autochthonous tribal extraction in the Ramdasi. The present study revealed much genetic heterogeneity in differently ranking Sikh caste populations of Punjab, mainly attributable to their different ethnic backgrounds, and provided a genetic basis to social stratification present in this religious community of Punjab, India.

Is the Alzheimer's disease cortical thickness signature a biological marker for memory?

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Busovaca, Edgar; Zimmerman, Molly E; Meier, Irene B; Griffith, Erica Y; Grieve, Stuart M; Korgaonkar, Mayuresh S; Williams, Leanne M; Brickman, Adam M

2016-06-01

Recent work suggests that analysis of the cortical thickness in key brain regions can be used to identify individuals at greatest risk for development of Alzheimer's disease (AD). It is unclear to what extent this "signature" is a biological marker of normal memory function - the primary cognitive domain affected by AD. We examined the relationship between the AD signature biomarker and memory functioning in a group of neurologically healthy young and older adults. Cortical thickness measurements and neuropsychological evaluations were obtained in 110 adults (age range 21-78, mean = 46) drawn from the Brain Resource International Database. The cohort was divided into young adult (n = 64, age 21-50) and older adult (n = 46, age 51-78) groups. Cortical thickness analysis was performed with FreeSurfer, and the average cortical thickness extracted from the eight regions that comprise the AD signature. Mean AD-signature cortical thickness was positively associated with performance on the delayed free recall trial of a list learning task and this relationship did not differ between younger and older adults. Mean AD-signature cortical thickness was not associated with performance on a test of psychomotor speed, as a control task, in either group. The results suggest that the AD signature cortical thickness is a marker for memory functioning across the adult lifespan.

[Biological markers for the status of vitamins B12 and D: the importance of some analytical aspects in relation to clinical interpretation of results].

Science.gov (United States)

Boulat, O; Rey, F; Mooser, V

2012-10-31

Biological markers for the status of vitamins B12 and D: the importance of some analytical aspects in relation to clinical interpretation of results When vitamin B12 deficiency is expressed clinically, the diagnostic performance of total cobalamin is identical to that of holotranscobalamin II. In subclinical B12 deficiency, the two aforementioned markers perform less well. Additional analysis of a second, functional marker (methylmalonate or homocysteine) is recommended. Different analytical approaches for 25-hydroxyvitamin D quantification, the marker of vitamin D deficiency, are not yet standardized. Measurement biases of up to +/- 20% compared with the original method used to establish threshold values are still observed.

Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms.

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Elad Segev

Full Text Available Finding optimal markers for microorganisms important in the medical, agricultural, environmental or ecological fields is of great importance. Thousands of complete microbial genomes now available allow us, for the first time, to exhaustively identify marker proteins for groups of microbial organisms. In this work, we model the biological task as the well-known mathematical "hitting set" problem, solving it based on both greedy and randomized approximation algorithms. We identify unique markers for 17 phenotypic and taxonomic microbial groups, including proteins related to the nitrite reductase enzyme as markers for the non-anammox nitrifying bacteria group, and two transcription regulation proteins, nusG and yhiF, as markers for the Archaea and Escherichia/Shigella taxonomic groups, respectively. Additionally, we identify marker proteins for three subtypes of pathogenic E. coli, which previously had no known optimal markers. Practically, depending on the completeness of the database this algorithm can be used for identification of marker genes for any microbial group, these marker genes may be prime candidates for the understanding of the genetic basis of the group's phenotype or to help discover novel functions which are uniquely shared among a group of microbes. We show that our method is both theoretically and practically efficient, while establishing an upper bound on its time complexity and approximation ratio; thus, it promises to remain efficient and permit the identification of marker proteins that are specific to phenotypic or taxonomic groups, even as more and more bacterial genomes are being sequenced.

Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research

Directory of Open Access Journals (Sweden)

Valdur Saks

2009-03-01

Full Text Available We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed.

Biological markers of oxidative stress: Applications to cardiovascular research and practice

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Edwin Ho

2013-01-01

Full Text Available Oxidative stress is a common mediator in pathogenicity of established cardiovascular risk factors. Furthermore, it likely mediates effects of emerging, less well-defined variables that contribute to residual risk not explained by traditional factors. Functional oxidative modifications of cellular proteins, both reversible and irreversible, are a causal step in cellular dysfunction. Identifying markers of oxidative stress has been the focus of many researchers as they have the potential to act as an “integrator” of a multitude of processes that drive cardiovascular pathobiology. One of the major challenges is the accurate quantification of reactive oxygen species with very short half-life. Redox-sensitive proteins with important cellular functions are confined to signalling microdomains in cardiovascular cells and are not readily available for quantification. A popular approach is the measurement of stable by-products modified under conditions of oxidative stress that have entered the circulation. However, these may not accurately reflect redox stress at the cell/tissue level. Many of these modifications are “functionally silent”. Functional significance of the oxidative modifications enhances their validity as a proposed biological marker of cardiovascular disease, and is the strength of the redox cysteine modifications such as glutathionylation. We review selected biomarkers of oxidative stress that show promise in cardiovascular medicine, as well as new methodologies for high-throughput measurement in research and clinical settings. Although associated with disease severity, further studies are required to examine the utility of the most promising oxidative biomarkers to predict prognosis or response to treatment.

[Immunological Markers in Organ Transplantation].

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Beckmann, J H; Heits, N; Braun, F; Becker, T

2017-04-01

The immunological monitoring in organ transplantation is based mainly on the determination of laboratory parameters as surrogate markers of organ dysfunction. Structural damage, caused by alloreactivity, can only be detected by invasive biopsy of the graft, which is why inevitably rejection episodes are diagnosed at a rather progressive stage. New non-invasive specific markers that enable transplant clinicians to identify rejection episodes at an earlier stage, on the molecular level, are needed. The accurate identification of rejection episodes and the establishment of operational tolerance permit early treatment or, respectively, a controlled cessation of immunosuppression. In addition, new prognostic biological markers are expected to allow a pre-transplant risk stratification thus having an impact on organ allocation and immunosuppressive regimen. New high-throughput screening methods allow simultaneous examination of hundreds of characteristics and the generation of specific biological signatures, which might give concrete information about acute rejection, chronic dysfunction as well as operational tolerance. Even though multiple studies and a variety of publications report about important advances on this subject, almost no new biological marker has been implemented in clinical practice as yet. Nevertheless, new technologies, in particular analysis of the genome, transcriptome, proteome and metabolome will make personalised transplantation medicine possible and will further improve the long-term results and graft survival rates. This article gives a survey of the limitations and possibilities of new immunological markers in organ transplantation. Georg Thieme Verlag KG Stuttgart · New York.

Biological ageing and frailty markers in breast cancer patients.

Science.gov (United States)

Brouwers, Barbara; Dalmasso, Bruna; Hatse, Sigrid; Laenen, Annouschka; Kenis, Cindy; Swerts, Evalien; Neven, Patrick; Smeets, Ann; Schöffski, Patrick; Wildiers, Hans

2015-05-01

Older cancer patients are a highly heterogeneous population in terms of global health and physiological reserves, and it is often difficult to determine the best treatment. Moreover, clinical tools currently used to assess global health require dedicated time and lack a standardized end score. Circulating markers of biological age and/or fitness could complement or partially substitute the existing screening tools. In this study we explored the relationship of potential ageing/frailty biomarkers with age and clinical frailty. On a population of 82 young and 162 older non-metastatic breast cancer patients, we measured mean leukocyte telomere length and plasma levels of interleukin-6 (IL-6), regulated upon activation, normal T cell expressed and secreted (RANTES), monocyte chemotactic protein 1 (MCP-1), insulin-like growth factor 1 (IGF-1). We also developed a new tool to summarize clinical frailty, designated Leuven Oncogeriatric Frailty Score (LOFS), by integrating GA results in a single, semi-continuous score. LOFS' median score was 8, on a scale from 0=frail to 10=fit. IL-6 levels were associated with chronological age in both groups and with clinical frailty in older breast cancer patients, whereas telomere length, IGF-1 and MCP-1 only correlated with age. Plasma IL-6 should be further explored as frailty biomarker in cancer patients.

Additional Prognostic Value of SUVmax Measured by F-18 FDG PET/CT over Biological Marker Expressions in Surgically Resected Cervical Cancer Patients.

Science.gov (United States)

Yun, Man Soo; Kim, Seong-Jang; Pak, Kyoungjune; Lee, Chang Hun

2015-01-01

We compared the prognostic ability of the maximum standardized uptake value (SUVmax) and various biological marker expressions to predict recurrence in patients with surgically resected cervical cancer. A retrospective review identified 60 patients with cervical cancer who received [18F]fluorodeoxyglucose positron emission tomography/computed tomography (F-18 FDG PET/CT) at the time of the diagnosis of cancer. The SUVmax, expressions of carbonic anhydrase-IX (CA-IX), glucose transporter 1 (GLUT-1), and vascular endothelial growth factor (VEGF), and known prognostic factors were investigated. The median follow-up time was 22.2 months (range 3.4-43.1 months). Using univariate analyses, the stage (stage II, p = 0.0066), SUVmax (> 6, p = 0.027), parametrial involvement (p value than biological marker expression in patients with surgically resected cervical cancer. © 2015 S. Karger GmbH, Freiburg.

The influence of framing on clinicians' judgments of the biological basis of behaviors.

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Kim, Nancy S; Ahn, Woo-kyoung; Johnson, Samuel G B; Knobe, Joshua

2016-03-01

Practicing clinicians frequently think about behaviors both abstractly (i.e., in terms of symptoms, as in the Diagnostic and Statistical Manual of Mental Disorders, 5th ed., DSM-5; American Psychiatric Association, 2013) and concretely (i.e., in terms of individual clients, as in DSM-5 Clinical Cases; Barnhill, 2013). Does abstract/concrete framing influence clinical judgments about behaviors? Practicing mental health clinicians (N = 74) were presented with hallmark symptoms of 6 disorders framed abstractly versus concretely, and provided ratings of their biological and psychological bases (Experiment 1) and the likely effectiveness of medication and psychotherapy in alleviating them (Experiment 2). Clinicians perceived behavioral symptoms in the abstract to be more biologically and less psychologically based than when concretely described, and medication was viewed as more effective for abstractly than concretely described symptoms. These findings suggest a possible basis for miscommunication and misalignment of views between primarily research-oriented and primarily practice-oriented clinicians; furthermore, clinicians may accept new neuroscience research more strongly in the abstract than for individual clients. (c) 2016 APA, all rights reserved).

Specific acyclic isoprenoids as biological markers of methanogenic bacteria in marine sediments.

Science.gov (United States)

Brassell, S C; Wardroper, A M; Thomson, I D; Maxwell, J R; Eglinton, G

1981-04-23

The widespread occurrence of extended hopanoids in sediments and petroleums illustrates the importance of bacterial lipid contributions to geological materials. In archaebacteria, however, hopanoids are absent; their role as structural components of biomembranes is fulfilled by acyclic isoprenoids. Recent studies of the lipid constituents of archaebacteria have greatly extended the range of acyclic isoprenoid skeletons known in organisms (Fig. 1). In particularly, isoprenoids with head-to-head linkages have been identified, and such compounds (for example, 3,7,11,15,18,22,26,30-octamethyldotriacontane, I) have been recognized in petroleum and as degradation products of Messel shale kerogen. Here we report the first recognition of 2,6,10,15,19-pentamethyleicosane (II), a known component of methanogens, in marine sediments of Recent to Cretaceous age (Table 1) and suggest that it and certain other acyclic isoprenoids may be used as biological markers for methanogens.

Biological basis of the sterile insect technique

International Nuclear Information System (INIS)

Lance, D.R.; McInnis, D.O.

2005-01-01

In principle, the sterile insect technique (SIT) is applicable to controlling a wide variety of insect pests, but biological factors, interacting with socio-economic and political forces, restrict its practical use to a narrower set of pest species and situations. This chapter reviews how the biology and ecology of a given pest affect the feasibility and logistics of developing and using the SIT against that pest insect. The subjects of pest abundance, distribution, and population dynamics are discussed in relation to producing and delivering sufficient sterile insects to control target populations. Pest movement and distribution are considered as factors that influence the feasibility and design of SIT projects, including the need for population- or area-wide management approaches. Biological characteristics, that affect the ability of sterile insects to interact with wild populations, are presented, including the nature of mating systems of pests, behavioural and physiological consequences of mass production and sterilization, and mechanisms that males use to block a female's acquisition and/or use of sperm from other males. An adequate knowledge of the biology of the pest species and potential target populations is needed, both for making sound decisions on whether integration of the SIT into an area-wide integrated pest management (AW-IPM) programme is appropriate, and for the efficient and effective application of the technique. (author)

Quality control in the neutron activation analysis of biological markers for selenium in epidemiological investigations

International Nuclear Information System (INIS)

Morris, J.S.; Ngwenyama, R.A.; Guthrie, J.M.; Brockman, J.D.; Spate, V.L.; Robertson, J.D.

2008-01-01

Instrumental neutron activation analysis is routinely used at the MURR to quantify selenium in prospectively-collected biologic markers including blood serum and toenails. These specimens are typically collected from well-defined cohort populations participating in investigations assessing selenium intake and incidence of chronic disease endpoints. These epidemiological investigations, whether observational (case-control) or clinical (intervention), typically generate thousands of samples. The purpose of this paper is to assess, through evaluation of quality control results, if the achievable accuracy and precision in the measurement of selenium using NAA is adequate to determine a relative risk of 1.2 at high confidence in epidemiological studies. (author)

Discrimination of uranium chemo-toxic and radio-toxic effects: definition of biological markers for evaluating professional risks in nuclear industry

International Nuclear Information System (INIS)

Darolles, Carine

2010-01-01

Uranium (U) is a heavy metal that is also considered as an alpha emitter. Thus the origin of U toxicity is both chemical and radiological. The identification of bio-markers to discriminate chemical and radiological toxicity for a given U compound is required to assess accurately the health effects of isotopic mixtures such as depleted U in 235 U with a low specific activity. Data from the literature show that the best candidates are cytogenetic markers. In the present work, the assessment of bio-markers of U contamination was performed on three cellular models (mouse fibroblasts, rat lymphocytes and human lymphocytes) that were exposed to different isotopic mixtures of U. The cytokinesis-block micronucleus (MN) centromere assay was performed to discriminate the chemo-toxic and radio-toxic effects of U. This study showed that the evaluation of micronuclei in bi-nucleated cells could not assess U genotoxicity accurately. Instead, the assessment of centromere-negative micronuclei and nucleo-plasmic bridges correlated with the radio-toxic effects of U. The evaluation of centromere-positive micronuclei and micronuclei in mono-nucleated cells correlated with the chemo-toxic effects of U. These cytogenetic markers should be validated on different biological models and could be proposed to discriminate radiological and chemical toxicity of a given isotopic mixture of U. These four cytogenetic markers could be a useful complement of the classical dosimetric bio-markers for the assessment of internal uranium contamination. (author)

Final report on 'biological effects of tritium as a basis of research and development in nuclear fusion'

International Nuclear Information System (INIS)

1987-12-01

The National Institute of Radiological Sciences, Japan, has undertaken a special study of ''biological effects of tritium as a basis of research and development in nuclear fusion'' over a 5-year period from April 1981 through March 1986. This is a final report, covering incorporation and metabolism of tritium, physical, chemical, and cellular effects of tritium, tritium damage to the mammalian tissue, and human exposure to tritium. The report is organized into five chapters, including ''Study of incorporation of tritium into the living body and its in vivo behavior''; ''Physical and chemical studies for the determination of relative biological effectiveness''; ''Analytical study on biological effects of tritium in cultured mammalian cells''; ''Study of tritium effects on the mammalian tissue, germ cells, and cell transformation''; and ''Changes in the hemopoietic stem cells and lymphocyte subsets in humans after exposure to some internal emitters''. (Namekawa, K.)

Physical basis for biological effect

International Nuclear Information System (INIS)

Goodhead, D.T.

1987-01-01

Absorbed dose, or particle fluence, alone, are poor predictors of the biological effectiveness of ionizing radiations. Various radiation 'quality' parameters have been proposed to account quantitatively for the differences due to type of radiation. These include LET, quality factor (Q), lineal energy, specific energy and Z 2 /β 2 . However, all of these have major shortcomings, largely because they fail to describe adequately the microscopic stochastic properties of radiation which are primarily responsible for their relative effectiveness. Most biophysical models of radiation action now agree that the biological effectiveness of radiations are to a large extent determined by their very localized spatial properties of energy deposition (perhaps DNA and associated structures) and that the probability of residual permanent cellular damage (after cellular repair) depends on the nature of this initial macromolecular damage. Common features of these models make it clear that major future advances in identifying critical physical parameters of radiations for general practical application, or to describe their fundamental mechanisms of action, require accurate knowledge of the spatial patterns of energy deposition down to distances of the order of nanometres. Therefore, adequate descriptions are required of the nature and spatial distribution of the initial charged particles and of the interaction-by-interaction structure of the ensuing charged particle tracks. Recent development and application of Monte Carlo track structure simulations have already made it possible to commence such analyses of radiobiological data. (author). 56 refs, 7 figs

Characterization of Fasciola spp. in Myanmar on the basis of spermatogenesis status and nuclear and mitochondrial DNA markers.

Science.gov (United States)

Ichikawa, Madoka; Bawn, Saw; Maw, Ni Ni; Htun, Lat Lat; Thein, Myint; Gyi, Aung; Sunn, Kyaw; Katakura, Ken; Itagaki, Tadashi

2011-12-01

Fasciola spp. in Myanmar were characterized on the basis of spermatogenesis status and DNA markers of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1). We collected 88 adult flukes from Yangon, Lashio, and Myitkyina. Spermatogenesis status was analyzed by the presence of sperm in the seminal vesicles, and 8 aspermic and 80 spermic flukes were detected. The flukes were identified on the basis of spermatogenesis status and ITS1 types which were analyzed by a PCR-RFLP method, and 80 spermic flukes were identified as F. gigantica. A very low detection rate of aspermic Fasciola sp. indicated that they are not established in Myanmar. In phylogenetic analyses, the 7 aspermic Fasciola sp. from Myitkyina displayed a haplotype in nad1 sequence, which was identical to that of aspermic Fasciola sp. from other Asian countries including China. Therefore, they were probably introduced from China through an infected domestic ruminant. On the other hand, 17 nad1 haplotypes detected in F. gigantica belonged to 2 clades unique to Myanmar, each with a distinct founder haplotype in a network analysis. This indicated a unique history of F. gigantica introduction into Myanmar involving ancient artificial movements of domestic ruminants. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Screening for the anti-inflammation quality markers of Xiaojin Pills based on HPLC-MS/MS method, COX-2 inhibition test and protein interaction network.

Science.gov (United States)

Xiong, Xi; He, Ya-Nan; Feng, Bi; Pan, Yuan; Zhang, Hai-Zhu; Ke, Xiu-Mei; Zhang, Yi; Yang, Ming; Han, Li; Zhang, Ding-Kun

2018-05-10

Nowadays, breast disorders seriously affect women's health in an increasing number. In China, Xiaojin Pills are commonly used in the treatment of breast diseases. Doctors have concluded that the combined use of Xiaojin Pills with conventional therapy can significantly improve the efficacy with fewer side effects. However, the prescription of Xiaojin Pills is complicated and their quality control methods cannot completely ensure the quality of Xiaojin Pills. On the basis of its mechanism, our study combined chemical evaluation and biological evaluation to identify the anti-inflammatory markers of Xiaojin Pills. In this manuscript, 13 compounds in Xiaojin Pills were quantified. At the same time, the cyclooxygenase-2 inhibition rates of different Xiaojin Pills were measured and the possible markers were screened by spectrum-effect relationship. Further, anti-inflammatory activities of markers were verified and protein interaction network was analyzed, identifying the components of Protocatechuate, Beta-Boswellic acid and Levistilide A as the anti-inflammatory quality markers of Xiaojin Pills. We hope our studies can provide a scientific theoretical basis for accurately quality control of Xiaojin Pills and reasonable suggestions for pharmaceutical companies and new ideas for the quality control of other medicines.

ASSESSMENT OF THE RESPONSE OF PATIENTS WITH CROHN'S DISEASE TO BIOLOGICAL THERAPY USING NEW NON-INVASIVE MARKERS: lactoferrin and calprotectin

Directory of Open Access Journals (Sweden)

Islaine Martins NOGUEIRA

2013-04-01

Full Text Available Context The use of fecal markers to monitor Crohn's disease is crucial for assessing the response to treatment. Objective To assess the inflammatory activity of Crohn's disease by comparing fecal markers (calprotectin and lactoferrin, colonoscopy combined with biopsy, and the Crohn's disease activity index (CDAI, as well as serum markers, before treatment with infliximab, after the end of induction, and after the end of maintenance. Methods Seventeen patients were included who had been previously diagnosed with Crohn's disease and were using conventional treatment but required the introduction of biological therapy with infliximab. Each patient underwent a colonoscopy with biopsy, serum, and fecal (calprotectin and lactoferrin tests to assess inflammatory activity, and CDAI assessments before treatment with infliximab, after induction (week 8, and after maintenance (week 32. Results The calprotectin levels exhibited significant reductions (P = 0.04 between the assessment before treatment with infliximab and the end of induction, which did not occur after the end of the maintenance phase. Lactoferrin remained positive throughout the three phases of the study. Regarding the histological assessment, a significant difference was found only between the assessment before treatment and after the end of maintenance (P = 0.036, and 60% of the patients exhibited histological improvements after the completion of the follow-up period. The CDAI exhibited a significant difference between the assessment before treatment with infliximab and after induction, as well as before treatment and after maintenance (P<0.01. Conclusion Calprotectin and lactoferrin are not useful for monitoring inflammatory activity in Crohn's disease patients who are subjected to biological therapy.

Use of anti-tumor necrosis factor biologics in the treatment of rheumatoid arthritis does not change human T-lymphotropic virus type 1 markers: a case series.

Science.gov (United States)

Umekita, Kunihiko; Umeki, Kazumi; Miyauchi, Shunichi; Ueno, Shiro; Kubo, Kazuyoshi; Kusumoto, Norio; Takajo, Ichiro; Nagatomo, Yasuhiro; Okayama, Akihiko

2015-09-01

Anti-tumor necrosis factor (anti-TNF) biologics are effective in the treatment of rheumatoid arthritis (RA); however, it is still not clear whether this treatment promotes the development of malignancies such as lymphoma. Human T-lymphotropic virus type 1 (HTLV-1), which is a causative agent of adult T-cell lymphoma (ATL), is prevalent in Japan. Many HTLV-1-positive patients with RA are assumed to exist; however, there have thus far been no reports on the effect of anti-TNF biologics on HTLV-1-positive patients. We analyzed the response to treatment with anti-TNF biologics and change of HTLV-1 markers in two cases of RA. The two cases showed no response based on the European League Against of Rheumatism response criteria 60-96 weeks after administration of anti-TNF biologics (infliximab and etanercept). No signs of ATL were observed and HTLV-1 markers, such as proviral load and clonality of HTLV-1-infected cells, showed no significant change in either of two cases. Therefore, treatment with anti-TNF biologics did not induce activation of HTLV-1, although the effect on RA was not as effective as in HTLV-1-negative patients in this limited study. Further long-term study with a greater number of patients is necessary to clarify the safety and efficacy of anti-TNF biologics in HTLV-1-positive patients with RA.

Identification of apple cultivars on the basis of simple sequence repeat markers.

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Liu, G S; Zhang, Y G; Tao, R; Fang, J G; Dai, H Y

2014-09-12

DNA markers are useful tools that play an important role in plant cultivar identification. They are usually based on polymerase chain reaction (PCR) and include simple sequence repeats (SSRs), inter-simple sequence repeats, and random amplified polymorphic DNA. However, DNA markers were not used effectively in the complete identification of plant cultivars because of the lack of known DNA fingerprints. Recently, a novel approach called the cultivar identification diagram (CID) strategy was developed to facilitate the use of DNA markers for separate plant individuals. The CID was designed whereby a polymorphic maker was generated from each PCR that directly allowed for cultivar sample separation at each step. Therefore, it could be used to identify cultivars and varieties easily with fewer primers. In this study, 60 apple cultivars, including a few main cultivars in fields and varieties from descendants (Fuji x Telamon) were examined. Of the 20 pairs of SSR primers screened, 8 pairs gave reproducible, polymorphic DNA amplification patterns. The banding patterns obtained from these 8 primers were used to construct a CID map. Each cultivar or variety in this study was distinguished from the others completely, indicating that this method can be used for efficient cultivar identification. The result contributed to studies on germplasm resources and the seedling industry in fruit trees.

Molecular markers in glioma.

Science.gov (United States)

Ludwig, Kirsten; Kornblum, Harley I

2017-09-01

Gliomas are the most malignant and aggressive form of brain tumors, and account for the majority of brain cancer related deaths. Malignant gliomas, including glioblastoma are treated with radiation and temozolomide, with only a minor benefit in survival time. A number of advances have been made in understanding glioma biology, including the discovery of cancer stem cells, termed glioma stem cells (GSC). Some of these advances include the delineation of molecular heterogeneity both between tumors from different patients as well as within tumors from the same patient. Such research highlights the importance of identifying and validating molecular markers in glioma. This review, intended as a practical resource for both clinical and basic investigators, summarizes some of the more well-known molecular markers (MGMT, 1p/19q, IDH, EGFR, p53, PI3K, Rb, and RAF), discusses how they are identified, and what, if any, clinical relevance they may have, in addition to discussing some of the specific biology for these markers. Additionally, we discuss identification methods for studying putative GSC's (CD133, CD15, A2B5, nestin, ALDH1, proteasome activity, ABC transporters, and label-retention). While much research has been done on these markers, there is still a significant amount that we do not yet understand, which may account for some conflicting reports in the literature. Furthermore, it is unlikely that the investigator will be able to utilize one single marker to prospectively identify and isolate GSC from all, or possibly, any gliomas.

Malignant transformation in vitro: criteria, biological markers, and application in environmental screening of carcinogens

International Nuclear Information System (INIS)

Borek, C.

1979-01-01

Biological markers which distinguish malignantly transformed fibroblasts from their normal counterpart include pleomorphic morphology, lowered requirement for nutritional factors, loss of density inhibition of growth, complex topography as discernible by scanning electron microscopy, loss in surface proteins, incomplete glycosylation of membrane glycolylipids and glycoproteins, increased production of specific proteases, decreased organization of the cytoskeleton, and acquisition of neoantigens. Several of these markers are not consistently found in transformed epithelial cells and therefore cannot serve to distinguish unequivocally neoplastic epithelial cells from the normal counterparts. The only criteria associated with the transformed nature of both fibroblasts and epithelial cells are the ability of the cells to proliferate in semisolid medium and to induce tumors in appropriate hosts. In vitro systems represent a powerful tool for screening the mutagenic/oncogenic potential of physical, chemical, and environmental agents. Fibroblasts rather than epithelial cells are preferred for this purpose at the present time because of the clear-cut phenotypic differences between the normal and the transformed cells. These systems have been useful in establishing that malignant transformation can be induced by doses as low as 1 rad of X rays or 0.1 rad of neutrons, and that fractionation at low dose levelsleads to enhanced transformation. They have been useful in identifying a large number of hazardous chemicals and in evaluating the relationship between the mutagenic and carcinogenic potential of radiation and chemicals

Adverse biological effects of Milan urban PM looking for suitable molecular markers of exposure

Directory of Open Access Journals (Sweden)

Mantecca Paride

2012-01-01

Full Text Available The results presented summarise the ones obtained in the coordinated research project Tosca, which extensively analysed the impact of Milan urban PM on human health. The molecular markers of exposure and effects of seasonally and size-fractionated PMs (summer and winter PM10, PM2.5 were investigated in in vitro (human lung cell lines and in vivo (mice systems. The results obtained by the analyses of cytotoxic, pro-inflammatory and genotoxic parameters demonstrate that the biological responses are strongly dependent upon the PM samples seasonal and dimensional variability, that ultimately reflect their chemical composition and source. In fact summer PM10, enriched in crustal elements and endotoxins, was the most cytotoxic and pro-inflammatory fraction, while fine winter PMs induced genotoxic effects and xenobiotic metabolizing enzymes (like CYP1B1 production, likely as a consequence of the higher content in combustion derived particles reach in PAHs and heavy toxic metals. These outcomes outline the need of a detailed knowledge of the PMs physico-chemical composition on a local scale, coupled with the biological hazard directly associated to PM exposure. Apparently this is the only way allowing scientists and police-makers to establish the proper relationships between the respirable PM quantity/quality and the health outcomes described by clinicians and epidemiologists.

Uniparental genetic markers in South Amerindians

Directory of Open Access Journals (Sweden)

Rafael Bisso-Machado

2012-01-01

Full Text Available A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.

Verification of the systematic position of California brome (Bromus carinatus Hook. and Arn., Poaceae, cv. 'Broma', on the basis of analysis of issr markers

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Agnieszka Sutkowska

2012-10-01

Full Text Available ‘Broma’ is a grass cultivar belonging to the species Bromus carinatus. In the Lists of Agricultural Plant Varieties of the Research Centre for Cultivar Testing (COBORU, it is shown as Bromus willdenowii (= B. catharticus, B. unioloides (List of Agricultural Plant Varieties 1989-2009, whereas already in 1984 Mirek demonstrated on the basis of morphological analysis that this was a different closely related species – B. carinatus. The aim of the present study was to verify the species affiliation of cv. ‘Broma’. The conducted analysis of ISSR molecular markers included representatives of cv. ‘Broma” as well as of B. carinatus and B. willdenowii. The method used allowed the identification of molecular markers of the above-mentioned taxa. The numerical analysis of the obtained results suggests that cv. ‘Broma’ should be classified in the species B. carinatus, not B. willdenowii.

Radiation biology as a basis for multidisciplinary cancer therapy

International Nuclear Information System (INIS)

Hosoya, N.

2017-01-01

The research field of radiation biology has progressed greatly thanks to the advances in molecular biology. DNA in the cell nucleus is the principal target of radiation. The biological effect of radiation can be determined by how the DNA damage is processed in the cell. In order to prevent deleterious biological effects due to DNA damage, the cells possess a system termed 'DNA damage response'. The DNA damage response finally induces cell cycle arrest, activation of DNA repair pathways, or cell death. If accurately repaired, DNA damage will result in survival of cells with no biological effects. If inaccurately repaired, DNA damage may result in survival of cells exhibiting genetic alterations, which can lead to the development of various diseases including cancer. If unrepaired, fatal DNA damage such as the DNA double-strand break will result in cell depth. Since radiation therapy and chemotherapy are designed to specifically kill cancer cells by inducing DNA double-strand breaks, it is important to take advantage of cancer-specific abnormalities in DNA damage response. In this review, I describe the impact of targeting DNA damage response in cancer therapy and show how progress in radiation biology has contributed to the development of novel therapeutic strategies. (author)

Biological and Chemical Removal of Primary Cilia Affects Mechanical Activation of Chondrogenesis Markers in Chondroprogenitors and Hypertrophic Chondrocytes.

Science.gov (United States)

Deren, Matthew E; Yang, Xu; Guan, Yingjie; Chen, Qian

2016-02-04

Chondroprogenitors and hypertrophic chondrocytes, which are the first and last stages of the chondrocyte differentiation process, respectively, are sensitive to mechanical signals. We hypothesize that the mechanical sensitivity of these cells depends on the cell surface primary cilia. To test this hypothesis, we removed the primary cilia by biological means with transfection with intraflagellar transport protein 88 (IFT88) siRNA or by chemical means with chloral hydrate treatment. Transfection of IFT88 siRNA significantly reduced the percentage of ciliated cells in both chondroprogenitor ATDC5 cells as well as primary hypertrophic chondrocytes. Cyclic loading (1 Hz, 10% matrix deformation) of ATDC5 cells in three-dimensional (3D) culture stimulates the mRNA levels of chondrogenesis marker Type II collagen (Col II), hypertrophic chondrocyte marker Type X collagen (Col X), and a molecular regulator of chondrogenesis and chondrocyte hypertrophy bone morphogenetic protein 2 (BMP-2). The reduction of ciliated chondroprogenitors abolishes mechanical stimulation of Col II, Col X, and BMP-2. In contrast, cyclic loading stimulates Col X mRNA levels in hypertrophic chondrocytes, but not those of Col II and BMP-2. Both biological and chemical reduction of ciliated hypertrophic chondrocytes reduced but failed to abolish mechanical stimulation of Col X mRNA levels. Thus, primary cilia play a major role in mechanical stimulation of chondrogenesis and chondrocyte hypertrophy in chondroprogenitor cells and at least a partial role in hypertrophic chondrocytes.

Biological and Chemical Removal of Primary Cilia Affects Mechanical Activation of Chondrogenesis Markers in Chondroprogenitors and Hypertrophic Chondrocytes

Directory of Open Access Journals (Sweden)

Matthew E. Deren

2016-02-01

Full Text Available Chondroprogenitors and hypertrophic chondrocytes, which are the first and last stages of the chondrocyte differentiation process, respectively, are sensitive to mechanical signals. We hypothesize that the mechanical sensitivity of these cells depends on the cell surface primary cilia. To test this hypothesis, we removed the primary cilia by biological means with transfection with intraflagellar transport protein 88 (IFT88 siRNA or by chemical means with chloral hydrate treatment. Transfection of IFT88 siRNA significantly reduced the percentage of ciliated cells in both chondroprogenitor ATDC5 cells as well as primary hypertrophic chondrocytes. Cyclic loading (1 Hz, 10% matrix deformation of ATDC5 cells in three-dimensional (3D culture stimulates the mRNA levels of chondrogenesis marker Type II collagen (Col II, hypertrophic chondrocyte marker Type X collagen (Col X, and a molecular regulator of chondrogenesis and chondrocyte hypertrophy bone morphogenetic protein 2 (BMP-2. The reduction of ciliated chondroprogenitors abolishes mechanical stimulation of Col II, Col X, and BMP-2. In contrast, cyclic loading stimulates Col X mRNA levels in hypertrophic chondrocytes, but not those of Col II and BMP-2. Both biological and chemical reduction of ciliated hypertrophic chondrocytes reduced but failed to abolish mechanical stimulation of Col X mRNA levels. Thus, primary cilia play a major role in mechanical stimulation of chondrogenesis and chondrocyte hypertrophy in chondroprogenitor cells and at least a partial role in hypertrophic chondrocytes.

The biological basis of plutonium safety standards

International Nuclear Information System (INIS)

Mole, R.H.

1976-01-01

Since no radiation injury or cancer in man can, as yet, be directly attributed to Pu, all safety standards for Pu must be determined by reference to other safety standards, development of which is discussed. A system of safety standards must be based on links with real damage, such as the requirement for 226 Ra in bone. The type of biological information required for making standards realistic is considered in relation to Pu and Ra in bone. Also considered are the possible effects of Pu in soft tissue such as bone marrow. Not only dose, but also the number of cells exposed to the dose are important biologically and cellular aspects are examined. Since there is no positive evidence of Pu toxicity relevant information on other α emitters must be examined. The observed effectiveness of Ra, daughters of 222 Ra and 232 Th in causing mutations and cancer, is surveyed. Reference is made to the necessity of improving the ICRP system, currently based on the critical organ concept, by recognising the need for summation of risks in other organs where exposure to Pu is concerned. Improved biological understanding particularly that of hereditary damage, in recent years leads to less pessimistic thinking on the effects of ionizing radiations. The immediate need appears to be for consistency in safety standards. (U.K.)

Evaluation of Accessory Lacrimal Gland in Muller's Muscle Conjunctival Resection Specimens for Precursor Cell Markers and Biological Markers of Dry Eye Disease.

Science.gov (United States)

Ali, Marwan; Shah, Dhara; Pasha, Zeeshan; Jassim, Sarmad H; Jassim Jaboori, Assraa; Setabutr, Pete; Aakalu, Vinay K

2017-04-01

The accessory lacrimal glands (ALGs) are an understudied component of the tear functional unit, even though they are important in the development of dry eye syndrome (DES). To advance our understanding of aging changes, regenerative potential, and histologic correlates to human characteristics, we investigated human ALG tissue from surgical samples to determine the presence or absence of progenitor cell markers and lacrimal epithelial markers and to correlate marker expression to relevant patient characteristics. ALG tissues obtained from Muller's muscle conjunctival resection (MMCR) specimens were created using tissue microarrays (TMAs). Immunofluorescence staining of MMCR sections was performed using primary antibodies specific to cell protein markers. Cell marker localization in TMAs was then assessed by two blinded observers using a standardized scoring system. Patient characteristics including age, race, and status of ocular surface health were then compared against expression of stem cell markers. Human ALG expressed a number of epithelial markers, and in particular, histatin-1 was well correlated with the expression of epithelial markers and was present in most acini. In addition, we noted the presence of precursor cell markers nestin, ABCG2, and CD90 in ALG tissue. There was a decrease in precursor cell marker expression with increasing age. Finally, we noted that a negative association was present between histatin-1 expression and DES. Thus, we report for the first time that human ALG tissues contain precursor marker-positive cells and that this marker expression may decrease with increasing age. Moreover, histatin-1 expression may be decreased in DES. Future studies will be performed to use these cell markers to isolate and culture lacrimal epithelial cells from heterogeneous tissues, determine the relevance of histatin-1 expression to DES, and isolate candidate precursor cells from ALG tissue.

Incorporation of conventional genetic markers and RAPD markers into an RFLP based map in maize

International Nuclear Information System (INIS)

Coe, E.H. Jr.; McMullen, M.D.; Polacco, M.; Davis, G.L.; Chao, S.

1998-01-01

Integration of classical genetic markers, in particular mutants, onto the maize Restriction Fragment Length Polymorphism (RFLP) map will provide the tools necessary to further our understanding of plant development and of complex traits. Initially integration was accomplished by visual alignment of common markers and sometimes involved the use of information from several different molecular maps to determine the relative placement of a single mutant. The maize core marker set was designed to provide a common set of markers which could be used for integration of map data. We have completed the mapping, of 56 mutants on chromosome one relative to the core marker set. Phenotypes included whole plant, seedling, and kernel effects and represented a variety of biological processes. Since these mutants were previously located to chromosome arm, mapping required the use of only seven markers per mutant to define the correct bin location. Two mistakes in marker order relative to the classical map were identified, as well as, six groups of mutants which require allelism testing. Placement of mutants and cDNAs into bins using, the core markers provides a necessary resource for identification of gene function in maize. (author)

Biological basis of heavy ion beams for cancer therapy

International Nuclear Information System (INIS)

Sakamoto, Kiyohiko

1985-01-01

Fast neutron therapy has started firstly and proton therapy has commenced secondly, fast neutron shows better biological effects compared to conventional radiations but its dose distribution is not good, and proton demonstrates excellent dose distribution but its biological effects are almost the same as that of conventional radiations. On the other hand, negative pi-mesons and heavy ions indicate high radiobiological effect and excellent dose distribution, therefore these particle radiations is considered to be more attractive for radiotherapeutic radiations to enhance cure rate of cancers. The biological strong points of these particles are as follows : 1) cells exposed to these particle radiations shows less recovery after irradiation compared to conventional radiations, 2) these radiations show high biological effects (high value of relative biological effectiveness = RBE) when the same dose is given, 3) big effects on hypoxic cells which exsist in tumor, i.e. the value of oxygen enhancement ratio (OER) is low, 4) the differences in radiosensitivity by stages of cell cycle are not so great (data was not shown in present paper), 5) biological effects at prepeak plateau region in depth dose curve formed by these particle radiations is less than that at peak region (therefore, if beam is modulated to cover tumor at spraed out broad peak, tumors is given more biological effect compared to normal tissues which is to be exposed to radiations at prepaeak region). Clinical trial using heavy ions are being performed at Lawrence Berkeley Laboratory which is only one facility to be able to try clinical trial. The results of clinical trials at Lawrence Berkeley Laboratory suggest to be very prospective to enhance tumor cure rate, however it is too early to estimate the effect of heavy ion therapy. (J.P.N.)

Source Identification of Human Biological Materials and Its Prospect in Forensic Science.

Science.gov (United States)

Zou, K N; Gui, C; Gao, Y; Yang, F; Zhou, H G

2016-06-01

Source identification of human biological materials in crime scene plays an important role in reconstructing the crime process. Searching specific genetic markers to identify the source of different human biological materials is the emphasis and difficulty of the research work of legal medical experts in recent years. This paper reviews the genetic markers which are used for identifying the source of human biological materials and studied widely, such as DNA methylation, mRNA, microRNA, microflora and protein, etc. By comparing the principles and methods of source identification of human biological materials using different kinds of genetic markers, different source of human biological material owns suitable marker types and can be identified by detecting single genetic marker or combined multiple genetic markers. Though there is no uniform standard and method for identifying the source of human biological materials in forensic laboratories at present, the research and development of a series of mature and reliable methods for distinguishing different human biological materials play the role as forensic evidence which will be the future development direction. Copyright© by the Editorial Department of Journal of Forensic Medicine.

Evolving Evidence for the Value of Neuroimaging Methods and Biological Markers in Subjects Categorized with Subjective Cognitive Decline.

Science.gov (United States)

Lista, Simone; Molinuevo, Jose L; Cavedo, Enrica; Rami, Lorena; Amouyel, Philippe; Teipel, Stefan J; Garaci, Francesco; Toschi, Nicola; Habert, Marie-Odile; Blennow, Kaj; Zetterberg, Henrik; O'Bryant, Sid E; Johnson, Leigh; Galluzzi, Samantha; Bokde, Arun L W; Broich, Karl; Herholz, Karl; Bakardjian, Hovagim; Dubois, Bruno; Jessen, Frank; Carrillo, Maria C; Aisen, Paul S; Hampel, Harald

2015-09-24

There is evolving evidence that individuals categorized with subjective cognitive decline (SCD) are potentially at higher risk for developing objective and progressive cognitive impairment compared to cognitively healthy individuals without apparent subjective complaints. Interestingly, SCD, during advancing preclinical Alzheimer's disease (AD), may denote very early, subtle cognitive decline that cannot be identified using established standardized tests of cognitive performance. The substantial heterogeneity of existing SCD-related research data has led the Subjective Cognitive Decline Initiative (SCD-I) to accomplish an international consensus on the definition of a conceptual research framework on SCD in preclinical AD. In the area of biological markers, the cerebrospinal fluid signature of AD has been reported to be more prevalent in subjects with SCD compared to healthy controls; moreover, there is a pronounced atrophy, as demonstrated by magnetic resonance imaging, and an increased hypometabolism, as revealed by positron emission tomography, in characteristic brain regions affected by AD. In addition, SCD individuals carrying an apolipoprotein ɛ4 allele are more likely to display AD-phenotypic alterations. The urgent requirement to detect and diagnose AD as early as possible has led to the critical examination of the diagnostic power of biological markers, neurophysiology, and neuroimaging methods for AD-related risk and clinical progression in individuals defined with SCD. Observational studies on the predictive value of SCD for developing AD may potentially be of practical value, and an evidence-based, validated, qualified, and fully operationalized concept may inform clinical diagnostic practice and guide earlier designs in future therapy trials.

Stereotactic core needle breast biopsy marker migration: An analysis of factors contributing to immediate marker migration.

Science.gov (United States)

Jain, Ashali; Khalid, Maria; Qureshi, Muhammad M; Georgian-Smith, Dianne; Kaplan, Jonah A; Buch, Karen; Grinstaff, Mark W; Hirsch, Ariel E; Hines, Neely L; Anderson, Stephan W; Gallagher, Katherine M; Bates, David D B; Bloch, B Nicolas

2017-11-01

To evaluate breast biopsy marker migration in stereotactic core needle biopsy procedures and identify contributing factors. This retrospective study analyzed 268 stereotactic biopsy markers placed in 263 consecutive patients undergoing stereotactic biopsies using 9G vacuum-assisted devices from August 2010-July 2013. Mammograms were reviewed and factors contributing to marker migration were evaluated. Basic descriptive statistics were calculated and comparisons were performed based on radiographically-confirmed marker migration. Of the 268 placed stereotactic biopsy markers, 35 (13.1%) migrated ≥1 cm from their biopsy cavity. Range: 1-6 cm; mean (± SD): 2.35 ± 1.22 cm. Of the 35 migrated biopsy markers, 9 (25.7%) migrated ≥3.5 cm. Patient age, biopsy pathology, number of cores, and left versus right breast were not associated with migration status (P> 0.10). Global fatty breast density (P= 0.025) and biopsy in the inner region of breast (P = 0.031) were associated with marker migration. Superior biopsy approach (P= 0.025), locally heterogeneous breast density, and t-shaped biopsy markers (P= 0.035) were significant for no marker migration. Multiple factors were found to influence marker migration. An overall migration rate of 13% supports endeavors of research groups actively developing new biopsy marker designs for improved resistance to migration. • Breast biopsy marker migration is documented in 13% of 268 procedures. • Marker migration is affected by physical, biological, and pathological factors. • Breast density, marker shape, needle approach etc. affect migration. • Study demonstrates marker migration prevalence; marker design improvements are needed.

Evaluation of Accessory Lacrimal Gland in Muller’s Muscle Conjunctival Resection Specimens for Precursor Cell Markers and Biological Markers of Dry Eye Disease

Science.gov (United States)

Ali, Marwan; Shah, Dhara; Pasha, Zeeshan; Jassim, Sarmad H.; Jaboori, Assraa Jassim; Setabutr, Pete; Aakalu, Vinay K.

2017-01-01

Purpose The accessory lacrimal glands (ALG) are an understudied component of the tear functional unit, even though they are important in the development of dry eye syndrome (DES). To advance our understanding of aging changes, regenerative potential and histologic correlates to human characteristics, we investigated human ALG tissue from surgical samples to determine the presence or absence of progenitor cell markers and lacrimal epithelial markers and to correlate marker expression to relevant patient characteristics. Materials and Methods ALG tissues obtained from Muller’s Muscle Conjunctival Resection (MMCR) specimens were created using tissue microarrays (TMAs). Immunofluorescence staining of MMCR sections was performed using primary antibodies specific to cell protein markers. Cell marker localization in TMAs was then assessed by two blinded observers using a standardized scoring system. Patient characteristics including age, race, and status of ocular surface health were then compared against expression of stem cell markers. Results Human ALG expressed a number of epithelial markers, and in particular, histatin-1 was well correlated with the expression of epithelial markers and was present in most acini. In addition, we noted the presence of precursor cell markers nestin, ABCG2 and CD90 in ALG tissue. There was a decrease in precursor cell marker expression with increasing age. Finally, we noted that a negative association was present between histatin-1 expression and DES. Conclusions Thus, we report for the first time that human ALG tissues contain precursor marker positive cells and that this marker expression may decrease with increasing age. Moreover, histatin-1 expression may be decreased in DES. Future studies will be performed to use these cell markers to isolate and culture lacrimal epithelial cells from heterogeneous tissues, determine the relevance of histatin-1 expression to DES and isolate candidate precursor cells from ALG tissue. PMID:27612554

Accuracy of marker-assisted selection with auxiliary traits

Indian Academy of Sciences (India)

Unknown

Genetic information on molecular markers is increasingly being used in plant and animal improvement programmes particularly as indirect means to improve a metric trait by selection either on an individual basis or on the basis of an index incorporating such information. This paper examines the utility of an index of ...

CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models.

Science.gov (United States)

Chen, Yuhui; Lawless, Conor; Gillespie, Colin S; Wu, Jake; Boys, Richard J; Wilkinson, Darren J

2010-05-01

Dynamic simulation modelling of complex biological processes forms the backbone of systems biology. Discrete stochastic models are particularly appropriate for describing sub-cellular molecular interactions, especially when critical molecular species are thought to be present at low copy-numbers. For example, these stochastic effects play an important role in models of human ageing, where ageing results from the long-term accumulation of random damage at various biological scales. Unfortunately, realistic stochastic simulation of discrete biological processes is highly computationally intensive, requiring specialist hardware, and can benefit greatly from parallel and distributed approaches to computation and analysis. For these reasons, we have developed the BASIS system for the simulation and storage of stochastic SBML models together with associated simulation results. This system is exposed as a set of web services to allow users to incorporate its simulation tools into their workflows. Parameter inference for stochastic models is also difficult and computationally expensive. The CaliBayes system provides a set of web services (together with an R package for consuming these and formatting data) which addresses this problem for SBML models. It uses a sequential Bayesian MCMC method, which is powerful and flexible, providing very rich information. However this approach is exceptionally computationally intensive and requires the use of a carefully designed architecture. Again, these tools are exposed as web services to allow users to take advantage of this system. In this article, we describe these two systems and demonstrate their integrated use with an example workflow to estimate the parameters of a simple model of Saccharomyces cerevisiae growth on agar plates.

Role of serum eosinophil cationic protein as a biological marker to assess the severity of bronchial asthma

International Nuclear Information System (INIS)

Begum, A.; Sattar, H.; Miah, R.A.; Saleh, A.A.; Hassan, R.; Salam, A

2012-01-01

Objective: The study was carried out to evaluate the role of serum eosinophil cationic protein (ECP) as a biological marker for the diagnosis and to assess the severity of bronchial asthma. Methodology: This observational cross-sectional study was conducted among 70 bronchial asthma patients and 45 disease controls (tuberculosis-15, chronic obstructive pulmonary disease-15, interstitial lung disease-15) enrolled from patients attending the outpatient department of the National Institute of Disease of the Chest and Hospital (NIDCH), Dhaka, Bangladesh during July 2010 to June 2011. Global Initiative of Asthma Management and Prevention (GINA) criteria were followed for selection of both atopic and non-atopic patients with intermittent or persistent (mild, moderate and severe) asthma. Serum level of eosinophil cationic protein (ECP), IgE, forced expiratory volume in 1 second (FEV 1% predicted) and circulatory eosinophil (CE) count were estimated. Results: Mean serum ECP level (28.8 +- 42.9 vs. 6.82 +- 3.5 ng/mL; P<0.001), IgE level (383.59 - 225.3 vs. 135 +- 131.8 IU/mL; P<0.001) and percent circulatory eosinophil count (9.95 +- 3.7 vs. 5.95 +- 1.4; P<0.024) were all found significantly raised among asthma patients than disease controls but % FEV1 was equivocal. All grades of persistent asthma patients had significantly (P<0.025 and P<0.002) higher mean ECP level than intermittent cases but serum IgE level and CE count did not differ significantly. FEV1 % predicted correlated well among moderate and severe persistent asthma but was equivocal for intermittent and mild persistent cases. Conclusion: This study has reinforced that serum eosinophil cationic protein is a dependable biological marker with more discriminatory power over other indicators for bronchial asthma and to assess its severity. (author)

Total and phosphorylated tau protein as biological markers of Alzheimer's disease.

LENUS (Irish Health Repository)

Hampel, Harald

2012-02-01

Advances in our understanding of tau-mediated neurodegeneration in Alzheimer\\'s disease (AD) are moving this disease pathway to center stage for the development of biomarkers and disease modifying drug discovery efforts. Immunoassays were developed detecting total (t-tau) and tau phosphorylated at specific epitopes (p-tauX) in cerebrospinal fluid (CSF), methods to analyse tau in blood are at the experimental beginning. Clinical research consistently demonstrated CSF t- and p-tau increased in AD compared to controls. Measuring these tau species proved informative for classifying AD from relevant differential diagnoses. Tau phosphorylated at threonine 231 (p-tau231) differentiated between AD and frontotemporal dementia, tau phosphorylated at serine 181 (p-tau181) enhanced classification between AD and dementia with Lewy bodies. T- and p-tau are considered "core" AD biomarkers that have been successfully validated by controlled large-scale multi-center studies. Tau biomarkers are implemented in clinical trials to reflect biological activity, mechanisms of action of compounds, support enrichment of target populations, provide endpoints for proof-of-concept and confirmatory trials on disease modification. World-wide quality control initiatives are underway to set required methodological and protocol standards. Discussions with regulatory authorities gain momentum defining the role of tau biomarkers for trial designs and how they may be further qualified for surrogate marker status.

Effectiveness of biologic and non-biologic antirheumatic drugs on anaemia markers in 153,788 patients with rheumatoid arthritis: New evidence from real-world data.

Science.gov (United States)

Paul, Sanjoy Ketan; Montvida, Olga; Best, Jennie H; Gale, Sara; Pethoe-Schramm, Attila; Sarsour, Khaled

2018-02-01

To evaluate the impact of treatment with disease-modifying antirheumatic drugs (DMARDs), including IL-6 receptor inhibitor tocilizumab (TCZ), on anaemia markers in patients with rheumatoid arthritis. Using the Centricity Electronic Medical Records from USA, patients with rheumatoid arthritis diagnosed between January 2000 and April 2016, who initiated TCZ (n = 3732); tofacitinib (TOFA, n = 3126); other biologic DMARD (obDMARD, n = 55,964); or other non-biologic DMARD (onbDMARD, n = 91,236) were identified. Changes in haemoglobin (Hb) and haematocrit (Hct) over 2 years of treatment initiation were evaluated, adjusting and balancing for confounders. Mean (95% CI) adjusted increase in Hb and Hct levels at 24 months in TCZ group were 0.23g/dL (0.14, 0.42) and 0.96% (0.41, 1.52) respectively. Among patients with anaemia in the TCZ group, Hb and Hct increased significantly by 0.72g/dL and 2.06%, respectively. Patients in the TCZ group were 86% (95% CI of OR: 1.43, 2.00) more likely to increase Hb ≥ 1g/dL compared to the other groups combined. No clinically significant changes in Hb were observed in the other groups. The obDMARD group demonstrated lower Hct increase than TCZ group, while no significant changes were observed in the remaining groups. Compared to those who initiated TCZ therapy after 1 year of diagnosis of rheumatoid arthritis, those who initiated earlier were 95% (OR = 1.95; 95% CI: 1.19, 3.21; p < 0.001) more likely to increase Hb within 6 months. This real-world study suggests significant increase in Hb and Hct levels after TCZ therapy in anaemic and non-anaemic patients with rheumatoid arthritis, compared with other biologic and non-biologic DMARDs. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Prognostic factors in non-muscle-invasive bladder tumors - I. Clinical prognostic factors: A review of the experience of the EORTC genito-urinary group - II. Biologic prognostic markers

NARCIS (Netherlands)

Kurth, Karl-Heinz; Sylvester, Richard J.

2007-01-01

Objectives: To summarize the most important clinical prognostic factors of non-muscle-invasive bladder cancer, as assessed by the European organization for Research and Treatment of Cancer (EORTC) Genito-Urinary Group, to present biologic markers involved in urothelial cell carcinoma, and to address

The Learning of Biology: A Structural Basis for Future Research

Science.gov (United States)

Murray, Darrel L.

1977-01-01

This article reviews recent research studies and experiences relating the learning theories of Ausubel to biology instruction. Also some suggestions are made for future research on the learning of biology. (MR)

EuroFIR-BASIS - a combined composition and biological activity database for bioactive compounds in plant-based foods

DEFF Research Database (Denmark)

Gry, Jørn; Black, Lucinda; Eriksen, Folmer Damsted

2007-01-01

Mounting evidence suggests that certain non-nutrient bioactive compounds promote optimal human health and reduce the risk of chronic disease. An Internet-deployed database, EuroFIR-BASIS, which uniquely combines food composition and biological effects data for plant-based bioactive compounds......, is being developed. The database covers multiple compound classes and 330 major food plants and their edible parts with data sourced from quality-assessed, peer-reviewed literature. The database will be a valuable resource for food regulatory and advisory bodies, risk authorities, epidemiologists...... and researchers interested in diet and health relationships, and product developers within the food industry....

Recent advances in candidate-gene and whole-genome approaches to the discovery of anthelmintic resistance markers and the description of drug/receptor interactions

Directory of Open Access Journals (Sweden)

Andrew C. Kotze

2014-12-01

Full Text Available Anthelmintic resistance has a great impact on livestock production systems worldwide, is an emerging concern in companion animal medicine, and represents a threat to our ongoing ability to control human soil-transmitted helminths. The Consortium for Anthelmintic Resistance and Susceptibility (CARS provides a forum for scientists to meet and discuss the latest developments in the search for molecular markers of anthelmintic resistance. Such markers are important for detecting drug resistant worm populations, and indicating the likely impact of the resistance on drug efficacy. The molecular basis of resistance is also important for understanding how anthelmintics work, and how drug resistant populations arise. Changes to target receptors, drug efflux and other biological processes can be involved. This paper reports on the CARS group meeting held in August 2013 in Perth, Australia. The latest knowledge on the development of molecular markers for resistance to each of the principal classes of anthelmintics is reviewed. The molecular basis of resistance is best understood for the benzimidazole group of compounds, and we examine recent work to translate this knowledge into useful diagnostics for field use. We examine recent candidate-gene and whole-genome approaches to understanding anthelmintic resistance and identify markers. We also look at drug transporters in terms of providing both useful markers for resistance, as well as opportunities to overcome resistance through the targeting of the transporters themselves with inhibitors. Finally, we describe the tools available for the application of the newest high-throughput sequencing technologies to the study of anthelmintic resistance.

Biological markers for anxiety disorders, OCD and PTSD: A consensus statement. Part II: Neurochemistry, neurophysiology and neurocognition

Science.gov (United States)

Bandelow, Borwin; Baldwin, David; Abelli, Marianna; Bolea-Alamanac, Blanca; Bourin, Michel; Chamberlain, Samuel R.; Cinosi, Eduardo; Davies, Simon; Domschke, Katharina; Fineberg, Naomi; Grünblatt, Edna; Jarema, Marek; Kim, Yong-Ku; Maron, Eduard; Masdrakis, Vasileios; Mikova, Olya; Nutt, David; Pallanti, Stefano; Pini, Stefano; Ströhle, Andreas; Thibaut, Florence; Vaghix, Matilde M.; Won, Eunsoo; Wedekind, Dirk; Wichniak, Adam; Woolley, Jade; Zwanzger, Peter; Riederer, Peter

2017-01-01

Objective Biomarkers are defined as anatomical, biochemical or physiological traits that are specific to certain disorders or syndromes. The objective of this paper is to summarise the current knowledge of biomarkers for anxiety disorders, obsessive-compulsive disorder (OCD) and posttraumatic stress disorder (PTSD). Methods Findings in biomarker research were reviewed by a task force of international experts in the field, consisting of members of the World Federation of Societies for Biological Psychiatry Task Force on Biological Markers and of the European College of Neuropsychopharmacology Anxiety Disorders Research Network. Results The present article (Part II) summarises findings on potential biomarkers in neurochemistry (neurotransmitters such as serotonin, norepinephrine, dopamine or GABA, neuropeptides such as cholecystokinin, neurokinins, atrial natriuretic peptide, or oxytocin, the HPA axis, neurotrophic factors such as NGF and BDNF, immunology and CO2 hypersensitivity), neurophysiology (EEG, heart rate variability) and neurocognition. The accompanying paper (Part I) focuses on neuroimaging and genetics. Conclusions Although at present, none of the putative biomarkers is sufficient and specific as a diagnostic tool, an abundance of high quality research has accumulated that should improve our understanding of the neurobiological causes of anxiety disorders, OCD and PTSD. PMID:27419272

Sequence characterized amplified region (SCAR) markers-based ...

African Journals Online (AJOL)

ajl yemi

2011-12-19

Dec 19, 2011 ... reverse transcription polymerase chain reaction (RT-PCR), differential-display .... were synthesized by Sangon Biological Engineering Technology and. Services ..... to cold tolerance to scar markers in common carp. J. Dalian.

EuroFIR eBASIS: application for health claims submissions and evaluations

DEFF Research Database (Denmark)

Kiely, M.; Black, L.J.; Plumb, J.

2010-01-01

Background: The European Food Information Resource (EuroFIR) network has established the eBASIS (Bioactive Substances in Food Information System) online food composition and biological effects database for plant-derived bioactive compounds (phytochemicals). On the basis of submitted evidence......, the European Food Safety Authority (EFSA) expert panel on Dietetic Products, Nutrition and Allergies assesses whether claims made under articles 13.1, 13.5 or 14 of the Regulation (EC) 1924/2006, which governs the use of nutrition and health claims on foods, are scientifically justified. This report evaluates...... the eBASIS biological effects database in the preparation and evaluation of health claims dossiers. Methods: The eBASIS biological effects database is a compilation of expert-evaluated data extracted from the literature, prioritising human intervention studies to investigate health effects...

Identification of biological/biochemical marker(s) for preterm delivery

DEFF Research Database (Denmark)

Thorsen, Poul; Schendel, Diana; Deshpande, Anjali D.

2001-01-01

Fetal and neonatal mortality and morbidity rates are strongly associated with gestational age for delivery: the risk for poor outcome increases as gestational age decreases. Attempts to predict preterm delivery (PTD, spontaneous delivery before 37 weeks' gestation) have been largely unsuccessful...... a nested case-control study of PTD in 84 cases and 400 controls has been performed. The second study is a nested case-control study of 675 PTD cases (equally divided into three gestational age categories of 24-29 weeks' gestation, 30-33 weeks' gestation, and 34-36 weeks' gestation) and 675 controls drawn...... study against PTD. The first phase of the clinical intervention study will be to establish a risk-assessment model based on the "best" combination of biological/biochemical measures and other factors associated with PTD in order to identify pregnant women at very high risk of PTD. The second phase...

Biological dosimetry of irradiation accidents

International Nuclear Information System (INIS)

Durand, V.; Chambrette, V.; Le Roy, A.; Paillole, N.; Sorokine, I.; Voisin, P.

1994-01-01

The biological dosimetry in radiation protection allows to evaluate the received dose by a potentially irradiated person from biological markers such chromosomal abnormalities. The technologies of Hybridization In Situ by Fluorescence (F.I.S.H) allow the detection of steady chromosomal aberrations of translocation type

Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges.

Science.gov (United States)

Kanthaswamy, S

2015-10-01

This review highlights the importance of domestic animal genetic evidence sources, genetic testing, markers and analytical approaches as well as the challenges this field is facing in view of the de facto 'gold standard' human DNA identification. Because of the genetic similarity between humans and domestic animals, genetic analysis of domestic animal hair, saliva, urine, blood and other biological material has generated vital investigative leads that have been admitted into a variety of court proceedings, including criminal and civil litigation. Information on validated short tandem repeat, single nucleotide polymorphism and mitochondrial DNA markers and public access to genetic databases for forensic DNA analysis is becoming readily available. Although the fundamental aspects of animal forensic genetic testing may be reliable and acceptable, animal forensic testing still lacks the standardized testing protocols that human genetic profiling requires, probably because of the absence of monetary support from government agencies and the difficulty in promoting cooperation among competing laboratories. Moreover, there is a lack in consensus about how to best present the results and expert opinion to comply with court standards and bear judicial scrutiny. This has been the single most persistent challenge ever since the earliest use of domestic animal forensic genetic testing in a criminal case in the mid-1990s. Crime laboratory accreditation ensures that genetic test results have the courts' confidence. Because accreditation requires significant commitments of effort, time and resources, the vast majority of animal forensic genetic laboratories are not accredited nor are their analysts certified forensic examiners. The relevance of domestic animal forensic genetics in the criminal justice system is undeniable. However, further improvements are needed in a wide range of supporting resources, including standardized quality assurance and control protocols for sample

Perspective Biological Markers for Autism Spectrum Disorders: Advantages of the Use of Receiver Operating Characteristic Curves in Evaluating Marker Sensitivity and Specificity

Directory of Open Access Journals (Sweden)

Provvidenza M. Abruzzo

2015-01-01

Full Text Available Autism Spectrum Disorders (ASD are a heterogeneous group of neurodevelopmental disorders. Recognized causes of ASD include genetic factors, metabolic diseases, toxic and environmental factors, and a combination of these. Available tests fail to recognize genetic abnormalities in about 70% of ASD children, where diagnosis is solely based on behavioral signs and symptoms, which are difficult to evaluate in very young children. Although it is advisable that specific psychotherapeutic and pedagogic interventions are initiated as early as possible, early diagnosis is hampered by the lack of nongenetic specific biological markers. In the past ten years, the scientific literature has reported dozens of neurophysiological and biochemical alterations in ASD children; however no real biomarker has emerged. Such literature is here reviewed in the light of Receiver Operating Characteristic (ROC analysis, a very valuable statistical tool, which evaluates the sensitivity and the specificity of biomarkers to be used in diagnostic decision making. We also apply ROC analysis to some of our previously published data and discuss the increased diagnostic value of combining more variables in one ROC curve analysis. We also discuss the use of biomarkers as a tool for advancing our understanding of nonsyndromic ASD.

Radiographic markers - A reservoir for bacteria?

International Nuclear Information System (INIS)

Tugwell, Jenna; Maddison, Adele

2011-01-01

Introduction: Amongst the most frequently handled objects in the radiology department are radiographic markers. They are personal accessories used with every patient, and are kept in the radiographers pockets when not utilised. Upon enquiry it was discovered that many radiographers disregarded the potential of these accessories to become a vector for cross-contamination thus never or rarely clean them. The aims of this study were therefore to identify if radiographic markers are a reservoir for bacteria and to establish an effective cleaning method for decontaminating them. Methodology: 25 radiographers/student radiographers were selected for this study. Swabbing of their markers prior and post cleaning took place. The microbiology laboratory subsequently analyzed the results by quantifying and identifying the bacteria present. The participants also completed a closed questionnaire regarding their markers (e.g. frequency of cleaning and type of marker) to help specify the results gained from the swabbing procedure. Results: From the sample swabbed, 92% were contaminated with various organisms including Staphylococcus and Bacillus species, the amount of bacteria present ranged from 0 to >50 CFU. There were no significant differences between disinfectant wipes and alcohol gel in decontaminating the markers. Both successfully reduced their bacterial load, with 80% of the markers post cleaning having 0 CFU. Conclusion: The results indicated that radiographic markers can become highly contaminated with various organisms thus serve as a reservoir for bacteria. In addition, the markers need to be cleaned on a regular basis, with either disinfectant wipes or alcohol gel to reduce their bacterial load.

Application of biological markers for the identification of oil-type pollutants in recent sediments: Alluvial formation of the Danube river, Oil refinery Pančevo

Directory of Open Access Journals (Sweden)

Rašović Aleksandar S.

2002-01-01

Full Text Available The purpose of this paper was to examine to which extent the abundance and distribution of certain biological markers may be used for the identification of oil-type pollutants in recent sediments and ground waters. The samples were taken from the area of the Oil Refinery Pančevo (alluvial formation of the Danube River. The organic matter of the investigated samples was isolated using an extraction method with chloroform. The group composition and usual biological markers were analyzed in the obtained extracts. n-Alkanes and acyclic isoprenoids, pristane and phytane were analyzed using gas chromatographie (GC analysis of saturated hydrocarbons. Polycyclic alkanes of the sterane and terpane type were analyzed using gas chromatography-mass spectrometry (GC-MS, i.e. by analyzing the carbamide non-adduct of the total alkane fraction (Single Ion Monitoring SIM-technique. The obtained results indicate that n-alkanes can be used for the identification of oil-type pollutants (for example, if the oil-pollutant is biodegraded or present in very low concentrations, and steranes and triterpanes can be used as very reliable indicators of oil-type pollution in recent sediments and ground waters.

[Serum anticholinergic activity: relationship with clinical symptoms in Alzheimer's disease and proposal of new biological marker].

Science.gov (United States)

Hori, Koji; Konishi, Kimiko; Hachisu, Mitsugu

2011-06-01

We reviewed the importance of measuring serum anticholinergic activity (SAA) in patients with Alzheimer's disease (AD). Since Tune and Coyle reported a simple method for assessing SAA using radioreceptor-binding assay, SAA is assumed to be the cumulative activity of parent medications and their metabolites and its relationship with delirium and cognitive functions has been debated. However, we evaluated the SAA in AD patients and SAA was correlated with prescription of antipsychotic medications, cognitive dysfunctions, severity of AD and psychotic symptoms, especially, with delusion and diurnal rhythm disturbance. From these results, we should not only pay attention to avoiding the prescription of medications with anticholinergic activity but also we speculated that AA appeared endogenously in AD and accelerated AD pathology. Moreover, there might be the possibility that SAA has predictive value for assessing the progressiveness of AD and as a biological marker for AD.

Characterization of tumorigenicity and radio-sensitivity markers by an ex vivo approach. In vivo identification of p53 dependent radio-sensitivity markers

International Nuclear Information System (INIS)

Alvarez, S.

2003-12-01

After a detailed discussion of the relationship between cancer and genetic instability, of the structure, activation mechanisms, activity and biological functions of the p53 protein, a presentation of p53 mutants, and a recall of the effects of ionizing radiations, the author reports a biology research during which he investigated a cell model established from rat embryo lungs treated with Benzo[a]pyrene and made of tumoral lines muted by the p53 gene. He tried to identify markers which could report differences of tumorigenicity and radio-sensitivity observed in these different lines. He also tried to characterize radio-sensitivity molecular markers dependent on the p53 gene in a context of normal cells

Molecular mechanisms of nematode-nematophagous microbe interactions: basis for biological control of plant-parasitic nematodes.

Science.gov (United States)

Li, Juan; Zou, Chenggang; Xu, Jianping; Ji, Xinglai; Niu, Xuemei; Yang, Jinkui; Huang, Xiaowei; Zhang, Ke-Qin

2015-01-01

Plant-parasitic nematodes cause significant damage to a broad range of vegetables and agricultural crops throughout the world. As the natural enemies of nematodes, nematophagous microorganisms offer a promising approach to control the nematode pests. Some of these microorganisms produce traps to capture and kill the worms from the outside. Others act as internal parasites to produce toxins and virulence factors to kill the nematodes from within. Understanding the molecular basis of microbe-nematode interactions provides crucial insights for developing effective biological control agents against plant-parasitic nematodes. Here, we review recent advances in our understanding of the interactions between nematodes and nematophagous microorganisms, with a focus on the molecular mechanisms by which nematophagous microorganisms infect nematodes and on the nematode defense against pathogenic attacks. We conclude by discussing several key areas for future research and development, including potential approaches to apply our recent understandings to develop effective biocontrol strategies.

Genetic diversity of maize genotypes on the basis of morpho ...

African Journals Online (AJOL)

Genetic diversity of maize genotypes on the basis of morpho-physiological and simple sequence repeat (SSR) markers. Ashish Kumar, Arunita Rakshit, Naresh K Mangilipelli, Y Varalaxmi, T Vijayalakshmi, Jainender M Vanaja, SK Yadav, B Venkateswarlu, M Maheswari ...

Prediction for steatosis in type-2 diabetes: clinico-biological markers versus 1H-MR spectroscopy

International Nuclear Information System (INIS)

Guiu, Boris; Krause, Denis; Cercueil, Jean-Pierre; Crevisy-Girod, Elodie; Binquet, Christine; Duvillard, Laurence; Masson, David; Lepage, Come; Hamza, Samia; Minello, Anne; Hillon, Patrick; Verges, Bruno; Petit, Jean-Michel

2012-01-01

The SteatoTest, fatty liver index (FLI) and hepatic steatosis index (HSI) are clinico-biological scores of steatosis validated in general or selected populations. Serum adiponectin (s-adiponectin) and retinol binding protein 4 (s-RBP4) are adipokines that could predict liver steatosis. We investigated whether the Steatotest, FLI, HSI, s-adiponectin and s-RBP4 could be valid predictors of liver steatosis in type-2 diabetic (T2D) patients. We enrolled 220 consecutive T2D patients. Reference standard was 3.0 T 1 H-MR spectroscopy (corrected for T1 and T2 decays). Intraclass correlation coefficients (ICCs), Kappa statistic measures of agreement, receiver operating characteristic (ROC) curves were assessed. Median liver fat content was 91 mg triglyceride/g liver tissue (range: 0-392). ICCs among the Steatotest, FLI, HSI, s-adiponectin, s-RBP4 and spectroscopy were low: 0.384, 0.281, 0.087, -0.297 and 0.048. Agreement between scores and spectroscopy was poor (Kappa range: 0.042-0.281). The areas under the ROC curves were low: 0.674, 0.647, 0.637, 0.616 and 0.540. S-adiponectin and s-RBP4 levels were strongly related to the presence of diabetic nephropathy (P = 0.0037 and P = 0.004; Mann-Whitney). The SteatoTest, FLI, HSI, s-adiponectin, s-RBP4 are not valid predictors of steatosis in T2D patients. Clino-biological markers cannot replace 1 H-MR spectroscopy for the assessment of liver fat in this population. (orig.)

Synthesis of (±)-I-125-iodobenzovesamicol - A cholinergic neuron marker

International Nuclear Information System (INIS)

Jung, Y.W.; Van Dort, M.E.; Wieland, D.M.

1990-01-01

The authors are focusing efforts on developing markers for the cholinergic neuron. Vesamicol (VA) has been adopted as a basis for the design of a presynaptic cholinergic nerve marker. Benzovesamicol, an analog of VA, is equipotent with VA and displays remarkable bulk tolerance in the 5-position. They have synthesized (±)-[I-125]-5-iodobenzovesamicol, and have conducted in vivo screening with it in mice

The bio markers of ionizing radiation; Los biomarcadores de las radaiciones ionizantes

Energy Technology Data Exchange (ETDEWEB)

Pernot, E.; Cardis, E.

2011-07-01

This article reviews bio markers currently used to study the biological effects of ionizing radiation and proposed a classification based on the time of onset of biological effects related to exposure time and persistence over time.

Investigating the Influence of Biological Sex on the Behavioral and Neural Basis of Face Recognition.

Science.gov (United States)

Scherf, K Suzanne; Elbich, Daniel B; Motta-Mena, Natalie V

2017-01-01

There is interest in understanding the influence of biological factors, like sex, on the organization of brain function. We investigated the influence of biological sex on the behavioral and neural basis of face recognition in healthy, young adults. In behavior, there were no sex differences on the male Cambridge Face Memory Test (CFMT)+ or the female CFMT+ (that we created) and no own-gender bias (OGB) in either group. We evaluated the functional topography of ventral stream organization by measuring the magnitude and functional neural size of 16 individually defined face-, two object-, and two place-related regions bilaterally. There were no sex differences in any of these measures of neural function in any of the regions of interest (ROIs) or in group level comparisons. These findings reveal that men and women have similar category-selective topographic organization in the ventral visual pathway. Next, in a separate task, we measured activation within the 16 face-processing ROIs specifically during recognition of target male and female faces. There were no sex differences in the magnitude of the neural responses in any face-processing region. Furthermore, there was no OGB in the neural responses of either the male or female participants. Our findings suggest that face recognition behavior, including the OGB, is not inherently sexually dimorphic. Face recognition is an essential skill for navigating human social interactions, which is reflected equally in the behavior and neural architecture of men and women.

Investigating the Influence of Biological Sex on the Behavioral and Neural Basis of Face Recognition

Science.gov (United States)

2017-01-01

Abstract There is interest in understanding the influence of biological factors, like sex, on the organization of brain function. We investigated the influence of biological sex on the behavioral and neural basis of face recognition in healthy, young adults. In behavior, there were no sex differences on the male Cambridge Face Memory Test (CFMT)+ or the female CFMT+ (that we created) and no own-gender bias (OGB) in either group. We evaluated the functional topography of ventral stream organization by measuring the magnitude and functional neural size of 16 individually defined face-, two object-, and two place-related regions bilaterally. There were no sex differences in any of these measures of neural function in any of the regions of interest (ROIs) or in group level comparisons. These findings reveal that men and women have similar category-selective topographic organization in the ventral visual pathway. Next, in a separate task, we measured activation within the 16 face-processing ROIs specifically during recognition of target male and female faces. There were no sex differences in the magnitude of the neural responses in any face-processing region. Furthermore, there was no OGB in the neural responses of either the male or female participants. Our findings suggest that face recognition behavior, including the OGB, is not inherently sexually dimorphic. Face recognition is an essential skill for navigating human social interactions, which is reflected equally in the behavior and neural architecture of men and women. PMID:28497111

A systematic review of secondhand smoke exposure in a car: Attributable changes in atmospheric and biological markers.

Science.gov (United States)

Raoof, Sana A; Agaku, Israel T; Vardavas, Constantine I

2015-05-01

Exposure to secondhand smoke (SHS) has been linked to disease, disability, and premature death. While several countries have enacted smoke-free legislations, exposure to SHS may still occur in unregulated private environments, such as in the family car. We performed a systematic review of peer-reviewed literature in PubMed and Web of Science up to May 2013. Articles were selected if they provided a quantitative measure of SHS exposure (biological or atmospheric markers); the study was conducted inside a car; and the assessed exposure was attributable to cigarette combustion. From 202 articles identified, 12 met the inclusion criteria. Among all studies that assessed smoking in cars with at least one window partially open, the particulate matter 2.5 μm or less in diameter (PM2.5) concentrations ranged from 47 μg/m(3) to 12,150 μg/m(3). For studies with all windows closed, PM2.5 ranged from 203.6 μg/m(3) to 13,150 μg/m(3). SHS concentration in a car was mediated by air-conditioning status, extent of airflow, and driving speed. Smoking in cars leads to extremely high exposure to SHS and increased concentration of atmospheric markers of exposure-even in the presence of air-conditioning or increased airflow from open windows. This clearly shows that the only way to protect nonsmokers, especially children, from SHS within cars is by eliminating tobacco smoking. © The Author(s) 2015.

Overweight and Obesity in Southern Italy: their association with social and life-style characteristics and their effect on levels of biologic markers.

Science.gov (United States)

Osella, Alberto R; Díaz, María Del Pilar; Cozzolongo, Rafaelle; Bonfiglio, Caterina; Franco, Isabella; Abrescia, Daniela Isabel; Bianco, Antonella; Giampiero, Elba Silvana; Petruzzi, José; Elsa, Lanzilota; Mario, Correale; Mastrosimni, Anna María; Giocchino, Leandro

2014-01-01

In the last decades, overweight and obesity have been transformed from minor public health issues to a major threat to public health affecting the most affluent societies and also the less developed ones. To estimate overweight-obesity prevalence in adults, their association with some social determinants and to assess the effect of these two conditions on levels of biologic and biochemical characteristics, by means of a population-based study. A random sample of the general population of Putignano was drawn. All participants completed a general pre-coded and a Food Frequency questionnaire; anthropometric measures were taken and a venous blood sample was drawn. All subjects underwent liver ultra-sonography. Data description was done by means of tables and then Quantile Regression was performed. Overall prevalence of overweight and obesity were 34.5% and 16.1% respectively. Both overweight and obesity were more frequent among male, married and low socio-economic position subjects. There were increasing frequencies of normal weight with higher levels of education. Overweight and obese subjects had more frequently Nonalcoholic Fatty Liver Disease, Hypertension and altered biochemical markers. Quantile regression showed a statistically significant association of age with overweight and obesity (maximum about 64.8 yo), gender (female) and low levels of education in both overweight and obesity. More than 10 gr/day of wine intake was associated with overweight. The prevention and treatment of overweight/obesity on a population wide basis are needed. Population-based strategies should also improve social and physical environmental contexts for healthful lifestyles.

Smart markers for watershed-based cell segmentation.

Directory of Open Access Journals (Sweden)

Can Fahrettin Koyuncu

Full Text Available Automated cell imaging systems facilitate fast and reliable analysis of biological events at the cellular level. In these systems, the first step is usually cell segmentation that greatly affects the success of the subsequent system steps. On the other hand, similar to other image segmentation problems, cell segmentation is an ill-posed problem that typically necessitates the use of domain-specific knowledge to obtain successful segmentations even by human subjects. The approaches that can incorporate this knowledge into their segmentation algorithms have potential to greatly improve segmentation results. In this work, we propose a new approach for the effective segmentation of live cells from phase contrast microscopy. This approach introduces a new set of "smart markers" for a marker-controlled watershed algorithm, for which the identification of its markers is critical. The proposed approach relies on using domain-specific knowledge, in the form of visual characteristics of the cells, to define the markers. We evaluate our approach on a total of 1,954 cells. The experimental results demonstrate that this approach, which uses the proposed definition of smart markers, is quite effective in identifying better markers compared to its counterparts. This will, in turn, be effective in improving the segmentation performance of a marker-controlled watershed algorithm.

Smart markers for watershed-based cell segmentation.

Science.gov (United States)

Koyuncu, Can Fahrettin; Arslan, Salim; Durmaz, Irem; Cetin-Atalay, Rengul; Gunduz-Demir, Cigdem

2012-01-01

Automated cell imaging systems facilitate fast and reliable analysis of biological events at the cellular level. In these systems, the first step is usually cell segmentation that greatly affects the success of the subsequent system steps. On the other hand, similar to other image segmentation problems, cell segmentation is an ill-posed problem that typically necessitates the use of domain-specific knowledge to obtain successful segmentations even by human subjects. The approaches that can incorporate this knowledge into their segmentation algorithms have potential to greatly improve segmentation results. In this work, we propose a new approach for the effective segmentation of live cells from phase contrast microscopy. This approach introduces a new set of "smart markers" for a marker-controlled watershed algorithm, for which the identification of its markers is critical. The proposed approach relies on using domain-specific knowledge, in the form of visual characteristics of the cells, to define the markers. We evaluate our approach on a total of 1,954 cells. The experimental results demonstrate that this approach, which uses the proposed definition of smart markers, is quite effective in identifying better markers compared to its counterparts. This will, in turn, be effective in improving the segmentation performance of a marker-controlled watershed algorithm.

Prognostic molecular markers in early breast cancer

International Nuclear Information System (INIS)

Esteva, Francisco J; Hortobagyi, Gabriel N

2004-01-01

A multitude of molecules involved in breast cancer biology have been studied as potential prognostic markers. In the present review we discuss the role of established molecular markers, as well as potential applications of emerging new technologies. Those molecules used routinely to make treatment decisions in patients with early-stage breast cancer include markers of proliferation (e.g. Ki-67), hormone receptors, and the human epidermal growth factor receptor 2. Tumor markers shown to have prognostic value but not used routinely include cyclin D 1 and cyclin E, urokinase-like plasminogen activator/plasminogen activator inhibitor, and cathepsin D. The level of evidence for other molecular markers is lower, in part because most studies were retrospective and not adequately powered, making their findings unsuitable for choosing treatments for individual patients. Gene microarrays have been successfuly used to classify breast cancers into subtypes with specific gene expression profiles and to evaluate prognosis. RT-PCR has also been used to evaluate expression of multiple genes in archival tissue. Proteomics technologies are in development

Biological (molecular and cellular) markers of toxicity

International Nuclear Information System (INIS)

Shugart, L.R.; D'Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

1991-01-01

Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO 6 -ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O 6 -ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP

Significance Of Immunohistochemical Markers In Diagnostics Of Urinary Bladder Cancer

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A.V. Medvedeva

2009-12-01

Full Text Available On the basis of surgical and biopsy material 106 patients with diseases of urinary bladder have been under study. They received treatment at Scientific Research Institute of Fundamental and Clinical Uronephrology of Saratov State Medical University. 13 immunohistochemical markers have been evaluated: markers of proliferative activity - Ki-67, PCNA, p63, suppressor of tumor growth - p53, markers of apoptosis - Bcl-2, Bax, receptor of epidermal growth factors - EGFR, cytokeratin profile - (CK7, CK8, CK10/13, CK 17, CK18, CK19, as well as their diagnostic significance for identifying the urinary bladder cancer

Parasites as Biological Tags for Stock Discrimination of Beaked Redfish (Sebastes mentella: Parasite Infra-Communities vs. Limited Resolution of Cytochrome Markers.

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Regina Klapper

Full Text Available The use of parasites as biological tags for discrimination of fish stocks has become a commonly used approach in fisheries management. Metazoan parasite community analysis and anisakid nematode population genetics based on a mitochondrial cytochrome marker were applied in order to assess the usefulness of the two parasitological methods for stock discrimination of beaked redfish Sebastes mentella of three fishing grounds in the North East Atlantic. Multivariate, model-based approaches demonstrated that the metazoan parasite fauna of beaked redfish from East Greenland differed from Tampen, northern North Sea, and Bear Island, Barents Sea. A joint model (latent variable model was used to estimate the effects of covariates on parasite species and identified four parasite species as main source of differences among fishing grounds; namely Chondracanthus nodosus, Anisakis simplex s.s., Hysterothylacium aduncum, and Bothriocephalus scorpii. Due to its high abundance and differences between fishing grounds, Anisakis simplex s.s. was considered as a major biological tag for host stock differentiation. Whilst the sole examination of Anisakis simplex s.s. on a population genetic level is only of limited use, anisakid nematodes (in particular, A. simplex s.s. can serve as biological tags on a parasite community level. This study confirmed the use of multivariate analyses as a tool to evaluate parasite infra-communities and to identify parasite species that might serve as biological tags. The present study suggests that S. mentella in the northern North Sea and Barents Sea is not sub-structured.

Identification of micro satellite markers on chromosomes of bread ...

African Journals Online (AJOL)

SERVER

2007-07-18

Jul 18, 2007 ... 2 Department of Biotechnology and Molecular Biology, CCS Haryana Agricultural University, ... markers closely linked to karnal bunt resistance in wheat. ... from leaf tissues using modified CTAB procedure (Saghai-Maroof et.

On the biological basis of musicality.

Science.gov (United States)

Honing, Henkjan

2018-03-15

In recent years, music and musicality have been the focus of an increasing amount of research effort. This has led to a growing role and visibility of the contribution of (bio)musicology to the field of neuroscience and cognitive sciences at large. While it has been widely acknowledged that there are commonalities between speech, language, and musicality, several researchers explain this by considering musicality as an epiphenomenon of language. However, an alternative hypothesis is that musicality is an innate and widely shared capacity for music that can be seen as a natural, spontaneously developing set of traits based on and constrained by our cognitive abilities and their underlying biology. A comparative study of musicality in humans and well-known animal models (monkeys, birds, pinnipeds) will further our insights on which features of musicality are exclusive to humans and which are shared between humans and nonhuman animals, contribute to an understanding of the musical phenotype, and further constrain existing evolutionary theories of music and musicality. © 2018 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

Structural Basis of Biological Nitrile Reduction*

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Chikwana, Vimbai M.; Stec, Boguslaw; Lee, Bobby W. K.; de Crécy-Lagard, Valérie; Iwata-Reuyl, Dirk; Swairjo, Manal A.

2012-01-01

The enzyme QueF catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), the only nitrile reduction reaction known in biology. We describe here two crystal structures of Bacillus subtilis QueF, one of the wild-type enzyme in complex with the substrate preQ0, trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the C55A mutant in complex with the substrate preQ0 bound noncovalently. The QueF enzyme forms an asymmetric tunnel-fold homodecamer of two head-to-head facing pentameric subunits, harboring 10 active sites at the intersubunit interfaces. In both structures, a preQ0 molecule is bound at eight sites, and in the wild-type enzyme, it forms a thioimide covalent linkage to the catalytic residue Cys-55. Both structural and transient kinetic data show that preQ0 binding, not thioimide formation, induces a large conformational change in and closure of the active site. Based on these data, we propose a mechanism for the activation of the Cys-55 nucleophile and subsequent hydride transfer. PMID:22787148

Occupational cosmic radiation exposure in Portuguese airline pilots: study of a possible correlation with oxidative biological markers.

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Silva, Rodrigo; Folgosa, Filipe; Soares, Paulo; Pereira, Alice S; Garcia, Raquel; Gestal-Otero, Juan Jesus; Tavares, Pedro; Gomes da Silva, Marco D R

2013-05-01

Several studies have sought to understand the health effects of occupational exposure to cosmic radiation. However, only few biologic markers or associations with disease outcomes have so far been identified. In the present study, 22 long- and 26 medium-haul male Portuguese airline pilots and 36 factory workers who did not fly regularly were investigated. The two groups were comparable in age and diet, were non-smokers, never treated with ionizing radiation and other factors. Cosmic radiation exposure in pilots was quantified based on direct monitoring of 51 flights within Europe, and from Europe to North and South America, and to Africa. Indirect dose estimates in pilots were performed based on the SIEVERT (Système informatisé d'évaluation par vol de l'exposition au rayonnement cosmique dans les transports aériens) software for 6,039 medium- and 1,366 long-haul flights. Medium-haul pilots had a higher cosmic radiation dose rate than long-haul pilots, that is, 3.3 ± 0.2 μSv/h and 2.7 ± 0.3 μSv/h, respectively. Biological tests for oxidative stress on blood and urine, as appropriate, at two time periods separated by 1 year, included measurements of antioxidant capacity, total protein, ferritin, hemoglobin, creatinine and 8-hydroxy-2-deoxyguanosine (8OHdG). Principal components analysis was used to discriminate between the exposed and unexposed groups based on all the biological tests. According to this analysis, creatinine and 8OHdG levels were different for the pilots and the unexposed group, but no distinctions could be made among the medium- and the long-haul pilots. While hemoglobin levels seem to be comparable between the studied groups, they were directly correlated with ferritin values, which were lower for the airline pilots.

Biological marker distribution in coexisting kerogen, bitumen and asphaltenes in Monterey Formation diatomite, California

Science.gov (United States)

Tannenbaum, E.; Ruth, E.; Huizinga, B. J.; Kaplan, I. R.

1986-01-01

Organic-rich (18.2%) Monterey Formation diatomite from California was studied. The organic matter consist of 94% bitumen and 6% kerogen. Biological markers from the bitumen and from pyrolysates of the coexisting asphaltenes and kerogen were analyzed in order to elucidate the relationship between the various fractions of the organic matter. While 17 alpha(H), 18 alpha(H), 21 alpha(H)-28,30-bisnorhopane was present in the bitumen and in the pryolysate of the asphaltenes, it was not detected in the pyrolysates of the kerogen. A C40-isoprenoid with "head to head" linkage, however, was present in pyrolysates of both kerogen and asphaltenes, but not in the bitumen from the diatomite. The maturation level of the bitumen, based on the extent of isomerization of steranes and hopanes, was that of a mature oil, whereas the pyrolysate from the kerogen showed a considerably lower maturation level. These relationships indicate that the bitumen may not be indigenous to the diatomite and that it is a mature oil that migrated into the rock. We consider the possibility, however, that some of the 28,30-bisnorhopane-rich Monterey Formation oils have not been generated through thermal degradation of kerogen, but have been expelled from the source rock at an early stage of diagenesis.

Prediction for steatosis in type-2 diabetes: clinico-biological markers versus {sup 1}H-MR spectroscopy

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Guiu, Boris; Krause, Denis; Cercueil, Jean-Pierre [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Radiology, 2 boulevard Marechal de Lattre de Tassigny, BP 77908, Dijon (France); Crevisy-Girod, Elodie [CHU (University Hospital), Department of Endocrinology, Diabetology, and Metabolic Diseases, BP 77908, Dijon (France); Binquet, Christine [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Biostatistics and Medical Informatics, BP 77908, Dijon (France); Duvillard, Laurence [University of Burgundy, INSERM U866, BP 87900, Dijon (France); Masson, David [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Biochemistry, BP 77908, Dijon (France); Lepage, Come; Hamza, Samia; Minello, Anne; Hillon, Patrick [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Hepatology, BP 77908, Dijon (France); Verges, Bruno; Petit, Jean-Michel [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Endocrinology, Diabetology, and Metabolic Diseases, BP 77908, Dijon (France)

2012-04-15

The SteatoTest, fatty liver index (FLI) and hepatic steatosis index (HSI) are clinico-biological scores of steatosis validated in general or selected populations. Serum adiponectin (s-adiponectin) and retinol binding protein 4 (s-RBP4) are adipokines that could predict liver steatosis. We investigated whether the Steatotest, FLI, HSI, s-adiponectin and s-RBP4 could be valid predictors of liver steatosis in type-2 diabetic (T2D) patients. We enrolled 220 consecutive T2D patients. Reference standard was 3.0 T {sup 1}H-MR spectroscopy (corrected for T1 and T2 decays). Intraclass correlation coefficients (ICCs), Kappa statistic measures of agreement, receiver operating characteristic (ROC) curves were assessed. Median liver fat content was 91 mg triglyceride/g liver tissue (range: 0-392). ICCs among the Steatotest, FLI, HSI, s-adiponectin, s-RBP4 and spectroscopy were low: 0.384, 0.281, 0.087, -0.297 and 0.048. Agreement between scores and spectroscopy was poor (Kappa range: 0.042-0.281). The areas under the ROC curves were low: 0.674, 0.647, 0.637, 0.616 and 0.540. S-adiponectin and s-RBP4 levels were strongly related to the presence of diabetic nephropathy (P = 0.0037 and P = 0.004; Mann-Whitney). The SteatoTest, FLI, HSI, s-adiponectin, s-RBP4 are not valid predictors of steatosis in T2D patients. Clino-biological markers cannot replace {sup 1}H-MR spectroscopy for the assessment of liver fat in this population. (orig.)

The impact of a prospective survey-based workplace intervention program on employee health, biologic stress markers, and organizational productivity.

Science.gov (United States)

Anderzén, Ingrid; Arnetz, Bengt B

2005-07-01

To study whether knowledge about psychosocial work indicators and a structured method to implement changes based on such knowledge comprise an effective management tool for enhancing organizational as well as employee health and well-being. White- collar employees representing 22 different work units were assessed before and after a 1-year intervention program. Subjective ratings on health and work environment, biologic markers, absenteeism, and productivity were measured. Significant improvements in performance feedback, participatory management, employeeship, skills development, efficiency, leadership, employee well-being, and work-related exhaustion were identified. The restorative hormone testosterone increased during the intervention and changes correlated with increased overall organizational well-being. Absenteeism decreased and productivity improved. Fact-based psychosocial workplace interventions are suggested to be an important process for enhancing employee well-being as well as organizational performance.

A life course approach to explore the biological embedding of socioeconomic position and social mobility through circulating inflammatory markers.

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Castagné, Raphaële; Delpierre, Cyrille; Kelly-Irving, Michelle; Campanella, Gianluca; Guida, Florence; Krogh, Vittorio; Palli, Domenico; Panico, Salvatore; Sacerdote, Carlotta; Tumino, Rosario; Kyrtopoulos, Soterios; Hosnijeh, Fatemeh Saberi; Lang, Thierry; Vermeulen, Roel; Vineis, Paolo; Stringhini, Silvia; Chadeau-Hyam, Marc

2016-04-27

Lower socioeconomic position (SEP) has consistently been associated with poorer health. To explore potential biological embedding and the consequences of SEP experiences from early life to adulthood, we investigate how SEP indicators at different points across the life course may be related to a combination of 28 inflammation markers. Using blood-derived inflammation profiles measured by a multiplex array in 268 participants from the Italian component of the European Prospective Investigation into Cancer and Nutrition cohort, we evaluate the association between early life, young adulthood and later adulthood SEP with each inflammatory markers separately, or by combining them into an inflammatory score. We identified an increased inflammatory burden in participants whose father had a manual occupation, through increased plasma levels of CSF3 (G-CSF; β = 0.29; P = 0.002), and an increased inflammatory score (β = 1.96; P = 0.029). Social mobility was subsequently modelled by the interaction between father's occupation and the highest household occupation, revealing a significant difference between "stable Non-manual" profiles over the life course versus "Manual to Non-manual" profiles (β = 2.38, P = 0.023). Low SEP in childhood is associated with modest increase in adult inflammatory burden; however, the analysis of social mobility suggests a stronger effect of an upward social mobility over the life course.

Chromium oxide (51Cr2O3 used as biological marker was not absorbed by fish

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G.Z. Sakita

2015-06-01

Full Text Available The aim of this study was to evaluate the rate absorption of radio-labeled chromium oxide (51Cr2O3, used as biological marker in nutrition studies with Nile tilapia Oreochromis niloticus. An experimental diet with approximately 58 µCi of specific activity of the element was encapsulated and fed daily to 35 adult Nile tilapia; a group of 35 fish was used as control feeding on a basal diet. At the beginning of the experiment five fish from each group were randomly selected and blood samples were drawn from control (BC and experimental fish (BE. Fish were then euthanized by anesthetic overdoses and samples of the liver tissue (LT, renal tissue (RT, stomach without content (S, intestine without content (I, gills tissue (GT, muscle tissue (fillet; MT, visceral fat (VF, content of the digestive tract (CTDE and water aquarium were collected from the experimental fish. The procedure was repeated daily for one week. Simple linear regressions were adjusted - days of collection vs. determination coefficients, and were established for statistical comparisons of the measured activity of 51Cr readings in sampled blood and tissues (logarithmic transformation for samples of the control and experimental fish. No differences (P>0.05 were detected between samples from BC fish and BE, RT, VF, MT and LT of treated fish, but samples of GT, I, S, CTDE and WA from the tanks holding fish which received the experimental diet differed from control (P<0.05. The experimental results indicate that the trivalent chromium in the form of 51Cr2O3 was not significantly absorbed by the gastrointestinal tract, gills or another possible route of absorption under these experimental conditions and with Nile tilapia. Therefore, this marker was shown to be inert and can be safely used in nutrition studies.

High prevalence of markers of coronary heart disease among Greenland Inuit

DEFF Research Database (Denmark)

Jørgensen, Marit Eika; Bjerregaard, Peter; Kjaergaard, Jens Jørgen

2008-01-01

were associated with CHD. CONCLUSION: The prevalence of markers of CHD was not different from that in Western populations. The Inuit is a population undergoing rapid social and health transitions, with the emergence of cardiovascular risk factors, and there is a need for critical rethinking...... of markers of CHD among Greenland Inuit, and to study associations between markers of CHD and behavioral and biological variables. DESIGN: We studied prevalence of angina pectoris (AP), self-reported myocardial infarction (MI), and ECG defined MI and ischaemia in a population survey among 1316 Inuit living...

The Effects of Short-Term Propofol and Dexmedetomidine on Lung Mechanics, Histology, and Biological Markers in Experimental Obesity.

Science.gov (United States)

Heil, Luciana Boavista Barros; Santos, Cíntia L; Santos, Raquel S; Samary, Cynthia S; Cavalcanti, Vinicius C M; Araújo, Mariana M P N; Poggio, Hananda; Maia, Lígia de A; Trevenzoli, Isis Hara; Pelosi, Paolo; Fernandes, Fatima C; Villela, Nivaldo R; Silva, Pedro L; Rocco, Patricia R M

2016-04-01

Administering anesthetics to the obese population requires caution because of a variety of reasons including possible interactions with the inflammatory process observed in obese patients. Propofol and dexmedetomidine have protective effects on pulmonary function and are widely used in short- and long-term sedation, particularly in intensive care unit settings in lean and obese subjects. However, the functional and biological effects of these drugs in obesity require further elucidation. In a model of diet-induced obesity, we compared the short-term effects of dexmedetomidine versus propofol on lung mechanics and histology, as well as biological markers of inflammation and oxidative stress modulation in obesity. Wistar rats (n = 56) were randomly fed a standard diet (lean) or experimental diet (obese) for 12 weeks. After this period, obese animals received sodium thiopental intraperitoneally and were randomly allocated into 4 subgroups: (1) nonventilated (n = 4) for molecular biology analysis only (control); (2) sodium thiopental (n = 8); (3) propofol (n = 8); and (4) dexmedetomidine (n = 8), which received continuous IV administration of the corresponding agents and were mechanically ventilated (tidal volume = 6 mL/kg body weight, fraction of inspired oxygen = 0.4, positive end-expiratory pressure = 3 cm H2O) for 1 hour. Compared with lean animals, obese rats did not present increased body weight but had higher total body and trunk fat percentages, airway resistance, and interleukin-6 levels in the lung tissue (P = 0.02, P = 0.0027, and P = 0.01, respectively). In obese rats, propofol, but not dexmedetomidine, yielded increased airway resistance, bronchoconstriction index (P = 0.016, P = 0.02, respectively), tumor necrosis factor-α, and interleukin-6 levels, as well as lower levels of nuclear factor-erythroid 2-related factor-2 and glutathione peroxidase (P = 0.001, Bonferroni-corrected t test). In this model of diet-induced obesity, a 1-hour propofol infusion

Are All Dads Equal? Biology Versus Marriage as a Basis for Paternal Investment.

Science.gov (United States)

Hofferth, Sandra L.; Anderson, Kermyt G.

2003-01-01

Using three different theoretical perspectives, examines the engagement, availability, participation, and warmth of residential fathers in married biological parent, unmarried biological parent, married stepparent, and cohabiting father families. Biology explains less of father involvement than anticipated once differences between fathers are…

Neurobiological Basis of Insight in Schizophrenia: A Systematic Review.

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Xavier, Rose Mary; Vorderstrasse, Allison

2016-01-01

Insight in schizophrenia is defined as awareness into illness, symptoms, and need for treatment and has long been associated with cognition, other psychopathological symptoms, and several adverse clinical and functional outcomes. However, the biological basis of insight is not clearly understood. The aim of this systematic review was to critically evaluate and summarize advances in the study of the biological basis of insight in schizophrenia and to identify gaps in this knowledge. A literature search of PubMed, CINAHL, PsycINFO, and EMBASE databases was conducted using search terms to identify articles relevant to the biology of insight in schizophrenia published in the last 6 years. Articles that focused on etiology of insight in schizophrenia and those that examined the neurobiology of insight in schizophrenia or psychoses were chosen for analysis. Articles on insight in conditions other than schizophrenia or psychoses and which did not investigate the neurobiological underpinnings of insight were excluded from the review. Twenty-six articles met the inclusion criteria for this review. Of the 26 articles, 3 focused on cellular abnormalities and 23 were neuroimaging studies. Preliminary data identify the prefrontal cortex, cingulate cortex, and regions of the temporal and parietal lobe (precuneus, inferior parietal lobule) and hippocampus as the neural correlates of insight. A growing body of literature attests to the neurobiological basis of insight in schizophrenia. Current evidence supports the neurobiological basis of insight in schizophrenia and identifies specific neural correlates for insight types and its dimensions. Further studies that examine the precise biological mechanisms of insight are needed to apply this knowledge to effective clinical intervention development.

Geriatric neuro-oncology: from mythology to biology.

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Weller, Michael; Platten, Michael; Roth, Patrick; Wick, Wolfgang

2011-12-01

Age has remained one of the most important determinants of risk for the development of certain brain tumors, of benefit from and tolerance of brain tumor treatment, and overall outcome. Regarding these three aspects, there are major differences across the spectrum of primary brain tumors depending on specific histology. Here, we review recent advances in understanding the biological basis of the prognostic marker 'age' in neuro-oncology. Contemporary population-based studies confirm the strong prognostic impact of age in many brain tumors. Elderly patients continue to be treated less aggressively than younger patients with the same tumors. However, biological factors may contribute to the negative prognostic impact of age. For instance, among gliomas, mutations of the isocitrate dehydrogenase genes, which are prognostically favorable, are much more common in younger patients. Moreover, complete responses defined by neuroimaging were much less durable in elderly as opposed to younger patients with primary central nervous system lymphoma in the German Primary Central Nervous System Lymphoma Study Group trial. A combination of age-adapted patterns of care and treatment-independent, tumor-intrinsic factors contributes to the poorer outcome of elderly patients with brain tumors. These factors need to be better distinguished and understood in order to improve outcome in elderly brain tumor patients.

Sequence-characterized markers from Begonia x tuberhybrida Voss..

Czech Academy of Sciences Publication Activity Database

Wiesner, Ivo; Wiesnerová, Dana

2008-01-01

Roč. 73, č. 6 (2008), s. 244-247 ISSN 1611-4426 R&D Projects: GA AV ČR 1QS500510566 Institutional research plan: CEZ:AV0Z50510513 Keywords : Begonia * genetic markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.300, year: 2008

Biological markers of generalized anxiety disorder.

Science.gov (United States)

Maron, Eduard; Nutt, David

2017-06-01

Generalized anxiety disorder (GAD) is a prevalent and highly disabling mental health condition; however, there is still much to learn with regard to pertinent biomarkers, as well as diagnosis, made more difficult by the marked and common overlap of GAD with affective and anxiety disorders. Recently, intensive research efforts have focused on GAD, applying neuroimaging, genetic, and blood-based approaches toward discovery of pathogenetic and treatment-related biomarkers. In this paper, we review the large amount of available data, and we focus in particular on evidence from neuroimaging, genetic, and neurochemical measurements in GAD in order to better understand potential biomarkers involved in its etiology and treatment. Overall, the majority of these studies have produced results that are solitary findings, sometimes inconsistent and not clearly replicable. For these reasons, they have not yet been translated into clinical practice. Therefore, further research efforts are needed to distinguish GAD from other mental disorders and to provide new biological insights into its pathogenesis and treatment.

EuroFIR eBASIS: application for health claims submissions and evaluations

NARCIS (Netherlands)

Kiely, M.; Black, L.J.; Plumb, J.; Kroon, P.; Hollman, P.C.H.; Larsen, J.C.; Speijers, G.; Kapsokefalou, M.; Sheehan, D.; Gry, J.; Finglas, P.M.

2010-01-01

Background: The European Food Information Resource (EuroFIR) network has established the eBASIS (Bioactive Substances in Food Information System) online food composition and biological effects database for plant-derived bioactive compounds (phytochemicals). On the basis of submitted evidence, the

Organisms modeling: The question of radial basis function networks

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Muzy Alexandre

2014-01-01

Full Text Available There exists usually a gap between bio-inspired computational techniques and what biologists can do with these techniques in their current researches. Although biology is the root of system-theory and artifical neural networks, computer scientists are tempted to build their own systems independently of biological issues. This publication is a first-step re-evalution of an usual machine learning technique (radial basis funtion(RBF networks in the context of systems and biological reactive organisms.

Use of mammary epithelial antigens as markers in mammary neoplasia

International Nuclear Information System (INIS)

Ceriani, R.L.; Peterson, J.A.; Blank, E.W.

1979-01-01

Cell-type specific antigens of the mammary epithelial cells can be used as markers of breast neoplasia. Methods are proposed for the detection of metastatic mammary tissue in vivo by injection of [ 125 I]-labeled antibodies against the mammary epithelial antigens. In addition, the reduced expression of mammary epithelial cell antigens in neoplastic breast cells, quantitated here on a cell per cell basis by flow cytofluorimetry, is a marker of neoplasia and an indication of a deletion accompanying the neoplastic transformation of these cells. (Auth.)

Gliomatosis cerebri: Prognosis based on current molecular markers.

Science.gov (United States)

Maharaj, Monish M; Phan, Kevin; Xu, Joshua; Fairhall, Jacob; Reddy, Rajesh; Rao, Prashanth J V

2017-09-01

This study aims to review the literature and identify key molecular markers affecting the prognosis of Gliomatosis cerebri (2) to evaluate the level of evidence and identify outstanding markers requiring further study. A literature search was conducted across 5 major databases using the key terms: "Molecular markers" AND "Gliomatosis cerebri" OR "diffuse astrocytoma." Critical appraisal and data presentation was performed inline with the PRISMA guidelines. Following search strategy implementation, 11 studies were included in the final review process. Our data demonstrates significant prognostic value associated with IDH1 132H mutation and variable evidence surrounding the role of INA expression, MGMT promoter methylation and other factors. However, there are significant limitations in the level of evidence obtained. As the genetic basis for the pathogenesis of Gliomatosis cerebri continues to widen, there is little data on markers aside from IDH1 mutation available. IDH1 132H mutation has been demonstrated to have significant effect on survival, particularly in patients with Gliomatosis cerebri type 2. Copyright © 2017 Elsevier Ltd. All rights reserved.

Selected biological markers in various vascular lesions of the head and neck

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Zuzanna Gronkiewicz

2014-10-01

Full Text Available Vascular anomalies are divided according to the contemporary system of classification into two groups: tumors and malformations. However, there is no consensus on juvenile angiofibroma’s place in that system. The general characteristics of selected markers of angiogenesis and tissue remodeling are presented in the series in the context of current knowledge in the field of pathophysiology of vascular lesions. The mentioned markers are currently the subjects of multidirectional studies in oncology, as they take part in the process of neoangiogenesis and proliferation of tumors. Nevertheless, they have not been widely examined in vascular lesions. The indirect goal of that series is to indicate the possible research direction on vascular lesions to determine their molecular profile, to create a more specific system of classification, and above all to develop new diagnostic and treatment methods.

Monoclonal carcinoembryonic antigen radioimmunoassay in prostatic cancer: Validation of the method and comparison to some other tumor-associated markers

International Nuclear Information System (INIS)

Stefanovic, V.; Ignjatovic, M.; Milosavljevic, B.; Dinic, A.; Nis Univ.

1987-01-01

The use of a monoclonal CEA RIA and of some other biological markers for a diagnosis of prostatic cancer was investigated. The increased level of serum CEA was found in both prostatic cancer and in non-malignant disease. The low sensitivity of the CEA monoclonal assay precludes its use for a clinical diagnosis of prostatic cancer. The simultaneous use of some other biological markers (PAP, TPA, β2-microglobulin and ferritin) did increase sensitivity. However, further studies should be directed to a much more specific and sensitive marker of the human prostatic adenocarcinoma. (orig.) [de

Monoclonal carcinoembryonic antigen radioimmunoassay in prostatic cancer: Validation of the method and comparison to some other tumor-associated markers

Energy Technology Data Exchange (ETDEWEB)

Stefanovic, V; Ignjatovic, M; Milosavljevic, B; Dinic, A

1987-04-01

The use of a monoclonal CEA RIA and of some other biological markers for a diagnosis of prostatic cancer was investigated. The increased level of serum CEA was found in both prostatic cancer and in non-malignant disease. The low sensitivity of the CEA monoclonal assay precludes its use for a clinical diagnosis of prostatic cancer. The simultaneous use of some other biological markers (PAP, TPA, ..beta..2-microglobulin and ferritin) did increase sensitivity. However, further studies should be directed to a much more specific and sensitive marker of the human prostatic adenocarcinoma.

Biological basis of total body irradiation

International Nuclear Information System (INIS)

Dubray, B.; Helfre, S.; Dendale, R.; Cosset, J.M.; Giraud, P.

1999-01-01

A comprehensive understanding of the radiobiological bases of total body irradiation (TBI) is made difficult by the large number of normal and malignant tissues that must be taken into account. In addition, tissue responses to irradiation are also sensitive to associated treatments, type of graft and a number of patient characteristics. Experimental studies have yielded a large body of data, the clinical relevance of which still requires definite validation through randomized trials. Fractionated TBI schemes are able to reduce late normal tissue toxicity, but the ultimate consequences of the fractional dose reduction do not appear to be equivocal. Thus, leukemia and lymphoma cells are probably more radio-biologically heterogeneous than previously thought, with several cell lines displaying relatively high radioresistance and repair capability patterns. The most primitive host-type hematopoietic stem cells are likely to be at least partly protected by TBI fractionation and may hamper late engraftment. Similarly, but with possibly conflicting consequences on the probability of engraftment, the persistence of a functional marrow stroma may also be fractionation-sensitive, while higher rejection rates have been reported after T-depletion grafts and fractionated TBI. in clinical practice (as for performance of relevant clinical trials), the influence of these results are rather limited by the heavy logistic constraints created by a sophisticated and time-consuming procedure. Lastly, clinicians are now facing an increasing incidence of second cancers, at least partly induced by irradiation, which jeopardize the long-term prospects of otherwise cured patients. (authors)

“LIFE COURSE SOCIOECONOMIC POSITION IS ASSOCIATED WITH INFLAMMATORY MARKERS: THE FRAMINGHAM OFFSPRING STUDY”

OpenAIRE

Pilote, Louise; Lynch, John W; Richard, Hugues; Almeida, Nisha; Benjamin, Emelia J; Murabito, Joanne M

2010-01-01

Associations between life course socioeconomic position (SEP) and novel biological risk markers for coronary heart disease such as inflammatory markers are not well understood. Most studies demonstrate inverse associations of life course SEP with C-reactive protein (CRP), interleukin-6 (IL-6) and fibrinogen, however little is known about associations between life course SEP and other inflammatory markers including intercellular adhesion molecule-1 (ICAM-1), tumor necrosis factor II (TNFR2), l...

Ya as Discourse Marker: Indonesian Stand – Up Comedy Strategy in Producing Laughter

Directory of Open Access Journals (Sweden)

Dientha Yuniar

2013-11-01

Full Text Available This paper would explore an analysis of discourse markers ya as Indonesian stand – up comedy strategy in producing laughter. The spotlight would focus on how ya, as the major marker, performed in professional stand-up comedy performance. How they used ya in 7-10 minutes performance could illustrate the basis natural performance in bursting laughter and the enhancement of audience’s response in laughter. It argued for an approach based upon two level functions of discourse markers by Brinton (1996; textual level and interpersonal level. Both functions determined the functions of discourse markers. The result explored the relationship not only the bursting laughter but also between stand – up technique and discourse markers. Finally, this study leads into examination of ya as Indonesian discourse marker into the development of humor research within linguistics study.

Developing maximal neuromuscular power: Part 1--biological basis of maximal power production.

Science.gov (United States)

Cormie, Prue; McGuigan, Michael R; Newton, Robert U

2011-01-01

This series of reviews focuses on the most important neuromuscular function in many sport performances, the ability to generate maximal muscular power. Part 1 focuses on the factors that affect maximal power production, while part 2, which will follow in a forthcoming edition of Sports Medicine, explores the practical application of these findings by reviewing the scientific literature relevant to the development of training programmes that most effectively enhance maximal power production. The ability of the neuromuscular system to generate maximal power is affected by a range of interrelated factors. Maximal muscular power is defined and limited by the force-velocity relationship and affected by the length-tension relationship. The ability to generate maximal power is influenced by the type of muscle action involved and, in particular, the time available to develop force, storage and utilization of elastic energy, interactions of contractile and elastic elements, potentiation of contractile and elastic filaments as well as stretch reflexes. Furthermore, maximal power production is influenced by morphological factors including fibre type contribution to whole muscle area, muscle architectural features and tendon properties as well as neural factors including motor unit recruitment, firing frequency, synchronization and inter-muscular coordination. In addition, acute changes in the muscle environment (i.e. alterations resulting from fatigue, changes in hormone milieu and muscle temperature) impact the ability to generate maximal power. Resistance training has been shown to impact each of these neuromuscular factors in quite specific ways. Therefore, an understanding of the biological basis of maximal power production is essential for developing training programmes that effectively enhance maximal power production in the human.

Generation and application of SSR markers in avocado

International Nuclear Information System (INIS)

Sharon, D.; Lavi, U.; Cregan, P.B.; Hillel, J.

1998-01-01

Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author)

Generation and application of SSR markers in avocado

Energy Technology Data Exchange (ETDEWEB)

Sharon, D; Lavi, U [Institute of Horticulture, ARO Volcani Center, Bet-Dagan (Israel); Cregan, P B [United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland (United States); Hillel, J [Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot (Israel)

1998-10-01

Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author) 20 refs, 3 figs, 8 tabs

Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers.

Science.gov (United States)

Marcheco-Teruel, Beatriz; Parra, Esteban J; Fuentes-Smith, Evelyn; Salas, Antonio; Buttenschøn, Henriette N; Demontis, Ditte; Torres-Español, María; Marín-Padrón, Lilia C; Gómez-Cabezas, Enrique J; Alvarez-Iglesias, Vanesa; Mosquera-Miguel, Ana; Martínez-Fuentes, Antonio; Carracedo, Angel; Børglum, Anders D; Mors, Ole

2014-07-01

We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives.

Science.gov (United States)

Vogt, Gunter

2018-03-01

In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions. Genome mining is expected to reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction, moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory, biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigenetic investigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation, tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish is further suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance of epigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies, environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratory lineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically edited strains.

Art and brain: the relationship of biology and evolution to art.

Science.gov (United States)

Zaidel, Dahlia W

2013-01-01

Visual art, as with all other arts, is spontaneously created only by humans and is ubiquitously present to various extents in all societies today. Exploring the deep roots of art from cognitive, neurological, genetic, evolutionary, archaeological, and biological perspectives is essential for the full understanding of why we have art, and what art is about. The cognitive basis of art is symbolic, abstract, and referential thinking. However, archaeological markers of symbolic activity by early humans are not associated with art production. There is an enormously large time gap between the activity and the appearance of sporadic art by early Homo sapiens, and another large time delay before appearance of enduring practice of art. The aesthetic aspect of art is not considered to be the initial impetus for creating it. Instead, archaeological markers suggest that the early beginnings of art are associated with development of stratified societies where external visual identifiers by way of body ornaments and decorations were used. The major contributing forces for the consistency in art-making are presumed to be the formation of socioculture, intragroup cooperation, increased group size, survival of skillful artisans, and favorable demographic conditions. The biological roots of art are hypothesized to parallel aspects of our ancestry, specifically animal courtship displays, where signals of health and genetic quality are exhibited for inspection by potential mates. Viewers assess displayed art for talent, skill, communicative, and aesthetic-related qualities. Interdisciplinary discussions of art reflect the current approach to full understanding of the nature of art. © 2013 Elsevier B.V. All rights reserved.

[Study on sequence characterized amplified region (SCAR) markers of Cornus officinalis].

Science.gov (United States)

Chen, Suiqing; Lu, Xiaolei; Wang, Lili

2011-05-01

To establish sequence characterized amplified region markers of Cornus officinalis and provide a scientific basis for molecular identification of C. officinalis. The random primer was screened through RAPD to obtain specific RAPD marker bands. The RAPD marker bands were separated, extracted, cloned and sequenced. Both ends of the sequence of RAPD marker bands were determined. A pair of specific primers was designed for conventional PCR reaction, and SCAR marker was acquired. Four pairs of primers were designed based on the sequence of RAPD marker bands. The DNA of the seven varieties of C. officinalis was amplified by using YST38 and YST43 primer. The results showed that seven varieties of C. officinalis were able to produce a single PCR product. It was an effective way to identify C. officinalis. The varieties with cylindrical and long-pear shape fruits amplified by YST38 showed a specific band, which could be used as the evidence of variety identification. Seven varieties of C. oficinalis were amplified by using primer YST39. But the size of band of the variety with spindly shape fruit (35,0400 bp) was about 300 bp, which was shorter than those of the variety with the other shape fruits of C. officinalis (650-700 bp). The variety with the spindly shape fruit could be identified through this difference. The primer YST92 could produce a fragment from 600-700 bp in the varieties with cylindrical and long-pear shape fruits, a fragment from 200-300 bp in the varieties with oval and short-cylindrical shape fruits and had no fragment in the varieties with long cylindrical, elliptic and short-pear shape fruits, which could be used to select the different shapes of C. officinalis. SCAR mark is established and can be used as the basis for breeding and distinguishing the verieties of C. officinalis.

Relationship between apoptotic markers in semen from fertile men and demographic, hormonal and seminal characteristics

DEFF Research Database (Denmark)

Specht, Ina; Spanò, Marcello; Hougaard, Karin S

2012-01-01

and biological correlates of the pro-apoptotic marker Fas and the anti-apoptotic marker Bcl-xL in sperm cells of fertile men. Six hundred and four men from Greenland, Poland and Ukraine were consecutively enrolled during their pregnant wife's antenatal visits. Semen analysis was performed as recommended...

Embedding filtering criteria into a wrapper marker selection method for brain tumor classification: an application on metabolic peak area ratios

International Nuclear Information System (INIS)

Kounelakis, M G; Zervakis, M E; Giakos, G C; Postma, G J; Buydens, L M C; Kotsiakis, X

2011-01-01

The purpose of this study is to identify reliable sets of metabolic markers that provide accurate classification of complex brain tumors and facilitate the process of clinical diagnosis. Several ratios of metabolites are tested alone or in combination with imaging markers. A wrapper feature selection and classification methodology is studied, employing Fisher's criterion for ranking the markers. The set of extracted markers that express statistical significance is further studied in terms of biological behavior with respect to the brain tumor type and grade. The outcome of this study indicates that the proposed method by exploiting the intrinsic properties of data can actually reveal reliable and biologically relevant sets of metabolic markers, which form an important adjunct toward a more accurate type and grade discrimination of complex brain tumors

Role of excision repair in postradiation recovery of biological activity of cellular DNA Bacillus subtilis

International Nuclear Information System (INIS)

Filippov, V.D.

1976-01-01

DNA extracted from UV-irradiated prototroph cells of Bacillus subtilis uvr + (45 sec. of UV light, 20% survivals) has a lowered transforming activity (TA) of markers purB and metB, and a lowered ratio TA pur/TA met. During the subsequent incubation of uvr + cells in glucose-salt medium free of nitrogen sources the TA of markers and the ratio between them increase. No increase is observed during the postradiation incubation under the same conditions or in a nutrition medium of uvr cells, deficient in escision of pyrimidine dimers. The increment of DNA begins approsimately in 30 min. after the beginning of incubation of irradiated uvr cells in nutrition medium. On the basis of these facts it is concluded that neither the replication of damaged DNA nor the postreplication repair, but only excision repair, can provide the recovery of biological (transforming) activity of cellular DNA in Bac. subtilis. The system given might be a suitable model for testing compounds which affect the activity of this process. The well-known inhibitors of dark repair, caffeine, proflavine to inhibit reversibly the initial steps of the process/ and especially acriflavine, delay the recovery of markers of cellular DNA in irradiated uvr + cells. Caffeine is proved to inhibit reversibly the initial steps of the process

Messina: a novel analysis tool to identify biologically relevant molecules in disease.

Directory of Open Access Journals (Sweden)

Mark Pinese

Full Text Available BACKGROUND: Morphologically similar cancers display heterogeneous patterns of molecular aberrations and follow substantially different clinical courses. This diversity has become the basis for the definition of molecular phenotypes, with significant implications for therapy. Microarray or proteomic expression profiling is conventionally employed to identify disease-associated genes, however, traditional approaches for the analysis of profiling experiments may miss molecular aberrations which define biologically relevant subtypes. METHODOLOGY/PRINCIPAL FINDINGS: Here we present Messina, a method that can identify those genes that only sometimes show aberrant expression in cancer. We demonstrate with simulated data that Messina is highly sensitive and specific when used to identify genes which are aberrantly expressed in only a proportion of cancers, and compare Messina to contemporary analysis techniques. We illustrate Messina by using it to detect the aberrant expression of a gene that may play an important role in pancreatic cancer. CONCLUSIONS/SIGNIFICANCE: Messina allows the detection of genes with profiles typical of markers of molecular subtype, and complements existing methods to assist the identification of such markers. Messina is applicable to any global expression profiling data, and to allow its easy application has been packaged into a freely-available stand-alone software package.

The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows.

Science.gov (United States)

Hardie, L C; VandeHaar, M J; Tempelman, R J; Weigel, K A; Armentano, L E; Wiggans, G R; Veerkamp, R F; de Haas, Y; Coffey, M P; Connor, E E; Hanigan, M D; Staples, C; Wang, Z; Dekkers, J C M; Spurlock, D M

2017-11-01

The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cows were from research herds located in the United States, Canada, the Netherlands, and the United Kingdom. Feed efficiency, defined as residual feed intake (RFI), was calculated within location as the residual of the regression of dry matter intake (DMI) on milk energy (MilkE), metabolic body weight (MBW), change in body weight, and systematic effects. For RFI, DMI, MilkE, and MBW, bivariate analyses were performed considering each trait as a separate trait within parity group to estimate variance components and genetic correlations between them. Animal relationships were established using a genomic relationship matrix. Genome-wide association studies were performed separately by parity group for RFI, DMI, MilkE, and MBW using the Bayes B method with a prior assumption that 1% of single nucleotide polymorphisms have a nonzero effect. One-megabase windows with greatest percentage of the total genetic variation explained by the markers (TGVM) were identified, and adjacent windows with large proportion of the TGVM were combined and reanalyzed. Heritability estimates for RFI were 0.14 (±0.03; ±SE) in primiparous cows and 0.13 (±0.03) in multiparous cows. Genetic correlations between primiparous and multiparous cows were 0.76 for RFI, 0.78 for DMI, 0.92 for MBW, and 0.61 for MilkE. No single 1-Mb window explained a significant proportion of the TGVM for RFI; however, after combining windows, significance was met on Bos taurus autosome 27 in primiparous cows, and nearly reached on Bos taurus autosome 4 in multiparous cows. Among other genes, these regions contain β-3 adrenergic receptor and the physiological candidate gene

Changes in the ER, PgR, HER2, p53 and Ki-67 biological markers between primary and recurrent breast cancer: discordance rates and prognosis

Directory of Open Access Journals (Sweden)

Tashima Rumiko

2011-10-01

Full Text Available Abstract Background In breast cancer, ER/PgR, HER2, and Ki-67 are important biological markers for predicting prognosis and making effective treatment decisions. In addition, changes in markers due to relapse are also clinically experienced; however, the frequency and clinical significance are still not fully understood. Thus, changes in markers and their correlations with prognosis were investigated. Patients and Methods Out of the patients with relapse from 1997 to March 2011, there were 97 consecutive patients from whom the lesion was resected and evaluated by immunostaining. The biopsy sites were chest wall, lymph node, ipsilateral breast tumor recurrence, lungs, bones, ovaries and brain. The markers sought were ER, PgR, HER2, p53 and Ki-67. Results The hormone receptor positive rate from the primary tumor to recurrence decreased from 63.9% to 57.7% and from 56.7% to 43.3% for ER and PgR, respectively. Changes in the positive/negative evaluation were seen at the rate of 10.3% and 25.8% for ER and PgR, respectively. The Ki-67 index increased significantly from a mean of 29.1% at primary tumor to 36.3% at relapse. When divided into 2 groups ( Conclusion Estrogen receptor and PgR decreased while Ki-67 increased due to relapse; however, the rate of change was high for PgR and Ki-67. Change in the subtypes was seen in 25%. In addition, PgR at relapse and Ki-67 at primary tumor were significant factors for post-relapse prognosis while PgR becoming negative was a poor prognostic factor. These findings are important for making effective treatment decisions.

Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars.

Science.gov (United States)

Costet, L; Le Cunff, L; Royaert, S; Raboin, L-M; Hervouet, C; Toubi, L; Telismart, H; Garsmeur, O; Rousselle, Y; Pauquet, J; Nibouche, S; Glaszmann, J-C; Hoarau, J-Y; D'Hont, A

2012-09-01

Modern sugarcane cultivars (Saccharum spp., 2n = 100-130) are high polyploid, aneuploid and of interspecific origin. A major gene (Bru1) conferring resistance to brown rust, caused by the fungus Puccinia melanocephala, has been identified in cultivar R570. We analyzed 380 modern cultivars and breeding materials covering the worldwide diversity with 22 molecular markers genetically linked to Bru1 in R570 within a 8.2 cM segment. Our results revealed a strong LD in the Bru1 region and strong associations between most of the markers and rust resistance. Two PCR markers, that flank the Bru1-bearing segment, were found completely associated with one another and only in resistant clones representing efficient molecular diagnostic for Bru1. On this basis, Bru1 was inferred in 86 % of the 194 resistant sugarcane accessions, revealing that it constitutes the main source of brown rust resistance in modern cultivars. Bru1 PCR diagnostic markers should be particularly useful to identify cultivars with potentially alternative sources of resistance to diversify the basis of brown rust resistance in breeding programs.

Cancer molecular markers: A guide to cancer detection and management.

Science.gov (United States)

Nair, Meera; Sandhu, Sardul Singh; Sharma, Anil Kumar

2018-02-08

Cancer is generally caused by the molecular alterations which lead to specific mutations. Advances in molecular biology have provided an impetus to the study of cancers with valuable prognostic and predictive significance. Over the hindsight various attempts have been undertaken by scientists worldwide, in the management of cancer; where, we have witnessed a number of molecular markers which allow the early detection of cancers and lead to a decrease in its mortality rate. Recent advances in oncology have led to the discovery of cancer markers that has allowed early detection and targeted therapy of tumors. In this context, current review provides a detail outlook on various molecular markers for diagnosis, prognosis and management of therapeutic response in cancer patients. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design

Directory of Open Access Journals (Sweden)

Shashi N. Goonetilleke

2018-01-01

Full Text Available In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb, application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.

cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications.

Science.gov (United States)

Wani, Gowher A; Shah, Manzoor A; Reshi, Zafar A; Atangana, Alain R; Khasa, Damase P

2014-07-01

A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation.

A case against bio markers as they are currently used in radioecological risk analyses: a problem of linkage

International Nuclear Information System (INIS)

Hinton, T.G.; Brechignac, F.

2005-01-01

Bio-markers are successfully used in human risk analyses as early indicators of contaminant exposure and predictors of deleterious effects. This has boosted the search for bio-markers in determining ecological risks to non-human biota, and particularly for assessments related to radioactive contaminants. There are difficulties, however, that prevent an easy transfer of the bio-marker concept from humans to non-human biota, as there are significant differences in endpoints of concern, units of observation and dose response relationships between human and ecological risk analyses. The use of bio-markers in ecological risk analyses currently lacks a linkage between molecular-level effects and quantifiable impacts observed in individuals and populations. This is important because ecological risk analyses generally target the population level of biological organisation. We highlight various examples that demonstrate the difficulties of linking individual responses to population-level impacts, such as indirect effects and compensatory interactions. Eco-toxicologists cope with such difficulties through the use of uncertainty or extrapolation factors. Extrapolation factors (EF) typically range from 1 to 1000 when linking effects observed in individuals to those predicted to occur in populations. We question what magnitude of EF will be required when going from a molecular level effect, measured by a bio-marker, all the way up to the population level of biological organisation. Particularly, we stress that a successful application of bio-markers to radioecological risk assessment can only be achieved once the connection has been made between changes in individual resource allocation-based life histories and population dynamics. This clearly emphasises the need to quantify the propagation of molecular and cellular level effects to higher levels of biological organisation, especially in the long-term via several generations of exposure. Finally, we identify pertinent research

Inflammatory markers in blood and serum tumor markers predict survival in patients with epithelial appendiceal neoplasms undergoing surgical cytoreduction and intraperitoneal chemotherapy.

Science.gov (United States)

Chua, Terence C; Chong, Chanel H; Liauw, Winston; Zhao, Jing; Morris, David L

2012-08-01

The study examines the role inflammatory and tumor markers as biomarkers to preoperatively predict outcome in patients with epithelial appendiceal neoplasm undergoing cytoreduction and intraperitoneal chemotherapy. Associations between baseline variables, tumor markers [CEA (carcinoembyronic antigen], CA125, CA199), inflammatory markers including neutrophils-lymphocyte ratio (NLR), platelet-lymphocyte ratio (PLR), and C-reactive protein (CRP) with progression-free survival (PFS) and overall survival (OS) were examined in patients undergoing surgical cytoreduction and intraperitoneal chemotherapy for epithelial appendiceal neoplasm. A total of 174 patients with epithelial appendiceal neoplasm (low-grade pseudomyxoma, n = 117; appendiceal cancer, n = 57) underwent cytoreduction. On univariate analysis, all 3 inflammatory and tumor markers predicted for both PFS and OS, respectively; NLR ≤ 2.6 (P = 0.01, P = 0.002), PLR ≤ 166 (P = 0.006, P = 0.016), CRP ≤ 12.5 (P = 0.001, P = 0.008), CEA (P 37 (P = 0.003), and a CRP > 12.5 (P = 0.013). A higher peritoneal cancer index (PCI > 24) was associated with elevation in CEA > 12, CA125 > 39, CA199 > 37, PLR > 166 and CRP > 12. The tumor histologic subtype was associated with CA 199 levels. The results from this investigation suggest that preoperative inflammatory markers in blood and serologic tumor markers may predict outcomes and are associated with tumor biology in patients with epithelial appendiceal neoplasm undergoing cytoreduction and intraperitoneal chemotherapy treatment.

Application of tumor markers in the immunodiagnosis of cancer

International Nuclear Information System (INIS)

Gelder, F.B.; Barr, L.H.; Goldman, L.I.

1983-01-01

Recently, research directed toward the detection of both tumor-specific and tumor-related products has intensified for several reasons. 1. The growing knowledge of tumor metabolism has lead some investigators to hypothesize that most, if not all, malignant tumors produce these substances. 2. The use of multiple tumor markers appears more valuable than application of single markers. 3. The availability of highly sensitive and specific immunological methods provides the tools to measure substances which previously could not be assayed. 4. As additional information evolves, the events associated with malignant transformation and tumor behaviour may become clear. Tumor-related products include immune markers, altered cell surface membranes, as well as fetal and/or ectopic proteins, to name but a few. The synthesis of fetal and/or ectopic proteins occurs in several cancers. These have served as the basis for most immunodiagnostic tests and comprise the major thrust of this review

Sensitivity improvements, in the determination of mercury in biological tissues by neutron activation analysis

Energy Technology Data Exchange (ETDEWEB)

Cornett, C R; Samudralwar, D L; Ehmann, W D [Kentucky Univ., Lexington, KY (United States). Dept. of Chemistry; Markesbery, W R [Kentucky Univ., Lexington, KY (United States)

1995-08-01

The possible association of dental amalgam surface exposure, brain mercury (Hg) levels, and pathological markers of Alzheimer`s disease (AD) in the brain is the subject of an on-going study in our laboratory. Two radiochemical neutron activation analysis methods and the use of instrumental neutron activation analysis (INAA) with Compton suppression spectrometry have been evaluated for improving our INAA Hg detection limit (2.8{+-}0.6 ng/g, wet-weight basis) in human tissue. Large numbers of samples dictated the use of a purely instrumental method or rapid, simple radiochemical separations. Human brain tissues and NIST biological standards were analyzed using a precipitation of Hg{sub 2}Cl{sub 2}, a solvent extraction utilizing sodium diethyldithiocarbomate, conventional INAA, and INAA with Compton suppression. The radiochemical precipitation of Hg{sub 2}Cl{sub 2} proved to be the most useful method for use in our study because it provided a simultaneous, quantitative determination of silver (Ag) and a Hg detection limit in brain tissue of 1.6{+-}0.1 ng/g (wet-weight basis). (author). 12 refs., 2 tabs.

Serum and urinary biochemical markers for knee and hip-osteoarthritis: a systematic review applying the consensus BIPED criteria

NARCIS (Netherlands)

Spil, W.E. van; Groot, J. de; Lems, W.F.; Oostveen, J.C.M.; Lafeber, F.P.J.G.

2010-01-01

Context: Molecules that are released into biological fluids during matrix metabolism of articular cartilage, subchondral bone, and synovial tissue could serve as biochemical markers of the process of osteoarthritis (OA). Unfortunately, actual breakthroughs in the biochemical OA marker field are

Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

Science.gov (United States)

Lau, Wendy C. P.; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam; Latif, Mohammad A.; Ramli, Asfaliza

2015-01-01

After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

Systems biology and biomarker discovery

Energy Technology Data Exchange (ETDEWEB)

Rodland, Karin D.

2010-12-01

Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

Environmental biology

International Nuclear Information System (INIS)

Tschumi, P.A.

1981-01-01

Environmental biology illustrates the functioning of ecosystems and the dynamics of populations with many examples from limnology and terrestrial ecology. On this basis, present environmental problems are analyzed. The present environmental crisis is seen as a result of the failure to observe ecological laws. (orig.) [de

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

DEFF Research Database (Denmark)

Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn

2011-01-01

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environment...

Improved ability of biological and previous caries multimarkers to predict caries disease as revealed by multivariate PLS modelling

Directory of Open Access Journals (Sweden)

Ericson Thorild

2009-11-01

Full Text Available Abstract Background Dental caries is a chronic disease with plaque bacteria, diet and saliva modifying disease activity. Here we have used the PLS method to evaluate a multiplicity of such biological variables (n = 88 for ability to predict caries in a cross-sectional (baseline caries and prospective (2-year caries development setting. Methods Multivariate PLS modelling was used to associate the many biological variables with caries recorded in thirty 14-year-old children by measuring the numbers of incipient and manifest caries lesions at all surfaces. Results A wide but shallow gliding scale of one fifth caries promoting or protecting, and four fifths non-influential, variables occurred. The influential markers behaved in the order of plaque bacteria > diet > saliva, with previously known plaque bacteria/diet markers and a set of new protective diet markers. A differential variable patterning appeared for new versus progressing lesions. The influential biological multimarkers (n = 18 predicted baseline caries better (ROC area 0.96 than five markers (0.92 and a single lactobacilli marker (0.7 with sensitivity/specificity of 1.87, 1.78 and 1.13 at 1/3 of the subjects diagnosed sick, respectively. Moreover, biological multimarkers (n = 18 explained 2-year caries increment slightly better than reported before but predicted it poorly (ROC area 0.76. By contrast, multimarkers based on previous caries predicted alone (ROC area 0.88, or together with biological multimarkers (0.94, increment well with a sensitivity/specificity of 1.74 at 1/3 of the subjects diagnosed sick. Conclusion Multimarkers behave better than single-to-five markers but future multimarker strategies will require systematic searches for improved saliva and plaque bacteria markers.

Evaluation of four single-locus markers for leishmania species discrimination by sequencing

NARCIS (Netherlands)

van der Auwera, Gert; Ravel, Christophe; Verweij, Jaco J.; Bart, Aldert; Schönian, Gabriele; Felger, Ingrid

2014-01-01

Several genetic markers have been described for discriminating Leishmania species. In most reported cases, one or a few polymorphisms are the basis of species identification, and the methods were validated on a limited number of strains from a particular geographical region. Therefore, most

Physical exercise, fitness and dietary pattern and their relationship with circadian blood pressure pattern, augmentation index and endothelial dysfunction biological markers: EVIDENT study protocol

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Nicolás Eguskiñe

2010-05-01

Full Text Available Abstract Background Healthy lifestyles may help to delay arterial aging. The purpose of this study is to analyze the relationship of physical activity and dietary pattern to the circadian pattern of blood pressure, central and peripheral blood pressure, pulse wave velocity, carotid intima-media thickness and biological markers of endothelial dysfunction in active and sedentary individuals without arteriosclerotic disease. Methods/Design Design: A cross-sectional multicenter study with six research groups. Subjects: From subjects of the PEPAF project cohort, in which 1,163 who were sedentary became active, 1,942 were sedentary and 2,346 were active. By stratified random sampling, 1,500 subjects will be included, 250 in each group. Primary measurements: We will evaluate height, weight, abdominal circumference, clinical and ambulatory blood pressure with the Radial Pulse Wave Acquisition Device (BPro, central blood pressure and augmentation index with Pulse Wave Application Software (A-Pulse and SphymgoCor System Px (Pulse Wave Analysis, pulse wave velocity (PWV with SphymgoCor System Px (Pulse Wave Velocity, nutritional pattern with a food intake frequency questionnaire, physical activity with the 7-day PAR questionnaire and accelerometer (Actigraph GT3X, physical fitness with the cycle ergometer (PWC-170, carotid intima-media thickness by ultrasound (Micromax, and endothelial dysfunction biological markers (endoglin and osteoprotegerin. Discussion Determining that sustained physical activity and the change from sedentary to active as well as a healthy diet improve circadian pattern, arterial elasticity and carotid intima-media thickness may help to propose lifestyle intervention programs. These interventions could improve the cardiovascular risk profile in some parameters not routinely assessed with traditional risk scales. From the results of this study, interventional approaches could be obtained to delay vascular aging that combine physical

Identify super quality markers from prototype-based pharmacokinetic markers of Tangzhiqing tablet (TZQ) based on in vitro dissolution/ permeation and in vivo absorption correlations.

Science.gov (United States)

Li, Ziqiang; Liu, Jia; Li, Yazhuo; Du, Xi; Li, Yanfen; Wang, Ruihua; Lv, Chunxiao; He, Xin; Wang, Baohe; Huang, Yuhong; Zhang, Deqin

2018-06-01

A quality marker (Q-marker) is defined as an inherent chemical compound that is used for the quality control of a drug. Its biological activities are closely related to safety and therapeutic effects. Generally, a multiple-component herbal medicine may have many Q-markers. We therefore proposed a concept of "super Q-marker" satisfying both the criterion of Q-markers and PK-markers to be used in more effective quality control of herbal medicine. The first aim was to find suitable prototype-based PK-markers from Tangzhiqing tablets (TZQ), a Chinese patent medicine. Then super Q-markers were expected to be identified from the prototype-based PK-markers based on an in vitro-in vivo correlation study. Potentially eligible prototype-based PK-markers were identified in a single- and multiple-dose pharmacokinetic study on TZQ in 30 healthy volunteers. The in vitro dissolution and permeation profiles of the prototype-based PK-markers of TZQ were evaluated by the physiologically-based drug dissolution/absorption simulating system (DDASS). An in vitro-in vivo correlation analysis was conducted between the dissolution/permeation behaviors in DDASS and the actual absorption profiles in human to test the transferability and traceability of the promising super Q-markers for TZQ. In human, plasma paeoniflorin and nuciferine as prototype-based PK-markers exhibited the appropriate pharmacokinetic properties, including dose-dependent systemic exposure (AUC, C max ) and a proper elimination half-life (1∼3h). In DDASS, it was predicted that paeoniflorin and nuciferine are highly permeable but the absorption rates are primarily limited by the dissolution rates. Moreover, the established in vitro-in vivo correlations of paeoniflorin and nuciferine were in support of the super Q-markers features. Paeoniflorin and nuciferine are identified as the super Q-markers from the prototype-based PK-markers of TZQ based on findings from a combination of in vitro, in vivo, and in vitro-in vivo

Application of petroleum markers to geochemical and environmental investigations

International Nuclear Information System (INIS)

Abu-Elgheit, M.A.; El-Gayar, M.S.; Hegazi, A.H.

1998-01-01

Application of trace-metal and biological markers to geochemical studies has shown that crude oils could be correlated or differentiated according to their geologic age. The V/Ni, V/Σ Ni, Mg, Fe, and pristine to phytane (Pr/Ph) markers were almost uniform in Gulf of Suez crude oils, revealing their same origin, yet showing marked differences in Western Desert crude oils, reflecting varying degrees of their maturity and migrational history. The significance of petroleum markers was extended to monitoring of oil spill sources. Weathering of spills usually renders their source identification questionable by infrared or gas chromatography profiles. Since evaporative loss light petroleum fractions does not appreciably affect the high-Molecular Weight components with which trace metals, isoprenoids, hopanes, and steranes are associated, V/Ni, Pr/Ph, m/z 191, and m/z 217 mass chromatogram fragments were found reliable in fingerprinting oil spill sources in Mediterranean waters

cpDNA Microsatellite Markers for Lemna minor (Araceae: Phylogeographic Implications

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Gowher A. Wani

2014-07-01

Full Text Available Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation.

Alteration of serum thymus and activation-regulated chemokine level during biologic therapy for psoriasis: Possibility as a marker reflecting favorable response to anti-interleukin-17A agents.

Science.gov (United States)

Shibuya, Takashi; Honma, Masaru; Iinuma, Shin; Iwasaki, Takeshi; Takahashi, Hidetoshi; Ishida-Yamamoto, Akemi

2018-06-01

Biologics show great efficacy in treating psoriasis, a chronic inflammatory skin disease. The high cost and side-effects of biologics, dose-reduction, elongation of administration interval and suspension are possible options. However, there has been no reliable biomarker we can use when we consider these moderations in therapy. This study was conducted to test the possibility of using serum thymus and activation-regulated chemokine (TARC) level as an indicator for step down of biologic therapy. Serum TARC level was measured in 70 psoriatic patients at Asahikawa Medical University, and a correlation of TARC and severity of skin lesions was analyzed. Referring to serum TARC level, psoriatic patients can be divided into two groups. One is a population in which serum TARC level is positively correlated with severity of skin lesions, and the other is a population with low psoriatic severity and high TARC level. Serum TARC level was higher in the group that achieved PASI-clear with biologics than in the group which did not achieve PASI-clear. Among biologics, the group treated with secukinumab, an anti-interleukin (IL)-17A agent, showed significantly higher TARC level compared with the group treated with anti-tumor necrosis factor agents. In certain populations achieving PASI-clear, serum TARC level may be a potent marker reflecting better response to IL-17A inhibitors, and in this case step down of treatment for psoriasis is possible. © 2018 Japanese Dermatological Association.

New basis set for the prediction of the specific rotation in flexible biological molecules

DEFF Research Database (Denmark)

Baranowska-Łaczkowska, Angelika; Z. Łaczkowski, Krzysztof Z. Łaczkowski; Henriksen, Christian

2016-01-01

are compared to those obtained with the (d-)aug-cc-pVXZ (X = D, T and Q) basis sets of Dunning et al. The ORP values are in good overall agreement with the aug-cc-pVTZ results making the ORP a good basis set for routine TD-DFT optical rotation calculations of conformationally flexible molecules. The results...

Biological basis of suicide and suicidal behavior

Science.gov (United States)

Pandey, Ghanshyam N

2013-01-01

Objective Suicide is a major public health concern as each year 30,000 people die by suicide in the US alone. In the teenage population, it is the second leading cause of death. There have been extensive studies of psychosocial factors associated with suicide and suicidal behavior. However, very little is known about the neurobiology of suicide. Recent research has provided some understanding of the neurobiology of suicide, which is the topic of this review. Methods Neurobiology of suicide has been studied using peripheral tissues, such as platelets, lymphocytes, and cerebral spinal fluid obtained from suicidal patients or from the postmortem brains of suicide victims. Results These studies have provided encouraging information with regard to the neurobiology of suicide. They show an abnormality of serotonergic mechanism, such as increased serotonin receptor subtypes and decreased serotonin metabolites, such as 5-hydroxyindoleacetic acid. These studies also suggest abnormalities of receptor-linked signaling mechanisms, such as phosphoinositide and adenylyl cyclase signaling mechanisms. Other biological systems that appear to be dysregulated in suicide are the hypothalamic-pituitary-adrenal (HPA) axis, and abnormalities of neurotrophins and neurotrophin receptors. More recently, several studies also indicate abnormalities of neuroimmune functions in suicide. Conclusions These studies have been discussed in detail in the following review. Some encouraging information has emerged, primarily related to some of these neurobiological mechanisms. It is hoped that neurobiological studies may eventually result in identifying appropriate biomarkers for suicidal behavior as well as appropriate therapeutic targets for its treatment. PMID:23773657

Molecular basis for mitochondrial signaling

CERN Document Server

2017-01-01

This book covers recent advances in the study of structure, function, and regulation of metabolite, protein and ion translocating channels, and transporters in mitochondria. A wide array of cutting-edge methods are covered, ranging from electrophysiology and cell biology to bioinformatics, as well as structural, systems, and computational biology. At last, the molecular identity of two important channels in the mitochondrial inner membrane, the mitochondrial calcium uniporter and the mitochondrial permeability transition pore have been established. After years of work on the physiology and structure of VDAC channels in the mitochondrial outer membrane, there have been multiple discoveries on VDAC permeation and regulation by cytosolic proteins. Recent breakthroughs in structural studies of the mitochondrial cholesterol translocator reveal a set of novel unexpected features and provide essential clues for defining therapeutic strategies. Molecular Basis for Mitochondrial Signaling covers these and many more re...

International consensus for neuroblastoma molecular diagnostics: report from the International Neuroblastoma Risk Group (INRG) Biology Committee

Science.gov (United States)

Ambros, P F; Ambros, I M; Brodeur, G M; Haber, M; Khan, J; Nakagawara, A; Schleiermacher, G; Speleman, F; Spitz, R; London, W B; Cohn, S L; Pearson, A D J; Maris, J M

2009-01-01

Neuroblastoma serves as a paradigm for utilising tumour genomic data for determining patient prognosis and treatment allocation. However, before the establishment of the International Neuroblastoma Risk Group (INRG) Task Force in 2004, international consensus on markers, methodology, and data interpretation did not exist, compromising the reliability of decisive genetic markers and inhibiting translational research efforts. The objectives of the INRG Biology Committee were to identify highly prognostic genetic aberrations to be included in the new INRG risk classification schema and to develop precise definitions, decisive biomarkers, and technique standardisation. The review of the INRG database (n=8800 patients) by the INRG Task Force finally enabled the identification of the most significant neuroblastoma biomarkers. In addition, the Biology Committee compared the standard operating procedures of different cooperative groups to arrive at international consensus for methodology, nomenclature, and future directions. Consensus was reached to include MYCN status, 11q23 allelic status, and ploidy in the INRG classification system on the basis of an evidence-based review of the INRG database. Standardised operating procedures for analysing these genetic factors were adopted, and criteria for proper nomenclature were developed. Neuroblastoma treatment planning is highly dependant on tumour cell genomic features, and it is likely that a comprehensive panel of DNA-based biomarkers will be used in future risk assignment algorithms applying genome-wide techniques. Consensus on methodology and interpretation is essential for uniform INRG classification and will greatly facilitate international and cooperative clinical and translational research studies. PMID:19401703

Natural hybridization in tropical spikerushes of Eleocharis subgenus Limnochloa (Cyperaceae): Evidence from morphology and DNA markers

Czech Academy of Sciences Publication Activity Database

Košnar, J.; Košnar, Ji.; Macek, Petr; Herbstová, Miroslava; Rejmánková, E.; Stech, M.

2010-01-01

Roč. 97, č. 7 (2010), s. 1229-1240 ISSN 0002-9122 Institutional research plan: CEZ:AV0Z60050516; CEZ:AV0Z50510513 Keywords : Belize * Cyperaceae * DNA markers * hybridization Subject RIV: EB - Genetics ; Molecular Biology; EB - Genetics ; Molecular Biology (BU-J) Impact factor: 3.052, year: 2010

Structural Biology Guides Antibiotic Discovery

Science.gov (United States)

Polyak, Steven

2014-01-01

Modern drug discovery programs require the contribution of researchers in a number of specialist areas. One of these areas is structural biology. Using X-ray crystallography, the molecular basis of how a drug binds to its biological target and exerts its mode of action can be defined. For example, a drug that binds into the active site of an…

Lod scores for gene mapping in the presence of marker map uncertainty.

Science.gov (United States)

Stringham, H M; Boehnke, M

2001-07-01

Multipoint lod scores are typically calculated for a grid of locus positions, moving the putative disease locus across a fixed map of genetic markers. Changing the order of a set of markers and/or the distances between the markers can make a substantial difference in the resulting lod score curve and the location and height of its maximum. The typical approach of using the best maximum likelihood marker map is not easily justified if other marker orders are nearly as likely and give substantially different lod score curves. To deal with this problem, we propose three weighted multipoint lod score statistics that make use of information from all plausible marker orders. In each of these statistics, the information conditional on a particular marker order is included in a weighted sum, with weight equal to the posterior probability of that order. We evaluate the type 1 error rate and power of these three statistics on the basis of results from simulated data, and compare these results to those obtained using the best maximum likelihood map and the map with the true marker order. We find that the lod score based on a weighted sum of maximum likelihoods improves on using only the best maximum likelihood map, having a type 1 error rate and power closest to that of using the true marker order in the simulation scenarios we considered. Copyright 2001 Wiley-Liss, Inc.

Molecular markers in bladder cancer: Novel research frontiers.

Science.gov (United States)

Sanguedolce, Francesca; Cormio, Antonella; Bufo, Pantaleo; Carrieri, Giuseppe; Cormio, Luigi

2015-01-01

Bladder cancer (BC) is a heterogeneous disease encompassing distinct biologic features that lead to extremely different clinical behaviors. In the last 20 years, great efforts have been made to predict disease outcome and response to treatment by developing risk assessment calculators based on multiple standard clinical-pathological factors, as well as by testing several molecular markers. Unfortunately, risk assessment calculators alone fail to accurately assess a single patient's prognosis and response to different treatment options. Several molecular markers easily assessable by routine immunohistochemical techniques hold promise for becoming widely available and cost-effective tools for a more reliable risk assessment, but none have yet entered routine clinical practice. Current research is therefore moving towards (i) identifying novel molecular markers; (ii) testing old and new markers in homogeneous patients' populations receiving homogeneous treatments; (iii) generating a multimarker panel that could be easily, and thus routinely, used in clinical practice; (iv) developing novel risk assessment tools, possibly combining standard clinical-pathological factors with molecular markers. This review analyses the emerging body of literature concerning novel biomarkers, ranging from genetic changes to altered expression of a huge variety of molecules, potentially involved in BC outcome and response to treatment. Findings suggest that some of these indicators, such as serum circulating tumor cells and tissue mitochondrial DNA, seem to be easily assessable and provide reliable information. Other markers, such as the phosphoinositide-3-kinase (PI3K)/AKT (serine-threonine kinase)/mTOR (mammalian target of rapamycin) pathway and epigenetic changes in DNA methylation seem to not only have prognostic/predictive value but also, most importantly, represent valuable therapeutic targets. Finally, there is increasing evidence that the development of novel risk assessment tools

Genome Target Evaluator (GTEvaluator: A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers.

Directory of Open Access Journals (Sweden)

Arnaud Felten

Full Text Available Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers. In the present study, we have developed GTEvaluator, a bioinformatics workflow which ranks genetic markers depending on their sensitivity and specificity towards groups of well-defined genomes. GTEvaluator identifies the most performant genetic markers to target individuals among a population. The individuals (i.e. a group of genomes within a collection are defined by any kind of particular phenotypic or biological properties inside a related population (i.e. collection of genomes. The performance of the genetic markers is computed by a distance value which takes into account both sensitivity and specificity. In this study we report two examples of GTEvaluator application. In the first example Bacillus phenotypic markers were evaluated for their capacity to distinguish B. cereus from B. thuringiensis. In the second experiment, GTEvaluator measured the performance of genetic markers dedicated to the molecular serotyping of Salmonella enterica. In one in silico experiment it was possible to test 64 markers onto 134 genomes corresponding to 14 different serotypes.

Changes in Oxidative Stress Markers and Biological Markers of Muscle Injury with Aging at Rest and in Response to an Exhaustive Exercise

Science.gov (United States)

Bouzid, Mohamed Amine; Hammouda, Omar; Matran, Regis; Robin, Sophie; Fabre, Claudine

2014-01-01

Purpose The aim of this study was to evaluate whether oxidative stress markers and biomarkers of muscle injury would be affected by aging at rest and in response to an incremental exhaustive exercise. Methods Fifteen young (20.3±2.8 years) and fifteen older adults (65.1±3.5 years) performed an incremental cycle ergometer test to exhaustion. Before and after exercise, oxidative stress [superoxide dismutase (SOD), glutathione peroxidase (GPX), glutathione reductase (GR), ascorbic acid, α-Tocopherol, malondialdehyde (MDA)] and muscle injury [creatine kinase (CK), lactate deshydrogenase (LDH)] biomarkers were assessed. Results At rest, there was no difference in oxidative stress markers and LDH level between the groups, however CK was significantly higher in the young group than the elderly group (pantioxidant efficiency and an increase in oxidative stress damage. Furthermore, older adults would not more susceptible to exercise-induced muscle injury than young people. PMID:24618679

Reconfiguration of face expressions based on the discrete capture data of radial basis function interpolation

Institute of Scientific and Technical Information of China (English)

ZHENG Guangguo; ZHOU Dongsheng; WEI Xiaopeng; ZHANG Qiang

2012-01-01

Compactly supported radial basis function can enable the coefficient matrix of solving weigh linear system to have a sparse banded structure, thereby reducing the complexity of the algorithm. Firstly, based on the compactly supported radial basis function, the paper makes the complex quadratic function （Multiquadric, MQ for short） to be transformed and proposes a class of compactly supported MQ function. Secondly, the paper describes a method that interpolates discrete motion capture data to solve the motion vectors of the interpolation points and they are used in facial expression reconstruction. Finally, according to this characteris- tic of the uneven distribution of the face markers, the markers are numbered and grouped in accordance with the density level, and then be interpolated in line with each group. The approach not only ensures the accuracy of the deformation of face local area and smoothness, but also reduces the time complexity of computing.

NABIC marker database: A molecular markers information network of agricultural crops.

Science.gov (United States)

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Biological Motion Perception in Autism

Directory of Open Access Journals (Sweden)

J Cusack

2011-04-01

Full Text Available Typically developing adults can readily recognize human actions, even when conveyed to them via point-like markers placed on the body of the actor (Johansson, 1973. Previous research has suggested that children affected by autism spectrum disorder (ASD are not equally sensitive to this type of visual information (Blake et al, 2003, but it remains unknown why ASD would impact the ability to perceive biological motion. We present evidence which looks at how adolescents and adults with autism are affected by specific factors which are important in biological motion perception, such as (eg, inter-agent synchronicity, upright/inverted, etc.

[Biology and culture: a dimension of collaboration between anthropology and epidemiology].

Science.gov (United States)

Song, Leiming; Wang, Ning

2016-01-01

Biology is the important basis of epidemiological study. Based on biology, psychology, social and cultural factors can influence human's health and disease incidence. The medical mode has changed from "biomedical mode" to "bio-psycho-social medical model" , but culture factor was neglected somewhat during this process, so paying attention to culture factor in anthropologic study and using it as biologic basis in epidemiologic study might be a dimension of collaboration between of anthropology and epidemiology.

Serum Calprotectin in Rheumatoid Arthritis: A Promising Diagnostic Marker, How Far Is It Related to Activity and Sonographic Findings?

Directory of Open Access Journals (Sweden)

H.E. Mansour

2017-03-01

Conclusion: Calprotectin was found to have high association with laboratory and ultrasonography markers of inflammation in RA patients, so it is recommended for use as a marker of inflammatory activity in RA patients especially for the follow-up of patients on biological therapy to assess its efficacy.

DNA damage markers in dermal fibroblasts in vitro reflect chronological donor age

DEFF Research Database (Denmark)

Waaijer, Mariëtte E C; Croco, Eleonora; Westendorp, Rudi G J

2016-01-01

The aging process is accompanied by an accumulation of cellular damage, which compromises the viability and function of cells and tissues. We aim to further explore the association between in vitro DNA damage markers and the chronological age of the donor, as well as long-lived family membership...... markers and long-lived family membership or cardiovascular disease. Results were comparable when fibroblasts were stressed in vitro with rotenone. In conclusion, we found that DNA damage foci of cultured fibroblasts are significantly associated with the chronological age, but not biological age...

The correlation between internal and external markers for abdominal tumors: Implications for respiratory gating

International Nuclear Information System (INIS)

Gierga, David P.; Brewer, Johanna; Sharp, Gregory C.; Betke, Margrit; Willett, Christopher G.; Chen, George T.Y.

2005-01-01

Purpose: The correlation of the respiratory motion of external patient markers and abdominal tumors was examined. Data of this type are important for image-guided therapy techniques, such as respiratory gating, that monitor the movement of external fiducials. Methods and Materials: Fluoroscopy sessions for 4 patients with internal, radiopaque tumor fiducial clips were analyzed by computer vision techniques. The motion of the internal clips and the external markers placed on the patient's abdominal skin surface were quantified and correlated. Results: In general, the motion of the tumor and external markers were well correlated. The maximum amount of peak-to-peak craniocaudal tumor motion was 2.5 cm. The ratio of tumor motion to external-marker motion ranged from 0.85 to 7.1. The variation in tumor position for a given external-marker position ranged from 2 to 9 mm. The period of the breathing cycle ranged from 2.7 to 4.5 seconds, and the frequency patterns for both the tumor and the external markers were similar. Conclusions: Although tumor motion generally correlated well with external fiducial marker motion, relatively large underlying tumor motion can occur compared with external-marker motion and variations in the tumor position for a given marker position. Treatment margins should be determined on the basis of a detailed understanding of tumor motion, as opposed to relying only on external-marker information

Approaches to establish Q-markers for the quality standards of traditional Chinese medicines.

Science.gov (United States)

Yang, Wenzhi; Zhang, Yibei; Wu, Wanying; Huang, Luqi; Guo, Dean; Liu, Changxiao

2017-07-01

Traditional Chinese medicine (TCM) has played a pivotal role in maintaining the health of Chinese people and is now gaining increasing acceptance around the global scope. However, TCM is confronting more and more concerns with respect to its quality. The intrinsic "multicomponent and multitarget" feature of TCM necessitates the establishment of a unique quality and bioactivity evaluation system, which is different from that of the Western medicine. However, TCM is investigated essentially as "herbal medicine" or "natural product", and the pharmacopoeia quality monographs are actually chemical-markers-based, which can ensure the consistency only in the assigned chemical markers, but, to some extent, have deviated from the basic TCM theory. A concept of "quality marker" (Q-marker), following the "property-effect-component" theory, is proposed. The establishment of Q-marker integrates multidisciplinary technologies like natural products chemistry, analytical chemistry, bionics, chemometrics, pharmacology, systems biology, and pharmacodynamics, etc. Q-marker-based fingerprint and multicomponent determination conduce to the construction of more scientific quality control system of TCM. This review delineates the background, definition, and properties of Q-marker, and the associated technologies applied for its establishment. Strategies and approaches for establishing Q-marker-based TCM quality control system are presented and highlighted with a few TCM examples.

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations.

Science.gov (United States)

Fuentes-Pardo, Angela P; Ruzzante, Daniel E

2017-10-01

Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology. © 2017 John Wiley & Sons Ltd.

cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications1

Science.gov (United States)

Wani, Gowher A.; Shah, Manzoor A.; Reshi, Zafar A.; Atangana, Alain R.; Khasa, Damase P.

2014-01-01

• Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation. PMID:25202636

Parameters of biological activity in colorectal cancer

Czech Academy of Sciences Publication Activity Database

Svobodová, Š.; Topolčan, O.; Holubec jr., L.; Levý, M.; Pecen, Ladislav; Svačina, Š.

2011-01-01

Roč. 31, č. 1 (2011), s. 373-378 ISSN 0250-7005 Institutional research plan: CEZ:AV0Z10300504 Keywords : colorectal cancer * biological activity * prognosis * tumor markers * angiogenetic factors * metalloproteinases * adhesion molecules Subject RIV: FD - Oncology ; Hematology Impact factor: 1.725, year: 2011

Molecular and biological interactions in colorectal cancer

NARCIS (Netherlands)

Heer, Pieter de

2007-01-01

The current thesis discusses the use of molecular and biological tumor markers to predict clinical outcome. By studying several key processes in the develepment of cancer as regulation of cell motility (non-receptor protein tyrosin adesion kinases, FAK, Src and paxillin, Apoptosis (caspase-3

E. Biological effects of radiation on man

International Nuclear Information System (INIS)

1976-01-01

This report firstly summarises information on the biological hazards of radiation and their relation to radiation dose, and hence estimates the biological risks associated with nuclear power production. Secondly, it describes the basis and present status of radiation protection standards in the nuclear power industry

Progress in hprt mutation assay and its application in radiation biology

International Nuclear Information System (INIS)

He Jing; Li Qiang

2008-01-01

hprt gene is an X-linked locus that has been well studied and widely used as a bio-marker in mutation detection, hprt mutation assay is a gene mutation test system in mammalian cells in vitro which has been used as a biological dosimeter. In this paper, the biological characteristics of hprt gene, hprt mutation detection methodology and the application of hprt mutation assay in radiation biology are comprehensively reviewed. (authors)

Biological marker compounds as indicators of the depositional history of the Maoming oil shale

Energy Technology Data Exchange (ETDEWEB)

Brassell, S.C.; Eglinton, G.; Mo, F.J.

1986-01-01

The Eocene Maoming oil shale from Guangdong Province occurs as a laterally uniform stratigraphic section, typically 20-25 m thick, from which the aliphatic hydrocarbon constituents of six representative samples were investigated using GC and C-GC-MS. The sediments evaluated included the basal lignite, a vitrinite lens from the overlying claystone, and four intervals from the massive oil shale bed. As expected, the lignite and vitrinite differ markedly from the oil shales. The lignite is dominated by bacterial hopanoids and components of higher plant origin, including C/sub 29/ steroids and triterpenoids such as oleanenes. Visually, the oil shale samples show corroded and degraded phytoclasts, spores, wispy particles of fluorescent organic material attributable to dinoflagellates and, especially in the uppermost sample, colonial algal bodies. The distributions of biological markers in the oil shales show many features in common, notably a dominance of dinoflagellate-derived 4-methylsteroids, and a significant proportion of higher-plant derived n-alkanes with marked odd-over-even carbon number predominance. Overall, they exhibit several features that resemble characteristics of the Messel shale. The hydrocarbons of the lowest shale horizon suggest that there may have been a gradual transition between deposition of the original peat and the subsequent oil shales. The aliphatic hydrocarbons of the uppermost shale are dominated by a number of C/sub 31/ and C/sub 33/ botryococcane homologues and other unusual branched alkanes possibly derived from green algae. All of the samples are immature. Overall, molecular and microscopic examination of the stratigraphic succession of the Maoming oil shale suggests a shallow, lacustrine environment within which peats were deposited. This lake subsequently deepened to support abundant algal populations, especially dinoflagellates, culminating in a dominance of botryococcoid algae.

Prediction of clinical infection in women with preterm labour with intact membranes: a score based on ultrasonographic, clinical and biological markers.

Science.gov (United States)

Kayem, Gilles; Maillard, Françoise; Schmitz, Thomas; Jarreau, Pierre H; Cabrol, Dominique; Breart, Gérard; Goffinet, François

2009-07-01

To predict maternal and neonatal clinical infection at admission in women hospitalized for preterm labour (PTL) with intact membranes. Prospective study of 371 women hospitalized for preterm labour with intact membranes. The primary outcome was clinical infection, defined by clinical chorioamnionitis at delivery or early-onset neonatal infection. Clinical infection was identified in 21 cases (5.7%) and was associated with earlier gestational age at admission for PTL, elevated maternal C-reactive protein (CRP) and white blood cell count (WBC), shorter cervical length, and a cervical funnelling on ultrasound. We used ROC curves to determine the cut-off values that minimized the number of false positives and false negatives. The cut-off points chosen were 30 weeks for gestational age at admission, 25 mm for cervical length, 8 mg/l for CRP and 12,000 c/mm(3) for WBC. Each of these variables was assigned a weight on the basis of the adjusted odds ratios in a clinical infection risk score (CIRS). We set a threshold corresponding to a specificity close to 90%, and calculated the positive and negative predictive values and likelihood ratios of each marker and of the CIRS. The CIRS had a sensitivity of 61.9%, while the sensitivity of the other markers ranged from 19.0% to 42.9%. Internal cross-validation was used to estimate the performance of the CIRS in new subjects. The diagnostic values found remained close to the initial values. A clinical infection risk score built from data known at admission for preterm labour helps to identify women and newborns at high risk of clinical infection.

Ácidos graxos como marcadores biológicos da ingestão de gorduras Fatty acids as biological markers of fat intake

Directory of Open Access Journals (Sweden)

Juliana dos Santos Vaz

2006-08-01

of dietary fat intake. The aim of this study is to evidence the metabolic aspects of some fatty acids and their role as markers of dietary fat intake, and to present the analytical methods used in their determination. Analysis of the fatty acid composition of adipose tissue provides long-term information on dietary fat intake, whereas the determination of the fatty acid composition of serum lipid fractions accounts for the short- and medium-term dietary intakes. The essential fatty acids, the saturated fatty acids with an odd number of carbon atoms (15:0 and 17:0 and the trans fatty acids are used as biological markers of dietary fat intake or of these individual components, since they are not synthesized endogenously. Gas chromatography and high-performance liquid chromatography are the main analytical methods used to determine fatty acid composition. At present, the most comprehensive evaluation of dietary fat intake comprises the determination of biological markers in association with dietary assessment methods.

DNA-based genetic markers for Rapid Cycling Brassica rapa (Fast Plants type designed for the teaching laboratory.

Directory of Open Access Journals (Sweden)

Eryn E. Slankster

2012-06-01

Full Text Available We have developed DNA-based genetic markers for rapid-cycling Brassica rapa (RCBr, also known as Fast Plants. Although markers for Brassica rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP based markers and 14 variable number tandem repeat (VNTR-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a nongenic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology.

Procalcitonin: A Reliable Marker for the Diagnosis of Neonatal Sepsis

Science.gov (United States)

Adib, Minoo; Bakhshiani, Zahra; Navaei, Fakhri; Saheb Fosoul, Fereshteh; Fouladi, Salomeh; Kazemzadeh, Hamidreza

2012-01-01

Objective(s) In the last few years, serum procalcitonin has been proposed as an early marker of infections in neonates, with varying results. In this study, we aimed to investigate the value of procalcitonin, and C- reactive protein in establishing the diagnosis of neonatal sepsis. Materials and Methods Blood samples were collected at admission from 69 neonates with suspected infection (admitted to the Neonatal Intensive Care Units at Alzahra and Dr Beheshti Hospital in and Fatema-Zahra in Najafabad from May 2005 to April 2006). Patients were categorized in different groups according to clinical symptoms of sepsis, bacteriological and laboratory results. Group I consisted of 20 newborns with positive blood cultures and other biological tests which suggested infection. Group II consisted of 49 neonates with negative blood cultures but had two or three of clinical signs of sepsis. The control group included 18 healthy neonates with physiological hyperbilirubinemia and no clinical and biological data of infection, referred to the hospital for bilirubin determination. Procalcitonin and C-reactive protein (CRP) were determined by immunoluminometric assay and nephlometry method respectively. Results Mean levels of procalcitonin and CRP in septic neonates (group I) were significantly higher than the other two groups (P< 0.005). Sensitivity, specificity, positive predictive value and negative predictive value were determined for all markers and compared with each other. Conclusion We conclude that procalcitonin is a better marker than CRP in the diagnosis of neonatal sepsis. PMID:23493845

From quality markers to data mining and intelligence assessment: A smart quality-evaluation strategy for traditional Chinese medicine based on quality markers.

Science.gov (United States)

Bai, Gang; Zhang, Tiejun; Hou, Yuanyuan; Ding, Guoyu; Jiang, Min; Luo, Guoan

2018-01-31

The quality of traditional Chinese medicine (TCM) forms the foundation of its clinical efficacy. The standardization of TCM is the most important task of TCM modernization. In recent years, there has been great progress in the quality control of TCM. However, there are still many issues related to the current quality standards, and it is difficult to objectively evaluate and effectively control the quality of TCM. To face these challenge, we summarized the current quality marker (Q-marker) research based on its characteristics and benefits, and proposed a reasonable and intelligentized quality evaluation strategy for the development and application of Q-markers. Ultra-performance liquid chromatography-quadrupole/time-of-flight with partial least squares-discriminant analysis was suggested to screen the chemical markers from Chinese medicinal materials (CMM), and a bioactive-guided evaluation method was used to select the Q-markers. Near-infrared spectroscopy (NIRS), based on the distinctive wavenumber zones or points from the Q-markers, was developed for its determination. Then, artificial intelligence algorithms were used to clarify the complex relationship between the Q-markers and their integral functions. Internet and mobile communication technology helped us to perform remote analysis and determine the information feedback of test samples. The quality control research, evaluation, standard establishment and quality control of TCM must be based on the systematic analysis of Q-markers to study and describe the material basis of TCM efficacy, define the chemical markers in the plant body, and understand the process of herb drug acquisition, change and transmission laws affecting metabolism and exposure. Based on the advantages of chemometrics, new sensor technologies, including infrared spectroscopy, hyperspectral imaging, chemical imaging, electronic nose and electronic tongue, have become increasingly important in the quality evaluation of CMM. Inspired by the

Biological basis of inhalation exposure of radon and its daughters

International Nuclear Information System (INIS)

Matsuoka, Osamu

1989-01-01

Since inhalation exposure by radon and its daughters is very specific type of internal exposure, it is necessary to understand its characteristic nature. The specificity originates from the nuclear feature of radon daughters and the biological micro-environment in the respiratory tract. Inhaled radon and its daughters exist in the respiratory tract as ions attached to air dusts and deposit on the mucus surface of the respiratory tract by various mechanisms such as impaction, sedimentation and diffusion. Deposition of radon daughters is predominant around the site of the fourth generation according to Weibel's model. Deposited particles with radon daughters are cleared by muco-ciliary transportation. Its speed is estimated to be about 1.0 cm/min, at the upper region. Alpha decay will happen during transportation in the respiratory tract. Radon has no tissue affinity metabolically. Therefore, the irradiation is limited to the epithelial cells of respiratory tract. The cell components within 30-70 micron in depth are irradiated with alpha particle. Biological effectiveness of alpha radiation is very high compared with beta or gamma radiation. The target cell for carcinogenesis by radon exposure is considered to be the basal cell of epithelium. Lung cancer induced by radon inhalation is recognized to be squamous cell carcinoma, small cell carcinoma, or oat-cell carcinoma and adenocarcinoma. The modification factors which influence the effect of radon exposure are co-inhalation of ore dust and smoking habit. According to epidemiological studies on lung cancer which occurred in uranium miners, it is suggested that the smoking habit strongly promotes lung cancer induction. (author)

Iterative h-minima-based marker-controlled watershed for cell nucleus segmentation.

Science.gov (United States)

Koyuncu, Can Fahrettin; Akhan, Ece; Ersahin, Tulin; Cetin-Atalay, Rengul; Gunduz-Demir, Cigdem

2016-04-01

Automated microscopy imaging systems facilitate high-throughput screening in molecular cellular biology research. The first step of these systems is cell nucleus segmentation, which has a great impact on the success of the overall system. The marker-controlled watershed is a technique commonly used by the previous studies for nucleus segmentation. These studies define their markers finding regional minima on the intensity/gradient and/or distance transform maps. They typically use the h-minima transform beforehand to suppress noise on these maps. The selection of the h value is critical; unnecessarily small values do not sufficiently suppress the noise, resulting in false and oversegmented markers, and unnecessarily large ones suppress too many pixels, causing missing and undersegmented markers. Because cell nuclei show different characteristics within an image, the same h value may not work to define correct markers for all the nuclei. To address this issue, in this work, we propose a new watershed algorithm that iteratively identifies its markers, considering a set of different h values. In each iteration, the proposed algorithm defines a set of candidates using a particular h value and selects the markers from those candidates provided that they fulfill the size requirement. Working with widefield fluorescence microscopy images, our experiments reveal that the use of multiple h values in our iterative algorithm leads to better segmentation results, compared to its counterparts. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

Biochemical markers for prediction of preclampsia: review of the literature.

Science.gov (United States)

Monte, Santo

2011-07-01

Preeclampsia (PE) is one of the most common diseases worldwide, complicating ~5% of all pregnancies.Although no major progress has been achieved in the treatment of PE, our ability to identify women at highrisk has increased considerably during the past decade.The early identification of patients with an increased risk for preeclampsia is therefore one of the most important goals in obstetrics. Today, several markers may offer the potential to be used, most likely in a combinatory analysis, as predictors or diagnostic tools. We present here the current knowledge on the biology of preeclampsia and review several biochemical markers which may be used to monitor preeclampsia in a future, that, we hope, is not to distant from today.

Voice analysis as an objective state marker in bipolar disorder

DEFF Research Database (Denmark)

Faurholt-Jepsen, M.; Busk, Jonas; Frost, M.

2016-01-01

Changes in speech have been suggested as sensitive and valid measures of depression and mania in bipolar disorder. The present study aimed at investigating (1) voice features collected during phone calls as objective markers of affective states in bipolar disorder and (2) if combining voice...... features, automatically generated objective smartphone data on behavioral activities and electronic self-monitored data were collected from 28 outpatients with bipolar disorder in naturalistic settings on a daily basis during a period of 12 weeks. Depressive and manic symptoms were assessed using...... and electronic self-monitored data increased the accuracy, sensitivity and specificity of classification of affective states slightly. Voice features collected in naturalistic settings using smartphones may be used as objective state markers in patients with bipolar disorder....

Tumor markers kits development for use in radioimmunometric assays

International Nuclear Information System (INIS)

Ahmed, B.

1997-01-01

The immunoassays such as RIA and IRMA are now widely used through the world for the quantitation of a variety of substances in the biological fluid for their high sensibility and specificity which required simple equipments. These techniques are also very used in Algeria for an effective amelioration of public heath The assays kits of RIA/IRMA of thyroid hormones are the most used, followed by peptidic hormones, steroids hormones and IRMA Tumor Markers (T.M) kits. In spite of the important demand, of tumor markers kits for the diagnosis and follow up of cancers their use are always insufficient due to the high cost. The research contract programme proposed by IAEA on the theme 'The Developments of IRMA Tumor Markers Kits' of prostate specific Antigen (PSA) and Tissue Polypeptide Specific Antigen (TPS) will allowed us to produce locally with best quality-price, the main reagents for PSA and TPS IRMA assays kits for diagnosis and follow up the prostate and breast cancers which are very spready in the country. This report include the following points: Generalities on the use of tumor markers in Algeria, programme for the Development of the PSA IRMA assay (schedule of protocols applied for each reagents; annual planning for assessing the programme activities) and conclusion

On the use of Locally Dense Basis Sets in the Calculation of EPR Hyperfine Couplings

DEFF Research Database (Denmark)

Hedegård, Erik D.; Sauer, Stephan P. A.; Milhøj, Birgitte O.

2013-01-01

The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c......The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site...

On the use of locally dense basis sets in the calculation of EPR hyperfine couplings

DEFF Research Database (Denmark)

Milhøj, Birgitte Olai; Hedegård, Erik D.; Sauer, Stephan P. A.

2013-01-01

The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c......The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site...

Biological variation of cystatin C

DEFF Research Database (Denmark)

Reinhard, Mark; Erlandsen, Erland; Randers, Else

2009-01-01

Introduction: Cystatin C has been investigated as a marker of the glomerular filtration rate. However, previous studies have reported conflicting results concerning the biological variation of cystatin C. The aim of the present study was to evaluate the biological variation of cystatin C...... in comparison to creatinine. Methods: Eight weekly morning blood samples were taken from twenty healthy volunteers (13 females, 7 males) aged 25-61 years. Mean creatinine clearance was 99.7 ml/min/1.73 m2 (range 61.8-139.5) and mean body mass index 23.9 kg/m2 (range 20.3-28.7). A total of 155 samples were...

Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana.

Science.gov (United States)

Wittenberg, Alexander H J; van der Lee, Theo; Cayla, Cyril; Kilian, Andrzej; Visser, Richard G F; Schouten, Henk J

2005-08-01

Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds of restriction site based polymorphisms between genotypes and does not require DNA sequence information or site-specific oligonucleotides. This paper demonstrates the potential of DArT for genetic mapping by validating the quality and molecular basis of the markers, using the model plant Arabidopsis thaliana. Restriction fragments from a genomic representation of the ecotype Landsberg erecta (Ler) were amplified by PCR, individualized by cloning and spotted onto glass slides. The arrays were then hybridized with labeled genomic representations of the ecotypes Columbia (Col) and Ler and of individuals from an F(2) population obtained from a Col x Ler cross. The scoring of markers with specialized software was highly reproducible and 107 markers could unambiguously be ordered on a genetic linkage map. The marker order on the genetic linkage map coincided with the order on the DNA sequence map. Sequencing of the Ler markers and alignment with the available Col genome sequence confirmed that the polymorphism in DArT markers is largely a result of restriction site polymorphisms.

COMPLICATIONS OF ALCOHOLIC LIVER DISEASE AND DIAGNOSTIC MARKERS

Directory of Open Access Journals (Sweden)

Milena Ilić

2011-12-01

Full Text Available Alcoholism is one of the leading diseases affecting people’s health and immunity worldwide. Nearly 30 thousand people in the USA die from chronic liver damage. The liver is the central organ in the metabolism of alcohol. Alcohol is primarily a hepatotoxic agent. Hepatotoxicity of alcohol is clinically manifested by the development of alcoholic fatty liver, alcoholic hepatitis and alcoholic cirrhosis. It is characterized by appropriate symptomatology, depending on the degree of liver damage. Excessive use of alcohol for a long period of time, along with malnutrition, genetic and ethnic predisposition, leads to alcoholic cirrhosis and the development of its complications. Portal hypertension damages other organs and organ systems, causing hepatopulmonary syndrome, hepatorenal syndrome, hepatic encephalopathy, spontaneous bacterial peritonitis, etc. For these reasons, alcoholism reduction is given priority, as well as reduction of morbidity and mortality of people with alcoholic chronic liver damage. Therefore, early diagnosis of alcohol abuse is necessary, as well as timely diagnosis of different degrees of alcoholic liver damage. The diagnosis of chronic alcoholic liver damage is set on the basis of confirmed data of alcohol consumption; liver function test (serum markers aminotransferase, gammaglutamyl transferase, prothrombin time, serum bilirubin and albumin level; serum markers of liver fibrosis. Fibrosis markers are directly involved in sedimentation and dissolution of extracellular matrix, i.e. in the process of fibrogenesis and fibrinolysis of liver tissues. They include markers and enzymes of metabolism, as well as cytokines and chemokines.

Fetal dose from radiotherapy photon beams: Physical basis, techniques to estimate radiation dose outside of the treatment field, biological effects and professional considerations

International Nuclear Information System (INIS)

Stovell, Marilyn; Blackwell, C. Robert

1997-01-01

Purpose/Objective: The presentation will review: 1. The physical basis of radiation dose outside of the treatment field. 2. Techniques to estimate and reduce fetal dose. 3. Clinical examples of fetal dose estimation and reduction. 4. Biological effects of fetal irradiation. 5. Professional considerations. Approximately 4000 women per year in the United States require radiotherapy during pregnancy. This report presents data and techniques that allow the medical physicist to estimate the radiation dose the fetus will receive and to reduce this dose with appropriate shielding. Out-of-beam data are presented for a variety of photon beams, including cobalt-60 gamma rays and x rays from 4 to 18 MV. Designs for simple and inexpensive to more complex and expensive types of shielding equipment are described. Clinical examples show that proper shielding can reduce the radiation dose to the fetus by 50%. In addition, a review of the biological aspects of irradiation enables estimates of the risks of lethality, growth retardation, mental retardation, malformation, sterility, cancer induction, and genetic defects to the fetus. A summary of professional considerations/recommendations is also provided as a guide for the radiation oncologist and medical physicist

Biological origins of color categorization

OpenAIRE

Skelton, Alice E.; Catchpole, Gemma; Abbott, Joshua T.; Bosten, Jenny M.; Franklin, Anna

2017-01-01

The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants’ categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mappe...

Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes

DEFF Research Database (Denmark)

Rohde, Palle Duun; Demontis, Ditte; Castro Dias Cuyabano, Beatriz

2016-01-01

was among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case–control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism......Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited...... genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT...

Zone analysis in biology articles as a basis for information extraction.

Science.gov (United States)

Mizuta, Yoko; Korhonen, Anna; Mullen, Tony; Collier, Nigel

2006-06-01

In the field of biomedicine, an overwhelming amount of experimental data has become available as a result of the high throughput of research in this domain. The amount of results reported has now grown beyond the limits of what can be managed by manual means. This makes it increasingly difficult for the researchers in this area to keep up with the latest developments. Information extraction (IE) in the biological domain aims to provide an effective automatic means to dynamically manage the information contained in archived journal articles and abstract collections and thus help researchers in their work. However, while considerable advances have been made in certain areas of IE, pinpointing and organizing factual information (such as experimental results) remains a challenge. In this paper we propose tackling this task by incorporating into IE information about rhetorical zones, i.e. classification of spans of text in terms of argumentation and intellectual attribution. As the first step towards this goal, we introduce a scheme for annotating biological texts for rhetorical zones and provide a qualitative and quantitative analysis of the data annotated according to this scheme. We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework.

Is there a Biological Basis for Therapeutic Applications of Millimetre Waves and THz Waves?

Science.gov (United States)

Mattsson, Mats-Olof; Zeni, Olga; Simkó, Myrtill

2018-03-01

Millimetre wave (MMW) and THz wave (THz) applications are already employed in certain industrial and medical environments for non-destructive quality control, and medical imaging, diagnosis, and therapy, respectively. The aim of the present study is to investigate if published experimental studies (in vivo and in vitro) provide evidence for "non-thermal" biological effects of MMW and THz. Such effects would occur in absence of tissue heating and associated damage and are the ones that can be exploited for therapeutic medical use. The investigated studies provide some evidence for both MMW and THz that can influence biological systems in a manner that is not obviously driven by tissue heating. However, the number of relevant studies is very limited which severely limits the drawing of any far-reaching conclusions. Furthermore, the studies have not addressed specific interaction mechanisms and do not provide hints for future mechanistic studies. Also, the studies do not indicate any specific importance regarding power density levels, frequencies, or exposure duration. It is also unclear if any specific biological endpoints are especially sensitive. Any therapeutic potential of MMW or THz has to be evaluated based on future high-quality studies dealing with physical, bio-physical, and biological aspects that have specific health-related perspectives in mind.

Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity.

Directory of Open Access Journals (Sweden)

Nicolas Heslot

Full Text Available Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L. genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

Science.gov (United States)

Heslot, Nicolas; Rutkoski, Jessica; Poland, Jesse; Jannink, Jean-Luc; Sorrells, Mark E.

2013-01-01

Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis. PMID:24040295

Biological variation of total prostate-specific antigen

DEFF Research Database (Denmark)

Söletormos, Georg; Semjonow, Axel; Sibley, Paul E C

2005-01-01

BACKGROUND: The objectives of this study were to determine whether a single result for total prostate-specific antigen (tPSA) can be used confidently to guide the need for prostate biopsy and by how much serial tPSA measurements must differ to be significant. tPSA measurements include both...... analytical and biological components of variation. The European Group on Tumor Markers conducted a literature survey to determine both the magnitude and impact of biological variation on single, the mean of replicate, and serial tPSA measurements. METHODS: The survey yielded 27 studies addressing the topic......, and estimates for the biological variation of tPSA could be derived from 12 of these studies. RESULTS: The mean biological variation was 20% in the concentration range 0.1-20 microg/L for men over 50 years. The biological variation means that the one-sided 95% confidence interval (CI) of the dispersion...

On the Informativeness of Dominant and Co-Dominant Genetic Markers for Bayesian Supervised Clustering

DEFF Research Database (Denmark)

Guillot, Gilles; Carpentier-Skandalis, Alexandra

2011-01-01

We study the accuracy of a Bayesian supervised method used to cluster individuals into genetically homogeneous groups on the basis of dominant or codominant molecular markers. We provide a formula relating an error criterion to the number of loci used and the number of clusters. This formula...

Biological Activity and Phytochemical Study of Scutellaria platystegia.

Science.gov (United States)

Madani Mousavi, Seyedeh Neda; Delazar, Abbas; Nazemiyeh, Hossein; Khodaie, Laleh

2015-01-01

This study aimed to determine biological activity and phytochemical study of Scutellaria platystegia (family Labiatae). Methanolic (MeOH) extract of aerial parts of S. platystegia and SPE fractions of methanolic extract (specially 20% and 40% methanolic fractions), growing in East-Azarbaijan province of Iran were found to have radical scavenging activity by DPPH (2, 2-diphenyl -1- pycryl hydrazyl) assay. Dichloromethane (DCM) extract of this plant exhibited animalarial activity by cell free method providing IC50 at 1.1876 mg/mL. Crude extracts did not exhibit any toxicity assessed by brine shrimp lethality assay. Phytochemical study of methanolic extract by using reverse phase HPLC method and NMR instrument for isolation and identification of pure compounds respectively, yielded 2-(4- hydroxy phenyl) ethyl-O-β-D- glucopyranoside from 10% and apigenin 7-O-glucoside, verbascoside and martynoside from 40% SPE fraction. Occurance of verbascoside and martynoside as biochemical markers appeared to be widespread in this genus. Antioxidant and antimalarial activity of MeOH and DCM extracts, respectively, as well as no general toxicity of them could provide a basis for further in-vitro and in-vivo studies and clinical trials to develop new therapeutical alternatives.

The diagnostic importance of the new marker KIM-1 in kidney damage

Directory of Open Access Journals (Sweden)

Zofia Marchewka

2013-07-01

Full Text Available In recent years, the rapid development of scientific research led to the introduction of strategies based on new markers that allow for estimation of the latent disease period before the clinical symptoms of actual kidney failure are revealed.The experimental tests carried out on animals and cell lines derived from the proximal tubule have made possible the detection of genes that are induced early after hypoxia [1].The protein products of these genes can be considered as useful markers for the diagnosis of renal failure. The induction of gene KIM-1 (called Kidney Injury Molecule-1 results in the formation of protein that can be considered as a diagnostic marker.This work describes the data on the structure, biological function and importance of determining the concentrations of KIM-1 in the diagnosis of drug-induced toxicity and kidney damage.

[The diagnostic importance of the new marker KIM-1 in kidney damage].

Science.gov (United States)

Marchewka, Zofia; Płonka, Joanna

2013-07-24

In recent years, the rapid development of scientific research led to the introduction of strategies based on new markers that allow for estimation of the latent disease period before the clinical symptoms of actual kidney failure are revealed. The experimental tests carried out on animals and cell lines derived from the proximal tubule have made possible the detection of genes that are induced early after hypoxia. The protein products of these genes can be considered as useful markers for the diagnosis of renal failure. The induction of gene KIM-1 (called Kidney Injury Molecule-1) results in the formation of protein that can be considered as a diagnostic marker. This work describes the data on the structure, biological function and importance of determining the concentrations of KIM-1 in the diagnosis of drug-induced toxicity and kidney damage.

Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers

Science.gov (United States)

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

Depression, osteoporosis, serotonin and cell membrane viscosity between biology and philosophical anthropology

OpenAIRE

Cocchi, Massimo; Tonello, Lucio; Gabrielli, Fabio; Pregnolato, Massimo

2011-01-01

Abstract Due to the relationship between biology and culture, we believe that depression, understood as a cultural and existential phenomenon, has clear markers in molecular biology. We begin from an existential analysis of depression constituting the human condition and then shift to analysis of biological data confirming, according to our judgment, its original (ontological) structure. In this way philosophy is involved at the anthropological level, in as much as it detects the underlying m...

A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis.

Directory of Open Access Journals (Sweden)

Dunja K Lamatsch

Full Text Available Sex-specific markers are a prerequisite for understanding reproductive biology, genetic factors involved in sex differences, mechanisms of sex determination, and ultimately the evolution of sex chromosomes. The Western mosquitofish, Gambusia affinis, may be considered a model species for sex-chromosome evolution, as it displays female heterogamety (ZW/ZZ, and is also ecologically interesting as a worldwide invasive species. Here, de novo RNA-sequencing on the gonads of sexually mature G. affinis was used to identify contigs that were highly transcribed in females but not in males (i.e., transcripts with ovary-specific expression. Subsequently, 129 primer pairs spanning 79 contigs were tested by PCR to identify sex-specific transcripts. Of those primer pairs, one female-specific DNA marker was identified, Sanger sequenced and subsequently validated in 115 fish. Sequence analyses revealed a high similarity between the identified sex-specific marker and the 3´ UTR of the aminomethyl transferase (amt gene of the closely related platyfish (Xiphophorus maculatus. This is the first time that RNA-seq has been used to successfully characterize a sex-specific marker in a fish species in the absence of a genome map. Additionally, the identified sex-specific marker represents one of only a handful of such markers in fishes.

A novel magnet based 3D printed marker wand as basis for repeated in-shoe multi segment foot analysis: a proof of concept.

Science.gov (United States)

Eerdekens, Maarten; Staes, Filip; Pilkington, Thomas; Deschamps, Kevin

2017-01-01

Application of in-shoe multi-segment foot kinematic analyses currently faces a number of challenges, including: (i) the difficulty to apply regular markers onto the skin, (ii) the necessity for an adequate shoe which fits various foot morphologies and (iii) the need for adequate repeatability throughout a repeated measure condition. The aim of this study therefore was to design novel magnet based 3D printed markers for repeated in-shoe measurements while using accordingly adapted modified shoes for a specific multi-segment foot model. Multi-segment foot kinematics of ten participants were recorded and kinematics of hindfoot, midfoot and forefoot were calculated. Dynamic trials were conducted to check for intra and inter-session repeatability when combining novel markers and modified shoes in a repeated measures design. Intraclass correlation coefficients were calculated to determine reliability. Both repeatability and reliability were proven to be good to excellent with maximum joint angle deviations of 1.11° for intra-session variability and 1.29° for same-day inter-session variability respectively and ICC values of >0.91. The novel markers can be reliably used in future research settings using in-shoe multi-segment foot kinematic analyses with multiple shod conditions.

Dielectric relaxation in biological systems physical principles, methods, and applications

CERN Document Server

Feldman, Yuri

2015-01-01

This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

Science.gov (United States)

Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

2014-09-01

The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

Intestinal Stem Cell Markers in the Intestinal Metaplasia of Stomach and Barrett's Esophagus.

Directory of Open Access Journals (Sweden)

Bo Gun Jang

Full Text Available Gastric intestinal metaplasia (IM is a highly prevalent preneoplastic lesion; however, the molecular mechanisms regulating its development remain unclear. We have previously shown that a population of cells expressing the intestinal stem cell (ISC marker LGR5 increases remarkably in IM. In this study, we further investigated the molecular characteristics of these LGR5+ cells in IM by examining the expression profile of several ISC markers. Notably, we found that ISC markers-including OLFM4 and EPHB2-are positively associated with the CDX2 expression in non-tumorous gastric tissues. This finding was confirmed in stomach lesions with or without metaplasia, which demonstrated that OLFM4 and EPHB2 expression gradually increased with metaplastic progression. Moreover, RNA in situ hybridization revealed that LGR5+ cells coexpress several ISC markers and remained confined to the base of metaplastic glands, reminiscent to that of normal intestinal crypts, whereas those in normal antral glands expressed none of these markers. Furthermore, a large number of ISC marker-expressing cells were diffusely distributed in gastric adenomas, suggesting that these markers may facilitate gastric tumorigenesis. In addition, Barrett's esophagus (BE-which is histologically similar to intestinal metaplasia-exhibited a similar distribution of ISC markers, indicating the presence of a stem cell population with intestinal differentiation potential. In conclusion, we identified that LGR5+ cells in gastric IM and BE coexpress ISC markers, and exhibit the same expression profile as those found in normal intestinal crypts. Taken together, these results implicate an intestinal-like stem cell population in the pathogenesis of IM, and provide an important basis for understanding the development and maintenance of this disease.

Markers

Science.gov (United States)

Healthy Schools Network, Inc., 2011

2011-01-01

Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

A reductionist approach to extract robust molecular markers from microarray data series - Isolating markers to track osseointegration.

Science.gov (United States)

Barik, Anwesha; Banerjee, Satarupa; Dhara, Santanu; Chakravorty, Nishant

2017-04-01

Complexities in the full genome expression studies hinder the extraction of tracker genes to analyze the course of biological events. In this study, we demonstrate the applications of supervised machine learning methods to reduce the irrelevance in microarray data series and thereby extract robust molecular markers to track biological processes. The methodology has been illustrated by analyzing whole genome expression studies on bone-implant integration (ossointegration). Being a biological process, osseointegration is known to leave a trail of genetic footprint during the course. In spite of existence of enormous amount of raw data in public repositories, researchers still do not have access to a panel of genes that can definitively track osseointegration. The results from our study revealed panels comprising of matrix metalloproteinases and collagen genes were able to track osseointegration on implant surfaces (MMP9 and COL1A2 on micro-textured; MMP12 and COL6A3 on superimposed nano-textured surfaces) with 100% classification accuracy, specificity and sensitivity. Further, our analysis showed the importance of the progression of the duration in establishment of the mechanical connection at bone-implant surface. The findings from this study are expected to be useful to researchers investigating osseointegration of novel implant materials especially at the early stage. The methodology demonstrated can be easily adapted by scientists in different fields to analyze large databases for other biological processes. Copyright © 2017 Elsevier Inc. All rights reserved.

A genetic linkage map of willow (Salix viminalis) based on AFLP and microsatelite markers

NARCIS (Netherlands)

Hanley, S.; Barker, J.H.A.; Ooijen, van J.W.; Aldam, C.; Harris, S.L.; Ahman, I.; Larsson, S.; Karp, A.

2002-01-01

The genus Salix (willow) contains a number of species of great value as biomass crops. Efforts to breed varieties with improved biomass yields and resistances to pests and diseases are limited by the lack of knowledge on the genetic basis of the traits. We have used AFLP and microsatellite markers

Genomic Signal Processing: Predicting Basic Molecular Biological Principles

Science.gov (United States)

Alter, Orly

2005-03-01

Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of

Systems Biology: Impressions from a Newcomer Graduate Student in 2016

Science.gov (United States)

Simpson, Melanie Rae

2016-01-01

As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

Identification of novel markers that demarcate the nucleolus during severe stress and chemotherapeutic treatment.

Science.gov (United States)

Su, Haitong; Kodiha, Mohamed; Lee, Sunghoon; Stochaj, Ursula

2013-01-01

The nucleolus, the ribosomal factory of the cell, has emerged as a key player that regulates many aspects of cell biology. Several thousand proteins associate at least transiently with nucleoli, thereby generating a highly dynamic compartment with a protein profile which is sensitive to changes in cell physiology and pharmacological agents. Powerful tools that reliably demarcate the nucleoli are a prerequisite to measure their composition and activities. Previously, we developed quantitative methods to measure fluorescently labeled molecules in nucleoli. While these tools identify nucleoli under control and mild stress conditions, the accurate detection of nucleolar boundaries under harsh experimental conditions is complicated by the lack of appropriate markers for the nucleolar compartment. Using fluorescence microscopy we have now identified new marker proteins to detect nucleoli upon (a) severe stress and (b) drug treatments that trigger a pronounced reorganization of nucleoli. Our results demonstrate that nucleolin is an ideal marker to delimit nucleoli when cells are exposed to heat or oxidative stress. Furthermore, we show for the first time that cellular apoptosis susceptibility protein (CAS) and human antigen R protein (HuR) are excluded from nucleoli and can be employed to delimit these compartments under severe conditions that redistribute major nucleolar proteins. As proof-of-principle, we used these markers to demarcate nucleoli in cells treated with pharmacological compounds that disrupt the nucleolar organization. Furthermore, to gain new insights into the biology of the nucleolus, we applied our protocols and quantified stress- and drug-induced changes in nucleolar organization and function. Finally, we show that CAS, HuR and nucleolin not only identify nucleoli in optical sections, but are also suitable to demarcate the nucleolar border following 3D reconstruction. Taken together, our studies present novel marker proteins that delimit nucleoli with

Identification of novel markers that demarcate the nucleolus during severe stress and chemotherapeutic treatment.

Directory of Open Access Journals (Sweden)

Haitong Su

Full Text Available The nucleolus, the ribosomal factory of the cell, has emerged as a key player that regulates many aspects of cell biology. Several thousand proteins associate at least transiently with nucleoli, thereby generating a highly dynamic compartment with a protein profile which is sensitive to changes in cell physiology and pharmacological agents. Powerful tools that reliably demarcate the nucleoli are a prerequisite to measure their composition and activities. Previously, we developed quantitative methods to measure fluorescently labeled molecules in nucleoli. While these tools identify nucleoli under control and mild stress conditions, the accurate detection of nucleolar boundaries under harsh experimental conditions is complicated by the lack of appropriate markers for the nucleolar compartment. Using fluorescence microscopy we have now identified new marker proteins to detect nucleoli upon (a severe stress and (b drug treatments that trigger a pronounced reorganization of nucleoli. Our results demonstrate that nucleolin is an ideal marker to delimit nucleoli when cells are exposed to heat or oxidative stress. Furthermore, we show for the first time that cellular apoptosis susceptibility protein (CAS and human antigen R protein (HuR are excluded from nucleoli and can be employed to delimit these compartments under severe conditions that redistribute major nucleolar proteins. As proof-of-principle, we used these markers to demarcate nucleoli in cells treated with pharmacological compounds that disrupt the nucleolar organization. Furthermore, to gain new insights into the biology of the nucleolus, we applied our protocols and quantified stress- and drug-induced changes in nucleolar organization and function. Finally, we show that CAS, HuR and nucleolin not only identify nucleoli in optical sections, but are also suitable to demarcate the nucleolar border following 3D reconstruction. Taken together, our studies present novel marker proteins that

Development and evaluation of microsatellite markers for Acer miyabei (Sapindaceae), a threatened maple species in East Asia.

Science.gov (United States)

Saeki, Ikuyo; Hirao, Akira S; Kenta, Tanaka

2015-06-01

Twelve microsatellite markers were developed and characterized in a threatened maple species, Acer miyabei (Sapindaceae), for use in population genetic analyses. Using Ion Personal Genome Machine (PGM) sequencing, we developed microsatellite markers with perfect di- and trinucleotide repeats. These markers were tested on a total of 44 individuals from two natural populations of A. miyabei subsp. miyabei f. miyabei in Hokkaido Island, Japan. The number of alleles per locus ranged from two to eight. The observed and expected heterozygosities per locus ranged from 0.05 to 0.75 and from 0.05 to 0.79, respectively. Some of the markers were successfully transferred to the closely related species A. campestre, A. platanoides, and A. pictum. The developed markers will be useful in characterizing the genetic structure and diversity of A. miyabei and will help to understand its spatial genetic variation, levels of inbreeding, and patterns of gene flow, thereby providing a basis for conservation.

Molecular identification and genetic variation of varieties of Styphnolobium japonicum (Fabaceae) using SRAP markers.

Science.gov (United States)

Sun, R X; Zhang, C H; Zheng, Y Q; Zong, Y C; Yu, X D; Huang, P

2016-05-06

Thirty-four Styphnolobium japonicum varieties were analyzed using sequence-related amplified polymorphism (SRAP) markers, to investigate genetic variation and test the effectiveness of SRAP markers in DNA fingerprint establishment. Twelve primer pairs were selected from 120 primer combinations for their reproducibility and high polymorphism. We found a total of 430 amplified fragments, of which 415 fragments were considered polymorphic with an average of 34.58 polymorphic fragments for each primer combination. The percentage of polymorphic fragments was 96.60%, and four primer pairs showed 100% polymorphism. Moreover, simple matched coefficients ranged between 0.68 and 0.89, with an average of 0.785, indicating that the genetic variation among varieties was relatively low. This could be because of the narrow genetic basis of the selected breeding material. Based on the similarity coefficient value of 0.76, the varieties were divided into four major groups. In addition, abundant and clear SRAP fingerprints were obtained and could be used to establish DNA fingerprints. In the DNA fingerprints, each variety had its unique pattern that could be easily distinguished from others. The results demonstrated that 34 varieties of S. japonicum had a relatively narrow genetic variation. Hence, a broadening of the genetic basis of breeding material is necessary. We conclude that establishment of DNA fingerprint is feasible by means of SRAP markers.

Quantum Mechanics predicts evolutionary biology.

Science.gov (United States)

Torday, J S

2018-07-01

Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.

Sleep spindles: a physiological marker of age-related changes in gray matter in brain regions supporting motor skill memory consolidation.

Science.gov (United States)

Fogel, Stuart; Vien, Catherine; Karni, Avi; Benali, Habib; Carrier, Julie; Doyon, Julien

2017-01-01

Sleep is necessary for the optimal consolidation of procedural learning, and in particular, for motor sequential skills. Motor sequence learning remains intact with age, but sleep-dependent consolidation is impaired, suggesting that memory deficits for procedural skills are specifically impacted by age-related changes in sleep. Age-related changes in spindles may be responsible for impaired motor sequence learning consolidation, but the morphological basis for this deficit is unknown. Here, we found that gray matter in the hippocampus and cerebellum was positively correlated with both sleep spindles and offline improvements in performance in young participants but not in older participants. These results suggest that age-related changes in gray matter in the hippocampus relate to spindles and may underlie age-related deficits in sleep-related motor sequence memory consolidation. In this way, spindles can serve as a biological marker for structural brain changes and the related memory deficits in older adults. Copyright © 2016 Elsevier Inc. All rights reserved.

Profiling tumor-associated markers for early detection of malignant mesothelioma: an epidemiologic study

Czech Academy of Sciences Publication Activity Database

Amati, M.; Tomasetti, M.; Scartozzi, M.; Mariotti, L.; Alleva, R.; Pignotti, E.; Borghi, B.; Valentino, M.; Governa, M.; Neužil, Jiří; Santarelli, L.

2008-01-01

Roč. 17, č. 1 (2008), s. 163-170 ISSN 1055-9965 R&D Projects: GA AV ČR IAA500520602 Institutional research plan: CEZ:AV0Z50520514; CEZ:AV0Z50520701 Keywords : malignant mesothelioma * tumor markers * asbestos Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.770, year: 2008

The biological basis of a universal constraint on color naming: cone contrasts and the two-way categorization of colors.

Science.gov (United States)

Xiao, Youping; Kavanau, Christopher; Bertin, Lauren; Kaplan, Ehud

2011-01-01

Many studies have provided evidence for the existence of universal constraints on color categorization or naming in various languages, but the biological basis of these constraints is unknown. A recent study of the pattern of color categorization across numerous languages has suggested that these patterns tend to avoid straddling a region in color space at or near the border between the English composite categories of "warm" and "cool". This fault line in color space represents a fundamental constraint on color naming. Here we report that the two-way categorization along the fault line is correlated with the sign of the L- versus M-cone contrast of a stimulus color. Moreover, we found that the sign of the L-M cone contrast also accounted for the two-way clustering of the spatially distributed neural responses in small regions of the macaque primary visual cortex, visualized with optical imaging. These small regions correspond to the hue maps, where our previous study found a spatially organized representation of stimulus hue. Altogether, these results establish a direct link between a universal constraint on color naming and the cone-specific information that is represented in the primate early visual system.

EFSA Panel on Biological Hazards (BIOHAZ); Scientific Opinion on VTEC-seropathotype and scientific criteria regarding pathogenicity assessment

DEFF Research Database (Denmark)

Hald, Tine; Baggesen, Dorte Lau

of verocytotoxins alone or genes encoding such verocytotoxins does not provide a sound scientific basis on which to assess risk to the consumer because there is no single or combination of marker(s) that fully define a ‘pathogenic’ VTEC. Strains positive for verocytotoxin 2 gene(vtx2)- and eae (intimin production...

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents.

Science.gov (United States)

Mayer, René E; Reischer, Georg H; Ixenmaier, Simone K; Derx, Julia; Blaschke, Alfred Paul; Ebdon, James E; Linke, Rita; Egle, Lukas; Ahmed, Warish; Blanch, Anicet R; Byamukama, Denis; Savill, Marion; Mushi, Douglas; Cristóbal, Héctor A; Edge, Thomas A; Schade, Margit A; Aslan, Asli; Brooks, Yolanda M; Sommer, Regina; Masago, Yoshifumi; Sato, Maria I; Taylor, Huw D; Rose, Joan B; Wuertz, Stefan; Shanks, Orin C; Piringer, Harald; Mach, Robert L; Savio, Domenico; Zessner, Matthias; Farnleitner, Andreas H

2018-05-01

Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750-4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log 10 7.2-8.0 marker equivalents (ME) 100 mL -1 ) and biologically treated wastewater samples (median log 10 4.6-6.0 ME 100 mL -1 ) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.

Human Biological Monitoring of Diisononyl Phthalate and Diisodecyl Phthalate: A Review

International Nuclear Information System (INIS)

Saravanabhavan, G.; Murray, J.

2012-01-01

High molecular-weight phthalates, such as diisononyl phthalate (Din), and diisodecyl phthalate (DIDP), are widely used as plasticizers in the manufacturing of polymers and consumer products. Human biological monitoring studies have employed the metabolites of DINP and DIDP as bio markers to assess human exposure. In this review, we summarize and analyze publicly available scientific data on chemistry, metabolism, and excretion kinetics, of DINP and DIDP, to identify specific and sensitive metabolites. Human biological monitoring data on DINP and DIDP are scrutinised to assess the suitability of these metabolites as bio markers of exposure. Results from studies carried out in animals and humans indicate that phthalates are metabolised rapidly and do not bio accumulate. During Phase-I metabolism, ester hydrolysis of DINP and DIDP leads to the formation of hydrolytic monoesters. These primary metabolites undergo further oxidation reactions to produce secondary metabolites. Hence, the levels of secondary metabolites of DINP and DIDP in urine are found to be always higher than the primary metabolites. Results from human biological monitoring studies have shown that the secondary metabolites of DINP and DIDP in urine were detected in almost all tested samples, while the primary metabolites were detected in only about 10% of the samples. This indicates that the secondary metabolites are very sensitive bio markers of DINP/DIDP exposure while primary metabolites are not. The NHANES data indicate that the median concentrations of MCIOP and MCINP (secondary metabolites of DINP and DIDP, resp.) at a population level are about 5.1 μg/L and 2.7 μg/L, respectively. Moreover, the available biological monitoring data suggest that infants/children are exposed to higher levels of phthalates than adults.

Deciphering the language between biological and synthetic materials

Directory of Open Access Journals (Sweden)

Paolo A. Netti

2014-06-01

Full Text Available Chemical signals propagating through aqueous environment are at the basis of the language utilized by living systems to exchange information. In the last years, molecular biology has partly disclosed the grammar and the syntax of this complex language revealing the fascinating world of molecular communication that is the foundation of biological development.

Quantum Biology at the Cellular Level - elements of the research program

OpenAIRE

Bordonaro, Michael; Ogryzko, Vasily

2013-01-01

Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at Cellular Level), a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. Key words. decoherence, macroscopic superpositions, basis-dependence, formal superposition, non-classical correlations,...

Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.).

Science.gov (United States)

Harmon, Monica; Lane, Thomas; Staton, Margaret; Coggeshall, Mark V; Best, Teodora; Chen, Chien-Chih; Liang, Haiying; Zembower, Nicole; Drautz-Moses, Daniela I; Hwee, Yap Zhei; Schuster, Stephan C; Schlarbaum, Scott E; Carlson, John E; Gailing, Oliver

2017-08-08

Sugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple. A set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species. Genic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change.

Bio-markers: traceability in food safety issues.

Science.gov (United States)

Raspor, Peter

2005-01-01

Research and practice are focusing on development, validation and harmonization of technologies and methodologies to ensure complete traceability process throughout the food chain. The main goals are: scale-up, implementation and validation of methods in whole food chains, assurance of authenticity, validity of labelling and application of HACCP (hazard analysis and critical control point) to the entire food chain. The current review is to sum the scientific and technological basis for ensuring complete traceability. Tracing and tracking (traceability) of foods are complex processes due to the (bio)markers, technical solutions and different circumstances in different technologies which produces various foods (processed, semi-processed, or raw). Since the food is produced for human or animal consumption we need suitable markers to be stable and traceable all along the production chain. Specific biomarkers can have a function in technology and in nutrition. Such approach would make this development faster and more comprehensive and would make possible that food effect could be monitored with same set of biomarkers in consumer. This would help to develop and implement food safety standards that would be based on real physiological function of particular food component.

Cultivar identification and genetic relationship of pineapple (Ananas comosus) cultivars using SSR markers.

Science.gov (United States)

Lin, Y S; Kuan, C S; Weng, I S; Tsai, C C

2015-11-25

The genetic relationships among 27 pineapple [Ananas comosus (L.) Merr.] cultivars and lines were examined using 16 simple sequence repeat (SSR) markers. The number of alleles per locus of the SSR markers ranged from 2 to 6 (average 3.19), for a total of 51 alleles. Similarity coefficients were calculated on the basis of 51 amplified bands. A dendrogram was created according to the 16 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed most of the cultivars and lines to be distinguished, with the exception of vegetative clones. According to the dendrogram, the 27 pineapple cultivars and lines were clustered into three main clusters and four individual clusters. As expected, the dendrogram showed that derived cultivars and lines are closely related to their parental cultivars; the genetic relationships between pineapple cultivars agree with the genealogy of their breeding history. In addition, the analysis showed that there is no obvious correlation between SSR markers and morphological characters. In conclusion, SSR analysis is an efficient method for pineapple cultivar identification and can offer valuable informative characters to identify pineapple cultivars in Taiwan.

Towards uranium dose-effects relationships for bio markers of oxidative stress in fish

International Nuclear Information System (INIS)

Buet, A.; Camilleri, V.; Simon, O.; Garnier-Laplace, J.

2004-01-01

Within the Envirhom program, the bioavailability of uranium, a widely spread metal in fresh waters, has been studied in various organisms to gain understanding of metal-organisms interactions. Experiments are still in progress to establish a comprehensive basis of early and delayed involved toxicological mechanisms. Uranium is known to be both radio-toxic and chemo-toxic. The cellular damage of radiation, but also of heavy metal exposure, is mainly associated with an oxidative injury due to the formation of reactive oxygen species. Moreover, the intensity of oxidative damages is dependant on the efficiency of antioxidant defense systems of the organism. In this context, short-term experiments were performed with juvenile rainbow trout (Onchorynchus mykiss) in order to (1) assess the response of some antioxidant parameters and other potential bio-markers and (2) to better characterize the kinetics of the responses in relation with U concentrations and exposure duration. Trout were exposed by direct pathway to a range of U concentrations in water (low, medium and high: 20, 100 and 500 μg U.L -1 respectively) during 10 days. Several antioxidant parameters were measured: the rate of reduced glutathione (GSH) that plays a major role in cellular detoxification and antioxidant defense, and the activities of superoxide dismutases (SOD) and catalase that are involved in the detoxification of oxygen reactive species. The activity of glutathione reductase (GR), that restores the pool of GSH was measured, as well as the activity of acetylcholinesterase (AChE), a marker of neurotoxicity. In parallel, U analysis were performed in gill, skin, muscle, skeleton, intestine, liver, kidneys and body residues of exposed trout in order to assess the dependence of biological responses with a potential uranium bioaccumulation in fish tissues. (author)

Enhanced expression of melanoma progression markers in mouse model of sleep apnea

Directory of Open Access Journals (Sweden)

S. Perini

2016-07-01

Full Text Available Introduction: Obstructive sleep apnea has been associated with higher cancer incidence and mortality. Increased melanoma aggressivity was reported in obstructive sleep apnea patients. Mice exposed to intermittent hypoxia (IH mimicking sleep apnea show enhanced melanoma growth. Markers of melanoma progression have not been investigated in this model. Objective: The present study examined whether IH affects markers of melanoma tumor progression. Methods: Mice were exposed to isocapnic IH to a nadir of 8% oxygen fraction for 14 days. One million B16F10 melanoma cells were injected subcutaneously. Immunohistochemistry staining for Ki-67, PCNA, S100-beta, HMB-45, Melan-A, TGF-beta, Caspase-1, and HIF-1alpha were quantified using Photoshop. Results: Percentage of positive area stained was higher in IH than sham IH group for Caspase-1, Ki-67, PCNA, and Melan-A. The greater expression of several markers of tumor aggressiveness, including markers of ribosomal RNA transcription (Ki-67 and of DNA synthesis (PCNA, in mice exposed to isocapnic IH than in controls provide molecular evidence for a apnea–cancer relationship. Conclusions: These findings have potential repercussions in the understanding of differences in clinical course of tumors in obstructive sleep apnea patients. Further investigation is necessary to confirm mechanisms of these descriptive results. Keywords: Apnea, Melanoma, Biological markers

Isolation, culture and biological characteristics of multipotent porcine skeletal muscle satellite cells.

Science.gov (United States)

Yang, Jinjuan; Liu, Hao; Wang, Kunfu; Li, Lu; Yuan, Hongyi; Liu, Xueting; Liu, Yingjie; Guan, Weijun

2017-12-01

Skeletal muscle has a huge regenerative potential for postnatal muscle growth and repair, which mainly depends on a kind of muscle progenitor cell population, called satellite cell. Nowadays, the majority of satellite cells were obtained from human, mouse, rat and other animals but rarely from pig. In this article, the porcine skeletal muscle satellite cells were isolated and cultured in vitro. The expression of surface markers of satellite cells was detected by immunofluorescence and RT-PCR assays. The differentiation capacity was assessed by inducing satellite cells into adipocytes, myoblasts and osteoblasts. The results showed that satellite cells isolated from porcine tibialis anterior were subcultured up to 12 passages and were positive for Pax7, Myod, c-Met, desmin, PCNA and NANOG but were negative for Myogenin. Satellite cells were also induced to differentiate into adipocytes, osteoblasts and myoblasts, respectively. These findings indicated that porcine satellite cells possess similar biological characteristics of stem cells, which may provide theoretical basis and experimental evidence for potential therapeutic application in the treatment of dystrophic muscle and other muscle injuries.

Biology relevant to space radiation

International Nuclear Information System (INIS)

Fry, R.J.M.

1996-01-01

The biological effects of the radiations to which mankind on earth are exposed are becoming known with an increasing degree of detail. This knowledge is the basis of the estimates of risk that, in turn, fosters a comprehensive and evolving radiation protection system. The substantial body of information has been, and is being, applied to questions about the biological effects of radiation is space and the associated risk estimates. The purpose of this paper is not to recount all the biological effect of radiation but to concentrate on those that may occur as a result from exposure to the radiations encountered in space. In general, the biological effects of radiation in space are the same as those on earth. However, the evidence that the effects on certain tissues by the heaviest-charged particles can be interpreted on the basis of our knowledge about other high-LET radiation is equivocal. This specific question will be discussed in greater detail later. It is important to point out the that there are only limited data about the effects on humans of two components of the radiations in space, namely protons and heavy ions. Thus predictions of effects on space crews are based on experimental systems exposed on earth at rates and fluences that are higher than those in space and one the effects of gamma or x rays with estimates of the equivalent doses using quality factors

Updating biological bases of social behavior.

Science.gov (United States)

O'Connor, Thomas G

2014-09-01

This month's collation of papers deals with social behaviors that operationalize key constructs in fields covered by the journal, including attachment theory and parenting; emotional regulation; psychopathology of several forms; general and specific cognitive abilities. Notably, many examples are offered of how these social behaviors link with biology. That is an obvious and important direction for clinical research insofar as it helps to erase a perceptual chasm and artificial duality between 'behavior' and 'biology'. But, although it must be the case that social behavior has biological connections of one sort or other, identifying reliable connections with practical application has proved to be a non-trivial challenge. In particular, the challenge seems to be in measuring social behavior meaningfully enough that it could be expected to have a biological pulse, and in measuring biological markers systematically enough that emergent-downstream effects would surface. Associations are not especially uncommon, but it has been a frustrating task in constructing a practically broad model from a bricolage of scattered and disconnected parts and findings in the literature. Several reports in this issue offer contrasts that may help move along this line of study. © 2014 Association for Child and Adolescent Mental Health.

[The development of a new marker of the training status in athletes].

Science.gov (United States)

Statsenko, E A; Kovkova, A V; Nekhaĭ, E V

2012-01-01

The present study was based on the mathematical modeling of the middle molecular weight peptides (MMWP) concentration in the blood. On the one hand, MMWP are the products of partial protein catabolism, on the other hand, they act as inductors of protein synthesis. We have developed a complex hormonal marker that allows estimating the adaptive reactions in the organism of the athletes. The marker integrates the known hormonal indices, such as testosterone to cortisol ratio and aldosterone to cortisol ratio (-1,271 + 0,206 x 1n(testosterone) + 1,108 x 1n(aldosterone))/1n(cortisol). The use of a mathematical model for the prediction of MMWP levels in the rowers' blood provides a basis for the application of the new marker for the evaluation of physical conditions of the high-class athletes engaged in other sports. By way of example, the estimation of its informative value for the examination of swimmers has demonstrated significant positive correlation between the predicted and observed MMWP levels (r = 0,4187; p = 0,050). Practicability of applying the newly proposed hormonal marker for monitoring adaptative reactions in athletes is confirmed by significant correlation of calculated values with the real time the freestyle swimmers spend to cover a 50 m distance (r = - 0,4454; p = 0,001).

Effect of lifelong football training on the expression of muscle molecular markers involved in healthy longevity

DEFF Research Database (Denmark)

Mancini, A; Vitucci, D; Labruna, G

2017-01-01

PURPOSE: We investigated whether lifelong football training affects the expression of healthy longevity-related muscle molecular markers. METHODS: Biopsies were collected from the vastus lateralis muscle of 10 lifelong football-trained men (68.2 ± 3.0 years) and of 10 active untrained healthy men...... the expression of key markers involved in muscle oxidative metabolism, and in the DNA repair and senescence suppression pathways, thus providing the molecular basis for healthy longevity....... (66.7 ± 1.3 years). Gene and protein expression was measured by RTqPCR on RNA and by western blotting on protein extracts from muscle biopsies, respectively. RESULTS: The expression of AMPKα1/α2, NAMPT, TFAM and PGC1α, which are markers of oxidative metabolism, and MyHC β isoform expression was higher...

Development of Simple Sequence Repeats (SSR) markers in Setaria italica (Poaceae) and cross-amplification in related species.

Science.gov (United States)

Lin, Heng-Sheng; Chiang, Chih-Yun; Chang, Song-Bin; Kuoh, Chang-Sheng

2011-01-01

Foxtail millet is one of the world's oldest cultivated crops. It has been adopted as a model organism for providing a deeper understanding of plant biology. In this study, 45 simple sequence repeats (SSR) markers of Setaria italica were developed. These markers showing polymorphism were screened in 223 samples from 12 foxtail millet populations around Taiwan. The most common dinucleotide and trinucleotide repeat motifs are AC/TG (84.21%) and CAT (46.15%). The average number of alleles (N(a)), the average heterozygosities observed (H(o)) and expected (H(e)) are 3.73, 0.714, 0.587, respectively. In addition, 24 SSR markers had shown transferability to six related Poaceae species. These new markers provide tools for examining genetic relatedness among foxtail millet populations and other related species. It is suitable for germplasm management and protection in Poaceae.

Biological Collections: Chasing the Ideal

Science.gov (United States)

Kamenski, P. A.; Sazonov, A. E.; Fedyanin, A. A.; Sadovnichy, V. A.

2016-01-01

This article is based on the results of an analysis of existing biological collections in Russia and abroad set up in the framework of the project “Scientific Basis of the National Biobank –Depository of Living Systems” by M.V. Lomonosov Moscow State University [1]. PMID:27437135

Control of the cassava mealybug in Africa: lessons from a biological ...

African Journals Online (AJOL)

Control of the cassava mealybug in Africa: lessons from a biological control project. ... Such studies are needed in order to attribute the observed effects to various causes and to advance the science of biological control. ( 4) It is concluded that biological control is the basis ofiPM but cannot usually be manipulated by the ...

Biological radiation effects

International Nuclear Information System (INIS)

Kiefer, J.

1989-01-01

The book covers all aspects of biological radiation effects. The physical basis is dealt with in some detail, and the effects at the subcellular and the cellular level are discussed, taking into account modern developments and techniques. The effects on the human organism are reviewed, both from the point of view of applications in medicine as well as with regard to radiation hazards (teratogenic, gonadal and carcinogenic effects)

Genomic markers for decision making: what is preventing us from using markers?

Science.gov (United States)

Coyle, Vicky M; Johnston, Patrick G

2010-02-01

The advent of novel genomic technologies that enable the evaluation of genomic alterations on a genome-wide scale has significantly altered the field of genomic marker research in solid tumors. Researchers have moved away from the traditional model of identifying a particular genomic alteration and evaluating the association between this finding and a clinical outcome measure to a new approach involving the identification and measurement of multiple genomic markers simultaneously within clinical studies. This in turn has presented additional challenges in considering the use of genomic markers in oncology, such as clinical study design, reproducibility and interpretation and reporting of results. This Review will explore these challenges, focusing on microarray-based gene-expression profiling, and highlights some common failings in study design that have impacted on the use of putative genomic markers in the clinic. Despite these rapid technological advances there is still a paucity of genomic markers in routine clinical use at present. A rational and focused approach to the evaluation and validation of genomic markers is needed, whereby analytically validated markers are investigated in clinical studies that are adequately powered and have pre-defined patient populations and study endpoints. Furthermore, novel adaptive clinical trial designs, incorporating putative genomic markers into prospective clinical trials, will enable the evaluation of these markers in a rigorous and timely fashion. Such approaches have the potential to facilitate the implementation of such markers into routine clinical practice and consequently enable the rational and tailored use of cancer therapies for individual patients.

Characterization and application of newly developed polymorphic microsatellite markers in the Ezo red fox (Vulpes vulpes schrencki).

Science.gov (United States)

Tada, T; Seki, Y; Kameyama, Y; Kikkawa, Y; Wada, K

2016-12-19

The Ezo red fox (Vulpes vulpes schrencki), a subspecies endemic to Hokkaido island, Japan, is a known host species for the tapeworm Echinococcus multilocularis. To develop tools for molecular ecological studies, we isolated 28 microsatellite regions from the genome of Ezo red fox, and developed 18 polymorphic microsatellite markers. These markers were characterized using 7 individuals and 22 fecal samples of the Ezo red fox. The number of alleles for these markers ranged from 1 to 7, and the observed heterozygosity, estimated on the basis of the genotypes of 7 individuals, ranged from 0.29 to 1.00. All markers, except DvNok5, were in Hardy-Weinberg equilibrium (P > 0.05), and no linkage disequilibrium was detected among these loci, except between DvNok14 and DvNok28 (P = 0.01). Moreover, six microsatellite loci were successfully genotyped using feces-derived DNA from the Ezo red fox. The markers developed in our study might serve as a useful tool for molecular ecological studies of the Ezo red fox.

Multi-Marker Strategy in Heart Failure: Combination of ST2 and CRP Predicts Poor Outcome.

Directory of Open Access Journals (Sweden)

Anne Marie Dupuy

Full Text Available Natriuretic peptides (BNP and NT-proBNP are recognized as gold-standard predictive markers in Heart Failure (HF. However, currently ST2 (member of the interleukin 1 receptor family has emerged as marker of inflammation, fibrosis and cardiac stress. We evaluated ST2 and CRP as prognostic markers in 178 patients with chronic heart failure in comparison with other classical markers such as clinical established parameters but also biological markers: NT-proBNP, hs-cTnT alone or in combination. In multivariate analysis, subsequent addition of ST2 led to age, CRP and ST2 as the only remaining predictors of all-cause mortality (HR 1.03, HR 1.61 and HR 2.75, respectively as well as of cardiovascular mortality (HR 1.00, HR 2.27 and HR 3.78, respectively. The combined increase of ST2 and CRP was significant for predicting worsened outcomes leading to identify a high risk subgroup that individual assessment of either marker. The same analysis was performed with ST2 in combination with Barcelona score. Overall, our findings extend previous data demonstrating that ST2 in combination with CRP as a valuable tool for identifying patients at risk of death.

Biological markers of asexuality: Handedness, birth order, and finger length ratios in self-identified asexual men and women.

Science.gov (United States)

Yule, Morag A; Brotto, Lori A; Gorzalka, Boris B

2014-02-01

Human asexuality is defined as a lack of sexual attraction to anyone or anything and it has been suggested that it may be best conceptualized as a sexual orientation. Non-right-handedness, fraternal birth order, and finger length ratio (2D:4D) are early neurodevelopmental markers associated with sexual orientation. We conducted an Internet study investigating the relationship between self-identification as asexual, handedness, number of older siblings, and self-measured finger-lengths in comparison to individuals of other sexual orientation groups. A total of 325 asexuals (60 men and 265 women; M age, 24.8 years), 690 heterosexuals (190 men and 500 women; M age, 23.5 years), and 268 non-heterosexuals (homosexual and bisexual; 64 men and 204 women; M age, 29.0 years) completed online questionnaires. Asexual men and women were 2.4 and 2.5 times, respectively, more likely to be non-right-handed than their heterosexual counterparts and there were significant differences between sexual orientation groups in number of older brothers and older sisters, and this depended on handedness. Asexual and non-heterosexual men were more likely to be later-born than heterosexual men, and asexual women were more likely to be earlier-born than non-heterosexual women. We found no significant differences between sexual orientation groups on measurements of 2D:4D ratio. This is one of the first studies to test and provide preliminary empirical support for an underlying neurodevelopmental basis to account for the lack of sexual attraction characteristic of asexuality.

The biological basis for the control of prenatal irradiation

International Nuclear Information System (INIS)

1988-01-01

The embryo and fetus have been generally considered to be more sensitive than the adult to the detrimental effects of radiation exposure. In particular, recent re-evaluations of epidemiological data on human population exposed to radiation have suggested that there may be greater sensitivity than heretofore recognized to the induction of mental retardation and reduced intelligence by exposure during gestation. To assist national authorities in evaluating this problem and establishing appropriate protection measures for limiting the dose to the embryo and fetus and, thus, to pregnant or potentially pregnant women, the Nuclear Energy Agency has appointed a Group of Consultants to assemble and evaluate the biological data relevant to the protection of the human conceptus, and to make recommendations for achieving this in the operational practice. The Group has surveyed the human data dealing with the biologcal effects of radiation exposure at low doses, and has supplemented this with information derived from animal studies. The Group has also taken full account of the studies and recommendations issued in this area by other international organizations, primarily the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) and the International Commission on Radiological Protection (ICRP). This report is published under the responsibility of the Secretary General of the OECD, and does not commit Member governments of the Organization

Characterization of a new Vaccinia virus isolate reveals the C23L gene as a putative genetic marker for autochthonous Group 1 Brazilian Vaccinia virus.

Directory of Open Access Journals (Sweden)

Felipe L Assis

Full Text Available Since 1999, several Vaccinia virus (VACV isolates, the etiological agents of bovine vaccinia (BV, have been frequently isolated and characterized with various biological and molecular methods. The results from these approaches have grouped these VACV isolates into two different clusters. This dichotomy has elicited debates surrounding the origin of the Brazilian VACV and its epidemiological significance. To ascertain vital information to settle these debates, we and other research groups have made efforts to identify molecular markers to discriminate VACV from other viruses of the genus Orthopoxvirus (OPV and other VACV-BR groups. In this way, some genes have been identified as useful markers to discriminate between the VACV-BR groups. However, new markers are needed to infer ancestry and to correlate each sample or group with its unique epidemiological and biological features. The aims of this work were to characterize a new VACV isolate (VACV DMTV-2005 molecularly and biologically using conserved and non-conserved gene analyses for phylogenetic inference and to search for new genes that would elucidate the VACV-BR dichotomy. The VACV DMTV-2005 isolate reported in this study is biologically and phylogenetically clustered with other strains of Group 1 VACV-BR, the most prevalent VACV group that was isolated during the bovine vaccinia outbreaks in Brazil. Sequence analysis of C23L, the gene that encodes for the CC-chemokine-binding protein, revealed a ten-nucleotide deletion, which is a new Group 1 Brazilian VACV genetic marker. This deletion in the C23L open reading frame produces a premature stop-codon that is shared by all Group 1 VACV-BR strains and may also reflect the VACV-BR dichotomy; the deletion can also be considered to be a putative genetic marker for non-virulent Brazilian VACV isolates and may be used for the detection and molecular characterization of new isolates.

Forging patterns and making waves from biology to geology: a commentary on Turing (1952) 'The chemical basis of morphogenesis'.

Science.gov (United States)

Ball, Philip

2015-04-19

Alan Turing was neither a biologist nor a chemist, and yet the paper he published in 1952, 'The chemical basis of morphogenesis', on the spontaneous formation of patterns in systems undergoing reaction and diffusion of their ingredients has had a substantial impact on both fields, as well as in other areas as disparate as geomorphology and criminology. Motivated by the question of how a spherical embryo becomes a decidedly non-spherical organism such as a human being, Turing devised a mathematical model that explained how random fluctuations can drive the emergence of pattern and structure from initial uniformity. The spontaneous appearance of pattern and form in a system far away from its equilibrium state occurs in many types of natural process, and in some artificial ones too. It is often driven by very general mechanisms, of which Turing's model supplies one of the most versatile. For that reason, these patterns show striking similarities in systems that seem superficially to share nothing in common, such as the stripes of sand ripples and of pigmentation on a zebra skin. New examples of 'Turing patterns' in biology and beyond are still being discovered today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

76 FR 35104 - Safety Zone; Waterway Closure, Atchafalaya River From Mile Marker 117 (Morgan City Railroad...

Science.gov (United States)

2011-06-16

...-AA00 Safety Zone; Waterway Closure, Atchafalaya River From Mile Marker 117 (Morgan City Railroad Bridge... with rising flood water in the Atchafalaya River. Basis and Purpose Captain of the Port Morgan City... safety zone is located on the specified waters of the Atchafalaya River between MM 117 (Morgan City...

Synthetic biology approaches for protein production optimization in bacterial cell factories

DEFF Research Database (Denmark)

Rennig, Maja; Andersen, Mikael Rørdam

devices and their fusion to antibiotic selection markers enables subsequent selection of high-expressing constructs. The approach is a simple and inexpensive alternative to advanced screening techniques. In addition, a second synthetic biology approach provides the means for fast and efficient plasmid...

A marker of biological age explains individual variation in the strength of the adult stress response.

Science.gov (United States)

Andrews, Clare; Nettle, Daniel; Larriva, Maria; Gillespie, Robert; Reichert, Sophie; Brilot, Ben O; Bedford, Thomas; Monaghan, Pat; Spencer, Karen A; Bateson, Melissa

2017-09-01

The acute stress response functions to prioritize behavioural and physiological processes that maximize survival in the face of immediate threat. There is variation between individuals in the strength of the adult stress response that is of interest in both evolutionary biology and medicine. Age is an established source of this variation-stress responsiveness diminishes with increasing age in a range of species-but unexplained variation remains. Since individuals of the same chronological age may differ markedly in their pace of biological ageing, we asked whether biological age-measured here via erythrocyte telomere length-predicts variation in stress responsiveness in adult animals of the same chronological age. We studied two cohorts of European starlings in which we had previously manipulated the rate of biological ageing by experimentally altering the competition experienced by chicks in the fortnight following hatching. We predicted that individuals with greater developmental telomere attrition, and hence greater biological age, would show an attenuated corticosterone (CORT) response to an acute stressor when tested as adults. In both cohorts, we found that birds with greater developmental telomere attrition had lower peak CORT levels and a more negative change in CORT levels between 15 and 30 min following stress exposure. Our results, therefore, provide strong evidence that a measure of biological age explains individual variation in stress responsiveness: birds that were biologically older were less stress responsive. Our results provide a novel explanation for the phenomenon of developmental programming of the stress response: observed changes in stress physiology as a result of exposure to early-life adversity may reflect changes in ageing.

Structural basis for target protein recognition by the protein disulfide reductase thioredoxin

DEFF Research Database (Denmark)

Maeda, Kenji; Hägglund, Per; Finnie, Christine

2006-01-01

Thioredoxin is ubiquitous and regulates various target proteins through disulfide bond reduction. We report the structure of thioredoxin (HvTrxh2 from barley) in a reaction intermediate complex with a protein substrate, barley alpha-amylase/subtilisin inhibitor (BASI). The crystal structure...... of this mixed disulfide shows a conserved hydrophobic motif in thioredoxin interacting with a sequence of residues from BASI through van der Waals contacts and backbone-backbone hydrogen bonds. The observed structural complementarity suggests that the recognition of features around protein disulfides plays...... a major role in the specificity and protein disulfide reductase activity of thioredoxin. This novel insight into the function of thioredoxin constitutes a basis for comprehensive understanding of its biological role. Moreover, comparison with structurally related proteins shows that thioredoxin shares...

Reference values of thirty-one frequently used laboratory markers for 75-year-old males and females

Science.gov (United States)

Ryden, Ingvar; Lind, Lars

2012-01-01

Background We have previously reported reference values for common clinical chemistry tests in healthy 70-year-old males and females. We have now repeated this study 5 years later to establish reference values also at the age of 75. It is important to have adequate reference values for elderly patients as biological markers may change over time, and adequate reference values are essential for correct clinical decisions. Methods We have investigated 31 frequently used laboratory markers in 75-year-old males (n = 354) and females (n = 373) without diabetes. The 2.5 and 97.5 percentiles for these markers were calculated according to the recommendations of the International Federation of Clinical Chemistry. Results Reference values are reported for 75-year-old males and females for 31 frequently used laboratory markers. Conclusion There were minor differences between reference intervals calculated with and without individuals with cardiovascular diseases. Several of the reference intervals differed from Scandinavian reference intervals based on younger individuals (Nordic Reference Interval Project). PMID:22300333

Single cell biology beyond the era of antibodies: relevance, challenges, and promises in biomedical research.

Science.gov (United States)

Abraham, Parvin; Maliekal, Tessy Thomas

2017-04-01

Research of the past two decades has proved the relevance of single cell biology in basic research and translational medicine. Successful detection and isolation of specific subsets is the key to understand their functional heterogeneity. Antibodies are conventionally used for this purpose, but their relevance in certain contexts is limited. In this review, we discuss some of these contexts, posing bottle neck for different fields of biology including biomedical research. With the advancement of chemistry, several methods have been introduced to overcome these problems. Even though microfluidics and microraft array are newer techniques exploited for single cell biology, fluorescence-activated cell sorting (FACS) remains the gold standard technique for isolation of cells for many biomedical applications, like stem cell therapy. Here, we present a comprehensive and comparative account of some of the probes that are useful in FACS. Further, we illustrate how these techniques could be applied in biomedical research. It is postulated that intracellular molecular markers like nucleostemin (GNL3), alkaline phosphatase (ALPL) and HIRA can be used for improving the outcome of cardiac as well as bone regeneration. Another field that could utilize intracellular markers is diagnostics, and we propose the use of specific peptide nucleic acid probes (PNPs) against certain miRNAs for cancer surgical margin prediction. The newer techniques for single cell biology, based on intracellular molecules, will immensely enhance the repertoire of possible markers for the isolation of cell types useful in biomedical research.

Elimination of ghost markers during dual sensor-based infrared tracking of multiple individual reflective markers

International Nuclear Information System (INIS)

Stroian, G.; Falco, T.; Seuntjens, J.P.

2004-01-01

The accuracy of dose delivery in radiotherapy is affected by the uncertainty in tumor localization. Motion of internal anatomy due to physiological processes such as respiration may lead to significant displacements which compromise tumor coverage and generate irradiation of healthy tissue. Real-time tracking with infrared-based systems is often used for tracking thoracic motion in radiation therapy. We studied the origin of ghost markers ('crosstalk') which may appear during dual sensor-based infrared tracking of independent reflective markers. Ghost markers occur when two or more reflective markers are coplanar with each other and with the sensors of the two camera-based infrared tracking system. Analysis shows that sensors are not points but they have a finite extent and this extent determines for each marker a 'ghost volume'. If one reflective marker enters the ghost volume of another marker, ghost markers will be reported by the tracking system; if the reflective markers belong to a surface their 'ghost volume' is reduced to a 'ghost surface' (ghost zone). Appearance of ghost markers is predicted for markers taped on the torso of an anthropomorphic phantom. This study illustrates the dependence of the shape, extent, and location of the ghost zones on the shape of the anthropomorphic phantom, the angle of view of the tracking system, and the distance between the tracking system and the anthropomorphic phantom. It is concluded that the appearance of ghost markers can be avoided by positioning the markers outside the ghost zones of the other markers. However, if this is not possible and the initial marker configuration is ghost marker-free, ghost markers can be eliminated during real-time tracking by virtue of the fact that they appear in the coordinate data sequence only temporarily

Development of Simple Sequence Repeats (SSR Markers in Setaria italica (Poaceae and Cross-Amplification in Related Species

Directory of Open Access Journals (Sweden)

Chih-Yun Chiang

2011-11-01

Full Text Available Foxtail millet is one of the world’s oldest cultivated crops. It has been adopted as a model organism for providing a deeper understanding of plant biology. In this study, 45 simple sequence repeats (SSR markers of Setaria italica were developed. These markers showing polymorphism were screened in 223 samples from 12 foxtail millet populations around Taiwan. The most common dinucleotide and trinucleotide repeat motifs are AC/TG (84.21% and CAT (46.15%. The average number of alleles (Na, the average heterozygosities observed (Ho and expected (He are 3.73, 0.714, 0.587, respectively. In addition, 24 SSR markers had shown transferability to six related Poaceae species. These new markers provide tools for examining genetic relatedness among foxtail millet populations and other related species. It is suitable for germplasm management and protection in Poaceae.

Curcumin, an active constiuent of the ancient medicinal herb Curcuma longa L.: some uses and the establishment and biological basis of medical efficacy.

Science.gov (United States)

Witkin, Jeffrey M; Li, Xia

2013-06-01

The root extract, curcumin (diferuloylmethane), is a constituent of the ancient herbal medicine Jiawei-Xiaoyaosan that has been used for dyspepsia, stress, and mood disorders. Curcumin engenders a diverse profile of biological actions that result in changes in oxidative stress, inflammation, and cell-death pathways. Combined with its historical use in medical practice and its safety profile, curcumin has been studied for its potential therapeutic applications in cancer, aging, endocrine, immunological, gastrointestinal, and cardiac diseases. In addition, data in animal models and in humans have also begun to be collected in stroke, Alzheimer's disease, and Parkinson's disease. A compelling new body of literature is also mounting to support the efficacy of curcumin in stress and mood disorders. Current understanding of the biological basis for antidepressant-relevant biochemical and behavioral changes shows convergence with some mechanisms known for standard antidepressants. In addition, the mechanisms of the antidepressant-like pharmacology of curcumin also appear to overlap with those of other disease states. Thus, ancient wisdom might be built into this interesting and newly-appreciated natural molecule. Although curcumin is a primary ingredient in anti-aging pills, cosmetic creams, eye treatments, diet products, etc, a key hurdle to the development of curcumin for disease treatment and prevention is overcoming its low oral bioavailability. Although multiple approaches to this problem are being examined, a solution to the bioavailability issue will be needed to ensure appropriate tissue exposures of curcumin in clinical investigation. Progress in this regard is underway.

Intangible life functorial connections in relational biology

CERN Document Server

Louie, A H

2017-01-01

This rare publication continues an exploratory journey in relational biology, a study of biology in terms of the organization of networked connections in living systems. It builds on the author’s two earlier monographs which looked at the epistemology of life and the ontogeny of life. Here the emphasis is on the intangibility of life, that the real nature of living systems is conveyed not by their tangible material basis but by their intangible inherent processes.    Relational biology is the approach that hails ‘function dictates structure’; it is mathematics decoded into biological realizations. Therefore, the work begins with a concise introduction to category theory, equiping the reader with the mathematical metalanguage of relation biology. The book is organized around three parts:   Part I is a comprehensive study of the most important functor in relational biology, the power set functor.  The author lays the set-theoretic foundations of the functorial connections in relational biology, explor...

Left Ventricular Hypertrophy: An allometric comparative analysis of different ECG markers

International Nuclear Information System (INIS)

Bonomini, MP; Valentinuzzi, M E; Arini, P D; Ingallina, F; Barone, V

2011-01-01

Allometry, in general biology, measures the relative growth of a part in relation to the whole living organism. Left ventricular hypertrophy (LVH) is the heart adaptation to excessive load (systolic or diastolic). The increase in left ventricular mass leads to an increase in the electrocardiographic voltages. Based on clinical data, we compared the allometric behavior of three different ECG markers of LVH. To do this, the allometric fit AECG δ + β (VM) relating left ventricular mass (estimated from ecocardiographic data) and ECG amplitudes (expressed as the Cornell-Voltage, Sokolow and the ECG overall voltage indexes) were compared. Besides, sensitivity and specificity for each index were analyzed. The more sensitive the ECG criteria, the better the allometric fit. In conclusion: The allometric paradigm should be regarded as the way to design new and more sensitive ECG-based LVH markers.

Tantalum markers in radiography

International Nuclear Information System (INIS)

Aronson, A.S.; Jonsson, N.; Alberius, P.

1985-01-01

The biocompatibility of two types of radiopaque tantalum markers was evaluated histologically. Reactions to pin markers (99.9% purity) and spherical markers (95.2% purity) were investigated after 3-6 weeks in rabbits and 5-48 weeks in children with abnormal growth. Both marker types were firmly attached to bone trabeculae; this was most pronounced in rabbit bone, and no adverse macroscopic reactions were observed. Microscopically, no reactions or only slight fibrosis of bone tissue were detected, while soft tissues only demonstrated a minor inflammatory reaction. Nevertheless, the need for careful preparation and execution of marker implantations is stressed, and particularly avoidance iof the use of emery in sharpening of cannulae. The bioinertness of tantalum was reconfirmed as was its suitability for use as skeletal and soft tissue radiographic markers. (orig.)

Development and characterization of novel microsatellite markers in Trillium govanianum: a threatened plant species from North-Western Himalaya.

Science.gov (United States)

Sharma, Vikas; Wani, Mohammad Saleem; Singh, Vijay; Kaur, Kuljit; Gupta, Raghbir Chand

2017-07-01

Trillium govanianum is a temperate forest understory plant species of high value belonging to the family Melanthiaceae. It is endemic to Himalayan region and facing a bottleneck situation due to reckless extractions from its natural strands. In the present study, 21 microsatellite markers were developed and characterized in 20 accessions of T. govanianum. Collectively, the polymorphic markers amplified 31 alleles in a range of 2-4 with an average of 2.6 alleles per marker. The mean observed heterozygosity (H o ), expected heterozygosity (H e ), and Shannon information index (I) were 0.46, 0.48, and 0.73, respectively. Average polymorphism information content (PIC) was 0.385. The cross-transferability in a related species, namely, Polygonatum verticillatum, showed amplification of ten markers. The newly developed microsatellite markers efficiently distinguished the different accessions on the basis of their geographic origin. Thus, these microsatellites can be useful in exploring genetic diversity in various existing populations of T. govanianum in north-western Himalaya, which may be useful for their conservation, management, and improvement in future.

Can microsatellite markers resolve phylogenetic relationships between closely related crested newt species (Triturus cristatus superspecies)?

Czech Academy of Sciences Publication Activity Database

Mikulíček, P.; Crnobrnja-Isailović, J.; Piálek, Jaroslav

2007-01-01

Roč. 28, č. 4 (2007), s. 467-474 ISSN 0173-5373 R&D Projects: GA ČR GA206/01/0695; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60930519 Keywords : crested newt * microsatelitte markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.929, year: 2007

[Basis for designing a medical course curriculum].

Science.gov (United States)

Villarreal, R; Bojalil, L F; Mercer, H

1977-01-01

This article sets forth the reasons for the structure given to the Division of Biology and Health on the Xochimilco campus of Metropolitan Autonomous University in Mexico: to adjust the university to the process of social change going forward in the country and gear the university to the problems of the present by avoiding the rigidity of its structure. The basic aspects of curriculum design are cited against a background of an historical analysis of the socioeconomic structure of education and health. The principles underlying the curriculum and the course work are then described on the basis of that analysis.

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy.

Science.gov (United States)

Matsuda, Atsushi; Schermelleh, Lothar; Hirano, Yasuhiro; Haraguchi, Tokuko; Hiraoka, Yasushi

2018-05-15

Correction of chromatic shift is necessary for precise registration of multicolor fluorescence images of biological specimens. New emerging technologies in fluorescence microscopy with increasing spatial resolution and penetration depth have prompted the need for more accurate methods to correct chromatic aberration. However, the amount of chromatic shift of the region of interest in biological samples often deviates from the theoretical prediction because of unknown dispersion in the biological samples. To measure and correct chromatic shift in biological samples, we developed a quadrisection phase correlation approach to computationally calculate translation, rotation, and magnification from reference images. Furthermore, to account for local chromatic shifts, images are split into smaller elements, for which the phase correlation between channels is measured individually and corrected accordingly. We implemented this method in an easy-to-use open-source software package, called Chromagnon, that is able to correct shifts with a 3D accuracy of approximately 15 nm. Applying this software, we quantified the level of uncertainty in chromatic shift correction, depending on the imaging modality used, and for different existing calibration methods, along with the proposed one. Finally, we provide guidelines to choose the optimal chromatic shift registration method for any given situation.

Molecular marker studies in riverine buffaloes, for characterization and diagnosis of genetic defects

International Nuclear Information System (INIS)

Yadav, B.R.

2005-01-01

The buffalo is probably the last livestock species to have been domesticated, with many genetic, physiological and behavioural traits not yet well understood. Molecular markers have been used for characterizing animals and breeds, diagnosing diseases and identifying anatomical and physiological anomalies. RFLP studies showed low heterozygosity, but genomic and oligonucleotide probes showed species-specific bands useful for identification of carcass or other unknown samples. Use of RAPD revealed band frequencies, band sharing frequencies, genetic distances, and genetic and identity indexes in different breeds. Bovine microsatellite primers indicate that 70.9% of bovine loci were conserved in buffalo. Allele numbers, sizes, frequencies, heterozygosity and polymorphism information content showed breed-specific patterns. Different marker types - genomic and oligonucleotide probes, RAPD and microsatellites - are useful in parent identification. Individual specific DNA fingerprinting techniques were applied with twin-born animal (XX/XY) chimerism, sex identification, anatomically defective and XO individuals. Molecular markers are a potential tool for geneticists and breeders to evaluate existing germplasm and to manipulate it to develop character-specific strains and to provide the basis for effective genetic conservation. (author)

Genome Analysis of the First Extensively Drug-Resistant (XDR Mycobacterium tuberculosis in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance.

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Chee Sian Kuan

Full Text Available The outbreak of extensively drug-resistant tuberculosis (XDR-TB has become an increasing problem in many TB-burdened countries. The underlying drug resistance mechanisms, including the genetic variation favored by selective pressure in the resistant population, are partially understood. Recently, the first case of XDR-TB was reported in Malaysia. However, the detailed genotype family and mechanisms of the formation of multiple drugs resistance are unknown. We sequenced the whole genome of the UM 1072388579 strain with a 2-kb insert-size library and combined with that from previously sequenced 500-bp-insert paired-end reads to produce an improved sequence with maximal sequencing coverage across the genome. In silico spoligotyping and phylogenetic analyses demonstrated that UM 1072388579 strain belongs to an ancestral-like, non-Beijing clade of East Asia lineage. This is supported by the presence of a number of lineage-specific markers, including fadD28, embA, nuoD and pks7. Polymorphism analysis showed that the drug-susceptibility profile is correlated with the pattern of resistance mutations. Mutations in drug-efflux pumps and the cell wall biogenesis pathway such as mmpL, pks and fadD genes may play an important role in survival and adaptation of this strain to its surrounding environment. In this work, fifty-seven putative promoter SNPs were identified. Among them, we identified a novel SNP located at -4 T allele of TetR/acrR promoter as an informative marker to recognize strains of East Asian lineage. Our work indicates that the UM 1072388579 harbors both classical and uncommon SNPs that allow it to escape from inhibition by many antibiotics. This study provides a strong foundation to dissect the biology and underlying resistance mechanisms of the first reported XDR M. tuberculosis in Malaysia.

Bladder tumor markers beyond cytology: International Consensus Panel on bladder tumor markers.

NARCIS (Netherlands)

Lokeshwar, V.B.; Habuchi, T.; Grossman, H.B.; Murphy, W.M.; Hautmann, S.H.; Hemstreet, G.P.; Bono, A.V.; Getzenberg, R.H.; Goebell, P.; Schmitz-Drager, B.J.; Schalken, J.A.; Fradet, Y.; Marberger, M.; Messing, E.; Droller, M.J.

2005-01-01

This is the first of 2 articles that summarize the findings of the International Consensus Panel on cytology and bladder tumor markers. The objectives of our panel were to reach a consensus on the areas where markers are needed, to define the attributes of an ideal tumor marker, and to identify

Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

Science.gov (United States)

Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

2016-01-01

Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

Mining the human phenome using allelic scores that index biological intermediates

NARCIS (Netherlands)

Evans, David M; Brion, Marie Jo A; Paternoster, Lavinia; Kemp, John P; McMahon, George; Munafò, Marcus; Whitfield, John B; Medland, Sarah E; Montgomery, Grant W; Timpson, Nicholas J; St Pourcain, Beate; Lawlor, Debbie A; Martin, Nicholas G; Dehghan, Abbas; Hirschhorn, Joel; Smith, George Davey; Alizadeh, Behrooz

2013-01-01

It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease

Depression, osteoporosis, serotonin and cell membrane viscosity between biology and philosophical anthropology

Directory of Open Access Journals (Sweden)

Gabrielli Fabio

2011-03-01

Full Text Available Abstract Due to the relationship between biology and culture, we believe that depression, understood as a cultural and existential phenomenon, has clear markers in molecular biology. We begin from an existential analysis of depression constituting the human condition and then shift to analysis of biological data confirming, according to our judgment, its original (ontological structure. In this way philosophy is involved at the anthropological level, in as much as it detects the underlying meanings of depression in the original biological-cultural horizon of human life. Considering the integration of knowledge it is the task of molecular biology to identify the aforementioned markers, to which the existential aspects of depression are linked to. In particular, recent works show the existence of a link between serotonin and osteoporosis as a result of a modified expression of the low-density lipoprotein receptor-related protein 5 gene. Moreover, it is believed that the hereditary or acquired involvement of tryptophan hydroxylase 2 (Tph2 or 5-hydroxytryptamine transporter (5-HTT is responsible for the reduced concentration of serotonin in the central nervous system, causing depression and affective disorders. This work studies the depression-osteoporosis relationship, with the aim of focusing on depressive disorders that concern the quantitative dynamic of platelet membrane viscosity and interactome cytoskeleton modifications (in particular Tubulin and Gsα protein as a possible condition of the involvement of the serotonin axis (gut, brain and platelet, not only in depression but also in connection with osteoporosis.

Biological conceptions of race and the motivation to cross racial boundaries.

Science.gov (United States)

Williams, Melissa J; Eberhardt, Jennifer L

2008-06-01

The present studies demonstrate that conceiving of racial group membership as biologically determined increases acceptance of racial inequities (Studies 1 and 2) and cools interest in interacting with racial outgroup members (Studies 3-5). These effects were generally independent of racial prejudice. It is argued that when race is cast as a biological marker of individuals, people perceive racial outgroup members as unrelated to the self and therefore unworthy of attention and affiliation. Biological conceptions of race therefore provide justification for a racially inequitable status quo and for the continued social marginalization of historically disadvantaged groups. (PsycINFO Database Record (c) 2008 APA, all rights reserved).

Biological and psychological predictors of posttraumatic stress disorder onset and chronicity. A one-year prospective study

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C. Gandubert

2016-06-01

Conclusions: This prospective study shows that peritraumatic psychological and biological markers are independent predictors of PTSD onset with specificities according to the stage of PTSD development; the psychological diathesis, i.e. peritraumatic distress and dissociation, being a better predictor of short-term dysfunction whereas biological diathesis was also predictive of development and maintenance of PTSD.

Quantum biology at the cellular level--elements of the research program.

Science.gov (United States)

Bordonaro, Michael; Ogryzko, Vasily

2013-04-01

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.

Science.gov (United States)

Wordley, Claire; Slate, Jon; Stapley, Jessica

2011-01-01

Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage. © 2010 Blackwell Publishing Ltd.

Estimating the CCSD basis-set limit energy from small basis sets: basis-set extrapolations vs additivity schemes

Energy Technology Data Exchange (ETDEWEB)

Spackman, Peter R.; Karton, Amir, E-mail: amir.karton@uwa.edu.au [School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009 (Australia)

2015-05-15

Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/L{sup α} two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol{sup –1}. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol{sup –1}.

Estimating the CCSD basis-set limit energy from small basis sets: basis-set extrapolations vs additivity schemes

International Nuclear Information System (INIS)

Spackman, Peter R.; Karton, Amir

2015-01-01

Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/L α two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol –1 . The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol –1

Molecular markers in the epidemiology and diagnosis of coccidioidomycosis.

Science.gov (United States)

Duarte-Escalante, Esperanza; Frías-De-León, María Guadalupe; Zúñiga, Gerardo; Martínez-Herrera, Erick; Acosta-Altamirano, Gustavo; Reyes-Montes, María Del Rocío

2014-01-01

The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Tumor markers in clinical oncology

International Nuclear Information System (INIS)

Novakovic, S.

2004-01-01

The subtle differences between normal and tumor cells are exploited in the detection and treatment of cancer. These differences are designated as tumor markers and can be either qualitative or quantitative in their nature. That means that both the structures that are produced by tumor cells as well as the structures that are produced in excessive amounts by host tissues under the influence of tumor cells can function as tumor markers. Speaking in general, the tumor markers are the specific molecules appearing in the blood or tissues and the occurrence of which is associated with cancer. According to their application, tumor markers can be roughly divided as markers in clinical oncology and markers in pathology. In this review, only tumor markers in clinical oncology are going to be discussed. Current tumor markers in clinical oncology include (i) oncofetal antigens, (ii) placental proteins, (iii) hormones, (iv) enzymes, (v) tumor-associated antigens, (vi) special serum proteins, (vii) catecholamine metabolites, and (viii) miscellaneous markers. As to the literature, an ideal tumor marker should fulfil certain criteria - when using it as a test for detection of cancer disease: (1) positive results should occur in the early stages of the disease, (2) positive results should occur only in the patients with a specific type of malignancy, (3) positive results should occur in all patients with the same malignancy, (4) the measured values should correlate with the stage of the disease, (5) the measured values should correlate to the response to treatment, (6) the marker should be easy to measure. Most tumor markers available today meet several, but not all criteria. As a consequence of that, some criteria were chosen for the validation and proper selection of the most appropriate marker in a particular malignancy, and these are: (1) markers' sensitivity, (2) specificity, and (3) predictive values. Sensitivity expresses the mean probability of determining an elevated tumor

Statistical strategies to reveal potential vibrational markers for in vivo analysis by confocal Raman spectroscopy

Science.gov (United States)

Oliveira Mendes, Thiago de; Pinto, Liliane Pereira; Santos, Laurita dos; Tippavajhala, Vamshi Krishna; Téllez Soto, Claudio Alberto; Martin, Airton Abrahão

2016-07-01

The analysis of biological systems by spectroscopic techniques involves the evaluation of hundreds to thousands of variables. Hence, different statistical approaches are used to elucidate regions that discriminate classes of samples and to propose new vibrational markers for explaining various phenomena like disease monitoring, mechanisms of action of drugs, food, and so on. However, the technical statistics are not always widely discussed in applied sciences. In this context, this work presents a detailed discussion including the various steps necessary for proper statistical analysis. It includes univariate parametric and nonparametric tests, as well as multivariate unsupervised and supervised approaches. The main objective of this study is to promote proper understanding of the application of various statistical tools in these spectroscopic methods used for the analysis of biological samples. The discussion of these methods is performed on a set of in vivo confocal Raman spectra of human skin analysis that aims to identify skin aging markers. In the Appendix, a complete routine of data analysis is executed in a free software that can be used by the scientific community involved in these studies.

Marker-assisted selection in fish and shellfish breeding schemes

International Nuclear Information System (INIS)

Martinez, V.

2007-01-01

The main goals of breeding programmes for fish and shellfish are to increase the profitability and sustainability of aquaculture. Traditionally, these have been carried out successfully using pedigree information by selecting individuals based on breeding values predicted for traits measured on candidates using an 'animal model'. This methodology assumes that phenotypes are explained by a large number of genes with small effects and random environmental deviations. However, information on individual genes with medium or large effects cannot be used in this manner. In selective breeding programmes using pedigree information, molecular markers have been used primarily for parentage assignment when tagging individual fish is difficult and to avoid causing common environmental effects from rearing families in separate tanks. The use of these techniques in such conventional breeding programmes is discussed in detail. Exploiting the great biological diversity of many fish and shellfish species, different experimental designs may use either chromosomal manipulations or large family sizes to increase the likelihood of finding the loci affecting quantitative traits, the so-called QTL, by screening the segregation of molecular markers. Using information on identified loci in breeding schemes in aquaculture is expected to be cost-effective compared with traditional breeding methods only when the accuracy of predicting breeding values is rather low, e.g. for traits with low heritability such as disease resistance or carcass quality. One of the problems facing aquaculture is that some of the resources required to locate QTL accurately, such as dense linkage maps, are not yet available for the many species. Recently, however, information from expressed sequence tag (EST) databases has been used for developing molecular markers such as microsatellites and single nucleotide polymorphisms (SNPs). Marker-assisted selection (MAS) or genome-wide marker-assisted selection (G-MAS) using

Biological variation and analytical imprecision of CA 125 in patients with ovarian cancer

DEFF Research Database (Denmark)

Tuxen, M K; Sölétormos, G; Rustin, G J

2000-01-01

Despite the availability of serial data on CA 125 in ovarian cancer, the problem of interpreting a change over time is still unsolved. Changes in marker concentrations are due not only to patients improving or deteriorating but also to analytical imprecision and normal intra-individual biological...... variation. The aim of this study was to assess the analytical imprecision (CV(A)) and the intra- and inter-individual biological variation (CV(I) and CV(G), respectively) of CA 125 in a group of 26 patients with clinically stable ovarian cancer. Furthermore, the critical difference for a change between two...... for serum tumor marker assessment during monitoring of patients with ovarian cancer. The cut-off value of CA 125 is of minor value in detecting unusual results for an individual subject, when previous measurements from an individual are available. These measurements should be preferred as reference...

Traditional and emerging molecular markers in neuroblastoma prognosis: the good, the bad and the ugly.

Science.gov (United States)

Poremba, C; Hero, B; Goertz, H G; Scheel, C; Wai, D; Schaefer, K L; Christiansen, H; Berthold, F; Juergens, H; Boecker, W; Dockhorn-Dworniczak, B

2001-01-01

Neuroblastomas (NB) are a heterogeneous group of childhood tumours with a wide range of likelihood for tumour progression. As traditional parameters do not ensure completely accurate prognostic grouping, new molecular markers are needed for assessing the individual patient's prognosis more precisely. 133 NB of all stages were analysed in blind-trial fashion for telomerase activity (TA), expression of surviving, and MYCN status. These data were correlated with other traditional prognostic indicators and disease outcome. TA is a powerful independent prognostic marker for all stages and is capable of differentiating between good and poor outcome in putative "favourable" clinical or biological subgroups of NB patients. High surviving expression is associated with an adverse outcome, but is more difficult to interprete than TA because survivin expression needs to be accurately quantified to be of predictive value. We propose an extended progression model for NB including emerging prognostic markers, with emphasis on telomerase activity.

THE ASSESSMENT OF BIOLOGICAL MARKERS IN PATIENTS WITH PREECLAMPSIA WHEN AN INFLAMMATORY PROCESS APPEARS

Directory of Open Access Journals (Sweden)

Eduard Crauciuc

2015-07-01

Full Text Available Preeclampsia represents a pathological state that is specific to regnancy, is characterized by high blood pressure de novo and significant proteinuria and appears after 20 weeks of pregnancy. The continuously increasing mortality caused by preeclampsia in our country totally justifies the fact that all efforts are directed towards primary and secondary prevention of the disease and underlines the necessity of urgent intervention at population level, together withthe implementation of a screening programme that is able to reduce the impact of this condition on the mother and the baby. The cases were gathered between 2003 and 2014. The patients were selected by studying the observation charts of the pregnant women hospitalized in ”Cuza Vodă” Clinical Hospital of Obstetrics and Gynecology Iaşi, having a pregnancy over 20 weeks, who came for a specialized consult and who were harvested CRP, without an infectious context or prematurely and spontaneously ruptured membranes. The comparison of the lab markers for the pregnantwomen with severe preeclampsia, depending on the plasmatic level of CRP over 12 mg/l, showed significantly higher values of fibrinogen, LDH, GOT, GPT, serum blood urea nitrogen, creatinine and urine proteins, while the mean number of white cells was significantly reduced (p<0,05. The study confirms the change in the inflammatory process markers, the hepatic and kidney function, associated with a high plasmatic level of CRP for pregnant women with severe preeclampsia.

DESIGNING EAP MATERIALS BASED ON INTERCULTURAL CORPUS ANALYSES: THE CASE OF LOGICAL MARKERS IN RESEARCH ARTICLES

Directory of Open Access Journals (Sweden)

Pilar Mur Dueñas

2009-10-01

Full Text Available The ultimate aim of intercultural analyses in English for Academic Purposes is to help non-native scholars function successfully in the international disciplinary community in English. The aim of this paper is to show how corpus-based intercultural analyses can be useful to design EAP materials on a particular metadiscourse category, logical markers, in research article writing. The paper first describes the analysis carried out of additive, contrastive and consecutive logical markers in a corpus of research articles in English and in Spanish in a particular discipline, Business Management. Differences were found in their frequency and also in the use of each of the sub-categories. Then, five activities designed on the basis of these results are presented. They are aimed at raising Spanish Business scholars' awareness of the specific uses and pragmatic function of frequent logical markers in international research articles in English.

Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers.

Science.gov (United States)

Sijen, Titia

2015-09-01

Human biological traces have the potential to present strong evidence for placing a suspect at a crime scene. In cases, the activity that led to deposition of an individual's cellular material is increasingly disputed, for which the identification of cell types could be crucial. This review aims to give an overview of the possibilities of the employment of mRNA, miRNA, DNA methylation and microbial markers for tissue identification in a forensic context. The biological background that renders these markers tissue-specificity is considered, as this can affect data interpretation. Furthermore, the forensic relevance of inferring certain cell types is discussed, as are the various methodologies that can be applied. Forensic stains can carry minute amounts of cell material that may be degraded or polluted and most likely cell material of multiple sources will be present. The interpretational challenges that are imposed by this compromised state will be discussed as well. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing

Czech Academy of Sciences Publication Activity Database

Wang, H.; Dai, K.; Xiao, J.; Yuan, C.; Zhao, R. L.; Doležel, Jaroslav; Wu, Y.; Cao, A.; Chen, P.; Zhang, S.; Wang, X.

2017-01-01

Roč. 18, FEB 15 (2017), č. článku 167. ISSN 1471-2164 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : triticum-aestivum l. * conferring resistance * wild relatives * mosaic-virus * plug markers * bread wheat * genome * gene * rye * improvement * Triticum aestivum * Haynaldia villosa * Molecular marker * Intron polymorphism Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 3.729, year: 2016

Reliability of Urinary Dehydration Markers in Elite Youth Boxers.

Science.gov (United States)

Zubac, Damir; Cular, Drazen; Marusic, Uros

2018-03-01

To determine the reliability and diagnostic accuracy of noninvasive urinary dehydration markers in field-based settings on a day-to-day basis in elite adolescent amateur boxers. Sixty-nine urine samples were collected daily from 23 athletes (17.3 ± 1.9 y) during their weight-stable phase and analyzed by field and laboratory measures of hydration status. Urine osmolality (U OSM ), urine specific gravity (U SG ), total protein content (T PC ), and body-mass stability were evaluated to determine fluid balance and hydration status. Overall macronutrient and water intake were determined using dietary records. According to their anthropometric characteristics, athletes were assigned into 2 groups: lightweight (L WB ) and heavyweight (H WB ) boxers. Data presented on U OSM demonstrated a uniform increment by 11.2% ± 12.8% (L WB ) and 19.9% ± 22.7% (H WB ) (P dehydration markers. Poor correlations were found between U SG and T PC metabolites (r = .27, P = .211). Urinary dehydration markers (both U SG and U OSM ) exhibit high variability and seem to be unreliable diagnostic tools to track actual body-weight loss in real-life settings. The ad libitum fluid intake was apparently inadequate to match acute fluid loss during and after intense preparation. The applicability of a single-time-point hydration-status assessment concept may preclude accurate assessment of actual body-weight deficits in youth boxers.

Microbiological control of sterilization efficiency by irradiation. Biological indicators. [Medical supplies

Energy Technology Data Exchange (ETDEWEB)

Bates, C [Institut National des Radioelements, Brussels (Belgium)

1977-01-01

The microbiological efficiency of the radiosterilization process was tested by means of biological indicators such as Micrococcus radiodurans R1 and Bacillus pumilus E601 for gamma and electron radiation doses ranging from 0.5 to 6 Mrad. The response of the biological indicators was studied in terms of conservation time, initial concentration of biological material, and sources of used radiation. Both the biological dosimetry of the process and the sterility after treatment were studied on the basis of inactivation curves.

Cystatin C: A new biochemical marker in livestock sector

Directory of Open Access Journals (Sweden)

Pravas Ranjan Sahoo

2016-09-01

Full Text Available The livestock sector contributes largely to the economy of India. Different systemic diseases like renal diseases, neurological and cardiovascular diseases cause huge loss in production and productive potential of livestock in India, which is considered as a major concern for both small and large ruminants. Early detection of diseseses is essential to combat the economic loss. An efficient biochemical marker can be developed which would provide more specific, sensitive and reliable measurement of functions of different organs. Determination of endogenous marker Cystatin C may fulfill the above need which can provide a detection platform not only for Kidney function but also for assaying other organs' function. Cystatin C is a low molecular weight protein which is removed from the bloodstream by glomerular filtration in the kidneys. Thus, it may act as a potential biological tool in diagnosis of renal and other systemic diseases in livestock. This mini-review focuses on the Cystatin C and its clinical importance which can be extensively employed in the livestock sector. [J Adv Vet Anim Res 2016; 3(3.000: 200-205

Checking the Course of Colorectal Carcinoma Follow up Using Mathematical Classification of Tumor Marker Profiles

Czech Academy of Sciences Publication Activity Database

Holubec jr., L.; Botterlich, N.; Topolčan, O.; Finek, J.; Pikner, R.; Pecen, Ladislav; Holubec, L.

2002-01-01

Roč. 23, Suppl.1 (2002), s. 57 ISSN 1010-4283. [Meeting of the International Society for Oncodevelopmental Biology and Medicine /30./. 08.09.2002-12.09.2002, Boston] R&D Projects: GA MŠk ME 438 Institutional research plan: AV0Z1030915 Keywords : tumor markers * colorectal CA * mathematical classification Subject RIV: BA - General Mathematics

REFORMASI SISTEM AKUNTANSI CASH BASIS MENUJU SISTEM AKUNTANSI ACCRUAL BASIS

Directory of Open Access Journals (Sweden)

Yuri Rahayu

2016-03-01

Full Text Available Abstract –  Accounting reform movement was born with the aim of structuring the direction of improvement . This movement is characterized by the enactment of the Act of 2003 and Act 1 of 2004, which became the basis of the birth of Government Regulation No.24 of 2005 on Government Accounting Standards ( SAP . The general,  accounting is based on two systems,  the cash basis  and the accrual basis. The facts speak far students still at problem with differences to the two methods that result in a lack of understanding on the treatment system for recording. The purpose method of research is particularly relevant to student references who are learning basic accounting so that it can provide information and more meaningful understanding of the accounting method cash basis and Accrual basis. This research was conducted through a normative approach, by tracing the document that references a study/library that combines source of reference that can be believed either from books and the internet are processed with a foundation of knowledge and experience of the author. The conclusion can be drawn that basically to be able to understand the difference of the system and the Cash Basis accrual student base treatment requires an understanding of both methods. To be able to have the ability and understanding of both systems required reading exercises and reference sources.   Keywords : Reform, cash basis, accrual basis   Abstrak - Gerakan reformasi akuntansi dilahirkan dengan tujuan penataan ke arah perbaikan. Gerakan ini  ditandai dengan dikeluarkannya  Undang-Undang tahun 2003 dan Undang-Undang No.1 Tahun 2004  yang menjadi dasar lahirnya Peraturan Pemerintah No.24 Tahun 2005 tentang Standar Akuntansi Pemerintah (SAP . Pada umumnya pencatatan akuntansi di dasarkan pada dua sistem yaitu basis kas (Cash Basis dan basis akrual  (Accrual Basis. Fakta berbicara Selama ini mahasiswa masih dibinggungkan dengan perbedaan ke dua metode itu sehingga

Identification of cancer stem cell markers in human malignant mesothelioma cells

Energy Technology Data Exchange (ETDEWEB)

Ghani, Farhana Ishrat; Yamazaki, Hiroto; Iwata, Satoshi; Okamoto, Toshihiro [Division of Clinical Immunology, Institute of Medical Science, University of Tokyo, Tokyo (Japan); Aoe, Keisuke; Okabe, Kazunori; Mimura, Yusuke [Departments of Medical Oncology, Yamaguchi-Ube Medical Center, Yamaguchi (Japan); Fujimoto, Nobukazu; Kishimoto, Takumi [Department of Respiratory Medicine, Okayama Rosai Hospital, Okayama (Japan); Yamada, Taketo [Department of Pathology, Keio University School of Medicine, Tokyo (Japan); Xu, C. Wilson [Drug Development Program, Nevada Cancer Institute, Las Vegas, NV (United States); Morimoto, Chikao, E-mail: morimoto@ims.u-tokyo.ac.jp [Division of Clinical Immunology, Institute of Medical Science, University of Tokyo, Tokyo (Japan); Drug Development Program, Nevada Cancer Institute, Las Vegas, NV (United States)

2011-01-14

Research highlights: {yields} We performed serial transplantation of surgical samples and established new cell lines of malignant mesothelioma. {yields} SP cell and expressions of CD9/CD24/CD26 were often observed in mesothelioma cell lines. {yields} SP and CD24{sup +} cells proliferated by asymmetric cell division-like manner. CD9{sup +} and CD24{sup +} cells have higher potential to generate spheroid colony. {yields} The marker-positive cells have clear tendency to generate larger tumors in mice. -- Abstract: Malignant mesothelioma (MM) is an aggressive and therapy-resistant neoplasm arising from the pleural mesothelial cells and usually associated with long-term asbestos exposure. Recent studies suggest that tumors contain cancer stem cells (CSCs) and their stem cell characteristics are thought to confer therapy-resistance. However, whether MM cell has any stem cell characteristics is not known. To understand the molecular basis of MM, we first performed serial transplantation of surgical samples into NOD/SCID mice and established new cell lines. Next, we performed marker analysis of the MM cell lines and found that many of them contain SP cells and expressed several putative CSC markers such as CD9, CD24, and CD26. Interestingly, expression of CD26 closely correlated with that of CD24 in some cases. Sorting and culture assay revealed that SP and CD24{sup +} cells proliferated by asymmetric cell division-like manner. In addition, CD9{sup +} and CD24{sup +} cells have higher potential to generate spheroid colony than negative cells in the stem cell medium. Moreover, these marker-positive cells have clear tendency to generate larger tumors in mouse transplantation assay. Taken together, our data suggest that SP, CD9, CD24, and CD26 are CSC markers of MM and could be used as novel therapeutic targets.

Molecular biology - Part II: Beneficial liaisons: Radiobiology meets cellular and molecular biology

International Nuclear Information System (INIS)

Stevenson, Mary Ann; Coleman, C. Norman

1997-01-01

Purpose: The purpose of this course is to familiarize radiation oncologists with the concepts and terminology of molecular and cellular biology that are especially relevant to radiation oncology. The ability of radiation oncologists to remain current with the new discoveries of modern biology is essential to the development of improved therapeutic strategies and, importantly, to the proper balance between investment in technology and biology. Objective: This year, this Refresher Course is part of a three-part ''series'' including Drs. McKenna and Dritschilo. The objective is to provide continuing education for the academic and practicing radiation oncologist, physicist and biologist in the modern biologic concepts of cancer and its treatment. An effort will be made to relate these general concepts to the clinic by providing a broad view as to potential new biological treatments which might enhance the efficacy of radiation therapy. The specific focus of this Course will vary from year to year. Some of the classic radiation biology models which form the basis of clinical practice and laboratory research will be examined and 'newer' models will be presented which take into account the emerging knowledge of cellular and molecular biology. A few techniques in molecular and cellular biology will be described to the extent necessary to understand their basic concepts and their applicability. Aspects of radiation biology which will be covered include cell cycle, radiation-induced changes in the cellular phenotype, and considerations of the effect of the tumor microenvironment. It is not the expectation that the attendees will become experts in the particular subjects presented. Rather, it is the intent to increase their curiosity as to the new knowledge that is emerging and to demonstrate that these seemingly complicated areas can be understood and appreciated with a modicum of the effort

Molecular biology - Part II: Beneficial liaisons: Radiobiology meets cellular and molecular biology

International Nuclear Information System (INIS)

Stevenson, Mary Ann; Coleman, C. Norman

1996-01-01

Purpose: The purpose of this course is to familiarize radiation oncologists with the concepts and terminology of molecular and cellular biology that are especially relevant to radiation oncology. The ability of radiation oncologists to remain current with the new discoveries of modern biology is essential to the development of improved therapeutic strategies and, importantly, to the proper balance between investment in technology and biology. Objective: This year, this Refresher Course is part of a three-part 'series' including Drs. Martin Brown and Amato Giaccia. The objective is to provide continuing education for the academic and practicing radiation oncologist, physicist and biologist in the modern biologic concepts of cancer and its treatment. An effort will be made to relate these general concepts to the clinic by providing a broad view as to potential new biological treatments which might enhance the efficacy of radiation therapy. The specific focus of this Course will vary from year to year. Some of the classic radiation biology models which form the basis of clinical practice and laboratory research will be examined and 'newer' models will be presented which take into account the emerging knowledge of cellular and molecular biology. A few techniques in molecular and cellular biology will be described to the extent necessary to understand their basic concepts and their applicability. Aspects of radiation biology which will be covered include cell cycle, radiation-induced changes in the cellular phenotype, and considerations of the effect of the tumor microenvironment. It is not the expectation that the attendees will become experts in the particular subjects presented. Rather, it is the intent to increase their curiosity as to the new knowledge that is emerging and to demonstrate that these seemingly complicated areas can be understood and appreciated with a modicum of the effort

Biological Markers for Pulpal Inflammation: A Systematic Review.

Directory of Open Access Journals (Sweden)

Dan-Krister Rechenberg

Full Text Available Pulpitis is mainly caused by an opportunistic infection of the pulp space with commensal oral microorganisms. Depending on the state of inflammation, different treatment regimes are currently advocated. Predictable vital pulp therapy depends on accurate determination of the pulpal status that will allow repair to occur. The role of several players of the host response in pulpitis is well documented: cytokines, proteases, inflammatory mediators, growth factors, antimicrobial peptides and others contribute to pulpal defense mechanisms; these factors may serve as biomarkers that indicate the status of the pulp. Therefore, the aim of this systematic review was to evaluate the presence of biomarkers in pulpitis.The electronic databases of MEDLINE, EMBASE, Scopus and other sources were searched for English and non-English articles published through February 2015. Two independent reviewers extracted information regarding study design, tissue or analyte used, outcome measures, results and conclusions for each article. The quality of the included studies was assessed using a modification of the Newcastle-Ottawa-Scale.From the initial 847 publications evaluated, a total of 57 articles were included in this review. In general, irreversible pulpitis was associated with different expression of various biomarkers compared to normal controls. These biomarkers were significantly expressed not only in pulp tissue, but also in gingival crevicular fluid that can be collected non-invasively, and in dentin fluid that can be analyzed without extirpating the entire pulpal tissue. Such data may then be used to accurately differentiate diseased from healthy pulp tissue. The interplay of pulpal biomarkers and their potential use for a more accurate and biologically based diagnostic tool in endodontics is envisaged.

Bragg Curve, Biological Bragg Curve and Biological Issues in Space Radiation Protection with Shielding

Science.gov (United States)

Honglu, Wu; Cucinotta, F.A.; Durante, M.; Lin, Z.; Rusek, A.

2006-01-01

The space environment consists of a varying field of radiation particles including high-energy ions, with spacecraft shielding material providing the major protection to astronauts from harmful exposure. Unlike low-LET gamma or X-rays, the presence of shielding does not always reduce the radiation risks for energetic charged particle exposure. Since the dose delivered by the charged particle increases sharply as the particle approaches the end of its range, a position known as the Bragg peak, the Bragg curve does not necessarily represent the biological damage along the particle traversal since biological effects are influenced by the track structure of both primary and secondary particles. Therefore, the biological Bragg curve is dependent on the energy and the type of the primary particle, and may vary for different biological endpoints. To achieve a Bragg curve distribution, we exposed cells to energetic heavy ions with the beam geometry parallel to a monolayer of fibroblasts. Qualitative analyses of gamma-H2AX fluorescence, a known marker of DSBs, indicated increased clustering of DNA damage before the Bragg peak, enhanced homogenous distribution at the peak, and provided visual evidence of high linear energy transfer (LET) particle traversal of cells beyond the Bragg peak. A quantitative biological response curve generated for micronuclei (MN) induction across the Bragg curve did not reveal an increased yield of MN at the location of the Bragg peak. However, the ratio of mono-to bi-nucleated cells, which indicates inhibition in cell progression, increased at the Bragg peak location. These results, along with other biological concerns, show that space radiation protection with shielding can be a complicated issue.

Introduction to bioengineering: melding of engineering and biological sciences.

Science.gov (United States)

Shoureshi, Rahmat A

2005-04-01

Engineering has traditionally focused on the external extensions of organisms, such as transportation systems, high-rise buildings, and entertainment systems. In contrast, bioengineering is concerned with inward processes of biologic organisms. Utilization of engineering principles and techniques in the analysis and solution of problems in medicine and biology is the basis for bioengineering. This article discusses subspecialties in bioengineering and presents examples of projects in this discipline.

Comparative polymorphism of sterlet fertilizers (Acipenser Ruthenus for microsatellite DNA markers

Directory of Open Access Journals (Sweden)

Ольга Олексіївна Малишева

2015-11-01

Full Text Available Based on microsatellite DNA markers in three (LG-19, LS-68 and LS-39 it is examined intraspecific genetic structure of sterlet fertilizers. As a result of this work it was found that this group of fish is in a balanced state in terms of the genetic polymorphism. On the basis of certain individual differences in allelic variants have been selected and combined the parental pairs for alternative genotypes. The results of the research allow optimize further work on the reproduction of sturgeon under artificial cultivation

Application of support vector machine model for enhancing the diagnostic value of tumor markers in gastric cancer

International Nuclear Information System (INIS)

Wang Hui; Huang Gang

2010-01-01

Objective: To evaluate the early diagnostic value of tumor markers for gastric cancer using support vector machine (SVM) model. Methods: Subjects involved in the study consisted of 262 cases with gastric cancer, 156 cases with benign gastric diseases and 149 healthy controls. From those subjects, five tumor markers, carcinoembryonic antigen (CEA), carbohydrate (CA) 125, CA19-9, alphafetoprotein (AFP) and CA50, were assayed and collected to make the datasets. To modify SVM model to fit the diagnostic classifiers, radial basis function was adopted and kernel function was optimized and validated by grid search and cross validation. For comparative study, methods of combination tests of five markers, Logistic regression, and decision tree were also used. Results: For gastric cancer, the diagnostic accuracy of the combination tests, Logistic regression, decision tree and SVM model were 46.2%, 64.5%, 63.9% and 95.1% respectively. SVM model significantly elevated the diagnostic value comparing with other three methods. Conclusion: The application of SVM model is of high value in enhancing the tumor marker for the diagnosis of gastric cancer. (authors)

Partitioning of genomic variance using biological pathways

DEFF Research Database (Denmark)

Edwards, Stefan McKinnon; Janss, Luc; Madsen, Per

and that these variants are enriched for genes that are connected in biological pathways or for likely functional effects on genes. These biological findings provide valuable insight for developing better genomic models. These are statistical models for predicting complex trait phenotypes on the basis of SNP......-data and trait phenotypes and can account for a much larger fraction of the heritable component. A disadvantage is that this “black-box” modelling approach conceals the biological mechanisms underlying the trait. We propose to open the “black-box” by building SNP-set genomic models that evaluate the collective...... action of multiple SNPs in genes, biological pathways or other external findings on the trait phenotype. As proof of concept we have tested the modelling framework on several traits in dairy cattle....

[Classification of organisms and structuralism in biology].

Science.gov (United States)

Vasil'eva, L I

2001-01-01

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.

Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia

Science.gov (United States)

Ju, Yiqian; Jiao, Yao; Feng, Lu; Pan, Huitang; Cheng, Tangren; Zhang, Qixiang

2016-01-01

The genetic control of plant architecture is a promising approach to breed desirable cultivars, particularly in ornamental flowers. In this study, the F1 population (142 seedlings) derived from Lagerstroemia fauriei (non-dwarf) × L. indica ‘Pocomoke’ (dwarf) was phenotyped for six traits (plant height (PH), internode length (IL), internode number, primary lateral branch height (PLBH), secondary lateral branch height and primary branch number), and the IL and PLBH traits were positively correlated with the PH trait and considered representative indexes of PH. Fifty non-dwarf and dwarf seedlings were pooled and subjected to a specific-locus amplified fragment sequencing (SLAF-seq) method, which screened 1221 polymorphic markers. A total of 3 markers segregating between bulks were validated in the F1 population, with the M16337 and M38412 markers highly correlated with the IL trait and the M25207 marker highly correlated with the PLBH trait. These markers provide a predictability of approximately 80% using a single marker (M25207) and a predictability of 90% using marker combinations (M16337 + M25207) in the F1 population, which revealed that the IL and the PLBH traits, especially the PLBH, were the decisive elements for PH in terms of molecular regulation. Further validation was performed in the BC1 population and a set of 28 Lagerstroemia stocks using allele-specific PCR (AS-PCR) technology, and the results showed the stability and reliability of the SNP markers and the co-determination of PH by multiple genes. Our findings provide an important theoretical and practical basis for the early prediction and indirect selection of PH using the IL and the PLBH, and the detected SNPs may be useful for marker-assisted selection (MAS) in crape myrtle. PMID:27404662

Advanced Test Reactor Safety Basis Upgrade Lessons Learned Relative to Design Basis Verification and Safety Basis Management

International Nuclear Information System (INIS)

G. L. Sharp; R. T. McCracken

2004-01-01

The Advanced Test Reactor (ATR) is a pressurized light-water reactor with a design thermal power of 250 MW. The principal function of the ATR is to provide a high neutron flux for testing reactor fuels and other materials. The reactor also provides other irradiation services such as radioisotope production. The ATR and its support facilities are located at the Test Reactor Area of the Idaho National Engineering and Environmental Laboratory (INEEL). An audit conducted by the Department of Energy's Office of Independent Oversight and Performance Assurance (DOE OA) raised concerns that design conditions at the ATR were not adequately analyzed in the safety analysis and that legacy design basis management practices had the potential to further impact safe operation of the facility.1 The concerns identified by the audit team, and issues raised during additional reviews performed by ATR safety analysts, were evaluated through the unreviewed safety question process resulting in shutdown of the ATR for more than three months while these concerns were resolved. Past management of the ATR safety basis, relative to facility design basis management and change control, led to concerns that discrepancies in the safety basis may have developed. Although not required by DOE orders or regulations, not performing design basis verification in conjunction with development of the 10 CFR 830 Subpart B upgraded safety basis allowed these potential weaknesses to be carried forward. Configuration management and a clear definition of the existing facility design basis have a direct relation to developing and maintaining a high quality safety basis which properly identifies and mitigates all hazards and postulated accident conditions. These relations and the impact of past safety basis management practices have been reviewed in order to identify lessons learned from the safety basis upgrade process and appropriate actions to resolve possible concerns with respect to the current ATR safety

Markers and mapping revisited: finding your gene.

Science.gov (United States)

Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

2009-01-01

This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of

Differential risk assessments from five hypoxia specific assays: The basis for biologically adapted individualized radiotherapy in advanced head and neck cancer patients

DEFF Research Database (Denmark)

Nordsmark, Marianne; Eriksen, Jesper Grau; Gebski, Val

2007-01-01

osteopontin measured by ELISA, tumour oxygenation status using pO(2) needle electrodes and tumour osteopontin, hypoxia inducible factor 1alpha (HIF-1alpha) and carboxyanhydrase 9 (CA9) by immunohistochemistry. The primary treatment was radiotherapy and the hypoxic radiosensitizer nimorazole. Loco......-regional tumour control was evaluated at 5 years. RESULTS: All five markers showed inter-tumour variability. Inter-marker correlations were inconsistent. Only plasma osteopontin inversely correlated with median tumour pO(2), (p=0.02, r=0.28) and CA9 correlated with HIF-1alpha (p...-Meier analysis high plasma osteopontin, high HIF-1alpha and high proportion of tumour pO(2)2.5mmHg (HP(2.5)) related significantly with poorer loco-regional control, whereas CA9 and tumour osteopontin failed to predict loco-regional control in this set dataset. When analyzing Hb, stage, and the five markers...

Quality transitivity and traceability system of herbal medicine products based on quality markers.

Science.gov (United States)

Liu, Changxiao; Guo, De-An; Liu, Liang

2018-05-15

Due to a variety of factors to affect the herb quality, the existing quality management model is unable to evaluate the process control. The development of the concept of "quality marker" (Q-marker) lays basis for establishing an independent process quality control system for herbal products. To ensure the highest degree of safety, effectiveness and quality process control of herbal products, it is aimed to establish a quality transitivity and traceability system of quality and process control from raw materials to finished herbal products. Based on the key issues and challenges of quality assessment, the current status of quality and process controls from raw materials to herbal medicinal products listed in Pharmacopoeia were analyzed and the research models including discovery and identification of Q-markers, analysis and quality management of risk evaluation were designed. Authors introduced a few new technologies and methodologies, such as DNA barcoding, chromatographic technologies, fingerprint analysis, chemical markers, bio-responses, risk management and solution for quality process control. The quality and process control models for herbal medicinal products were proposed and the transitivity and traceability system from raw materials to the finished products was constructed to improve the herbal quality from the entire supply and production chain. The transitivity and traceability system has been established based on quality markers, especially on how to control the production process under Good Engineering Practices, as well as to implement the risk management for quality and process control in herbal medicine production. Copyright © 2018 Elsevier GmbH. All rights reserved.

Synthetic strategies for efficient conjugation of organometallic complexes with pendant protein reactive markers

KAUST Repository

Jantke, Dominik; Marziale, Alexander N.; Reiner, Thomas; Kraus, Florian; Herdtweck, Eberhardt; Raba, Andreas; Eppinger, Jö rg

2013-01-01

Site-directed conjugation of metal centers to proteins is fundamental for biological and bioinorganic applications of transition metals. However, methods for the site-selective introduction of metal centers remain scarce. Herein, we present broadly applicable synthetic strategies for the conjugation of bioactive molecules with a range of organometallic complexes. Following three different synthetic strategies, we were able to synthesize a small library of metal conjugated protein markers featuring different types of protein reactive sites (epoxides, phenylphosphonates, fluorosulfonates and fluorophosphonate groups) as well as different late transition metals (iron, ruthenium, rhodium, palladium and platinum). The products were isolated in moderate to excellent yields and high purity. Furthermore, X-ray diffraction of the metalated protein markers corroborates structural integrity of the metal complex and the protein reactive site. © 2013 Elsevier B.V. All rights reserved.

Synthetic strategies for efficient conjugation of organometallic complexes with pendant protein reactive markers

KAUST Repository

Jantke, Dominik

2013-11-01

Site-directed conjugation of metal centers to proteins is fundamental for biological and bioinorganic applications of transition metals. However, methods for the site-selective introduction of metal centers remain scarce. Herein, we present broadly applicable synthetic strategies for the conjugation of bioactive molecules with a range of organometallic complexes. Following three different synthetic strategies, we were able to synthesize a small library of metal conjugated protein markers featuring different types of protein reactive sites (epoxides, phenylphosphonates, fluorosulfonates and fluorophosphonate groups) as well as different late transition metals (iron, ruthenium, rhodium, palladium and platinum). The products were isolated in moderate to excellent yields and high purity. Furthermore, X-ray diffraction of the metalated protein markers corroborates structural integrity of the metal complex and the protein reactive site. © 2013 Elsevier B.V. All rights reserved.

Noninvasive biological sensor system for detection of drunk driving.

Science.gov (United States)

Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

2011-01-01

Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

Sunflower Hybrid Breeding: From Markers to Genomic Selection.

Science.gov (United States)

Dimitrijevic, Aleksandra; Horn, Renate

2017-01-01

In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi , or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches

Sunflower Hybrid Breeding: From Markers to Genomic Selection

Directory of Open Access Journals (Sweden)

Aleksandra Dimitrijevic

2018-01-01

Full Text Available In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare

Sunflower Hybrid Breeding: From Markers to Genomic Selection

Science.gov (United States)

Dimitrijevic, Aleksandra; Horn, Renate

2018-01-01

In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches

Mining the Human Phenome Using Allelic Scores That Index Biological Intermediates

DEFF Research Database (Denmark)

Evans, David M; Brion, Marie Jo A; Paternoster, Lavinia

2013-01-01

It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease...... aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we...

Biological image construction by using Raman radiation and Pca: preliminary results

International Nuclear Information System (INIS)

Martinez E, J. C.; Cordova F, T.; Hugo R, V.

2015-10-01

Full text: In the last years, the Raman spectroscopy (Rs) technique has had some applications in the study and analysis of biological samples, due to it is able to detect concentrations or presence of certain organic and inorganic compounds of medical interest. In this work, raw data were obtained through measurements in selected points on a square regions in order to detect specific organic / inorganic compounds on biological samples. Gold nano stars samples were prepared and coated with membrane markers (CD 10+ and CD 19+) and diluted in leukemic B lymphocytes. Each data block was evaluated independently by the method of principal component analysis (Pca) in order to find representative dimensionless values (Cp) for each Raman spectrum in a specific coordinate. Each Cp was normalized in a range of 0-255 in order to generate a representative image of 8 bits of the region under study. Data acquisition was performed with Raman microscopy system Renishaw in Via in the range of 550 to 1700 cm-1 with a 785 nm laser source, with a power of 17 m W and 15 s of exposure time were used for each spectrum. In preliminary results could detect the presence of molecular markers CD 10+ and CD 19+ with gold nano stars and discrimination between both markers. The results suggest conducting studies with specific concentrations organic and inorganic materials. (Author)

Biological image construction by using Raman radiation and Pca: preliminary results

Energy Technology Data Exchange (ETDEWEB)

Martinez E, J. C. [IPN, Unidad Profesional Interdisciplinaria de Ingenieria, Campus Guanajuato, Av. Mineral de Valenciana 200, Col. Fracc. Industrial Puerto Interior, 36275 Silao, Guanajuato (Mexico); Cordova F, T. [Universidad de Guanajuato, DIC, Departamento de Ingenieria Fisica, Loma del Bosque No. 103, Col. Lomas del Campestre, 37150 Leon, Guanajuato (Mexico); Hugo R, V., E-mail: jcmartineze@ipn.mx [Universidad de Guadalajara, Centro Universitario de Tonala, Morelos No. 180, 69584 Tonala, Jalisco (Mexico)

2015-10-15

Full text: In the last years, the Raman spectroscopy (Rs) technique has had some applications in the study and analysis of biological samples, due to it is able to detect concentrations or presence of certain organic and inorganic compounds of medical interest. In this work, raw data were obtained through measurements in selected points on a square regions in order to detect specific organic / inorganic compounds on biological samples. Gold nano stars samples were prepared and coated with membrane markers (CD 10+ and CD 19+) and diluted in leukemic B lymphocytes. Each data block was evaluated independently by the method of principal component analysis (Pca) in order to find representative dimensionless values (Cp) for each Raman spectrum in a specific coordinate. Each Cp was normalized in a range of 0-255 in order to generate a representative image of 8 bits of the region under study. Data acquisition was performed with Raman microscopy system Renishaw in Via in the range of 550 to 1700 cm-1 with a 785 nm laser source, with a power of 17 m W and 15 s of exposure time were used for each spectrum. In preliminary results could detect the presence of molecular markers CD 10+ and CD 19+ with gold nano stars and discrimination between both markers. The results suggest conducting studies with specific concentrations organic and inorganic materials. (Author)

[Progress in molecular biology of a semi-mangrove, Millettia pinnata].

Science.gov (United States)

Huang, Jianzi; Zhang, Wanke; Huang, Rongfeng; Zheng, Yizhi

2015-04-01

Millettia pinnata L. is a leguminous tree with great potential in biodiesel applications and also a typical semi-mangrove. In this review, we presented several aspects about the recent research progress in molecular biology of M. pinnata. We descrived several types of molecular markers used to assess the genetic diversity and phylogeny of this species, genome and transcriptome analyses based on high-throughput sequencing platform accomplished for this species, and several gene and genomic sequences of this species isolated for further research. Finally, based on the current research progress, we proposed some orientations for future molecular biology research on M. pinnata.

How could Decision Support System Based on Non-Linear Model Help to Interpret Tumor Marker Measurments in Oncology

Czech Academy of Sciences Publication Activity Database

Pecen, Ladislav; Eben, Kryštof; Vondráček, Jiří; Holubec, L.; Topolčan, O.; Pikner, R.; Kausitz, J.; Nekulová, M.; Šimíčková, M.

2002-01-01

Roč. 23, Suppl.1 (2002), s. 38 ISSN 1010-4283. [Meeting of the International Society for Oncodevelopmental Biology and Medicine /30./. 08.09.2002-12.09.2002, Boston] Institutional research plan: AV0Z1030915 Keywords : tumor markers * decision support systems Subject RIV: BA - General Mathematics

The molecular biology of WHO grade I astrocytomas.

Science.gov (United States)

Marko, Nicholas F; Weil, Robert J

2012-12-01

World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood.

Marker Registration Technique for Handwritten Text Marker in Augmented Reality Applications

Science.gov (United States)

Thanaborvornwiwat, N.; Patanukhom, K.

2018-04-01

Marker registration is a fundamental process to estimate camera poses in marker-based Augmented Reality (AR) systems. We developed AR system that creates correspondence virtual objects on handwritten text markers. This paper presents a new method for registration that is robust for low-content text markers, variation of camera poses, and variation of handwritten styles. The proposed method uses Maximally Stable Extremal Regions (MSER) and polygon simplification for a feature point extraction. The experiment shows that we need to extract only five feature points per image which can provide the best registration results. An exhaustive search is used to find the best matching pattern of the feature points in two images. We also compared performance of the proposed method to some existing registration methods and found that the proposed method can provide better accuracy and time efficiency.

PROTEOMIC AND EPIGENOMIC MARKERS OF SEPSIS-INDUCED DELIRIUM (SID

Directory of Open Access Journals (Sweden)

Adonis eSfera

2015-10-01

Full Text Available In elderly population sepsis is one of the leading causes of intensive care unit (ICU admissions in the United States. Sepsis-induced delirium (SID is the most frequent cause of delirium in ICU (1. Together delirium and SID represent under recognized public health problems which place an increasing financial burden on the US health care system, currently estimated at 143 to 152 billion dollars per year (2. The interest in SID was recently reignited as it was demonstrated that, contrary to prior beliefs, cognitive deficits induced by this condition may be irreversible and lead to dementia (3-4. Conversely, it is construed that diagnosing SID early or mitigating its full blown manifestations may preempt geriatric cognitive disorders. Biological markers specific for sepsis and SID would facilitate the development of potential therapies, monitor the disease process and at the same time enable elderly individuals to make better informed decisions regarding surgeries which may pose the risk of complications, including sepsis and delirium.This article proposes a battery of peripheral blood markers to be used for diagnostic and prognostic purposes in sepsis and SID. Though each individual marker may not be specific enough, we believe that together as a battery they may achieve the necessary accuracy to answer two important questions: who may be vulnerable to the development of sepsis, and who may develop SID and irreversible cognitive deficits following sepsis?

The molecular basis of jaundice: An old symptom revisited.

Science.gov (United States)

Gazzin, Silvia; Masutti, Flora; Vitek, Libor; Tiribelli, Claudio

2017-08-01

Increased serum bilirubin level is a widely used diagnostic marker for hepatic illnesses. Nevertheless, mild elevation of unconjugated serum bilirubin (such as in Gilbert syndrome) has been recently demonstrated to correlate with low risk of chronic inflammatory and/or oxidative stress-mediated diseases. In accord, a low serum bilirubin level has emerged as an important predisposing factor or a biomarker of these pathologic conditions including cardiovascular, tumour, and possibly neurodegenerative diseases. Bilirubin possesses multiple biological actions with interaction in a complex network of enzymatic and signalling pathways. The fact that the liver is the main organ controlling the bioavailability of bilirubin emphasizes the central role of this organ in human health. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

Science.gov (United States)

Kang, Tianyu; Ding, Wei; Zhang, Luoyan; Ziemek, Daniel; Zarringhalam, Kourosh

2017-12-19

Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers. In this paper, we develop a biological network-based regularized artificial neural network model for prediction of phenotype from transcriptomic measurements in clinical trials. To improve model sparsity and the overall reproducibility of the model, we incorporate regularization for simultaneous shrinkage of gene sets based on active upstream regulatory mechanisms into the model. We benchmark our method against various regression, support vector machines and artificial neural network models and demonstrate the ability of our method in predicting the clinical outcomes using clinical trial data on acute rejection in kidney transplantation and response to Infliximab in ulcerative colitis. We show that integration of prior biological knowledge into the classification as developed in this paper, significantly improves the robustness and generalizability of predictions to independent datasets. We provide a Java code of our algorithm along with a parsed version of the STRING DB database. In summary, we present a method for prediction of clinical phenotypes using baseline genome-wide expression data that makes use of prior biological knowledge on gene-regulatory interactions in order to increase robustness and reproducibility of omic-scale markers. The integrated group-wise regularization methods increases the interpretability of biological signatures and gives stable performance estimates across independent test sets.

Current research in Radiation Biology and Biochemistry Division

International Nuclear Information System (INIS)

Tarachand, U.; Singh, B.B.

1995-01-01

The Radiation Biology and Biochemistry Division, Bhabha Atomic Research Centre, Bombay has been engaged in research in the frontier areas of (i) radiation biology related to tumour therapy and injury caused by free radicals; (ii) molecular basis of diseases of physiological origin; (iii) molecular aspects of chemical carcinogenesis and (iv) structure of genome and genome related functions. The gist of research and development activities carried out in the Division during the last two years are documented

Current research in Radiation Biology and Biochemistry Division

Energy Technology Data Exchange (ETDEWEB)

Tarachand, U; Singh, B B [eds.; Bhabha Atomic Research Centre, Bombay (India). Radiation Biology and Biochemistry Div.

1996-12-31

The Radiation Biology and Biochemistry Division, Bhabha Atomic Research Centre, Bombay has been engaged in research in the frontier areas of (i) radiation biology related to tumour therapy and injury caused by free radicals; (ii) molecular basis of diseases of physiological origin; (iii) molecular aspects of chemical carcinogenesis and (iv) structure of genome and genome related functions. The gist of research and development activities carried out in the Division during the last two years are documented.

Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test

KAUST Repository

Cai, T.

2012-06-25

In recent years, genome-wide association studies (GWAS) and gene-expression profiling have generated a large number of valuable datasets for assessing how genetic variations are related to disease outcomes. With such datasets, it is often of interest to assess the overall effect of a set of genetic markers, assembled based on biological knowledge. Genetic marker-set analyses have been advocated as more reliable and powerful approaches compared with the traditional marginal approaches (Curtis and others, 2005. Pathways to the analysis of microarray data. TRENDS in Biotechnology 23, 429-435; Efroni and others, 2007. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One 2, 425). Procedures for testing the overall effect of a marker-set have been actively studied in recent years. For example, score tests derived under an Empirical Bayes (EB) framework (Liu and others, 2007. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 63, 1079-1088; Liu and others, 2008. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC bioinformatics 9, 292-2; Wu and others, 2010. Powerful SNP-set analysis for case-control genome-wide association studies. American Journal of Human Genetics 86, 929) have been proposed as powerful alternatives to the standard Rao score test (Rao, 1948. Large sample tests of statistical hypotheses concerning several parameters with applications to problems of estimation. Mathematical Proceedings of the Cambridge Philosophical Society, 44, 50-57). The advantages of these EB-based tests are most apparent when the markers are correlated, due to the reduction in the degrees of freedom. In this paper, we propose an adaptive score test which up- or down-weights the contributions from each member of the marker-set based on the Z-scores of

Effectiveness of Vascular Markers (Immunohistochemical Stains) in Soft Tissue Sarcomas.

Science.gov (United States)

Naeem, Namra; Mushtaq, Sajid; Akhter, Noreen; Hussain, Mudassar; Hassan, Usman

2018-05-01

To ascertain the effectiveness of IHC markers of vascular origin like CD31, CD34, FLI1 and ERG in vascular soft tissue sarcomas including angiosarcomas, Kaposi sarcomas, epithelioid hemangioendothelioma and a non-vascular soft tissue sarcoma (Epithelioid sarcoma). Descriptive study. Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, from 2011 to 2017. Diagnosed cases of angiosarcomas (n=48), epithelioid hemangioendothelioma (n=9), Kaposi sarcoma (n=9) and epithelioid sarcoma (n=20) were selected. Immunohistochemical staining as performed on formalin fixed paraffin embedded sections. The sections were stained for the following markers: CD34 (VENTANA clone Q Bend 10), CD31 (Leica clone 1 A 10), FLI1 (CELL MARQUE clone MRQ-1) and ERG (CELL MARQUE clone EP111). A complete panel of CD34, CD31 and ERG was applied on 8/48 cases of angiosarcomas with triple positivity in 6 cases. Eight cases showed positivity for only CD31 and ERG and 2 cases showed positivity for only ERG. A complete panel of CD34, CD31 and ERG was applied on 3/9 cases of epithelioid hemangioendothelioma with positivity for all markers in 2 cases. Combined positivity for ERG and CD34 was seen in 2 cases and on 4 cases only CD31 immunohistochemical was solely applied with 100% positivity. FLI1 was not applied on any case. Among 9 cases of Kaposi sarcoma, ERG, CD34 and CD31 in combination were applied on only 1 case with triple positivity. Remaining cases show positivity for either CD34, CD31 or FLI1. Majority of cases of epithelioid sarcomas were diagnosed on the basis of cytokeratin and CD34 positivity with loss of INI1. The other vascular markers showed negativity in all cases. Among these four markers, ERG immunohistochemical stain is highly effective for endothelial differentiation due to its specific nuclear staining pattern in normal blood vessel endothelial cells (internal control) as well as neoplastic cells of vascular tumors and lack of background staining.

Pig Manure Contamination Marker Selection Based on the Influence of Biological Treatment on the Dominant Fecal Microbial Groups▿

Science.gov (United States)

Marti, Romain; Dabert, Patrick; Pourcher, Anne-Marie

2009-01-01

The objective of this study was to identify a microbial marker for pig manure contamination. We quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. The partial 16S rRNA genes of Bacteroides-Prevotella, Eubacterium-Clostridiaceae, Bacillus-Streptococcus-Lactobacillus (BSL), and Bifidobacterium group isolates were amplified and analyzed by capillary electrophoresis single-strand conformation polymorphism. The most dominant bacterial populations were identified by cloning and sequencing their 16S rRNA genes. The results showed that Bifidobacterium spp. and, to a lesser extent, members of the BSL group, were less affected by the aerobic treatment than either Eubacterium-Clostridiaceae or Bacteroides-Prevotella. Two Bifidobacterium species found in raw manure were still present in manure during land application, suggesting that they can survive outside the pig intestinal tract and also survive aerobic treatment. The 16S-23S rRNA internal transcribed spacer of one species, Bifidobacterium thermacidophilum subsp. porcinum, was sequenced, and a specific pair of primers was designed for its detection in the environment. With this nested PCR assay, this potential marker was not detected in samples from 30 bovine, 30 poultry, and 28 human fecal samples or in 15 urban wastewater effluents. As it was detected in runoff waters after spreading of pig manure, we propose this marker as a suitable microbial indicator of pig manure contamination. PMID:19525269

Pig manure contamination marker selection based on the influence of biological treatment on the dominant fecal microbial groups.

Science.gov (United States)

Marti, Romain; Dabert, Patrick; Pourcher, Anne-Marie

2009-08-01

The objective of this study was to identify a microbial marker for pig manure contamination. We quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. The partial 16S rRNA genes of Bacteroides-Prevotella, Eubacterium-Clostridiaceae, Bacillus-Streptococcus-Lactobacillus (BSL), and Bifidobacterium group isolates were amplified and analyzed by capillary electrophoresis single-strand conformation polymorphism. The most dominant bacterial populations were identified by cloning and sequencing their 16S rRNA genes. The results showed that Bifidobacterium spp. and, to a lesser extent, members of the BSL group, were less affected by the aerobic treatment than either Eubacterium-Clostridiaceae or Bacteroides-Prevotella. Two Bifidobacterium species found in raw manure were still present in manure during land application, suggesting that they can survive outside the pig intestinal tract and also survive aerobic treatment. The 16S-23S rRNA internal transcribed spacer of one species, Bifidobacterium thermacidophilum subsp. porcinum, was sequenced, and a specific pair of primers was designed for its detection in the environment. With this nested PCR assay, this potential marker was not detected in samples from 30 bovine, 30 poultry, and 28 human fecal samples or in 15 urban wastewater effluents. As it was detected in runoff waters after spreading of pig manure, we propose this marker as a suitable microbial indicator of pig manure contamination.

Development of SSR markers for a Tibetan medicinal plant, Lancea tibetica (Phrymaceae), based on RAD sequencing.

Science.gov (United States)

Tian, Zunzhe; Zhang, Faqi; Liu, Hairui; Gao, Qingbo; Chen, Shilong

2016-11-01

Lancea tibetica (Phrymaceae), a Tibetan medicinal plant, is endemic to the Qinghai-Tibet Plateau. The over-exploitation of wild L. tibetica has led to the destruction of many populations. To enhance protection and management, biological research, especially population genetic studies, should be carried out on L. tibetica . Simple sequence repeat (SSR) markers of L. tibetica were developed to analyze population diversity. Four thousand four hundred and forty-one SSR loci were identified for L. tibetica based on restriction-site associated DNA (RAD) sequencing on the Illumina HiSeq platform. One hundred SSR loci were arbitrarily selected for primer design, and 38 of them were successfully amplified. These markers were tested on 56 individuals from three populations of L. tibetica , and 10 markers displayed polymorphisms. The total number of alleles per locus ranged from three to eight, and observed and expected heterozygosities ranged from 0.200 to 1.000 and 0.683 to 0.879, respectively. We tested for cross-amplification of these 10 markers in the related species L. hirsuta and found that nine could be successfully amplified. The SSR markers characterized here are the first to be developed and tested in L. tibetica . They will be useful for future population genetic studies on L. tibetica and closely related species.

Ghost marker detection and elimination in marker-based optical tracking systems for real-time tracking in stereotactic body radiotherapy

International Nuclear Information System (INIS)

Yan, Guanghua; Li, Jonathan; Huang, Yin; Mittauer, Kathryn; Lu, Bo; Liu, Chihray

2014-01-01

Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position

Ghost marker detection and elimination in marker-based optical tracking systems for real-time tracking in stereotactic body radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Yan, Guanghua, E-mail: yan@ufl.edu; Li, Jonathan; Huang, Yin; Mittauer, Kathryn; Lu, Bo; Liu, Chihray [Department of Radiation Oncology, University of Florida, Gainesville, Florida 32610 (United States)

2014-10-15

Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position

A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance.

Science.gov (United States)

Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Islam, Kh Nurul; Latif, Mohammad Abdul

2013-11-14

Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1-6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding

A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

Directory of Open Access Journals (Sweden)

Mohammad Abdul Latif

2013-11-01

Full Text Available Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR, and they are typically composed of 1–6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS

Oligometastatic prostate cancer: shaping the definition with molecular imaging and an improved understanding of tumor biology.

Science.gov (United States)

Joice, Gregory A; Rowe, Steven P; Pienta, Kenneth J; Gorin, Michael A

2017-11-01

The aim of this review is to discuss how novel imaging modalities and molecular markers are shaping the definition of oligometastatic prostate cancer. To effectively classify a patient as having oligometastatic prostate cancer, diagnostic tests must be sensitive enough to detect subtle sites of metastatic disease. Conventional imaging modalities can readily detect widespread polymetastatic disease but do not have the sensitivity necessary to reliably classify patients as oligometastatic. Molecular imaging using both metabolic- and molecularly-targeted radiotracers has demonstrated great promise in aiding in our ability to define the oligometastatic state. Perhaps the most promising data to date have been generated with radiotracers targeting prostate-specific membrane antigen. In addition, early studies are beginning to define biologic markers in the oligometastatic state that may be indicative of disease with minimal metastatic potential. Recent developments in molecular imaging have allowed for improved detection of metastatic prostate cancer allowing for more accurate staging of patients with oligometastatic disease. Future development of biologic markers may assist in defining the oligometastatic state and determining prognosis.

The biologically equivalent dose BED - Is the approach for calculation of this factor really a reliable basis?

International Nuclear Information System (INIS)

Jensen, J.M.; Zimmermann, J.

2000-01-01

To predict the effect on tumours in radiotherapy, especially relating to irreversible effects, but also to realize the retrospective assessment the so called L-Q-model is relied on at present. Internal specific organ parameters, such as α, β, γ, T p , T k , and ρ, as well as external parameters, so as D, d, n, V, and V ref , were used for determination of the biologically equivalent dose BED. While the external parameters are determinable with small deviations, the internal parameters depend on biological varieties and dispersons: In some cases the lowest value is assumed to be Δ=±25%. This margin of error goes on to the biologically equivalent dose by means of the principle of superposition of errors. In some selected cases (lung, kidney, skin, rectum) these margins of error were calculated exemplarily. The input errors especially of the internal parameters cause a mean error Δ on the biologically equivalent dose and a dispersion of the single fraction dose d dependent on the organ taking into consideration, of approximately 8-30%. Hence it follows only a very critical and cautious application of those L-Q-algorithms in expert proceedings, and in radiotherapy more experienced based decisions are recommended, instead of acting only upon simple two-dimensional mechanistic ideas. (orig.) [de

Biochemical markers of bone turnover

International Nuclear Information System (INIS)

Kim, Deog Yoon

1999-01-01

Biochemical markers of bone turnover has received increasing attention over the past few years, because of the need for sensitivity and specific tool in the clinical investigation of osteoporosis. Bone markers should be unique to bone, reflect changes of bone less, and should be correlated with radiocalcium kinetics, histomorphometry, or changes in bone mass. The markers also should be useful in monitoring treatment efficacy. Although no bone marker has been established to meet all these criteria, currently osteocalcin and pyridinium crosslinks are the most efficient markers to assess the level of bone turnover in the menopausal and senile osteoporosis. Recently, N-terminal telopeptide (NTX), C-terminal telopeptide (CTX) and bone specific alkaline phosphatase are considered as new valid markers of bone turnover. Recent data suggest that CTX and free deoxypyridinoline could predict the subsequent risk of hip fracture of elderly women. Treatment of postmenopausal women with estrogen, calcitonin and bisphosphonates demonstrated rapid decrease of the levels of bone markers that correlated with the long-term increase of bone mass. Factors such as circadian rhythms, diet, age, sex, bone mass and renal function affect the results of biochemical markers and should be appropriately adjusted whenever possible. Each biochemical markers of bone turnover may have its own specific advantages and limitations. Recent advances in research will provide more sensitive and specific assays

National survey on internal quality control for tumour markers in clinical laboratories in China.

Science.gov (United States)

Wang, Wei; Zhong, Kun; Yuan, Shuai; He, Falin; Du, Yuxuan; Hu, Zhehui; Wang, Zhiguo

2018-06-15

This survey was initiated to obtain knowledge on the current situation of internal quality control (IQC) practice for tumour markers (TMs) in China. Additionally, we tried to acquire the most appropriate quality specifications. This survey was a current status survey. The IQC information had been collected via online questionnaires. All of 1821 clinical laboratories which participated in the 2016 TMs external quality assessment (EQA) programme had been enrolled. The imprecision evaluation criteria were the minimal, desirable, and optimal allowable imprecisions based on biological variations, and 1/3 total allowable error (TEa) and 1/4 TEa. A total of 1628 laboratories answered the questionnaires (89%). The coefficients of variation (CVs) of the IQC of participant laboratories varied greatly from 1% (5 th percentile) to 13% (95 th percentile). More than 82% (82 - 91%) of participant laboratories two types of CVs met 1/3 TEa except for CA 19-9. The percentiles of current CVs were smaller than cumulative CVs. A number of 1240 laboratories (76%) reported their principles and systems used. The electrochemiluminescence was the most used principle (45%) and had the smallest CVs. The performance of laboratories for TMs IQC has yet to be improved. On the basis of the obtained results, 1/3 TEa would be realistic and attainable quality specification for TMs IQC for clinical laboratories in China.

Marker Detection in Aerial Images

KAUST Repository

Alharbi, Yazeed

2017-04-09

The problem that the thesis is trying to solve is the detection of small markers in high-resolution aerial images. Given a high-resolution image, the goal is to return the pixel coordinates corresponding to the center of the marker in the image. The marker has the shape of two triangles sharing a vertex in the middle, and it occupies no more than 0.01% of the image size. An improvement on the Histogram of Oriented Gradients (HOG) is proposed, eliminating the majority of baseline HOG false positives for marker detection. The improvement is guided by the observation that standard HOG description struggles to separate markers from negatives patches containing an X shape. The proposed method alters intensities with the aim of altering gradients. The intensity-dependent gradient alteration leads to more separation between filled and unfilled shapes. The improvement is used in a two-stage algorithm to achieve high recall and high precision in detection of markers in aerial images. In the first stage, two classifiers are used: one to quickly eliminate most of the uninteresting parts of the image, and one to carefully select the marker among the remaining interesting regions. Interesting regions are selected by scanning the image with a fast classifier trained on the HOG features of markers in all rotations and scales. The next classifier is more precise and uses our method to eliminate the majority of the false positives of standard HOG. In the second stage, detected markers are tracked forward and backward in time. Tracking is needed to detect extremely blurred or distorted markers that are missed by the previous stage. The algorithm achieves 94% recall with minimal user guidance. An average of 30 guesses are given per image; the user verifies for each whether it is a marker or not. The brute force approach would return 100,000 guesses per image.

Biological Correlates of Empathy

Directory of Open Access Journals (Sweden)

E. Timucin Oral

2010-04-01

Full Text Available Empathy can be defined as the capacity to know emotionally what another is experiencing from within the frame of reference of that other person and the capacity to sample the feelings of another or it can be metaphorized as to put oneself in another’s shoes. Although the concept of empathy was firstly described in psychological theories, researches studying the biological correlates of psychological theories have been increasing recently. Not suprisingly, dinamically oriented psychotherapists Freud, Kohut, Basch and Fenichel had suggested theories about the biological correlates of empathy concept and established the basis of this modality decades ago. Some other theorists emphasized the importance of empathy in the early years of lifetime regarding mother-child attachment in terms of developmental psychology and investigated its role in explanation of psychopathology. The data coming from some of the recent brain imaging and animal model studies also seem to support these theories. Although increased activity in different brain regions was shown in many of the brain imaging studies, the role of cingulate cortex for understanding mother-child relationship was constantly emphasized in nearly all of the studies. In addition to these studies, a group of Italian scientists has defined a group of neurons as “mirror neurons” in their studies observing rhesus macaque monkeys. Later, they also defined mirror neurons in human studies, and suggested them as “empathy neurons”. After the discovery of mirror neurons, the hopes of finding the missing part of the puzzle for understanding the biological correlates of empathy raised again. Although the roles of different biological parameters such as skin conductance and pupil diameter for defining empathy have not been certain yet, they are going to give us the opportunity to revise the inconsistent basis of structural validity in psychiatry and to stabilize descriptive validity. In this review, the

Subattomole sensitivity in biological accelerator mass spectrometry.

Science.gov (United States)

Salehpour, Mehran; Possnert, Göran; Bryhni, Helge

2008-05-15

The Uppsala University 5 MV Pelletron tandem accelerator has been used to study (14)C-labeled biological samples utilizing accelerator mass spectrometry (AMS) technology. We have adapted a sample preparation method for small biological samples down to a few tens of micrograms of carbon, involving among others, miniaturizing of the graphitization reactor. Standard AMS requires about 1 mg of carbon with a limit of quantitation of about 10 amol. Results are presented for a range of small sample sizes with concentrations down to below 1 pM of a pharmaceutical substance in human blood. It is shown that (14)C-labeled molecular markers can be routinely measured from the femtomole range down to a few hundred zeptomole (10 (-21) mol), without the use of any additional separation methods.

Physical, biological and clinical basis of light ions using in radiotherapy: EULIMA project

International Nuclear Information System (INIS)

Chauvel, P.

1991-01-01

Improving the efficiency of radiotherapy is a constant concern in oncology: more than half of the patients who contract cancer receive radiotherapy at some stage. Use of charged particles in radiotherapy represents indisputable progress in localization of the dose delivered to tumour masses, thereby allowing reduction of dose received by adjacent healthy tissues. Protons improve the physical selectivity of the irradiation, i.e. the dose distribution. High-LET (Linear Energy Transfer) radiations produce different biological effects, decreasing the differences in radiosensitivity, and allowing radiation therapy to control radioresistant tumours. Fast neutrons represent the most known of these high-LET particles, but they suffer of a relatively poor physical selectivity. The two approaches (physical selectivity and biological advantages) are joined in by light ions (Carbon, Oxygen, Neon). Highly selective high-LET radiation therapy can be performed for radioresistant tumours without damage to healthy tissues. Preliminary results obtained in Berkeley (USA) demonstrate an improved local control of unresectable, slowly growing tumours, confirming what could be extrapolated from proton and neutrontherapy. Furthermore, radioactive light ion beams can be used to verify the accuracy of treatment planning by checking the range of the particle with a PET camera, and in the future for the treatment itself. In the framework of its programme Europe against Cancer, the Commission of the European Communities participates in the funding of the EULIMA (European Light Ion Medical Accelerator) project feasibility study, aiming to design an hospital-based light ion therapy facility in Europe [fr

Biological effects of drinking-water mineral composition on calcium balance and bone remodeling markers.

Science.gov (United States)

Roux, S; Baudoin, C; Boute, D; Brazier, M; De La Guéronniere, V; De Vernejoul, M C

2004-01-01

To compare the effects of 2 drinking waters containing similar calcium (Ca) concentration in order to analyze the role of ions other than Ca on bone metabolism. These mineral drinking-waters differed by their mineral composition primarily concerning the concentration of bicarbonate (HCO3-), high in the HB, and sulfate, high in HS water. Of 60 included women, 39 completed the study. Patients were randomly assigned to an intake of 1 liter per day of mineral water HB or HS for 28 d, followed by cross-over to the alternative drinking-water for a further 28 d. At baseline and after each period of one month, Ca metabolism parameters, acid-base status, and bone remodeling markers were measured. Changes in Ca metabolism were significant in the HB group where the ionized Ca increased and the PTH decreased. Serum pH showed a similar increase whatever the used drinking water compared to baseline. In the HB group, significant increase in urine pH, and significant decrease in AT-HCO3- and NH4+ were observed. Bone resorption markers, urinary CTx/Cr, Pyr/Cr, and D-Pyr/Cr, significantly decreased in the HB group compared to baseline, and were not significantly modified in the HS group. These results showed a beneficial effect of the bicarbonaterich HB water on bone metabolism. This may account for a better bioavailability of the Ca, a greater alkalinization, and a larger decrease in PTH level secondary to a higher ionized Ca level. The higher content of silica in HB water may have also participated to the positive action on bone balance that was observed. In this short term study, these data underlined the potential role of the mineral drinking water composition on bone metabolism.

From dysplastic nevus to melanoma: functional proteomic approach for the identification of bio markers

International Nuclear Information System (INIS)

De Pol, A.

2009-01-01

The project ultimately aims to identify bio markers from serum or other biological fluids helpful for early diagnosis of melanoma. Parametric analysis combined with advanced skin imaging technology, such as con focal microscopy, is directed to the identification of different types of benign melanocyte lesions, as well as to the characterization of different melanomas and dysplastic nevi, in order to understand different tumour progression behaviours and to identify possible melanoma precursors

Introduction to radiation biology

International Nuclear Information System (INIS)

Uma Devi, P.; Satish Rao, B.S.; Nagarathnam, A.

2000-01-01

This book is arranged in a logical sequence, starting from radiation physics and radiation chemistry, followed by molecular, subcellular and cellular effects and going on to the level of organism. Topics covered include applied radiobiology like modifiers of radiosensitivity, predictive assay, health physics, human genetics and radiopharmaceuticals. The topics covered are : 1. Radiation Physics, 2. Detection and Measurement of Radiation, 3. Radiation Chemistry, 4. DNA Damage and Repair, 5. Chromosomal Aberrations and Gene Mutations, 6. Cellular Radiobiology 7. Acute Radiation Effects, 8. Delayed Effects of Radiation, 9. Biological Basis of Radiotherapy, 10. Chemical Modifiers of Radiosensitivity, 11. Hyperthermia, 12. High LET Radiations in Cancer, Therapy, 13. Predictive Assays, 14. Radiation Effects on Embryos, 15. Human Radiation Genetics, 16. Radiolabelled Compounds in Biology and Medicine and 17. Radiological Health

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel.

Science.gov (United States)

Huang, Ling; Deng, Xiaohui; Li, Ronghua; Xia, Yanshi; Bai, Guihua; Siddique, Kadambot H M; Guo, Peiguo

2018-04-20

Simple Sequence Repeat (SSR) is one of the most effective markers used in plant and animal genetic research and molecular breeding programs. Silver staining is a widely used method for the detection of SSR markers in a polyacrylamide gel. However, conventional protocols for silver staining are technically demanding and time-consuming. Like many other biological laboratory techniques, silver staining protocols have been steadily optimized to improve detection efficiency. Here, we report a simplified silver staining method that significantly reduces reagent costs and enhances the detection resolution and picture clarity. The new method requires two major steps (impregnation and development) and three reagents (silver nitrate, sodium hydroxide, and formaldehyde), and only 7 min of processing for a non-denaturing polyacrylamide gel. Compared to previously reported protocols, this new method is easier, quicker and uses fewer chemical reagents for SSR detection. Therefore, this simple, low-cost, and effective silver staining protocol will benefit genetic mapping and marker-assisted breeding by a quick generation of SSR marker data.

Changes in urinary amino acids excretion in relationship with muscle activity markers over a professional cycling stage race: in search of fatigue markers.

Science.gov (United States)

Corsetti, Roberto; Barassi, Alessandra; Perego, Silvia; Sansoni, Veronica; Rossi, Alessandra; Damele, Clara Anna Linda; Melzi D'Eril, Gianlodovico; Banfi, Giuseppe; Lombardi, Giovanni

2016-01-01

The aim of this study was to identify the relationship between metabolic effort, muscular damage/activity indices, and urinary amino acids profile over the course of a strenuous prolonged endurance activity, as a cycling stage race is, in order to identify possible fatigue markers. Nine professional cyclists belonging to a single team, competing in the Giro d'Italia cycling stage race, were anthropometrically characterized and sampled for blood and urine the day before the race started, and on days 12 and 23 of the race. Diet was kept the same over the race, and power output and energy expenditure were recorded. Sera were assayed for muscle markers (lactate dehydrogenase, aspartate aminotransferase, and creatine kinase activities, and blood urea nitrogen), and creatinine, all corrected for plasma volume changes. Urines were profiled for amino acid concentrations, normalized on creatinine excretion. Renal function, in terms of glomerular filtration rate, was monitored by MDRD equation corrected on body surface area. Creatine kinase activity and blood urea were increased during the race as did serum creatinine while kidney function remained stable. Among the amino acids, taurine, glycine, cysteine, leucine, carnosine, 1-methyl histidine, and 3-methyl histidine showed a net decreased, while homocysteine was increased. Taurine and the dipeptide carnosine (β-alanyl-L-histidine) were significantly correlated with the muscle activity markers and the indices of effort. In conclusion, the metabolic profile is modified strikingly due to the effort. Urinary taurine and carnosine seem useful tools to evaluate the muscle damage and possibly the fatigue status on a long-term basis.

Quality Markers in Cardiology. Main Markers to Measure Quality of Results (Outcomes) and Quality Measures Related to Better Results in Clinical Practice (Performance Metrics). INCARDIO (Indicadores de Calidad en Unidades Asistenciales del Área del Corazón): A SEC/SECTCV Consensus Position Paper.

Science.gov (United States)

López-Sendón, José; González-Juanatey, José Ramón; Pinto, Fausto; Cuenca Castillo, José; Badimón, Lina; Dalmau, Regina; González Torrecilla, Esteban; López-Mínguez, José Ramón; Maceira, Alicia M; Pascual-Figal, Domingo; Pomar Moya-Prats, José Luis; Sionis, Alessandro; Zamorano, José Luis

2015-11-01

Cardiology practice requires complex organization that impacts overall outcomes and may differ substantially among hospitals and communities. The aim of this consensus document is to define quality markers in cardiology, including markers to measure the quality of results (outcomes metrics) and quality measures related to better results in clinical practice (performance metrics). The document is mainly intended for the Spanish health care system and may serve as a basis for similar documents in other countries. Copyright © 2015 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

[Circadian markers and genes in bipolar disorder].

Science.gov (United States)

Yeim, S; Boudebesse, C; Etain, B; Belliviera, F

2015-09-01

Bipolar disorder is a severe and complex multifactorial disease, characterized by alternance of acute episodes of depression and mania/hypomania, interspaced by euthymic periods. The etiological determinants of bipolar disorder yet, are still poorly understood. For the last 30 years, chronobiology is an important field of investigation to better understand the pathophysiology of bipolar disorder. We conducted a review using Medline, ISI Database, EMBase, PsyInfo up to January 2015, using the following keywords combinations: "mood disorder", "bipolar disorder", "depression", "unipolar disorder", "major depressive disorder", "affective disorder", for psychiatric conditions; and "circadian rhythms", "circadian markers", "circadian gene", "clock gene", "melatonin" for circadian rhythms. The search critera was presence of word in any field of the article. Quantitative and qualitative circadian abnormalities are associated with bipolar disorders both during acute episodes and euthymic periods, suggesting that these altered circadian rhythms may represent biological trait markers of the disorder. These circadian dysfunctions were assessed by various validated tools including polysomnography, actigraphy, sleep diaries, chronotype assessments and blood melatonin/cortisol measures. Other altered endogenous circadian activities have also been reported in bipolar patients, such as hormones secretion, core body temperature or fibroblasts activity. Moreover, these markers were also altered in healthy relatives of bipolar patients, suggesting a degree of heritability. Several genetic association studies have also showed associations between multiple circadian genes and bipolar disorder, such as CLOCK, ARTNL1, GSK3β, PER3, NPAS2, NR1D1, TIMELESS, RORA, RORB, and CSNK1ε. Thus, these circadian gene variants may contribute to the genetic susceptibility of the disease. Furthermore, the study of the clock system may help to better understand some phenotypic aspects like the

HNS{sup +} and HSN{sup +} cations: Electronic states, spin-rovibronic spectroscopy with planetary and biological implications

Energy Technology Data Exchange (ETDEWEB)

Trabelsi, Tarek; Hochlaf, Majdi, E-mail: hochlaf@univ-mlv.fr [Laboratoire Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, 5 Blvd. Descartes, 77454 Marne-la-Vallée (France); Ben Yaghlane, Saida [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications—LSAMA, Université de Tunis El Manar, Tunis (Tunisia); Al Mogren, Muneerah Mogren [Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Francisco, Joseph S. [Department of Chemistry, University of Nebraska-Lincoln, 433 Hamilton Hall, Lincoln, Nebraska 68588-0304 (United States)

2016-08-28

Ab initio methods in conjunction with a large basis set are used to compute the potential energy surfaces of the 12 lowest electronic states of the HNS{sup +} and HSN{sup +} isomeric forms. These potentials are used in discussions of the metastability of these cations and plausible mechanisms for the H{sup +}/H + SN{sup +}/SN, S/S{sup +} + NH{sup +}/NH, N/N{sup +} + SH{sup +}/SH ion-molecule reactions. Interestingly, the low rovibrational levels of HSN{sup +}(1{sup 2}A″) and HNS{sup +}(1{sup 2}A″) electronically excited ions are predicted to be long-lived. Both ions are suggested to be a suitable candidate for light-sensitive NO{sup ⋅} donor in vivo and as a possible marker for the detection of intermediates in nitrites + H{sub 2}S reactions at the cellular level. The full spin rovibronic levels of HNS{sup +} are presented, which may assist in the experimental identification of HNS{sup +} and HSN{sup +} ions and in elucidating their roles in astrophysical and biological media.

Insomnia with Objective Short Sleep Duration: the Most Biologically Severe Phenotype of the Disorder

Science.gov (United States)

Vgontzas, Alexandros N.; Fernandez-Mendoza, Julio; Liao, Duanping; Bixler, Edward O.

2013-01-01

Summary Until recently, the association of chronic insomnia with significant medical morbidity was not established and its diagnosis was based solely on subjective complaints. We present evidence that insomnia with objective short sleep duration is the most biologically severe phenotype of the disorder, as it is associated with cognitive-emotional and cortical arousal, activation of both limbs of the stress system, and a higher risk for hypertension, impaired heart rate variability, diabetes, neurocognitive impairment, and mortality. Also, it appears that objective short sleep duration is a biological marker of genetic predisposition to chronic insomnia. In contrast, insomnia with objective normal sleep duration is associated with cognitive-emotional and cortical arousal and sleep misperception but not with signs of activation of both limbs of the stress system or medical complications. Furthermore, the first phenotype is associated with unremitting course, whereas the latter is more likely to remit. We propose that short sleep duration in insomnia is a reliable marker of the biological severity and medical impact of the disorder. Objective measures of sleep obtained in the home environment of the patient would become part of the routine assessment of insomnia patients in a clinician’s office setting. We speculate that insomnia with objective short sleep duration has primarily biological roots and may respond better to biological treatments, whereas insomnia with objective normal sleep duration has primarily psychological roots and may respond better to psychological interventions alone. PMID:23419741

Insomnia with objective short sleep duration: the most biologically severe phenotype of the disorder.

Science.gov (United States)

Vgontzas, Alexandros N; Fernandez-Mendoza, Julio; Liao, Duanping; Bixler, Edward O

2013-08-01

Until recently, the association of chronic insomnia with significant medical morbidity was not established and its diagnosis was based solely on subjective complaints. We present evidence that insomnia with objective short sleep duration is the most biologically severe phenotype of the disorder, as it is associated with cognitive-emotional and cortical arousal, activation of both limbs of the stress system, and a higher risk for hypertension, impaired heart rate variability, diabetes, neurocognitive impairment, and mortality. Also, it appears that objective short sleep duration is a biological marker of genetic predisposition to chronic insomnia. In contrast, insomnia with objective normal sleep duration is associated with cognitive-emotional and cortical arousal and sleep misperception but not with signs of activation of both limbs of the stress system or medical complications. Furthermore, the first phenotype is associated with unremitting course, whereas the latter is more likely to remit. We propose that short sleep duration in insomnia is a reliable marker of the biological severity and medical impact of the disorder. Objective measures of sleep obtained in the home environment of the patient would become part of the routine assessment of insomnia patients in a clinician's office setting. We speculate that insomnia with objective short sleep duration has primarily biological roots and may respond better to biological treatments, whereas insomnia with objective normal sleep duration has primarily psychological roots and may respond better to psychological interventions alone. Copyright © 2012 Elsevier Ltd. All rights reserved.

Assessment of prostatic fiducial marker introduction: patient morbidity, staff satisfaction and improved treatment field placement

International Nuclear Information System (INIS)

Brown, Simon; Lehman, Margot; Ferrari-Anderson, Janet; Glyde, Alan; Burmeister, Elizabeth; Nicol, David

2011-01-01

Increased accuracy when using fiducial markers for prostate localisation is well documented. This project aimed to establish the improvement in accuracy when using gold markers for daily prostate localisation, to assess patient satisfaction and morbidity from the transrectal implantation of gold seed markers and establish staff attitudes towards the newly introduced processes. Twenty patients with prostate cancer had three gold seeds implanted into the base, apex and central zone of the prostate transrectally using ultrasound guidance. Surveys were conducted to assess staff and patient satisfaction with the process of gold seed localisation. The gold markers were used to localise the prostate on a daily basis using megavoltage electronic portal imaging. Measurements were taken to establish the increase in accuracy when using gold fiducial markers compared with using the surrounding bony anatomy. Inter-fraction motion (1 standard deviation (SD)) of the fiducial markers was 2.20, 4.28 and 4.27 mm in the LR, SI and AP directions, respectively. Intra-fraction prostate motion (1 SD) was measured as 0.8 mm LR, 1.1 mm SI and 2.0 mm AP. The patient survey showed that the insertion and associated side effects were acceptable, with 5% of patients stating that the seed insertion was worse than the prostate biopsy, and 23.1% of patients experienced short duration (1–2 days) haematuria. The staff survey showed that daily online image guidance was achievable without affecting patient throughput. Thirty percent of treatment staff believed that performing online daily localisation did not add any extra time to a standard treatment, and the remaining 70% thought that the added time was minimal (2–4 min). Gold fiducial markers are an accurate, reliable and tolerable method of daily prostate localisation.

Networks as a Privileged Way to Develop Mesoscopic Level Approaches in Systems Biology

OpenAIRE

Alessandro Giuliani

2014-01-01

The methodologies advocated in computational biology are in many cases proper system-level approaches. These methodologies are variously connected to the notion of “mesosystem” and thus on the focus on relational structures that are at the basis of biological regulation. Here, I describe how the formalization of biological systems by means of graph theory constitutes an extremely fruitful approach to biology. I suggest the epistemological relevance of the notion of graph resides in its multil...

Marine Carotenoids and Cardiovascular Risk Markers

Directory of Open Access Journals (Sweden)

Lorenza Speranza

2011-06-01

Full Text Available Marine carotenoids are important bioactive compounds with physiological activities related to prevention of degenerative diseases.found principally in plants, with potential antioxidant biological properties deriving from their chemical structure and interaction with biological membranes. They are substances with very special and remarkable properties that no other groups of substances possess and that form the basis of their many, varied functions and actions in all kinds of living organisms. The potential beneficial effects of marine carotenoids have been studied particularly in astaxanthin and fucoxanthin as they are the major marine carotenoids. Both these two carotenoids show strong antioxidant activity attributed to quenching singlet oxygen and scavenging free radicals. The potential role of these carotenoids as dietary anti-oxidants has been suggested to be one of the main mechanisms for their preventive effects against cancer and inflammatory diseases. The aim of this short review is to examine the published studies concerning the use of the two marine carotenoids, astaxanthin and fucoxanthin, in the prevention of cardiovascular diseases.

Uses of chemotherapy together with radiation, and its biological basis

International Nuclear Information System (INIS)

Watanabe, Ikuo; Terashima, Toyozo

1978-01-01

Effect of use of anticancer drugs together with radiation, especially effects of Actinomycin D (AMD), Bleomycin (BLM), and Adriamycin (Ad) which seemed to have synergistic effect, and other substances which have possibility to have synergistic effect were described. It was clarified that AMD out of them showed synergistic effect to inhibit repair of sublethel damage induced by irradiation in addition to anticancer effect itself. Therefore, it is thought that use of AMD is effective especially to cancer with high radioresistance and it is better to administer this drug just before or just after irradiation. It seems to be better to administer at one time with high concentration in the allowable range. It is difficult to come to a conclusion as to BLM and Ad, generalized as well as the conclusion of AMD, but it seems to be better to use BLM and Ad together with irradiation at the same time. As BLM is highly effective especially to epithelial cells, it must be necessary to investigate whether there is a difference of characteristics between cells. In any case, there are two great factors, the concentration and action time (containing the time remaining in vivo) of drugs, and moreover, another factor, time relation to irradiation is added. Therefore, an experiment schedule is complicated so much, and it is important to study quantitatively on the basis of systematic experimental plan. As to clinical application of them, it is necessary to perform an experiment in vitro which is exullent in estimation and an experiment in vivo which certified the effects in keeping organic cooperation. (Tsunoda, M.)

Selection of chemical markers for the quality control of medicinal plants of the genus Cecropia.

Science.gov (United States)

Rivera-Mondragón, Andrés; Ortíz, Orlando O; Bijttebier, Sebastiaan; Vlietinck, Arnold; Apers, Sandra; Pieters, Luc; Caballero-George, Catherina

2017-12-01

Several Cecropia (Cecropiaceae) species are traditionally used in Latin America for the treatment of a variety of diseases including diabetes, arterial hypertension, asthma, bronchitis, anxiety, and inflammation. At present, a number of commercial products based on these plants have been introduced into the market with very little information on methods for guaranteeing their quality and safety. This work proposes potential chemical markers for the quality control of the raw materials of Cecropia obtusifolia Bertol., Cecropia peltata L., Cecropia glaziovii Snethl., Cecropia pachystachya Trécul, and Cecropia hololeuca Miq. The Herbal Chemical Marker Ranking System (Herb MaRS) developed by the National Institute of Complementary Medicine (NICM) at the University of Western Sydney was used for selecting chemical markers for the quality control of selected medicinal species of Cecropia. This review covers the period from 1982 to 2016. Chlorogenic acid, flavonoidal glycosides (orientin, isoorientin, vitexin, isovitexin, and rutin), catechin, epicatechin, procyanidins (B2, B5, and C1), steroids (β-sitosterol), and triterpenoids (α-amyrin, pomolic, tormentic and ursolic acids) were selected as chemical markers for the quality control of the leaves. It is necessary to establish comprehensive standards for guaranteeing quality, safety and efficacy of herbal drugs. The selection of adequate chemical markers for quality control purposes requires a good knowledge about the chemical composition of medicinal plants and their associated biological properties. To the best of our knowledge this review article is the first to address the identification and quantitative determination of the chemical markers for the genus Cecropia.

Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

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Manoj Kumar Mishra

2011-06-01

Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

Nodes and biological processes identified on the basis of network analysis in the brain of the senescence accelerated mice as an Alzheimer’s disease animal model

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Xiao-Rui eCheng

2013-10-01

Full Text Available Harboring the behavioral and histopathological signatures of Alzheimer’s disease (AD, senescence accelerated mouse-prone 8 (SAMP8 mice are currently considered a robust model for studying AD. However, the underlying mechanisms, prioritized pathways and genes in SAMP8 mice linked to AD remain unclear. In this study, we provide a biological interpretation of the molecular underpinnings of SAMP8 mice. Our results were derived from differentially expressed genes in the hippocampus and cerebral cortex of SAMP8 mice compared to age-matched SAMR1 mice at 2, 6, and 12 months of age using cDNA microarray analysis. On the basis of PPI, MetaCore and the co-expression network, we constructed a distinct genetic sub-network in the brains of SAMP8 mice. Next, we determined that the regulation of synaptic transmission and apoptosis were disrupted in the brains of SAMP8 mice. We found abnormal gene expression of RAF1, MAPT, PTGS2, CDKN2A, CAMK2A, NTRK2, AGER, ADRBK1, MCM3AP and STUB1, which may have initiated the dysfunction of biological processes in the brains of SAMP8 mice. Specifically, we found microRNAs, including miR-20a, miR-17, miR-34a, miR-155, miR-18a, miR-22, miR-26a, miR-101, miR-106b and miR-125b, that might regulate the expression of nodes in the sub-network. Taken together, these results provide new insights into the biological and genetic mechanisms of SAMP8 mice and add an important dimension to our understanding of the neuro-pathogenesis in SAMP8 mice from a systems perspective.

Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

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Doerge RW

2003-06-01

Full Text Available Abstract Background It has been reported in the quantitative trait locus (QTL literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach. We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. Results Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. Conclusion We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

Prediction of hepatocellular carcinoma biological behavior in patient selection for liver transplantation

Science.gov (United States)

Cillo, Umberto; Giuliani, Tommaso; Polacco, Marina; Herrero Manley, Luz Maria; Crivellari, Gino; Vitale, Alessandro

2016-01-01

Morphological criteria have always been considered the benchmark for selecting hepatocellular carcinoma (HCC) patients for liver transplantation (LT). These criteria, which are often inappropriate to express the tumor’s biological behavior and aggressiveness, offer only a static view of the disease burden and are frequently unable to correctly stratify the tumor recurrence risk after LT. Alpha-fetoprotein (AFP) and its progression as well as AFP-mRNA, AFP-L3%, des-γ-carboxyprothrombin, inflammatory markers and other serological tests appear to be correlated with post-transplant outcomes. Several other markers for patient selection including functional imaging studies such as 18F-FDG-PET imaging, histological evaluation of tumor grade, tissue-specific biomarkers, and molecular signatures have been outlined in the literature. HCC growth rate and response to pre-transplant therapies can further contribute to the transplant evaluation process of HCC patients. While AFP, its progression, and HCC response to pre-transplant therapy have already been used as a part of an integrated prognostic model for selecting patients, the utility of other markers in the transplant setting is still under investigation. This article intends to review the data in the literature concerning predictors that could be included in an integrated LT selection model and to evaluate the importance of biological aggressiveness in the evaluation process of these patients. PMID:26755873

Prognostic significance of new immunohistochemical markers in refractory classical Hodgkin lymphoma: a study of 59 cases.

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Danielle Canioni

2009-07-01

Full Text Available Although most classical Hodgkin lymphoma patients are cured, a significant minority fail after primary therapy and may die as result of their disease. To date, there is no consensus on biological markers that add value to usual parameters (which comprise the International Prognostic Score used at diagnosis to predict outcome. We evaluated 59 patients (18 with primary refractory or early relapse disease and 41 responders for bcl2, Ki67, CD20, TiA1 and c-kit expression by semi-quantitative immunohistochemical study and correlated the results with the response to treatment.The results showed that expression of bcl2 and CD20 in Hodgkin and Reed Sternberg cells, and expression of TiA1 in micro-environmental lymphocytes, and c-kit positive mast cells in microenvironment, were independent prognostic markers. These novel cHL markers could be used in association with clinical parameters to identify newly diagnosed patients with favorable or unfavorable prognosis and to better tailor treatment for different risk groups.

Biology Branch

Energy Technology Data Exchange (ETDEWEB)

Baldwin, W F

1974-12-31

Progress is reported on the following studies in biochemistry and molecular biology: study of long pyrimidine polynucleotides in DNA; isolation of thymine dimers from Schizosaccharomyces pombe; thermal stability of high molecular weight RNA; nucleases of Micrococcus radiodurans; effect of ionizing radiation on M. radiodurans cell walls and cell membranes; chemical modification of nucleotides; exonucleases of M. radiodurans; and enzymatic basis of repair of radioinduced damage in M. radiodurans. Genetics, development, and population studies include repair pathways and mutation induction in yeast; induction of pure mutant clones in yeast; radiosensitivity of bacteriophage T4; polyacrylamide gel electrophoresis of bacteriophage T4; radiation genetics of Dahibominus; and radiation studies on bitting flies. (HLW)

Relationship between bone scintigraphy and tumor markers in patients with breast cancer

International Nuclear Information System (INIS)

Yildiz, M.; Oral, B.

2004-01-01

The aim of this study is to specify the precise role of bone scintigraphy and serum carcinoembryonic antigen (CEA) and breast cancer-associated antigen (CA) 15-3 assays in the monitoring of breast cancers in order to optimize their use and to determine whether it is possible to guide the prescription of bone scan by the use of CEA and CA 15-3 assays in the monitoring of breast cancer. For this purpose, from November 1997 to May 2002, 98 consecutive female breast cancer patients (median age, 52 years; range 35-77 years) underwent bone scintigraphy during follow-up. In these patients values of tumor markers were compared with the results of bone scintigraphy. Some of the patients with bone metastasis were checked repeatedly at intervals of 6 to 12 months, resulting in 49 patients with bone metastasis and 74 patients without bone metastasis being included in the study. In patients with bone metastasis, serum CEA levels were abnormal in 23/49 cases and CA 15-3 serum concentrations were elevated above the cut-off in 33/49 cases. Among patients without bone metastasis, CEA and CA 15-3 serum concentrations were normal in 50/74 and 55/74 cases respectively. The combination of the two markers improved the diagnostic sensitivity. Although serial tumor marker measurements are an efficient and cost effective method of monitoring disease progression, it does not allow prediction of the bone scan results; so it is not justifiable to reject a bone scintigraphy on the basis of these markers. (author)

Embodied Feeling and Reason in Decision-Making: Assessing the Somatic-Marker Hypothesis

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Warren TenHouten

2016-04-01

Full Text Available Whether or not reason and affect are complementary depends on the task at hand. In ordinary circumstances, problemsolving and decision-making involve both somatic feelings and limbic-structure-based emotions. Feelings, experienced as states of the body, can contribute to decision-making by triggering heuristic cues and rapidly eliminating negative behavioral alternatives, in part by providing what Damasio call somatic markers (Damasio, Tranel and Damasio, 1991; Damasio, 1994, 1999, 2003. However, if task-performance is motivated by potentially large rewards, with high demands on short-term memory and on concentration, the dorsolateral prefrontal cortexcan inhibit affects manifested in the medial prefrontal cortex in order to carry out the necessary cognitive operations. We interpret these two different mental task situations using dual process models. Although experimental evidence from studies of normal subjects and frontal-lobe-damaged patients performing the Iowa Gambling Task has been interpreted as supportive of the somatic-marker hypothesis (SMH, we show that this evidence has been called into question due to faulty study designs. However, studies of normal and psychopathic subjects playing the ultimatum game show that pulse-rate deceleration occurring during the brief period preceding decision-making constitutes a somatic marker. Compared to normal controls, psychopaths show less somatic (electro dermal activity and act with cool, economic rationality, accepting unfair (<50/50 offers that normal subjects reject on the basis of non-economic values of fairness. The somatic-marker hypothesis is discussed and criticized, and various theories based on this hypothesis are identified.

FSH-FSHR3-stem cells in ovary surface epithelium: basis for adult ovarian biology, failure, aging, and cancer.

Science.gov (United States)

Bhartiya, Deepa; Singh, Jarnail

2015-01-01

Despite extensive research, genetic basis of premature ovarian failure (POF) and ovarian cancer still remains elusive. It is indeed paradoxical that scientists searched for mutations in FSH receptor (FSHR) expressed on granulosa cells, whereas more than 90% of cancers arise in ovary surface epithelium (OSE). Two distinct populations of stem cells including very small embryonic-like stem cells (VSELs) and ovarian stem cells (OSCs) exist in OSE, are responsible for neo-oogenesis and primordial follicle assembly in adult life, and are modulated by FSH via its alternatively spliced receptor variant FSHR3 (growth factor type 1 receptor acting via calcium signaling and the ERK/MAPK pathway). Any defect in FSH-FSHR3-stem cell interaction in OSE may affect folliculogenesis and thus result in POF. Ovarian aging is associated with a compromised microenvironment that does not support stem cell differentiation into oocytes and further folliculogenesis. FSH exerts a mitogenic effect on OSE and elevated FSH levels associated with advanced age may provide a continuous trigger for stem cells to proliferate resulting in cancer, thus supporting gonadotropin theory for ovarian cancer. Present review is an attempt to put adult ovarian biology, POF, aging, and cancer in the perspective of FSH-FSHR3-stem cell network that functions in OSE. This hypothesis is further supported by the recent understanding that: i) cancer is a stem cell disease and OSE is the niche for ovarian cancer stem cells; ii) ovarian OCT4-positive stem cells are regulated by FSH; and iii) OCT4 along with LIN28 and BMP4 are highly expressed in ovarian cancers. © 2015 Society for Reproduction and Fertility.

Utility of MRI versus tumor markers for post-treatment surveillance of marker-positive CNS germ cell tumors.

Science.gov (United States)

Cheung, Victoria; Segal, Devorah; Gardner, Sharon L; Zagzag, David; Wisoff, Jeffrey H; Allen, Jeffrey C; Karajannis, Matthias A

2016-09-01

Patients with marker-positive central nervous system (CNS) germ cell tumors are typically monitored for tumor recurrence with both tumor markers (AFP and b-hCG) and MRI. We hypothesize that the recurrence of these tumors will always be accompanied by an elevation in tumor markers, and that surveillance MRI may not be necessary. We retrospectively identified 28 patients with CNS germ cell tumors treated at our institution that presented with an elevated serum or cerebrospinal fluid (CSF) tumor marker at the time of diagnosis. We then identified those who had a tumor recurrence after having been in remission and whether each recurrence was detected via MRI changes, elevated tumor markers, or both. Four patients suffered a tumor recurrence. Only one patient had simultaneously elevated tumor markers and MRI evidence of recurrence. Two patients had evidence of recurrence on MRI without corresponding elevations in serum or CSF tumor markers. One patient had abnormal tumor markers with no evidence of recurrence on MRI until 6 months later. We conclude that in patients with marker-positive CNS germ cell tumors who achieve complete remission, continued surveillance imaging in addition to measurement of tumor markers is indicated to detect recurrences.

The use of caffeine as a biological marker of human exposure and response to polycyclic and polyhalogenated aromatic hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Campbell, M.E

1987-06-05

The use of caffeine as a non-invasive biological marker of PAH-inducible P-450 enzyme induction in humans is assessed through caffeine biotransformation studies using human liver preparations, and through caffeine ingestion studies of human populations exposed to diverse polycyclic and polyhalogenated aromatic hydrocarbons (PAHs and HAHs). In vitro studies indicate that all N-demethylations from caffeine and its primary metabolites are mediated in large part by PAH-inducible P-450 in human liver microsomes, whereas corresponding methylxanthine hydroxylations are in large and variable part mediated by other enzymes that are apparently not inducible by PAHs. It is proposed that a caffeine metabolite ratio (CMR), based on paraxanthine 7-demethylation products relative to a paraxanthine 8-hydroxylation product measured in the urine after caffeine ingestion, reflects PAH-inducible P-450 activity. In vivo studies demonstrate that mean CMR values are significantly higher in smokers and lower in oral contraceptive users, and that CMR values correlate highly with systemic caffeine clearance. Furthermore, mean CMR and CBT (caffeine breath test) values determined for six populations of varying age, and PAH and HAH exposure demonstrated a significant correlation. The participation of xanthine oxidase in the metabolism of caffeine, and proposes the use of the urinary ratio of 1-methyluric acid to 1-methylxanthine as an index of xanthine oxidase activity is also demonstrated. The data suggest that xanthine oxidase activity is not altered by gender, age, oral contraceptive use, PAH and HAH exposure. The data support the use of the CMR as an indicator of PAH-inducible P-450 activity, and show that xanthine oxidase is resistant to induction by PAHs and HAHs. 300 refs., 41 figs., 35 tabs.

The Implementation of Research-based Learning on Biology Seminar Course in Biology Education Study Program of FKIP UMRAH

Science.gov (United States)

Amelia, T.

2018-04-01

Biology Seminar is a course in Biology Education Study Program of Faculty of Teacher Training and Education University of Maritim Raja Ali Haji (FKIP UMRAH) that requires students to have the ability to apply scientific attitudes, perform scientific writing and undertake scientific publications on a small scale. One of the learning strategies that can drive the achievement of learning outcomes in this course is Research-Based Learning. Research-Based Learning principles are considered in accordance with learning outcomes in Biology Seminar courses and generally in accordance with the purpose of higher education. On this basis, this article which is derived from a qualitative research aims at describing Research-based Learning on Biology Seminar course. Based on a case study research, it was known that Research-Based Learning on Biology Seminar courses is applied through: designing learning activities around contemporary research issues; teaching research methods, techniques and skills explicitly within program; drawing on personal research in designing and teaching courses; building small-scale research activities into undergraduate assignment; and infusing teaching with the values of researchers.

The Molecular Biology of Pestiviruses.

Science.gov (United States)

Tautz, Norbert; Tews, Birke Andrea; Meyers, Gregor

2015-01-01

Pestiviruses are among the economically most important pathogens of livestock. The biology of these viruses is characterized by unique and interesting features that are both crucial for their success as pathogens and challenging from a scientific point of view. Elucidation of these features at the molecular level has made striking progress during recent years. The analyses revealed that major aspects of pestivirus biology show significant similarity to the biology of human hepatitis C virus (HCV). The detailed molecular analyses conducted for pestiviruses and HCV supported and complemented each other during the last three decades resulting in elucidation of the functions of viral proteins and RNA elements in replication and virus-host interaction. For pestiviruses, the analyses also helped to shed light on the molecular basis of persistent infection, a special strategy these viruses have evolved to be maintained within their host population. The results of these investigations are summarized in this chapter. © 2015 Elsevier Inc. All rights reserved.

Development of cost-effective Hordeum chilense DNA markers: molecular aids for marker-assisted cereal breeding.

Science.gov (United States)

Hernández, P; Dorado, G; Ramírez, M C; Laurie, D A; Snape, J W; Martín, A

2003-01-01

Hordeum chilense is a potential source of useful genes for wheat breeding. The use of this wild species to increase genetic variation in wheat will be greatly facilitated by marker-assisted introgression. In recent years, the search for the most suitable DNA marker system for tagging H. chilense genomic regions in a wheat background has lead to the development of RAPD and SCAR markers for this species. RAPDs represent an easy way of quickly generating suitable introgression markers, but their use is limited in heterogeneous wheat genetic backgrounds. SCARs are more specific assays, suitable for automatation or multiplexing. Direct sequencing of RAPD products is a cost-effective approach that reduces labour and costs for SCAR development. The use of SSR and STS primers originally developed for wheat and barley are additional sources of genetic markers. Practical applications of the different marker approaches for obtaining derived introgression products are described.

Elucidating polyploidization of bermudagrasses as assessed by organelle and nuclear DNA markers.

Science.gov (United States)

Gulsen, Osman; Ceylan, Ahmet

2011-12-01

Clarification of relationships among ploidy series of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to elucidate polyploidization among Cynodon accessions with different ploidy series collected from Turkey based on chloroplast and nuclear DNA. Forty Cynodon accessions including 7 diploids, 3 triploids, 10 tetraploids, 11 pentaploids, and 9 hexaploids were analyzed using chloroplast DNA restriction fragment-length polymorphism (cpDNA RFLP), chloroplast DNA simple sequence repeat (cpDNA SSR), and nuclear DNA markers based on neighbor-joining (NJ) and principle component analyses (PCA). All three-marker systems with two statistical algorithms clustered the diploids apart from the other ploidy levels. Assuming autopolyploidy, spontaneous polyploidization followed by rapid diversification among the higher ploidy levels than the diploids is likely in Cynodon's evolution. Few tetraploid and hexaploid accessions were clustered with or closely to the group of diploids, supporting the hypothesis above. Eleven haplotypes as estimated by cpDNA RFLP and SSR markers were detected. This study indicated that the diploids had different organelle genome from the rest of the ploidy series and provided valuable insight into relationships among ploidy series of Cynodon accessions based on cp and nuclear DNAs.

Specific Protein Markers for Stem Cell Cross-Talk with Neighboring Cells in the Environment

OpenAIRE

Park, Kyung Soo; Shin, Seung Won; Choi, Jeong-Woo; Um, Soong Ho

2013-01-01

A stem cell interacts with the neighboring cells in its environment. To maintain a living organism’s metabolism, either cell-cell or cell-environment interactions may be significant. Usually, these cells communicate with each other through biological signaling by interactive behaviors of primary proteins or complementary chemicals. The signaling intermediates offer the stem cell’s functionality on its metabolism. With the rapid advent of omics technologies, various specific markers by which s...

Transferability of molecular markers from major legumes to Lathyrus spp. for their application in mapping and diversity studies.

Science.gov (United States)

Almeida, Nuno Felipe; Trindade Leitão, Susana; Caminero, Constantino; Torres, Ana Maria; Rubiales, Diego; Vaz Patto, Maria Carlota

2014-01-01

Lathyrus cicera L. (chickling pea) and L. sativus L. (grass pea) have great potential among grain legumes due to their adaptability to inauspicious environments, high protein content and resistance to serious diseases. Nevertheless, due to its past underused, further activities are required to exploit this potential and to capitalise on the advances in molecular biology that enable improved Lathyrus spp. breeding programmes. In this study we evaluated the transferability of molecular markers developed for closely related legume species to Lathyrus spp. (Medicago truncatula, pea, lentil, faba bean and lupin) and tested the application of those new molecular tools on Lathyrus mapping and diversity studies. Genomic and expressed sequence tag microsatellite, intron-targeted amplified polymorphic, resistance gene analogue and defence-related gene markers were tested. In total 128 (27.7 %) and 132 (28.6 %) molecular markers were successfully cross-amplified, respectively in L. cicera and L. sativus. In total, the efficiency of transferability from genomic microsatellites was 5 %, and from gene-based markers, 55 %. For L. cicera, three cleaved amplified polymorphic sequence markers and one derived cleaved amplified polymorphic sequence marker based on the cross-amplified markers were also developed. Nine of those molecular markers were suitable for mapping in a L. cicera recombinant inbred line population. From the 17 molecular markers tested for diversity analysis, six (35 %) in L. cicera and seven (41 %) in L. sativus were polymorphic and discriminate well all the L. sativus accessions. Additionally, L. cicera accessions were clearly distinguished from L. sativus accessions. This work revealed a high number of transferable molecular markers to be used in current genomic studies in Lathyrus spp. Although their usefulness was higher on diversity studies, they represent the first steps for future comparative mapping involving these species.

Fiducial marker guided stereotactic liver radiotherapy: Is a time delay between marker implantation and planning CT needed?

DEFF Research Database (Denmark)

Worm, Esben S; Bertholet, Jenny; Høyer, Morten

2016-01-01

To minimize the risk of marker migration in fiducial marker guided liver SBRT it is common to add a delay of a week between marker implantation and planning CT. This study found that such a delay is unnecessary and could be avoided to minimize the treatment preparation time.......To minimize the risk of marker migration in fiducial marker guided liver SBRT it is common to add a delay of a week between marker implantation and planning CT. This study found that such a delay is unnecessary and could be avoided to minimize the treatment preparation time....

Postgraduate studies in radiation biology in Europe

International Nuclear Information System (INIS)

Trott, K.R.; Lohmann, P.H.M.; Zeeland, A.A. van; Natarajan, A.T.; Schibilla, H.; Chadwick, K.; Kellerer, A.M.; Steinhaeusler, F.

1998-01-01

The present system of radiobiological research in universities and research centres is no longer able to train radiobiologists who have a comprehensive understanding of the entire field of radiation biology including both 'classical' and molecular radiation biology. However, such experts are needed in view of the role radiation protection plays in our societies. No single institution in Europe could now run a 1-year, full-time course which covers all aspects of the radiobiological basis of radiation protection. Therefore, a cooperative action of several universities from different EU member states has been developed and is described herein. (orig.)

Mutant germplasm characterization using molecular markers. A manual

International Nuclear Information System (INIS)

2002-01-01

Plant biotechnology applications must not only respond to the challenge of improving food security and fostering socio-economic development, but in doing so, promote the conservation, diversification and sustainable use of plant genetic resources for food and agriculture. Nowadays the biotechnology toolbox available to plant breeders offers several new possibilities for increasing productivity, crop diversification and production, while developing a more sustainable agriculture. This training course focuses on one of the most promising set of techniques used in modern crop improvement programmes, i.e. on molecular markers. These are rapidly being adopted by plant breeders and molecular biologists as effective and appropriate tools for basic and applied studies addressing biological components in agricultural production systems. Their use in applied breeding programmes can range from facilitating the appropriate choice of parents for crosses, to mapping/tagging of gene blocks associated with economically important traits (often termed 'quantitative trait loci' (QTLs)). Gene tagging and QTL mapping in turn permit marker-assisted selection (MAS) in backcross, pedigree, and population improvement programmes, thereby facilitating more efficient incremental improvement of specific individual target traits. And through comparative genomics, molecular markers can be used in ways that allow us to more effectively discover and efficiently exploit biodiversity and the evolutionary relationships between organisms. Substantial progress has been made in recent years in mapping, tagging and isolating many agriculturally important genes using molecular markers due in large part to improvements in the techniques that have been developed to help find markers of interest. Among the techniques that are particularly promising are Restriction Fragment Length Polymorphism (RFLPs), Amplified Fragment Length Polymorphism (AFLPs), Random Amplified Polymorphic DNA (RAPDs), Microsatellites

Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn.

Science.gov (United States)

Cha, Thye San; Anne-Marie, Kaben; Chuah, Tse Seng

2014-02-01

Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.

Mind-body therapies and control of inflammatory biology: A descriptive review.

Science.gov (United States)

Bower, Julienne E; Irwin, Michael R

2016-01-01

The use of mind-body therapies, including Tai Chi, Qigong, yoga, and meditation, has grown steadily in recent years. These approaches have been shown to be effective in reducing symptoms and improving quality of life, and research has begun to examine the impact of these therapies on biological processes, including inflammation. A review of 26 randomized controlled trials was conducted to describe the effects of mind-body therapies (MBTs) on circulating, cellular, and genomic markers of inflammation. This qualitative evaluation showed mixed effects of MBTs on circulating inflammatory markers, including CRP and IL-6, and on measures of stimulated cytokine production. More consistent findings were seen for genomic markers, with trials showing decreased expression of inflammation-related genes and reduced signaling through the proinflammatory transcription factor NF-κB. Potential mechanisms for these effects are discussed, including alterations in neuroendocrine, neural, and psychological and behavioral processes. Copyright © 2015 Elsevier Inc. All rights reserved.

Radiopaque anastomosis marker

International Nuclear Information System (INIS)

Elliott, D.P.; Halseth, W.L.

1977-01-01

This invention relates to split ring markers fabricated in whole or in part from a radiopaque material, usually metal, having the terminal ends thereof and a medial portion formed to define eyelets by means of which said marker can be sutured to the tissue at the site of an anastomosis to provide a visual indication of its location when examined fluoroscopically

Self-interest and Altruism: Pluralism as a Basis for Leadership in Business

OpenAIRE

Jay Joseph

2015-01-01

The paper outlines the case for pluralism between self-interest (egoism) and altruism in business leadership. Scientific progression demonstrating pluralism is discussed, providing a multidisciplinary view of pluralism from evolutionary biology, psychology, moral philosophy, economic theory and organisational behavior. Findings show that myopic views of self-interest and altruism were once dominant in a number of fields however shifts in contemporary theory have provided a basis for pluralism...

Development and application of sequence-tagged microsatellite site (STMS) markers in chickpea (Cicer arietinum), banana (Musa spp.) and their major pathogens, Ascochyta rabiei and Mycosphaerella fijiensis

International Nuclear Information System (INIS)

Winter, P.; Kaemmer, D.; Paff, T.; Geistlinger, J.; Neu, C.; Kahl, G.

2001-01-01

DNA markers of various kinds have found widespread application in many facets of plant breeding and plant pathogen control. Yet another marker type, sequence-tagged microsatellite (STMS) markers, provides the markers of choice for nearly every crop because of their co-dominant nature, reliability, ease of application and high polymorphic information content. We report here on the development of a whole set of STMS markers and the respective, selected primer sequences for two important crops, chickpea (Cicer arietinum L.) and banana (Musa acuminata), and for their most devastating fungal pathogens, Ascochyta rabiei and Mycosphaerella fijiensis, respectively. These markers were generated either by direct screening of size-selected genomic libraries with microsatellite-complementary oligonucleotides, or by enrichment of DNA fragments containing microsatellite sequences. A total of 69 markers for chickpea, 15 markers for M. acuminata, 19 markers for A rabiei and 11 markers for M. fijiensis, selected on the basis of their high information content and ease of use are presented here. These can be applied for mapping of the respective genomes, for various population studies, and cultivar and isolate identification. We further demonstrate that several of these markers can potentially be applied across species boundaries and thus could increase the marker repertoire also for other species of the genus Cicer, Musa and for Ascochyta-type pathogens of bean, and potentially also of lentil and pea. (author)

Frameworking memory and serotonergic markers.

Science.gov (United States)

Meneses, Alfredo

2017-07-26

The evidence for neural markers and memory is continuously being revised, and as evidence continues to accumulate, herein, we frame earlier and new evidence. Hence, in this work, the aim is to provide an appropriate conceptual framework of serotonergic markers associated with neural activity and memory. Serotonin (5-hydroxytryptamine [5-HT]) has multiple pharmacological tools, well-characterized downstream signaling in mammals' species, and established 5-HT neural markers showing new insights about memory functions and dysfunctions, including receptors (5-HT1A/1B/1D, 5-HT2A/2B/2C, and 5-HT3-7), transporter (serotonin transporter [SERT]) and volume transmission present in brain areas involved in memory. Bidirectional influence occurs between 5-HT markers and memory/amnesia. A growing number of researchers report that memory, amnesia, or forgetting modifies neural markers. Diverse approaches support the translatability of using neural markers and cerebral functions/dysfunctions, including memory formation and amnesia. At least, 5-HT1A, 5-HT4, 5-HT6, and 5-HT7 receptors and SERT seem to be useful neural markers and therapeutic targets. Hence, several mechanisms cooperate to achieve synaptic plasticity or memory, including changes in the expression of neurotransmitter receptors and transporters.

The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes.

Science.gov (United States)

Urantowka, Adam Dawid; Kroczak, Aleksandra; Mackiewicz, Paweł

2017-07-14

Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods. Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in

Pedigrees or markers: Which are better in estimating relatedness and inbreeding coefficient?

Science.gov (United States)

Wang, Jinliang

2016-02-01

Individual inbreeding coefficient (F) and pairwise relatedness (r) are fundamental parameters in population genetics and have important applications in diverse fields such as human medicine, forensics, plant and animal breeding, conservation and evolutionary biology. Traditionally, both parameters are calculated from pedigrees, but are now increasingly estimated from genetic marker data. Conceptually, a pedigree gives the expected F and r values, FP and rP, with the expectations being taken (hypothetically) over an infinite number of individuals with the same pedigree. In contrast, markers give the realised (actual) F and r values at the particular marker loci of the particular individuals, FM and rM. Both pedigree (FP, rP) and marker (FM, rM) estimates can be used as inferences of genomic inbreeding coefficients FG and genomic relatedness rG, which are the underlying quantities relevant to most applications (such as estimating inbreeding depression and heritability) of F and r. In the pre-genomic era, it was widely accepted that pedigrees are much better than markers in delineating FG and rG, and markers should better be used to validate, amend and construct pedigrees rather than to replace them. Is this still true in the genomic era when genome-wide dense SNPs are available? In this simulation study, I showed that genomic markers can yield much better estimates of FG and rG than pedigrees when they are numerous (say, 10(4) SNPs) under realistic situations (e.g. genome and population sizes). Pedigree estimates are especially poor for species with a small genome, where FG and rG are determined to a large extent by Mendelian segregations and may thus deviate substantially from their expectations (FP and rP). Simulations also confirmed that FM, when estimated from many SNPs, can be much more powerful than FP for detecting inbreeding depression in viability. However, I argue that pedigrees cannot be replaced completely by genomic SNPs, because the former allows for

The use of ovarian reserve markers in IVF clinical practice: a national consensus.

Science.gov (United States)

La Marca, Antonio; Ferraretti, Anna Pia; Palermo, Roberto; Ubaldi, Filippo M

2016-01-01

Ovarian reserve markers have been documented to perform very well in the clinical practice. While this is widely recognized, still now there is no consensus on how to use new biomarkers in the clinical practice. This study was conducted among Italian IVF centres using the Delphi technique, a validated consensus-building process. Briefly three consecutive questionnaires were developed for clinicians in charge of IVF centres. In the first rounds, participants were asked to rate the importance of a list of statements regarding the categorization of ovarian response and the diagnostic role of biomarkers. In round 3, participants were asked to rate their agreement and consensus on the list of statements derived from the first two rounds. There were 120 respondents. Consensus was achieved for many points: (a) poor ovarian response is predicted on the basis of the following: AMH  3 ng/ml or AFC > 14; (c) day 3 FSH measurement should always be associated to estradiol; (d) AMH can be measured on a random basis; (e) the measurement of the AFC with the 2D technology may be considered adequate and (f) the AFC should be measured in the early follicular phase and consists in the total number of 2-9 mm follicles in both the ovaries. The present study suggests that extensive consensus on the importance and use of new ovarian reserve markers to improve IVF safety and performance is already present among clinicians.

Using the logical basis of phylogenetics as the framework for teaching biology

Directory of Open Access Journals (Sweden)

Charles Morphy D. Santos

2008-01-01

Full Text Available The influence of the evolutionary theory is widespread in modern worldview. Due to its great explanatory power and pervasiveness, the theory of evolution should be used as the organizing theme in biology teaching. For this purpose, the essential concepts of phylogenetic systematics are useful as a didactic instrument. The phylogenetic method was the first objective set of rules to implement in systematics the evolutionary view that the organisms are all connected at some hierarchical level due to common ancestry, as suggested by Darwin and Wallace. Phylogenetic systematics was firstly proposed by the German Entomologist Willi Hennig in 1950 and had considerably importance in the decrease of the role of essentialism and subjectivity in classificatory studies, becoming one of the paradigms in biological systematics. Based on cladograms, a general phylogenetic reference system allows to the depiction and representation of large amounts of biological information in branching diagrams. Besides, the phylogenetic approach sheds light upon typical misconceptions concerning evolution and related concepts that directly affect students' comprehension about the evolutionary process and the hierarchical structure of the living world. The phylogenetic method is also a form of introducing students to some of the philosophical and scientific idiosyncrasies, providing them the ability to understand concepts such as hypothesis, theory, paradigm and falsifiability. The students are incited to use arguments during the process of accepting or denying scientific hypotheses, which overcomes the mere assimilation of knowledge previously elaborated.A influência da teoria evolutiva é disseminada na visão de mundo moderna. Devido a seu grande poder explanatório e penetração, a teoria da evolução deve ser usada como o tema organizador do ensino de biologia. Para esse propósito, os conceitos essenciais da sistemática filogenética são úteis como instrumentos did

System requirements and design description for the document basis database interface (DocBasis)

International Nuclear Information System (INIS)

Lehman, W.J.

1997-01-01

This document describes system requirements and the design description for the Document Basis Database Interface (DocBasis). The DocBasis application is used to manage procedures used within the tank farms. The application maintains information in a small database to track the document basis for a procedure, as well as the current version/modification level and the basis for the procedure. The basis for each procedure is substantiated by Administrative, Technical, Procedural, and Regulatory requirements. The DocBasis user interface was developed by Science Applications International Corporation (SAIC)

The diagnostic value of preoperative inflammatory markers in craniopharyngioma: a multicenter cohort study.

Science.gov (United States)

Chen, Ming; Zheng, Shi-Hao; Yang, Min; Chen, Zhi-Hua; Li, Shi-Ting

2018-05-01

To compare the different levels of preoperative inflammatory markers in peripheral blood samples between craniopharyngioma (CP) and other sellar region tumors so as to explore their differential diagnostic value. The level of white blood cell (WBC), neutrophil, lymphocyte, monocyte, platelet, albumin, neutrophil lymphocyte ratio (NLR), derived NLR (dNLR), platelet lymphocyte ratio (PLR), monocyte lymphocyte ratio (MLR) and prognostic nutritional index (PNI) were compared between the CP and other sellar region tumors. A receiver operating characteristics (ROC) curve analysis was performed to evaluate the diagnostic significance of the peripheral blood inflammatory markers and their paired combinations for CP including its pathological types. Patients with CP had higher levels of pre-operative WBC, lymphocyte and PNI. The papillary craniopharyngioma (PCP) group had higher neutrophil count and NLR than the adamantinomatous craniopharyngioma (ACP) and healthy control groups whereas the ACP group had higher platelet count and PNI than the PCP and healthy control groups. There were not any significant differences in preoperative inflammatory markers between the primary and recurrent CP groups. The AUC values of WBC, neutrophil, NLR + PLR and dNLR + PLR in PCP were all higher than 0.7. Inflammation seems to be closely correlated with CP's development. The preoperative inflammatory markers including WBC, neutrophil, NLR + PLR and dNLR + PLR may differentially diagnose PCP, pituitary tumor (PT) and Rathke cleft cyst (RCC). In addition, some statistical results in this study indirectly proved previous experimental conclusions and strictly matched CP's biological features.

Myxozoans as biological tags for stock identification of the Argentine hake, Merluccius hubbsi (Gadiformes: Merlucciidae)

Czech Academy of Sciences Publication Activity Database

Cantatore, D.M.P.; Irigoitia, M.M.; Holzer, Astrid S.; Timi, J.T.

2016-01-01

Roč. 143, č. 6 (2016), s. 732-740 ISSN 0031-1820 Institutional support: RVO:60077344 Keywords : biological markers * Kudoa rosenbuschi * Myxoproteus meridionalis * Fabespora sp. * common hake * stock discrimination * South West Atlantic Subject RIV: EH - Ecology, Behaviour Impact factor: 2.713, year: 2016

[Differential diagnosis of primary and secondary mathematical learning disability – indications from the dyscalculia test Basis-Math 4–8].

Science.gov (United States)

Krinzinger, Helga

2016-09-01

Studies in children with AD(H)D without mathematical learning disability (MLD) as well as studies on the effects of methylphenidate on arithmetic have shown that most deficits in mathematics and most error types commonly described as specific to developmental dyscalculia (e. g., finger-counting, fact-retrieval deficit, complex counting, difficulties with carry/borrow procedures, self-corrections) cannot be classified as such and should thus not be used for the differential diagnosis of primary dyscalculia and secondary MLD. This article proposes using the overall score in the dyscalculia test Basis-Math 4-8 (Moser Opitz et al., 2010) as well as implausible subtraction errors as a marker for dyscalculia and the number of self-corrections made during the test as a cognitive marker for attention deficits. Hierarchical cluster analyses were calculated in a sample of 51 clinically referred children with normal IQ and suspicion of MLD, using IQ, years of schooling, overall score of the Basis-Math 4–8 and number of self-corrections in this test as variables. The results revealed a subgroup with primary dyscalculia as well as three subgroups with secondary MLD (two with attention deficit hyperactivity disorder, one with depression and one small subgroup with high IQ). In conclusion, the Basis-Math 4–8 (Moser Opitz et al., 2010) can offer substantial information for the differential diagnosis of dyscalculia and secondary deficits in mathematics due to attention problems and enable optimization of treatment decisions for the different groups.

Biologically inspired technologies in NASA's morphing project

Science.gov (United States)

McGowan, Anna-Maria R.; Cox, David E.; Lazos, Barry S.; Waszak, Martin R.; Raney, David L.; Siochi, Emilie J.; Pao, S. Paul

2003-07-01

For centuries, biology has provided fertile ground for hypothesis, discovery, and inspiration. Time-tested methods used in nature are being used as a basis for several research studies conducted at the NASA Langley Research Center as a part of Morphing Project, which develops and assesses breakthrough vehicle technologies. These studies range from low drag airfoil design guided by marine and avian morphologies to soaring techniques inspired by birds and the study of small flexible wing vehicles. Biology often suggests unconventional yet effective approaches such as non-planar wings, dynamic soaring, exploiting aeroelastic effects, collaborative control, flapping, and fibrous active materials. These approaches and other novel technologies for future flight vehicles are being studied in NASA's Morphing Project. This paper will discuss recent findings in the aeronautics-based, biologically-inspired research in the project.

Early bichemical markers of effects: Enzyme induction, oncogene activation and markers of oxidative damage

DEFF Research Database (Denmark)

Poulsen, Henrik E.; Loft, Steffen

1995-01-01

Early bichemical marker, enzyme induction, oncogene activation, oxidative damage, low-density lipoprotein......Early bichemical marker, enzyme induction, oncogene activation, oxidative damage, low-density lipoprotein...

Controllability and observability of Boolean networks arising from biology

Science.gov (United States)

Li, Rui; Yang, Meng; Chu, Tianguang

2015-02-01

Boolean networks are currently receiving considerable attention as a computational scheme for system level analysis and modeling of biological systems. Studying control-related problems in Boolean networks may reveal new insights into the intrinsic control in complex biological systems and enable us to develop strategies for manipulating biological systems using exogenous inputs. This paper considers controllability and observability of Boolean biological networks. We propose a new approach, which draws from the rich theory of symbolic computation, to solve the problems. Consequently, simple necessary and sufficient conditions for reachability, controllability, and observability are obtained, and algorithmic tests for controllability and observability which are based on the Gröbner basis method are presented. As practical applications, we apply the proposed approach to several different biological systems, namely, the mammalian cell-cycle network, the T-cell activation network, the large granular lymphocyte survival signaling network, and the Drosophila segment polarity network, gaining novel insights into the control and/or monitoring of the specific biological systems.

Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast.

Science.gov (United States)

Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

2015-06-01

To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences.

Association between Urinary Excretion of Cortisol and Markers of Oxidatively Damaged DNA and RNA in Humans

DEFF Research Database (Denmark)

Joergensen, Anders; Broedbaek, Kasper; Weimann, Allan

2011-01-01

Chronic psychological stress is associated with accelerated aging, but the underlying biological mechanisms are not known. Prolonged elevations of the stress hormone cortisol is suspected to play a critical role. Through its actions, cortisol may potentially induce oxidatively generated damage...... to cellular constituents such as DNA and RNA, a phenomenon which has been implicated in aging processes. We investigated the relationship between 24 h excretion of urinary cortisol and markers of oxidatively generated DNA and RNA damage, 8-oxo-7,8-dihydro-2'-deoxyguanosine and 8-oxo-7,8-dihydroguanosine......, in a sample of 220 elderly men and women (age 65 - 83 years). We found a robust association between the excretion of cortisol and the oxidation markers (R(2)¿=¿0.15, P...

GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses.

Science.gov (United States)

Fredslund, Jakob; Madsen, Lene H; Hougaard, Birgit K; Sandal, Niels; Stougaard, Jens; Bertioli, David; Schauser, Leif

2006-07-01

The web program GeMprospector (URL: http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main) allows users to automatically design large sets of cross-species genetic marker candidates targeting either legumes or grasses. The user uploads a collection of ESTs from one or more legume or grass species, and they are compared with a database of clusters of homologous EST and genomic sequences from other legumes or grasses, respectively. Multiple sequence alignments between submitted ESTs and their homologues in the appropriate database form the basis of automated PCR primer design in conserved exons such that each primer set amplifies an intron. The only user input is a collection of ESTs, not necessarily from more than one species, and GeMprospector can boost the potential of such an EST collection by combining it with a large database to produce cross-species genetic marker candidates for legumes or grasses.

New Hypothesis and Theory about Functions of Sleep and Dreams

Directory of Open Access Journals (Sweden)

Nikola N. Ilanković

2014-03-01

Conclusion: IEP-P1 could be a new biological marker to distinction of sleep organization in different psychotic states and other states of altered consciousness. The developed statistical models could be the basis for new hypothesis and theories about functions of sleep and dreams.

Marker based standardization of polyherbal formulation (SJT-DI-02 by high performance thin layer chromatography method

Directory of Open Access Journals (Sweden)

Bhakti J Ladva

2014-01-01

Full Text Available Background: Preparation of highly standardized herbal products with respect to chemical composition and biological activity is considered to be a valuable approach in this field. SJT-DI-02 polyherbal formulation was successfully developed at our institute and filed for patent at Mumbai patent office. Objective: The present work was marker based standardization of patented, novel and efficacious polyherbal formulation namely SJT-DI-02 for the treatment of diabetes. The SJT-DI-02 was comprised of dried extracts of rhizomes of Acorus calamus, leaves of Aegle marmelose, fruits of Benincasa hispida, roots of Chlorophytum arendinaceum, seeds of Eugenia jambolana, leaves of Ocimum sanctum, pericarp of Punica granatum, seeds of Tamarindus indica. Selected plants were collected, dried and extracted with suitable solvents. The formulation was prepared by mixing different fractions of extracts. Materials and Methods: For successful and best standardization, first of all selection and procurement was carried out. Selection is done on the basis of therapeutic efficacy and amount of the marker present in the particular plant part. At the time of procurement side by side phytochemical screening and estimation of phytoconstituents was carried out. After completion of preliminary screening using characterized markers, we tried to develop best TLC systems using selected solvent composition. Finally well-developed TLC systems were applied in HPTLC. In the present study polyherbal formulation was standardized by using different four markers. TLC Densitometric methods were developed using HPTLC for the quantification of these marker compounds. Solvent systems were optimized to achieve best resolution of the marker compounds from other components of the sample extract. The identity of the bands in the sample extracts were confirmed by comparing the Rf and the absorption spectra by overlaying their UV absorption spectra with those of their respective standards. The

ALDH1A3: A Marker of Mesenchymal Phenotype in Gliomas Associated with Cell Invasion.

Directory of Open Access Journals (Sweden)

Wenlong Zhang

Full Text Available Aldehyde dehydrogenases (ALDH is a family of enzymes including 19 members. For now, ALDH activity had been wildly used as a marker of cancer stem cells (CSCs. But biological functions of relevant isoforms and their clinical applications are still controversial. Here, we investigate the clinical significance and potential function of ALDH1A3 in gliomas. By whole-genome transcriptome microarray and mRNA sequencing analysis, we compared the expression of ALDH1A3 in high- and low- grade gliomas as well as different molecular subtypes. Microarray analysis was performed to identify the correlated genes of ALDH1A3. We further used Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways analysis to explore the biological function of ALDH1A3. Finally, by mRNA knockdown we revealed the relationship between ALDH1A3 and the ability of tumor invasion. ALDH1A3 overexpression was significantly associated with high grade as well as the higher mortality of gliomas in survival analysis. ALDH1A3 was characteristically highly expressed in Mesenchymal (Mes subtype gliomas. Moreover, we found that ALDH1A3 was most relevant to extracellular matrix organization and cell adhesion biological process, and the ability of tumor invasion was suppressed after ALDH1A3 knockdown in vitro. In conclusion, ALDH1A3 can serve as a novel marker of Mes phenotype in gliomas with potential clinical prognostic value. The expression of ALDH1A3 is associated with tumor cell invasion.

Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.

Directory of Open Access Journals (Sweden)

Humira Sonah

Full Text Available Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice and dicots (Arabidopsis, Medicago and Populus was performed. A total of 797,863 simple sequence repeats (SSRs were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database 'BraMi' (Brachypodium microsatellite markers of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot-dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium

Receptor studies in biological psychiatry

International Nuclear Information System (INIS)

Fujiwara, Yutaka

1992-01-01

Recent advances in the pharmacological treatment of endogenous psychosis have led to the development of biological studies in psychiatry. Studies on neurotransmitter receptors were reviewed in order to apply positron-emission tomograph (PET) for biological psychiatry. The dopamine (DA) hypothesis for schizophrenia was advanced on the basis of the observed effects of neuroleptics and methamphetamine, and DA(D 2 ) receptor supersensitivity measured by PET and receptor binding in the schizophrenic brain. The clinical potencies of neuroleptics for schizophrenia were correlated with their abilities to inhibit the D 2 receptor, and not other receptors. The σ receptor was expected to be a site of antipsychotic action. However, the potency of drugs action on it was not correlated with clinical efficacy. Haloperidol binds with high affinity to the σ receptor, which may mediate acute dystonia, an extrapyramidal side effect of neuroleptics. Behavioral and neurochemical changes induced by methamphetamine treatment were studied as an animal model of schizophrenia, and both a decrease of D 2 receptor density and an increase of DA release were detected. The monoamine hypothesis for manic-depressive psychosis was advanced on the basis of the effect of reserpine, monoamine oxidase inhibitor and antidepressants. 3 H-clonidine binding sites were increased in platelet membranes of depressive patients, 3 H-imipramine binding sites were decreased. The GABA A receptor is the target site for the action of anxiolytics and antiepileptics such as benzodiazepines and barbiturates. Recent developments in molecular biology techniques have revealed the structure of receptor proteins, which are classified into two receptor families, the G-protein coupled type (D 2 ) and the ion-channel type (GABA A ). (J.P.N.)

The relation between histological, tumor-biological and clinical parameters in deep and superficial leiomyosarcoma and leiomyoma.

NARCIS (Netherlands)

Pijpe, Justin; Broers, Gerben H Torn; Plaat, Boudewijn E Ch; Hundeiker, M; Otto, F; Mastik, Mirjam F; Hoekstra, Harald J; Graaf, Winette T A van der; van den Berg, Eva; Molenaar, Willemina M

2002-01-01

Purpose: Leiomyosarcomas (LMS) of deep and superficial tissues were examined to identify prognostic markers explaining their different biological behaviour and to define differences between cutaneous and subcutaneous LMS. LMS and leiomyomas (LM) of the skin were compared to and consistent

Using genetic markers to orient the edges in quantitative trait networks: the NEO software.

Science.gov (United States)

Aten, Jason E; Fuller, Tova F; Lusis, Aldons J; Horvath, Steve

2008-04-15

Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting the edges of a trait network. The availability of hundreds of thousands of genetic markers poses new challenges: how to relate (anchor) traits to multiple genetic markers, how to score the genetic evidence in favor of an edge orientation, and how to weigh the information from multiple markers. We develop and implement Network Edge Orienting (NEO) methods and software that address the challenges of inferring unconfounded and directed gene networks from microarray-derived gene expression data by integrating mRNA levels with genetic marker data and Structural Equation Model (SEM) comparisons. The NEO software implements several manual and automatic methods for incorporating genetic information to anchor traits. The networks are oriented by considering each edge separately, thus reducing error propagation. To summarize the genetic evidence in favor of a given edge orientation, we propose Local SEM-based Edge Orienting (LEO) scores that compare the fit of several competing causal graphs. SEM fitting indices allow the user to assess local and overall model fit. The NEO software allows the user to carry out a robustness analysis with regard to genetic marker selection. We demonstrate the utility of NEO by recovering known causal relationships in the sterol homeostasis pathway using liver gene expression data from an F2 mouse cross. Further, we use NEO to study the relationship between a disease gene and a biologically important gene co-expression module in liver tissue. The NEO software can be used to orient the edges of gene co-expression networks or quantitative trait

Biological origins of color categorization.

Science.gov (United States)

Skelton, Alice E; Catchpole, Gemma; Abbott, Joshua T; Bosten, Jenny M; Franklin, Anna

2017-05-23

The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants' categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mapped infants' categorical recognition memory for hue onto a stimulus array used previously to document the color lexicons of 110 nonindustrialized languages. Following familiarization to a given hue, infants' response to a novel hue indicated that their recognition memory parses the hue continuum into red, yellow, green, blue, and purple categories. Infants' categorical distinctions aligned with common distinctions in color lexicons and are organized around hues that are commonly central to lexical categories across languages. The boundaries between infants' categorical distinctions also aligned, relative to the adaptation point, with the cardinal axes that describe the early stages of color representation in retinogeniculate pathways, indicating that infant color categorization may be partly organized by biological mechanisms of color vision. The findings suggest that color categorization in language and thought is partially biologically constrained and have implications for broader debate on how biology, culture, and communication interact in human cognition.

A small population of resident limb bud mesenchymal cells express few MSC-associated markers, but the expression of these markers is increased immediately after cell culture.

Science.gov (United States)

Marín-Llera, Jessica Cristina; Chimal-Monroy, Jesús

2018-05-01

Skeletal progenitors are derived from resident limb bud mesenchymal cells of the vertebrate embryos. However, it remains poorly understood if they represent stem cells, progenitors, or multipotent mesenchymal stromal cells (MSC). Derived-MSC of different adult tissues under in vitro experimental conditions can differentiate into the same cellular lineages that are present in the limb. Here, comparing non-cultured versus cultured mesenchymal limb bud cells, we determined the expression of MSC-associated markers, the in vitro differentiation capacity and their gene expression profile. Results showed that in freshly isolated limb bud mesenchymal cells, the proportion of cells expressing Sca1, CD44, CD105, CD90, and CD73 is very low and a low expression of lineage-specific genes was observed. However, recently seeded limb bud mesenchymal cells acquired Sca1 and CD44 markers and the expression of the key differentiation genes Runx2 and Sox9, while Scx and Pparg genes decreased. Also, their chondrogenic differentiation capacity decreased through cellular passages while the osteogenic increased. Our findings suggest that the modification of the cell adhesion process through the in vitro method changed the limb mesenchymal cell immunophenotype leading to the expression and maintenance of common MSC-associated markers. These findings could have a significant impact on MSC study and isolation strategy because they could explain common variations observed in the MSC immunophenotype in different tissues. © 2018 International Federation for Cell Biology.

26 CFR 1.1014-4 - Uniformity of basis; adjustment to basis.

Science.gov (United States)

2010-04-01

...) INCOME TAX (CONTINUED) INCOME TAXES Basis Rules of General Application § 1.1014-4 Uniformity of basis... to property acquired by bequest, devise, or inheritance relate back to the death of the decedent... prescribing a general uniform basis rule for property acquired from a decedent is, on the one hand, to tax the...

Individualization of controlled ovarian stimulation in vitro fertilization using ovarian reserve markers.

Science.gov (United States)

Grisendi, Valentina; La Marca, Antonio

2017-06-01

In assisted reproduction technologies (ART) the controlled ovarian stimulation (COS) therapy is the starting point from which a good oocytes retrieval depends. Treatment individualization is based on ovarian response prediction, which largely depends on a woman's ovarian reserve. Anti-Müllerian hormone (AMH) and antral follicle count (AFC) are considered the most accurate and reliable markers of ovarian reserve. A literature search was carried out for studies that addressed the ability of AMH and AFC to predict poor and/or excessive ovarian response in IVF cycles. According to the predicted response to ovarian stimulation (poor- normal- or high-response) is today possible not only to personalize pre-treatment counseling with the couple, but also to individualize the ovarian stimulation protocol, choosing among GnRH-agonists or antagonists for endogenous follicle-stimulating hormone (FSH) suppression and formulating the FSH starting dose most adequate for the single patients. In this review we discuss how to choose the best COS therapy for the single patient, on the basis of the markers-guided ovarian response prediction.

Biological Roles of Aberrantly Expressed Glycosphingolipids and Related Enzymes in Human Cancer Development and Progression

Directory of Open Access Journals (Sweden)

Dinghao Zhuo

2018-05-01

Full Text Available Glycosphingolipids (GSLs, which consist of a hydrophobic ceramide backbone and a hydrophilic carbohydrate residue, are an important type of glycolipid expressed in surface membranes of all animal cells. GSLs play essential roles in maintenance of plasma membrane stability, in regulation of numerous cellular processes (including adhesion, proliferation, apoptosis, and recognition, and in modulation of signal transduction pathways. GSLs have traditionally been classified as ganglio-series, lacto-series, or globo-series on the basis of their diverse types of oligosaccharide chains. Structures and functions of specific GSLs are also determined by their oligosaccharide chains. Different cells and tissues show differential expression of GSLs, and changes in structures of GSL glycan moieties occur during development of numerous types of human cancer. Association of GSLs and/or related enzymes with initiation and progression of cancer has been documented in 100s of studies, and many such GSLs are useful markers or targets for cancer diagnosis or therapy. In this review, we summarize (i recent studies on aberrant expression and distribution of GSLs in common human cancers (breast, lung, colorectal, melanoma, prostate, ovarian, leukemia, renal, bladder, gastric; (ii biological functions of specific GSLs in these cancers.

76 FR 72724 - Advisory Committee For Biological Sciences; Notice of Meeting

Science.gov (United States)

2011-11-25

... Science Foundation, 4201 Wilson Blvd., Arlington, VA 22230. Type of Meeting: Open. Contact Person: Chuck... research that is the basis for the 21st century bio-economy and the undergraduate and graduate biology...

Mathematics, structuralism and biology.

Science.gov (United States)

Saunders, P T

1988-01-01

A new approach is gaining ground in biology, one that has much in common with the structuralist tradition in other fields. It is very much in the spirit of an earlier view of biology and indeed of science in general. It is also, though this is not generally recognized, in the spirit of twentieth century physics. As in modern physics, however, it is not a question of ignoring all the progress that has been made within the former paradigm. On the contrary, the aim is to use it as a basis for setting out in a somewhat different direction. Complex phenomena do not generally lend themselves to reductionist analyses which seek explanation only in terms of detailed mechanisms, but a proper scientific discussion of structure must make full use of what we have already learned - by whatever means - about the processes that underly the phenomena we are trying to understand.

Peripheral blood and neuropsychological markers for the onset of action of antidepressant drugs in patients with Major Depressive Disorder

Directory of Open Access Journals (Sweden)

Hiemke Christoph

2011-01-01

Full Text Available Abstract Background In Major Depressive Disorder (MDD, treatment outcomes with currently available strategies are often disappointing. Therefore, it is sensible to develop new strategies to increase remission rates in acutely depressed patients. Many studies reported that true drug response can be observed within 14 days (early improvement of antidepressant treatment. The identical time course of symptom amelioration after early improvement in patients treated with antidepressants of all classes or with placebo strongly suggests a common biological mechanism, which is not specific for a particular antidepressant medication. However, the biology underlying early improvement and final treatment response is not understood and there is no established biological marker as yet, which can predict treatment response for the individual patient before initiation or during the course of antidepressant treatment. Peripheral blood markers and executive functions are particularly promising candidates as markers for the onset of action and thus the prediction of final treatment outcome in MDD. Methods/Design The present paper presents the rationales, objectives and methods of a multi-centre study applying close-meshed repetitive measurements of peripheral blood and neuropsychological parameters in patients with MDD and healthy controls during a study period of eight weeks for the identification of biomarkers for the onset of antidepressants' action in patients with MDD. Peripheral blood parameters and depression severity are assessed in weekly intervals from baseline to week 8, executive performance in bi-weekly intervals. Patients are participating in a randomized controlled multi-level clinical trial, healthy controls are matched according to mean age, sex and general intelligence. Discussion This investigation will help to identify a biomarker or a set of biomarkers with decision-making quality in the treatment of MDD in order to increase the currently

Why we cannot conclude that sexual orientation is primarily a biological phenomenon.

Science.gov (United States)

Byne, W

1997-01-01

While all mental phenomena must have an ultimate biological substrate, the precise contribution of biological factors to the development of sexual orientation remains to be elucidated. Does biology merely provide the slate of neural circuitry upon which sexual orientation is inscribed by experience? Do biological factors directly wire the brain so that it will support a particular orientation? Or do biological factors influence sexual orientation only indirectly, perhaps by influencing personality variables that in turn influence how one interacts with and shapes the environment as it contributes to the social relationships and experiences that shape sexual orientation as it emerges developmentally? Recent neurostructural and genetic linkage evidence pertaining to sexual orientation must be viewed tentatively until it has been adequately corroborated and integrated with psychological and cultural models. Moreover, even a reliable and robust correlation between a biological marker and sexual orientation would be equally compatible with the second and third possibilities delineated above. Yet if the third possibility more closely approximates reality, the search for predisposing biological factors will result in incomplete and misleading findings until their interactions with environmental factors are taken into account and controlled for in adequate longitudinal studies.

Genome-Wide Development of MicroRNA-Based SSR Markers in Medicago truncatula with Their Transferability Analysis and Utilization in Related Legume Species.

Science.gov (United States)

Min, Xueyang; Zhang, Zhengshe; Liu, Yisong; Wei, Xingyi; Liu, Zhipeng; Wang, Yanrong; Liu, Wenxian

2017-11-18

Microsatellite (simple sequence repeats, SSRs) marker is one of the most widely used markers in marker-assisted breeding. As one type of functional markers, MicroRNA-based SSR (miRNA-SSR) markers have been exploited mainly in animals, but the development and characterization of miRNA-SSR markers in plants are still limited. In the present study, miRNA-SSR markers for Medicago truncatula ( M. truncatula ) were developed and their cross-species transferability in six leguminous species was evaluated. A total of 169 primer pairs were successfully designed from 130 M. truncatula miRNA genes, the majority of which were mononucleotide repeats (70.41%), followed by dinucleotide repeats (14.20%), compound repeats (11.24%) and trinucleotide repeats (4.14%). Functional classification of SSR-containing miRNA genes showed that all targets could be grouped into three Gene Ontology (GO) categories: 17 in biological process, 11 in molecular function, and 14 in cellular component. The miRNA-SSR markers showed high transferability in other six leguminous species, ranged from 74.56% to 90.53%. Furthermore, 25 Mt - miRNA-SSR markers were used to evaluate polymorphisms in 20 alfalfa accessions, and the polymorphism information content (PIC) values ranged from 0.39 to 0.89 with an average of 0.71, the allele number per marker varied from 3 to 18 with an average of 7.88, indicating a high level of informativeness. The present study is the first time developed and characterized of M. truncatula miRNA-SSRs and demonstrated their utility in transferability, these novel markers will be valuable for genetic diversity analysis, marker-assisted selection and genotyping in leguminous species.

Development and validation of genic-SSR markers in sesame by RNA-seq.

Science.gov (United States)

Zhang, Haiyang; Wei, Libin; Miao, Hongmei; Zhang, Tide; Wang, Cuiying

2012-07-16

Sesame (Sesamum indicum L.) is one of the most important oil crops; however, a lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of samples from different sesame growth and developmental stages, and mining of genic-SSR markers to identify valuable markers for sesame molecular genetics research. In this study, 75 bp and 100 bp paired-end RNA-seq was used to sequence 24 cDNA libraries, and 42,566 uni-transcripts were assembled from more than 260 million filtered reads. The total length of uni-transcript sequences was 47.99 Mb, and 7,324 SSRs (SSRs ≥15 bp) and 4,440 SSRs (SSRs ≥18 bp) were identified. On average, there was one genic-SSR per 6.55 kb (SSRs ≥15 bp) or 10.81 kb (SSRs ≥18 bp). Among perfect SSRs (≥18 bp), di-nucleotide motifs (48.01%) were the most abundant, followed by tri- (20.96%), hexa- (25.37%), penta- (2.97%), tetra- (2.12%), and mono-nucleotides (0.57%). The top four motif repeats were (AG/CT)n [1,268 (34.51%)], (CA/TG)n [281 (7.65%)], (AT/AT)n [215 (5.85%)], and (GAA/TTC)n [131 (3.57%)]. A total of 2,164 SSR primer pairs were identified in the 4,440 SSR-containing sequences (≥18 bp), and 300 SSR primer pairs were randomly chosen for validation. These SSR markers were amplified and validated in 25 sesame accessions (24 cultivated accessions, one wild species). 276 (92.0%) primer pairs yielded PCR amplification products in 24 cultivars. Thirty two primer pairs (11.59%) exhibited polymorphisms. Moreover, 203 primer pairs (67.67%) yielded PCR amplicons in the wild accession and 167 (60.51%) were polymorphic between species. A UPGMA dendrogram based on genetic similarity coefficients showed that the correlation between genotype and geographical source was low and that the genetic basis of sesame in China is narrow, as previously reported. The 32 polymorphic primer pairs were validated using an F2 mapping population; 18 primer pairs exhibited polymorphisms between the parents, and 14

A systems biology-based classifier for hepatocellular carcinoma diagnosis.

Directory of Open Access Journals (Sweden)

Yanqiong Zhang

Full Text Available AIM: The diagnosis of hepatocellular carcinoma (HCC in the early stage is crucial to the application of curative treatments which are the only hope for increasing the life expectancy of patients. Recently, several large-scale studies have shed light on this problem through analysis of gene expression profiles to identify markers correlated with HCC progression. However, those marker sets shared few genes in common and were poorly validated using independent data. Therefore, we developed a systems biology based classifier by combining the differential gene expression with topological features of human protein interaction networks to enhance the ability of HCC diagnosis. METHODS AND RESULTS: In the Oncomine platform, genes differentially expressed in HCC tissues relative to their corresponding normal tissues were filtered by a corrected Q value cut-off and Concept filters. The identified genes that are common to different microarray datasets were chosen as the candidate markers. Then, their networks were analyzed by GeneGO Meta-Core software and the hub genes were chosen. After that, an HCC diagnostic classifier was constructed by Partial Least Squares modeling based on the microarray gene expression data of the hub genes. Validations of diagnostic performance showed that this classifier had high predictive accuracy (85.88∼92.71% and area under ROC curve (approximating 1.0, and that the network topological features integrated into this classifier contribute greatly to improving the predictive performance. Furthermore, it has been demonstrated that this modeling strategy is not only applicable to HCC, but also to other cancers. CONCLUSION: Our analysis suggests that the systems biology-based classifier that combines the differential gene expression and topological features of human protein interaction network may enhance the diagnostic performance of HCC classifier.

Biomarkers of Nanoparticles Impact on Biological Systems

Science.gov (United States)

Mikhailenko, V.; Ieleiko, L.; Glavin, A.; Sorochinska, J.

Studies of nanoscale mineral fibers have demonstrated that the toxic and carcinogenic effects are related to the surface area and surface activity of inhaled particles. Particle surface characteristics are considered to be key factors in the generation of free radicals and reactive oxygen species and are related to the development of apoptosis or cancer. Existing physico-chemical methods do not always allow estimation of the nanoparticles impact on organismal and cellular levels. The aim of this study was to develop marker system for evaluation the toxic and carcinogenic effects of nanoparticles on cells. The markers are designed with respect to important nanoparticles characteristics for specific and sensitive assessment of their impact on biological system. We have studied DNA damage, the activity of xanthine oxidoreductase influencing the level of free radicals, bioenergetic status, phospholipids profile and formation of 1H-NMR-visible mobile lipid domains in Ehrlich carcinoma cells. The efficiency of the proposed marker system was tested in vivo and in vitro with the use of C60 fullerene nanoparticles and multiwalled carbon nanotubes. Our data suggest that multiwalled carbon nanotubes and fullerene C60 may pose genotoxic effect, change energy metabolism and membrane structure, alter free radical level via xanthine oxidase activation and cause mobile lipid domains formation as determined in vivo and in vitro studies on Ehrlich carcinoma cells.

The Road Ahead to Cure Alzheimer’s Disease: Development of Biological Markers and Neuroimaging Methods for Prevention Trials Across all Stages and Target Populations

Science.gov (United States)

Cavedo, E.; Lista, S.; Khachaturian, Z.; Aisen, P.; Amouyel, P.; Herholz, K.; Jack, C.R.; Sperling, R.; Cummings, J.; Blennow, K.; O’Bryant, S.; Frisoni, G.B.; Khachaturian, A.; Kivipelto, M.; Klunk, W.; Broich, K.; Andrieu, S.; de Schotten, M. Thiebaut; Mangin, J.-F.; Lammertsma, A.A.; Johnson, K.; Teipel, S.; Drzezga, A.; Bokde, A.; Colliot, O.; Bakardjian, H.; Zetterberg, H.; Dubois, B.; Vellas, B.; Schneider, L.S.; Hampel, H.

2015-01-01

Alzheimer’s disease (AD) is a slowly progressing non-linear dynamic brain disease in which pathophysiological abnormalities, detectable in vivo by biological markers, precede overt clinical symptoms by many years to decades. Use of these biomarkers for the detection of early and preclinical AD has become of central importance following publication of two international expert working group’s revised criteria for the diagnosis of AD dementia, mild cognitive impairment (MCI) due to AD, prodromal AD and preclinical AD. As a consequence of matured research evidence six AD biomarkers are sufficiently validated and partly qualified to be incorporated into operationalized clinical diagnostic criteria and use in primary and secondary prevention trials. These biomarkers fall into two molecular categories: biomarkers of amyloid-beta (Aβ) deposition and plaque formation as well as of tau-protein related hyperphosphorylation and neurodegeneration. Three of the six gold-standard (“core feasible) biomarkers are neuroimaging measures and three are cerebrospinal fluid (CSF) analytes. CSF Aβ1-42 (Aβ1-42), also expressed as Aβ1-42 : Aβ1-40 ratio, T-tau, and P-tau Thr181 & Thr231 proteins have proven diagnostic accuracy and risk enhancement in prodromal MCI and AD dementia. Conversely, having all three biomarkers in the normal range rules out AD. Intermediate conditions require further patient follow-up. Magnetic resonance imaging (MRI) at increasing field strength and resolution allows detecting the evolution of distinct types of structural and functional abnormality pattern throughout early to late AD stages. Anatomical or volumetric MRI is the most widely used technique and provides local and global measures of atrophy. The revised diagnostic criteria for “prodromal AD” and “mild cognitive impairment due to AD” include hippocampal atrophy (as the fourth validated biomarker), which is considered an indicator of regional neuronal injury. Advanced image analysis

Analysing malaria drug trials on a per-individual or per-clone basis: a comparison of methods.

Science.gov (United States)

Jaki, Thomas; Parry, Alice; Winter, Katherine; Hastings, Ian

2013-07-30

There are a variety of methods used to estimate the effectiveness of antimalarial drugs in clinical trials, invariably on a per-person basis. A person, however, may have more than one malaria infection present at the time of treatment. We evaluate currently used methods for analysing malaria trials on a per-individual basis and introduce a novel method to estimate the cure rate on a per-infection (clone) basis. We used simulated and real data to highlight the differences of the various methods. We give special attention to classifying outcomes as cured, recrudescent (infections that never fully cleared) or ambiguous on the basis of genetic markers at three loci. To estimate cure rates on a per-clone basis, we used the genetic information within an individual before treatment to determine the number of clones present. We used the genetic information obtained at the time of treatment failure to classify clones as recrudescence or new infections. On the per-individual level, we find that the most accurate methods of classification label an individual as newly infected if all alleles are different at the beginning and at the time of failure and as a recrudescence if all or some alleles were the same. The most appropriate analysis method is survival analysis or alternatively for complete data/per-protocol analysis a proportion estimate that treats new infections as successes. We show that the analysis of drug effectiveness on a per-clone basis estimates the cure rate accurately and allows more detailed evaluation of the performance of the treatment. Copyright © 2012 John Wiley & Sons, Ltd.

Safety Basis Report

International Nuclear Information System (INIS)

R.J. Garrett

2002-01-01

As part of the internal Integrated Safety Management Assessment verification process, it was determined that there was a lack of documentation that summarizes the safety basis of the current Yucca Mountain Project (YMP) site characterization activities. It was noted that a safety basis would make it possible to establish a technically justifiable graded approach to the implementation of the requirements identified in the Standards/Requirements Identification Document. The Standards/Requirements Identification Documents commit a facility to compliance with specific requirements and, together with the hazard baseline documentation, provide a technical basis for ensuring that the public and workers are protected. This Safety Basis Report has been developed to establish and document the safety basis of the current site characterization activities, establish and document the hazard baseline, and provide the technical basis for identifying structures, systems, and components (SSCs) that perform functions necessary to protect the public, the worker, and the environment from hazards unique to the YMP site characterization activities. This technical basis for identifying SSCs serves as a grading process for the implementation of programs such as Conduct of Operations (DOE Order 5480.19) and the Suspect/Counterfeit Items Program. In addition, this report provides a consolidated summary of the hazards analyses processes developed to support the design, construction, and operation of the YMP site characterization facilities and, therefore, provides a tool for evaluating the safety impacts of changes to the design and operation of the YMP site characterization activities

Safety Basis Report

Energy Technology Data Exchange (ETDEWEB)

R.J. Garrett

2002-01-14

As part of the internal Integrated Safety Management Assessment verification process, it was determined that there was a lack of documentation that summarizes the safety basis of the current Yucca Mountain Project (YMP) site characterization activities. It was noted that a safety basis would make it possible to establish a technically justifiable graded approach to the implementation of the requirements identified in the Standards/Requirements Identification Document. The Standards/Requirements Identification Documents commit a facility to compliance with specific requirements and, together with the hazard baseline documentation, provide a technical basis for ensuring that the public and workers are protected. This Safety Basis Report has been developed to establish and document the safety basis of the current site characterization activities, establish and document the hazard baseline, and provide the technical basis for identifying structures, systems, and components (SSCs) that perform functions necessary to protect the public, the worker, and the environment from hazards unique to the YMP site characterization activities. This technical basis for identifying SSCs serves as a grading process for the implementation of programs such as Conduct of Operations (DOE Order 5480.19) and the Suspect/Counterfeit Items Program. In addition, this report provides a consolidated summary of the hazards analyses processes developed to support the design, construction, and operation of the YMP site characterization facilities and, therefore, provides a tool for evaluating the safety impacts of changes to the design and operation of the YMP site characterization activities.

Study on the radiation-induced biological responses based on the analysis of metabolites

International Nuclear Information System (INIS)

Jo, Sungkee; Jung, Uhee; Park, Haeran; Roh, Changhyun; Shin, Heejune; Ryu, Dongkyoung

2013-01-01

1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation

Study on the radiation-induced biological responses based on the analysis of metabolites

Energy Technology Data Exchange (ETDEWEB)

Jo, Sungkee; Jung, Uhee; Park, Haeran; Roh, Changhyun; Shin, Heejune; Ryu, Dongkyoung

2013-01-15

1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation.

The physical basis of biochemistry the foundations of molecular biophysics

CERN Document Server

Bergethon, Peter R

1998-01-01

The objective of this book is to provide a unifying approach to the study of biophysical chemistry for the advanced undergraduate who has had a year of physics, organic chem­ istry, calculus, and biology. This book began as a revised edition of Biophysical Chemistry: Molecules to Membranes, which Elizabeth Simons and I coauthored. That short volume was written in an attempt to provide a concise text for a one-semester course in biophysical chemistry at the graduate level. The experience of teaching biophysical chemistry to bi­ ologically oriented students over the last decade has made it clear that the subject requires a more fundamental text that unifies the many threads of modem science: physics, chem­ istry, biology, mathematics, and statistics. This book represents that effort. This volume is not a treatment of modem biophysical chemistry with its rich history and many contro­ versies, although a book on that topic is also needed. The Physical Basis of Biochemistry is an introduction to the philosophy...

Transformation of tobacco cpDNA with fusion E7GGG/GUS gene and homologous recombination mediated elimination of the marker gene

Czech Academy of Sciences Publication Activity Database

Bříza, Jindřich; Vlasák, Josef; Ryba, Š.; Ludvíková, V.; Niedermeierová, Hana

2013-01-01

Roč. 27, č. 2 (2013), s. 3644-3648 ISSN 1310-2818 R&D Projects: GA AV ČR IAA500960903 Institutional support: RVO:60077344 Keywords : E7GGG oncogene * chloroplast transformation * marker-free plant * homologous recombination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.379, year: 2013