Researchers Hooked on Teaching. Noted Scholars Discuss the Synergies of Teaching and Research. Foundations for Organizational Science Series.

ERIC Educational Resources Information Center

Andre, Rae, Ed.; Frost, Peter J., Ed.

This collection of 19 essays is organized into a narrative of the teaching-research dilemma. The essays include: (1) "Struggling With Balance" (Cynthia V. Fukami); (2) "My Career as a Teacher: Promise, Failure, Redemption" (Howard E. Aldrich); (3) "Teaching and Research: A Puzzling Dichotomy" (Barbara A. Gutek); (4)…

Whole Wiskott‑Aldrich syndrome protein gene deletion identified by high throughput sequencing.

PubMed

He, Xiangling; Zou, Runying; Zhang, Bing; You, Yalan; Yang, Yang; Tian, Xin

2017-11-01

Wiskott‑Aldrich syndrome (WAS) is a rare X‑linked recessive immunodeficiency disorder, characterized by thrombocytopenia, small platelets, eczema and recurrent infections associated with increased risk of autoimmunity and malignancy disorders. Mutations in the WAS protein (WASP) gene are responsible for WAS. To date, WASP mutations, including missense/nonsense, splicing, small deletions, small insertions, gross deletions, and gross insertions have been identified in patients with WAS. In addition, WASP‑interacting proteins are suspected in patients with clinical features of WAS, in whom the WASP gene sequence and mRNA levels are normal. The present study aimed to investigate the application of next generation sequencing in definitive diagnosis and clinical therapy for WAS. A 5 month‑old child with WAS who displayed symptoms of thrombocytopenia was examined. Whole exome sequence analysis of genomic DNA showed that the coverage and depth of WASP were extremely low. Quantitative polymerase chain reaction indicated total WASP gene deletion in the proband. In conclusion, high throughput sequencing is useful for the verification of WAS on the genetic profile, and has implications for family planning guidance and establishment of clinical programs.

R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome.

PubMed

Sarkar, Koustav; Han, Seong-Su; Wen, Kuo-Kuang; Ochs, Hans D; Dupré, Loïc; Seidman, Michael M; Vyas, Yatin M

2017-12-15

Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. We sought to define how dysfunctional gene transcription is causally linked to the degree of T H cell deficiency and genomic instability in the XLT/WAS clinical spectrum. In human T H 1- or T H 2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in T H 1 cells relative to T H 2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (T H 1 genes) in T H 1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (T H 2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. Transcriptional R-loop imbalance is a novel molecular defect causative in T H 1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum

Genetic characteristics of eighty-seven patients with the Wiskott-Aldrich syndrome.

PubMed

Gulácsy, Vera; Freiberger, Tomas; Shcherbina, Anna; Pac, Malgorzata; Chernyshova, Liudmyla; Avcin, Tadej; Kondratenko, Irina; Kostyuchenko, Larysa; Prokofjeva, Tatjana; Pasic, Srdjan; Bernatowska, Ewa; Kutukculer, Necil; Rascon, Jelena; Iagaru, Nicolae; Mazza, Cinzia; Tóth, Beáta; Erdos, Melinda; van der Burg, Mirjam; Maródi, László

2011-02-01

The Wiskott-Aldrich syndrome (WAS) is an X-linked recessive immune deficiency disorder characterized by thrombocytopenia, small platelet size, eczema, recurrent infections, and increased risk of autoimmune disorders and malignancies. WAS is caused by mutations in the WASP gene which encodes WASP, a 502-amino acid protein. WASP plays a critical role in actin cytoskeleton organization and signalling, and functions of immune cells. We present here the results of genetic analysis of patients with WAS from eleven Eastern and Central European (ECE) countries and Turkey. Clinical and haematological information of 87 affected males and 48 carrier females from 77 WAS families were collected. The WASP gene was sequenced from genomic DNA of patients with WAS, as well as their family members to identify carriers. In this large cohort, we identified 62 unique mutations including 17 novel sequence variants. The mutations were scattered throughout the WASP gene and included single base pair changes (17 missense and 11 nonsense mutations), 7 small insertions, 18 deletions, and 9 splice site defects. Genetic counselling and prenatal diagnosis were applied in four affected families. This study was part of the J Project aimed at identifying genetic basis of primary immunodeficiency disease in ECE countries. This report provides the first comprehensive overview of the molecular genetic and demographic features of WAS in ECE. Copyright © 2010 Elsevier Ltd. All rights reserved.

Glycan Arrays: From Basic Biochemical Research to Bioanalytical and Biomedical Applications

NASA Astrophysics Data System (ADS)

Geissner, Andreas; Seeberger, Peter H.

2016-06-01

A major branch of glycobiology and glycan-focused biomedicine studies the interaction between carbohydrates and other biopolymers, most importantly, glycan-binding proteins. Today, this research into glycan-biopolymer interaction is unthinkable without glycan arrays, tools that enable high-throughput analysis of carbohydrate interaction partners. Glycan arrays offer many applications in basic biochemical research, for example, defining the specificity of glycosyltransferases and lectins such as immune receptors. Biomedical applications include the characterization and surveillance of influenza strains, identification of biomarkers for cancer and infection, and profiling of immune responses to vaccines. Here, we review major applications of glycan arrays both in basic and applied research. Given the dynamic nature of this rapidly developing field, we focus on recent findings.

Research advance of stability mechanism on physicochemical, biochemical and microorganism trait of wine

NASA Astrophysics Data System (ADS)

Nan, Lijun; Li, Yashan; Cui, Changwei; Ning, Na; Huang, Jing; Xu, Chengdong; Zhang, Xiaofang; Yang, Ruiqun; Zhong, Yingxue

2018-04-01

The stability of wine is an important feature during the wine aging, which is mainly reflected in the balance of color, taste and aroma during the wine aging. During the wine fermentation, the role of microbes and enzymes including the interaction between them caused the mutual penetration, combination, decomposition and transformation among the substances in connection with color, aroma and taste in wine, which led to the instability of wine. After the fermentation of wine, the long aging period could just stabilize the wine. Still, the quality of wine had changed a lot. Based on the indicative changes in wine, such as microbiological interactions, biochemical reactions as well as interactions between the microorganism and biochemical reactions, the impact of changes of the basic biochemical and physicochemical indices on the stability of red wine were reviewed, and developmental suggestions in the future were also put forward in this paper, in order to reveal the mechanism of instability through the effect of dynamic change on the stability of red wine and analyze the unstable root of the red wine, which could lay a foundation for further research, and provide help for actual production.

Successful Reduced Intensity Allogeneic Transplant With Full Donor Chimerism and Good Quality of Life in Adolescent Patient With Wiskott-Aldrich Syndrome.

PubMed

Ali, Salah; Gacsadi, Anna; McDougall, Elizabeth; Armstrong, Christine; Krueger, Joerg; Schechter, Tal; Ali, Muhammad

2017-07-01

Wiskott-Aldrich syndrome (WAS) is an X-linked disease characterized by microthrombocytopenia, eczema, immune deficiency, and autoimmune phenomena. Allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative treatment. Myeloablative conditioning is the most common regimen used for HSCT in patients with WAS to avoid the risk of mixed donor chimerism and autoimmunity post-HSCT. There is limited data on the use of reduced intensity conditioning for HSCT in patients with WAS. Here, we report a case with severe phenotype of WAS transplanted successfully with reduced intensity conditioning, which is an acceptable conditioning regimen and can be considered in patients with WAS with significantly impaired organ functions.

Wiskott-Aldrich syndrome protein deficiency in B cells results in impaired peripheral homeostasis

PubMed Central

Meyer-Bahlburg, Almut; Becker-Herman, Shirly; Humblet-Baron, Stephanie; Khim, Socheath; Weber, Michele; Bouma, Gerben; Thrasher, Adrian J.; Batista, Facundo D.

2008-01-01

To more precisely identify the B-cell phenotype in Wiskott-Aldrich syndrome (WAS), we used 3 distinct murine in vivo models to define the cell intrinsic requirements for WAS protein (WASp) in central versus peripheral B-cell development. Whereas WASp is dispensable for early bone marrow B-cell development, WASp deficiency results in a marked reduction in each of the major mature peripheral B-cell subsets, exerting the greatest impact on marginal zone and B1a B cells. Using in vivo bromodeoxyuridine labeling and in vitro functional assays, we show that these deficits reflect altered peripheral homeostasis, partially resulting from an impairment in integrin function, rather than a developmental defect. Consistent with these observations, we also show that: (1) WASp expression levels increase with cell maturity, peaking in those subsets exhibiting the greatest sensitivity to WASp deficiency; (2) WASp+ murine B cells exhibit a marked selective advantage beginning at the late transitional B-cell stage; and (3) a similar in vivo selective advantage is manifest by mature WASp+ human B cells. Together, our data provide a better understanding of the clinical phenotype of WAS and suggest that gene therapy might be a useful approach to rescue altered B-cell homeostasis in this disease. PMID:18687984

Foamy Virus Vector-mediated Gene Correction of a Mouse Model of Wiskott–Aldrich Syndrome

PubMed Central

Uchiyama, Toru; Adriani, Marsilio; Jagadeesh, G Jayashree; Paine, Adam; Candotti, Fabio

2012-01-01

The Wiskott–Aldrich syndrome (WAS) is an X-linked disorder characterized by eczema, thrombocytopenia and immunodeficiency. Hematopoietic cell transplantation can cure the disease and gene therapy is being tested as an alternative treatment option. In this study, we assessed the use of foamy virus (FV) vectors as a gene transfer system for WAS, using a Was knockout (KO) mouse model. Preliminary experiments using FV vectors expressing the green fluorescent protein under the transcriptional control of the endogenous WAS promoter or a ubiquitously acting chromatin opening element allowed us to define transduction conditions resulting in high (>40%) and long-term in-vivo marking of blood cells after transplantation. In following experiments, Was KO mice were treated with FV vectors containing the human WAS complementary DNA (cDNA). Transplanted animals expressed the WAS protein (WASp) in T and B lymphocytes, as well as platelets and showed restoration of both T-cell receptor-mediated responses and B-cell migration. We also observed recovery of platelet adhesion and podosome formation in dendritic cells (DCs) of treated mice. These data demonstrate that FV vectors can be effective for hematopoietic stem cell (HSC)-directed gene correction of WAS. PMID:22215016

Deletion of Wiskott–Aldrich syndrome protein triggers Rac2 activity and increased cross-presentation by dendritic cells

PubMed Central

Baptista, Marisa A. P.; Keszei, Marton; Oliveira, Mariana; Sunahara, Karen K. S.; Andersson, John; Dahlberg, Carin I. M.; Worth, Austen J.; Liedén, Agne; Kuo, I-Chun; Wallin, Robert P. A.; Snapper, Scott B.; Eidsmo, Liv; Scheynius, Annika; Karlsson, Mikael C. I.; Bouma, Gerben; Burns, Siobhan O.; Forsell, Mattias N. E.; Thrasher, Adrian J.; Nylén, Susanne; Westerberg, Lisa S.

2016-01-01

Wiskott–Aldrich syndrome (WAS) is caused by loss-of-function mutations in the WASp gene. Decreased cellular responses in WASp-deficient cells have been interpreted to mean that WASp directly regulates these responses in WASp-sufficient cells. Here, we identify an exception to this concept and show that WASp-deficient dendritic cells have increased activation of Rac2 that support cross-presentation to CD8+ T cells. Using two different skin pathology models, WASp-deficient mice show an accumulation of dendritic cells in the skin and increased expansion of IFNγ-producing CD8+ T cells in the draining lymph node and spleen. Specific deletion of WASp in dendritic cells leads to marked expansion of CD8+ T cells at the expense of CD4+ T cells. WASp-deficient dendritic cells induce increased cross-presentation to CD8+ T cells by activating Rac2 that maintains a near neutral pH of phagosomes. Our data reveals an intricate balance between activation of WASp and Rac2 signalling pathways in dendritic cells. PMID:27425374

The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of Tachinid flies.

PubMed

Zhao, Zhe; Su, Tian-Juan; Chesters, Douglas; Wang, Shi-di; Ho, Simon Y W; Zhu, Chao-Dong; Chen, Xiao-Lin; Zhang, Chun-Tian

2013-01-01

Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene.

The Mitochondrial Genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the Evolutionary Timescale of Tachinid Flies

PubMed Central

Zhao, Zhe; Su, Tian-juan; Chesters, Douglas; Wang, Shi-di; Ho, Simon Y. W.; Zhu, Chao-dong; Chen, Xiao-lin; Zhang, Chun-tian

2013-01-01

Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene. PMID:23626734

Wiskott-Aldrich Syndrome (WAS)

MedlinePlus

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Measures of Biochemical Sociology

ERIC Educational Resources Information Center

Snell, Joel; Marsh, Mitchell

2008-01-01

In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

Wiskott-Aldrich syndrome protein is required for NK cell cytotoxicity and colocalizes with actin to NK cell-activating immunologic synapses

NASA Astrophysics Data System (ADS)

Orange, Jordan S.; Ramesh, Narayanaswamy; Remold-O'Donnell, Eileen; Sasahara, Yoji; Koopman, Louise; Byrne, Michael; Bonilla, Francisco A.; Rosen, Fred S.; Geha, Raif S.; Strominger, Jack L.

2002-08-01

The Wiskott-Aldrich syndrome (WAS) is a primary immunodeficiency disorder caused by a mutation in WAS protein (WASp) that results in defective actin polymerization. Although the function of many hematopoietic cells requires WASp, the specific expression and function of this molecule in natural killer (NK) cells is unknown. Here, we report that WAS patients have increased percentages of peripheral blood NK cells and that fresh enriched NK cells from two patients with a WASp mutation have defective cytolytic function. In normal NK cells, WASp was expressed and localized to the activating immunologic synapse (IS) with filamentous actin (F-actin). Perforin also localized to the NK cell-activating IS but at a lesser frequency than F-actin and WASp. The accumulation of F-actin and WASp at the activating IS was decreased significantly in NK cells that had been treated with the inhibitor of actin polymerization, cytochalasin D. NK cells from WAS patients lacked expression of WASp and accumulated F-actin at the activating IS infrequently. Thus, WASp has an important function in NK cells. In patients with WASp mutations, the resulting NK cell defects are likely to contribute to their disease.

A Program on Biochemical and Biomedical Engineering.

ERIC Educational Resources Information Center

San, Ka-Yiu; McIntire, Larry V.

1989-01-01

Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

Research on: A. Reclamation of borrow pits and denuded lands; B. Biochemical aspects of mycorrhizae of forest trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marx, D.H.

1990-12-01

This report furnishes a list of compiled and ongoing studies and a list of publications which resulted from the research accomplished by Institute scientists and other collaborators. The research accomplished can be placed in four categories: I. Research on borrow pit rehabilitation with 12 publications; II. Research on artificial regeneration of southern pines with 34 publications; III. Research on artificial regeneration of eastern hardwoods with 16 publications; and IV. Cooperative research with the University of Georgia on biochemical aspects of mycorrhizae with 5 publications. Major accomplishments of this research are: 1. Procedures to successfully reclaim borrow pits with sludge, subsoilingmore » and seedlings with specific mycorrhizae. 2. Protocols to successfully artificially regenerate southern pines (particularly ling leaf pine) and certain eastern hardwoods. 3. Basic understanding of the biochemistry of mycorrhizae and the discovery of a new pathway for sucrose utilization in plants. 67 refs.« less

Overview of the DOE/SERI Biochemical Conversion Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, J D

1986-09-01

The Solar Energy Research Institute manages a program of research and development on the biochemical conversion of renewable lignocellulosic materials to liquid fuels for the Department of Energy's Biofuels and Municipal Waste Technology Division. The Biochemical Conversion Program is mission oriented so effort is concentrated on technologies which appear to have the greatest potential for being adopted by the private sector to economically convert lignocellulosic materials into high value liquid transportation fuels such as ethanol. The program is structured to supply the technology for such fuels to compete economically first as an octane booster or fuel additive, and, with additionalmore » improvements, as a neat fuel. 18 refs., 3 figs., 1 tab.« less

Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation.

PubMed

Ducka, Anna M; Joel, Peteranne; Popowicz, Grzegorz M; Trybus, Kathleen M; Schleicher, Michael; Noegel, Angelika A; Huber, Robert; Holak, Tad A; Sitar, Tomasz

2010-06-29

Three classes of proteins are known to nucleate new filaments: the Arp2/3 complex, formins, and the third group of proteins that contain ca. 25 amino acid long actin-binding Wiskott-Aldrich syndrome protein homology 2 domains, called the WH2 repeats. Crystal structures of the complexes between the actin-binding WH2 repeats of the Spire protein and actin were determined for the Spire single WH2 domain D, the double (SpirCD), triple (SpirBCD), quadruple (SpirABCD) domains, and an artificial Spire WH2 construct comprising three identical D repeats (SpirDDD). SpirCD represents the minimal functional core of Spire that can nucleate actin filaments. Packing in the crystals of the actin complexes with SpirCD, SpirBCD, SpirABCD, and SpirDDD shows the presence of two types of assemblies, "side-to-side" and "straight-longitudinal," which can serve as actin filament nuclei. The principal feature of these structures is their loose, open conformations, in which the sides of actins that normally constitute the inner interface core of a filament are flipped inside out. These Spire structures are distant from those seen in the filamentous nuclei of Arp2/3, formins, and in the F-actin filament.

Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation

PubMed Central

Ducka, Anna M.; Joel, Peteranne; Popowicz, Grzegorz M.; Trybus, Kathleen M.; Schleicher, Michael; Noegel, Angelika A.; Huber, Robert; Holak, Tad A.; Sitar, Tomasz

2010-01-01

Three classes of proteins are known to nucleate new filaments: the Arp2/3 complex, formins, and the third group of proteins that contain ca. 25 amino acid long actin-binding Wiskott-Aldrich syndrome protein homology 2 domains, called the WH2 repeats. Crystal structures of the complexes between the actin-binding WH2 repeats of the Spire protein and actin were determined for the Spire single WH2 domain D, the double (SpirCD), triple (SpirBCD), quadruple (SpirABCD) domains, and an artificial Spire WH2 construct comprising three identical D repeats (SpirDDD). SpirCD represents the minimal functional core of Spire that can nucleate actin filaments. Packing in the crystals of the actin complexes with SpirCD, SpirBCD, SpirABCD, and SpirDDD shows the presence of two types of assemblies, “side-to-side” and “straight-longitudinal,” which can serve as actin filament nuclei. The principal feature of these structures is their loose, open conformations, in which the sides of actins that normally constitute the inner interface core of a filament are flipped inside out. These Spire structures are distant from those seen in the filamentous nuclei of Arp2/3, formins, and in the F-actin filament. PMID:20538977

Know-how and know-why in biochemical engineering.

PubMed

von Stockar, U; Valentinotti, S; Marison, I; Cannizzaro, C; Herwig, C

2003-08-01

This contribution analyzes the position of biochemical engineering in general and bioprocess engineering particularly in the force fields between fundamental science and applications, and between academia and industry. By using culture technology as an example, it can be shown that bioprocess engineering has moved slowly but steadily from an empirical art concerned with mainly know-how to a science elucidating the know-why of culture behavior. Highly powerful monitoring tools enable biochemical engineers to understand and explain quantitatively the activity of cellular culture on a metabolic basis. Among these monitoring tools are not just semi-online analyses of culture broth by HPLC, GC and FIA, but, increasingly, also noninvasive methods such as midrange IR, Raman and capacitance spectroscopy, as well as online calorimetry. The detailed and quantitative insight into the metabolome and the fluxome that bioprocess engineers are establishing offers an unprecedented opportunity for building bridges between molecular biology and engineering biosciences. Thus, one of the major tasks of biochemical engineering sciences is not developing new know-how for industrial applications, but elucidating the know-why in biochemical engineering by conducting research on the underlying scientific fundamentals.

Two sisters with clinical diagnosis of Wiskott-Aldrich Syndrome: Is the condition in the family autosomal recessive?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kondoh, T.; Hayashi, K.; Matsumoto, T.

1995-10-09

We report two sisters in a family representing manifestations of Wiskott-Aldrich syndrome (WAS), an X-linked immunodeficiency disorder. An elder sister had suffered from recurrent infections, small thrombocytopenic petechiae, purpura, and eczema for 7 years. The younger sister had the same manifestations as the elder sister`s for a 2-year period, and died of intracranial bleeding at age 2 years. All the laboratory data of the two patients were compatible with WAS, although they were females. Sialophorin analysis with the selective radioactive labeling method of this protein revealed that in the elder sister a 115-KD band that should be specific for sialophorinmore » was reduced in quantity, and instead an additional 135-KD fragment was present as a main band. Polymerase chain reaction (PCR) analysis of the sialophorin gene and single-strand conformation polymorphism (SSCP) analysis of the PCR product demonstrated that there were no detectable size-change nor electrophoretic mobility change in the DNA from both patients. The results indicated that their sialophorin gene structure might be normal. Studies on the mother-daughter transmission of X chromosome using a pERT84-MaeIII polymorphic marker mapped at Xp21 and HPRT gene polymorphism at Xq26 suggested that each sister had inherited a different X chromosome from the mother. Two explanations are plausible for the occurrence of the WAS in our patients: the WAS in the patients is attributable to an autosomal gene mutation which may regulate the sialophorin gene expression through the WAS gene, or, alternatively, the condition in this family is an autosomal recessive disorder separated etiologically from the X-linked WAS. 17 refs., 6 figs., 1 tab.« less

Novel mutations in the Wiskott-Aldrich syndrome protein gene and their effects on transcriptional, translational, and clinical phenotypes.

PubMed

Lemahieu, V; Gastier, J M; Francke, U

1999-01-01

Wiskott-Aldrich syndrome (WAS) is an X-linked recessive immunodeficiency characterized by thrombocytopenia, eczema, and recurrent infections, and caused by mutations in the WAS protein (WASP) gene. WASP contains several functional domains through which it interacts with proteins involved in intracellular signaling and regulation of the actin cytoskeleton. In this report, 17 WASP gene mutations were identified, 12 of which are novel. DNA of affected males and obligate carriers was PCR amplified and analyzed by SSCA, heteroduplex analysis, and direct sequencing. The effects of the mutations at the mRNA and protein level were ascertained by RT-PCR and Western blot analyses. All missense mutations were located in exons 1-4. Most of the nonsense, frameshift and splice site mutations were found in exons 6-11. Mutations that alter splice sites led to the synthesis of several types of mRNAs, a fraction of which represented the normally spliced product. The presence of normally spliced transcripts was correlated with a milder phenotype. When one such case was studied by Western blotting, reduced amounts of normal-size WASP were present. In other cases as well, a correlation was found between the amount of normal or mutant WASP present and the phenotypes of the affected individuals. No protein was detected in two individuals with severe WAS. Reduced levels of a normal-size WASP with a missense mutation were seen in two individuals with XLT. It is concluded that mutation analysis at the DNA level is not sufficient for predicting clinical course. Studies at the transcript and protein level are needed for a better assessment.

A large kindred with X-linked neutropenia with an I294T mutation of the Wiskott-Aldrich syndrome gene.

PubMed

Beel, Karolien; Cotter, Melanie M; Blatny, Jan; Bond, Jonathan; Lucas, Geoff; Green, Frances; Vanduppen, Vik; Leung, Daisy W; Rooney, Sean; Smith, Owen P; Rosen, Michael K; Vandenberghe, Peter

2009-01-01

X-linked neutropenia (XLN, OMIM #300299) is a rare form of severe congenital neutropenia. It was originally described in a three-generation family with five affected members that had an L270P mutation in the GTP-ase binding domain (GBD) of the Wiskott-Aldrich syndrome protein (WASP) [Devriendt et al (2001) Nature Genetics, Vol. 27, 313-317]. Here, we report and describe a large three-generation family with XLN, with 10 affected males and eight female carriers. A c.882T>C mutation was identified in the WAS gene, resulting in an I294T mutation. The infectious course is variable and mild in view of the profound neutropenia. In addition to the original description, low-normal IgA levels, low to low-normal platelet counts and reduced natural killer (NK)-cell counts also appear as consistent XLN features. However, inverted CD4/CD8 ratios were not found in this family, nor were cases identified with myelodysplastic syndrome or acute myeloid leukaemia. Female carriers exhibited a variable attenuated phenotype. Like L270P WASP, I294T WASP is constitutively active towards actin polymerization. In conclusion, this largest XLN kindred identified to date provides new independent genetic evidence that mutations disrupting the auto-inhibitory GBD of WASP are the cause of XLN. Reduced NK cells, low to low normal platelet counts and low to low-normal IgA levels are also features of XLN.

Balanced Biochemical Reactions: A New Approach to Unify Chemical and Biochemical Thermodynamics

PubMed Central

Sabatini, Antonio; Vacca, Alberto; Iotti, Stefano

2012-01-01

A novel procedure is presented which, by balancing elements and electric charge of biochemical reactions which occur at constant pH and pMg, allows assessing the thermodynamics properties of reaction ΔrG ′0, ΔrH ′0, ΔrS ′0 and the change in binding of hydrogen and magnesium ions of these reactions. This procedure of general applicability avoids the complex calculations required by the use of the Legendre transformed thermodynamic properties of formation ΔfG ′0, ΔfH ′0 and ΔfS ′0 hitherto considered an obligatory prerequisite to deal with the thermodynamics of biochemical reactions. As a consequence, the term “conditional” is proposed in substitution of “Legendre transformed” to indicate these thermodynamics properties. It is also shown that the thermodynamic potential G is fully adequate to give a criterion of spontaneous chemical change for all biochemical reactions and then that the use of the Legendre transformed G′ is unnecessary. The procedure proposed can be applied to any biochemical reaction, making possible to re-unify the two worlds of chemical and biochemical thermodynamics, which so far have been treated separately. PMID:22247780

Accurate atom-mapping computation for biochemical reactions.

PubMed

Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

2012-11-26

The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

Exploring the remote sensing of foliar biochemical concentrations with AVIRIS data

NASA Technical Reports Server (NTRS)

Smith, Geoffrey M.; Curran, Paul J.

1992-01-01

Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data shows promise for the estimation of foliar biochemical concentrations at the scale of the canopy. There are, however, several problems associated with the use of AVIRIS data in this way and these are detailed in recent Plant Biochemical Workshop Report. The research reported was concentrated upon three of these problems: field sampling of forest canopies, wet laboratory assay of foliar chemicals, and the visualization of AVIRIS data.

Decreased expression of Wiskott-Aldrich syndrome protein family verprolin-homologous protein 2 may be involved in the development of pre-eclampsia.

PubMed

Li, Juan; Luo, Xin; Xiao, Xiaoqiu; Zhang, Xuemei; Qi, Hongbo; Liu, Xiru; Zhang, Hua; Gao, Li; Yang, Zhongmei

2014-01-01

Wiskott–Aldrich syndrome protein family verprolin-homologous protein 2 (WAVE2) is a protein that mediates actin cytoskeletal reorganization and lamellipodia protrusion formation, which are required for cell migration and invasion. The primary purpose of this study was to determine whether there is an association between reactive oxygen species (ROS) and WAVE2 in pre-eclampsia, and whether WAVE2 expression in trophoblast cells is vulnerable to oxidative stress. This study observed excessive generation of ROS and decreased expression of WAVE2 in pre-eclamptic placentas compared with normotensive controls. Moreover, there was a significant negative correlation between ROS and WAVE2 protein in pre-eclamptic placenta (P < 0.001). An in-vitro model of hypoxia–reoxygenation (H/R) was used to imitate oxidative stress in placental trophoblasts, and it was found that the expression of WAVE2 protein in trophoblasts was decreased after H/R treatment. Additionally, compared with normoxia, decreased cell proliferation, higher cell apoptosis and attenuated cell migration and invasion were detected in trophoblasts exposed to H/R. In conclusion, the findings strongly suggest that excessive oxidative stress can decrease WAVE2 expression in trophoblasts and that the decreased expression of WAVE2 in trophoblast cells may be involved in the development of pre-eclampsia. Copyright © 2013 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Development of Convergence Nanoparticles (Phase II): Detection and Therapeutics of Pathogen Targets by Using Multi-Mode Hybrid Nanoparticle Probe

DTIC Science & Technology

2010-04-05

Chloride (Aldrich 45011, 5g) 1 -Ethyl- 3 -[ 3 - dimethylaminopropyl ]carbodiimide hydrochloride (Pierce 25952-53-8, 25g) Oleylamine (Aldrich O7805, 500g...email: jcheon@yonsei.ac.kr Table of Content 1 . Abstract 2. Introduction 3 . Approach 4. Results and discussions 5. Pay-off 6. Summary 7...highly accurate detection and therapeutics of biological pathogens. 3 . Approaches 1 ) Approach Our research was focused on the development of

Complete integrability of information processing by biochemical reactions

NASA Astrophysics Data System (ADS)

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-11-01

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on spin systems - has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis-Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy - based on completely integrable hydrodynamic-type systems of PDEs - which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions.

Complete integrability of information processing by biochemical reactions.

PubMed

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-11-04

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on spin systems - has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis-Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy - based on completely integrable hydrodynamic-type systems of PDEs - which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions.

Abelson Interactor 1 (Abi1) and Its Interaction with Wiskott-Aldrich Syndrome Protein (Wasp) Are Critical for Proper Eye Formation in Xenopus Embryos*

PubMed Central

Singh, Arvinder; Winterbottom, Emily F.; Ji, Yon Ju; Hwang, Yoo-Seok; Daar, Ira O.

2013-01-01

Abl interactor 1 (Abi1) is a scaffold protein that plays a central role in the regulation of actin cytoskeleton dynamics as a constituent of several key protein complexes, and homozygous loss of this protein leads to embryonic lethality in mice. Because this scaffold protein has been shown in cultured cells to be a critical component of pathways controlling cell migration and actin regulation at cell-cell contacts, we were interested to investigate the in vivo role of Abi1 in morphogenesis during the development of Xenopus embryos. Using morpholino-mediated translation inhibition, we demonstrate that knockdown of Abi1 in the whole embryo, or specifically in eye field progenitor cells, leads to disruption of eye morphogenesis. Moreover, signaling through the Src homology 3 domain of Abi1 is critical for proper movement of retinal progenitor cells into the eye field and their appropriate differentiation, and this process is dependent upon an interaction with the nucleation-promoting factor Wasp (Wiskott-Aldrich syndrome protein). Collectively, our data demonstrate that the Abi1 scaffold protein is an essential regulator of cell movement processes required for normal eye development in Xenopus embryos and specifically requires an Src homology 3 domain-dependent interaction with Wasp to regulate this complex morphogenetic process. PMID:23558677

Nanoparticles as biochemical sensors

PubMed Central

El-Ansary, Afaf; Faddah, Layla M

2010-01-01

There is little doubt that nanoparticles offer real and new opportunities in many fields, such as biomedicine and materials science. Such particles are small enough to enter almost all areas of the body, including cells and organelles, potentially leading to new approaches in nanomedicine. Sensors for small molecules of biochemical interest are of critical importance. This review is an attempt to trace the use of nanomaterials in biochemical sensor design. The possibility of using nanoparticles functionalized with antibodies as markers for proteins will be elucidated. Moreover, capabilities and applications for nanoparticles based on gold, silver, magnetic, and semiconductor materials (quantum dots), used in optical (absorbance, luminescence, surface enhanced Raman spectroscopy, surface plasmon resonance), electrochemical, and mass-sensitive sensors will be highlighted. The unique ability of nanosensors to improve the analysis of biochemical fluids is discussed either through considering the use of nanoparticles for in vitro molecular diagnosis, or in the biological/biochemical analysis for in vivo interaction with the human body. PMID:24198472

Biochemical responses of the Skylab crewman

NASA Technical Reports Server (NTRS)

Leach, C. S.; Rambaut, P. C.

1974-01-01

The biochemical investigations of the Skylab crewmen were designed to study the physiological changes that were observed on flight crews returning from previous space flight missions as well as to study those changes expected to result from prolonged weightless exposure. These studies can be divided into two broad categories. One category included routine blood studies similar to those used in clinical medical practice. The second included research-type endocrine analyses used to investigate more thoroughly the metabolic/endocrine responses to the space flight environment. The premission control values indicated that all Skylab crewmen were healthy and were free from biochemical abnormalities. The routine results during and after flight showed slight but significant changes in electrolytes, glucose, total protein, osmolality, uric acid, cholesterol, and creatinine. Plasma hormal changes included adrenocorticotrophic hormone, cortisol, angiotensin I, aldosterone, insulin, and thyroxine. The 24-hour urine analyses results revealed increased excretion of cortisol, catecholamines, antidiuretic hormone, and aldosterone as well as excretion of significant electrolyte and uric acid during the Skylab flights.

Misleading biochemical laboratory test results

PubMed Central

Nanji, Amin A.

1984-01-01

This article reviews the general and specific factors that interfere with the performance of common biochemical laboratory tests and the interpretation of their results. The clinical status of the patient, drug interactions, and in-vivo and in-vitro biochemical interactions and changes may alter the results obtained from biochemical analysis of blood constituents. Failure to recognize invalid laboratory test results may lead to injudicious and dangerous management of patients. PMID:6375845

Biochemical transformation of coals

DOEpatents

Lin, Mow S.; Premuzic, Eugene T.

1999-03-23

A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

Biochemical transformation of coals

DOEpatents

Lin, M.S.; Premuzic, E.T.

1999-03-23

A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed. 7 figs.

Present status of biochemical research on the insecticide resistance problem*

PubMed Central

Agosin, Moises

1963-01-01

In order to provide a rational basis for the development of new insecticides, a thorough understanding of resistance mechanisms is necessary and this presupposes a detailed knowledge of the normal biochemical pathways in insects. The author reviews recent progress in this field, particularly the work on enzymatic detoxication of insecticides which appears to be the most important single factor in the production of resistance. The mechanisms include dehydrochlorination and α-methylenic oxidation (DDT), hydrolysis by phosphatases or carboxyesterases (organophosphorus compounds), and oxidation by microsomal enzyme systems (various classes of insecticides). Much work still needs to be done on the enzyme systems involved, especially in relation to substrate specificity and the effect of enzyme inhibitors that might act as synergists of insecticides. PMID:20604178

Biochemical-Pathway Diversity in Archaebacteria

DTIC Science & Technology

1990-08-30

Classification) (U) Biochemical-pathway diversity in Archaebacteria 12 PERSONAL AUTHOR(S) I Jensen, Roy-A. i3o. TYPE OF REN" RT 12b. Tki~ 0’E D-30-9 4...by block numtb.sj FIEL I ROU I SIGRLJP Archaebacteria , biochemical diversity, prephenate 06 03. 1 dehydratase, aromatic amino acid biosynthesis t...1988 RE10SE: lo assess the extent to which the archaebacteria possess unique biochemical features of aromatic amino acid biosynthesis and regulation and

An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing.

PubMed

Wu, Zujian; Pang, Wei; Coghill, George M

2015-01-01

Both qualitative and quantitative model learning frameworks for biochemical systems have been studied in computational systems biology. In this research, after introducing two forms of pre-defined component patterns to represent biochemical models, we propose an integrative qualitative and quantitative modelling framework for inferring biochemical systems. In the proposed framework, interactions between reactants in the candidate models for a target biochemical system are evolved and eventually identified by the application of a qualitative model learning approach with an evolution strategy. Kinetic rates of the models generated from qualitative model learning are then further optimised by employing a quantitative approach with simulated annealing. Experimental results indicate that our proposed integrative framework is feasible to learn the relationships between biochemical reactants qualitatively and to make the model replicate the behaviours of the target system by optimising the kinetic rates quantitatively. Moreover, potential reactants of a target biochemical system can be discovered by hypothesising complex reactants in the synthetic models. Based on the biochemical models learned from the proposed framework, biologists can further perform experimental study in wet laboratory. In this way, natural biochemical systems can be better understood.

Biochemical abnormalities in neonatal seizures.

PubMed

Sood, Arvind; Grover, Neelam; Sharma, Roshan

2003-03-01

The presence of seizure does not constitute a diagnoses but it is a symptom of an underlying central nervous system disorder due to systemic or biochemical disturbances. Biochemical disturbances occur frequently in the neonatal seizures either as an underlying cause or as an associated abnormality. In their presence, it is difficult to control seizure and there is a risk of further brain damage. Early recognition and treatment of biochemical disturbances is essential for optimal management and satisfactory long term outcome. The present study was conducted in the department of pediatrics in IGMC Shimla on 59 neonates. Biochemical abnormalities were detected in 29 (49.15%) of cases. Primary metabolic abnormalities occurred in 10(16.94%) cases of neonatal seizures, most common being hypocalcaemia followed by hypoglycemia, other metabolic abnormalities include hypomagnesaemia and hyponateremia. Biochemical abnormalities were seen in 19(38.77%) cases of non metabolic seizure in neonates. Associated metabolic abnormalities were observed more often with Hypoxic-ischemic-encephalopathy (11 out of 19) cases and hypoglycemia was most common in this group. No infant had hyponateremia, hyperkelemia or low zinc level.

Increased expression of Wiskott-Aldrich syndrome protein family verprolin-homologous protein 2 correlated with poor prognosis of hepatocellular carcinoma.

PubMed

Yang, Lian-Yue; Tao, Yi-Ming; Ou, Di-Peng; Wang, Wei; Chang, Zhi-Gang; Wu, Fan

2006-10-01

Because of its role in cell migration, the Wiskott-Aldrich syndrome protein family verprolin-homologous protein (WAVE) 2 has been implicated in cancer metastasis. Evidence to support such a role of WAVE2 in human cancer, however, is lacking. We thus examined the expression of WAVE2 in hepatocellular carcinoma (HCC) tissues to test whether the levels of WAVE2 expression correlated to the progression of HCC. Samples of 112 HCC patients were determined immunohistochemically for WAVE2 expression and the correlation of WAVE2 levels with prognosis was analyzed. Among the 112 cases, 31 paired HCC and paracarcinomatous liver tissue specimens were analyzed for WAVE2 levels by reverse transcription-PCR and Western blotting, respectively. Among 112 cases of HCCs, the immunohistochemistry data indicated significant increase of WAVE2 expression levels in 71 cases. Importantly, the increased WAVE2 expression correlated with the multiple tumor nodules (P = 0.008), the absence of capsular formation (P = 0.035), Edmondson-Steiner grade (P = 0.009), vein invasion (P = 0.023), and a shortened median survival time (326 versus 512 days; P = 0.003). Multivariable Cox regression analysis revealed the WAVE2 expression level was an independent factor for prognosis. The immunohistochemistry data were further confirmed by results of reverse transcription-PCR and Western analysis of 31 HCC cases, in which the WAVE2 mRNA and protein in HCC tissues were significantly elevated when compared with paracarcinomatous liver tissue (P < 0.001). WAVE2 expression is elevated in HCC tissues, which correlates with a poor prognosis, suggesting WAVE2 as a candidate prognostic marker of HCC.

Coexpression of actin-related protein 2 and Wiskott-Aldrich syndrome family verproline-homologous protein 2 in adenocarcinoma of the lung.

PubMed

Semba, Seitaro; Iwaya, Keiichi; Matsubayashi, Jun; Serizawa, Hiromi; Kataba, Hiroaki; Hirano, Takashi; Kato, Harubumi; Matsuoka, Takeshi; Mukai, Kiyoshi

2006-04-15

Highly invasive and metastatic cancer cells, such as adenocarcinoma of the lung cells, form irregular protrusions by assembling a branched network of actin filaments. In mammalian cells, the actin-related protein 2 and 3 (Arp2/3) complex initiates actin assembly to form lamellipodial protrusions by binding to Wiskott-Aldrich syndrome (WASP)/WASP family verproline-homologous protein 2 (WAVE2). In this study, colocalization of Arp2 and WAVE2 in adenocarcinoma of the lung was investigated to elucidate its prognostic value. Immunohistochemical staining of Arp2 and WAVE2 was done on mirror sections of 115 adenocarcinomas of the lung from pathologic stage IA to IIIA classes. Kaplan-Meier disease-free survival and overall survival curves were analyzed to determine the prognostic significance of the coexpression of Arp2 and WAVE2. Immunoreactivity for both Arp2 and WAVE2 was detected in the same cancer cells in 78 (67.8%) of the 115 lung cancer specimens. The proportion of cancer cells expressing both Arp2 and WAVE2 was significantly higher in cases with lymph-node metastasis (P = 0.0046), and significantly lower in bronchioloalveolar carcinomas (P < 0.0001). The patients whose cancer cells coexpressed them had a shorter disease-free survival time (P < 0.0001) and overall survival time (P < 0.0001). Multivariate Cox regression analysis revealed that coexpression of Arp2 and WAVE2 is an independent risk factor for tumor recurrence. Coexpression of Arp2 and WAVE2 is correlated with poorer patient outcome, and may be involved in the mechanism of cancer metastasis.

Airpower Journal Index, 1987-1996

DTIC Science & Technology

1998-07-01

AirpowerJournal Airpower Research Institute Author Index Aldrich, Maj Richard W. "The International Legal Implications of Information Warfare," vol . 10...no . 3 (Fall 1996) : 99-110. Aldrich, Maj Richard W., and Maj Norman K. Thompson . "Verifying Chemical and Biological Weapons Treaties: Is the...Perspective," vol . 3, no . 4 (Winter 1989) : 10-33. Casebeer, 1st Lt William D. ; Col Richard Szafranski ; and Dr. James H. Toner. "Military Ethics," vol. 8

Complete integrability of information processing by biochemical reactions

PubMed Central

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-01-01

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling – based on spin systems – has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis–Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy – based on completely integrable hydrodynamic-type systems of PDEs – which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions. PMID:27812018

A novel optical fiber biochemical sensor based on long period grating

NASA Astrophysics Data System (ADS)

Mao, Xianhui; Liao, Yanbiao; Zhang, Min; Lai, Shurong; Yin, Haibo

2007-09-01

In this paper, our present work, which aimed at investigating a novel optical fiber biochemical sensor based on long period grating (LPG), is introduced. Biochemical sensor is one of the most attractive fields of sensor research, especially with the development and occurrence of all kinds of novel theory and technology such as LPG. When there is a refraction index periodic perturbation, the guiding mode and cladding mode in LPG couple with each other. This make the LPG is sensitive to the ambient refractive index. This means it can be a novel bio-chemical sensor when it is applied in the fields of biochemistry. After investigating the principle of coupling in LPG, where the formulas of resonance wave length and band width are induced by 3-layer step index model, we developed an optical fiber biochemical sensor. The structure of its probe is designed by coating some function films whose thickness is between several tens and several hundreds nanometers on the cladding of optical fiber. Experiments of monitoring the saline separateness process of Bovine Serum Albumin (BSA) and Mice-Immunoglobulin G (M-IgG) by using the developed LPG sensor have been done. The monitoring indicated that for the BSA, the saline separateness occurs when the saturation is between 50% and 60%, for the M-IgG, the percentage is between 30%-40%. Besides the monitoring, the experiments could also analyze the effects of protein type (different molecule structure), protein consistency and saline saturation to saline separateness. The experimental results show that the optical fiber biochemical sensor based on LPG has many advantages such as simple structure, high sensitivity and miniature. It has a promising future in many research fields and application fields.

BNDB - the Biochemical Network Database.

PubMed

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

2007-10-02

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

Autonomous bio-chemical decontaminator (ABCD) against weapons of mass destruction

NASA Astrophysics Data System (ADS)

Hyacinthe, Berg P.

2006-05-01

The proliferation of weapons of mass destruction (WMD) and the use of such elements pose an eminent asymmetric threat with disastrous consequences to the national security of any nation. In particular, the use of biochemical warfare agents against civilians and unprotected troops in international conflicts or by terrorists against civilians is considered as a very peculiar threat. Accordingly, taking a quarantine-before-inhalation approach to biochemical warfare, the author introduces the notion of autonomous biochemical decontamination against WMD. In the unfortunate event of a biochemical attack, the apparatus proposed herein is intended to automatically detect, identify, and more importantly neutralize a biochemical threat. Along with warnings concerning a cyber-WMD nexus, various sections cover discussions on human senses and computer sensors, corroborating evidence related to detection and neutralization of chemical toxins, and cyber-assisted olfaction in stand alone, peer-to-peer, and network settings. In essence, the apparatus can be used in aviation and mass transit security to initiate mass decontamination by dispersing a decontaminant aerosol or to protect the public water supply against a potential bioterrorist attack. Future effort may involve a system-on-chip (SoC) embodiment of this apparatus that allows a safer environment for the emerging phenomenon of cyber-assisted olfaction and morph cell phones into ubiquitous sensors/decontaminators. Although this paper covers mechanisms and protocols to avail a neutralizing substance, further research will need to explore the substance's various pharmacological profiles and potential side effects.

Explorations into Chemical Reactions and Biochemical Pathways.

PubMed

Gasteiger, Johann

2016-12-01

A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

40 CFR 158.2010 - Biochemical pesticides data requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions are identified within the test notes. Definitions that apply to all biochemical data requirements... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides...

40 CFR 158.2010 - Biochemical pesticides data requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions are identified within the test notes. Definitions that apply to all biochemical data requirements... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides...

40 CFR 158.2010 - Biochemical pesticides data requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions are identified within the test notes. Definitions that apply to all biochemical data requirements... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides...

40 CFR 158.2010 - Biochemical pesticides data requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions are identified within the test notes. Definitions that apply to all biochemical data requirements... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides...

40 CFR 158.2010 - Biochemical pesticides data requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions are identified within the test notes. Definitions that apply to all biochemical data requirements... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides...

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

PubMed

Adalsteinsson, David; McMillen, David; Elston, Timothy C

2004-03-08

Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Biochemical Conversion: Using Enzymes, Microbes, and Catalysis to Make Fuels and Chemicals

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2013-07-26

This fact sheet describes the Bioenergy Technologies Office's biochemical conversion work and processes. BETO conducts collaborative research, development, and demonstration projects to improve several processing routes for the conversion of cellulosic biomass.

An Efficacy and Pharmacokinetic Evaluation of a Dose of Diazepam That Will Reduce the Incidence of Convulsions in Indian Rhesus Monkeys Pretreated with Pyridostigmine Bromide, Challenged with Soman, and Treated with Atropine and Pralidoxime Chloride with the Diazepam

DTIC Science & Technology

1990-12-01

benzophenone (Aldrich 23:985-2), tetrabutylammonium nitrate (Kodak 9664), sodium lauryl sulfate (dodecyl sulfide, sodium salt) (Aldrich 86-201-0), helium gas...phase buffer for the initial identity confirmation using a Supelco LC-I column by dissolving 6.0 g of sodium lauryl sulfate and 1.0 g of...water, glacial acetic acid (Baker Reagent’Grade), tetrabutylammonium chloride (Aldrich g8. percent), sodium lauryl sulfate (Aldrich 98 percent), sodium

The underlying pathway structure of biochemical reaction networks

PubMed Central

Schilling, Christophe H.; Palsson, Bernhard O.

1998-01-01

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function. PMID:9539712

Causal correlation of foliar biochemical concentrations with AVIRIS spectra using forced entry linear regression

NASA Technical Reports Server (NTRS)

Dawson, Terence P.; Curran, Paul J.; Kupiec, John A.

1995-01-01

A major goal of airborne imaging spectrometry is to estimate the biochemical composition of vegetation canopies from reflectance spectra. Remotely-sensed estimates of foliar biochemical concentrations of forests would provide valuable indicators of ecosystem function at regional and eventually global scales. Empirical research has shown a relationship exists between the amount of radiation reflected from absorption features and the concentration of given biochemicals in leaves and canopies (Matson et al., 1994, Johnson et al., 1994). A technique commonly used to determine which wavelengths have the strongest correlation with the biochemical of interest is unguided (stepwise) multiple regression. Wavelengths are entered into a multivariate regression equation, in their order of importance, each contributing to the reduction of the variance in the measured biochemical concentration. A significant problem with the use of stepwise regression for determining the correlation between biochemical concentration and spectra is that of 'overfitting' as there are significantly more wavebands than biochemical measurements. This could result in the selection of wavebands which may be more accurately attributable to noise or canopy effects. In addition, there is a real problem of collinearity in that the individual biochemical concentrations may covary. A strong correlation between the reflectance at a given wavelength and the concentration of a biochemical of interest, therefore, may be due to the effect of another biochemical which is closely related. Furthermore, it is not always possible to account for potentially suitable waveband omissions in the stepwise selection procedure. This concern about the suitability of stepwise regression has been identified and acknowledged in a number of recent studies (Wessman et al., 1988, Curran, 1989, Curran et al., 1992, Peterson and Hubbard, 1992, Martine and Aber, 1994, Kupiec, 1994). These studies have pointed to the lack of a physical

Pheochromocytoma-paraganglioma: Biochemical and genetic diagnosis.

PubMed

Cano Megías, Marta; Rodriguez Puyol, Diego; Fernández Rodríguez, Loreto; Sención Martinez, Gloria Lisette; Martínez Miguel, Patricia

Pheochromocytomas and paragangliomas are tumours derived from neural crest cells, which can be diagnosed by biochemical measurement of metanephrine and methoxytyramine. Advances in genetic research have identified many genes involved in the pathogenesis of these tumours, suggesting that up to 35-45% may have an underlying germline mutation. These genes have a singular transcriptional signature and can be grouped into 2 clusters (or groups): cluster 1 (VHL and SHDx), involved in angiogenesis and hypoxia pathways; and cluster 2 (MEN2 and NF1), linked to the kinase signalling pathway. In turn, these genes are associated with a characteristic biochemical phenotype (noradrenergic and adrenergic), and clinical features (location, biological behaviour, age of presentation, etc.) in a large number of cases. Early diagnosis of these tumours, accompanied by a correct genetic diagnosis, should eventually become a priority to enable better treatment, early detection of complications, proper screening of family members and related tumours, as well as an improvement in the overall prognosis of these patients. Copyright © 2016 Sociedad Española de Nefrología. Published by Elsevier España, S.L.U. All rights reserved.

Unification of some biochemical methods of research in the pre- and post-flight periods

NASA Technical Reports Server (NTRS)

Tigranyan, R. A.

1980-01-01

The biochemical methods for determination of various parameters and factors during pre- and post-flight periods, as used by American and Soviet teams dealing with space flight medicine are compared. The emphasis is on the exchange of information on the study of the blood and urine content of space travelers before and after space flight. A series of electrolytic, enzymatic, and hormonal factors is discussed.

Serum Biochemical Phenotypes in the Domestic Dog

PubMed Central

Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.

2016-01-01

The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

Physiological, Biochemical, and Molecular Mechanisms of Heat Stress Tolerance in Plants

PubMed Central

Hasanuzzaman, Mirza; Nahar, Kamrun; Alam, Md. Mahabub; Roychowdhury, Rajib; Fujita, Masayuki

2013-01-01

High temperature (HT) stress is a major environmental stress that limits plant growth, metabolism, and productivity worldwide. Plant growth and development involve numerous biochemical reactions that are sensitive to temperature. Plant responses to HT vary with the degree and duration of HT and the plant type. HT is now a major concern for crop production and approaches for sustaining high yields of crop plants under HT stress are important agricultural goals. Plants possess a number of adaptive, avoidance, or acclimation mechanisms to cope with HT situations. In addition, major tolerance mechanisms that employ ion transporters, proteins, osmoprotectants, antioxidants, and other factors involved in signaling cascades and transcriptional control are activated to offset stress-induced biochemical and physiological alterations. Plant survival under HT stress depends on the ability to perceive the HT stimulus, generate and transmit the signal, and initiate appropriate physiological and biochemical changes. HT-induced gene expression and metabolite synthesis also substantially improve tolerance. The physiological and biochemical responses to heat stress are active research areas, and the molecular approaches are being adopted for developing HT tolerance in plants. This article reviews the recent findings on responses, adaptation, and tolerance to HT at the cellular, organellar, and whole plant levels and describes various approaches being taken to enhance thermotolerance in plants. PMID:23644891

Characterizing autism spectrum disorders by key biochemical pathways.

PubMed

Subramanian, Megha; Timmerman, Christina K; Schwartz, Joshua L; Pham, Daniel L; Meffert, Mollie K

2015-01-01

The genetic and phenotypic heterogeneity of autism spectrum disorders (ASD) presents a substantial challenge for diagnosis, classification, research, and treatment. Investigations into the underlying molecular etiology of ASD have often yielded mixed and at times opposing findings. Defining the molecular and biochemical underpinnings of heterogeneity in ASD is crucial to our understanding of the pathophysiological development of the disorder, and has the potential to assist in diagnosis and the rational design of clinical trials. In this review, we propose that genetically diverse forms of ASD may be usefully parsed into entities resulting from converse patterns of growth regulation at the molecular level, which lead to the correlates of general synaptic and neural overgrowth or undergrowth. Abnormal brain growth during development is a characteristic feature that has been observed both in children with autism and in mouse models of autism. We review evidence from syndromic and non-syndromic ASD to suggest that entities currently classified as autism may fundamentally differ by underlying pro- or anti-growth abnormalities in key biochemical pathways, giving rise to either excessive or reduced synaptic connectivity in affected brain regions. We posit that this classification strategy has the potential not only to aid research efforts, but also to ultimately facilitate early diagnosis and direct appropriate therapeutic interventions.

Characterizing autism spectrum disorders by key biochemical pathways

PubMed Central

Subramanian, Megha; Timmerman, Christina K.; Schwartz, Joshua L.; Pham, Daniel L.; Meffert, Mollie K.

2015-01-01

The genetic and phenotypic heterogeneity of autism spectrum disorders (ASD) presents a substantial challenge for diagnosis, classification, research, and treatment. Investigations into the underlying molecular etiology of ASD have often yielded mixed and at times opposing findings. Defining the molecular and biochemical underpinnings of heterogeneity in ASD is crucial to our understanding of the pathophysiological development of the disorder, and has the potential to assist in diagnosis and the rational design of clinical trials. In this review, we propose that genetically diverse forms of ASD may be usefully parsed into entities resulting from converse patterns of growth regulation at the molecular level, which lead to the correlates of general synaptic and neural overgrowth or undergrowth. Abnormal brain growth during development is a characteristic feature that has been observed both in children with autism and in mouse models of autism. We review evidence from syndromic and non-syndromic ASD to suggest that entities currently classified as autism may fundamentally differ by underlying pro- or anti-growth abnormalities in key biochemical pathways, giving rise to either excessive or reduced synaptic connectivity in affected brain regions. We posit that this classification strategy has the potential not only to aid research efforts, but also to ultimately facilitate early diagnosis and direct appropriate therapeutic interventions. PMID:26483618

MicroRNA-214-5p Inhibits the Invasion and Migration of Hepatocellular Carcinoma Cells by Targeting Wiskott-Aldrich Syndrome Like.

PubMed

Li, Hongdan; Wang, Haoqi; Ren, Zhen

2018-01-01

This study aims to explore the effects of microRNA-214-5p (miR-214-5p) on the invasion and migration of Hepatocellular Carcinoma cells (HCC). Hepatocellular Carcinoma tissues and adjacent normal tissues from 44 hepatocellular carcinoma patients were prepared for this study. The HepG2 and BEL-7402 cells were transfected with miR-214-5p mimic and inhibitor. qRT-PCR was performed to detect the expressions of miR-214-5p. Transwell assays were used to detect the invasion and migration assays in HepG2 and BEL-7402 cells. A dual-luciferase reporter assay was conducted to examine the effect of miR-214-5p on Wiskott-Aldrich Syndrome Like (WASL/ N-WASP). Western blot and qRT-PCR were used to measure the expressions of the E-cadherin, N-cadherin and Vimentin proteins. Transwell chamber assays were performed to detect cell invasion and migration. Compared with normal tissues, HCC tissues demonstrated significantly lower expression of miR-214-5p. Overexpression of miR-214-5p significantly inhibited the migration and invasion of HCC cells and inhibition of miR-214-5p promoted the migration and invasion. Additionally, miR-214-5p suppressed the epithelial-mesenchymal transition (EMT). Further study showed WASL was a putative target gene of miR-214-5p. Up-regulating the expression of WASL could reverse the inhibition effect of miR-214-5p on invasion and migration. Our data suggested that miR-214-5p inhibited the invasion and migration of HepG2 and BEL-7402 by targeting WASL in Hepatocellular carcinoma. © 2018 The Author(s). Published by S. Karger AG, Basel.

Arsenic Uptake, Toxicity, Detoxification, and Speciation in Plants: Physiological, Biochemical, and Molecular Aspects

PubMed Central

Abbas, Ghulam; Murtaza, Behzad; Bibi, Irshad; Shahid, Muhammad; Khan, Muhammad Imran; Amjad, Muhammad; Hussain, Munawar; Natasha

2018-01-01

Environmental contamination with arsenic (As) is a global environmental, agricultural and health issue due to the highly toxic and carcinogenic nature of As. Exposure of plants to As, even at very low concentration, can cause many morphological, physiological, and biochemical changes. The recent research on As in the soil-plant system indicates that As toxicity to plants varies with its speciation in plants (e.g., arsenite, As(III); arsenate, As(V)), with the type of plant species, and with other soil factors controlling As accumulation in plants. Various plant species have different mechanisms of As(III) or As(V) uptake, toxicity, and detoxification. This review briefly describes the sources and global extent of As contamination and As speciation in soil. We discuss different mechanisms responsible for As(III) and As(V) uptake, toxicity, and detoxification in plants, at physiological, biochemical, and molecular levels. This review highlights the importance of the As-induced generation of reactive oxygen species (ROS), as well as their damaging impacts on plants at biochemical, genetic, and molecular levels. The role of different enzymatic (superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase) and non-enzymatic (salicylic acid, proline, phytochelatins, glutathione, nitric oxide, and phosphorous) substances under As(III/V) stress have been delineated via conceptual models showing As translocation and toxicity pathways in plant species. Significantly, this review addresses the current, albeit partially understood, emerging aspects on (i) As-induced physiological, biochemical, and genotoxic mechanisms and responses in plants and (ii) the roles of different molecules in modulation of As-induced toxicities in plants. We also provide insight on some important research gaps that need to be filled to advance our scientific understanding in this area of research on As in soil-plant systems. PMID:29301332

Influence of low-frequency vibration on changes of biochemical parameters of living rats

NASA Astrophysics Data System (ADS)

Kasprzak, Cezary; Damijan, Zbigniew; Panuszka, Ryszard

2004-05-01

The aim of the research was to investigate how some selected biochemical parameters of living rats depend on exposure of low-frequency vibrations. Experiments were run on 30 Wistar rats randomly segregated into three groups: (I) 20 days old (before puberty), (II) 70th day after; (III) control group. The exposure was repeated seven times, for 3 h, at the same time of day. Vibrations applied during the first tests of the experiment had acceleration 1.22 m/s2 and frequency 20 Hz. At the 135th day the rats' bones were a subject of morphometric/biochemical examination. The results of biochemical tests proved decrease in LDL and HDL cholesterol levels for exposed rats as well as the Ca contents in blood plasma. There was evident increasing of Ca in blood plasma in exposed rats for frequency of exposition.

Improving Marine Ecosystem Models with Biochemical Tracers

NASA Astrophysics Data System (ADS)

Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

2018-01-01

Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

Biochemical Engineering Fundamentals

ERIC Educational Resources Information Center

Bailey, J. E.; Ollis, D. F.

1976-01-01

Discusses a biochemical engineering course that is offered as part of a chemical engineering curriculum and includes topics that influence the behavior of man-made or natural microbial or enzyme reactors. (MLH)

Biochemical Activities of 320 ToxCast Chemicals Evaluated Across 239 Functional Targets

EPA Science Inventory

EPA’s ToxCast research program is profiling chemical bioactivity in order to generate predictive signatures of toxicity. The present study evaluated 320 chemicals across 239 biochemical assays. ToxCast phase I chemicals include 309 unique structures, most of which are pesticide ...

Biochemical transformation of solid carbonaceous material

DOEpatents

Lin, Mow S.; Premuzic, Eugene T.

2001-09-25

A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

Combination therapy for biochemically recurrent prostate cancer tested in new trial | Center for Cancer Research

Cancer.gov

Prostate-specific antigen (PSA) is an enzyme released by the prostate gland and is found in abnormally high concentrations in the blood of men with prostate cancer. “Biochemical recurrence” is when PSA levels continue to rise after initial treatment for prostate cancer, such as surgery or radiation. Marijo Bilusic, M.D., of the Genitourinary Malignancies Branch is leading the

Simulation studies in biochemical signaling and enzyme reactions

NASA Astrophysics Data System (ADS)

Nelatury, Sudarshan R.; Vagula, Mary C.

2014-06-01

Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

Bias due to Preanalytical Dilution of Rodent Serum for Biochemical Analysis on the Siemens Dimension Xpand Plus

PubMed Central

Johns, Jennifer L.; Moorhead, Kaitlin A.; Hu, Jing; Moorhead, Roberta C.

2018-01-01

Clinical pathology testing of rodents is often challenging due to insufficient sample volume. One solution in clinical veterinary and exploratory research environments is dilution of samples prior to analysis. However, published information on the impact of preanalytical sample dilution on rodent biochemical data is incomplete. The objective of this study was to evaluate the effects of preanalytical sample dilution on biochemical analysis of mouse and rat serum samples utilizing the Siemens Dimension Xpand Plus. Rats were obtained from end of study research projects. Mice were obtained from sentinel testing programs. For both, whole blood was collected via terminal cardiocentesis into empty tubes and serum was harvested. Biochemical parameters were measured on fresh and thawed frozen samples run straight and at dilution factors 2–10. Dilutions were performed manually, utilizing either ultrapure water or enzyme diluent per manufacturer recommendations. All diluted samples were generated directly from the undiluted sample. Preanalytical dilution caused clinically unacceptable bias in most analytes at dilution factors four and above. Dilution-induced bias in total calcium, creatinine, total bilirubin, and uric acid was considered unacceptable with any degree of dilution, based on the more conservative of two definitions of acceptability. Dilution often caused electrolyte values to fall below assay range precluding evaluation of bias. Dilution-induced bias occurred in most biochemical parameters to varying degrees and may render dilution unacceptable in the exploratory research and clinical veterinary environments. Additionally, differences between results obtained at different dilution factors may confound statistical comparisons in research settings. Comparison of data obtained at a single dilution factor is highly recommended. PMID:29497614

Determination of Urease Biochemical Properties of Asparagus Bean (Vigna unguiculata ssp sesquipedalis L.)

NASA Astrophysics Data System (ADS)

Zusfahair; Ningsih, D. R.; Fatoni, A.; Pertiwi, D. S.

2018-04-01

Urease is enzyme that plays a role in nitrogen metabolism during plant germination. Plants that produce a lot of urease are grains. This study used asparagus bean as source of urease. The purpose of this research is to learn the effect of germination time on the activity of urease enzyme from asparagus bean and its biochemical properties. The research was started by germination of asparagus bean on day 2, 4, 6, 8, 10 and 12. Asparagus bean sprouts were extracted using acetone and separated by centrifugation to obtain the crude extract of urease. The biochemical properties of the crude extract of urease was further determined including: the effect of temperature, pH, substrate concentration, and metal addition to urease activity. The urease activity is determined by the Nessler method. The germination time of asparagus bean in yielding urease enzyme reached the optimum activity on the 8th day with activity value of 593.7 U/mL. The biochemical properties of urease from asparagus bean have optimum activity at 35 °C, pH 7.0 and substrate concentration 0.125% with activity value of 600 U/mL. Addition of CaCl2, SnCl2 and ZnCl2 metals decrease the activity of urease.

Scaling up semi-arid grassland biochemical content from the leaf to the canopy level: challenges and opportunities.

PubMed

He, Yuhong; Mui, Amy

2010-01-01

Remote sensing imagery is being used intensively to estimate the biochemical content of vegetation (e.g., chlorophyll, nitrogen, and lignin) at the leaf level. As a result of our need for vegetation biochemical information and our increasing ability to obtain canopy spectral data, a few techniques have been explored to scale leaf-level biochemical content to the canopy level for forests and crops. However, due to the contribution of non-green materials (i.e., standing dead litter, rock, and bare soil) from canopy spectra in semi-arid grasslands, it is difficult to obtain information about grassland biochemical content from remote sensing data at the canopy level. This paper summarizes available methods used to scale biochemical information from the leaf level to the canopy level and groups these methods into three categories: direct extrapolation, canopy-integrated approach, and inversion of physical models. As for semi-arid heterogeneous grasslands, we conclude that all methods are useful, but none are ideal. It is recommended that future research should explore a systematic upscaling framework which combines spatial pattern analysis, canopy-integrated approach, and modeling methods to retrieve vegetation biochemical content at the canopy level.

Xeroderma pigmentosum: biochemical and genetic characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cleaver, J.E.; Bootsma, D.

1975-01-01

Biochemical and genetic studies on xeroderma pigmentosum are reviewed under the following headings: clinical features of xeroderma pigmentosum; karyotype; cell killing and host cell reactivation after irradiation or exposure to chemical carcinogens; SV40 transformation of xeroderma pigmentosum cells; biochemical defects in the common and de Sanctis-Cacchione forms of xeroderma pigmentosum; cell hybridization and complementation groups; biochemical defects in the xeroderma pigmentosum variant and the role of caffeine in DNA repair; DNA repair in xeroderma pigmentosum heterozygotes; response of xeroderma pigmentosum cells to various mutagens and chemical carcinogens; other high and low repair diseases; and possible significance of DNA repair inmore » theories of aging and carcinogenesis. (HLW)« less

CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

PubMed

Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

2014-09-01

Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

Research and design of an optical system of biochemical analyzer based on the narrow-band pass filter

NASA Astrophysics Data System (ADS)

Xiao, Ze-xin; Chen, Kuan

2008-03-01

Biochemical analyzer is one of the important instruments in the clinical diagnosis, and its optical system is the important component. The operation of this optical system can be regard as three parts. The first is transforms the duplicate colored light as the monochromatic light. The second is transforms the light signal of the monochromatic, which have the information of the measured sample, as the electric signal by use the photoelectric detector. And the last is to send the signal to data processing system by use the control system. Generally, there are three types monochromators: prism, optical grating and narrow-band pass filter. Thereinto, the narrow-band pass filter were widely used in the semi-auto biochemical analyzer. Through analysed the principle of biochemical analyzer base on the narrow-band pass filter, we known that the optical has three features. The first is the optical path of the optical system is a non- imaging system. The second, this system is wide spectrum region that contain visible light and ultraviolet spectrum. The third, this is a little aperture and little field monochromatic light system. Therefore, design idea of this optical system is: (1) luminous energy in the system less transmission loss; (2) detector coupled to the luminous energy efficient; mainly correct spherical aberration. Practice showed the point of Image quality evaluation: (1) dispersion circle diameter equal the receiving device pixel effective width of 125%, and the energy distribution should point target of 80% of energy into the receiving device pixel width of the effective diameter in this dispersion circle; (2) With MTF evaluation, the requirements in 20lp/ mm spatial frequency, the MTF values should not be lower than 0.6. The optical system should be fit in with ultraviolet and visible light width spectrum, and the detector image plane can but suited the majority visible light spectrum when by defocus optimization, and the image plane of violet and ultraviolet

Biochemical mechanisms of cisplatin cytotoxicity.

PubMed

Cepeda, Victoria; Fuertes, Miguel A; Castilla, Josefina; Alonso, Carlos; Quevedo, Celia; Pérez, Jose M

2007-01-01

Since the discovery by Rosenberg and collaborators of the antitumor activity of cisplatin 35 years ago, three platinum antitumor drugs (cisplatin, carboplatin and oxaliplatin) have enjoyed a huge clinical and commercial hit. Ever since the initial discovery of the anticancer activity of cisplatin, major efforts have been devoted to elucidate the biochemical mechanisms of antitumor activity of cisplatin in order to be able to rationally design novel platinum based drugs with superior pharmacological profiles. In this report we attempt to provide a current picture of the known facts pertaining to the mechanism of action of the drug, including those involved in drug uptake, DNA damage signals transduction, and cell death through apoptosis or necrosis. A deep knowledge of the biochemical mechanisms, which are triggered in the tumor cell in response to cisplatin injury not only may lead to the design of more efficient platinum antitumor drugs but also may provide new therapeutic strategies based on the biochemical modulation of cisplatin activity.

Improved prediction of biochemical recurrence after radical prostatectomy by genetic polymorphisms.

PubMed

Morote, Juan; Del Amo, Jokin; Borque, Angel; Ars, Elisabet; Hernández, Carlos; Herranz, Felipe; Arruza, Antonio; Llarena, Roberto; Planas, Jacques; Viso, María J; Palou, Joan; Raventós, Carles X; Tejedor, Diego; Artieda, Marta; Simón, Laureano; Martínez, Antonio; Rioja, Luis A

2010-08-01

Single nucleotide polymorphisms are inherited genetic variations that can predispose or protect individuals against clinical events. We hypothesized that single nucleotide polymorphism profiling may improve the prediction of biochemical recurrence after radical prostatectomy. We performed a retrospective, multi-institutional study of 703 patients treated with radical prostatectomy for clinically localized prostate cancer who had at least 5 years of followup after surgery. All patients were genotyped for 83 prostate cancer related single nucleotide polymorphisms using a low density oligonucleotide microarray. Baseline clinicopathological variables and single nucleotide polymorphisms were analyzed to predict biochemical recurrence within 5 years using stepwise logistic regression. Discrimination was measured by ROC curve AUC, specificity, sensitivity, predictive values, net reclassification improvement and integrated discrimination index. The overall biochemical recurrence rate was 35%. The model with the best fit combined 8 covariates, including the 5 clinicopathological variables prostate specific antigen, Gleason score, pathological stage, lymph node involvement and margin status, and 3 single nucleotide polymorphisms at the KLK2, SULT1A1 and TLR4 genes. Model predictive power was defined by 80% positive predictive value, 74% negative predictive value and an AUC of 0.78. The model based on clinicopathological variables plus single nucleotide polymorphisms showed significant improvement over the model without single nucleotide polymorphisms, as indicated by 23.3% net reclassification improvement (p = 0.003), integrated discrimination index (p <0.001) and likelihood ratio test (p <0.001). Internal validation proved model robustness (bootstrap corrected AUC 0.78, range 0.74 to 0.82). The calibration plot showed close agreement between biochemical recurrence observed and predicted probabilities. Predicting biochemical recurrence after radical prostatectomy based on

Analysis of p21-Activated Kinase Function in Neurofibromatosis Type 2

DTIC Science & Technology

2010-01-01

6,6′-dithiobis) for 10 min, before stimulation with 10% FCS (PAA, Pasching, Austria), 0.5 μM forskolin (Sigma-Aldrich, St. Louis, USA), 10 nM β1...0.5 μM forskolin (Sigma-Aldrich), 10 nM β1- heregulin144–244 (Genentech), 0.5 mM 3-isobutyl-1-methylxanthin (IBMX, Sigma-Aldrich) and 2.5 μg/ml...0.5 μM forskolin (Sigma-Aldrich), 10 nM β1-heregulin144–244 (Genentech), 0.5 mM 3-isobutyl-1-methylxanthin and 2.5 μg/ml insulin (both from Sigma

How to investigate neuro-biochemical relationships on a regional level in humans? Methodological considerations for combining functional with biochemical imaging.

PubMed

Duncan, Niall W; Wiebking, Christine; Muñoz-Torres, Zeidy; Northoff, Georg

2014-01-15

There is an increasing interest in combining different imaging modalities to investigate the relationship between neural and biochemical activity. More specifically, imaging techniques like MRS and PET that allow for biochemical measurement are combined with techniques like fMRI and EEG that measure neural activity in different states. Such combination of neural and biochemical measures raises not only technical issues, such as merging the different data sets, but also several methodological issues. These methodological issues – ranging from hypothesis generation and hypothesis-guided use of technical facilities to target measures and experimental measures – are the focus of this paper. We discuss the various methodological problems and issues raised by the combination of different imaging methodologies in order to investigate neuro-biochemical relationships on a regional level in humans. For example, the choice of transmitter and scan type is discussed, along with approaches to allow the establishment of particular specificities (such as regional or biochemical) to in turn make results fully interpretable. An algorithm that can be used as a form of checklist for designing such multimodal studies is presented. The paper concludes that while several methodological and technical caveats needs to be overcome and addressed, multimodal imaging of the neuro-biochemical relationship provides an important tool to better understand the physiological mechanisms of the human brain.

How to investigate neuro-biochemical relationships on a regional level in humans? Methodological considerations for combining functional with biochemical imaging.

PubMed

Duncan, Niall W; Wiebking, Christine; Munoz-Torres, Zeidy; Northoff, Georg

2013-10-25

There is an increasing interest in combining different imaging modalities to investigate the relationship between neural and biochemical activity. More specifically, imaging techniques like MRS and PET that allow for biochemical measurement are combined with techniques like fMRI and EEG that measure neural activity in different states. Such combination of neural and biochemical measures raises not only technical issues, such as merging the different data sets, but also several methodological issues. These methodological issues - ranging from hypothesis generation and hypothesis-guided use of technical facilities to target measures and experimental measures - are the focus of this paper. We discuss the various methodological problems and issues raised by the combination of different imaging methodologies in order to investigate neuro-biochemical relationships on a regional level in humans. For example, the choice of transmitter and scan type is discussed, along with approaches to allow the establishment of particular specificities (such as regional or biochemical) to in turn make results fully interpretable. An algorithm that can be used as a form of checklist for designing such multimodal studies is presented. The paper concludes that while several methodological and technical caveats needs to be overcome and addressed, multimodal imaging of the neuro-biochemical relationship provides an important tool to better understand the physiological mechanisms of the human brain. Copyright © 2013. Published by Elsevier B.V.

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

Complexity and performance of on-chip biochemical assays

NASA Astrophysics Data System (ADS)

Kopf-Sill, Anne R.; Nikiforov, Theo; Bousse, Luc J.; Nagle, Rob; Parce, J. W.

1997-03-01

The use of microchips for performing biochemical processes has the potential to reduce reagent use and thus assay costs, increase throughput, and automate complex processes. We are building a multifunctional platform that provides sensing and actuation functions for a variety of microchip- based biochemical and analytical processes. Here we describe recent experiments that include on-chip dilution, reagent mixing, reaction, separation, and detection for important classes of biochemical assays. Issues in chip design and control are discussed.

[Mitochondrial diseases in children including Leigh syndrome--biochemical and molecular background].

PubMed

Pronicka, Ewa; Piekutowska-Abramczuk, Dorota; Pronicki, Maciej

2008-01-01

Mitochondrial diseases in children are more frequently caused by mutations in nuclear DNA then in mtDNA. Special clinical phenotypes are associated with the mutations in SURF1 gene, in SCO2 gene and with mtDNA depletion syndromes. Leigh syndrome is the most common clinical presentation of various mitochondrial disorders during childhood. Elevation of lactate in blood, cerebrospinal fluid and urine is a simple biochemical marker of mitochondrial disorders but its specificity and sensitivity are low. Biochemical investigation of muscle biopsy and search for mitochondrial mutations remain a gold standard in the diagnosis. The standarized diagnostic criteria to establish level of diagnostic certainty (possible, probable, definite) are proposed to be used in practice; these include clinical features, neuroimaging and muscle biopsy investigations. Further research directions to improve our understanding of mitochondrial pathologies in children are suggested.

[INVITED] Tilted fiber grating mechanical and biochemical sensors

NASA Astrophysics Data System (ADS)

Guo, Tuan; Liu, Fu; Guan, Bai-Ou; Albert, Jacques

2016-04-01

The tilted fiber Bragg grating (TFBG) is a new kind of fiber-optic sensor that possesses all the advantages of well-established Bragg grating technology in addition to being able to excite cladding modes resonantly. This device opens up a multitude of opportunities for single-point sensing in hard-to-reach spaces with very controllable cross-sensitivities, absolute and relative measurements of various parameters, and an extreme sensitivity to materials external to the fiber without requiring the fiber to be etched or tapered. Over the past five years, our research group has been developing multimodal fiber-optic sensors based on TFBG in various shapes and forms, always keeping the device itself simple to fabricate and compatible with low-cost manufacturing. This paper presents a brief review of the principle, fabrication, characterization, and implementation of TFBGs, followed by our progress in TFBG sensors for mechanical and biochemical applications, including one-dimensional TFBG vibroscopes, accelerometers and micro-displacement sensors; two-dimensional TFBG vector vibroscopes and vector rotation sensors; reflective TFBG refractometers with in-fiber and fiber-to-fiber configurations; polarimetric and plasmonic TFBG biochemical sensors for in-situ detection of cell, protein and glucose.

Biochemical Characterization of Prions.

PubMed

Fiorini, Michele; Bongianni, Matilde; Monaco, Salvatore; Zanusso, Gianluigi

2017-01-01

Prion disease or transmissible spongiform encephalopathies are characterized by the presence of the abnormal form of the prion protein (PrP Sc ). The pathological and transmissible properties of PrP Sc are enciphered in its secondary and tertiary structures. Since it's well established that different strains of prions are linked to different conformations of PrP Sc , biochemical characterization of prions seems a preliminary but reliable approach to detect, analyze, and compare prion strains. Experimental biochemical procedures might be helpful in distinguishing PrP Sc physicochemical properties and include resistance to proteinase K (PK) digestion, insolubility in nonionic detergents, PK-resistance under denaturing conditions and sedimentation properties in sucrose gradients. This biochemical approach has been extensively applied in human prion disorders and subsequently expanded for PrP Sc characterization in animals. In particular, in sporadic Creutzfedlt-Jakob disease (sCJD) PrP Sc is characterized by two main glycotypes conventionally named Type 1 and Type 2, based on the apparent gel migration at 21 and 19kDa of the PrP Sc PK-resistant fragment. An additional PrP Sc type was identified in sCJD characterized by an unglycosylated dominant glycoform pattern and in 2010 a variably protease-sensitive prionopathy (VPSPr) was reported showing a PrP Sc with an electrophoretic ladder like pattern. Additionally, the presence of PrP Sc truncated fragments completes the electrophoretic characterization of different prion strains. By two-dimensional (2D) electrophoretic analysis additional PrP Sc pattern was identified, since this procedure provides information about the isoelectric point and the different peptides length related to PK cleavage, as well as to glycosylation extent or GPI anchor presence. We here provide and extensive review on PrP Sc biochemical analysis in human and animal prion disorders. Further, we show that PrP Sc glycotypes observed in CJD share

Estimating Biochemical Parameters of Tea (camellia Sinensis (L.)) Using Hyperspectral Techniques

NASA Astrophysics Data System (ADS)

Bian, M.; Skidmore, A. K.; Schlerf, M.; Liu, Y.; Wang, T.

2012-07-01

Tea (Camellia Sinensis (L.)) is an important economic crop and the market price of tea depends largely on its quality. This research aims to explore the potential of hyperspectral remote sensing on predicting the concentration of biochemical components, namely total tea polyphenols, as indicators of tea quality at canopy scale. Experiments were carried out for tea plants growing in the field and greenhouse. Partial least squares regression (PLSR), which has proven to be the one of the most successful empirical approach, was performed to establish the relationship between reflectance and biochemical concentration across six tea varieties in the field. Moreover, a novel integrated approach involving successive projections algorithms as band selection method and neural networks was developed and applied to detect the concentration of total tea polyphenols for one tea variety, in order to explore and model complex nonlinearity relationships between independent (wavebands) and dependent (biochemicals) variables. The good prediction accuracies (r2 > 0.8 and relative RMSEP < 10 %) achieved for tea plants using both linear (partial lease squares regress) and nonlinear (artificial neural networks) modelling approaches in this study demonstrates the feasibility of using airborne and spaceborne sensors to cover wide areas of tea plantation for in situ monitoring of tea quality cheaply and rapidly.

[NUTRITIONAL STATUS BY ANTHROPOMETRIC AND BIOCHEMICAL PARAMETERS OF COLLEGE BASKETBALL PLAYERS].

PubMed

Godoy-Cumillaf, Andrés Esteban Roberto; Cárcamo-Araneda, Cristian Rodolfo; Hermosilla-Rodríguez, Freddy Patricio; Oyarzún-Ruiz, Jean Pierre; Viveros-Herrera, José Francisco Javier

2015-12-01

in relation to the student population, their class schedules, hours of study, budget shortages, among others, do not allow them to have good eating habits and sedentary ago. Within this context are the sports teams, which must deal with the above. knowing the nutritional status of a group of college basketball players (BU) by anthropometric and biochemical parameters. the research provides a non-experimental, descriptive, transversal, with a quantitative approach The sample was selected on a non-probabilistic approach. which included 12 players design. Anthropometric parameters for body mass index (BMI), somatotype and body composition was assessed. For biochemical glucose, triglycerides and cholesterol. have a BMI of 24.6 (kg/m2), are classified as endomesomorfas (5,5-4,3-1,2) have a fat mass 39.9% and 37.8% of muscle mass, glucose values are 68.7 (mg/dl), triglycerides 128 (mg/dl) and 189 cholesterol (mg/dl). the BU have normal values for BMI and biochemical parameters, but dig deeper greater amount of adipose tissue is found as reported by body composition and somatotype, a situation that could be related to poor eating habits, however is required further study to reach a categorical conclusion. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Biochemical Disincentives to Fertilizing Cellulosic Ethanol Crops

NASA Astrophysics Data System (ADS)

Gallagher, M. E.; Hockaday, W. C.; Snapp, S.; McSwiney, C.; Baldock, J.

2010-12-01

Corn grain biofuel crops produce the highest yields when the cropping ecosystem is not nitrogen (N)-limited, achieved by application of fertilizer. There are environmental consequences for excessive fertilizer application to crops, including greenhouse gas emissions, hypoxic “dead zones,” and health problems from N runoff into groundwater. The increase in corn acreage in response to demand for alternative fuels (i.e. ethanol) could exacerbate these problems, and divert food supplies to fuel production. A potential substitute for grain ethanol that could reduce some of these impacts is cellulosic ethanol. Cellulosic ethanol feedstocks include grasses (switchgrass), hardwoods, and crop residues (e.g. corn stover, wheat straw). It has been assumed that these feedstocks will require similar N fertilization rates to grain biofuel crops to maximize yields, but carbohydrate yield versus N application has not previously been monitored. We report the biochemical stocks (carbohydrate, protein, and lignin in Mg ha-1) of a corn ecosystem grown under varying N levels. We measured biochemical yield in Mg ha-1 within the grain, leaf and stem, and reproductive parts of corn plants grown at seven N fertilization rates (0-202 kg N ha-1), to evaluate the quantity and quality of these feedstocks across a N fertilization gradient. The N fertilization rate study was performed at the Kellogg Biological Station-Long Term Ecological Research Site (KBS-LTER) in Michigan. Biochemical stocks were measured using 13C nuclear magnetic resonance spectroscopy (NMR), combined with a molecular mixing model (Baldock et al. 2004). Carbohydrate and lignin are the main biochemicals of interest in ethanol production since carbohydrate is the ethanol feedstock, and lignin hinders the carbohydrate to ethanol conversion process. We show that corn residue carbohydrate yields respond only weakly to N fertilization compared to grain. Grain carbohydrate yields plateau in response to fertilization at

Hypomagnesemia predicts postoperative biochemical hypocalcemia after thyroidectomy.

PubMed

Luo, Han; Yang, Hongliu; Zhao, Wanjun; Wei, Tao; Su, Anping; Wang, Bin; Zhu, Jingqiang

2017-05-25

To investigate the role of magnesium in biochemical and symptomatic hypocalcemia, a retrospective study was conducted. Less-than-total thyroidectomy patients were excluded from the final analysis. Identified the risk factors of biochemical and symptomatic hypocalcemia, and investigated the correlation by logistic regression and correlation test respectively. A total of 304 patients were included in the final analysis. General incidence of hypomagnesemia was 23.36%. Logistic regression showed that gender (female) (OR = 2.238, p = 0.015) and postoperative hypomagnesemia (OR = 2.010, p = 0.017) were independent risk factors for biochemical hypocalcemia. Both Pearson and partial correlation tests indicated there was indeed significant relation between calcium and magnesium. However, relative decreasing of iPTH (>70%) (6.691, p < 0.001) and hypocalcemia (2.222, p = 0.046) were identified as risk factors of symptomatic hypocalcemia. The difference remained significant even in normoparathyroidism patients. Postoperative hypomagnesemia was independent risk factor of biochemical hypocalcemia. Relative decline of iPTH was predominating in predicting symptomatic hypocalcemia.

Phaeochromocytoma: diagnostic challenges for biochemical screening and diagnosis.

PubMed

Barron, Jeffrey

2010-08-01

The aim of this article is to provide knowledge of the origin of catecholamines and metabolites so that there can be an informed approach to the methods for biochemical screening for a possible phaeochromocytoma; The article includes a review of catecholamine and metadrenaline metabolism, with methods used in biochemical screening. In the adrenal medulla and a phaeochromocytoma, catecholamines continuously leak from chromaffin granules into the cytoplasm and are converted to metadrenalines. For a phaeochromocytoma to become biochemically detectable, metnoradrenaline secretion needs to rise fourfold, whereas noradrenaline secretion needs to rise 15-fold. The prevalence of a sporadic phaeochromocytoma is low; therefore false-positive results exceed true-positive results. Assay sensitivity is high because it is important not to miss a possible phaeochromocytoma. The use of urine or plasma fractionated metadrenalines as the first-line test has been recommended due to improved sensitivity. A negative result excludes a phaeochromocytoma. Only after a sporadic phaeochromocytoma has been diagnosed biochemically is it cost effective to request imaging. Sensitivities and specificities of the assays differ according to pre-test probabilities of the presence of a phaeochromocytoma, with hereditary and incidentalomas having a higher pre-test probability than sporadic phaeochromocytoma. In conclusion, in screening for a possible phaeochromocytoma, biochemical investigations should be completed first to exclude or establish the diagnosis. The preferred biochemical screening test is fractionated metadrenalines, including methoxytyramine so as not to miss dopamine-secreting tumours.

eQuilibrator--the biochemical thermodynamics calculator.

PubMed

Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

2012-01-01

The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

eQuilibrator—the biochemical thermodynamics calculator

PubMed Central

Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

2012-01-01

The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

Biochemical adaptation to ocean acidification.

PubMed

Stillman, Jonathon H; Paganini, Adam W

2015-06-01

The change in oceanic carbonate chemistry due to increased atmospheric PCO2  has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2 . From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid-base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the

Biochemical Testing in Thyroid Disorders.

PubMed

Esfandiari, Nazanene H; Papaleontiou, Maria

2017-09-01

This article summarizes the main principles for the appropriate use of laboratory testing in the diagnosis and management of thyroid disorders, as well as controversies that have arisen in association with some of these biochemical tests. To place a test in perspective, its sensitivity and accuracy should be taken into account. Ordering the correct laboratory tests facilitates the early diagnosis of a thyroid disorder and allows for timely and appropriate treatment. This article focuses on a comprehensive update regarding thyroid-stimulating hormone, thyroxine/triiodothyronine, thyroid autoantibodies, thyroglobulin, and calcitonin. Clinical uses of these biochemical tests are outlined. Copyright © 2017 Elsevier Inc. All rights reserved.

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.

PubMed

Pahle, Jürgen

2009-01-01

Computer simulations have become an invaluable tool to study the sometimes counterintuitive temporal dynamics of (bio-)chemical systems. In particular, stochastic simulation methods have attracted increasing interest recently. In contrast to the well-known deterministic approach based on ordinary differential equations, they can capture effects that occur due to the underlying discreteness of the systems and random fluctuations in molecular numbers. Numerous stochastic, approximate stochastic and hybrid simulation methods have been proposed in the literature. In this article, they are systematically reviewed in order to guide the researcher and help her find the appropriate method for a specific problem.

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches

PubMed Central

2009-01-01

Computer simulations have become an invaluable tool to study the sometimes counterintuitive temporal dynamics of (bio-)chemical systems. In particular, stochastic simulation methods have attracted increasing interest recently. In contrast to the well-known deterministic approach based on ordinary differential equations, they can capture effects that occur due to the underlying discreteness of the systems and random fluctuations in molecular numbers. Numerous stochastic, approximate stochastic and hybrid simulation methods have been proposed in the literature. In this article, they are systematically reviewed in order to guide the researcher and help her find the appropriate method for a specific problem. PMID:19151097

Biochemical phenotypes to discriminate microbial subpopulations and improve outbreak detection.

PubMed

Galar, Alicia; Kulldorff, Martin; Rudnick, Wallis; O'Brien, Thomas F; Stelling, John

2013-01-01

Clinical microbiology laboratories worldwide constitute an invaluable resource for monitoring emerging threats and the spread of antimicrobial resistance. We studied the growing number of biochemical tests routinely performed on clinical isolates to explore their value as epidemiological markers. Microbiology laboratory results from January 2009 through December 2011 from a 793-bed hospital stored in WHONET were examined. Variables included patient location, collection date, organism, and 47 biochemical and 17 antimicrobial susceptibility test results reported by Vitek 2. To identify biochemical tests that were particularly valuable (stable with repeat testing, but good variability across the species) or problematic (inconsistent results with repeat testing), three types of variance analyses were performed on isolates of K. pneumonia: descriptive analysis of discordant biochemical results in same-day isolates, an average within-patient variance index, and generalized linear mixed model variance component analysis. 4,200 isolates of K. pneumoniae were identified from 2,485 patients, 32% of whom had multiple isolates. The first two variance analyses highlighted SUCT, TyrA, GlyA, and GGT as "nuisance" biochemicals for which discordant within-patient test results impacted a high proportion of patient results, while dTAG had relatively good within-patient stability with good heterogeneity across the species. Variance component analyses confirmed the relative stability of dTAG, and identified additional biochemicals such as PHOS with a large between patient to within patient variance ratio. A reduced subset of biochemicals improved the robustness of strain definition for carbapenem-resistant K. pneumoniae. Surveillance analyses suggest that the reduced biochemical profile could improve the timeliness and specificity of outbreak detection algorithms. The statistical approaches explored can improve the robust recognition of microbial subpopulations with routinely available

Biochemical Phenotypes to Discriminate Microbial Subpopulations and Improve Outbreak Detection

PubMed Central

Galar, Alicia; Kulldorff, Martin; Rudnick, Wallis; O'Brien, Thomas F.; Stelling, John

2013-01-01

Background Clinical microbiology laboratories worldwide constitute an invaluable resource for monitoring emerging threats and the spread of antimicrobial resistance. We studied the growing number of biochemical tests routinely performed on clinical isolates to explore their value as epidemiological markers. Methodology/Principal Findings Microbiology laboratory results from January 2009 through December 2011 from a 793-bed hospital stored in WHONET were examined. Variables included patient location, collection date, organism, and 47 biochemical and 17 antimicrobial susceptibility test results reported by Vitek 2. To identify biochemical tests that were particularly valuable (stable with repeat testing, but good variability across the species) or problematic (inconsistent results with repeat testing), three types of variance analyses were performed on isolates of K. pneumonia: descriptive analysis of discordant biochemical results in same-day isolates, an average within-patient variance index, and generalized linear mixed model variance component analysis. Results: 4,200 isolates of K. pneumoniae were identified from 2,485 patients, 32% of whom had multiple isolates. The first two variance analyses highlighted SUCT, TyrA, GlyA, and GGT as “nuisance” biochemicals for which discordant within-patient test results impacted a high proportion of patient results, while dTAG had relatively good within-patient stability with good heterogeneity across the species. Variance component analyses confirmed the relative stability of dTAG, and identified additional biochemicals such as PHOS with a large between patient to within patient variance ratio. A reduced subset of biochemicals improved the robustness of strain definition for carbapenem-resistant K. pneumoniae. Surveillance analyses suggest that the reduced biochemical profile could improve the timeliness and specificity of outbreak detection algorithms. Conclusions The statistical approaches explored can improve the

WASp Family Verprolin-homologous Protein-2 (WAVE2) and Wiskott-Aldrich Syndrome Protein (WASp) Engage in Distinct Downstream Signaling Interactions at the T Cell Antigen Receptor Site*

PubMed Central

Pauker, Maor H.; Reicher, Barak; Joseph, Noah; Wortzel, Inbal; Jakubowicz, Shlomi; Noy, Elad; Perl, Orly; Barda-Saad, Mira

2014-01-01

T cell antigen receptor (TCR) engagement has been shown to activate pathways leading to actin cytoskeletal polymerization and reorganization, which are essential for lymphocyte activation and function. Several actin regulatory proteins were implicated in regulating the actin machinery, such as members of the Wiskott-Aldrich syndrome protein (WASp) family. These include WASp and the WASp family verprolin-homologous protein-2 (WAVE2). Although WASp and WAVE2 share several structural features, the precise regulatory mechanisms and potential redundancy between them have not been fully characterized. Specifically, unlike WASp, the dynamic molecular interactions that regulate WAVE2 recruitment to the cell membrane and specifically to the TCR signaling complex are largely unknown. Here, we identify the molecular mechanism that controls the recruitment of WAVE2 in comparison with WASp. Using fluorescence resonance energy transfer (FRET) and novel triple-color FRET (3FRET) technology, we demonstrate how WAVE2 signaling complexes are dynamically regulated during lymphocyte activation in vivo. We show that, similar to WASp, WAVE2 recruitment to the TCR site depends on protein-tyrosine kinase, ZAP-70, and the adaptors LAT, SLP-76, and Nck. However, in contrast to WASp, WAVE2 leaves this signaling complex and migrates peripherally together with vinculin to the membrane leading edge. Our experiments demonstrate that WASp and WAVE2 differ in their dynamics and their associated proteins. Thus, this study reveals the differential mechanisms regulating the function of these cytoskeletal proteins. PMID:25342748

Remote sensing of forest canopy and leaf biochemical contents

NASA Technical Reports Server (NTRS)

Peterson, David L.; Matson, Pamela A.; Card, Don H.; Aber, John D.; Wessman, Carol; Swanberg, Nancy; Spanner, Michael

1988-01-01

Recent research on the remote sensing of forest leaf and canopy biochemical contents suggests that the shortwave IR region contains this information; laboratory analyses of dry ground leaves have yielded reliable predictive relationships between both leaf nitrogen and lignin with near-IR spectra. Attention is given to the application of these laboratory techniques to a limited set of spectra from fresh, whole leaves of conifer species. The analysis of Airborne Imaging Spectrometer data reveals that total water content variations in deciduous forest canopies appear as overall shifts in the brightness of raw spectra.

Correlations between female breast density and biochemical markers.

PubMed

Kim, Ji-Hye; Lee, Hae-Kag; Cho, Jae-Hwan; Park, Hyong-Keun; Yang, Han-Jun

2015-07-01

[Purpose] The aim of this study was to identify biochemical markers related to breast density. The study was performed with 200 patients who received mammography and biochemical marker testing between March 1, 2014 to October 1, 2014. [Subjects and Methods] Following the American College of Radiology, Breast Imaging Reporting and Data System (ACR BI-RADS), breast parenchymal pattern density from mammography was categorized into four grades: grade 1, almost entirely fat; grade 2, fibroglandular densities; grade 3, heterogeneously dense; and grade 4, extremely dense. Regarding biochemical markers, subjects underwent blood and urine tests after a 12-h fast. We analyzed correlations among breast density, general characteristics, and biochemical markers. [Results] Breast density-related factors were age, height, weight, body mass index (BMI), hematocrit, MCH, RDW, AST, ALT, ALP, uric acid, γGT, triglycerides, total cholesterol, HDL-cholesterol, and LDL-cholesterol. [Conclusion] The results can be used as basic and comparative data for the prevention and early control of breast cancer.

Stochastic hybrid systems for studying biochemical processes.

PubMed

Singh, Abhyudai; Hespanha, João P

2010-11-13

Many protein and mRNA species occur at low molecular counts within cells, and hence are subject to large stochastic fluctuations in copy numbers over time. Development of computationally tractable frameworks for modelling stochastic fluctuations in population counts is essential to understand how noise at the cellular level affects biological function and phenotype. We show that stochastic hybrid systems (SHSs) provide a convenient framework for modelling the time evolution of population counts of different chemical species involved in a set of biochemical reactions. We illustrate recently developed techniques that allow fast computations of the statistical moments of the population count, without having to run computationally expensive Monte Carlo simulations of the biochemical reactions. Finally, we review different examples from the literature that illustrate the benefits of using SHSs for modelling biochemical processes.

Accelerator mass spectrometry in biomedical research

NASA Astrophysics Data System (ADS)

Vogel, J. S.; Turteltaub, K. W.

1994-06-01

Biological effects occur in natural systems at chemical concentrations of parts per billion (1:10 9) or less. Affected biomolecules may be separable in only milligram or microgram quantities. Quantification at attomole sensitivity is needed to study these interactions. AMS measures isotope concentrations to parts per 10 13-15 on milligram-sized samples and is ideal for quantifying long-lived radioisotopic labels for tracing biochemical pathways in natural systems. 14C-AMS has now been coupled to a variety of organic separation and definition technologies. Our primary research investigates pharmacokinetics and genotoxicities of toxins and drugs at very low doses. Human subjects research using AMS includes nutrition, toxicity and elemental balance studies. 3H, 41Ca and 26Al are also traced by AMS for fundamental biochemical kinetic research. Expansion of biomedical AMS awaits further development of biochemical and accelerator technologies designed specifically for these applications.

Organic solvent pretreatment of lignocellulosic biomass for biofuels and biochemicals: A review.

PubMed

Zhang, Ke; Pei, Zhijian; Wang, Donghai

2016-01-01

Lignocellulosic biomass represents the largest potential volume and lowest cost for biofuel and biochemical production. Pretreatment is an essential component of biomass conversion process, affecting a majority of downstream processes, including enzymatic hydrolysis, fermentation, and final product separation. Organic solvent pretreatment is recognized as an emerging way ahead because of its inherent advantages, such as the ability to fractionate lignocellulosic biomass into cellulose, lignin, and hemicellulose components with high purity, as well as easy solvent recovery and solvent reuse. Objectives of this review were to update and extend previous works on pretreatment of lignocellulosic biomass for biofuels and biochemicals using organic solvents, especially on ethanol, methanol, ethylene glycol, glycerol, acetic acid, and formic acid. Perspectives and recommendations were given to fully describe implementation of proper organic solvent pretreatment for future research. Copyright © 2015 Elsevier Ltd. All rights reserved.

40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

Code of Federal Regulations, 2011 CFR

2011-07-01

... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections 158.2081...

40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

Code of Federal Regulations, 2012 CFR

2012-07-01

... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections 158.2081...

40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

Code of Federal Regulations, 2014 CFR

2014-07-01

... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections 158.2081...

40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

Code of Federal Regulations, 2010 CFR

2010-07-01

... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections 158.2081...

40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

Code of Federal Regulations, 2013 CFR

2013-07-01

... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections 158.2081...

Incidence of Abnormal Liver Biochemical Tests in Hyperthyroidism

PubMed Central

Lin, Tiffany Y.; Shekar, Anshula O.; Li, Ning; Yeh, Michael W.; Saab, Sammy; Wilson, Mark; Leung, Angela M.

2017-01-01

Objective Abnormal serum liver function tests are common in patients with untreated thyrotoxicosis, even prior to the initiation of antithyroidal medications that may worsen their severity. There is a wide range of the incidence of these abnormalities in the published literature. The aim of this study was to assess the risks factors and threshold of thyrotoxicosis severity for developing an abnormal liver biochemical test upon the diagnosis of new thyrotoxicosis. Design Single-institution retrospective cohort study. Patients Patients ≥18 years old receiving medical care at a large, academic, urban U.S. medical center between 2002–2016. Measurements Inclusion criteria were a serum thyroid stimulating hormone [TSH] concentration < 0.3 mIU/L or ICD-9 code for thyrotoxicosis, with thyrotoxicosis confirmed by either a concurrent elevated serum triiodothyronine (T3) and/or thyroxine (T4) concentration [total or free] within 3 months), and an available liver biochemical test(s) within 6 months of thyrotoxicosis. The biochemical liver tests assessed were serum aspartate transaminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (AP), gamma-glutamyltransferase (GGT), total bilirubin, and conjugated bilirubin concentrations. Results In this cohort of 1,514 subjects, the overall incidence of any biochemical liver test abnormality within 6 months of thyrotoxicosis was 39%. An initial serum TSH concentration <0.02 mIU/L, male gender, and African-American race were significant predictors of an abnormal serum liver biochemical test within 6 months of the diagnosis of new-onset untreated thyrotoxicosis. Conclusions This study identifies risk factors for patients who develop an abnormal serum liver biochemical test result within 6 months of a diagnosis of untreated thyrotoxicosis. PMID:28199740

Incidence of abnormal liver biochemical tests in hyperthyroidism.

PubMed

Lin, Tiffany Y; Shekar, Anshula O; Li, Ning; Yeh, Michael W; Saab, Sammy; Wilson, Mark; Leung, Angela M

2017-05-01

Abnormal serum liver function tests are common in patients with untreated thyrotoxicosis, even prior to the initiation of antithyroidal medications that may worsen the severity of the abnormal serum liver biochemistries. There is a wide range of the incidence of these abnormalities in the published literature. The aim of this study was to assess the risks factors and threshold of thyrotoxicosis severity for developing an abnormal liver biochemical test upon the diagnosis of new thyrotoxicosis. Single-institution retrospective cohort study. Patients of ≥18 years old receiving medical care at a large, academic, urban US medical centre between 2002-2016. Inclusion criteria were a serum thyroid stimulating hormone (TSH) concentration of <0·3 mIU/l or ICD-9 code for thyrotoxicosis, with thyrotoxicosis confirmed by either a concurrent elevated serum triiodothyronine (T3) or thyroxine (T4) concentration ([total or free] within 3 months), and an available liver biochemical test(s) within 6 months of thyrotoxicosis. The biochemical liver tests assessed were serum aspartate transaminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (AP), gamma-glutamyltransferase (GGT), total bilirubin, and conjugated bilirubin concentrations. In this cohort of 1514 subjects, the overall incidence of any biochemical liver test abnormality within 6 months of thyrotoxicosis was 39%. An initial serum TSH concentration <0·02 mIU/l, male gender, and African-American race were significant predictors of an abnormal serum liver biochemical test within 6 months of the diagnosis of new-onset untreated thyrotoxicosis. This study identifies risk factors for patients who develop an abnormal serum liver biochemical test result within 6 months of a diagnosis of untreated thyrotoxicosis. © 2017 John Wiley & Sons Ltd.

An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems.

PubMed

Wu, Zujian; Pang, Wei; Coghill, George M

Computational modelling of biochemical systems based on top-down and bottom-up approaches has been well studied over the last decade. In this research, after illustrating how to generate atomic components by a set of given reactants and two user pre-defined component patterns, we propose an integrative top-down and bottom-up modelling approach for stepwise qualitative exploration of interactions among reactants in biochemical systems. Evolution strategy is applied to the top-down modelling approach to compose models, and simulated annealing is employed in the bottom-up modelling approach to explore potential interactions based on models constructed from the top-down modelling process. Both the top-down and bottom-up approaches support stepwise modular addition or subtraction for the model evolution. Experimental results indicate that our modelling approach is feasible to learn the relationships among biochemical reactants qualitatively. In addition, hidden reactants of the target biochemical system can be obtained by generating complex reactants in corresponding composed models. Moreover, qualitatively learned models with inferred reactants and alternative topologies can be used for further web-lab experimental investigations by biologists of interest, which may result in a better understanding of the system.

Biochemical, endocrine, and hematological factors in human oxygen tolerance extension: Predictive studies 6

NASA Technical Reports Server (NTRS)

Lambertsen, C. J.; Clark, J. M.

1992-01-01

The Predictive Studies VI (Biochemical, endocrine, and hematological factors in human oxygen tolerance extension) Program consisted of two related areas of research activity, integrated in design and performance, that were each based on an ongoing analysis of human organ oxygen tolerance data obtained for the continuous oxygen exposures of the prior Predictive Studies V Program. The two research areas effectively blended broad investigation of systematically varied intermittent exposure patterns in animals with very selective evaluation of specific exposure patterns in man.

Optical tweezers and multiphoton microscopies integrated photonic tool for mechanical and biochemical cell processes studies

NASA Astrophysics Data System (ADS)

de Thomaz, A. A.; Faustino, W. M.; Fontes, A.; Fernandes, H. P.; Barjas-Castro, M. d. L.; Metze, K.; Giorgio, S.; Barbosa, L. C.; Cesar, C. L.

2007-09-01

The research in biomedical photonics is clearly evolving in the direction of the understanding of biological processes at the cell level. The spatial resolution to accomplish this task practically requires photonics tools. However, an integration of different photonic tools and a multimodal and functional approach will be necessary to access the mechanical and biochemical cell processes. This way we can observe mechanicaly triggered biochemical events or biochemicaly triggered mechanical events, or even observe simultaneously mechanical and biochemical events triggered by other means, e.g. electricaly. One great advantage of the photonic tools is its easiness for integration. Therefore, we developed such integrated tool by incorporating single and double Optical Tweezers with Confocal Single and Multiphoton Microscopies. This system can perform 2-photon excited fluorescence and Second Harmonic Generation microscopies together with optical manipulations. It also can acquire Fluorescence and SHG spectra of specific spots. Force, elasticity and viscosity measurements of stretched membranes can be followed by real time confocal microscopies. Also opticaly trapped living protozoas, such as leishmania amazonensis. Integration with CARS microscopy is under way. We will show several examples of the use of such integrated instrument and its potential to observe mechanical and biochemical processes at cell level.

Biotinidase deficiency: Genotype-biochemical phenotype association in Brazilian patients

PubMed Central

Borsatto, Taciane; Sperb-Ludwig, Fernanda; Lima, Samyra E.; S. Carvalho, Maria R.; S. Fonseca, Pablo A.; S. Camelo, José; M. Ribeiro, Erlane; F. V. de Medeiros, Paula; M. Lourenço, Charles; F. M. de Souza, Carolina; Boy, Raquel; Félix, Têmis M.; M. Bittar, Camila; L. C. Pinto, Louise; C. Neto, Eurico; J. Blom, Henk; D. Schwartz, Ida V.

2017-01-01

Introduction The association between the BTD genotype and biochemical phenotype [profound biotinidase deficiency (BD), partial BD or heterozygous activity] is not always consistent. This study aimed to investigate the genotype-biochemical phenotype association in patients with low biotinidase activity. Methods All exons, the 5'UTR and the promoter of the BTD gene were sequenced in 72 Brazilian individuals who exhibited low biotinidase activity. For each patient, the expected biochemical phenotype based on the known genotype was compared with the observed biochemical phenotype. Additional non-genetic factors that could affect the biotinidase activity were also analysed. Results Most individuals were identified by neonatal screening (n = 66/72). When consecutive results for the same patient were compared, age, prematurity and neonatal jaundice appeared to affect the level of biotinidase activity. The biochemical phenotype at the time of the second blood collection changed in 11/22 patients compared to results from the first sample. Three novel variants were found: c.1337T>C (p.L446P), c.1466A>G (p.N489S) and c.962G>A (p.W321*). Some patients with the same genotype presented different biochemical phenotypes. The expected and observed biochemical phenotypes agreed in 68.5% of cases (concordant patients). The non-coding variants c.-183G>A, c.-315A>G and c.-514C>T were present in heterozygosis in 5/17 discordant patients. In addition, c.-183G>A and c.-514C>T were also present in 10/37 concordant patients. Conclusions The variants found in the promoter region do not appear to have a strong impact on biotinidase activity. Since there is a disparity between the BTD genotype and biochemical phenotype, and biotinidase activity may be affected by both genetic and non-genetic factors, we suggest that the diagnosis of BD should be based on more than one measurement of plasma biotinidase activity. DNA analysis can be of additional relevance to differentiate between partial BD and

Biochemical studies in patients with hyperinsulinaemic hypoglycaemia.

PubMed

Al-Otaibi, Hessah; Senniappan, Senthil; Alam, Syeda; Hussain, Khalid

2013-11-01

Hyperinsulinaemic hypoglycaemia (HH) is characterised by the dysregulated secretion of insulin from the pancreatic β-cell. It is a major cause of severe and persistent hypoglycaemia in the newborn period. There have been no previous studies assessing the various biochemical alterations at the time of hypoglycaemia in relation to the severity of the hypoglycaemia. Biochemical and clinical data were collected on 90 neonates (gestational age range, 32-42 weeks) with a diagnosis of HH [(based on glucose requirement  > 8 mg/kg/min) and the biochemical profile of insulin action (low beta-hydroxybutyrate and fatty acid concentrations)] who had undergone fasting studies. The results showed that (a) the serum insulin level measured at the time of hypoglycaemia had no correlation with the severity of hypoglycaemia, (b) the serum insulin level was undetectable despite severe hypoglycaemia in a significant proportion of patients, (c) there was no correlation between the birth weight and the insulin level at the time of hypoglycaemia, (d) the suppression of ketogenesis was more marked than that of the non-esterified fatty acids. This study suggests that the diagnosis of HH should not rely solely on a raised serum insulin level at the time of hypoglycaemia but on the constellation of clinical and biochemical findings.

Biochemical mutagens affect the preservation of fungi and biodiversity estimations.

PubMed

Paterson, R Russell M; Lima, Nelson

2013-01-01

Many fungi have significant industrial applications or biosafety concerns and maintaining the original characteristics is essential. The preserved fungi have to represent the situation in nature for posterity, biodiversity estimations, and taxonomic research. However, spontaneous fungal mutations and secondary metabolites affecting producing fungi are well known. There is increasing interest in the preservation of microbes in Biological Resource Centers (BRC) to ensure that the organisms remain viable and stable genetically. It would be anathema if they contacted mutagens routinely. However, for the purpose of this discussion, there are three potential sources of biochemical mutagens when obtaining individual fungi from the environment: (a) mixtures of microorganisms are plated routinely onto growth media containing mutagenic antibiotics to control overgrowth by contaminants, (b) the microbial mixtures may contain microorganisms capable of producing mutagenic secondary metabolites, and (c) target fungi for isolation may produce "self" mutagens in pure culture. The probability that these compounds could interact with fungi undermines confidence in the preservation process and the potential effects of these biochemical mutagens are considered for the first time on strains held in BRC in this review.

40 CFR 82.11 - Exports of class I controlled substances to Article 5 Parties.

Code of Federal Regulations, 2010 CFR

2010-07-01

... AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) PROTECTION OF STRATOSPHERIC OZONE Production and Consumption...) CFC-11 Honeywell 7,150 Sigma Aldrich 1 CFC-113 Fisher Scientific 5 Honeywell 313,686 Sigma Aldrich 48...

Biochemical characteristics among Mycobacterium bovis BCG substrains.

PubMed

Hayashi, Daisuke; Takii, Takemasa; Mukai, Tetsu; Makino, Masahiko; Yasuda, Emi; Horita, Yasuhiro; Yamamoto, Ryuji; Fujiwara, Akiko; Kanai, Keita; Kondo, Maki; Kawarazaki, Aya; Yano, Ikuya; Yamamoto, Saburo; Onozaki, Kikuo

2010-05-01

In order to evaluate the biochemical characteristics of 14 substrains of Mycobacterium bovis bacillus Calmette Guérin (BCG) - Russia, Moreau, Japan, Sweden, Birkhaug, Danish, Glaxo, Mexico, Tice, Connaught, Montreal, Phipps, Australia and Pasteur - we performed eight different biochemical tests, including those for nitrate reduction, catalase, niacin accumulation, urease, Tween 80 hydrolysis, pyrazinamidase, p-amino salicylate degradation and resistance to thiophene 2-carboxylic acid hydrazide. Catalase activities of the substrains were all low. Data for nitrate reduction, niacin accumulation, Tween 80 hydrolysis, susceptibility to hydrogen peroxide and nitrate, and optimal pH for growth were all variable among these substrains. These findings suggest that the heterogeneities of biochemical characteristics are relevant to the differences in resistance of BCG substrains to environmental stress. The study also contributes to the re-evaluation of BCG substrains for use as vaccines.

Biochemical Characterization of Prion Strains in Bank Voles

PubMed Central

Pirisinu, Laura; Marcon, Stefano; Di Bari, Michele Angelo; D’Agostino, Claudia; Agrimi, Umberto; Nonno, Romolo

2013-01-01

Prions exist as different strains exhibiting distinct disease phenotypes. Currently, the identification of prion strains is still based on biological strain typing in rodents. However, it has been shown that prion strains may be associated with distinct PrPSc biochemical types. Taking advantage of the availability of several prion strains adapted to a novel rodent model, the bank vole, we investigated if any prion strain was actually associated with distinctive PrPSc biochemical characteristics and if it was possible to univocally identify strains through PrPSc biochemical phenotypes. We selected six different vole-adapted strains (three human-derived and three animal-derived) and analyzed PrPSc from individual voles by epitope mapping of protease resistant core of PrPSc (PrPres) and by conformational stability and solubility assay. Overall, we discriminated five out of six prion strains, while two different scrapie strains showed identical PrPSc types. Our results suggest that the biochemical strain typing approach here proposed was highly discriminative, although by itself it did not allow us to identify all prion strains analyzed. PMID:25437201

Craniometaphyseal dysplasia with obvious biochemical abnormality and rickets-like features.

PubMed

Wu, Bo; Jiang, Yan; Wang, Ou; Li, Mei; Xing, Xiao-Ping; Xia, Wei-Bo

2016-05-01

Craniometaphyseal dysplasia (CMD) is a rare genetic disorder that is characterized by progressive sclerosis of the craniofacial bones and metaphyseal widening of long bones, and biochemical indexes were mostly normal. To further the understanding of the disease from a biochemical perspective, we reported a CMD case with obviously abnormal biochemical indexes. A 1-year-old boy was referred to our clinic. Biochemical test showed obviously increased alkaline phosphatase (ALP) and parathyroid hormone (PTH), mild hypocalcemia and hypophosphatemia. Moreover, significant elevated receptor activator of nuclear factor kappa-B ligand (RANKL) level, but normal β-C-terminal telopeptide of type I collagen (β-CTX) concentration were revealed. He was initially suspected of rickets, because the radiological examination also showed broadened epiphysis in his long bones. Supplementation with calcium and calcitriol alleviated biochemical abnormality. However, the patient gradually developed osteosclerosis which was inconformity with rickets. Considering that he was also presented with facial paralysis and nasal obstruction symptom, the diagnosis of craniometaphyseal dysplasia was suspected, and then was confirmed by the mutation analysis of ANKH of the proband and his family, which showed a de novo heterozygous mutation (C1124-1126delCCT) on exon 9. Our study revealed that obvious biochemical abnormality and rickets-like features might present as uncommon characteristics in CMD patients, and the calcium and calcitriol supplementation could alleviate biochemical abnormalities. Furthermore, although early osteoclast differentiation factor was excited in CMD patient, activity of osteoclast was still inert. Copyright © 2016. Published by Elsevier B.V.

Varenicline in Autism: Theory and Case Report of Clinical and Biochemical Changes.

PubMed

Mostafavi, Mojdeh; Hardy, Paul; Arnold, L Eugene

2016-11-01

To explore the potential benefits of varenicline (CHANTIX ® ), a highly specific partial agonist of neuronal α4β2 nicotinic acetylcholine receptors (nAChR), for autistic symptoms, and present resulting biochemical changes in light of dopamine-related genotype. The clinical and biochemical changes exhibited by a 19-year-old severely autistic man following the use of low-dose varenicline in an ABA experiment of nature, and his genotype, were extracted from chart review. Clinical outcome was measured by the Ohio Autism Clinical Impression Scale and 12 relevant urine and saliva metabolites were measured by Neuroscience Laboratory. With varenicline, this patient improved clinically and autonomic biochemical indicators in saliva and urine normalized, including dopamine, 3,4-dihydroxyphenylacetic acid (DOPAC), epinephrine, norepinephrine, taurine, and histamine levels. In addition, with varenicline, the dopamine D1 receptor (DRD1) antibody titer as well as the percent of baseline calmodulin-dependent protein kinase II (CaM KII) activity dropped significantly. When varenicline stopped, he deteriorated; when it was resumed, he again improved. Doses of 0.5, 1, and 2 mg daily were tried before settling on a dose of 1.5 mg daily. He has remained on varenicline for over a year with no noticeable side effects. This report is, to the best of our knowledge, only the second to demonstrate positive effects of varenicline in autism, the first to show it in a severe case, and the first to show normalization of biochemical parameters related to genotype. As with the previous report, these encouraging results warrant further controlled research before clinical recommendations can be made.

A Biochemical Approach to the Problem of Dyslexia.

ERIC Educational Resources Information Center

Baker, Sidney McDonald

1985-01-01

The paper presents the case of a sixth-grade boy, labeled dyslexic, who responded positively to a biochemical approach. Remedy of iron, zinc, and Vitamin B-6 deficiencies as well as an imbalance of fatty acids resulted in improvements in hair and skin and also in reading. A biochemical approach to behavior problems is proposed. (Author/CL)

Developments in commercially produced microbials at Biochem Products

Treesearch

John Lublinkhof; Douglas H. Ross

1985-01-01

Biochem Products is part of a large industrial and scientific family - the Solvay Group. Solvay, headquartered in Brussels, Belgium is a multinational company with 46,000 employees worldwide. In the U.S., our working partners include a large polymer manufacturer, a peroxygen producer and a leading poultry and animal health products company. Biochem Products is a...

Management Options for Biochemically Recurrent Prostate Cancer.

PubMed

Fakhrejahani, Farhad; Madan, Ravi A; Dahut, William L

2017-05-01

Prostate cancer is the most common solid tumor malignancy in men worldwide. Treatment with surgery and radiation can be curative in organ-confined disease. Unfortunately, about one third of men develop biochemically recurrent disease based only on rising prostate-specific antigen (PSA) in the absence of visible disease on conventional imaging. For these patients with biochemical recurrent prostate cancer, there is no uniform guideline for subsequent management. Based on available data, it seems prudent that biochemical recurrent prostate cancer should initially be evaluated for salvage radiation or prostatectomy, with curative intent. In selected cases, high-intensity focused ultrasound and cryotherapy may be considered in patients that meet very narrow criteria as defined by non-randomized trials. If salvage options are not practical or unsuccessful, androgen deprivation therapy (ADT) is a standard option for disease control. While some patients prefer ADT to manage the disease immediately, others defer treatment because of the associated toxicity. In the absence of definitive randomized data, patients may be followed using PSA doubling time as a trigger to initiate ADT. Based on retrospective data, a PSA doubling time of less than 3-6 months has been associated with near-term development of metastasis and thus could be used signal to initiate ADT. Once treatment is begun, patients and their providers can choose between an intermittent and continuous ADT strategy. The intermittent approach may limit side effects but in patients with metastatic disease studies could not exclude a 20% greater risk of death. In men with biochemical recurrence, large studies have shown that intermittent therapy is non-inferior to continuous therapy, thus making this a reasonable option. Since biochemically recurrent prostate cancer is defined by technological limitations of radiographic detection, as new imaging (i.e., PSMA) strategies are developed, it may alter how the disease is

Kombucha tea fermentation: Microbial and biochemical dynamics.

PubMed

Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

2016-03-02

Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

Functional Polymers and Sequential Copolymers by Phase Transfer Catalysis. Synthesis of Thermotropic Side-Chain Liquid Crystalline Polymers Containing a Poly(2,6-Dimethyl-1,4-Phenylene Oxide) Main Chain.

DTIC Science & Technology

1986-10-01

bromovalerate (Aldrich, 99%), 5-bromovaleronitrile (Aldrich, 95%), and 11-bromoundecanoic acid (Aldrich, 99%) were used without further purification. 4...atic proton’s). 71 Cm, 4 aromatic X~tons). C. Synthesis of 4- 4-oxybipheny1 butyrnc acid , 4-(4-inethoxy 4’-oxy- I hen 1 butyrnc acid , 5-(4-oxybipheny1...valeric acid , 5-(4-inethoxy-4-oxy- bi heny1 valeric acid . 11- 4-ox bipheny1 undecanoic acid and 11- 4-inethox -4 -ox biphenylundecanoic acid . The

Maximizing the Biochemical Resolving Power of Fluorescence Microscopy

PubMed Central

Esposito, Alessandro; Popleteeva, Marina; Venkitaraman, Ashok R.

2013-01-01

Most recent advances in fluorescence microscopy have focused on achieving spatial resolutions below the diffraction limit. However, the inherent capability of fluorescence microscopy to non-invasively resolve different biochemical or physical environments in biological samples has not yet been formally described, because an adequate and general theoretical framework is lacking. Here, we develop a mathematical characterization of the biochemical resolution in fluorescence detection with Fisher information analysis. To improve the precision and the resolution of quantitative imaging methods, we demonstrate strategies for the optimization of fluorescence lifetime, fluorescence anisotropy and hyperspectral detection, as well as different multi-dimensional techniques. We describe optimized imaging protocols, provide optimization algorithms and describe precision and resolving power in biochemical imaging thanks to the analysis of the general properties of Fisher information in fluorescence detection. These strategies enable the optimal use of the information content available within the limited photon-budget typically available in fluorescence microscopy. This theoretical foundation leads to a generalized strategy for the optimization of multi-dimensional optical detection, and demonstrates how the parallel detection of all properties of fluorescence can maximize the biochemical resolving power of fluorescence microscopy, an approach we term Hyper Dimensional Imaging Microscopy (HDIM). Our work provides a theoretical framework for the description of the biochemical resolution in fluorescence microscopy, irrespective of spatial resolution, and for the development of a new class of microscopes that exploit multi-parametric detection systems. PMID:24204821

Fast and Cost-Effective Biochemical Spectrophotometric Analysis of Solution of Insect "Blood" and Body Surface Elution.

PubMed

Łoś, Aleksandra; Strachecka, Aneta

2018-05-09

Using insect hemolymph ("blood") and insect body surface elutions, researchers can perform rapid and cheap biochemical analyses to determine the insect's immunology status. The authors of this publication describe a detailed methodology for a quick marking of the concentration of total proteins and evaluation of the proteolytic system activity (acid, neutral, and alkaline proteases and protease inhibitors), as well as a methodology for quick "liver" tests in insects: alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and urea and glucose concentration analyses. The meaning and examples of an interpretation of the results of the presented methodology for biochemical parameter determination are described for the example of honey bees.

Biochemical Education in Brazil.

ERIC Educational Resources Information Center

Vella, F.

1988-01-01

Described are discussions held concerning the problems of biochemical education in Brazil at a meeting of the Sociedade Brazileira de Bioquimica in April 1988. Also discussed are other visits that were made to universities in Brazil. Three major recommendations to improve the state of biochemistry education in Brazil are presented. (CW)

Luteal phase deficiency in regularly menstruating women: prevalence and overlap in identification based on clinical and biochemical diagnostic criteria.

PubMed

Schliep, Karen C; Mumford, Sunni L; Hammoud, Ahmad O; Stanford, Joseph B; Kissell, Kerri A; Sjaarda, Lindsey A; Perkins, Neil J; Ahrens, Katherine A; Wactawski-Wende, Jean; Mendola, Pauline; Schisterman, Enrique F

2014-06-01

Although adequate luteal hormone production is essential for establishing pregnancy, luteal phase deficiency (LPD) is poorly characterized among eumenorrheic women. We assessed the prevalence and overlap of two established LPD diagnostic criteria: short luteal phase duration less than10 days (clinical LPD) and suboptimal luteal progesterone of 5 ng/mL or less (biochemical LPD) and their relationship with reproductive hormone concentrations. We conducted a prospective study in western New York (2005-2007) following 259 women, aged 18-44 years, for up to two menstrual cycles. Among ovulatory cycles with recorded cycle lengths (n = 463), there were 41 cycles (8.9%) with clinical LPD, 39 cycles (8.4%) with biochemical LPD, and 20 cycles (4.3%) meeting both criteria. Recurrent clinical and biochemical LPD was observed in eight (3.4%) and five (2.1%) women, respectively. Clinical and biochemical LPD were each associated with lower follicular estradiol (both P ≤ .001) and luteal estradiol (P = .03 and P = .02, respectively) after adjusting for age, race, and percentage body fat. Clinical, but not biochemical, LPD was associated with lower LH and FSH across all phases of the cycle (P ≤ .001). Clinical and biochemical LPD were evident among regularly menstruating women. Estradiol was lower in LPD cycles under either criterion, but LH and FSH were lower only in association with shortened luteal phase (ie, clinical LPD), indicating that clinical and biochemical LPD may reflect different underlying mechanisms. Identifying ovulation in combination with a well-timed luteal progesterone measurement may serve as a cost-effective and specific tool for LPD assessment by clinicians and researchers.

Weak Perturbations of Biochemical Oscillators

NASA Astrophysics Data System (ADS)

Gailey, Paul

2001-03-01

Biochemical oscillators may play important roles in gene regulation, circadian rhythms, physiological signaling, and sensory processes. These oscillations typically occur inside cells where the small numbers of reacting molecules result in fluctuations in the oscillation period. Some oscillation mechanisms have been reported that resist fluctuations and produce more stable oscillations. In this paper, we consider the use of biochemical oscillators as sensors by comparing inherent fluctuations with the effects of weak perturbations to one of the reactants. Such systems could be used to produce graded responses to weak stimuli. For example, a leading hypothesis to explain geomagnetic navigation in migrating birds and other animals is based on magnetochemical reactions. Because the magnitude of magnetochemical effects is small at geomagnetic field strengths, a sensitive, noise resistant detection scheme would be required.

Discovering Reliable Sources of Biochemical Thermodynamic Data to Aid Students' Understanding

ERIC Educational Resources Information Center

Me´ndez, Eduardo; Cerda´, María F.

2016-01-01

Students of physical chemistry in biochemical disciplines need biochemical examples to capture the need, not always understood, of a difficult area in their studies. The use of thermodynamic data in the chemical reference state may lead to incorrect interpretations in the analysis of biochemical examples when the analysis does not include relevant…

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis.

PubMed

Lee, Jessica J Y; Gottlieb, Michael M; Lever, Jake; Jones, Steven J M; Blau, Nenad; van Karnebeek, Clara D M; Wasserman, Wyeth W

2018-05-01

Phenomics is the comprehensive study of phenotypes at every level of biology: from metabolites to organisms. With high throughput technologies increasing the scope of biological discoveries, the field of phenomics has been developing rapid and precise methods to collect, catalog, and analyze phenotypes. Such methods have allowed phenotypic data to be widely used in medical applications, from assisting clinical diagnoses to prioritizing genomic diagnoses. To channel the benefits of phenomics into the field of inborn errors of metabolism (IEM), we have recently launched IEMbase, an expert-curated knowledgebase of IEM and their disease-characterizing phenotypes. While our efforts with IEMbase have realized benefits, taking full advantage of phenomics requires a comprehensive curation of IEM phenotypes in core phenomics projects, which is dependent upon contributions from the IEM clinical and research community. Here, we assess the inclusion of IEM biochemical phenotypes in a core phenomics project, the Human Phenotype Ontology. We then demonstrate the utility of biochemical phenotypes using a text-based phenomics method to predict gene-disease relationships, showing that the prediction of IEM genes is significantly better using biochemical rather than clinical profiles. The findings herein provide a motivating goal for the IEM community to expand the computationally accessible descriptions of biochemical phenotypes associated with IEM in phenomics resources.

[Biochemical failure after curative treatment for localized prostate cancer].

PubMed

Zouhair, Abderrahim; Jichlinski, Patrice; Mirimanoff, René-Olivier

2005-12-07

Biochemical failure after curative treatment for localized prostate cancer is frequent. The diagnosis of biochemical failure is clear when PSA levels rise after radical prostatectomy, but may be more difficult after external beam radiation therapy. The main difficulty once biochemical failure is diagnosed is to distinguish between local and distant failure, given the low sensitivity of standard work-up exams. Metabolic imaging techniques currently under evaluation may in the future help us to localize the site of failures. There are several therapeutic options depending on the initial curative treatment, each with morbidity risks that should be considered in multidisciplinary decision-making.

Validation of artificial neural network models for predicting biochemical markers associated with male infertility.

PubMed

Vickram, A S; Kamini, A Rao; Das, Raja; Pathy, M Ramesh; Parameswari, R; Archana, K; Sridharan, T B

2016-08-01

Seminal fluid is the secretion from many glands comprised of several organic and inorganic compounds including free amino acids, proteins, fructose, glucosidase, zinc, and other scavenging elements like Mg(2+), Ca(2+), K(+), and Na(+). Therefore, in the view of development of novel approaches and proper diagnosis to male infertility, overall understanding of the biochemical and molecular composition and its role in regulation of sperm quality is highly desirable. Perhaps this can be achieved through artificial intelligence. This study was aimed to elucidate and predict various biochemical markers present in human seminal plasma with three different neural network models. A total of 177 semen samples were collected for this research (both fertile and infertile samples) and immediately processed to prepare a semen analysis report, based on the protocol of the World Health Organization (WHO [2010]). The semen samples were then categorized into oligoasthenospermia (n=35), asthenospermia (n=35), azoospermia (n=22), normospermia (n=34), oligospermia (n=34), and control (n=17). The major biochemical parameters like total protein content, fructose, glucosidase, and zinc content were elucidated by standard protocols. All the biochemical markers were predicted by using three different artificial neural network (ANN) models with semen parameters as inputs. Of the three models, the back propagation neural network model (BPNN) yielded the best results with mean absolute error 0.025, -0.080, 0.166, and -0.057 for protein, fructose, glucosidase, and zinc, respectively. This suggests that BPNN can be used to predict biochemical parameters for the proper diagnosis of male infertility in assisted reproductive technology (ART) centres. AAS: absorption spectroscopy; AI: artificial intelligence; ANN: artificial neural networks; ART: assisted reproductive technology; BPNN: back propagation neural network model; DT: decision tress; MLP: multilayer perceptron; PESA: percutaneous

WASp family verprolin-homologous protein-2 (WAVE2) and Wiskott-Aldrich syndrome protein (WASp) engage in distinct downstream signaling interactions at the T cell antigen receptor site.

PubMed

Pauker, Maor H; Reicher, Barak; Joseph, Noah; Wortzel, Inbal; Jakubowicz, Shlomi; Noy, Elad; Perl, Orly; Barda-Saad, Mira

2014-12-12

T cell antigen receptor (TCR) engagement has been shown to activate pathways leading to actin cytoskeletal polymerization and reorganization, which are essential for lymphocyte activation and function. Several actin regulatory proteins were implicated in regulating the actin machinery, such as members of the Wiskott-Aldrich syndrome protein (WASp) family. These include WASp and the WASp family verprolin-homologous protein-2 (WAVE2). Although WASp and WAVE2 share several structural features, the precise regulatory mechanisms and potential redundancy between them have not been fully characterized. Specifically, unlike WASp, the dynamic molecular interactions that regulate WAVE2 recruitment to the cell membrane and specifically to the TCR signaling complex are largely unknown. Here, we identify the molecular mechanism that controls the recruitment of WAVE2 in comparison with WASp. Using fluorescence resonance energy transfer (FRET) and novel triple-color FRET (3FRET) technology, we demonstrate how WAVE2 signaling complexes are dynamically regulated during lymphocyte activation in vivo. We show that, similar to WASp, WAVE2 recruitment to the TCR site depends on protein-tyrosine kinase, ZAP-70, and the adaptors LAT, SLP-76, and Nck. However, in contrast to WASp, WAVE2 leaves this signaling complex and migrates peripherally together with vinculin to the membrane leading edge. Our experiments demonstrate that WASp and WAVE2 differ in their dynamics and their associated proteins. Thus, this study reveals the differential mechanisms regulating the function of these cytoskeletal proteins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Universal dynamical properties preclude standard clustering in a large class of biochemical data.

PubMed

Gomez, Florian; Stoop, Ralph L; Stoop, Ruedi

2014-09-01

Clustering of chemical and biochemical data based on observed features is a central cognitive step in the analysis of chemical substances, in particular in combinatorial chemistry, or of complex biochemical reaction networks. Often, for reasons unknown to the researcher, this step produces disappointing results. Once the sources of the problem are known, improved clustering methods might revitalize the statistical approach of compound and reaction search and analysis. Here, we present a generic mechanism that may be at the origin of many clustering difficulties. The variety of dynamical behaviors that can be exhibited by complex biochemical reactions on variation of the system parameters are fundamental system fingerprints. In parameter space, shrimp-like or swallow-tail structures separate parameter sets that lead to stable periodic dynamical behavior from those leading to irregular behavior. We work out the genericity of this phenomenon and demonstrate novel examples for their occurrence in realistic models of biophysics. Although we elucidate the phenomenon by considering the emergence of periodicity in dependence on system parameters in a low-dimensional parameter space, the conclusions from our simple setting are shown to continue to be valid for features in a higher-dimensional feature space, as long as the feature-generating mechanism is not too extreme and the dimension of this space is not too high compared with the amount of available data. For online versions of super-paramagnetic clustering see http://stoop.ini.uzh.ch/research/clustering. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Recommendations for terminology and databases for biochemical thermodynamics.

PubMed

Alberty, Robert A; Cornish-Bowden, Athel; Goldberg, Robert N; Hammes, Gordon G; Tipton, Keith; Westerhoff, Hans V

2011-05-01

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature. Copyright © 2011 Elsevier B.V. All rights reserved.

Conditions for duality between fluxes and concentrations in biochemical networks

PubMed Central

Fleming, Ronan M.T.; Vlassis, Nikos; Thiele, Ines; Saunders, Michael A.

2016-01-01

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality. The condition prescribes that, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes. PMID:27345817

Conditions for duality between fluxes and concentrations in biochemical networks

DOE PAGES

Fleming, Ronan M. T.; Vlassis, Nikos; Thiele, Ines; ...

2016-06-23

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We alsomore » provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality.The condition prescribes that, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes« less

Conditions for duality between fluxes and concentrations in biochemical networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fleming, Ronan M. T.; Vlassis, Nikos; Thiele, Ines

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We alsomore » provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality.The condition prescribes that, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes« less

Self-organizing ontology of biochemically relevant small molecules

PubMed Central

2012-01-01

Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of

Advances in citric acid fermentation by Aspergillus niger: biochemical aspects, membrane transport and modeling.

PubMed

Papagianni, Maria

2007-01-01

Citric acid is regarded as a metabolite of energy metabolism, of which the concentration will rise to appreciable amounts only under conditions of substantive metabolic imbalances. Citric acid fermentation conditions were established during the 1930s and 1940s, when the effects of various medium components were evaluated. The biochemical mechanism by which Aspergillus niger accumulates citric acid has continued to attract interest even though its commercial production by fermentation has been established for decades. Although extensive basic biochemical research has been carried out with A. niger, the understanding of the events relevant for citric acid accumulation is not completely understood. This review is focused on citric acid fermentation by A. niger. Emphasis is given to aspects of fermentation biochemistry, membrane transport in A. niger and modeling of the production process.

A Course in... Biochemical Engineering.

ERIC Educational Resources Information Center

Ng, Terry K-L.; And Others

1988-01-01

Describes a chemical engineering course for senior undergraduates and first year graduate students in biochemical engineering. Discusses five experiments used in the course: aseptic techniques, dissolved oxygen measurement, oxygen uptake by yeast, continuous sterilization, and cultivation of microorganisms. (MVL)

A grid layout algorithm for automatic drawing of biochemical networks.

PubMed

Li, Weijiang; Kurata, Hiroyuki

2005-05-01

Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/

40 CFR 158.2050 - Biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides human health... § 158.2050 Biochemical pesticides human health assessment data requirements table. (a) General. (1... table shows the data requirements for biochemical pesticides human health assessment. The test notes are...

40 CFR 158.2050 - Biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides human health... § 158.2050 Biochemical pesticides human health assessment data requirements table. (a) General. (1... table shows the data requirements for biochemical pesticides human health assessment. The test notes are...

40 CFR 158.2050 - Biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides human health... § 158.2050 Biochemical pesticides human health assessment data requirements table. (a) General. (1... table shows the data requirements for biochemical pesticides human health assessment. The test notes are...

40 CFR 158.2050 - Biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides human health... § 158.2050 Biochemical pesticides human health assessment data requirements table. (a) General. (1... table shows the data requirements for biochemical pesticides human health assessment. The test notes are...

40 CFR 158.2050 - Biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides human health... § 158.2050 Biochemical pesticides human health assessment data requirements table. (a) General. (1... table shows the data requirements for biochemical pesticides human health assessment. The test notes are...

Luteal Phase Deficiency in Regularly Menstruating Women: Prevalence and Overlap in Identification Based on Clinical and Biochemical Diagnostic Criteria

PubMed Central

Schliep, Karen C.; Mumford, Sunni L.; Hammoud, Ahmad O.; Stanford, Joseph B.; Kissell, Kerri A.; Sjaarda, Lindsey A.; Perkins, Neil J.; Ahrens, Katherine A.; Wactawski-Wende, Jean; Mendola, Pauline

2014-01-01

Context: Although adequate luteal hormone production is essential for establishing pregnancy, luteal phase deficiency (LPD) is poorly characterized among eumenorrheic women. Objective: We assessed the prevalence and overlap of two established LPD diagnostic criteria: short luteal phase duration less than10 days (clinical LPD) and suboptimal luteal progesterone of 5 ng/mL or less (biochemical LPD) and their relationship with reproductive hormone concentrations. Design, Setting, and Participants: We conducted a prospective study in western New York (2005–2007) following 259 women, aged 18–44 years, for up to two menstrual cycles. Results: Among ovulatory cycles with recorded cycle lengths (n = 463), there were 41 cycles (8.9%) with clinical LPD, 39 cycles (8.4%) with biochemical LPD, and 20 cycles (4.3%) meeting both criteria. Recurrent clinical and biochemical LPD was observed in eight (3.4%) and five (2.1%) women, respectively. Clinical and biochemical LPD were each associated with lower follicular estradiol (both P ≤ .001) and luteal estradiol (P = .03 and P = .02, respectively) after adjusting for age, race, and percentage body fat. Clinical, but not biochemical, LPD was associated with lower LH and FSH across all phases of the cycle (P ≤ .001). Conclusions: Clinical and biochemical LPD were evident among regularly menstruating women. Estradiol was lower in LPD cycles under either criterion, but LH and FSH were lower only in association with shortened luteal phase (ie, clinical LPD), indicating that clinical and biochemical LPD may reflect different underlying mechanisms. Identifying ovulation in combination with a well-timed luteal progesterone measurement may serve as a cost-effective and specific tool for LPD assessment by clinicians and researchers. PMID:24606080

Fundamental Reactive Characterization of Novel Nano-Scale Assembled Fuel/Oxidizers Using a New Mass-Spectrometry T-Jump Approach

DTIC Science & Technology

2014-03-01

Flame 2009, 156, (2), 322-333. 130 YEAR 4: The report has two sections 1. Ignition Initiation of Various Nanothermites 2. Alane as a dopant in...Lake ~ 236 Diiodine pentoxide (I2O5) Sigma-Aldrich < 50 Tin (IV) oxide (SnO2) Sigma-Aldrich < 50 Cobalt (II, III) oxide (Co3O4) Sigma-Aldrich < 50...and O2 (g)[53]. AgI (s) then undergoes melting at 831 K. Cobalt (II, III) oxide (Co3O4) decomposes around 1173 K into CoO (s) and O2 (g). The

Development of a new first-aid biochemical detector

NASA Astrophysics Data System (ADS)

Hu, Jingfei; Liao, Haiyang; Su, Shilin; Ding, Hao; Liu, Suquan

2016-10-01

The traditional biochemical detector exhibits poor adaptability, inconvenient carrying and slow detection, which can't meet the needs of first-aid under field condition like natural or man-made disasters etc. Therefore a scheme of first-aid biochemical detector based on MOMES Micro Spectrometer, UV LED and Photodiode was proposed. An optical detection structure combined continuous spectrum sweep with fixed wavelength measurement was designed, which adopted mobile detection optical path consisting of Micro Spectrometer and Halogen Lamp to detect Chloride (Cl-), Creatinine (Cre), Glucose (Glu), Hemoglobin (Hb). The UV LED and Photodiode were designed to detect Potassium (K-), Carbon dioxide (CO2), Sodium (Na+). According to the field diagnosis and treatment requirements, we designed the embedded control hardware circuit and software system, the prototype of first-aid biochemical detector was developed and the clinical trials were conducted. Experimental results show that the sample's absorbance repeatability is less than 2%, the max coefficient of variation (CV) in the batch repeatability test of all 7 biochemical parameters in blood samples is 4.68%, less than the clinical requirements 10%, the correlation coefficient (R2) in the clinical contrast test with AU5800 is almost greater than 0.97. To sum up, the prototype meets the requirements of clinical application.

Microfluidics meets metabolomics to reveal the impact of Campylobacter jejuni infection on biochemical pathways.

PubMed

Mortensen, Ninell P; Mercier, Kelly A; McRitchie, Susan; Cavallo, Tammy B; Pathmasiri, Wimal; Stewart, Delisha; Sumner, Susan J

2016-06-01

Microfluidic devices that are currently being used in pharmaceutical research also have a significant potential for utilization in investigating exposure to infectious agents. We have established a microfluidic device cultured with Caco-2 cells, and utilized metabolomics to investigate the biochemical responses to the bacterial pathogen Campylobacter jejuni. In the microfluidic devices, Caco-2 cells polarize at day 5, are uniform, have defined brush borders and tight junctions, and form a mucus layer. Metabolomics analysis of cell culture media collected from both Caco-2 cell culture systems demonstrated a more metabolic homogenous biochemical profile in the media collected from microfluidic devices, compared with media collected from transwells. GeneGo pathway mapping indicated that aminoacyl-tRNA biosynthesis was perturbed by fluid flow, suggesting that fluid dynamics and shear stress impacts the cells translational quality control. Both microfluidic device and transwell culturing systems were used to investigate the impact of Campylobacter jejuni infection on biochemical processes. Caco-2 cells cultured in either system were infected at day 5 with C. jejuni 81-176 for 48 h. Metabolomics analysis clearly differentiated C. jejuni 81-176 infected and non-infected medias collected from the microfluidic devices, and demonstrated that C. jejuni 81-176 infection in microfluidic devices impacts branched-chain amino acid metabolism, glycolysis, and gluconeogenesis. In contrast, no distinction was seen in the biochemical profiles of infected versus non-infected media collected from cells cultured in transwells. Microfluidic culturing conditions demonstrated a more metabolically homogenous cell population, and present the opportunity for studying host-pathogen interactions for extended periods of time.

Microfluidics Meets Metabolomics to Reveal the Impact of Campylobacter jejuni Infection on Biochemical Pathways

PubMed Central

Mortensen, Ninell P.; Mercier, Kelly A.; McRitchie, Susan; Cavallo, Tammy B.; Pathmasiri, Wimal; Stewart, Delisha; Sumner, Susan J.

2016-01-01

Microfluidic devices that are currently being used in pharmaceutical research also have a significant potential for utilization in investigating exposure to infectious agents. We have established a microfluidic device cultured with Caco-2 cells, and utilized metabolomics to investigate the biochemical responses to the bacterial pathogen Campylobacter jejuni. In the microfluidic devices, Caco-2 cells polarize at day 5, are uniform, have defined brush borders and tight junctions, and form a mucus layer. Metabolomics analysis of cell culture media collected from both Caco-2 cell culture systems demonstrated a more metabolic homogenous biochemical profile in the media collected from microfluidic devices, compared with media collected from transwells. GeneGo pathway mapping indicated that aminoacyl-tRNA biosynthesis was perturbed by fluid flow, suggesting that fluid dynamics and shear stress impacts the cells translational quality control. Both microfluidic device and transwell culturing systems were used to investigate the impact of Campylobacter jejuni infection on biochemical processes. Caco-2 cells cultured in either system were infected at day 5 with C. jejuni 81-176 for 48 hours. Metabolomics analysis clearly differentiated C. jejuni 81-176 infected and non-infected medias collected from the microfluidic devices, and demonstrated that C. jejuni 81-176 infection in microfluidic devices impacts branched-chain amino acid metabolism, glycolysis, and gluconeogenesis. In contrast, no distinction was seen in the biochemical profiles of infected versus non-infected media collected from cells cultured in transwells. Microfluidic culturing conditions demonstrated a more metabolically homogenous cell population, and present the opportunity for studying host-pathogen interactions for extended periods of time. PMID:27231016

Multidimensional biochemical information processing of dynamical patterns

NASA Astrophysics Data System (ADS)

Hasegawa, Yoshihiko

2018-02-01

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

Stoichiometric network theory for nonequilibrium biochemical systems.

PubMed

Qian, Hong; Beard, Daniel A; Liang, Shou-dan

2003-02-01

We introduce the basic concepts and develop a theory for nonequilibrium steady-state biochemical systems applicable to analyzing large-scale complex isothermal reaction networks. In terms of the stoichiometric matrix, we demonstrate both Kirchhoff's flux law sigma(l)J(l)=0 over a biochemical species, and potential law sigma(l) mu(l)=0 over a reaction loop. They reflect mass and energy conservation, respectively. For each reaction, its steady-state flux J can be decomposed into forward and backward one-way fluxes J = J+ - J-, with chemical potential difference deltamu = RT ln(J-/J+). The product -Jdeltamu gives the isothermal heat dissipation rate, which is necessarily non-negative according to the second law of thermodynamics. The stoichiometric network theory (SNT) embodies all of the relevant fundamental physics. Knowing J and deltamu of a biochemical reaction, a conductance can be computed which directly reflects the level of gene expression for the particular enzyme. For sufficiently small flux a linear relationship between J and deltamu can be established as the linear flux-force relation in irreversible thermodynamics, analogous to Ohm's law in electrical circuits.

Multidimensional biochemical information processing of dynamical patterns.

PubMed

Hasegawa, Yoshihiko

2018-02-01

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

PubMed

Qian, Hong; Beard, Daniel A

2005-04-22

The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.

68Ga Bombesin PET/MRI in Patients with Biochemically Recurrent Prostate Cancer and Noncontributory Conventional Imaging

DTIC Science & Technology

2017-10-01

REPORT DATE: October 2017 TYPE OF REPORT: Annual PREPARED FOR: U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702...AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012 11. SPONSOR...prostate cancer (PCa). Methods : We enrolled 15 men with biochemically recurrent PCa from May to Sep 2017, 63-79 year-old (mean±standard deviation (SD

Biochemical upgrading of oils

DOEpatents

Premuzic, Eugene T.; Lin, Mow S.

1999-01-12

A process for biochemical conversion of heavy crude oils is provided. The process includes contacting heavy crude oils with adapted biocatalysts. The resulting upgraded oil shows, a relative increase in saturated hydrocarbons, emulsions and oxygenates and a decrease in compounds containing in organic sulfur, organic nitrogen and trace metals. Adapted microorganisms which have been modified under challenged growth processes are also disclosed.

Biochemical upgrading of oils

DOEpatents

Premuzic, E.T.; Lin, M.S.

1999-01-12

A process for biochemical conversion of heavy crude oils is provided. The process includes contacting heavy crude oils with adapted biocatalysts. The resulting upgraded oil shows, a relative increase in saturated hydrocarbons, emulsions and oxygenates and a decrease in compounds containing organic sulfur, organic nitrogen and trace metals. Adapted microorganisms which have been modified under challenged growth processes are also disclosed. 121 figs.

Utility of biochemical verification of tobacco cessation in the Department of Veterans Affairs.

PubMed

Noonan, Devon; Jiang, Yunyun; Duffy, Sonia A

2013-03-01

Research on the validity of self-report tobacco use has varied by the population studied and has yet to be examined among smokers serviced by the Department of Veterans Affairs (VA). The purpose of this study was to determine the predictors of returning a biochemical urine test and the specificity and sensitivity of self-reported tobacco use status compared to biochemical verification. This was a sub-analysis of the larger Tobacco Tactics research study, a pre-/post-non-randomized control design study to implement and evaluate a smoking cessation intervention in three large VA hospitals. Inpatient smokers completed baseline demographic, health history and tobacco use measures. Patients were sent a follow-up survey at six-months to assess tobacco use and urine cotinine levels. A total of 645 patients returned six-month surveys of which 578 also returned a urinary cotinine strip at six-months. Multivariate analysis of the predictors of return rate revealed those more likely to return biochemical verification of their smoking status were younger, more likely to be thinking about quitting smoking, have arthritis, and less likely to have heart disease. The sensitivity and specificity of self-report tobacco use were 97% (95% confidence interval=0.95-0.98) and 93% (95% confidence interval=0.84-0.98) respectively. The misclassification rate among self-reported quitters was 21%. The misclassification rate among self-reported tobacco users was 1%. The sensitivity and specificity of self-report tobacco use were high among veteran smokers, yet among self-report quitters that misclassification rate was high at 21% suggesting that validating self-report tobacco measures is warranted in future studies especially in populations that are prone to misclassification. Copyright © 2012 Elsevier Ltd. All rights reserved.

Prostate-specific antigen screening impacts on biochemical recurrence in patients with clinically localized prostate cancer.

PubMed

Hashimoto, Takeshi; Ohori, Makoto; Shimodaira, Kenji; Kaburaki, Naoto; Hirasawa, Yosuke; Satake, Naoya; Gondo, Tatsuo; Nakagami, Yoshihiro; Namiki, Kazunori; Ohno, Yoshio

2018-06-01

To clarify the impact of prostate-specific antigen screening on surgical outcomes of prostate cancer. Patients who underwent radical prostatectomy were divided into two groups according to prostate-specific antigen testing opportunity (group 1, prostate-specific antigen screening; group 2, non-prostate-specific antigen screening). Perioperative clinical characteristics were compared using the Wilcoxon rank-sum and χ 2 -tests. Cox proportional hazards models were used to identify independent predictors of postoperative biochemical recurrence-free survival. In total, 798 patients (63.2%) and 464 patients (36.8%) were categorized into groups 1 and 2, respectively. Group 2 patients were more likely to have a higher prostate-specific antigen level and age at diagnosis and larger prostate volume. Clinical T stage, percentage of positive cores and pathological Gleason score did not differ between the groups. The 5-year biochemical recurrence-free survival rate was 83.9% for group 1 and 71.0% for group 2 (P < 0.001). On multivariate analysis, prostate-specific antigen testing opportunity (hazard ratio 2.530; P < 0.001) was an independent predictive factor for biochemical recurrence after surgery, as well as pathological T stage, pathological Gleason score, positive surgical margin and lymphovascular invasion. Additional analyses showed that prostate-specific antigen screening had a greater impact on biochemical recurrence in a younger patients, patients with a high prostate-specific antigen level, large prostate volume and D'Amico high risk, and patients meeting the exclusion criteria of the Prostate Cancer Research International Active Surveillance study. Detection by screening results in favorable outcomes after surgery. Prostate-specific antigen screening might contribute to reducing biochemical recurrence in patients with localized prostate cancer. © 2018 The Japanese Urological Association.

Impaired telomere length and telomerase activity in peripheral blood leukocytes and granulosa cells in patients with biochemical primary ovarian insufficiency.

PubMed

Xu, Xiaofei; Chen, Xinxia; Zhang, Xiruo; Liu, Yixun; Wang, Zhao; Wang, Peng; Du, Yanzhi; Qin, Yingying; Chen, Zi-Jiang

2017-01-01

Are telomere length and telomerase activity associated with biochemical primary ovarian insufficiency (POI)? Shortened telomere length and diminished telomerase activity were associated with biochemical POI. POI is a result of pathological reproductive aging and encompasses occult, biochemical and overt stages. Studies have indicated telomere length as a biomarker for biological aging. A total of 120 patients with biochemical POI and 279 control women were recruited by the Center for Reproductive Medicine of Shandong University. Telomere length in peripheral blood leukocytes (LTL) and granulosa cells (GTL) was measured using a modified Quantitative Polymerase Chain Reaction technique. The relative telomerase activity (RTA) in granulosa cells was detected using a modified quantitative-telomeric repeat amplification protocol assay. After adjusting for age, patients with biochemical POI (n = 120) exhibited significantly shorter LTLs (0.75 ± 0.09 vs 1.79 ± 0.12, P < 0.001; OR = 0.54, 95% CI = 0.43-0.68) and GTLs (0.78 ± 0.09 vs 1.90 ± 0.23, P < 0.001; OR = 0.54, 95% CI = 0.41-0.70) than the controls (n = 279 for LTLs; n = 90 for GTLs). Significantly diminished RTAs in granulosa cells were detected in patients with biochemical POI (n = 31) compared with the controls (n = 38) (1.57 ± 0.59 vs 4.63 ± 0.93, P = 0.025; OR = 0.84, 95% CI = 0.72-0.98). N/A. The cross-sectional nature of this study might have its limit in telomere length as well as telomerase activity along with the progressing decline in ovarian function. These findings suggest that telomere length and telomerase activity may be considered as indicators for progression of ovarian decline. This research was supported by the National Basic Research Program of China (973 Program) (2012CB944700), Science research foundation item of no-earnings health vocation (201402004) and the National Natural Science Foundation of China (31471352, 81270662, 81471509, 81300461, 81522018

[Design of high-efficiency double compound parabolic concentrator system in near infrared noninvasive biochemical analysis].

PubMed

Gao, Jing; Lu, Qi-Peng; Peng, Zhong-Qi; Ding, Hai-Quan; Gao, Hong-Zhi

2013-05-01

High signal-to-noise ratio (SNR) of system is necessary to obtain accurate blood components in near infrared noninvasive biochemical analysis. In order to improve SNR of analytical system, high-efficiency double compound parabolic concentrator (DCPC) system was researched, which was aimed at increasing light utilization efficiency. Firstly, with the request of collection efficiency in near infrared noninvasive biochemical analysis, the characteristic of emergent rays through compound parabolic concentrator (CPC) was analyzed. Then the maximum focusing angle range of the first stage CPC was determined. Secondly, the light utilization efficiency of truncated type was compared with standard DCPC, thus the best structure parameters of DCPC system were optimized. Lastly, combined with optical parameters of skin tissue, calculations were operated when incident wavelength is 1 000 nm. The light utilization efficiency of DCPC system, CPC-focusing mirror system, and non-optical collecting system was calculated. The results show that the light utilization efficiency of the three optical systems is 1.46%, 0.84% and 0.26% respectively. So DCPC system enhances collecting ability for human diffuse reflection light, and helps improve SNR of noninvasive biochemical analysis system and overall analysis accuracy effectively.

77 FR 8869 - Granting of Request for Early Termination of the Waiting Period Under the Premerger Notification...

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... DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances...-3 Strathmore Road, Natick, Massachusetts 01760-2447, made application by letter to the Drug... controlled substances: Drug Schedule Mephedrone (4-Methyl-N-methylcathinone) I (1248). MDPV (3,4...

40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... efficacy data unless the pesticide product bears a claim to control public health pests, such as pest... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070...

40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... efficacy data unless the pesticide product bears a claim to control public health pests, such as pest... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070...

40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... efficacy data unless the pesticide product bears a claim to control public health pests, such as pest... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070...

40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... efficacy data unless the pesticide product bears a claim to control public health pests, such as pest... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070...

40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... efficacy data unless the pesticide product bears a claim to control public health pests, such as pest... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070...

Biochemical correlates in an animal model of depression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, J.O.

1986-01-01

A valid animal model of depression was used to explore specific adrenergic receptor differences between rats exhibiting aberrant behavior and control groups. Preliminary experiments revealed a distinct upregulation of hippocampal beta-receptors (as compared to other brain regions) in those animals acquiring a response deficit as a result of exposure to inescapable footshock. Concurrent studies using standard receptor binding techniques showed no large changes in the density of alpha-adrenergic, serotonergic, or dopaminergic receptor densities. This led to the hypothesis that the hippocampal beta-receptor in responses deficient animals could be correlated with the behavioral changes seen after exposure to the aversive stimulus.more » Normalization of the behavior through the administration of antidepressants could be expected to reverse the biochemical changes if these are related to the mechanism of action of antidepressant drugs. This study makes three important points: (1) there is a relevant biochemical change in the hippocampus of response deficient rats which occurs in parallel to a well-defined behavior, (2) the biochemical and behavioral changes are normalized by antidepressant treatments exhibiting both serotonergic and adrenergic mechanisms of action, and (3) the mode of action of antidepressants in this model is probably a combination of serotonergic and adrenergic influences modulating the hippocampal beta-receptor. These results are discussed in relation to anatomical and biochemical aspects of antidepressant action.« less

Alternative aircraft anti-icing formulations with reduced aquatic toxicity and biochemical oxygen demand

USGS Publications Warehouse

Gold, Harris; Joback, Kevin; Geis, Steven; Bowman, George; Mericas, Dean; Corsi, Steven R.; Ferguson, Lee

2010-01-01

The current research was conducted to identify alternative aircraft and pavement deicer and anti-icer formulations with improved environmental characteristics compared to currently used commercial products (2007). The environmental characteristics of primary concern are the biochemical oxygen demand (BOD) and aquatic toxicity of the fully formulated products. Except when the distinction among products is necessary for clarity, “deicer” will refer to aircraft-deicing fluids (ADFs), aircraft anti-icing fluids (AAFs), and pavementdeicing materials (PDMs).

Measurement of biochemical oxygen demand of the leachates.

PubMed

Fulazzaky, Mohamad Ali

2013-06-01

Biochemical oxygen demand (BOD) of the leachates originally from the different types of landfill sites was studied based on the data measured using the two manometric methods. The measurements of BOD using the dilution method were carried out to assess the typical physicochemical and biological characteristics of the leachates together with some other parameters. The linear regression analysis was used to predict rate constants for biochemical reactions and ultimate BOD values of the different leachates. The rate of a biochemical reaction implicated in microbial biodegradation of pollutants depends on the leachate characteristics, mass of contaminant in the leachate, and nature of the leachate. Character of leachate samples for BOD analysis of using the different methods may differ significantly during the experimental period, resulting in different BOD values. This work intends to verify effect of the different dilutions for the manometric method tests on the BOD concentrations of the leachate samples to contribute to the assessment of reaction rate and microbial consumption of oxygen.

40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... for biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2... be available for human or livestock consumption. 13. Data on fish are required for all pesticides... for human consumption. 14. Data are required when a pesticide is to be applied directly to water that...

40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

... for biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2... be available for human or livestock consumption. 13. Data on fish are required for all pesticides... for human consumption. 14. Data are required when a pesticide is to be applied directly to water that...

40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

... for biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2... be available for human or livestock consumption. 13. Data on fish are required for all pesticides... for human consumption. 14. Data are required when a pesticide is to be applied directly to water that...

40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

... for biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2... be available for human or livestock consumption. 13. Data on fish are required for all pesticides... for human consumption. 14. Data are required when a pesticide is to be applied directly to water that...

40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

... for biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2... be available for human or livestock consumption. 13. Data on fish are required for all pesticides... for human consumption. 14. Data are required when a pesticide is to be applied directly to water that...

What is the biochemical and physiological rationale for using cold-water immersion in sports recovery? A systematic review.

PubMed

Bleakley, Chris M; Davison, Gareth W

2010-02-01

Cold-water immersion (CWI) is a popular recovery intervention after exercise. The scientific rationale is not clear, and there are no clear guidelines for its use. The aim of this review was to study the physiological and biochemical effect of short periods of CWI. A computer-based literature search, citation tracking and related articles searches were undertaken. Primary research studies using healthy human participants, immersed in cold water (<15 degrees C), for 5 min durations or less were included. Data were extracted on body temperature, cardiovascular, respiratory and biochemical response. 16 studies were included. Sample size was restricted, and there was a large degree of study heterogeneity. CWI was associated with an increase in heart rate, blood pressure, respiratory minute volume and metabolism. Decreases in end tidal carbon dioxide partial pressure and a decrease in cerebral blood flow were also reported. There was evidence of increases in peripheral catecholamine concentration, oxidative stress and a possible increase in free-radical-species formation. The magnitude of these responses may be attenuated with acclimatisation. CWI induces significant physiological and biochemical changes to the body. Much of this evidence is derived from full body immersions using resting healthy participants. The physiological and biochemical rationale for using short periods of CWI in sports recovery still remains unclear.

40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

Code of Federal Regulations, 2013 CFR

2013-07-01

... test notes are shown in paragraph (e) of this section. Table—EUP Biochemical Pesticides Nontarget... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Experimental use permit biochemical... FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

Code of Federal Regulations, 2011 CFR

2011-07-01

... test notes are shown in paragraph (e) of this section. Table—EUP Biochemical Pesticides Nontarget... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Experimental use permit biochemical... FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

Code of Federal Regulations, 2012 CFR

2012-07-01

... test notes are shown in paragraph (e) of this section. Table—EUP Biochemical Pesticides Nontarget... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Experimental use permit biochemical... FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

Code of Federal Regulations, 2014 CFR

2014-07-01

... test notes are shown in paragraph (e) of this section. Table—EUP Biochemical Pesticides Nontarget... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Experimental use permit biochemical... FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

77 FR 31307 - Foreign-Trade Zone 41-Milwaukee, WI; Application for Reorganization (Expansion of Service Area...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-25

... limit for a general-purpose zone project. The application was submitted pursuant to the Foreign-Trade... temporary sites as ``usage-driven'' sites: Site 12 (113.4 acres)-- Sigma-Aldrich Corporation, 5485 County Road ``V'', Sheboygan Falls, Sheboygan County; and, Site 13 (15.1 acres)--Sigma-Aldrich Corporation...

[Biochemical indicators of anaphylactic shock and the application in forensic medicine].

PubMed

Mi, Li; Chen, Jie; Gao, Wei-Min; Du, Zhong-Bo; Cao, Zhi-Peng; Zhang, Yuan; Zhu, Bao-Li

2014-04-01

Fatal anaphylactic shock is common in forensic practice. However, it is difficult to diagnose for lacking specific pathological and morphologic changes in forensic autopsy. The application of some biochemical indicators is of great significance. This paper reviews the biological characteristics of some biochemical indicators and detection methods. The forensic application, problems and prospects of these indicators are also introduced in details. The stable biochemical indicators, IgE, tryptase and chymase, show great potential and advantages in the identification of fatal anaphylactic shock in forensic medicine.

Physiological and molecular biochemical mechanisms of bile formation

PubMed Central

Reshetnyak, Vasiliy Ivanovich

2013-01-01

This review considers the physiological and molecular biochemical mechanisms of bile formation. The composition of bile and structure of a bile canaliculus, biosynthesis and conjugation of bile acids, bile phospholipids, formation of bile micellar structures, and enterohepatic circulation of bile acids are described. In general, the review focuses on the molecular physiology of the transporting systems of the hepatocyte sinusoidal and apical membranes. Knowledge of physiological and biochemical basis of bile formation has implications for understanding the mechanisms of development of pathological processes, associated with diseases of the liver and biliary tract. PMID:24259965

New biochemical markers: from bench to bedside.

PubMed

Zaninotto, Martina; Mion, Monica Maria; Novello, Enrica; Altinier, Sara; Plebani, Mario

2007-05-01

Evaluation of patients presenting to hospital with chest pain or other signs or symptoms suggesting acute coronary syndrome (ACS) is problematic, time-consuming and sometimes expensive, even if new biochemical markers, such as troponins, have improved the ability to detect cardiac injury. However, patients with normal troponin values are not necessarily risk-free for major cardiac events. Recent investigations indicate that the overall patient risk may be assessed earlier than before, thanks to new knowledge acquired concerning the pathobiology of atherosclerosis and molecular events involved in the progression of disease, thus allowing the development of new biochemical markers. Some selected markers are released during the different phases of development of cardiovascular disease and may be useful for the diagnosis of patients with cardiovascular disease. In particular, the identification of emerging markers that provide relevant information on the inflammatory process, and the development of biomarkers whose circulating concentrations suggest the status of plaque instability and rupture, seems to be of particular value in prognosis and risk stratification. The overall expectations for a cardiovascular biochemical marker are not only its biological plausibility but also the availability at a reasonable cost of rapid, high quality assays, and their correct interpretation by clinicians using optimal cut-offs. The crossing from bench to bedside for each new marker discovered, must be associated with concurrent advances in the characterization of analytical features and the development of routine assay, in the assessment of analytical performance and in interpretative reporting of test results as well as in the training of physicians to use the array of biomarkers available appropriately and to interpret them correctly. This approach calls for the coordinated support of clinicians, technology experts, statisticians and the industry so that new biochemical

Optimal Information Processing in Biochemical Networks

NASA Astrophysics Data System (ADS)

Wiggins, Chris

2012-02-01

A variety of experimental results over the past decades provide examples of near-optimal information processing in biological networks, including in biochemical and transcriptional regulatory networks. Computing information-theoretic quantities requires first choosing or computing the joint probability distribution describing multiple nodes in such a network --- for example, representing the probability distribution of finding an integer copy number of each of two interacting reactants or gene products while respecting the `intrinsic' small copy number noise constraining information transmission at the scale of the cell. I'll given an overview of some recent analytic and numerical work facilitating calculation of such joint distributions and the associated information, which in turn makes possible numerical optimization of information flow in models of noisy regulatory and biochemical networks. Illustrating cases include quantification of form-function relations, ideal design of regulatory cascades, and response to oscillatory driving.

Improved biochemical preservation of lung slices during cold storage.

PubMed

Bull, D A; Connors, R C; Reid, B B; Albanil, A; Stringham, J C; Karwande, S V

2000-05-15

Development of lung preservation solutions typically requires whole-organ models which are animal and labor intensive. These models rely on physiologic rather than biochemical endpoints, making accurate comparison of the relative efficacy of individual solution components difficult. We hypothesized that lung slices could be used to assess preservation of biochemical function during cold storage. Whole rat lungs were precision cut into slices with a thickness of 500 microm and preserved at 4 degrees C in the following solutions: University of Wisconsin (UW), Euro-Collins (EC), low-potassium-dextran (LPD), Kyoto (K), normal saline (NS), or a novel lung preservation solution (NPS) developed using this model. Lung biochemical function was assessed by ATP content (etamol ATP/mg wet wt) and capacity for protein synthesis (cpm/mg protein) immediately following slicing (0 h) and at 6, 12, 18, and 24 h of cold storage. Six slices were assayed at each time point for each solution. The data were analyzed using analysis of variance and are presented as means +/- SD. ATP content was significantly higher in the lung slices stored in NPS compared with all other solutions at each time point (P < 0.0001). Protein synthesis was significantly higher in the lung slices stored in NPS compared with all other solutions at 6, 12, and 18 h of preservation (P < 0.05). This lung slice model allows the rapid and efficient screening of lung preservation solutions and their components using quantifiable biochemical endpoints. Using this model, we have developed a novel solution that improves the biochemical preservation of lung slices during cold storage. Copyright 2000 Academic Press.

Metabolic network failures in Alzheimer’s disease: A biochemical road map

PubMed Central

Toledo, Jon B.; Arnold, Matthias; Kastenmüuller, Gabi; Chang, Rui; Baillie, Rebecca A.; Han, Xianlin; Thambisetty, Madhav; Tenenbaum, Jessica D.; Suhre, Karsten; Thompson, J. Will; St. John-Williams, Lisa; MahmoudianDehkordi, Siamak; Rotroff, Daniel M.; Jack, John R.; Motsinger-Reif, Alison; Risacher, Shannon L.; Blach, Colette; Lucas, Joseph E.; Massaro, Tyler; Louie, Gregory; Zhu, Hongjie; Dallmann, Guido; Klavins, Kristaps; Koal, Therese; Kim, Sungeun; Nho, Kwangsik; Shen, Li; Casanova, Ramon; Varma, Sudhir; Legido-Quigley, Cristina; Moseley, M. Arthur; Zhu, Kuixi; Henrion, Marc Y. R.; van der Lee, Sven J.; Harms, Amy C.; Demirkan, Ayse; Hankemeier, Thomas; van Duijn, Cornelia M.; Trojanowski, John Q.; Shaw, Leslie M.; Saykin, Andrew J.; Weiner, Michael W.; Doraiswamy, P. Murali; Kaddurah-Daouk, Rima

2018-01-01

Introduction The Alzheimer’s Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer’s disease (AD) and propel the development of critically needed therapies. In response to their recommendations, big data at multiple levels are being generated and integrated to study network failures in disease. We used metabolomics as a global biochemical approach to identify peripheral metabolic changes in AD patients and correlate them to cerebrospinal fluid pathology markers, imaging features, and cognitive performance. Methods Fasting serum samples from the Alzheimer’s Disease Neuroimaging Initiative (199 control, 356 mild cognitive impairment, and 175 AD participants) were analyzed using the AbsoluteIDQ-p180 kit. Performance was validated in blinded replicates, and values were medication adjusted. Results Multivariable-adjusted analyses showed that sphingomyelins and ether-containing phosphatidylcholines were altered in preclinical biomarker-defined AD stages, whereas acylcarnitines and several amines, including the branched-chain amino acid valine and α-aminoadipic acid, changed in symptomatic stages. Several of the analytes showed consistent associations in the Rotterdam, Erasmus Rucphen Family, and Indiana Memory and Aging Studies. Partial correlation networks constructed for Aβ1–42, tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes. Coexpression networks interconnected key metabolic effectors of disease. Discussion Metabolomics identified key disease-related metabolic changes and disease-progression-related changes. Defining metabolic changes during AD disease trajectory and its relationship to clinical phenotypes provides a powerful roadmap for drug and biomarker discovery. PMID:28341160

Biosensors and bioelectronics on smartphone for portable biochemical detection.

PubMed

Zhang, Diming; Liu, Qingjun

2016-01-15

Smartphone has been widely integrated with sensors, such as test strips, sensor chips, and hand-held detectors, for biochemical detections due to its portability and ubiquitous availability. Utilizing built-in function modules, smartphone is often employed as controller, analyzer, and displayer for rapid, real-time, and point-of-care monitoring, which can significantly simplify design and reduce cost of the detecting systems. This paper presents a review of biosensors and bioelectronics on smartphone for portable biochemical detections. The biosensors and bioelectronics based on smartphone can mainly be classified into biosensors using optics, surface plasmon resonance, electrochemistry, and near-field communication. The developments of these biosensors and bioelectronics on smartphone are reviewed along with typical biochemical detecting cases. Sensor strategies, detector attachments, and coupling methods are highlighted to show designs of the compact, lightweight, and low-cost sensor systems. The performances and advantages of these designs are introduced with their applications in healthcare diagnosis, environment monitoring, and food evaluation. With advances in micro-manufacture, sensor technology, and miniaturized electronics, biosensor and bioelectronic devices on smartphone can be used to perform biochemical detections as common and convenient as electronic tag readout in foreseeable future. Copyright © 2015 Elsevier B.V. All rights reserved.

Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.

PubMed

Sen, Dilara; Keung, Albert J

2018-01-01

The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.

Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination.

PubMed

Woodman, Andrew; Arnold, Jamie J; Cameron, Craig E; Evans, David J

2016-08-19

Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3' non-coding region we have further developed a cell-based assay (the 3'CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Interpretation of false positive results of biochemical prenatal tests].

PubMed

Sieroszewski, Piotr; Słowakiewicz, Katarzyna; Perenc, Małgorzata

2010-03-01

Modern, non-invasive prenatal diagnostics based on biochemical and ultrasonographic markers of fetal defects allows us to calculate the risk of fetal chromosomal aneuploidies with high sensitivity and specificity An introduction of biochemical, non-invasive prenatal tests turned out to result in frequent false positive results of these tests in cases when invasive diagnostics does not confirm fetal defects. However prospective analysis of these cases showed numerous complications in the third trimester of the pregnancies.

From molecules to mating: Rapid evolution and biochemical studies of reproductive proteins

PubMed Central

Wilburn, Damien B.; Swanson, Willie J.

2015-01-01

Sexual reproduction and the exchange of genetic information are essential biological processes for species across all branches of the tree of life. Over the last four decades, biochemists have continued to identify many of the factors that facilitate reproduction, but the molecular mechanisms that mediate this process continue to elude us. However, a recurring observation in this research has been the rapid evolution of reproductive proteins. In animals, the competing interests of males and females often result in arms race dynamics between pairs of interacting proteins. This phenomenon has been observed in all stages of reproduction, including pheromones, seminal fluid components, and gamete recognition proteins. In this article, we review how the integration of evolutionary theory with biochemical experiments can be used to study interacting reproductive proteins. Examples are included from both model and non-model organisms, and recent studies are highlighted for their use of state-of-the-art genomic and proteomic techniques. Significance Despite decades of research, our understanding of the molecular mechanisms that mediate fertilization remain poorly characterized. To date, molecular evolutionary studies on both model and non-model organisms have provided some of the best inferences to elucidating the molecular underpinnings of animal reproduction. This review article details how biochemical and evolutionary experiments have jointly enhanced the field for 40 years, and how recent work using high-throughput genomic and proteomic techniques have shed additional insights into this crucial biological process. PMID:26074353

Advanced Nanoporous Materials for Micro-Gravimetric Sensing to Trace-Level Bio/Chemical Molecules

PubMed Central

Xu, Pengcheng; Li, Xinxin; Yu, Haitao; Xu, Tiegang

2014-01-01

Functionalized nanoporous materials have been developed recently as bio/chemical sensing materials. Due to the huge specific surface of the nano-materials for molecular adsorption, high hopes have been placed on gravimetric detection with micro/nano resonant cantilevers for ultra-sensitive sensing of low-concentration bio/chemical substances. In order to enhance selectivity of the gravimetric resonant sensors to the target molecules, it is crucial to modify specific groups onto the pore-surface of the nano-materials. By loading the nanoporous sensing material onto the desired region of the mass-type transducers like resonant cantilevers, the micro-gravimetric bio/chemical sensors can be formed. Recently, such micro-gravimetric bio/chemical sensors have been successfully applied for rapid or on-the-spot detection of various bio/chemical molecules at the trace-concentration level. The applicable nanoporous sensing materials include mesoporous silica, zeolite, nanoporous graphene oxide (GO) and so on. This review article focuses on the recent achievements in design, preparation, functionalization and characterization of advanced nanoporous sensing materials for micro-gravimetric bio/chemical sensing. PMID:25313499

[Biochemical markers of bone remodeling: pre-analytical variations and guidelines for their use. SFBC (Société Française de Biologie Clinique) Work Group. Biochemical markers of bone remodeling].

PubMed

Garnero, P; Bianchi, F; Carlier, M C; Genty, V; Jacob, N; Kamel, S; Kindermans, C; Plouvier, E; Pressac, M; Souberbielle, J C

2000-01-01

Biochemical markers of bone turnover have been developed over the past 20 years that are more specific for bone tissue than conventional ones such as total alkaline phosphatase and urinary hydroxyproline. They have been widely used in clinical research and in clinical trials of new therapies as secondary end points of treatment efficacy. Most of the interest has been devoted to their use in postmenopausal osteoporosis, a condition characterized by subtle modifications of bone metabolism that cannot be detected readily by conventional markers of bone turnover. Although several recent studies have suggested that biochemical markers may be used for the management of the individual patient in routine clinical practice, this has not been clearly defined and is a matter of debate. Because of the crucial importance to clarify this issue, the Société Francaise de Biologie Clinique prompted an expert committee to summarize the available data and to make recommendations. The following paper includes a review on the biochemical and analytical aspects of the markers of bone formation and resorption and on the sources of variability such as sex, age, menstrual cycle, pregnancy and lactation, physical activity, seasonal variation and effects of diseases and treatments. We will also describe the effects of pre-analytical factors on the measurements of the different markers. Finally based on that review, we will make practical recommendations for the use of these markers in order to minimize the variability of the measurements and improve the clinical interpretation of the data.

[Design and experiment of micro biochemical detector based on micro spectrometer].

PubMed

Yu, Qing-hua; Wen, Zhi-yu; Chen, Gang; Dai, Wei-wei; Liu, Nian-ci; Wu, Xin

2012-03-01

According to the requirements of rapid detection of important life parameters for the sick and wounded, a new micro bio-chemical detection configuration was proposed utilizing continuous spectroscopy analysis, which was founded on MOEMS and embedded technology. The configuration was developed as so much research work was carried out on the detecting objects and methods. Important parameters such as stray light, absorbance linearity, absorbance ratability, stability and temperature accuracy of the instrument were tested, which are all in good agreement with the design requirements. Clinic tests show that it can detect multiple life parameters quickly (Na+, GLU, Hb eg.).

Biochemical differences in ethnic groups in Durango, Mexico.

PubMed

Lares-Asseff, Ismael; Lujín-García, Azalia; Sosa-Macías, Martha; Lazalde-Ramos, Blanca; Loera-Castañeda, Veronica; Galaviz-Hernández, Carlos; Villanueva-Fierro, Ignacio

2012-01-01

The aim of this study was to assess biochemical differences between Tepehuano indigenous people, and Mennonite and Mestizo populations of Durango, Mexico. Our study involved 334 volunteers aged 15 to 80 years; 132 Mennonite and 130 Mestizo individuals from Nuevo Ideal Municipality and 72 Tepehuano indigenous people from Mezquital Durango were evaluated. A clinical history and fast determination of aspartate aminotransferase (AST), alanine aminotransferase (ALT), uric acid, urea and creatinine were performed on each studied case. Statistically significant differences between the three studied groups were found for age, weight and height (P < .05), with higher values observed in men. The highest plasma urea levels were found in Mennonite compared to Mestizo people, followed by the Tepehuano indigenous. Higher biochemical parameters were found in men (vs women) in the studied groups. The percentage of individuals with abnormal levels for AST, ALT and uric acid were higher in Tepehuano indigenous people than in Mestizo, whereas the urea and creatinine percentages were higher in Mestizo people. The differences found on biochemical tests, could be explained by differences in lifestyle such as diet and sanitary habits.

Circadian Clocks: Unexpected Biochemical Cogs.

PubMed

Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie

2015-10-05

A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ∼ 24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Raman spectroscopy of oral tissues: correlation of spectral and biochemical markers

NASA Astrophysics Data System (ADS)

Singh, S. P.; Krishna, C. Murali

2014-03-01

Introduction Optical spectroscopic methods are being explored as novel tools for early and non-invasive cancer diagnosis. Both ex vivo and in vivo Raman spectroscopic studies carried out in oral cancer over the past decade have demonstrated that spectra of normal tissues are rich in lipids while tumor spectra show predominance of proteins. An accurate understanding of spectral features with respect to the biochemical composition is a pre-requisite before transferring these technologies for routine clinical usage. Therefore, in the present study, we have carried out Raman and biochemical studies on same tissues to correlate spectral markers and biochemical composition of normal and tumor oral tissues. Materials and Methods Spectra of 20 pairs of normal and tumor oral tissues were acquired using fiber-optic probe coupled HE-785 Raman spectrometer. Intensity associated with lipid (1440 cm-1) and protein (1450 and 1660 cm-1) bands were computed using curve-deconvolution method. Same tissues were then subjected to biochemical estimations of major biomolecules i.e., protein, lipid and phospholipids. Results and Discussion The intensity of the lipid band was found to be higher in normal tissues with respect to tumors, and the protein band was higher in tumors compared to normal tissues. Biochemical estimation yielded similar results i.e. high protein to lipid or phospholipid ratio in tumors with-respect to normal tissues. These differences were found to be statistically significant. Conclusion Findings of curve-deconvolution and biochemical estimation correlate very well and corroborate the spectral profile noted in earlier studies.

Modeling of uncertainties in biochemical reactions.

PubMed

Mišković, Ljubiša; Hatzimanikatis, Vassily

2011-02-01

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to

40 CFR 158.2081 - Experimental use permit biochemical pesticides product chemistry data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Experimental use permit biochemical... Pesticides § 158.2081 Experimental use permit biochemical pesticides product chemistry data requirements...: (d) Table. The following table shows the data requirements for experimental use permit biochemical...

40 CFR 158.2081 - Experimental use permit biochemical pesticides product chemistry data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Experimental use permit biochemical... Pesticides § 158.2081 Experimental use permit biochemical pesticides product chemistry data requirements...: (d) Table. The following table shows the data requirements for experimental use permit biochemical...

40 CFR 158.2081 - Experimental use permit biochemical pesticides product chemistry data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Experimental use permit biochemical... Pesticides § 158.2081 Experimental use permit biochemical pesticides product chemistry data requirements...: (d) Table. The following table shows the data requirements for experimental use permit biochemical...

40 CFR 158.2081 - Experimental use permit biochemical pesticides product chemistry data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Experimental use permit biochemical... Pesticides § 158.2081 Experimental use permit biochemical pesticides product chemistry data requirements...: (d) Table. The following table shows the data requirements for experimental use permit biochemical...

40 CFR 158.2081 - Experimental use permit biochemical pesticides product chemistry data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Experimental use permit biochemical... Pesticides § 158.2081 Experimental use permit biochemical pesticides product chemistry data requirements...: (d) Table. The following table shows the data requirements for experimental use permit biochemical...

2009 Biochemical Conversion Platform Review Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferrell, John

2009-12-01

This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Biochemical Conversion platform review meeting, held on April 14-16, 2009, at the Sheraton Denver Downtown, Denver, Colorado.

Length of positive surgical margin after radical prostatectomy as a predictor of biochemical recurrence.

PubMed

Shikanov, Sergey; Song, Jie; Royce, Cassandra; Al-Ahmadie, Hikmat; Zorn, Kevin; Steinberg, Gary; Zagaja, Gregory; Shalhav, Arieh; Eggener, Scott

2009-07-01

Length and location of positive surgical margins are independent predictors of biochemical recurrence after open radical prostatectomy. We assessed their impact on biochemical recurrence in a large robotic prostatectomy series. Data were collected prospectively from 1,398 men undergoing robotic radical prostatectomy for clinically localized prostate cancer from 2003 to 2008 at a single institution. The associations of preoperative prostate specific antigen, pathological Gleason score, pathological stage and positive surgical margin parameters (location, length and focality) with biochemical recurrence rate were evaluated. Margin status and length were measured by a single uropathologist. Biochemical recurrence was defined as serum prostate specific antigen greater than 0.1 ng/ml on 2 consecutive tests. Cox regression models were constructed to evaluate predictors of biochemical recurrence. Of 1,398 consecutive patients who underwent robotic prostatectomy positive margins were present in 243 (17%) (11% of pathological T2 and 41% of T3). Preoperative prostate specific antigen, pathological stage, Gleason score, margin status, and margin length as a continuous and categorical variable (less than 1, 1 to 3, more than 3 mm) were independent predictors of biochemical recurrence. Patients with negative margins and those with a positive margin less than 1 mm had similar rates of biochemical recurrence (log rank test p = 0.18). Surgical margin location was not independently associated with biochemical recurrence. Margin status and length are independent predictors of biochemical recurrence following robotic radical prostatectomy. Although longer followup and validation studies are necessary for confirmation, patients with a positive margin less than 1 mm appear to have similar recurrence rates as those with negative margins.

Improved biochemical preservation of heart slices during cold storage.

PubMed

Bull, D A; Reid, B B; Connors, R C; Albanil, A; Stringham, J C; Karwande, S V

2000-01-01

Development of myocardial preservation solutions requires the use of whole organ models which are animal and labor intensive. These models rely on physiologic rather than biochemical endpoints, making accurate comparison of the relative efficacy of individual solution components difficult. We hypothesized that myocardial slices could be used to assess preservation of biochemical function during cold storage. Whole rat hearts were precision cut into slices with a thickness of 200 microm and preserved at 4 degrees C in one of the following solutions: Columbia University (CU), University of Wisconsin (UW), D5 0.2% normal saline with 20 meq/l KCL (QNS), normal saline (NS), or a novel cardiac preservation solution (NPS) developed using this model. Myocardial biochemical function was assessed by ATP content (etamoles ATP/mg wet weight) and capacity for protein synthesis (counts per minute (cpm)/mg protein) immediately following slicing (0 hours), and at 6, 12, 18, and 24 hours of cold storage. Six slices were assayed at each time point for each solution. The data were analyzed using analysis of variance and are presented as the mean +/- standard deviation. ATP content was higher in the heart slices stored in the NPS compared to all other solutions at 6, 12, 18 and 24 hours of cold storage (p < 0.05). Capacity for protein synthesis was higher in the heart slices stored in the NPS compared to all other solutions at 6, 12, and 18 hours of cold storage (p < 0.05). CONCLUSIONS This myocardial slice model allows the rapid and efficient screening of cardiac preservation solutions and their components using quantifiable biochemical endpoints. Using this model, we have developed a novel preservation solution which improves the biochemical function of myocardial slices during cold storage.

Rapid Methods for Biochemical Testing of Anaerobic Bacteria

PubMed Central

Schreckenberger, Paul C.; Blazevic, Donna J.

1974-01-01

Rapid biochemical tests for nitrate, indole, gelatin, starch, esculin, and o-nitrophenyl-β-D-galactopyranoside were performed on 112 strains of anaerobic bacteria. All tests were incubated under aerobic conditions, and results were recorded within 4 h. The tests for nitrate, indole, and starch showed a 95% or greater correlation when compared to the standard biochemical tests. Tests for esculin and gelatin showed an agreement of 86 and 77%, respectively. PathoTec test strips for nitrate, indole, esculin, o-nitrophenyl-β-D-galactopyranoside, Voges-Proskauer, and urease were also tested and showed encouraging results. PMID:4613268

Changes in Biochemical Properties of the Blood in Winter Swimmers.

PubMed

Teleglow, Aneta; Marchewka, Jakub; Marchewka, Anna; Kulpa, Jan

The aim of the study was to investigate the effects of winter swimming on biochemical indicators of the blood. The subjects - winter swimmers - belonged to the Krakow Walrus Club "Kaloryfer" - "The Heater". The study group consisted of 11 men, aged 30-50 years, 'walrusing' throughout the whole season from November to March. Statistically significant changes throughout the 'walrusing' season were observed for the following biochemical parameters: a decrease in sodium (mmol/1), chloride (mmol/1), alpha-2 globulin(g/1), gamma globulin (g/1), IgG (g/1), and an increase in albumin (g/1), indicator A/G, IgA (g/l ), Herpes simplex virus IgM. Seasonal effort of winter swimmers has a positive influence on biochemical blood parameters.

[Impact of Gleason score on biochemical recurrence free survival after radical prostatectomy with positive surgical margins].

PubMed

Roux, V; Eyraud, R; Brureau, L; Gourtaud, G; Senechal, C; Fofana, M; Blanchet, P

Research of predictive factors of biochemical recurrence to guide the establishment of an adjuvant treatment after radical prostatectomy for cancer with positive surgical margins. A retrospective cohort of 1577 afro-caribbean patients undergoing radical prostatectomy operated between 1st January 2000 and 1st July 2013 was analyzed. In this cohort, 406 patients had positive surgical margin, we excluded 11 patients who received adjuvant therapy (radiotherapy, hormonotherapy, radio-hormonotherapy) and 2 patients for whom histological analysis of the surgical specimen was for a pT4 pathological stage. After a descriptive analysis, we used a Cox model to look for predictors of survival without biochemical recurrence then, depending on the significant variables, we separated our population into six groups: stage pT2 with Gleason score≤3+4 (group 1), stage pT2 with a score of Gleason≥4+3 (group 2), stage pT3a with a Gleason core≤3+4 (group 3), pT3a stage with a score of Gleason≥4+3 (group 4), stage pT3b with a Gleason score≤3+4 (group 5) and stage pT3b Gleason≥with a score of 4+3 (group 6) and compared survival without biochemical recurrence using a log rank test. After radical prostatectomy with surgical margins with an anatomopathological stage≤pT3b, a Gleason score≥4+3 had a pejorative survival without biochemical recurrence than pathological stage (P<0.001). In multivariate analysis, predictors of survival without biochemical recurrence after radical prostatectomy with positive surgical margins were the majority Gleason postoperative (P<0.0001), pathological stage (P=0.049) adjusted preoperative PSA (P=0.826), with the body mass index (BMI) (P=0.59) and tumor volume (P=0.95). A high postoperatively Gleason score (≥4+3) has a better predictive value of biochemical recurrence than pathological stage pT2 or pT3 at the patients having been treated for prostate cancer by radical prostatectomy with positive surgical margins. 4. Copyright �

CLINICAL FACTORS ASSOCIATED WITH BIOCHEMICAL ADRENAL-CORTISOL INSUFFICIENCY IN HOSPITALIZED PATIENTS

PubMed Central

Ben-Shlomo, Anat; Mirocha, James; Liu, Ning-Ai; Sheinin, Renee C.; Melmed, Shlomo

2014-01-01

Background Diagnosis of adrenal-cortisol insufficiency is often misleading in hospitalized patients as clinical and biochemical features overlap with co-morbidities. We analyzed clinical determinants associated with a biochemical diagnosis of adrenal-cortisol insufficiency in non-ICU hospitalized patients. Methods In a retrospective cohort study we reviewed 4668 inpatients with random morning cortisol levels ≤15 μg/dL hospitalized in our center between 2003 and 2010. Using serum cortisol threshold level of 18 μg/dL 30 and/or 60 minutes after cortrosyn (250 μg) injection to define biochemical adrenal-cortisol status, we characterized and compared insufficient (n=108, serum cortisol ≤18 μg/dL) and sufficient ( n=394; serum cortisol >18 μg/dL) non-ICU hospitalized patients. Results Commonly reported clinical and routine biochemical adrenal-cortisol insufficiency features were similar between insufficient and sufficient inpatients. Biochemical adrenal-cortisol insufficiency was associated with increased frequency of liver disease, specifically hepatitis C (p=0.01) and prior orthotopic liver transplantation (p<0.001), HIV (p=0.005) and reported preexisting male hypogonadism (p<0.001) as compared to biochemical adrenal-cortisol sufficiency group. Forty percent of insufficient inpatients were not treated with glucocorticoids after diagnosis. Multivariable logistic analysis demonstrated that inpatients with higher cortisol levels (p=0.0001), higher diastolic blood pressure (p=0.05) and females (p=0.009) were more likely not to be treated, while those with previous short-term glucocorticoid treatment (p=0.002), had other co-existing endocrine diseases (p=0.005) or received an inhospital endocrinology consultation (p<0.0001) were more likely to be replaced with glucocorticoids. Conclusions Commonly reported adrenal-cortisol insufficiency features do not reliably identify hospitalized patients biochemically confirmed to have this disorder. Co-morbidities including

Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways

PubMed Central

Vinnakota, Kalyan C.; Wu, Fan; Kushmerick, Martin J.; Beard, Daniel A.

2009-01-01

The operation of biochemical systems in vivo and in vitro is strongly influenced by complex interactions between biochemical reactants and ions such as H+, Mg2+, K+, and Ca2+. These are important second messengers in metabolic and signaling pathways that directly influence the kinetics and thermodynamics of biochemical systems. Herein we describe the biophysical theory and computational methods to account for multiple ion binding to biochemical reactants and demonstrate the crucial effects of ion binding on biochemical reaction kinetics and thermodynamics. In simulations of realistic systems, the concentrations of these ions change with time due to dynamic buffering and competitive binding. In turn, the effective thermodynamic properties vary as functions of cation concentrations and important environmental variables such as temperature and overall ionic strength. Physically realistic simulations of biochemical systems require incorporating all of these phenomena into a coherent mathematical description. Several applications to physiological systems are demonstrated based on this coherent simulation framework. PMID:19216922

Chemical and biochemical thermodynamics: Is it time for a reunification?

PubMed

Iotti, Stefano; Raff, Lionel; Sabatini, Antonio

2017-02-01

The thermodynamics of chemical reactions in which all species are explicitly considered with atoms and charge balanced is compared with the transformed thermodynamics generally used to treat biochemical reactions where atoms and charges are not balanced. The transformed thermodynamic quantities suggested by Alberty are obtained by execution of Legendre transformation of the usual thermodynamic potentials. The present analysis demonstrates that the transformed values for Δ r G' 0 and Δ r H' 0 can be obtained directly without performing Legendre transformations by simply writing the chemical reactions with all the pseudoisomers explicitly included and charges balanced. The appropriate procedures for computing the stoichiometric coefficients for the pseudoisomers are fully explained by means of an example calculation for the biochemical ATP hydrolysis reaction. It is concluded that the analysis has reunited the "two separate worlds" of conventional thermodynamics and transformed thermodynamics. In addition, it is also shown that the value of the conditional Gibbs energy of reaction, Δ r G', for a biochemical reaction is the same of the value of Δ r G for any chemical reaction involving pseudoisomers of the biochemical reagents. Copyright © 2016 Elsevier B.V. All rights reserved.

Biochemical processes of oligotrophic peat deposits of Vasyugan Mire

NASA Astrophysics Data System (ADS)

Inisheva, L. I.; Sergeeva, M. A.

2009-04-01

The problem of peat and mire ecosystems functioning and their rational use is the main problem of biosphere study. This problem also refers to forecasting of biosphere changes results which are global and anthropogenic. According to many scientists' research the portion of mires in earth carbon balance is about 15% of world's stock. The aim of this study is to investigate biochemical processes in oligotrophic deposits in North-eastern part of Vasyugan Mire. The investigations were made on the territory of scientific-research ground (56˚ 03´ and 56˚ 57´ NL, 82˚ 22´ and 82˚ 42´ EL). It is situated between two rivers Bakchar and Iksa (in outskirts of the village Polynyanka, Bakchar region, Tomsk oblast). Evolution of investigated mire massif began with the domination of eutrophic phytocenosis - Filicinae, then sedge. Later transfer into oligotrophic phase was accompanied by formation of meter high-moor peat deposit. The age of three-meter peat deposit reaches four thousand years. Biochemical processes of carbon cycle cover the whole peat deposit, but the process activity and its direction in different layers are defined by genesis and duration of peat formation. So, the number of cellulose-fermenting aerobes in researched peat deposits ranges from 16.8 to 75.5 million CFU/g, and anaerobic bacteria from 9.6 to 48.6 million CFU/g. The high number of aerobes is characteristic for high water levels, organizing by raised bog peats. Their number decreases along the profile in 1.7 - 2 times. The number of microflora in peat deposit is defined by the position in the landscape profile (different geneses), by the depth, by hydrothermic conditions of years and individual months. But microflora activity shows along all depth of peat deposit. We found the same in the process of studying of micromycete complex structure. There was revealed either active component micromycete complex - mycelium, or inert one - spores in a meter layer of peat deposit. If mushrooms

Detection of Biochemical Pathogens, Laser Stand-off Spectroscopy, Quantum Coherence, and Many Body Quantum Optics

DTIC Science & Technology

2012-02-24

AND SUBTITLE Detection of Biochemical Pathogens, Laser Stand-off Spectroscopy, Quantum Coherence, and Many Body Quantum Optics 6. AUTHORS Marian O...Maximum 200 words) Results of our earlier research in the realm of quantum optics were extended in order to solve the challenging technical problems of...efficient methods of generating UV light via quantum coherence. 14. SUBJECT TERMS Quantum coherence, quantum optics, lasers 15. NUMBER OF PAGES 15

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

PubMed Central

Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang

2018-01-01

Abstract SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements. PMID:29092055

Biochemical Thermodynamics under near Physiological Conditions

ERIC Educational Resources Information Center

Mendez, Eduardo

2008-01-01

The recommendations for nomenclature and tables in Biochemical Thermodynamics approved by IUBMB and IUPAC in 1994 can be easily introduced after the chemical thermodynamic formalism. Substitution of the usual standard thermodynamic properties by the transformed ones in the thermodynamic equations, and the use of appropriate thermodynamic tables…

Biochemical Approaches to Improved Nitrogen Fixation

USDA-ARS?s Scientific Manuscript database

Improving symbiotic nitrogen fixation by legumes has emerged again as an important topic on the world scene due to the energy crisis and lack of access to nitrogen fertilizer in developing countries. We have taken a biochemical genomics approach to improving symbiotic nitrogen fixation in legumes. L...

Visualizing Antimicrobials in Bacterial Biofilms: Three-Dimensional Biochemical Imaging Using TOF-SIMS.

PubMed

Davies, Sarah K; Fearn, Sarah; Allsopp, Luke P; Harrison, Freya; Ware, Ecaterina; Diggle, Stephen P; Filloux, Alain; McPhail, David S; Bundy, Jacob G

2017-01-01

Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight-secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection. IMPORTANCE Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples-both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium

Optical devices for biochemical sensing in flame hydrolysis deposited glass

NASA Astrophysics Data System (ADS)

Ruano-Lopez, Jesus M.

Previous research in the field of Flame Hydrolysis Deposition (FHD) of glasses has focused on the production of low cost optical devices for the field of telecommunications. The originality of this doctoral research resides in the exploration of this technology in the fabrication of optical bio-chemical sensors, with integrated "Lab-on-a-chip" devices. To achieve this goal, we have combined and applied different microfabrication processes for the manufacture of sensor platforms using FHD. These structures are unique in that they take advantage of the intrinsic benefits of the microfabrication process, such as, miniaturisation and mass production, and combine them with the properties of FHD glass, namely: low loss optical transducing mechanisms, planar technologies and monolithic integration. This thesis demonstrates that FHD is a suitable technology for biosensing and Lab- on-a-Chip applications. The objective is to provide future researchers with the necessary tools to accomplish an integrated analytical system based on FHD. We have designed, fabricated, and successfully tested a FHD miniaturised sensor, which comprised optical and microfluidic circuitry, in the framework of low volume fluorescence assays. For the first time, volumes as low as 570 pL were analysed with a Cyanine-5 fluorophore with a detection limit of 20 pM, or ca. 6000 molecules (+/-3sigma) for this platform. The fabrication of the sensor generated a compilation of processes that were then utilised to produce other possible optical platforms for bio-chemical sensors in FHD, e.g. arrays and microfluidics. The "catalogue" of methods used included new recipes for reactive ion etching, glass deposition and bonding techniques that enabled the development of the microfluidic circuitry, integrated with an optical circuitry. Furthermore, we developed techniques to implement new tasks such as optical signal treatment using integrated optical structures, planar arraying of sensors, a separating element for

Crossover Comparison of the Pharmacokinetics of Atropine and Pralidoxime Chloride in Three Multichambered Autoinjector Systems and the Mark 1. Task 90-15

DTIC Science & Technology

1991-03-30

tetrabutylanmmonium nitrate (Kodak 9664), sodium lauryl sulfate (dodecyl sulfide, sodium salt) (Aldrich 86-201-0), helium gas, and nitrogen gas. D ...shall be U.S. Army MeJical Research referred to Commander, U.S. Army Medical Research and Development Command, ATTN: S’~ D -R1 - ,Fort Detr ick...Protocols APPENDIX 8 I . SOPS APPENDIX C Pharrnacokinetic Analysis Data for Individual Animals I. APPENDIX D , Sample Phamnacokinetic Modeling Program

Reconstructing biochemical pathways from time course data.

PubMed

Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

2007-03-01

Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.

A revision of the Nearctic species of Liancalus (Diptera: Dolichopodidae)

Treesearch

Justin B. Runyon; Richard L. Hurley

2015-01-01

The genus Liancalus Loew is revised for the Nearctic Region. Seven species are documented from this region including two new species: Liancalus genualis Loew, L. hydrophilus Aldrich, L. limbatus Van Duzee, L. pterodactyl sp. n., L. querulus Osten Sacken, L. similis Aldrich, and L. sonorus sp. n. Lectotypes are designated for the following species: L. genualis, L....

The use of biochemical methods in extraterrestrial life detection

NASA Astrophysics Data System (ADS)

McDonald, Gene

2006-08-01

Instrument development for in situ extraterrestrial life detection focuses primarily on the ability to distinguish between biological and non-biological material, mostly through chemical analysis for potential biosignatures (e.g., biogenic minerals, enantiomeric excesses). In constrast, biochemical analysis techniques commonly applied to Earth life focus primarily on the exploration of cellular and molecular processes, not on the classification of a given system as biological or non-biological. This focus has developed because of the relatively large functional gap between life and non-life on Earth today. Life on Earth is very diverse from an environmental and physiological point of view, but is highly conserved from a molecular point of view. Biochemical analysis techniques take advantage of this similarity of all terrestrial life at the molecular level, particularly through the use of biologically-derived reagents (e.g., DNA polymerases, antibodies), to enable analytical methods with enormous sensitivity and selectivity. These capabilities encourage consideration of such reagents and methods for use in extraterrestrial life detection instruments. The utility of this approach depends in large part on the (unknown at this time) degree of molecular compositional differences between extraterrestrial and terrestrial life. The greater these differences, the less useful laboratory biochemical techniques will be without significant modification. Biochemistry and molecular biology methods may need to be "de-focused" in order to produce instruments capable of unambiguously detecting a sufficiently wide range of extraterrestrial biochemical systems. Modern biotechnology tools may make that possible in some cases.

Biochemical tests of placental function for assessment in pregnancy.

PubMed

Neilson, James P

2012-08-15

Biochemical tests of placental or feto-placental function were widely used in the 1960s and 1970s in high-risk pregnancies to try to predict, and thus try to avoid, adverse fetal outcome. To assess the effects of performing biochemical tests of placental function in high-risk, low-risk, or unselected pregnancies. We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (10 May 2012). Controlled trials (randomized or 'quasi-randomized') that compare the use of biochemical tests of placental function in pregnancy with non-use. Trial quality was assessed and data were extracted by the review author. A single eligible trial of poor quality was identified. It involved 622 women with high-risk pregnancies who had had plasma (o)estriol estimations. Women were allocated to have their (o)estriol results revealed or concealed on the basis of hospital record number (with attendant risk of selection bias). There were no obvious differences in perinatal mortality (relative risk (RR) 0.88, 95% confidence interval (CI) 0.36 to 2.13) or planned delivery (RR 0.97, 95% CI 0.81 to 1.15) between the two groups. The available trial data do not support the use of (o)estriol estimation in high-risk pregnancies. The single small trial available does not have the power to exclude a beneficial effect but this is probably of historical interest since biochemical testing has been superseded by biophysical testing in antepartum fetal assessment.

Proteins Annexin A2 and PSA in Prostate Cancer Biopsies Do Not Predict Biochemical Failure.

PubMed

Lamb, David S; Sondhauss, Sven; Dunne, Jonathan C; Woods, Lisa; Delahunt, Brett; Ferguson, Peter; Murray, Judith; Nacey, John N; Denham, James W; Jordan, T William

2017-12-01

We previously reported the use of mass spectrometry and western blotting to identify proteins from tumour regions of formalin-fixed paraffin-embedded biopsies from 16 men who presented with apparently localized prostate cancer, and found that annexin A2 (ANXA2) appeared to be a better predictor of subsequent biochemical failure than prostate-specific antigen (PSA). In this follow-up study, ANXA2 and PSA were measured using western blotting of proteins extracted from biopsies from 37 men from a subsequent prostate cancer trial. No significant differences in ANXA2 and PSA levels were observed between men with and without biochemical failure. The statistical effect sizes were small, d=0.116 for ANXA2, and 0.266 for PSA. ANXA2 and PSA proteins measured from biopsy tumour regions are unlikely to be good biomarkers for prediction of the clinical outcome of prostate cancer presenting with apparently localized disease. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

40 CFR 158.2083 - Experimental use permit biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

... pesticides human health assessment data requirements table. 158.2083 Section 158.2083 Protection of... Biochemical Pesticides § 158.2083 Experimental use permit biochemical pesticides human health assessment data... determine the human health assessment data requirements for a particular biochemical pesticide product. (2...

40 CFR 158.2083 - Experimental use permit biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... pesticides human health assessment data requirements table. 158.2083 Section 158.2083 Protection of... Biochemical Pesticides § 158.2083 Experimental use permit biochemical pesticides human health assessment data... determine the human health assessment data requirements for a particular biochemical pesticide product. (2...

40 CFR 158.2083 - Experimental use permit biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

... pesticides human health assessment data requirements table. 158.2083 Section 158.2083 Protection of... Biochemical Pesticides § 158.2083 Experimental use permit biochemical pesticides human health assessment data... determine the human health assessment data requirements for a particular biochemical pesticide product. (2...

40 CFR 158.2083 - Experimental use permit biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

... pesticides human health assessment data requirements table. 158.2083 Section 158.2083 Protection of... Biochemical Pesticides § 158.2083 Experimental use permit biochemical pesticides human health assessment data... determine the human health assessment data requirements for a particular biochemical pesticide product. (2...

40 CFR 158.2083 - Experimental use permit biochemical pesticides human health assessment data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

... pesticides human health assessment data requirements table. 158.2083 Section 158.2083 Protection of... Biochemical Pesticides § 158.2083 Experimental use permit biochemical pesticides human health assessment data... determine the human health assessment data requirements for a particular biochemical pesticide product. (2...

A Small Stem Loop Structure Of The Ebola Virus Trailer Is Essential For Replication And Interacts With Heat Shock Protein A8

DTIC Science & Technology

2016-12-02

agarose gel electrophoresis TR-16-205 Nucleic Acids Research, 2016 3 (Seakem GTG , Sigma-Aldrich) and purified using the QI- Aquick Gel Extraction Kit... gtg +cga 1923-1938 3′ LNA2 +caa+aaa+ga+aa+gaa+gaa 3E-5E eGFP, 3E-5E plasmid containing enhanced green fluorescent protein; aiSHAPE, antisense-interfered

Biochemical reactions of ozone in plants

Treesearch

J. Brian Mudd

1998-01-01

Plants react biochemically to ozone in three phases: with constitutive chemicals in the apoplastic fluid and cell membranes; by forming messenger molecules by the affected constitutive materials (ethylene); and by responding to the messenger molecules with pathogenic RNAs and proteins. For instance, plant reactions with ozone result in constitutive molecules such as...

Biochemical Reconstitution of the WAVE Regulatory Complex

PubMed Central

Chen, Baoyu; Padrick, Shae B.; Henry, Lisa; Rosen, Michael K.

2014-01-01

The WAVE regulatory complex (WRC) is a 400-KDa heteropentameric protein assembly that plays a central role in controlling actin cytoskeletal dynamics in many cellular processes. The WRC acts by integrating diverse cellular cues and stimulating the actin nucleating activity of the Arp2/3 complex at membranes. Biochemical and biophysical studies of the underlying mechanisms of these processes require large amounts of purified WRC. Recent success in recombinant expression, reconstitution, purification and crystallization of the WRC has greatly advanced our understanding of the inhibition, activation and membrane recruitment mechanisms of this complex. But many important questions remain to be answered. Here we summarize and update the methods developed in our laboratory, which allow reliable and flexible production of tens of milligrams of recombinant WRC of crystallographic quality, sufficient for many biochemical and structural studies. PMID:24630101

[The effect of space flight on metabolism: the results of biochemical research in rat experiments on the Kosmos biosatellites].

PubMed

Popova, I A; Grigor'ev, A I

1992-01-01

Cosmos biosatellites research program was the unique possibility to study the metabolic features influenced by space flight factors. Based on the existing ideas about relationships between some metabolic responses, the state of metabolism and the systems of its control in the rats flown in space was evaluated to differentiate the processes occurred in microgravity, possibly under effect of this factor and during first postflight hours. The biochemical results of studying the rats exposed to space environments during 7, 14, 18.5 and 19.5 days and sacrificed 4-11 h after landing (Cosmos-782, -936, -1129, -1667, -2044 flight) are used. The major portion of data are in line with understanding that after landing when the microgravity-adapted rats again return to 1-g environments they display an acute stress reaction. A postflight stress reaction is manifested itself in a specific way as compared to adequate and well studied model of acute and chronic stress and dictates subsequent metabolic changes. Postflight together with the acute stressful and progressing readaptation shifts the metabolic signs of previous adaptation to microgravity are shown up. In the absence of engineering feasibility to control or record the state of metabolism inflight it can only presupposed what metabolic status is typical of the animals in space environments and that its development is triggered by a decreased secretion of the biologically active growth hormone. This concept is confirmed by the postflight data.

A systematic petri net approach for multiple-scale modeling and simulation of biochemical processes.

PubMed

Chen, Ming; Hu, Minjie; Hofestädt, Ralf

2011-06-01

A method to exploit hybrid Petri nets for modeling and simulating biochemical processes in a systematic way was introduced. Both molecular biology and biochemical engineering aspects are manipulated. With discrete and continuous elements, the hybrid Petri nets can easily handle biochemical factors such as metabolites concentration and kinetic behaviors. It is possible to translate both molecular biological behavior and biochemical processes workflow into hybrid Petri nets in a natural manner. As an example, penicillin production bioprocess is modeled to illustrate the concepts of the methodology. Results of the dynamic of production parameters in the bioprocess were simulated and observed diagrammatically. Current problems and post-genomic perspectives were also discussed.

Aspects on the Physiological and Biochemical Foundations of Neurocritical Care

PubMed Central

Nordström, Carl-Henrik; Koskinen, Lars-Owe; Olivecrona, Magnus

2017-01-01

Neurocritical care (NCC) is a branch of intensive care medicine characterized by specific physiological and biochemical monitoring techniques necessary for identifying cerebral adverse events and for evaluating specific therapies. Information is primarily obtained from physiological variables related to intracranial pressure (ICP) and cerebral blood flow (CBF) and from physiological and biochemical variables related to cerebral energy metabolism. Non-surgical therapies developed for treating increased ICP are based on knowledge regarding transport of water across the intact and injured blood–brain barrier (BBB) and the regulation of CBF. Brain volume is strictly controlled as the BBB permeability to crystalloids is very low restricting net transport of water across the capillary wall. Cerebral pressure autoregulation prevents changes in intracranial blood volume and intracapillary hydrostatic pressure at variations in arterial blood pressure. Information regarding cerebral oxidative metabolism is obtained from measurements of brain tissue oxygen tension (PbtO2) and biochemical data obtained from intracerebral microdialysis. As interstitial lactate/pyruvate (LP) ratio instantaneously reflects shifts in intracellular cytoplasmatic redox state, it is an important indicator of compromised cerebral oxidative metabolism. The combined information obtained from PbtO2, LP ratio, and the pattern of biochemical variables reveals whether impaired oxidative metabolism is due to insufficient perfusion (ischemia) or mitochondrial dysfunction. Intracerebral microdialysis and PbtO2 give information from a very small volume of tissue. Accordingly, clinical interpretation of the data must be based on information of the probe location in relation to focal brain damage. Attempts to evaluate global cerebral energy state from microdialysis of intraventricular fluid and from the LP ratio of the draining venous blood have recently been presented. To be of clinical relevance, the

The Use of Stimulable Bioluminescence from Marine Dinoflagellates as a Means of Detecting Toxicity in the Marine Environment

DTIC Science & Technology

1993-04-01

measure the acute and sublethal effects of heavy metals ( tributyltin , copper, and zinc) and storm drain effluent on the light output from marine...heavy metals ( tributyltin , copper, and zinc) and storm drain effluent on the light output from marine bioluminescent dinoflagellates (Pyrocystis...pentahydrate and zinc sulfate heptahydrate (Aldrich Chemical Co.); tributyltin chloride (Aldrich Chemical Co.); American Society for Testing and Materials

Biochemical basis for the biological clock

NASA Technical Reports Server (NTRS)

Morre, D. James; Chueh, Pin-Ju; Pletcher, Jake; Tang, Xiaoyu; Wu, Lian-Ying; Morre, Dorothy M.

2002-01-01

NADH oxidases at the external surface of plant and animal cells (ECTO-NOX proteins) exhibit stable and recurring patterns of oscillations with potentially clock-related, entrainable, and temperature-compensated period lengths of 24 min. To determine if ECTO-NOX proteins might represent the ultradian time keepers (pacemakers) of the biological clock, COS cells were transfected with cDNAs encoding tNOX proteins having a period length of 22 min or with C575A or C558A cysteine to alanine replacements having period lengths of 36 or 42 min. Here we demonstrate that such transfectants exhibited 22, 36, or 40 to 42 h circadian patterns in the activity of glyceraldehyde-3-phosphate dehydrogenase, a common clock-regulated protein, in addition to the endogenous 24 h circadian period length. The fact that the expression of a single oscillatory ECTO-NOX protein determines the period length of a circadian biochemical marker (60 X the ECTO-NOX period length) provides compelling evidence that ECTO-NOX proteins are the biochemical ultradian drivers of the cellular biological clock.

A Randomized Phase 2 Trial of 177Lu Radiolabeled Anti-PSMA Biochemically Monoclonal Antibody J591 in Patients with High-Risk Castrate, Biochemically Relapsed Prostate Cancer

DTIC Science & Technology

2010-09-01

relapsed prostate cancer (PC) after local therapy. J Clin Oncol 28: 15s, 2010 (suppl; Abstr TPS248) Presentation: Poster presentation, 2010 ASCO...Annual Meeting V. Conclusions Biochemical relapse is common after local therapy for prostate cancer. Based on the physical properties of 177Lu...ketoconazole in patients (pts) with high-risk castrate biochemically relapsed prostate cancer (PC) after local therapy. S. T. Tagawa, J. Osborne, P. J

ReactPRED: a tool to predict and analyze biochemical reactions.

PubMed

Sivakumar, Tadi Venkata; Giri, Varun; Park, Jin Hwan; Kim, Tae Yong; Bhaduri, Anirban

2016-11-15

Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same. ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application. ReactPRED is available at: https://sourceforge.net/projects/reactpred/ CONTACT: anirban.b@samsung.com or ty76.kim@samsung.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Variations in biochemical values for common laboratory tests: a comparison among multi-ethnic Israeli women cohort.

PubMed

Birk, Ruth; Heifetz, Eliyahu M

2018-04-28

Biochemical laboratory values are an essential tool in medical diagnosis, treatment, and follow-up; however, they are known to vary between populations. Establishment of ethnicity-adjusted reference values is recommended by health organizations. To investigate the ethnicity element in biochemical lab values studying women of different ethnic groups. Biochemical lab values (n = 27) of 503 adult Israeli women of three ethnicities (Jewish Ashkenazi, Jewish Sephardic, and Bedouin Arab) attending a single medical center were analyzed. Biochemical data were extracted from medical center records. Ethnic differences of laboratory biochemicals were studied using ANCOVA to analyze the center of the distribution as well as quartile regression analysis to analyze the upper and lower limits, both done with an adjustment for age. Significant ethnic differences were found in almost half (n = 12) of the biochemical laboratory tests. Ashkenazi Jews exhibited significantly higher mean values compared to Bedouins in most of the biochemical tests, including albumin, alkaline phosphatase, calcium, cholesterol, cholesterol LDL and HDL, cholesterol LDL calc., folic acid, globulin, and iron saturation, while the Bedouins exhibited the highest mean values in the creatinine and triglycerides. For most of these tests, Sephardic Jews exhibited biochemical mean levels in between the two other groups. Compared to Ashkenazi Jews, Sephardic Jews had a significant shift to lower values in cholesterol LDL. Ethnic subpopulations have distinct distributions in biochemical laboratory test values, which should be taken into consideration in medical practice enabling precision medicine.

[Circulating miR-152 helps early prediction of postoperative biochemical recurrence of prostate cancer].

PubMed

Chen, Jun-Feng; Liao, Yu-Feng; Ma, Jian-Bo; Mao, Qi-Feng; Jia, Guang-Cheng; Dong, Xue-Jun

2017-07-01

To investigate the value of circulating miR-152 in the early prediction of postoperative biochemical recurrence of prostate cancer. Sixty-six cases of prostate cancer were included in this study, 35 with and 31 without biochemical recurrence within two years postoperatively, and another 31 healthy individuals were enrolled as normal controls. The relative expression levels of circulating miR-152 in the serum of the subjects were detected by qRT-PCR, its value in the early diagnosis of postoperative biochemical recurrence of prostate cancer was assessed by ROC curve analysis, and the correlation of its expression level with the clinicopathological parameters of the patients were analyzed. The expression of circulating miR-152 was significantly lower in the serum of the prostate cancer patients than in the normal controls (t = －5.212, P = 0.001), and so was it in the patients with than in those without postoperative biochemical recurrence (t = －5.727, P = 0.001). The ROC curve for the value of miR-152 in the early prediction of postoperative biochemical recurrence of prostate cancer showed the area under the curve (AUC) to be 0.906 (95% CI: 0.809－0.964), with a sensitivity of 91.4% and a specificity of 80.6%. The expression level of miR-152 was correlated with the Gleason score, clinical stage of prostate cancer, biochemical recurrence, and bone metastasis (P <0.05), decreasing with increased Gleason scores and elevated clinical stage of the malignancy. No correlation, however, was found between the miR-152 expression and the patients' age or preoperative PSA level (P >0.05). The expression level of circulating miR-152 is significantly reduced in prostate cancer patients with biochemical recurrence after prostatectomy and could be a biomarker in the early prediction of postoperative biochemical recurrence of the malignancy.

Real-time biochemical sensor based on Raman scattering with CMOS contact imaging.

PubMed

Muyun Cao; Yuhua Li; Yadid-Pecht, Orly

2015-08-01

This work presents a biochemical sensor based on Raman scattering with Complementary metal-oxide-semiconductor (CMOS) contact imaging. This biochemical optical sensor is designed for detecting the concentration of solutions. The system is built with a laser diode, an optical filter, a sample holder and a commercial CMOS sensor. The output of the system is analyzed by an image processing program. The system provides instant measurements with a resolution of 0.2 to 0.4 Mol. This low cost and easy-operated small scale system is useful in chemical, biomedical and environmental labs for quantitative bio-chemical concentration detection with results reported comparable to a highly cost commercial spectrometer.

Thermodynamic considerations on Ca2+-induced biochemical reactions in living cells

NASA Astrophysics Data System (ADS)

Lucia, Umberto; Ponzetto, Antonio

2016-02-01

Cells can be regarded as complex engines that execute a series of chemical reactions. Energy transformations, thermo-electro-chemical processes and transport phenomena can occur across cell membranes. Different, related thermo-electro-biochemical behaviour can occur between health and disease states. Analysis of the irreversibility related to ion fluxes can represent a new approach to study and control the biochemical behaviour of living cells.

Thermodynamics of Computational Copying in Biochemical Systems

NASA Astrophysics Data System (ADS)

Ouldridge, Thomas E.; Govern, Christopher C.; ten Wolde, Pieter Rein

2017-04-01

Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that, as in computation, a canonical biochemical readout network generates correlations; extracting no work from these correlations sets a lower bound on dissipation. For general input, the biochemical network cannot reach this bound, even with arbitrarily slow reactions or weak thermodynamic driving. It faces an accuracy-dissipation trade-off that is qualitatively distinct from and worse than implied by the bound, and more complex steady-state copy processes cannot perform better. Nonetheless, the cost remains close to the thermodynamic bound unless accuracy is extremely high. Additionally, we show that biomolecular reactions could be used in thermodynamically optimal devices under exogenous manipulation of chemical fuels, suggesting an experimental system for testing computational thermodynamics.

Are There Any Promising Biochemical Correlates of Achievement Behavior and Motivation? The Evidence for Serum Uric Acid and Serum Cholesterol

ERIC Educational Resources Information Center

Kasl, Stanislav V.

1974-01-01

This review examines the available evidence in support of the argument that serum uric acid (SUA) possesses considerable promise as an indicator of one type of biochemical influence on achievement behavior. The evidence arguing for further research into the role of serum cholesterol in achievement behavior is also examined. (Author/JR)

Biochemical Diagnosis in Substance and Non-substance Addiction.

PubMed

Shen, Wenwen; Liu, Huifeng; Xie, Xiaohu; Liu, Haixiong; Zhou, Wenhua

2017-01-01

An optimal biochemical marker for addiction would be some easily traced molecules in body specimens, which indicates indulgent addictive behaviors, or susceptibility to certain addictive stimuli. In this chapter, we discussed existing literature about possible biomarkers, and classified them into three categories: origin forms and metabolites of substances, markers from biochemical responses to certain addiction, and genetic and epigenetic biomarkers suggesting susceptibility to addiction. In every category, we examined studies concerning certain type of addiction one by one, with focuses mainly on opiates, psychostimulants, and pathological gambling. Several promising molecules were highlighted, including those of neurotrophic factors, inflammatory factors, and indicators of vascular injury, and genetic and epigenetic biomarkers such as serum miRNAs. DNA methylation signatures and signal nucleotide polymorphism of candidate gene underlying the addiction.

Integration of electrochemistry in micro-total analysis systems for biochemical assays: recent developments.

PubMed

Xu, Xiaoli; Zhang, Song; Chen, Hui; Kong, Jilie

2009-11-15

Micro-total analysis systems (microTAS) integrate different analytical operations like sample preparation, separation and detection into a single microfabricated device. With the outstanding advantages of low cost, satisfactory analytical efficiency and flexibility in design, highly integrated and miniaturized devices from the concept of microTAS have gained widespread applications, especially in biochemical assays. Electrochemistry is shown to be quite compatible with microanalytical systems for biochemical assays, because of its attractive merits such as simplicity, rapidity, high sensitivity, reduced power consumption, and sample/reagent economy. This review presents recent developments in the integration of electrochemistry in microdevices for biochemical assays. Ingenious microelectrode design and fabrication methods, and versatility of electrochemical techniques are involved. Practical applications of such integrated microsystem in biochemical assays are focused on in situ analysis, point-of-care testing and portable devices. Electrochemical techniques are apparently suited to microsystems, since easy microfabrication of electrochemical elements and a high degree of integration with multi-analytical functions can be achieved at low cost. Such integrated microsystems will play an increasingly important role for analysis of small volume biochemical samples. Work is in progress toward new microdevice design and applications.

Biochemical characterization of the selenoproteome in Gallus gallus via bioinformatics analysis: structure-function relationships and interactions of binding molecules.

PubMed

Zhu, Shi-Yong; Li, Xue-Nan; Sun, Xiao-Chen; Lin, Jia; Li, Wei; Zhang, Cong; Li, Jin-Long

2017-02-22

Knowledge about mammalian selenoproteins is increasing. However, the selenoproteome of birds remains considerably less understood, especially concerning its biochemical characterization, structure-function relationships and the interactions of binding molecules. In this work, the SECIS elements, subcellular localization, protein domains and interactions of binding molecules of the selenoproteome in Gallus gallus were analyzed using bioinformatics tools. We carried out comprehensive analyses of the structure-function relationships and interactions of the binding molecules of selenoproteins, to provide biochemical characterization of the selenoproteome in Gallus gallus. Our data provided a wealth of information on the biochemical functions of bird selenoproteins. Members of the selenoproteome were found to be involved in various biological processes in chickens, such as in antioxidants, maintenance of the redox balance, Se transport, and interactions with metals. Six membrane-bound selenoproteins (SelI, SelK, SelS, SelT, DIO1 and DIO3) played important roles in maintaining the membrane integrity. Chicken selenoproteins were classified according to their ligand binding sites as zinc-containing matrix metalloselenoproteins (Sep15, MsrB1, SelW and SelM), POP-containing selenoproteins (GPx1-4), FAD-interacting selenoproteins (TrxR1-3), secretory transport selenoproteins (GPx3 and SelPa) and other selenoproteins. The results of our study provided new evidence for the unknown biological functions of the selenoproteome in birds. Future research is required to confirm the novel biochemical functions of bird selenoproteins.

Performance limits and trade-offs in entropy-driven biochemical computers.

PubMed

Chu, Dominique

2018-04-14

It is now widely accepted that biochemical reaction networks can perform computations. Examples are kinetic proof reading, gene regulation, or signalling networks. For many of these systems it was found that their computational performance is limited by a trade-off between the metabolic cost, the speed and the accuracy of the computation. In order to gain insight into the origins of these trade-offs, we consider entropy-driven computers as a model of biochemical computation. Using tools from stochastic thermodynamics, we show that entropy-driven computation is subject to a trade-off between accuracy and metabolic cost, but does not involve time-trade-offs. Time trade-offs appear when it is taken into account that the result of the computation needs to be measured in order to be known. We argue that this measurement process, although usually ignored, is a major contributor to the cost of biochemical computation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification of biochemical features of defective Coffea arabica L. beans.

PubMed

Casas, María I; Vaughan, Michael J; Bonello, Pierluigi; McSpadden Gardener, Brian; Grotewold, Erich; Alonso, Ana P

2017-05-01

Coffee organoleptic properties are based in part on the quality and chemical composition of coffee beans. The presence of defective beans during processing and roasting contribute to off flavors and reduce overall cup quality. A multipronged approach was undertaken to identify specific biochemical markers for defective beans. To this end, beans were split into defective and non-defective fractions and biochemically profiled in both green and roasted states. A set of 17 compounds in green beans, including organic acids, amino acids and reducing sugars; and 35 compounds in roasted beans, dominated by volatile compounds, organic acids, sugars and sugar alcohols, were sufficient to separate the defective and non-defective fractions. Unsorted coffee was examined for the presence of the biochemical markers to test their utility in detecting defective beans. Although the green coffee marker compounds were found in all fractions, three of the roasted coffee marker compounds (1-methylpyrrole, 5-methyl- 2-furfurylfuran, and 2-methylfuran) were uniquely present in defective fractions. Published by Elsevier Ltd.

Label-Free Imaging and Biochemical Characterization of Bovine Sperm Cells

PubMed Central

Ferrara, Maria Antonietta; Di Caprio, Giuseppe; Managò, Stefano; De Angelis, Annalisa; Sirleto, Luigi; Coppola, Giuseppe; De Luca, Anna Chiara

2015-01-01

A full label-free morphological and biochemical characterization is desirable to select spermatozoa during preparation for artificial insemination. In order to study these fundamental parameters, we take advantage of two attractive techniques: digital holography (DH) and Raman spectroscopy (RS). DH presents new opportunities for studying morphological aspect of cells and tissues non-invasively, quantitatively and without the need for staining or tagging, while RS is a very specific technique allowing the biochemical analysis of cellular components with a spatial resolution in the sub-micrometer range. In this paper, morphological and biochemical bovine sperm cell alterations were studied using these techniques. In addition, a complementary DH and RS study was performed to identify X- and Y-chromosome-bearing sperm cells. We demonstrate that the two techniques together are a powerful and highly efficient tool elucidating some important criterions for sperm morphological selection and sex-identification, overcoming many of the limitations associated with existing protocols. PMID:25836358

Quantitative biochemical characterization and biotechnological production of caspase modulator, XIAP: Therapeutic implications for apoptosis-associated diseases.

PubMed

Yun, Si-Eun; Nam, Min-Kyung; Rhim, Hyangshuk

2018-07-01

Regulating apoptosis is a common and essential therapeutic strategy for cancer and neurodegenerative disorders. Based on basic studies of apoptotic mechanisms, various researches have attempted to overcome the pathogenesis of such diseases by activating or inhibiting apoptosis. Generally, the biochemical characteristics of the target molecules should be evaluated along with understanding of their mechanisms of action during drug development. Among apoptotic regulators, XIAP serves as a potent negative regulator to block apoptosis through the inhibition of caspase (CASP)-9 and -3/7. Although XIAP is an attractive target with such apoptotic-modulating property, biochemical and biophysical studies of XIAP are still challenging. In this study, the CASP-9 and -3/7 inhibitors XIAP, 242Δ and Δ230 were prepared using the pGEX expression system and biochemically characterized. These inhibitors were expressed in Escherichia coli at a concentration of ≥20 mg/L culture under a native condition with 0.01 mM IPTG induction. Notably, using a simple and rapid affinity purification technique, these CASP-9 and -3/7 inhibitors have been purified, yielding ≥5 mg/L culture at approximately 90% purity. We have determined that HtrA2 specifically binds to the BIR2 and BIR3 of XIAP at a 1:1 molecular ratio. Moreover, in vitro cell-free CASP-9 and -3/7 activation-apoptosis assays have demonstrated that these purified XIAP proteins dramatically inhibit CASP-9 and -3/7 action. Our system is suitable for biochemical studies, such as quantitation of the number of molecules acting on the apoptosis regulation, and provides a basis and insights that can be applied to the development of therapeutic agents for neurodegenerative disorders and cancer. Copyright © 2018 Elsevier B.V. All rights reserved.

Slot-waveguide biochemical sensor.

PubMed

Barrios, Carlos A; Gylfason, Kristinn B; Sánchez, Benito; Griol, Amadeu; Sohlström, H; Holgado, M; Casquel, R

2007-11-01

We report an experimental demonstration of an integrated biochemical sensor based on a slot-waveguide microring resonator. The microresonator is fabricated on a Si3N4-SiO2 platform and operates at a wavelength of 1.3 microm. The transmission spectrum of the sensor is measured with different ambient refractive indices ranging from n=1.33 to 1.42. A linear shift of the resonant wavelength with increasing ambient refractive index of 212 nm/refractive index units (RIU) is observed. The sensor detects a minimal refractive index variation of 2x10(-4) RIU.

40 CFR 180.1127 - Biochemical pesticide plant floral volatile attractant compounds: cinnamaldehyde, cinnamyl...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticide plant floral... (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1127 Biochemical pesticide plant floral volatile attractant compounds...

40 CFR 180.1127 - Biochemical pesticide plant floral volatile attractant compounds: cinnamaldehyde, cinnamyl...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticide plant floral... (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1127 Biochemical pesticide plant floral volatile attractant compounds...

Biochemical recurrence after radical prostatectomy: what does it mean?

PubMed Central

Tourinho-Barbosa, Rafael; Srougi, Victor; Nunes-Silva, Igor; Baghdadi, Mohammed; Rembeyo, Gregory; Eiffel, Sophie S.; Barret, Eric; Rozet, Francois; Galiano, Marc; Cathelineau, Xavier; Sanchez-Salas, Rafael

2018-01-01

ABSTRACT Background Radical prostatectomy (RP) has been used as the main primary treatment for prostate cancer (PCa) for many years with excellent oncologic results. However, approximately 20-40% of those patients has failed to RP and presented biochemical recurrence (BCR). Prostatic specific antigen (PSA) has been the pivotal tool for recurrence diagnosis, but there is no consensus about the best PSA threshold to define BCR until this moment. The natural history of BCR after surgical procedure is highly variable, but it is important to distinguish biochemical and clinical recurrence and to find the correct timing to start multimodal treatment strategy. Also, it is important to understand the role of each clinical and pathological feature of prostate cancer in BCR, progression to metastatic disease and cancer specific mortality (CSM). Review design A simple review was made in Medline for articles written in English language about biochemical recurrence after radical prostatectomy. Objective To provide an updated assessment of BCR definition, its meaning, PCa natural history after BCR and the weight of each clinical/pathological feature and risk group classifications in BCR, metastatic disease and CSM. PMID:29039897

Biochemical and nutritional components of selected honey samples.

PubMed

Chua, Lee Suan; Adnan, Nur Ardawati

2014-01-01

The purpose of this study was to investigate the relationship of biochemical (enzymes) and nutritional components in the selected honey samples from Malaysia. The relationship is important to estimate the quality of honey based on the concentration of these nutritious components. Such a study is limited for honey samples from tropical countries with heavy rainfall throughout the year. A number of six honey samples that commonly consumed by local people were collected for the study. Both the biochemical and nutritional components were analysed by using standard methods from Association of Official Analytical Chemists (AOAC). Individual monosaccharides, disaccharides and 17 amino acids in honey were determined by using liquid chromatographic method. The results showed that the peroxide activity was positively correlated with moisture content (r = 0.8264), but negatively correlated with carbohydrate content (r = 0.7755) in honey. The chromatographic sugar and free amino acid profiles showed that the honey samples could be clustered based on the type and maturity of honey. Proline explained for 64.9% of the total variance in principle component analysis (PCA). The correlation between honey components and honey quality has been established for the selected honey samples based on their biochemical and nutritional concentrations. PCA results revealed that the ratio of sucrose to maltose could be used to measure honey maturity, whereas proline was the marker compound used to distinguish honey either as floral or honeydew.

Biochemical and Cellular Assessment of Acetabular Chondral Flaps Identified During Hip Arthroscopy.

PubMed

Hariri, Sanaz; Truntzer, Jeremy; Smith, Robert Lane; Safran, Marc R

2015-06-01

To analyze chondral flaps debrided during hip arthroscopy to determine their biochemical and cellular composition. Thirty-one full-thickness acetabular chondral flaps were collected during hip arthroscopy. Biochemical analysis was undertaken in 21 flaps from 20 patients, and cellular viability was determined in 10 flaps from 10 patients. Biochemical analysis included concentrations of (1) DNA (an indicator of chondrocyte content), (2) hydroxyproline (an indicator of collagen content), and (3) glycosaminoglycan (an indicator of chondrocyte biosynthesis). Higher values for these parameters indicated more healthy tissue. The flaps were examined to determine the percentage of viable chondrocytes. The percentage of acetabular chondral flap specimens that had concentrations within 1 SD of the mean values reported in previous normal cartilage studies was 38% for DNA, 0% for glycosaminoglycan, and 43% for hydroxyproline. The average cellular viability of our acetabular chondral flap specimens was 39% (SD, 14%). Only 2 of the 10 specimens had more than half the cells still viable. There was no correlation between (1) the gross examination of the joint or knowledge of the patient's demographic characteristics and symptoms and (2) biochemical properties and cell viability of the flap, with one exception: a degenerative appearance of the surrounding cartilage correlated with a higher hydroxyproline concentration. Although full-thickness acetabular chondral flaps can appear normal grossly, the biochemical properties and percentage of live chondrocytes in full-thickness chondral flaps encountered in hip arthroscopy show that this tissue is not normal. There has been recent interest in repairing chondral flaps encountered during hip arthroscopy. These data suggest that acetabular chondral flaps are not biochemically and cellularly normal. Although these flaps may still be valuable mechanically and/or as a scaffold in some conductive or inductive capacity, further study is

Transport of Bacillus thuringiensis var. Kurstaki Via Fomites

DTIC Science & Technology

2011-01-01

Dick- inson and Co., Fisher Scientific) with cycloheximide (50 mg/ L, Sigma-Aldrich), and colony counts were obtained after overnight incubation at 37...soy agar (Beckton Dickinson and Co., Fisher Scientific) with cycloheximide (50 mg/L, Sigma- Aldrich), and colony counts were obtained after overnight...Miguel and colleagues reported the reaer- osolization of pollen , pollen fragments, animal dander, and mold from paved surfaces.16 Turnbull and col

Metabonomics and medicine: the Biochemical Oracle.

PubMed

Mitchell, Steve; Holmes, Elaine; Carmichael, Paul

2002-10-01

Occasionally, a new idea emerges that has the potential to revolutionize an entire field of scientific endeavour. It is now within our grasp to be able to detect subtle perturbations within the phenomenally complex biochemical matrix of living organisms. The discipline of metabonomics promises an all-encompassing approach to understanding total, yet fundamental, changes occurring in disease processes, drug toxicity and cell function.

Pathological and 3 Tesla Volumetric Magnetic Resonance Imaging Predictors of Biochemical Recurrence after Robotic Assisted Radical Prostatectomy: Correlation with Whole Mount Histopathology.

PubMed

Tan, Nelly; Shen, Luyao; Khoshnoodi, Pooria; Alcalá, Héctor E; Yu, Weixia; Hsu, William; Reiter, Robert E; Lu, David Y; Raman, Steven S

2018-05-01

, staging and positive surgical margins, significantly predicted biochemical recurrence. This suggests an important new imaging biomarker. Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Examining the Relationship between Gender and Drug-Using Behaviors in Adolescents: The Use of Diagnostic Assessments and Biochemical Analyses of Urine Samples.

ERIC Educational Resources Information Center

James, William H.; Moore, David D.

1999-01-01

Examines the relationship between gender and drug use among adolescents using diagnostic assessments and biochemical analyses of urine samples. Statistical significance was found in the relationship between gender and marijuana use. The study confirms that more research is needed in this area. (Author/MKA)

Do Ultrasensitive Prostate Specific Antigen Measurements Have a Role in Predicting Long-Term Biochemical Recurrence-Free Survival in Men after Radical Prostatectomy?

PubMed

Sokoll, Lori J; Zhang, Zhen; Chan, Daniel W; Reese, Adam C; Bivalacqua, Trinity J; Partin, Alan W; Walsh, Patrick C

2016-02-01

less than 0.1 ng/ml after radical prostatectomy a tenfold lower cutoff (0.01 ng/ml) stratified biochemical recurrence-free survival and was a significant independent predictor of biochemical recurrence, as were pathological features. Prostate specific antigen concentrations in men without pathological evidence of prostate cancer suggest that a higher prostate specific antigen concentration (0.03 ng/ml) in the ultrasensitive range may be needed to define the detection threshold. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Feasibility of biochemical verification in a web-based smoking cessation study.

PubMed

Cha, Sarah; Ganz, Ollie; Cohn, Amy M; Ehlke, Sarah J; Graham, Amanda L

2017-10-01

Cogent arguments have been made against the need for biochemical verification in population-based studies with low-demand characteristics. Despite this fact, studies involving digital interventions (low-demand) are often required in peer review to report biochemically verified abstinence. To address this discrepancy, we examined the feasibility and costs of biochemical verification in a web-based study conducted with a national sample. Participants were 600U.S. adult current smokers who registered on a web-based smoking cessation program and completed surveys at baseline and 3months. Saliva sampling kits were sent to participants who reported 7-day abstinence at 3months, and analyzed for cotinine. The response rate at 3-months was 41.2% (n=247): 93 participants reported 7-day abstinence (38%) and were mailed a saliva kit (71% returned). The discordance rate was 36.4%. Participants with discordant responses were more likely to report 3-month use of nicotine replacement therapy or e-cigarettes than those with concordant responses (79.2% vs. 45.2%, p=0.007). The total cost of saliva sampling was $8280 ($125/sample). Biochemical verification was both time- and cost-intensive, and yielded a relatively small number of samples due to low response rates and use of other nicotine products during the follow-up period. There was a high rate of discordance of self-reported abstinence and saliva testing. Costs for data collection may be prohibitive for studies with large sample sizes or limited budgets. Our findings echo previous statements that biochemical verification is not necessary in population-based studies, and add evidence specific to technology-based studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biochemical abnormalities in Pearson syndrome.

PubMed

Crippa, Beatrice Letizia; Leon, Eyby; Calhoun, Amy; Lowichik, Amy; Pasquali, Marzia; Longo, Nicola

2015-03-01

Pearson marrow-pancreas syndrome is a multisystem mitochondrial disorder characterized by bone marrow failure and pancreatic insufficiency. Children who survive the severe bone marrow dysfunction in childhood develop Kearns-Sayre syndrome later in life. Here we report on four new cases with this condition and define their biochemical abnormalities. Three out of four patients presented with failure to thrive, with most of them having normal development and head size. All patients had evidence of bone marrow involvement that spontaneously improved in three out of four patients. Unique findings in our patients were acute pancreatitis (one out of four), renal Fanconi syndrome (present in all patients, but symptomatic only in one), and an unusual organic aciduria with 3-hydroxyisobutyric aciduria in one patient. Biochemical analysis indicated low levels of plasma citrulline and arginine, despite low-normal ammonia levels. Regression analysis indicated a significant correlation between each intermediate of the urea cycle and the next, except between ornithine and citrulline. This suggested that the reaction catalyzed by ornithine transcarbamylase (that converts ornithine to citrulline) might not be very efficient in patients with Pearson syndrome. In view of low-normal ammonia levels, we hypothesize that ammonia and carbamylphosphate could be diverted from the urea cycle to the synthesis of nucleotides in patients with Pearson syndrome and possibly other mitochondrial disorders. © 2015 Wiley Periodicals, Inc.

In silico characterization of microbial electrosynthesis for metabolic engineering of biochemicals

PubMed Central

2011-01-01

Background A critical concern in metabolic engineering is the need to balance the demand and supply of redox intermediates such as NADH. Bioelectrochemical techniques offer a novel and promising method to alleviate redox imbalances during the synthesis of biochemicals and biofuels. Broadly, these techniques reduce intracellular NAD+ to NADH and therefore manipulate the cell's redox balance. The cellular response to such redox changes and the additional reducing power available to the cell can be harnessed to produce desired metabolites. In the context of microbial fermentation, these bioelectrochemical techniques can be used to improve product yields and/or productivity. Results We have developed a method to characterize the role of bioelectrosynthesis in chemical production using the genome-scale metabolic model of E. coli. The results in this paper elucidate the role of bioelectrosynthesis and its impact on biomass growth, cellular ATP yields and biochemical production. The results also suggest that strain design strategies can change for fermentation processes that employ microbial electrosynthesis and suggest that dynamic operating strategies lead to maximizing productivity. Conclusions The results in this paper provide a systematic understanding of the benefits and limitations of bioelectrochemical techniques for biochemical production and highlight how electrical enhancement can impact cellular metabolism and biochemical production. PMID:21967745

Flow Injection Technique for Biochemical Analysis with Chemiluminescence Detection in Acidic Media

PubMed Central

Chen, Jing; Fang, Yanjun

2007-01-01

A review with 90 references is presented to show the development of acidic chemiluminescence methods for biochemical analysis by use of flow injection technique in the last 10 years. A brief discussion of both the chemiluminescence and flow injection technique is given. The proposed methods for biochemical analysis are described and compared according to the used chemiluminescence system.

Label-free optical resonant sensors for biochemical applications

NASA Astrophysics Data System (ADS)

Ciminelli, Caterina; Campanella, Clarissa Martina; Dell'Olio, Francesco; Campanella, Carlo Edoardo; Armenise, Mario Nicola

2013-03-01

For a number of years, the scientific community has been paying growing attention to the monitoring and enhancement of public health and the quality of life through the detection of all dangerous agents for the human body, including gases, proteins, virus, and bacterial agents. When these agents are detected through label-free biochemical sensors, the molecules are not modified structurally or functionally by adding fluorescent or radioactive dyes. This work focuses on label-free optical ring resonator-based configurations suited for bio-chemical sensing, highlighting their physical aspects and specific applications. Resonant wavelength shift and the modal splitting occurring when the analyte interacts with microresonant structures are the two major physical aspects analyzed in this paper. Competitive optical platforms proposed in the literature are also illustrated together with their properties and performance.

[Biochemical principles of early saturnism recognition].

PubMed

Tsimakuridze, M P; Mansuradze, E A; Zurashvili, D G; Tsimakuridze, M P

2009-03-01

The aim of the work is to determine the major sensitive criteria of biochemical indicators that allow timely discovery of negative influence of lead on organism and assist in early diagnosis of primary stages of saturnism. The workers of Georgian typographies, performing technological processes of letterpress printing were observed. Professional groups having contact with lead aerosols (main group of 66 people) and the workers of the same typography not being in touch with the poison (control group of 24 people) were studied. It was distinguished that, protracted professional contact with lead causes moderate increase of lead, coproporphyrin and DALA in daily urine in most cases; it is more clearly evidenced in the professional groups of lead smelters and lino operators and less clearly among typesetter and printers. Upon the checkup of people, having a direct contact with lead, biochemical analysis of urine should be given a preference, especially the determination of quantitative content of lead and coproporphyrin in urine with the aim of revealing the lead carrier, which is one of the first signals for occupational lookout and medical monitoring of the similar contingent.

Physiological, biochemical and transcriptional analysis of onion bulbs during storage

PubMed Central

Chope, Gemma A.; Cools, Katherine; Hammond, John P.; Thompson, Andrew J.; Terry, Leon A.

2012-01-01

Background and Aims During the transition from endo-dormancy to eco-dormancy and subsequent growth, the onion bulb undergoes the transition from sink organ to source, to sustain cell division in the meristematic tissue. The mechanisms controlling these processes are not fully understood. Here, a detailed analysis of whole onion bulb physiological, biochemical and transcriptional changes in response to sprouting is reported, enabling a better knowledge of the mechanisms regulating post-harvest onion sprout development. Methods Biochemical and physiological analyses were conducted on different cultivars (‘Wellington’, ‘Sherpa’ and ‘Red Baron’) grown at different sites over 3 years, cured at different temperatures (20, 24 and 28 °C) and stored under different regimes (1, 3, 6 and 6 → 1 °C). In addition, the first onion oligonucleotide microarray was developed to determine differential gene expression in onion during curing and storage, so that transcriptional changes could support biochemical and physiological analyses. Key Results There were greater transcriptional differences between samples at harvest and before sprouting than between the samples taken before and after sprouting, with some significant changes occurring during the relatively short curing period. These changes are likely to represent the transition from endo-dormancy to sprout suppression, and suggest that endo-dormancy is a relatively short period ending just after curing. Principal component analysis of biochemical and physiological data identified the ratio of monosaccharides (fructose and glucose) to disaccharide (sucrose), along with the concentration of zeatin riboside, as important factors in discriminating between sprouting and pre-sprouting bulbs. Conclusions These detailed analyses provide novel insights into key regulatory triggers for sprout dormancy release in onion bulbs and provide the potential for the development of biochemical or transcriptional markers for sprout

Biochemical Applications in the Analytical Chemistry Lab

ERIC Educational Resources Information Center

Strong, Cynthia; Ruttencutter, Jeffrey

2004-01-01

An HPLC and a UV-visible spectrophotometer are identified as instruments that helps to incorporate more biologically-relevant experiments into the course, in order to increase the students understanding of selected biochemistry topics and enhances their ability to apply an analytical approach to biochemical problems. The experiment teaches…

Survey of Biochemical Education in Japanese Universities.

ERIC Educational Resources Information Center

Kagawa, Yasuo

1995-01-01

Reports findings of questionnaires sent to faculty in charge of biochemical education in medical schools and other programs from dentistry to agriculture. Total class hours have declined since 1984. New trends include bioethics and computer-assisted learning. Tables show trends in lecture hours, lecture content, laboratory hours, core subject…

The role of thermodynamics in biochemical engineering

NASA Astrophysics Data System (ADS)

von Stockar, Urs

2013-09-01

This article is an adapted version of the introductory chapter of a book whose publication is imminent. It bears the title "Biothermodynamics - The role of thermodynamics in biochemical engineering." The aim of the paper is to give a very short overview of the state of biothermodynamics in an engineering context as reflected in this book. Seen from this perspective, biothermodynamics may be subdivided according to the scale used to formalize the description of the biological system into three large areas: (i) biomolecular thermodynamics (most fundamental scale), (ii) thermodynamics of metabolism (intermediary scale), and (iii) whole-cell thermodynamics ("black-box" description of living entities). In each of these subareas, the main available theoretical approaches and the current and the potential applications are discussed. Biomolecular thermodynamics (i) is especially well developed and is obviously highly pertinent for the development of downstream processing. Its use ought to be encouraged as much as possible. The subarea of thermodynamics of live cells (iii), although scarcely applied in practice, is also expected to enhance bioprocess research and development, particularly in predicting culture performances, for understanding the driving forces for cellular growth, and in developing, monitoring, and controlling cellular cultures. Finally, there is no question that thermodynamic analysis of cellular metabolism (ii) is a promising tool for systems biology and for many other applications, but quite a large research effort is still needed before it may be put to practical use.

40 CFR 158.2082 - Experimental use permit biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

... biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2. The same... human or livestock consumption. 12. Data on fish are required for all pesticides applied directly to... pesticides residue data requirements table. 158.2082 Section 158.2082 Protection of Environment ENVIRONMENTAL...

40 CFR 158.2082 - Experimental use permit biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

... biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2. The same... human or livestock consumption. 12. Data on fish are required for all pesticides applied directly to... pesticides residue data requirements table. 158.2082 Section 158.2082 Protection of Environment ENVIRONMENTAL...

40 CFR 158.2082 - Experimental use permit biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

... biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2. The same... human or livestock consumption. 12. Data on fish are required for all pesticides applied directly to... pesticides residue data requirements table. 158.2082 Section 158.2082 Protection of Environment ENVIRONMENTAL...

40 CFR 158.2082 - Experimental use permit biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2. The same... human or livestock consumption. 12. Data on fish are required for all pesticides applied directly to... pesticides residue data requirements table. 158.2082 Section 158.2082 Protection of Environment ENVIRONMENTAL...

40 CFR 158.2082 - Experimental use permit biochemical pesticides residue data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

... biochemical agents in the biochemical human health assessment data requirements, § 158.2050. 2. The same... human or livestock consumption. 12. Data on fish are required for all pesticides applied directly to... pesticides residue data requirements table. 158.2082 Section 158.2082 Protection of Environment ENVIRONMENTAL...

Salivary testosterone may not serve as a screening test in the diagnosis of biochemical hyperandrogenism.

PubMed

Ambroziak, Urszula; Kuryłowicz, Alina; Kępczyńska-Nyk, Anna; Kondracka, Agnieszka; Gajda, Sylvia; Sieńko, Damian

2018-06-01

The diagnosis of biochemical hyperandrogenism is still challenging because a set of appropriate, recommended diagnostic tests has not been established. In our study, we aimed to answer the question of whether salivary testosterone is a reliable test to establish the diagnosis of biochemical hyperandrogenism as compared to serum total testosterone (TT) measured either by liquid chromatography-tandem mass spectrometry (LC-MS/MS) or immunoassay and to assess which set of biochemical tests would be the most appropriate for the identification of biochemical hyperandrogenism. A total of 39 women, aged 18-45 years, with clinical or biochemical hyperandrogenism and 41 healthy individuals, aged 19-45 years, were enrolled in the study. Salivary testosterone was measured using the Salimetrics test. Serum TT was measured either using the LC-MS/MS method or immunoassay, and dehydroepiandrosterone sulphate (DHEA-S) and androstenedione were measured using LC-MS/MS. In 15 of 17 (88%) patients with elevated serum TT measured by LC-MS/MS and in 14 of 16 (87%) measured with immunoassay, salivary testosterone showed normal levels. In 11 of 39 women (28%) with normal serum testosterone levels, DHEA-S was elevated. All patients with elevated androstenedione presented with an elevated concentration of either serum testosterone or DHEA-S. Salivary testosterone measurement may lead to the underdiagnosis of biochemical hyperandrogenism. Both serum testosterone and DHEA-S should be measured in the endocrine work-up toward biochemical hyperandrogenism. © 2018 Japan Society of Obstetrics and Gynecology.

[Biochemical changes in apoptosis and methods for their determination (review)].

PubMed

Sedláková, A; Kohút, A; Kalina, I

1999-08-01

Apoptosis or programmed cell death is a physiological process which occurs at different biological states as well as at disease process. Morphologically it is characterized by the chromatine condensation and other changes with preserved integrity of plasmatic membrane. The major and most frequently studied biochemical characteristic of apoptosis is a DNA fragmentation. In our paper attention is directed to the early biochemical changes in cell membranes, i.g., the externalization of phosphatidylserine, hydrolysis of sphingomyeline on the ceramide and activation of phospholipases especially phospholipase A2. In one part we described the changes of cysteine proteases (caspases), which play a key role in the execution of apoptosis. These biochemical changes are associated with ceramide signalization of apoptosis. Briefly are presented also some dates about apoptosis induction with reactive oxygen radicals and the role of the arachidonic acid metabolites in this process. We consider the investigation and determination of these changes as important parameters of apoptosis at some diseases, e.g., cancer or degenerative diseases, and of their treatment.

Design of a biochemical circuit motif for learning linear functions

PubMed Central

Lakin, Matthew R.; Minnich, Amanda; Lane, Terran; Stefanovic, Darko

2014-01-01

Learning and adaptive behaviour are fundamental biological processes. A key goal in the field of bioengineering is to develop biochemical circuit architectures with the ability to adapt to dynamic chemical environments. Here, we present a novel design for a biomolecular circuit capable of supervised learning of linear functions, using a model based on chemical reactions catalysed by DNAzymes. To achieve this, we propose a novel mechanism of maintaining and modifying internal state in biochemical systems, thereby advancing the state of the art in biomolecular circuit architecture. We use simulations to demonstrate that the circuit is capable of learning behaviour and assess its asymptotic learning performance, scalability and robustness to noise. Such circuits show great potential for building autonomous in vivo nanomedical devices. While such a biochemical system can tell us a great deal about the fundamentals of learning in living systems and may have broad applications in biomedicine (e.g. autonomous and adaptive drugs), it also offers some intriguing challenges and surprising behaviours from a machine learning perspective. PMID:25401175

Design of a biochemical circuit motif for learning linear functions.

PubMed

Lakin, Matthew R; Minnich, Amanda; Lane, Terran; Stefanovic, Darko

2014-12-06

Learning and adaptive behaviour are fundamental biological processes. A key goal in the field of bioengineering is to develop biochemical circuit architectures with the ability to adapt to dynamic chemical environments. Here, we present a novel design for a biomolecular circuit capable of supervised learning of linear functions, using a model based on chemical reactions catalysed by DNAzymes. To achieve this, we propose a novel mechanism of maintaining and modifying internal state in biochemical systems, thereby advancing the state of the art in biomolecular circuit architecture. We use simulations to demonstrate that the circuit is capable of learning behaviour and assess its asymptotic learning performance, scalability and robustness to noise. Such circuits show great potential for building autonomous in vivo nanomedical devices. While such a biochemical system can tell us a great deal about the fundamentals of learning in living systems and may have broad applications in biomedicine (e.g. autonomous and adaptive drugs), it also offers some intriguing challenges and surprising behaviours from a machine learning perspective.

MATLAB-Based Teaching Modules in Biochemical Engineering

ERIC Educational Resources Information Center

Lee, Kilho; Comolli, Noelle K.; Kelly, William J.; Huang, Zuyi

2015-01-01

Mathematical models play an important role in biochemical engineering. For example, the models developed in the field of systems biology have been used to identify drug targets to treat pathogens such as Pseudomonas aeruginosa in biofilms. In addition, competitive binding models for chromatography processes have been developed to predict expanded…

An Inductive Logic Programming Approach to Validate Hexose Binding Biochemical Knowledge.

PubMed

Nassif, Houssam; Al-Ali, Hassan; Khuri, Sawsan; Keirouz, Walid; Page, David

2010-01-01

Hexoses are simple sugars that play a key role in many cellular pathways, and in the regulation of development and disease mechanisms. Current protein-sugar computational models are based, at least partially, on prior biochemical findings and knowledge. They incorporate different parts of these findings in predictive black-box models. We investigate the empirical support for biochemical findings by comparing Inductive Logic Programming (ILP) induced rules to actual biochemical results. We mine the Protein Data Bank for a representative data set of hexose binding sites, non-hexose binding sites and surface grooves. We build an ILP model of hexose-binding sites and evaluate our results against several baseline machine learning classifiers. Our method achieves an accuracy similar to that of other black-box classifiers while providing insight into the discriminating process. In addition, it confirms wet-lab findings and reveals a previously unreported Trp-Glu amino acids dependency.

State-of-the-Art of (Bio)Chemical Sensor Developments in Analytical Spanish Groups

PubMed Central

Plata, María Reyes; Contento, Ana María; Ríos, Angel

2010-01-01

(Bio)chemical sensors are one of the most exciting fields in analytical chemistry today. The development of these analytical devices simplifies and miniaturizes the whole analytical process. Although the initial expectation of the massive incorporation of sensors in routine analytical work has been truncated to some extent, in many other cases analytical methods based on sensor technology have solved important analytical problems. Many research groups are working in this field world-wide, reporting interesting results so far. Modestly, Spanish researchers have contributed to these recent developments. In this review, we summarize the more representative achievements carried out for these groups. They cover a wide variety of sensors, including optical, electrochemical, piezoelectric or electro-mechanical devices, used for laboratory or field analyses. The capabilities to be used in different applied areas are also critically discussed. PMID:22319260

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PubMed Central

Kaltenbacher, Barbara; Hasenauer, Jan

2017-01-01

Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics. PMID:28114351

Study on color difference estimation method of medicine biochemical analysis

NASA Astrophysics Data System (ADS)

Wang, Chunhong; Zhou, Yue; Zhao, Hongxia; Sun, Jiashi; Zhou, Fengkun

2006-01-01

The biochemical analysis in medicine is an important inspection and diagnosis method in hospital clinic. The biochemical analysis of urine is one important item. The Urine test paper shows corresponding color with different detection project or different illness degree. The color difference between the standard threshold and the test paper color of urine can be used to judge the illness degree, so that further analysis and diagnosis to urine is gotten. The color is a three-dimensional physical variable concerning psychology, while reflectance is one-dimensional variable; therefore, the estimation method of color difference in urine test can have better precision and facility than the conventional test method with one-dimensional reflectance, it can make an accurate diagnose. The digital camera is easy to take an image of urine test paper and is used to carry out the urine biochemical analysis conveniently. On the experiment, the color image of urine test paper is taken by popular color digital camera and saved in the computer which installs a simple color space conversion (RGB -> XYZ -> L *a *b *)and the calculation software. Test sample is graded according to intelligent detection of quantitative color. The images taken every time were saved in computer, and the whole illness process will be monitored. This method can also use in other medicine biochemical analyses that have relation with color. Experiment result shows that this test method is quick and accurate; it can be used in hospital, calibrating organization and family, so its application prospect is extensive.

The Dearth of Mental Health Research in Occupational Therapy.

ERIC Educational Resources Information Center

Gibson, Diane

1984-01-01

Reasons for the lack of research in occupational therapy include small numbers of doctoral level occupational therapists, the psychobehavioral/biochemical dichotomy, the lack of a theoretical framework, the level of research instruction, the impact of a predominantly female profession, and the attitudes of institutions. (SK)

[Analysis of biochemical markers in serum of guinea pigs after death caused by hypothermia].

PubMed

Li, Shi-ying; Deng, Kai-fei; Shao, Yu; Li, Zheng-dong; Qin, Zhi-qiang; Chen, Yi-jiu; Huang, Ping

2014-08-01

To explore the changes and rules of biochemical markers in serum of guinea pigs after death caused by hypothermia and to provide references for fatal hypothermia diagnosis by serum biochemical markers. Twenty guinea pigs were randomly divided into experimental group and control group. The guinea pigs in the experimental group were kept at -30 °C until death, while the ones in control group were decapitated after same survival intervals at 25 °C. The serum was extracted from the whole blood of right ventricular immediately. Subsequently, a series of serum biochemical markers were analyzed by auto bio-chemical analyzer. The levels of glucose, uric acid, creatinine and urea nitrogen in the experimental group were significantly higher than those in control group, respectively (P<0.05). Compared with the control group, the levels of total protein and albumin were significantly lower in the experimental group (P<0.05). There were no significantly differences of the levels of other markers such as serum enzymes and ions observed between the two groups. There are characteristic changes of some specific serum biochemical markers in fatal hypothermia, which may be potentially useful for auxiliary diagnosis of fatal hypothermia.

Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory.

PubMed

Heuett, William J; Beard, Daniel A; Qian, Hong

2008-05-15

Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RTBS and STBS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA).

BioCluster: tool for identification and clustering of Enterobacteriaceae based on biochemical data.

PubMed

Abdullah, Ahmed; Sabbir Alam, S M; Sultana, Munawar; Hossain, M Anwar

2015-06-01

Presumptive identification of different Enterobacteriaceae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochemical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is labor-intensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and similarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface (GUI) tool named BioCluster. This tool was designed for automated clustering and identification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering (HC) and the Improved Hierarchical Clustering (IHC), a modified algorithm that was developed specifically for the clustering and identification of Enterobacteriaceae species. IHC takes into account the variability in result of 1-47 biochemical tests within this Enterobacteriaceae family. This tool also provides different options to optimize the clustering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that BioCluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http://microbialgen.du.ac.bd/biocluster/. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

CELLULAR, BIOCHEMICAL, AND MOLECULAR TECHNIQUES IN DEVELOPMENTAL TOXICOLOGY

EPA Science Inventory

Cellular, molecular and biochemical approaches vastly expand the possibilities for revealing the underlying mechanisms of developmental toxicity. The increasing interest in embryonic development as a model system for the study of gene expression has resulted in a cornucopia of i...

Morphological, kinetic, membrane biochemical and genetic aspects of intestinal enteroplasticity

PubMed Central

Drozdowski, Laurie A; Clandinin, M Tom; Thomson, Alan BR

2009-01-01

The process of intestinal adaptation (“enteroplasticity”) is complex and multifaceted. Although a number of trophic nutrients and non-nutritive factors have been identified in animal studies, successful, reproducible clinical trials in humans are awaited. Understanding mechanisms underlying this adaptive process may direct research toward strategies that maximize intestinal function and impart a true clinical benefit to patients with short bowel syndrome, or to persons in whom nutrient absorption needs to be maximized. In this review, we consider the morphological, kinetic and membrane biochemical aspects of enteroplasticity, focus on the importance of nutritional factors, provide an overview of the many hormones that may alter the adaptive process, and consider some of the possible molecular profiles. While most of the data is derived from rodent studies, wherever possible, the results of human studies of intestinal enteroplasticity are provided. PMID:19230039

Lipemia interferences in routine clinical biochemical tests.

PubMed

Calmarza, Pilar; Cordero, José

2011-01-01

Lipemic specimens are a common and frequent, but yet unresolved problem in clinical chemistry, and may produce significant interferences in the analytical results of different biochemical parameters. The aim of this study was to examine the effect of lipid removal using ultracentrifugation of lipemic samples, on some routine biochemistry parameters. Among all the samples obtained daily in our laboratory, the ones which were visibly muddy were selected and underwent to a process of ultracentrifugation, being determined a variety of biochemical tests before and after ultracentrifugation. A total of 110 samples were studied. We found significant differences in all the parameters studied except for total bilirubin, glucose, gamma-glutamyl transferase (GGT) and aspartate aminotransferase (AST). The greatest differences in the parameters analyzed were found in the concentration of alanine aminotransferase (ALT) (7.36%) and the smallest ones in the concentration of glucose (0.014%). Clinically significant interferences were found for phosphorus, creatinine, total protein and calcium. Lipemia causes clinically significant interferences for phosphorus, creatinine, total protein and calcium measurement and those interferences could be effectively removed by ultracentrifugation.

Effect of age on biochemical disease-free outcome in patients with T1-T3 prostate cancer treated with definitive radiotherapy in an equal-access health care system: a radiation oncology report of the Department of Defense Center for Prostate Disease Research.

PubMed

Johnstone, Peter A S; Riffenburgh, Robert H; Moul, Judd W; Sun, Leon; Wu, Hongyu; McLeod, David G; Kane, Christopher J; Martin, Douglas D; Kusuda, Leo; Lance, Raymond; Douglas, Robert; Donahue, Timothy; Beat, Michael G; Foley, John; Chung, Andrew; Soderdahl, Douglas; Do, Jason; Amling, Christopher L

2003-03-15

It has traditionally been a common perception that young age is a negative prognostic factor in prostate cancer (CaP). Furthermore, many urologists believe that younger patients are better suited to surgery rather than radiotherapy (RT) because of this perception. However, the data on the effect of age on outcome in patients with CaP are unclear. The records of the Department of Defense Center for Prostate Disease Research were queried for the biochemical disease-free results of patients after definitive RT and analyzed by age. The records of 1018 patients with T1-T3 CaP treated with definitive RT between 1988 and 2000 were reviewed. The records of patients receiving adjuvant hormonal therapy or adjuvant or salvage RT postoperatively were excluded. Biochemical failure was calculated by the American Society for Therapeutic Radiology and Oncology criteria. The median potential follow-up was 85.3 months as of December 31, 2001. Age did not affect biochemical disease-free survival significantly when considered as <60 vs. >/=60 years (p = 0.646), by decade (p = 0.329), or as a continuous variable (correlation coefficient r = 0.017, regression slope = 0.007, with p = 0.588 and R(2) < 0.001). Using multiple regression analysis, age was still not significant (p = 0.408). Other variables analyzed were pretreatment prostate-specific antigen level (p < 0.001), Gleason sum (p = 0.023), stage (p = 0.828), and RT dose (p = 0.033). Age and biochemical disease-free survival after RT for CaP are not related. Age may not be a valid factor in choosing between primary treatment options for CaP.

Adult amphibian epidermal proteins: biochemical characterization and developmental appearance.

PubMed

Reeves, O R

1975-08-01

The keratin-like proteins (KLPs) from the epidermis of adult frogs of the species Xenopus laevis have been isolated and biochemically characterized by means of polyacrylamide gel electrophoresis, amino acid analysis, tryptic peptide mapping, amino-terminal end-group analysis and isoelectric focusing. One particular protein fraction of rather unusual amino acid composition found only in epidermal tissue was isolated in quantity by preparative gel electrophoresis and monospecific antibodies prepared against it. Using this anti-KLP antibody preparation it was possible to show that at least one kine of keratin-like protein characteristic of the adult epidermis first appears within the larval epidermis during metamorphosis. This is the first reported biochemical characterization of a tissue-specific protien from adult amphibian skin.

Exercise-induced biochemical changes and their potential influence on cancer: a scientific review

PubMed Central

Thomas, Robert James; Kenfield, Stacey A; Jimenez, Alfonso

2017-01-01

Aim To review and discuss the available international literature regarding the indirect and direct biochemical mechanisms that occur after exercise, which could positively, or negatively, influence oncogenic pathways. Methods The PubMed, MEDLINE, Embase and Cochrane libraries were searched for papers up to July 2016 addressing biochemical changes after exercise with a particular reference to cancer. The three authors independently assessed their appropriateness for inclusion in this review based on their scientific quality and relevance. Results 168 papers were selected and categorised into indirect and direct biochemical pathways. The indirect effects included changes in vitamin D, weight reduction, sunlight exposure and improved mood. The direct effects included insulin-like growth factor, epigenetic effects on gene expression and DNA repair, vasoactive intestinal peptide, oxidative stress and antioxidant pathways, heat shock proteins, testosterone, irisin, immunity, chronic inflammation and prostaglandins, energy metabolism and insulin resistance. Summary Exercise is one of several lifestyle factors known to lower the risk of developing cancer and is associated with lower relapse rates and better survival. This review highlights the numerous biochemical processes, which explain these potential anticancer benefits. PMID:27993842

Automatising the analysis of stochastic biochemical time-series

PubMed Central

2015-01-01

Background Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these frameworks it is possible to analyse complex models under a variety of configurations, eventually selecting the best setting of, e.g., parameters for a target system. Motivation This operational pipeline relies on the ability to interpret the predictions of a model, often represented as simulation time-series. Thus, an efficient data analysis pipeline is crucial to automatise time-series analyses, bearing in mind that errors in this phase might mislead the modeller's conclusions. Results For this reason we have developed an intuitive framework-independent Python tool to automate analyses common to a variety of modelling approaches. These include assessment of useful non-trivial statistics for simulation ensembles, e.g., estimation of master equations. Intuitive and domain-independent batch scripts will allow the researcher to automatically prepare reports, thus speeding up the usual model-definition, testing and refinement pipeline. PMID:26051821

Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory

PubMed Central

Heuett, William J; Beard, Daniel A; Qian, Hong

2008-01-01

Background Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RTBS and STBS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA). PMID:18482450

The biochemical properties of antibodies and their fragments

USDA-ARS?s Scientific Manuscript database

Immunoglobulins (Ig) or antibodies are a powerful molecular recognition tools that can be used to identify minute quantities of a given target analyte. Their antigen binding properties define both the sensitivity and selectivity of an immunoassay. Understanding the biochemical properties of this c...

Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardona-Felix, Cesar S.; Lara-Gonzalez, Samuel; Brieba, Luis G.

2012-02-08

Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeastmore » and parasitic protozoa.« less

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

PubMed

Papin, Jason A; Reed, Jennifer L; Palsson, Bernhard O

2004-12-01

As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.

Chapter A7. Section 7.0. Five-Day Biochemical Oxygen Demand

USGS Publications Warehouse

Delzer, Gregory C.; McKenzie, Stuart W.

1999-01-01

The presence of a sufficient concentration of dissolved oxygen is critical to maintaining the aquatic life and aesthetic quality of streams and lakes. Determinng how organic matter affects the concentration of dissolved oxygen (DO) in a stream or lake is integral to water-quality management. The decay of organic matter in water is measured as biochemical or chemical oxygen demand. This report describes the field protocols used by U.S. Geological Survey (USGS) personnel to determine the five-day test for biochemical oxygen demand.

Biochemical markers in the assessment of bone disease

NASA Technical Reports Server (NTRS)

Bikle, D. D.

1997-01-01

As the mean age of our population increases, increasing attention has been paid to the diseases associated with aging, including diseases of the skeleton such as osteoporosis. Effective means of treating and possibly preventing such skeletal disorders are emerging, making their early recognition an important goal for the primary care physician. Although bone density measurements and skeletal imaging studies remain of primary diagnostic importance in this regard, a large number of assays for biochemical markers of bone formation and resorption are being developed that promise to complement the densitometry measurements and imaging studies, providing an assessment of the rates of bone turnover and an earlier evaluation of the effects of therapy. In this review, emphasizing the recent literature, the major biochemical markers currently in use or under active investigation are described, and their application in a number of diseases of the skeleton including osteoporosis is evaluated.

Biochemical process of low level radioactive liquid simulation waste containing detergent

NASA Astrophysics Data System (ADS)

Kundari, Noor Anis; Putra, Sugili; Mukaromah, Umi

2015-12-01

Research of biochemical process of low level radioactive liquid waste containing detergent has been done. Thse organic liquid wastes are generated in nuclear facilities such as from laundry. The wastes that are cotegorized as hazard and poison materials are also radioactive. It must be treated properly by detoxification of the hazard and decontamination of the radionuclides to ensure that the disposal of the waste meets the requirement of standard quality of water. This research was intended to determine decontamination factor and separation efficiensies, its kinetics law, and to produce a supernatant that ensured the environmental quality standard. The radioactive element in the waste was thorium with activity of 5.10-5 Ci/m3. The radioactive liquid waste which were generated in simulation plant contains detergents that was further processed by aerobic biochemical process using SGB 103 bacteria in a batch reactor equipped with aerators. Two different concentration of samples were processed and analyzed for 212 hours and 183 hours respectively at a room temperature. The product of this process is a liquid phase called as supernatant and solid phase material called sludge. The chemical oxygen demand (COD), biological oxygen demand (BOD), suspended solid (SS), and its alpha activity were analyzed. The results show that the decontamination factor and the separation efficiency of the lower concentration samples are higher compared to the samples with high concentration. Regarding the decontamination factor, the result for 212 hours processing of waste with detergent concentration of 1.496 g/L was 3.496 times, whereas at the detergent concentration of 0.748 g/L was 15.305 times for 183 hours processing. In case of the separation efficiency, the results for both samples were 71.396% and 93.465% respectively. The Bacterial growth kinetics equation follow Monod's model and the decreasing of COD and BOD were first order with the rate constant of 0.01 hour-1.

Biochemical process of low level radioactive liquid simulation waste containing detergent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kundari, Noor Anis, E-mail: nooranis@batan.go.id; Putra, Sugili; Mukaromah, Umi

Research of biochemical process of low level radioactive liquid waste containing detergent has been done. Thse organic liquid wastes are generated in nuclear facilities such as from laundry. The wastes that are cotegorized as hazard and poison materials are also radioactive. It must be treated properly by detoxification of the hazard and decontamination of the radionuclides to ensure that the disposal of the waste meets the requirement of standard quality of water. This research was intended to determine decontamination factor and separation efficiensies, its kinetics law, and to produce a supernatant that ensured the environmental quality standard. The radioactive elementmore » in the waste was thorium with activity of 5.10{sup −5} Ci/m{sup 3}. The radioactive liquid waste which were generated in simulation plant contains detergents that was further processed by aerobic biochemical process using SGB 103 bacteria in a batch reactor equipped with aerators. Two different concentration of samples were processed and analyzed for 212 hours and 183 hours respectively at a room temperature. The product of this process is a liquid phase called as supernatant and solid phase material called sludge. The chemical oxygen demand (COD), biological oxygen demand (BOD), suspended solid (SS), and its alpha activity were analyzed. The results show that the decontamination factor and the separation efficiency of the lower concentration samples are higher compared to the samples with high concentration. Regarding the decontamination factor, the result for 212 hours processing of waste with detergent concentration of 1.496 g/L was 3.496 times, whereas at the detergent concentration of 0.748 g/L was 15.305 times for 183 hours processing. In case of the separation efficiency, the results for both samples were 71.396% and 93.465% respectively. The Bacterial growth kinetics equation follow Monod’s model and the decreasing of COD and BOD were first order with the rate constant of

A New Solid/Liquid Hypergolic System: 3-amino-1,2,4-triazine and Nitric Acid

DTIC Science & Technology

2016-04-01

PROGRAM ELEMENT NUMBER 6. AUTHOR(S) William M Sherrill, William M Sickels, Eric J Bukowski, Eric C Johnson, and Joseph E Banning 5d. PROJECT ...on an Anasazi Instruments 90 MHz NMR. Dimethyl sulfoxide (DMSO)-D6 was obtained from Sigma -Aldrich and used as received. All NMR chemical shifts...were obtained from Sigma -Aldrich and were used as received. Approved for public release; distribution is unlimited. 7 5.2 Synthesis of 3-amino

Physiological, behavioral and biochemical adaptations of intertidal fishes to hypoxia.

PubMed

Richards, Jeffrey G

2011-01-15

Hypoxia survival in fish requires a well-coordinated response to either secure more O(2) from the hypoxic environment or to limit the metabolic consequences of an O(2) restriction at the mitochondria. Although there is a considerable amount of information available on the physiological, behavioral, biochemical and molecular responses of fish to hypoxia, very little research has attempted to determine the adaptive value of these responses. This article will review current attempts to use the phylogenetically corrected comparative method to define physiological and behavioral adaptations to hypoxia in intertidal fish and further identify putatively adaptive biochemical traits that should be investigated in the future. In a group of marine fishes known as sculpins, from the family Cottidae, variation in hypoxia tolerance, measured as a critical O(2) tension (P(crit)), is primarily explained by variation in mass-specific gill surface area, red blood cell hemoglobin-O(2) binding affinity, and to a lesser extent variation in routine O(2) consumption rate (M(O(2))). The most hypoxia-tolerant sculpins consistently show aquatic surface respiration (ASR) and aerial emergence behavior during hypoxia exposure, but no phylogenetically independent relationship has been found between the thresholds for initiating these behaviors and P(crit). At O(2) levels below P(crit), hypoxia survival requires a rapid reorganization of cellular metabolism to suppress ATP consumption to match the limited capacity for O(2)-independent ATP production. Thus, it is reasonable to speculate that the degree of metabolic rate suppression and the quantity of stored fermentable fuel is strongly selected for in hypoxia-tolerant fishes; however, these assertions have not been tested in a phylogenetic comparative model.

A stopped-flow calorimeter for biochemical applications.

PubMed Central

Howarth, J V; Millar, N C; Gutfreund, H

1987-01-01

A rapid-response stopped-flow calorimeter for small samples of reagents is described. The construction, performance characteristics and operational limitations are described, along with an example of its ability to resolve the kinetics of an enzyme-catalysed hydrolysis. It is thought likely that the method would find useful application in a variety of chemical and biochemical investigations. PMID:3435478

Development and use of biochemical markers in osteoarthritis: current update.

PubMed

Bay-Jensen, Anne C; Thudium, Christian S; Mobasheri, Ali

2018-01-01

There is an increasing demand for noninvasive and descriptive biochemical markers (biomarkers) in osteoarthritis; for enabling early drug development (including translational research), evaluating clinical trial at an early stage and for subtyping. Purpose of the review is to review and comment on current availability of such biomarkers. Many different biomarkers have been tested in the last 18 months. The main focus has been on testing whether the biomarkers, whether is reflect joint tissue turnover or inflammatory status, can differentiate osteoarthritis patients from healthy controls or whether the biomarkers are associated with progression. Less than a handful of studies, investigate the role of the biomarkers as response markers. Thus, there is still a great need for developing biomarkers that reflect disease activity and thereby can be used for treatment response or patient phenotyping. Osteoarthritis is the most common form of joint disease. This presents the osteoarthritis research community and pharmaceutical companies developing disease-modifying osteoarthritis drugs (DMOADs) with great opportunities. There are different osteoarthritis subtypes, which complicates the traditional approaches for developing new treatments. If we can identify new markers that can distinguish different subtypes, this can greatly facilitate drug development from early discovery to late clinical development.

MARCKS promotes invasion and is associated with biochemical recurrence in prostate cancer

PubMed Central

Dorris, Emma; O'Neill, Amanda; Hanrahan, Karen; Treacy, Ann; Watson, R. William

2017-01-01

Background Overtreatment of low-grade prostate cancer is a recognised problem for clinicians and patients. However, under-treatment runs the risk of missing the opportunity for cure in those who could benefit. Identification of new biomarkers of disease progression, including metastases, is required to better stratify and appropriately treat these patients. The ability to predict if prostate cancer will recur is an important clinical question that would impact treatment options for patients. Studies in other cancers have associated MARCKS with metastasis. Methods Tissue microarrays of local prostatectomy samples from a cohort of biochemical recurrent and non-biochemical recurrent tumours were assayed for MARCKS protein expression. Prostate cancer cell lines were transfected with siRNA targeting MARCKS or a control and functional endpoints of migration, invasion, proliferation, viability and apoptosis were measured. Actin was visualised by fluorescent microscopy and evidence of a cadherin switch and activation of the AKT pathway were assayed. Results MARCKS was upregulated in biochemical recurrent patients compared to non-biochemical recurrent. Knockdown of MARCKS reduced migration and invasion of prostate cancer cells, reduced MMP9 mRNA expression, as well as decreasing cell spreading and increased cell:cell adhesion in prostate cancer cell colonies. Knockdown of MARCKS had no effect on proliferation, viability or apoptosis of the prostate cancer cells. Conclusions In conclusion, MARCKS promotes migration and invasion and is associated with biochemical recurrence in localised prostate cancer tumours. The mechanisms by which this occurs have yet to be fully elucidated but lack of a cadherin switch indicates it is not via epithelial-to-mesenchymal transition. Actin rearrangement indicates that MARCKS promotes invasion through regulating the architecture of the cell. PMID:29069765

A Novel MiRNA-Based Predictive Model for Biochemical Failure Following Post-Prostatectomy Salvage Radiation Therapy

PubMed Central

Stegmaier, Petra; Drendel, Vanessa; Mo, Xiaokui; Ling, Stella; Fabian, Denise; Manring, Isabel; Jilg, Cordula A.; Schultze-Seemann, Wolfgang; McNulty, Maureen; Zynger, Debra L.; Martin, Douglas; White, Julia; Werner, Martin; Grosu, Anca L.; Chakravarti, Arnab

2015-01-01

Purpose To develop a microRNA (miRNA)-based predictive model for prostate cancer patients of 1) time to biochemical recurrence after radical prostatectomy and 2) biochemical recurrence after salvage radiation therapy following documented biochemical disease progression post-radical prostatectomy. Methods Forty three patients who had undergone salvage radiation therapy following biochemical failure after radical prostatectomy with greater than 4 years of follow-up data were identified. Formalin-fixed, paraffin-embedded tissue blocks were collected for all patients and total RNA was isolated from 1mm cores enriched for tumor (>70%). Eight hundred miRNAs were analyzed simultaneously using the nCounter human miRNA v2 assay (NanoString Technologies; Seattle, WA). Univariate and multivariate Cox proportion hazards regression models as well as receiver operating characteristics were used to identify statistically significant miRNAs that were predictive of biochemical recurrence. Results Eighty eight miRNAs were identified to be significantly (p<0.05) associated with biochemical failure post-prostatectomy by multivariate analysis and clustered into two groups that correlated with early (≤ 36 months) versus late recurrence (>36 months). Nine miRNAs were identified to be significantly (p<0.05) associated by multivariate analysis with biochemical failure after salvage radiation therapy. A new predictive model for biochemical recurrence after salvage radiation therapy was developed; this model consisted of miR-4516 and miR-601 together with, Gleason score, and lymph node status. The area under the ROC curve (AUC) was improved to 0.83 compared to that of 0.66 for Gleason score and lymph node status alone. Conclusion miRNA signatures can distinguish patients who fail soon after radical prostatectomy versus late failures, giving insight into which patients may need adjuvant therapy. Notably, two novel miRNAs (miR-4516 and miR-601) were identified that significantly improve

Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks

PubMed Central

Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M.

2017-01-01

Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. PMID:28566513

Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks.

PubMed

Meng, X Flora; Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M

2017-05-01

Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. © 2017 The Author(s).

Connecting Biochemical Photosynthesis Models with Crop Models to Support Crop Improvement

PubMed Central

Wu, Alex; Song, Youhong; van Oosterom, Erik J.; Hammer, Graeme L.

2016-01-01

The next advance in field crop productivity will likely need to come from improving crop use efficiency of resources (e.g., light, water, and nitrogen), aspects of which are closely linked with overall crop photosynthetic efficiency. Progress in genetic manipulation of photosynthesis is confounded by uncertainties of consequences at crop level because of difficulties connecting across scales. Crop growth and development simulation models that integrate across biological levels of organization and use a gene-to-phenotype modeling approach may present a way forward. There has been a long history of development of crop models capable of simulating dynamics of crop physiological attributes. Many crop models incorporate canopy photosynthesis (source) as a key driver for crop growth, while others derive crop growth from the balance between source- and sink-limitations. Modeling leaf photosynthesis has progressed from empirical modeling via light response curves to a more mechanistic basis, having clearer links to the underlying biochemical processes of photosynthesis. Cross-scale modeling that connects models at the biochemical and crop levels and utilizes developments in upscaling leaf-level models to canopy models has the potential to bridge the gap between photosynthetic manipulation at the biochemical level and its consequences on crop productivity. Here we review approaches to this emerging cross-scale modeling framework and reinforce the need for connections across levels of modeling. Further, we propose strategies for connecting biochemical models of photosynthesis into the cross-scale modeling framework to support crop improvement through photosynthetic manipulation. PMID:27790232

Diagnostic value of the biochemical tests in patients with purulent pericarditis.

PubMed

Ekim, Meral; Ekim, Hasan

2014-07-01

Purulent pericarditis is a collection of purulent effusion in the pericardial space. It has become a rare entity with the increased availability and use of antibiotics. In contrast to pleural empyema, there are few data regarding the biochemical parameters of purulent pericardial effusion to aid diagnosis. Therefore, in this study, we have evaluated the diagnostic utility of biochemical tests in patients with purulent pericarditis. Between September 2004 and September 2012, we treated fifteen children with purulent pericarditis and tamponade. There were 8 boys and 7 girls, ranging in age from 8 months to 14 years, with a mean age of 5.3 ± 3.2 years. Echocardiographic diagnosis of cardiac tamponade was made in all patients. All patients underwent immediate surgical drainage due to cardiac tamponade. The diagnosis of purulent pericarditis was supported by biochemical tests. Anterior mini-thoracotomy or subxiphoid approach was performed for surgical drainage. The most common clinical findings were tamponade, hepatomegaly, tachycardia, fever refractory antibiotic therapy, dyspnea, tachypnea, cough, and increased jugular venous pressure. Central venous pressure decreased and arterial tension increased immediately after the evacuation of purulent effusion during operation in all patients. The pericardial effusion had high lactic dehydrogenase, and low glucose concentration, confirming purulent pericarditis. Also, pH (mean± SD) was 7.01 ± 0.06. The culture of pericardial effusions and blood samples were negative. Biochemical tests are useful guideline when assessing the pericardial effusions. However, these tests should be interpreted with the clinical and operative findings.

Connecting Biochemical Photosynthesis Models with Crop Models to Support Crop Improvement.

PubMed

Wu, Alex; Song, Youhong; van Oosterom, Erik J; Hammer, Graeme L

2016-01-01

The next advance in field crop productivity will likely need to come from improving crop use efficiency of resources (e.g., light, water, and nitrogen), aspects of which are closely linked with overall crop photosynthetic efficiency. Progress in genetic manipulation of photosynthesis is confounded by uncertainties of consequences at crop level because of difficulties connecting across scales. Crop growth and development simulation models that integrate across biological levels of organization and use a gene-to-phenotype modeling approach may present a way forward. There has been a long history of development of crop models capable of simulating dynamics of crop physiological attributes. Many crop models incorporate canopy photosynthesis (source) as a key driver for crop growth, while others derive crop growth from the balance between source- and sink-limitations. Modeling leaf photosynthesis has progressed from empirical modeling via light response curves to a more mechanistic basis, having clearer links to the underlying biochemical processes of photosynthesis. Cross-scale modeling that connects models at the biochemical and crop levels and utilizes developments in upscaling leaf-level models to canopy models has the potential to bridge the gap between photosynthetic manipulation at the biochemical level and its consequences on crop productivity. Here we review approaches to this emerging cross-scale modeling framework and reinforce the need for connections across levels of modeling. Further, we propose strategies for connecting biochemical models of photosynthesis into the cross-scale modeling framework to support crop improvement through photosynthetic manipulation.

Sensors, Volume 3, Part II, Chemical and Biochemical Sensors Part II

NASA Astrophysics Data System (ADS)

Göpel, Wolfgang; Jones, T. A.; Kleitz, Michel; Lundström, Ingemar; Seiyama, Tetsuro

1997-06-01

'Sensors' is the first self-contained series to deal with the whole area of sensors. It describes general aspects, technical and physical fundamentals, construction, function, applications and developments of the various types of sensors. This is the second of two volumes focusing on chemical and biochemical sensors. It includes a detailed description of biosensors which often make use of transducer properties of the basic sensors and usually have additional biological components. This volume provides a unique overview of the applications, the possibilities and limitations of sensors in comparison with conventional instrumentation in analytical chemistry. Specific facettes of applications are presented by specialists from different fields including environmental, biotechnological, medical, or chemical process control. This book is an indispensable reference work for both specialits and newcomers, researchers and developers.

Surrogate biochemical markers: precise measurement for strategic drug and biologics development.

PubMed

Lee, J W; Hulse, J D; Colburn, W A

1995-05-01

More efficient drug and biologics development is necessary for future success of pharmaceutical and biotechnology companies. One way to achieve this objective is to use rationally selected surrogate markers to improve the early decision-making process. Using typical clinical chemistry methods to measure biochemical markers may not ensure adequate precision and reproducibility. In contrast, using analytical methods that meet good laboratory practices along with rational selection and validation of biochemical markers can give those who use them a competitive advantage over those who do not by providing meaningful data for earlier decision making.

Temperature-programmed natural convection for micromixing and biochemical reaction in a single microfluidic chamber.

PubMed

Kim, Sung-Jin; Wang, Fang; Burns, Mark A; Kurabayashi, Katsuo

2009-06-01

Micromixing is a crucial step for biochemical reactions in microfluidic networks. A critical challenge is that the system containing micromixers needs numerous pumps, chambers, and channels not only for the micromixing but also for the biochemical reactions and detections. Thus, a simple and compatible design of the micromixer element for the system is essential. Here, we propose a simple, yet effective, scheme that enables micromixing and a biochemical reaction in a single microfluidic chamber without using any pumps. We accomplish this process by using natural convection in conjunction with alternating heating of two heaters for efficient micromixing, and by regulating capillarity for sample transport. As a model application, we demonstrate micromixing and subsequent polymerase chain reaction (PCR) for an influenza viral DNA fragment. This process is achieved in a platform of a microfluidic cartridge and a microfabricated heating-instrument with a fast thermal response. Our results will significantly simplify micromixing and a subsequent biochemical reaction that involves reagent heating in microfluidic networks.

A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions.

PubMed

Samal, Satya Swarup; Grigoriev, Dima; Fröhlich, Holger; Weber, Andreas; Radulescu, Ovidiu

2015-12-01

Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The gist of the method is the notion of tropical equilibration that provides approximate descriptions of slow invariant manifolds. Compared to extant numerical algorithms such as the intrinsic low-dimensional manifold method, our approach is symbolic and utilizes orders of magnitude instead of precise values of the model parameters. Application of this method to a large collection of biochemical network models supports the idea that the number of dynamical variables in minimal models of cell physiology can be small, in spite of the large number of molecular regulatory actors.

Biochemical characterization of an isoprene synthase from Campylopus introflexus (heath star moss).

PubMed

Lantz, Alexandra T; Cardiello, Joseph F; Gee, Taylor A; Richards, Michaelin G; Rosenstiel, Todd N; Fisher, Alison J

2015-09-01

Each year, plants emit terragram quantities of the reactive hydrocarbon isoprene (2-methyl-1,3-butadiene) into the earth's atmosphere. In isoprene-emitting plants, the enzyme isoprene synthase (ISPS) catalyzes the production of isoprene from the isoprenoid intermediate dimethylallyl diphosphate (DMADP). While isoprene is emitted from all major classes of land plants, to date ISPSs from angiosperms only have been characterized. Here, we report the identification and initial biochemical characterization of a DMADP-dependent ISPS from the isoprene-emitting bryophyte Campylopus introflexus (heath star moss). The partially-purified C. introflexus ISPS (CiISPS) exhibited a Km for DMADP of 0.37 ± 0.28 mM, a pH optimum of 8.6 ± 0.5, and a temperature optimum of 40 ± 3 °C in vitro. Like ISPSs from angiosperms, the CiISPS required the presence of a divalent cation. However, unlike angiosperm ISPSs, the CiISPS utilized Mn(2+) preferentially over Mg(2+). Efforts are currently underway in our laboratory to further purify the CiISPS and clone the cDNA sequence encoding this novel enzyme. Our discovery of the first bryophyte ISPS paves the way for future studies concerning the evolutionary origins of isoprene emission in land plants and may help generate new bryophyte model systems for physiological and biochemical research on plant isoprene function. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Biochemical diagnosis of phaeochromocytoma: two instructive case reports.

PubMed Central

Stewart, M F; Reed, P; Weinkove, C; Moriarty, K J; Ralston, A J

1993-01-01

The biochemical features of two patients with phaeochromocytomas illustrate the inadvisability of depending on a single group of analytes for the diagnosis. The first case presented as a surgical emergency with retroperitoneal haemorrhage. Biochemical diagnosis was difficult since total 24 hour urinary free catecholamine excretion was within normal limits in two out of three samples, and only marginally raised in the third with an atypical preponderance of adrenaline. Plasma catecholamine concentrations were also normal. But urinary excretion of the catecholamine metabolites, metadrenaline and 4-hydroxy-3-methoxy mandelic acid (HMMA), was consistently raised. In contrast, the second patient presenting with headache and labile hypertension showed normal metabolite excretion in the face of grossly increased free noradrenaline excretion and raised plasma noradrenaline concentrations. It is therefore recommend that, as well as urinary free catecholamines, one group of their main metabolites, the 3-methoxy amines (normetadrenaline and metadrenaline) or HMMA, should routinely be measured whenever a phaeochromocytoma is suspected. PMID:8463426

A Biochemical Oscillator Using Excitatory Molecules for Nanonetworks.

PubMed

Shitiri, Ethungshan; Cho, Ho-Shin

2016-10-01

For nanonetworks to be able to achieve large-scale functionality, such as to respond collectively to a trigger, synchrony between nanomachines is essential. However, to facilitate synchronization, some sort of physical clocking mechanism is required, such as the oscillators driven by auto-inhibitory molecules or by auto-inducing molecules. In this study, taking inspiration from the widely studied biological oscillatory phenomena called Calcium (Ca 2+ ) oscillations, we undertake a different approach to design an oscillator. Our model employs three different types of excitatory molecules that work in tandem to generate oscillatory phenomenon in the concentration levels of the molecule of interest. The main objective of the study is to model a high frequency biochemical oscillator, along with the investigations to identify and determine the parameters that affect the period of the oscillations. The investigations entail and highlight the design of the reserve unit, a reservoir of the molecule of interest, as a key factor in realizing a high frequency stable biochemical oscillator.

Biochemically Silent Abdominal Paragangliomas in Patients with Mutations in the Succinate Dehydrogenase Subunit B Gene

PubMed Central

Timmers, Henri J. L. M.; Pacak, Karel; Huynh, Thanh T.; Abu-Asab, Mones; Tsokos, Maria; Merino, Maria J.; Baysal, Bora E.; Adams, Karen T.; Eisenhofer, Graeme

2008-01-01

Context: Patients with adrenal and extra-adrenal abdominal paraganglioma (PGL) almost invariably have increased plasma and urine concentrations of metanephrines, the O-methylated metabolites of catecholamines. We report four cases of biochemically silent abdominal PGL, in which metanephrines were normal despite extensive disease. Objective: Our objective was to identify the mechanism underlying the lack of catecholamine hypersecretion and metabolism to metanephrines in biochemically silent PGL. Design: This is a descriptive study. Setting: The study was performed at a referral center. Patients: One index case and three additional patients with large abdominal PGL and metastases but with the lack of evidence of catecholamine production, six patients with metastatic catecholamine-producing PGL and a mutation of the succinate dehydrogenase subunit B (SDHB) gene, and 136 random patients with catecholamine-producing PGL were included in the study. Main Outcome Measures: Plasma, urine, and tumor tissue concentrations of catecholamines and metabolites were calculated with electron microscopy and tyrosine hydroxylase immunohistochemistry. Results: All four patients with biochemically silent PGL had an underlying SDHB mutation. In the index case, the tumor tissue concentration of catecholamines (1.8 nmol/g) was less than 0.01% that of the median (20,410 nmol/g) for the 136 patients with catecholamine-producing tumors. Electron microscopy showed the presence of normal secretory granules in all four biochemically silent PGLs. Tyrosine hydroxylase immunoreactivity was negligible in the four biochemically silent PGLs but abundant in catecholamine-producing PGLs. Conclusions: Patients with SDHB mutations may present with biochemically silent abdominal PGLs due to defective catecholamine synthesis resulting from the absence of tyrosine hydroxylase. Screening for tumors in patients with SDHB mutations should not be limited to biochemical tests of catecholamine excess. PMID

Characterization of physical and biochemical changes in plasma treated spinach seed during germination

NASA Astrophysics Data System (ADS)

Hye Ji, Sang; Ki, Se Hoon; Kang, Min Ho; Choi, Jin Sung; Park, Yeunsoo; Oh, Jaesung; Kim, Seong Bong; Yoo, Suk Jae; Choi, Eun Ha; Park, Gyungsoon

2018-04-01

Despite the accumulating data on the effect of plasma on seed germination, mechanisms of plasma action need more extensive research. In a previous study, we observed that high voltage nanosecond pulsed plasma enhanced the germination of spinach seeds and subsequent seedling growth. As a follow-up study, we investigated the physico-chemical, biochemical, and molecular changes in seed after plasma treatment, focusing on the early germination stage, to elucidate mechanism(s) for the stimulating effects of plasma on seed germination. The primary radicle protruded from seeds exposed to high voltage nanosecond pulsed plasma (one shot) slightly faster than the control seeds. The hydrophilicity of the seed surface significantly increased after treatment with high voltage nanosecond pulsed plasma (one shot). However, a very subtle increase in water uptake by plasma treated seeds was observed. Raman and FTIR spectroscopy analyses on chloroform extract of seed coats demonstrated no significant chemical etching on the surface of plasma treated seeds. This may be related to no dramatic increase in water absorption by seeds. The level of GA hormone and starch hydrolysis inside the plasma treated seeds was significantly elevated within 24 h. Taken together, our results suggest that high voltage nanosecond pulsed plasma may not only enhance hydrophilicity of the seed surface but also stimulate biochemical and molecular processes inside seed, leading to enhanced embryonic development.

Influence of Biochemical Features of Burkholderia pseudomallei Strains on Identification Reliability by Vitek 2 System.

PubMed

Zakharova, Irina B; Lopasteyskaya, Yana A; Toporkov, Andrey V; Viktorov, Dmitry V

2018-01-01

Burkholderia pseudomallei is a Gram-negative saprophytic soil bacterium that causes melioidosis, a potentially fatal disease endemic in wet tropical areas. The currently available biochemical identification systems can misidentify some strains of B. pseudomallei . The aim of the present study was to identify the biochemical features of B. pseudomallei , which can affect its correct identification by Vitek 2 system. The biochemical patterns of 40 B. pseudomallei strains were obtained using Vitek 2 GN cards. The average contribution of biochemical tests in overall dissimilarities between correctly and incorrectly identified strains was assessed using nonmetric multidimensional scaling. It was found ( R statistic of 0.836, P = 0.001) that a combination of negative N-acetyl galactosaminidase, β-N-acetyl glucosaminidase, phosphatase, and positive D-cellobiase (dCEL), tyrosine arylamidase (TyrA), and L-proline arylamidase (ProA) tests leads to low discrimination of B. pseudomallei , whereas a set of positive dCEL and negative N-acetyl galactosaminidase, TyrA, and ProA determines the wrong identification of B. pseudomallei as Burkholderia cepacia complex. The further expansion of the Vitek 2 identification keys is needed for correct identification of atypical or regionally distributed biochemical profiles of B. pseudomallei .

Research Links Nutrition to Behavior Disorders.

ERIC Educational Resources Information Center

Schauss, Alexander G.

1985-01-01

Social and medical research studies are examined that show the dramatic effects of biochemical and nutritional factors on antisocial behavior. They include studies of cobalt levels in hair samples of violent and nonviolent criminals, effects of diet on chronic delinquents, and effects of vitamin/mineral supplements on behaviorally disordered…

Biochemical and cytochemical evaluation of heterozygote individuals with glucose-6-phosphate dehydrogenase deficiency.

PubMed

Gurbuz, Nilgun; Aksu, Tevfik Aslan; Van Noorden, Cornelis J F

2005-01-01

The aim of this study was to diagnose heterozygous glucose-6-phosphate dehydrogenase (G6PD) deficient females by an inexpensive cytochemical G6PD staining method that is easy to perform, allowing diagnosis of G6PD deficiency without cumbersome genetic analysis. Three subject groups were included in the study. The first group consisted of 15 hemizygous deficient males. The second and the third group were composed of 15 heterozygous deficient females and 15 healthy individuals, respectively. Biochemical determination and cytochemical staining of G6PD activity were performed in samples of all subjects. Results obtained with the cytochemical staining method correlated significantly with the biochemical data (p < 0.001), but a only 51-68% of the erythrocytes were stained positively in females with normal biochemical G6PD activity despite their having a G6PD-deficient child. This observation clearly indicates that these individuals are heterozygously deficient. These findings show that the cytochemical staining method to detect G6PD activity in erythrocytes is reliable, sensitive and specific and is superior to the biochemical method. Therefore, this method can be used routinely to detect heterozygous G6PD deficiency.

A biochemical method for assessing the neurotoxic effects of misonidazole in the rat.

PubMed Central

Rose, G. P.; Dewar, A. J.; Stratford, I. J.

1980-01-01

A proven biochemical method for assessing chemically induced neurotoxicity has been applied to the study of the toxic effects of misonidazole (MISO) in the rat. This involves the fluorimetric measurement of beta-glucuronidase and beta-galactosidase activities in homogenates of rat nervous tissue. The tissues analysed were sciatic/posterior tibial nerve (SPTN) cut into 4 sections, trigeminal ganglia and cerebellum. MISO administered i.p. to Wistar rats in doses greater than 300 mg/kg/day for 7 consecutive days produced maximal increases in both beta-glucuronidase and beta-galactosidase activities in th SPTN at 4 weeks (140-180% of control values). The highest increases were associated with the most distal secretion of the nerve. Significant enzyme-activity changes were also found in the trigeminal ganglia and cerebellum of MISO-dosed rats. The greatest activity occurred 4-5 weeks after dosing, and was dose-related. It is concluded that, in the rat, MISO can produce biochemical changes consistent with a dying-back peripheral neuropathy, and biochemical changes suggestive of cerebellar damage. This biochemical approach would appear to offer a convenient quantitative method for the detection of neurotoxic effects of other potential radio-sensitizing drugs. PMID:7459223

A comparative biochemical profile of some cyprinids fish in Dukan Lake, Kurdistan-Iraq

NASA Astrophysics Data System (ADS)

Azeez, Darya Mohammed; Mohammed, Sarbaz Ibrahim

2017-09-01

The present study was carried out to demonstrate the baseline values for some serum biochemical parameters for 64 adult freshwater fish including seven species belong to family Cyprinidae, have been collected in Dukan Lake, Kurdistan region-Iraq. Fishes were weighed, measured, and collect blood for blood chemistry. Serum biochemical analyses were determined using (Cobas C 311) full automatic chemical analyzer. The result of comparative study of serum biochemical parameters of all Cyprinidae species showed that serum glucose was (459.10±106.99 mg/dl) and direct bilirubin was (0.056±0.021mg/dl) in Barbus grypus, serum total protein (3.511± 0.0484gm/dl) and HDL (133.11±0.4231mg/dl) in Cyprinus carpio, serum cholesterol (338.33±43.923 mg/dl) and LDL (86.11±11.871mg/dl) in Carassius carassius, serum triglyceride (420.0±28.8mg/dl) and ALK (113.93±20.65U/L) in Chondrostoma regium, serum AST and serum ALT in Capoeta trutta, were significantly higher when compared to other species. In a conclusion there is variation in biochemical values among species of same family.

Biochemical and Biophysical Cues in Matrix Design for Chronic and Diabetic Wound Treatment

PubMed Central

Xiao, Yun; Ahadian, Samad

2017-01-01

Progress in biomaterial science and engineering and increasing knowledge in cell biology have enabled us to develop functional biomaterials providing appropriate biochemical and biophysical cues for tissue regeneration applications. Tissue regeneration is particularly important to treat chronic wounds of people with diabetes. Understanding and controlling the cellular microenvironment of the wound tissue are important to improve the wound healing process. In this study, we review different biochemical (e.g., growth factors, peptides, DNA, and RNA) and biophysical (e.g., topographical guidance, pressure, electrical stimulation, and pulsed electromagnetic field) cues providing a functional and instructive acellular matrix to heal diabetic chronic wounds. The biochemical and biophysical signals generally regulate cell–matrix interactions and cell behavior and function inducing the tissue regeneration for chronic wounds. Some technologies and devices have already been developed and used in the clinic employing biochemical and biophysical cues for wound healing applications. These technologies can be integrated with smart biomaterials to deliver therapeutic agents to the wound tissue in a precise and controllable manner. This review provides useful guidance in understanding molecular mechanisms and signals in the healing of diabetic chronic wounds and in designing instructive biomaterials to treat them. PMID:27405960

Scientific issues and potential remote-sensing requirements for plant biochemical content

NASA Technical Reports Server (NTRS)

Peterson, David L.; Hubbard, G. S.

1992-01-01

Application of developments in imaging spectrometry to the study of terrestrial ecosystems, which began in 1983, demonstrate the potential to estimate lignin and nitrogen concentrations of plant canopies by remote-sensing techniques. Estimation of these parameters from the first principles of radiative transfer and the interactions of light with plant materials is not presently possible, principally because of lack of knowledge about internal leaf scattering and specific absorption involving biochemical compounds. From the perspective of remote-sensing instrumentation, sensors are needed to support derivative imaging spectroscopy. Biochemical absorption features tend to occur in functional groupings throughout the 1100- to 2500-nm region. Derivative spectroscopy improves the information associated with the weaker, narrower absorption features of biochemical absorption that are superimposed on the strong absolute variations due to foliar biomass, pigments, and leaf water content of plant canopies. Preliminary sensor specifications call for 8-nm bandwidths at 2-nm centers in four spectral regions (about 400 bands total) and a signal-to-noise performance of at least 1000:1 for 20 percent albedo targets in the 2000-nm region.

ESTIMATING GASEOUS EXCHANGES BETWEEN THE ATMOSPHERE AND PLANTS USING A COUPLED BIOCHEMICAL DRY DEPOSITION MODEL

EPA Science Inventory

To study gaseous exchanges between the soil, biosphere and atmosphere, a biochemical model was coupled with the latest version of Meyers Multi-Layer Deposition Model. The biochemical model describes photosynthesis and respiration and their coupling with stomatal resistance for...

Biochemical markers of cartilage metabolism are associated with walking biomechanics 6-months following anterior cruciate ligament reconstruction.

PubMed

Pietrosimone, Brian; Loeser, Richard F; Blackburn, J Troy; Padua, Darin A; Harkey, Matthew S; Stanley, Laura E; Luc-Harkey, Brittney A; Ulici, Veronica; Marshall, Stephen W; Jordan, Joanne M; Spang, Jeffery T

2017-10-01

The purpose of our study was to determine the association between biomechanical outcomes of walking gait (peak vertical ground reaction force [vGRF], vGRF loading rate [vGRF-LR], and knee adduction moment [KAM]) 6 months following anterior cruciate ligament reconstruction (ACLR) and biochemical markers of serum type-II collagen turnover (collagen type-II cleavage product to collagen type-II C-propeptide [C2C:CPII]), plasma degenerative enzymes (matrix metalloproteinase-3 [MMP-3]), and a pro-inflammatory cytokine (interleukin-6 [IL-6]). Biochemical markers were evaluated within the first 2 weeks (6.5 ± 3.8 days) following ACL injury and again 6 months following ACLR in eighteen participants. All peak biomechanical outcomes were extracted from the first 50% of the stance phase of walking gait during a 6-month follow-up exam. Limb symmetry indices (LSI) were used to normalize the biomechanical outcomes in the ACLR limb to that of the contralateral limb (ACLR/contralateral). Bivariate correlations were used to assess associations between biomechanical and biochemical outcomes. Greater plasma MMP-3 concentrations after ACL injury and at the 6-month follow-up exam were associated with lesser KAM LSI. Lesser KAM was associated with greater plasma IL-6 at the 6-month follow-up exam. Similarly, lesser vGRF-LR LSI was associated with greater plasma MMP-3 concentrations at the 6-month follow-up exam. Lesser peak vGRF LSI was associated with higher C2C:CPII after ACL injury, yet this association was not significant after accounting for walking speed. Therefore, lesser biomechanical loading in the ACLR limb, compared to the contralateral limb, 6 months following ACLR may be related to deleterious joint tissue metabolism that could influence future cartilage breakdown. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2288-2297, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Complexity reduction of biochemical rate expressions.

PubMed

Schmidt, Henning; Madsen, Mads F; Danø, Sune; Cedersund, Gunnar

2008-03-15

The current trend in dynamical modelling of biochemical systems is to construct more and more mechanistically detailed and thus complex models. The complexity is reflected in the number of dynamic state variables and parameters, as well as in the complexity of the kinetic rate expressions. However, a greater level of complexity, or level of detail, does not necessarily imply better models, or a better understanding of the underlying processes. Data often does not contain enough information to discriminate between different model hypotheses, and such overparameterization makes it hard to establish the validity of the various parts of the model. Consequently, there is an increasing demand for model reduction methods. We present a new reduction method that reduces complex rational rate expressions, such as those often used to describe enzymatic reactions. The method is a novel term-based identifiability analysis, which is easy to use and allows for user-specified reductions of individual rate expressions in complete models. The method is one of the first methods to meet the classical engineering objective of improved parameter identifiability without losing the systems biology demand of preserved biochemical interpretation. The method has been implemented in the Systems Biology Toolbox 2 for MATLAB, which is freely available from http://www.sbtoolbox2.org. The Supplementary Material contains scripts that show how to use it by applying the method to the example models, discussed in this article.

Mathematical treatment of isotopologue and isotopomer speciation and fractionation in biochemical kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maggi, F.M.; Riley, W.J.

2009-11-01

We present a mathematical treatment of the kinetic equations that describe isotopologue and isotopomer speciation and fractionation during enzyme-catalyzed biochemical reactions. These equations, presented here with the name GEBIK (general equations for biochemical isotope kinetics) and GEBIF (general equations for biochemical isotope fractionation), take into account microbial biomass and enzyme dynamics, reaction stoichiometry, isotope substitution number, and isotope location within each isotopologue and isotopomer. In addition to solving the complete GEBIK and GEBIF, we also present and discuss two approximations to the full solutions under the assumption of biomass-free and enzyme steady-state, and under the quasi-steady-state assumption as applied tomore » the complexation rate. The complete and approximate approaches are applied to observations of biological denitrification in soils. Our analysis highlights that the full GEBIK and GEBIF provide a more accurate description of concentrations and isotopic compositions of substrates and products throughout the reaction than do the approximate forms. We demonstrate that the isotopic effects of a biochemical reaction depend, in the most general case, on substrate and complex concentrations and, therefore, the fractionation factor is a function of time. We also demonstrate that inverse isotopic effects can occur for values of the fractionation factor smaller than 1, and that reactions that do not discriminate isotopes do not necessarily imply a fractionation factor equal to 1.« less

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

PubMed Central

Rialle, Stéphanie; Felicori, Liza; Dias-Lopes, Camila; Pérès, Sabine; El Atia, Sanaâ; Thierry, Alain R.; Amar, Patrick; Molina, Franck

2010-01-01

Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks. Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/ Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20628073

Acidic deposition, cation mobilization, and biochemical indicators of stress in healthy red spruce

USGS Publications Warehouse

Shortle, W.C.; Smith, K.T.; Minocha, R.; Lawrence, G.B.; David, M.B.

1997-01-01

Dendrochemical and biochemical markers link stress in apparently healthy red spruce trees (Picea rubens) to acidic deposition. Acidic deposition to spruce forests of the northeastern USA increased sharply during the 1960s. Previous reports related visible damage of trees at high elevations to root and soil processes. In this report, dendrochemical and foliar biochemical markers indicate perturbations in biological processes in healthy red spruce trees across the northeastern USA. Previous research on the dendrochemistry of red spruce stemwood indicated that under uniform environmental conditions, stemwood concentrations of Ca and Mg decreased with increasing radial distance from the pith. For nine forest locations, frequency analysis shows that 28 and 52% of samples of red spruce stemwood formed in the 1960s are enriched in Ca and Mg, respectively, relative to wood formed prior to and after the 1960s. This enrichment in trees throughout the northeastern USA may be interpretable as a signal of increased availability of essential cations in forest soils. Such a temporary increase in the availability of Ca and Mg could be caused by cation mobilization, a consequence of increased acidic deposition. During cation mobilization, essential Ca and Mg as well as potentially harmful Al become more available for interaction with binding sites in the soil and absorbing roots. As conditions which favor cation mobilization continue, Ca and Mg can be leached or displaced from the soil. A measure of the interaction between Ca and Al is the Al/Ca binding ratio (molar charge ratio of exchangeable Al to exchangeable Ca). As the Al/Ca binding ratio in the root zone increased from 0.3 to 1.9, the foliar concentration of the biochemical stress marker putrescine also increased from 45 to 145 nm g-1. The correlation of the putrescine concentration to the Al/Ca binding ratio (adj. r2 = 0.68, P < 0.027) suggests that foliar stress may be linked to soil chemistry.

Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea.

PubMed

Pergolizzi, Giulia; Wagner, Gerd K; Bowater, Richard Peter

2016-08-31

DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD + ) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD + affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes. ©2016 The Author(s).

Diagnostic value of the biochemical tests in patients with purulent pericarditis

PubMed Central

Ekim, Meral; Ekim, Hasan

2014-01-01

Objectives: Purulent pericarditis is a collection of purulent effusion in the pericardial space. It has become a rare entity with the increased availability and use of antibiotics. In contrast to pleural empyema, there are few data regarding the biochemical parameters of purulent pericardial effusion to aid diagnosis. Therefore, in this study, we have evaluated the diagnostic utility of biochemical tests in patients with purulent pericarditis. Methods: Between September 2004 and September 2012, we treated fifteen children with purulent pericarditis and tamponade. There were 8 boys and 7 girls, ranging in age from 8 months to 14 years, with a mean age of 5.3 ± 3.2 years. Echocardiographic diagnosis of cardiac tamponade was made in all patients. All patients underwent immediate surgical drainage due to cardiac tamponade. The diagnosis of purulent pericarditis was supported by biochemical tests. Anterior mini-thoracotomy or subxiphoid approach was performed for surgical drainage. Results: The most common clinical findings were tamponade, hepatomegaly, tachycardia, fever refractory antibiotic therapy, dyspnea, tachypnea, cough, and increased jugular venous pressure. Central venous pressure decreased and arterial tension increased immediately after the evacuation of purulent effusion during operation in all patients. The pericardial effusion had high lactic dehydrogenase, and low glucose concentration, confirming purulent pericarditis. Also, pH (mean± SD) was 7.01 ± 0.06. The culture of pericardial effusions and blood samples were negative. Conclusion: Biochemical tests are useful guideline when assessing the pericardial effusions. However, these tests should be interpreted with the clinical and operative findings. PMID:25097529

Resource Management Technology: Los Alamos Technical Capabilities for Emergency Management,

DTIC Science & Technology

1983-07-18

synthetic fuels from coal (analogous to the Fischer-Tropsch process), olefin polymerization, and flue - gas desulfurization . In order to successfully...world. It has been a major research effort here for decades. Also, in the area of desulfurization of flue gases, Los Alamos scientists have been...Tectonic and Geochemical Controls on Copper-Molybdenum Porphyry Mineralization in the Southwestern United States (M. J. Aldrich and A. W. Laughlin) 1.0.6

Antioxidant dieckol downregulates the Rac1/ROS signaling pathway and inhibits Wiskott-Aldrich syndrome protein (WASP)-family verprolin-homologous protein 2 (WAVE2)-mediated invasive migration of B16 mouse melanoma cells.

PubMed

Park, Sun Joo; Kim, Yong Tae; Jeon, You Jin

2012-04-01

Reactive oxygen species (ROS) generation is linked to dynamic actin cytoskeleton reorganization, which is involved in tumor cell motility and metastasis. Thus, inhibition of ROS generation and actin polymerization in tumor cells may represent an effective anticancer strategy. However, the molecular basis of this signaling pathway is currently unknown. Here, we show that the Ecklonia cava-derived antioxidant dieckol downregulates the Rac1/ROS signaling pathway and inhibits Wiskott-Aldrich syndrome protein (WASP)-family verprolin-homologous protein 2 (WAVE2)-mediated invasive migration of B16 mouse melanoma cells. Steady-state intracellular ROS levels were higher in malignant B16F10 cells than in parental, nonmetastatic B16F0 cells. Elevation of ROS by H(2)O(2) treatment increased migration and invasion ability of B16F0 cells to level similar to that of B16F10 cells, suggesting that intracellular ROS signaling mediates the prometastatic properties of B16 mouse melanoma cells. ROS levels and the cell migration and invasion ability of B16 melanoma cells correlated with Rac1 activation and WAVE2 expression. Overexpression of dominant negative Rac1 and depletion of WAVE2 by siRNA suppressed H(2)O(2)-induced cell invasion of B16F0 and B16F10 cells. Similarly, dieckol attenuates the ROS-mediated Rac1 activation and WAVE2 expression, resulting in decreased migration and invasion of B16 melanoma cells. In addition, we found that dieckol decreases association between WAVE2 and NADPH oxidase subunit p47(phox). Therefore, this finding suggests that WAVE2 acts to couple intracellular Rac1/ROS signaling to the invasive migration of B16 melanoma cells, which is inhibited by dieckol.

Antioxidant Dieckol Downregulates the Rac1/ROS Signaling Pathway and Inhibits Wiskott-Aldrich Syndrome Protein (WASP)-Family Verprolin-Homologous Protein 2 (WAVE2)-Mediated Invasive Migration of B16 Mouse Melanoma Cells

PubMed Central

Park, Sun Joo; Kim, Yong Tae; Jeon, You Jin

2012-01-01

Reactive oxygen species (ROS) generation is linked to dynamic actin cytoskeleton reorganization, which is involved in tumor cell motility and metastasis. Thus, inhibition of ROS generation and actin polymerization in tumor cells may represent an effective anticancer strategy. However, the molecular basis of this signaling pathway is currently unknown. Here, we show that the Ecklonia cava-derived antioxidant dieckol downregulates the Rac1/ROS signaling pathway and inhibits Wiskott-Aldrich syndrome protein (WASP)-family verprolin-homologous protein 2 (WAVE2)-mediated invasive migration of B16 mouse melanoma cells. Steady-state intracellular ROS levels were higher in malignant B16F10 cells than in parental, nonmetastatic B16F0 cells. Elevation of ROS by H2O2 treatment increased migration and invasion ability of B16F0 cells to level similar to that of B16F10 cells, suggesting that intracellular ROS signaling mediates the prometastatic properties of B16 mouse melanoma cells. ROS levels and the cell migration and invasion ability of B16 melanoma cells correlated with Rac1 activation and WAVE2 expression. Overexpression of dominant negative Rac1 and depletion of WAVE2 by siRNA suppressed H2O2-induced cell invasion of B16F0 and B16F10 cells. Similarly, dieckol attenuates the ROS-mediated Rac1 activation and WAVE2 expression, resulting in decreased migration and invasion of B16 melanoma cells. In addition, we found that dieckol decreases association between WAVE2 and NADPH oxidase subunit p47phox. Therefore, this finding suggests that WAVE2 acts to couple intracellular Rac1/ROS signaling to the invasive migration of B16 melanoma cells, which is inhibited by dieckol. PMID:22441674

Biochemical identification of the mallard, Anas platyrhynchos, and black duck, A. rubripes

USGS Publications Warehouse

Morgan, R.P.; Noe, L.A.; Henny, C.J.

1976-01-01

1. Eleven tissue systems from mallards and black ducks were examined for soluble proteins, lactate dehydrogenases and non-specific esterases through discontinuous polyacrylamide techniques.2. Biochemical relationships between the black duck and mallard are extremely similar.3. Hemoglobins and lactate dehydrogenase appear to be common in electrophoretic mobility between the two species.4. Approximately 89% of the soluble proteins and 58% of the non-specific esterases are common among the two species, indicating both biochemical similarity at the genus level and species-specificity.

[Some biochemical parameters in the placenta in discoordinated and powerless labors].

PubMed

Sitnikova, O G; Peretiatko, L P; Sharygin, S A; Kuz'menko, G N; Popova, I G

2009-11-01

A number of biochemical parameters (total nitrites and nitrates (NO(x)), cyclic guanosine monophosphate (cGMP), nitrotyrosine, medium-weight molecules (MCM) in the placenta were determined in women with gestosis during discoordinated and powerless labor. Thirty placentas (10 placentas from parturients after discoordinated labor, 10 from those after powerless labor, 10 placentas as a control group) were examined. Changes in the parameters under study were found to result in the development of nitroxide and oxidant stresses and endotoxicosis. The biochemical parameters should be considered as placental criteria for the differential diagnosis of labor anomalies in gestosis, such as powerless and discoordinated labors.

Biochemical functionalization of peptide nanotubes with phage displayed peptides

NASA Astrophysics Data System (ADS)

Swaminathan, Swathi; Cui, Yue

2016-09-01

The development of a general approach for the biochemical functionalization of peptide nanotubes (PNTs) could open up existing opportunities in both fundamental studies as well as a variety of applications. PNTs are spontaneously assembled organic nanostructures made from peptides. Phage display has emerged as a powerful approach for identifying selective peptide binding motifs. Here, we demonstrate for the first time the biochemical functionalization of PNTs via peptides identified from a phage display peptide library. The phage-displayed peptides are shown to recognize PNTs. These advances further allow for the development of bifunctional peptides for the capture of bacteria and the self-assembly of silver particles onto PNTs. We anticipate that these results could provide significant opportunities for using PNTs in both fundamental studies and practical applications, including sensors and biosensors nanoelectronics, energy storage devices, drug delivery, and tissue engineering.

Diabetes, Biochemical Markers of Bone Turnover, Diabetes Control, and Bone

PubMed Central

Starup-Linde, Jakob

2012-01-01

Diabetes mellitus is known to have late complications including micro vascular and macro vascular disease. This review focuses on another possible area of complication regarding diabetes; bone. Diabetes may affect bone via bone structure, bone density, and biochemical markers of bone turnover. The aim of the present review is to examine in vivo from humans on biochemical markers of bone turnover in diabetics compared to non-diabetics. Furthermore, the effect of glycemic control on bone markers and the similarities and differences of type 1- and type 2-diabetics regarding bone markers will be evaluated. A systematic literature search was conducted using PubMed, Embase, Cinahl, and SveMed+ with the search terms: “Diabetes mellitus,” “Diabetes mellitus type 1,” “Insulin dependent diabetes mellitus,” “Diabetes mellitus type 2,” “Non-insulin dependent diabetes mellitus,” “Bone,” “Bone and Bones,” “Bone diseases,” “Bone turnover,” “Hemoglobin A Glycosylated,” and “HbA1C.” After removing duplicates from this search 1,188 records were screened by title and abstract and 75 records were assessed by full text for inclusion in the review. In the end 43 records were chosen. Bone formation and resorption markers are investigated as well as bone regulating systems. T1D is found to have lower osteocalcin and CTX, while osteocalcin and tartrate-resistant acid are found to be lower in T2D, and sclerostin is increased and collagen turnover markers altered. Other bone turnover markers do not seem to be altered in T1D or T2D. A major problem is the lack of histomorphometric studies in humans linking changes in turnover markers to actual changes in bone turnover and further research is needed to strengthen this link. PMID:23482417

Sonographic assessment of petroleum-induced hepatotoxicity in Nigerians: does biochemical assessment underestimate liver damage?

PubMed

Anakwue, Angel-Mary; Anakwue, Raphael; Okeji, Mark; Idigo, Felicitas; Agwu, Kenneth; Nwogu, Uloma

2017-03-01

Exposure to petroleum products has been shown to have significant adverse effects on the liver which can manifest either as morphological or physiological changes. The aim of the study was to assess the effects of chronic exposure to some petroleum products on the liver of exposed workers using sonography and to determine whether biochemical assessments underestimated hepatotoxicity. Abdominal ultrasound was performed on 415 exposed workers in order to evaluate liver echogenicity and size. Also, biochemical assessment of the liver was done to evaluate its function. Statistically significant increase in the liver parenchymal echogenicity and the liver size was seen in the exposed workers compared with control (p ≤ 0.05). These increased as the exposure duration increased. It was also noted that out of 16.87% (N=70) exposed workers with abnormal liver echopattern, only 2.65% (N=11) had alanine aminotransferase above the reference range. The study revealed evidence of ultrasound detectable hepatotoxicity among the exposed subjects. Sonography appeared to detect petroleum products-induced hepatic toxicity more than biochemical assays suggesting that biochemical assessment may have underestimated toxicity.

Characterization of Bioderived Polyhydroxyalkanoates by Size Exclusion Chromatography

NASA Astrophysics Data System (ADS)

Negulescu, Ioan; Cueto, Rafael; Rusch, Kelly; Gutierrez-Wing, Teresa; Stevens, Benjamin

2008-03-01

The plant derived polyesters, better known as polyhydroxyalkanoates, PHAs, are renewable and sustainable: [-O-CH(CH3)-(CH2)x-CO-]n. If x = 0 PHA is Poly(lactic acid), PLA; if x = 1 or 2 it is Poly(hydroxy butyrate), PHB, or Poly(hydroxy valerate), PHV. SEC and light scattering have been used before for determination of the absolute molecular mass of PLA dissolved in CHCl3 (Malmgren et al., J. Thermal Anal. Calorim., 2006, 83, 35-40). To our best knowledge there is no publication on the determination of the absolute MW of other PHAs. The bioderived polymers analyzed in this work were four catalog PHA samples: PHB Fluka 81329, PHB Natural Aldrich 363502, 95PHB/5PHV Aldrich 403105, and 92PHB/8PHV Aldrich 403113. SEC/LS instrumentation used: three Phenogel (1K-10000K) columns + a guard column, an Agilent pump and Wyatt Heleos MALS, QUELS (DLS), ViscoStar and rEX DRI detectors, all in series. The experimental dn/dc of PHB in CHCl3 (0.0336 ml/g at 658nm) allowed the determination of absolute MW of all PHA samples: PHB Fluka Mw 345,100 Mn 218,400; PHB Aldrich Mw 335,700 Mn 185,000; 92PHB/8PHV Mw 144,700 Mn 91,970; 95PHB/5PHV Mw 253,000 Mn 193,800.

Linking stable isotopes and biochemical responses in Balanus glandula under sewage influence.

PubMed

Laitano, M V; Díaz-Jaramillo, M; Rodriguez, Y E; Ducós, E; Panarello, H O; Fernández-Gimenez, A V

2018-02-01

In the present study, we analyzed the influence of untreated sewage exposure on carbon (δ13C) and nitrogen (δ15N) isotopic composition and several biochemical responses in the barnacle Balanus glandula. The main objective was to evaluate whether changes in stable isotopes signature do reflect biochemical sub-lethal effects in a sewage influence gradient. Stable isotopes analysis showed differences in isotope signatures between close sewage influence and distant sites, being δ13C signatures stronger than that of δ15N. Regarding biochemical effects, although organisms close to the effluent would be clearly exposed to contaminants (increased GST activity) the oxidative stress would not be too evident (peroxidases and ACAP not affected). The most affected physiological aspect was the digestive one, reflected in increased alkaline proteases and lipases activities. A clear relation between δ15N and GST activity was found, showing to δ15N as an indicator of potential exposure to chemical contaminants.

Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond

PubMed Central

Ge, Hao; Qian, Hong

2011-01-01

A theory for an non-equilibrium phase transition in a driven biochemical network is presented. The theory is based on the chemical master equation (CME) formulation of mesoscopic biochemical reactions and the mathematical method of large deviations. The large deviations theory provides an analytical tool connecting the macroscopic multi-stability of an open chemical system with the multi-scale dynamics of its mesoscopic counterpart. It shows a corresponding non-equilibrium phase transition among multiple stochastic attractors. As an example, in the canonical phosphorylation–dephosphorylation system with feedback that exhibits bistability, we show that the non-equilibrium steady-state (NESS) phase transition has all the characteristics of classic equilibrium phase transition: Maxwell construction, a discontinuous first-derivative of the ‘free energy function’, Lee–Yang's zero for a generating function and a critical point that matches the cusp in nonlinear bifurcation theory. To the biochemical system, the mathematical analysis suggests three distinct timescales and needed levels of description. They are (i) molecular signalling, (ii) biochemical network nonlinear dynamics, and (iii) cellular evolution. For finite mesoscopic systems such as a cell, motions associated with (i) and (iii) are stochastic while that with (ii) is deterministic. Both (ii) and (iii) are emergent properties of a dynamic biochemical network. PMID:20466813

Influence of Biochemical Features of Burkholderia pseudomallei Strains on Identification Reliability by Vitek 2 System

PubMed Central

Zakharova, Irina B; Lopasteyskaya, Yana A; Toporkov, Andrey V; Viktorov, Dmitry V

2018-01-01

Background: Burkholderia pseudomallei is a Gram-negative saprophytic soil bacterium that causes melioidosis, a potentially fatal disease endemic in wet tropical areas. The currently available biochemical identification systems can misidentify some strains of B. pseudomallei. The aim of the present study was to identify the biochemical features of B. pseudomallei, which can affect its correct identification by Vitek 2 system. Materials and Methods: The biochemical patterns of 40 B. pseudomallei strains were obtained using Vitek 2 GN cards. The average contribution of biochemical tests in overall dissimilarities between correctly and incorrectly identified strains was assessed using nonmetric multidimensional scaling. Results: It was found (R statistic of 0.836, P = 0.001) that a combination of negative N-acetyl galactosaminidase, β-N-acetyl glucosaminidase, phosphatase, and positive D-cellobiase (dCEL), tyrosine arylamidase (TyrA), and L-proline arylamidase (ProA) tests leads to low discrimination of B. pseudomallei, whereas a set of positive dCEL and negative N-acetyl galactosaminidase, TyrA, and ProA determines the wrong identification of B. pseudomallei as Burkholderia cepacia complex. Conclusion: The further expansion of the Vitek 2 identification keys is needed for correct identification of atypical or regionally distributed biochemical profiles of B. pseudomallei. PMID:29563716

A MULTILAYER BIOCHEMICAL DRY DEPOSITION MODEL 1. MODEL FORMULATION

EPA Science Inventory

A multilayer biochemical dry deposition model has been developed based on the NOAA Multilayer Model (MLM) to study gaseous exchanges between the soil, plants, and the atmosphere. Most of the parameterizations and submodels have been updated or replaced. The numerical integration ...

The dynamics of blood biochemical parameters in cosmonauts during long-term space flights

NASA Astrophysics Data System (ADS)

Markin, Andrei; Strogonova, Lubov; Balashov, Oleg; Polyakov, Valery; Tigner, Timoty

Most of the previously obtained data on cosmonauts' metabolic state concerned certain stages of the postflight period. In this connection, all conclusions, as to metabolism peculiarities during the space flight, were to a large extent probabilistic. The purpose of this work was study of metabolism characteristics in cosmonauts directly during long-term space flights. In the capillary blood samples taken from a finger, by "Reflotron IV" biochemical analyzer, "Boehringer Mannheim" GmbH, Germany, adapted to weightlessness environments, the activity of GOT, GPT, CK, gamma-GT, total and pancreatic amylase, as well as concentration of hemoglobin, glucose, total bilirubin, uric acid, urea, creatinine, total, HDL- and LDL cholesterol, triglycerides had been determined. HDL/LDL-cholesterol ratio also was computed. The crewmembers of 6 main missions to the "Mir" orbital station, a total of 17 cosmonauts, were examined. Biochemical tests were carryed out 30-60 days before lounch, and in the flights different stages between the 25-th and the 423-rd days of flights. In cosmonauts during space flight had been found tendency to increase, in compare with basal level, GOT, GPT, total amylase activity, glucose and total cholesterol concentration, and tendency to decrease of CK activity, hemoglobin, HDL-cholesterol concentration, and HDL/LDL — cholesterol ratio. Some definite trends in variations of other determined biochemical parameters had not been found. The same trends of mentioned biochemical parameters alterations observed in majority of tested cosmonauts, allows to suppose existence of connection between noted metabolic alterations with influence of space flight conditions upon cosmonaut's body. Variations of other studied blood biochemical parameters depends on, probably, pure individual causes.

Chronic histiocytic intervillositis - Clinical, biochemical and radiological findings: An observational study.

PubMed

Koby, Lawrence; Keating, Sarah; Malinowski, Ann Kinga; D'Souza, Rohan

2018-04-01

Chronic histiocytic intervillositis (CHI) of the placenta although rare, has a high recurrence rate, is associated with serious adverse pregnancy outcomes and has no available treatment. This study aims to determine clinical, biochemical and radiological factors associated with CHI, to guide management of subsequent pregnancies. This retrospective observational study included consecutive cases with a histopathologic diagnosis of CHI after 18 weeks of gestation, between 2001 and 2014, and no controls. Clinical (maternal, fetal and delivery outcomes), biochemical (first- and second-trimester biomarkers for fetal aneuploidy and serum alkaline phosphatase) and radiological (second- and third-trimester fetal, placental and Doppler ultrasound) factors associated with a histopathological diagnosis of CHI were identified and results presented as percentages. Outcomes of subsequent pregnancies were described. Of 231 identified cases of 'intervillositis', 33 were confirmed to have CHI, of which only 4/33 (12.1%) had prior uncomplicated term deliveries. During pregnancy, 10/18 (55.5%) had abnormal first-trimester screening, 4/16 (25%) had abnormal second-trimester screening, 6/19 (31.6%) had at least one elevated alkaline phosphatase level, and 15/20 (75%) had at least one abnormal feature on mid-trimester placental ultrasound. In subsequent pregnancies that were closely followed with a combination of biochemical and radiologic tests, there were no cases of fetal loss, and lower incidence of fetal growth restriction and preterm birth. No clinical, biochemical or radiological finding is consistently associated with CHI and adverse outcomes thereof. Whether the incorporation of these tests in individualized care-plans could improve outcomes in subsequent pregnancies needs to be studied further. Copyright © 2018 Elsevier Ltd. All rights reserved.

A scalable moment-closure approximation for large-scale biochemical reaction networks

PubMed Central

Kazeroonian, Atefeh; Theis, Fabian J.; Hasenauer, Jan

2017-01-01

Abstract Motivation: Stochastic molecular processes are a leading cause of cell-to-cell variability. Their dynamics are often described by continuous-time discrete-state Markov chains and simulated using stochastic simulation algorithms. As these stochastic simulations are computationally demanding, ordinary differential equation models for the dynamics of the statistical moments have been developed. The number of state variables of these approximating models, however, grows at least quadratically with the number of biochemical species. This limits their application to small- and medium-sized processes. Results: In this article, we present a scalable moment-closure approximation (sMA) for the simulation of statistical moments of large-scale stochastic processes. The sMA exploits the structure of the biochemical reaction network to reduce the covariance matrix. We prove that sMA yields approximating models whose number of state variables depends predominantly on local properties, i.e. the average node degree of the reaction network, instead of the overall network size. The resulting complexity reduction is assessed by studying a range of medium- and large-scale biochemical reaction networks. To evaluate the approximation accuracy and the improvement in computational efficiency, we study models for JAK2/STAT5 signalling and NFκB signalling. Our method is applicable to generic biochemical reaction networks and we provide an implementation, including an SBML interface, which renders the sMA easily accessible. Availability and implementation: The sMA is implemented in the open-source MATLAB toolbox CERENA and is available from https://github.com/CERENADevelopers/CERENA. Contact: jan.hasenauer@helmholtz-muenchen.de or atefeh.kazeroonian@tum.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881983

Early hypofractionated salvage radiotherapy for postprostatectomy biochemical recurrence.

PubMed

Kruser, Tim J; Jarrard, David F; Graf, Andrew K; Hedican, Sean P; Paolone, David R; Wegenke, John D; Liu, Glenn; Geye, Heather M; Ritter, Mark A

2011-06-15

Postprostatectomy adjuvant or salvage radiotherapy, when using standard fractionation, requires 6.5 to 8 weeks of treatment. The authors report on the safety and efficacy of an expedited radiotherapy course for salvage prostate radiotherapy. A total of 108 consecutive patients were treated with salvage radiation therapy to 65 grays (Gy) in 26 fractions of 2.5 Gy. Median follow-up was 32.4 months. Median presalvage prostate-specific antigen (PSA) was 0.44 (range, 0.05-9.50). Eighteen (17%) patients received androgen deprivation after surgery or concurrently with radiation. The actuarial freedom from biochemical failure for the entire group at 4 years was 67% ± 5.3%. An identical 67% control rate was seen at 5 years for the first 50 enrolled patients, whose median follow-up was longer at 43 months. One acute grade 3 genitourinary toxicity occurred, with no acute grade 3 gastrointestinal and no late grade 3 toxicities observed. On univariate analysis, higher Gleason score (P = .006), PSA doubling time ≤12 months (P = .03), perineural invasion (P = .06), and negative margins (P = .06) showed association with unsuccessful salvage. On multivariate analysis, higher Gleason score (P = .057) and negative margins (P = .088) retained an association with biochemical failure. Hypofractionated radiotherapy (65 Gy in 2.5 Gy fractions in about 5 weeks) reduces the length of treatment by from 1-½ to 3 weeks relative to other treatment schedules commonly used, produces low rates of toxicity, and demonstrates encouraging efficacy at 4 to 5 years. Hypofractionation may provide a convenient, resource-efficient, and well-tolerated salvage approach for the estimated 20,000 to 35,000 US men per year experiencing biochemical recurrence after prostatectomy. Copyright © 2010 American Cancer Society.

Recent Advances on the Use of Biochemical Extracts as Filaricidal Agents

PubMed Central

Al-Abd, Nazeh M.; Nor, Zurainee Mohamed; Al-Adhroey, Abdulelah H.; Suhaimi, Anwar; Sivanandam, S.

2013-01-01

Lymphatic filariasis is a parasitic infection that causes a devastating public health and socioeconomic burden with an estimated infection of over 120 million individuals worldwide. The infection is caused by three closely related nematode parasites, namely, Wuchereria bancrofti, Brugia malayi, and B. timori, which are transmitted to human through mosquitoes of Anopheles, Culex, and Aedes genera. The species have many ecological variants and are diversified in terms of their genetic fingerprint. The rapid spread of the disease and the genetic diversification cause the lymphatic filarial parasites to respond differently to diagnostic and therapeutic interventions. This in turn prompts the current challenge encountered in its management. Furthermore, most of the chemical medications used are characterized by adverse side effects. These complications urgently warrant intense prospecting on bio-chemicals that have potent efficacy against either the filarial worms or thier vector. In lieu of this, we presented a review on recent literature that reported the efficacy of filaricidal biochemicals and those employed as vector control agents. In addition, methods used for biochemical extraction, screening procedures, and structure of the bioactive compounds were also presented. PMID:24298292

Is Preoperative Biochemical Testing for Pheochromocytoma Necessary for All Adrenal Incidentalomas?

PubMed Central

Jun, Joo Hyun; Ahn, Hyun Joo; Lee, Sangmin M.; Kim, Jie Ae; Park, Byung Kwan; Kim, Jee Soo; Kim, Jung Han

2015-01-01

Abstract This study examined whether imaging phenotypes obtained from computed tomography (CT) can replace biochemical tests to exclude pheochromocytoma among adrenal incidentalomas (AIs) in the preoperative setting. We retrospectively reviewed the medical records of all patients (n = 251) who were admitted for operations and underwent adrenal-protocol CT for an incidentally discovered adrenal mass from January 2011 to December 2012. Various imaging phenotypes were assessed for their screening power for pheochromocytoma. Final diagnosis was confirmed by biopsy, biochemical tests, and follow-up CT. Pheochromocytomas showed similar imaging phenotypes as malignancies, but were significantly different from adenomas. Unenhanced attenuation values ≤10 Hounsfield units (HU) showed the highest specificity (97%) for excluding pheochromocytoma as a single phenotype. A combination of size ≤3 cm, unenhanced attenuation values ≤ 10 HU, and absence of suspicious morphology showed 100% specificity for excluding pheochromocytoma. Routine noncontrast CT can be used as a screening tool for pheochromocytoma by combining 3 imaging phenotypes: size ≤3 cm, unenhanced attenuation values ≤10 HU, and absence of suspicious morphology, and may substitute for biochemical testing in the preoperative setting. PMID:26559265

Upgrading Laccase Production and Biochemical Properties: Strategies and Challenges.

PubMed

Bertrand, Brandt; Martínez-Morales, Fernando; Trejo-Hernández, María R

2017-07-01

Improving laccases continues to be crucial in novel biotechnological developments and industrial applications, where they are concerned. This review breaks down and explores the potential of the strategies (conventional and modern) that can be used for laccase enhancement (increased production and upgraded biochemical properties such as stability and catalytic efficiency). The challenges faced with these approaches are briefly discussed. We also shed light on how these strategies merge and give rise to new options and advances in this field of work. Additionally, this article seeks to serve as a guide for students and academic researchers interested in laccases. This document not only gives basic information on laccases, but also provides updated information on the state of the art of various technologies that are used in this line of investigation. It also gives the readers an idea of the areas extensively studied and the areas where there is still much left to be done. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1015-1034, 2017. © 2017 American Institute of Chemical Engineers.

Biochemical and morphological changes associated with macrophages and osteoclasts when challenged with infection - biomed 2011.

PubMed

Wiggers, Erin Callie; Johnson, William; Tucci, Michelle; Benghuzzi, Hamed

2011-01-01

Osteomyelitis is a bacterial infection of the bone that occurs frequently as a complication of open fractures and various kinds of orthopedic surgery. This infection can often lead to more extensive surgeries and even death of the patient. In animal models of osteomyelitis, the site of infection by Staphylococcus aureus was observed to have high numbers of both macrophages and osteoclasts, both of which may contribute to large amounts of osteolysis and tissue damage. In order to evaluate the immune response in both types of cells, two cells lines, a macrophage cell line and a macrophage cell line stimulated to become osteoclasts by the addition of receptor activator of nuclear-factor B (RANKL), were exposed to lipopolysaccharides, opsonized S. aureus, and unopsonized S. aureus. The results showed that both cell types activated a biochemical cascade that included the release of cytokines and nitric oxide associated with cell damage and death in response to infection. However, macrophages and osteoclasts differed in response magnitude, most likely due to differences in cell-membrane receptors. This data supports the growing body of research that links the immune and skeletal systems. Further understanding of biochemical pathways shared by the two systems could lead to significant advances in the treatment of osteomyelitis and the success of prostheses.

Adiabatic coarse-graining and simulations of stochastic biochemical networks

PubMed Central

Sinitsyn, N. A.; Hengartner, Nicolas; Nemenman, Ilya

2009-01-01

We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach is similar to the Born–Oppenheimer approximation in quantum mechanics and follows from the stochastic path integral representation of the cumulant generating function of reaction events. In applications with a small number of chemical reactions, it produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, interpretable representation and can be used for high-accuracy, low-complexity coarse-grained numerical simulations. As an example, we derive the coarse-grained description for a chain of biochemical reactions and show that the coarse-grained and the microscopic simulations agree, but the former is 3 orders of magnitude faster. PMID:19525397

Prostate cancer: role of pretreatment multiparametric 3-T MRI in predicting biochemical recurrence after radical prostatectomy.

PubMed

Park, Jung Jae; Kim, Chan Kyo; Park, Sung Yoon; Park, Byung Kwan; Lee, Hyun Moo; Cho, Seong Whi

2014-05-01

The purpose of this study is to retrospectively investigate whether pretreatment multiparametric MRI findings can predict biochemical recurrence in patients who underwent radical prostatectomy (RP) for localized prostate cancer. In this study, 282 patients with biopsy-proven prostate cancer who received RP underwent pretreatment MRI using a phased-array coil at 3 T, including T2-weighted imaging (T2WI), diffusion-weighted imaging (DWI), and dynamic contrast-enhanced MRI (DCE-MRI). MRI variables included apparent tumor presence on combined imaging sequences, extracapsular extension, and tumor size on DWI or DCE-MRI. Clinical variables included baseline prostate-specific antigen (PSA) level, clinical stage, and Gleason score at biopsy. The relationship between clinical and imaging variables and biochemical recurrence was evaluated using Cox regression analysis. After a median follow-up of 26 months, biochemical recurrence developed in 61 patients (22%). Univariate analysis revealed that all the imaging and clinical variables were significantly associated with biochemical recurrence (p < 0.01). On multivariate analysis, however, baseline PSA level (p = 0.002), Gleason score at biopsy (p = 0.024), and apparent tumor presence on combined T2WI, DWI, and DCE-MRI (p = 0.047) were the only significant independent predictors of biochemical recurrence. Of the independent predictors, apparent tumor presence on combined T2WI, DWI, and DCE-MRI showed the highest hazard ratio (2.38) compared with baseline PSA level (hazard ratio, 1.05) and Gleason score at biopsy (hazard ratio, 1.34). The apparent tumor presence on combined T2WI, DWI, and DCE-MRI of pretreatment MRI is an independent predictor of biochemical recurrence after RP. This finding may be used to construct a predictive model for biochemical recurrence after surgery.

Chemical and Biochemical Approaches in the Study of Histone Methylation and Demethylation

PubMed Central

Li, Keqin Kathy; Luo, Cheng; Wang, Dongxia; Jiang, Hualiang; Zheng, Y. George

2014-01-01

Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and provide information otherwise difficulty to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation (ChIP), chemical ligation, mass spectrometry (MS), biochemical assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of the biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic application in the clinic. PMID:22777714

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Bingke; Cheng, Hui-Chun; Brautigam, Chad A.

Vibrio parahaemolyticus protein L (VopL) is an actin nucleation factor that induces stress fibers when injected into eukaryotic host cells. VopL contains three N-terminal Wiskott-Aldrich homology 2 (WH2) motifs and a unique VopL C-terminal domain (VCD). We describe crystallographic and biochemical analyses of filament nucleation by VopL. The WH2 element of VopL does not nucleate on its own and requires the VCD for activity. The VCD forms a U-shaped dimer in the crystal, stabilized by a terminal coiled coil. Dimerization of the WH2 motifs contributes strongly to nucleation activity, as do contacts of the VCD to actin. Our data leadmore » to a model in which VopL stabilizes primarily lateral (short-pitch) contacts between actin monomers to create the base of a two-stranded filament. Stabilization of lateral contacts may be a common feature of actin filament nucleation by WH2-based factors.« less

Modelling biochemical reaction systems by stochastic differential equations with reflection.

PubMed

Niu, Yuanling; Burrage, Kevin; Chen, Luonan

2016-05-07

In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effect of race on biochemical disease-free outcome in patients with prostate cancer treated with definitive radiation therapy in an equal-access health care system: radiation oncology report of the Department of Defense Center for Prostate Disease Research.

PubMed

Johnstone, Peter A S; Kane, Christopher J; Sun, Leon; Wu, Hongyu; Moul, Judd W; McLeod, David G; Martin, Douglas D; Kusuda, Leo; Lance, Raymond; Douglas, Robert; Donahue, Timothy; Beat, Michael G; Foley, John; Baldwin, Dalton; Soderdahl, Douglas; Do, Jason; Amling, Christopher L

2002-11-01

To report on the first collaboration of the Department of Defense Center for Prostate Disease Research concerned with the relationship between African American race and biochemical disease-free outcomes after definitive radiation therapy. Information from the medical records of 1,806 patients (1,349 white, 343 African American, 42 of "other" races, and 72 of "unknown" races) treated with definitive radiation therapy between 1973 and 2000 was reviewed. Patients receiving adjuvant hormonal therapy or postoperative adjuvant or salvage radiation therapy were excluded. Biochemical failure was calculated in over 96% of cases by using ASTRO criteria; patients with fewer than three follow-up visits were considered to have biochemical failure with a prostate-specific antigen (PSA) value more than 10-fold the previous value or with any value greater than 50.0 ng/mL. Median radiation therapy doses were similar. The median follow-up was 58.4 months. Kaplan-Meier tests, Cox proportional hazards regression analysis, and log-rank tests were used for data analysis. There was no statistically significant difference in biochemical disease-free survival according to race when patients were stratified according to T stage. African American race conferred a negative prognosis for patients with lesions of Gleason biopsy score 7 (P =.004) but not for patients with lesions of Gleason score 2-4 (P =.14), 5-6 (P =.79), or 8-10 (P =.86). Similarly, African American race conferred a negative prognosis in patients with PSA values of 20.1-50.0 ng/mL (P =.01) at presentation but not in patients with PSA values less than or equal to 4.0 ng/mL (P =.84), 4.1-10.0 ng/mL (P =.71), 10.1-20.0 ng/mL (P =.75), or above 50.0 ng/mL (P =.15) at presentation. At multivariate analysis, race was not a statistically significant predictor of outcome. In the equal-access health care system of the Department of Defense, African American race is not associated with a consistently negative prognosis in patients

Reye's Syndrome: A Review of Research Studies.

ERIC Educational Resources Information Center

Lopez, Thomas P.; And Others

1982-01-01

Clinical and pathological studies of Reye's syndrome indicate that symptoms range from influenza-related encephalitis-type disease to cranial pressure, cerebral edema, hemorrhage, and coma. Biochemical research on the blood, ammonia, and the liver is increasing in sophistication, and hopes for future insight into the etiology of Reye's syndrome…

A Diagrammatic Language for Biochemical Networks

NASA Astrophysics Data System (ADS)

Maimon, Ron

2002-03-01

I present a diagrammatic language for representing the structure of biochemical networks. The language is designed to represent modular structure in a computational fasion, with composition of reactions replacing functional composition. This notation is used to represent arbitrarily large networks efficiently. The notation finds its most natural use in representing biological interaction networks, but it is a general computing language appropriate to any naturally occuring computation. Unlike lambda-calculus, or text-derived languages, it does not impose a tree-structure on the diagrams, and so is more effective at representing biological fucntion than competing notations.

Interaction of metal oxide nanoparticles with higher terrestrial plants: Physiological and biochemical aspects.

PubMed

Du, Wenchao; Tan, Wenjuan; Peralta-Videa, Jose R; Gardea-Torresdey, Jorge L; Ji, Rong; Yin, Ying; Guo, Hongyan

2017-01-01

Multiple applications of metal oxide nanoparticles (MONPs) could result in their accumulation in soil, threatening higher terrestrial plants. Several reports have shown the effects of MONPs on plants. In this review, we analyze the most recent reports about the physiological and biochemical responses of plants to stress imposed by MONPs. Findings demonstrate that MONPs may be taken up and accumulated in plant tissues causing adverse or beneficial effects on seed germination, seedling elongation, photosynthesis, antioxidative stress response, agronomic, and yield characteristics. Given the importance of determining the potential risks of MONPs on crops and other terrestrial higher plants, research questions about field long-term conditions, transgenernational phytotoxicity, genotype specific sensitivity, and combined pollution problems should be considered. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Official Positions for FRAX® clinical regarding biochemical markers from Joint Official Positions Development Conference of the International Society for Clinical Densitometry and International Osteoporosis Foundation on FRAX®.

PubMed

McCloskey, Eugene V; Vasikaran, Samuel; Cooper, Cyrus

2011-01-01

The best indirect evidence that increased bone turnover contributes to fracture risk is the fact that most of the proven therapies for osteoporosis are inhibitors of bone turnover. The evidence base that we can use biochemical markers of bone turnover in the assessment of fracture risk is somewhat less convincing. This relates to natural variability in the markers, problems with the assays, disparity in the statistical analyses of relevant studies and the independence of their contribution to fracture risk. More research is clearly required to address these deficiencies before biochemical markers might contribute a useful independent risk factor for inclusion in FRAX(®). Copyright © 2011. Published by Elsevier Inc.

Can Stress-Induced Biochemical Differences drive Variation in the Hydrogen Isotope Composition of Leaf Wax n-Alkanes from Terrestrial Higher Plants?

NASA Astrophysics Data System (ADS)

Eley, Y.; Pedentchouk, N.; Dawson, L.

2014-12-01

Recent research has identified that interspecies variation in leaf wax n-alkane 2H/1H from plants growing at the same geographical location can exceed 100‰. These differences cannot easily be explained by mechanisms that influence the isotopic composition of leaf water. Biochemical processes are therefore likely to drive some of this variability. Currently, however, little is known about the relative importance of different biochemical processes in shaping n-alkane hydrogen isotope composition. To explore this issue, we combined n-alkane δ2H analysis with measurements of: (i) the percentage content of leaf C and N; and (ii) foliar δ15N, from seven plants growing at Stiffkey salt marsh, Norfolk, UK. These species differ biochemically in respect of the protective compounds they produce under salt or water stressed conditions, with monocots generally producing more carbohydrates, and dicots producing more nitrogenous compounds. We found that monocots had higher %C, while dicots had higher %N and 15N-enriched leaf tissue. We identified a systematic relationship between the nature of the dominant protective compound produced (carbohydrate vs. nitrogenous) and n-alkane 2H/1H: species with a greater proportion of carbohydrates have more negative δ2H values. These findings might imply that shifts in the relative contribution of H to pyruvate from NADPH (2H-depleted) and recycled carbohydrates (2H-enriched) can influence n-alkane δ2H. The 2H-depletion of monocot n-alkanes relative to dicots may therefore be due to a greater proportion of NADPH-derived H incorporated into pyruvate because of their enhanced demand for carbohydrates. The production of protective compounds in plant species is a common response to a range of abiotic stresses (e.g. high UV irradiation, drought, salinity, high/low temperature). Species-specific biochemical responses to stress could therefore influence n-alkane 2H/1H across a range of habitats. This study highlights the importance of detailed

Biochemical and biomechanical characterisation of equine cervical facet joint cartilage.

PubMed

O'Leary, S A; White, J L; Hu, J C; Athanasiou, K A

2018-04-15

The equine cervical facet joint is a site of significant pathology. Located bilaterally on the dorsal spine, these diarthrodial joints work in conjunction with the intervertebral disc to facilitate appropriate spinal motion. Despite the high prevalence of pathology in this joint, the facet joint is understudied and thus lacking in viable treatment options. The goal of this study was to characterise equine facet joint cartilage and provide a comprehensive database describing the morphological, histological, biochemical and biomechanical properties of this tissue. Descriptive cadaver studies. A total of 132 facet joint surfaces were harvested from the cervical spines of six skeletally mature horses (11 surfaces per animal) for compiling biomechanical and biochemical properties of hyaline cartilage of the equine cervical facet joints. Gross morphometric measurements and histological staining were performed on facet joint cartilage. Creep indentation and uniaxial strain-to-failure testing were used to determine the biomechanical compressive and tensile properties. Biochemical assays included quantification of total collagen, sulfated glycosaminoglycan and DNA content. The facet joint surfaces were ovoid in shape with a flat articular surface. Histological analyses highlighted structures akin to articular cartilage of other synovial joints. In general, biomechanical and biochemical properties did not differ significantly between the inferior and superior joint surfaces as well as among spinal levels. Interestingly, compressive and tensile properties of cervical facet articular cartilage were lower than those of articular cartilage from other previously characterised equine joints. Removal of the superficial zone reduced the tissue's tensile strength, suggesting that this zone is important for the tensile integrity of the tissue. Facet surfaces were sampled at a single, central location and do not capture the potential topographic variation in cartilage properties. This

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

PubMed Central

Shao, Zengyi; Zhao, Hua; Zhao, Huimin

2009-01-01

The assembly of large recombinant DNA encoding a whole biochemical pathway or genome represents a significant challenge. Here, we report a new method, DNA assembler, which allows the assembly of an entire biochemical pathway in a single step via in vivo homologous recombination in Saccharomyces cerevisiae. We show that DNA assembler can rapidly assemble a functional d-xylose utilization pathway (∼9 kb DNA consisting of three genes), a functional zeaxanthin biosynthesis pathway (∼11 kb DNA consisting of five genes) and a functional combined d-xylose utilization and zeaxanthin biosynthesis pathway (∼19 kb consisting of eight genes) with high efficiencies (70–100%) either on a plasmid or on a yeast chromosome. As this new method only requires simple DNA preparation and one-step yeast transformation, it represents a powerful tool in the construction of biochemical pathways for synthetic biology, metabolic engineering and functional genomics studies. PMID:19074487

A pretreatment nomogram for prediction of biochemical failure after primary cryoablation of the prostate.

PubMed

Elshafei, Ahmed; Kovac, Evan; Dhar, Nivedita; Levy, David; Polascik, Thomas; Mouraviev, Vladimir; Yu, Changhong; Jones, J Stephen

2015-09-01

To create a predictive nomogram for biochemical failure following primary whole-gland cryoablation of the prostate for localized prostate cancer (LPCa). We retrospectively analyzed 2,242 patients from the Cryo On-Line Database (COLD) who were treatment naive and had undergone primary whole gland cryoablation of the prostate for biopsy-confirmed LPCa. Kaplan-Meier (KM) curves estimating 5 year biochemical progression-free survival (bPFS) were generated. Multivariable Cox proportional hazards analysis (CoxPH) was performed in order to construct the nomogram. The nomogram was internally validated using the bootstrap technique. Overall, the KM estimated 5 year bPFS was 72.8%. Stratified by D'Amico risk, The KM estimated 5 year bPFS was 82.6%, 71.1%, and 57.8% for low-, intermediate-, and high-risk groups, respectively. Statistically significant predictors of biochemical outcomes from CoxPH analysis were pre-treatment prostate specific antigen (PTPSA) (P < 0.001), total prostate volume (P = 0.004), clinical stage (P = 0.034), and Gleason score (0.004). A nomogram for predicted 5 year biochemical progression free probability was constructed with a concordance index of 0.652. An online risk calculator was also generated. To the best of our knowledge, this is the first predictive nomogram for biochemical outcomes after primary whole gland cryoablation of the prostate using socio-demographic, pretreatment, clinical, and prostate biopsy data. Our nomogram and online risk calculator can guide both patients and urologists for shared decision making regarding definitive treatment options. © 2015 Wiley Periodicals, Inc.

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

PubMed

Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

2011-09-01

Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

Checklist and distribution maps of the blow flies of Venezuela (Diptera, Calliphoridae, Mesembrinellidae)

PubMed Central

Velásquez, Yelitza; Martínez-Sánchez, Ana Isabel; Thomas, Arianna; Rojo, Santos

2017-01-01

Abstract A checklist of the 39 species of blow flies (Calliphoridae and Mesembrinellidae) so far known to occur in Venezuela is provided, based on a thorough literature review and the examination of ca. 500 specimens deposited in the main entomological collections of the country. Data from the literature and museum collections were used to generate distribution maps for 37 species. Three species are recorded from Venezuela for the first time: Chrysomya putoria (Wiedemann, 1830), Mesembrinella spicata Aldrich, 1925 and Mesembrinella umbrosa Aldrich, 1922. PMID:28228670

Tank cultivation of the red algae Palmaria mollis: Effects of nutrients on growth rate, biochemical quality, and epiphytic growth

NASA Astrophysics Data System (ADS)

Ben, D.; Langdon, C. J.

2016-02-01

Pacific dulse (Palmaria mollis) is a candidate for aquaculture production in Oregon due to its high protein content, fast growth rate, and ability to fare in cold water conditions. Current cultivation methods use the F/2 medium to supply nutrients to macroalgae cultures. The F/2 medium is a costly mixture of nitrate, phosphate, trace metals and vitamins. The F/2 medium has been the standard for microalgae cultivation, but research has lacked on the necessity of all or part of this mixture for macroalgae cultivation. This study is designed to contribute to the development of Pacific dulse cultivation by measuring how different fertilizer regimens affect the growth, biochemical composition, and quality of Palmaria mollis (C-3 variety) in hopes to reduce the production cost. I hypothesis that dulse will not require additional nutrients during summer cultivation, due to summer upwelling conditions. Experiments were conducted in a flow-through water system, controlling for flow rate, stocking density, and nutrient supplementation. To test this, two replicates of four nutrient regimes were organized: no supplemental nutrients, all nutrients (standard F/2 medium), nitrate/phosphate only, and nitrate/phosphate with trace metals. Each tank was monitored weekly for color quality, epiphytic growth, specific growth rate, production and a final biochemical analysis. This study has preliminarily concluded that supplemental nutrients have no significant effect on production or biochemical quality, but does have an effect quality of epiphytic growth.

Biochemical component identification by plasmonic improved whispering gallery mode optical resonance based sensor

NASA Astrophysics Data System (ADS)

Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Saetchnikov, Anton V.; Schweiger, Gustav; Ostendorf, Andreas

2014-05-01

Experimental data on detection and identification of variety of biochemical agents, such as proteins, microelements, antibiotic of different generation etc. in both single and multi component solutions under varied in wide range concentration analyzed on the light scattering parameters of whispering gallery mode optical resonance based sensor are represented. Multiplexing on parameters and components has been realized using developed fluidic sensor cell with fixed in adhesive layer dielectric microspheres and data processing. Biochemical component identification has been performed by developed network analysis techniques. Developed approach is demonstrated to be applicable both for single agent and for multi component biochemical analysis. Novel technique based on optical resonance on microring structures, plasmon resonance and identification tools has been developed. To improve a sensitivity of microring structures microspheres fixed by adhesive had been treated previously by gold nanoparticle solution. Another technique used thin film gold layers deposited on the substrate below adhesive. Both biomolecule and nanoparticle injections caused considerable changes of optical resonance spectra. Plasmonic gold layers under optimized thickness also improve parameters of optical resonance spectra. Biochemical component identification has been also performed by developed network analysis techniques both for single and for multi component solution. So advantages of plasmon enhancing optical microcavity resonance with multiparameter identification tools is used for development of a new platform for ultra sensitive label-free biomedical sensor.

Metstoich--Teaching Quantitative Metabolism and Energetics in Biochemical Engineering

ERIC Educational Resources Information Center

Wong, Kelvin W. W.; Barford, John P.

2010-01-01

Metstoich, a metabolic calculator developed for teaching, can provide a novel way to teach quantitative metabolism to biochemical engineering students. It can also introduce biochemistry/life science students to the quantitative aspects of life science subjects they have studied. Metstoich links traditional biochemistry-based metabolic approaches…

A MULTILAYER BIOCHEMICAL DRY DEPOSITION MODEL 2. MODEL EVALUATION

EPA Science Inventory

The multilayer biochemical dry deposition model (MLBC) described in the accompanying paper was tested against half-hourly eddy correlation data from six field sites under a wide range of climate conditions with various plant types. Modeled CO₂, O₃, SO_2<...

The Stereochemistry of Biochemical Molecules: A Subject to Revisit

ERIC Educational Resources Information Center

Centelles, Josep J.; Imperial, Santiago

2005-01-01

Although Fischer's convention for stereoisomers is useful for simple molecules, the stereochemistry of complex biochemical molecules is often poorly indicated in textbooks. This article reports on errors in stereochemistry of complex hydrosoluble vitamin B12 molecule. Twenty-five popular biochemistry textbooks were examined for their treatment of…

Usefulness of biochemical remission and transient elastography in monitoring disease course in autoimmune hepatitis.

PubMed

Hartl, Johannes; Ehlken, Hanno; Sebode, Marcial; Peiseler, Moritz; Krech, Till; Zenouzi, Roman; von Felden, Johann; Weiler-Normann, Christina; Schramm, Christoph; Lohse, Ansgar W

2017-11-24

Liver fibrosis regression but also progression may occur in patients with autoimmune hepatitis (AIH) under treatment. There is a need for non-invasive surrogate markers for fibrosis development in AIH to better guide immunosuppressive treatment. The aims of the study were to assess the impact of complete biochemical remission defined as normalisation of aminotransferases and IgG on histological activity and fibrosis development, and the value of repeat transient elastography (TE) measurement for monitoring disease progression in AIH. A total of 131 liver biopsies from 60 patients with AIH and more than 900 TE from 125 patients with AIH, 130 with primary biliary cholangitis (PBC) and 100 with primary sclerosing cholangitis (PSC), were evaluated. Time intervals between TE were at least 12 months. Patients with AIH were treated for at least six months at first TE. In contrast to PBC and PSC, a decrease of liver stiffness (LS) was observed in the whole group of patients with AIH (-6.2%/year; 95% CI -12.6% to -0.2%; p = 0.04). The largest decrease of LS was observed in patients with severe fibrosis at baseline (F4: -11.7%/year; 95% CI -19% to -3.5%; p = 0.006). Complete biochemical remission was strongly linked to regression of LS ("remission": -7.5%/year vs. "no remission": +1.7%/year, p <0.001). Similarly, complete biochemical remission predicted low histological disease activity and was the only independent predictor for histological fibrosis regression (relative risk3.66; 95% CI1.54-10.2; p = 0.001). Patients with F3/F4-fibrosis, who remained in biochemical remission showed a considerable decrease of fibrosis stage (3.7 ± 0.5 to 1.8 ± 1.7; p = 0.007) on histological follow-up. This study demonstrates that complete biochemical remission is a reliable predictor of a good prognosis in AIH and leads to fibrosis regression that can be monitored by TE. Autoimmune hepatitis is an inflammatory disease of the liver, which often progresses to

Long-term treatment outcomes of acromegaly patients presenting biochemically-uncontrolled at a tertiary pituitary center.

PubMed

Carmichael, John D; Broder, Michael S; Cherepanov, Dasha; Chang, Eunice; Mamelak, Adam; Said, Qayyim; Neary, Maureen P; Bonert, Vivien

2017-08-04

Acromegaly is a rare, slowly progressive disorder resulting from excessive growth hormone (GH) production by a pituitary somatotroph tumor. The objective of this study was to examine acromegaly treatment outcomes during long-term care at a specialized pituitary center in patients presenting with lack of biochemical control. Data came from an acromegaly registry at the Cedars-Sinai Medical Center Pituitary Center (center). Acromegaly patients included in this study were those who presented biochemically-uncontrolled for care at the center. Biochemical control status, based on serum insulin-like growth factor-1 values, was determined at presentation and at study end. Patient characteristics and acromegaly treatments were reported before and after presentation by presenting treatment status and final biochemical control status. Data on long-term follow-up were recorded from 1985 through June 2013. Seventy-four patients presented uncontrolled: 40 untreated (54.1%) and 34 (45.9%) previously-treated. Mean (SD) age at diagnosis was 43.2 (14.7); 32 (43.2%) were female patients. Of 65 patients with tumor size information, 59 (90.8%) had macroadenomas. Prior treatments among the 34 previously-treated patients were pituitary surgery alone (47.1%), surgery and medication (41.2%), and medication alone (11.8%). Of the 40 patients without prior treatment, 82.5% achieved control by study end. Of the 34 with prior treatment, 50% achieved control by study end. This observational study shows that treatment outcomes of biochemically-uncontrolled acromegaly patients improve with directed care, particularly for those that initially present untreated. Patients often require multiple modalities of treatment, many of which are offered with the highest quality at specialized pituitary centers. Despite specialized care, some patients were not able to achieve biochemical control with methods of treatment that were available at the time of their treatment, showing the need for additional

Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species.

PubMed

Santos, André S; Ramos, Rommel T; Silva, Artur; Hirata, Raphael; Mattos-Guaraldi, Ana L; Meyer, Roberto; Azevedo, Vasco; Felicori, Liza; Pacheco, Luis G C

2018-05-11

Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov Models (HMMs) to detect enzymes participating in the various pathways and performed ab initio protein structure modeling and molecular docking to confirm specific results. We found a differential distribution among the various strains of genes that code for some important enzymes, such as beta-phosphoglucomutase and fructokinase, and also for individual components of carbohydrate transport systems, including the fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) and the ribose-specific ATP-binging cassette (ABC) transporter. Horizontal gene transfer plays a role in the biochemical variability of the isolates, as some genes needed for sucrose fermentation were seen to be present in genomic islands. Noteworthy

A review of the management of positive biochemical screening for phaeochromocytoma and paraganglioma: a salutary tale.

PubMed

Garrahy, A; Casey, R; Wall, D; Bell, M; O'Shea, P M

2015-07-01

Phaeochromocytomas (PC) and paragangliomas (PGL) are rare neuroendocrine tumours of chromaffin cells. Diagnosis depends on biochemical evidence of excessive production of catecholamines. This is straightforward when test results are orders of magnitude above the concentrations expected in healthy individuals and those with essential hypertension. Equivocal results pose a management dilemma. We reviewed biochemical screens that were positive and the ensuing management for PC/PGL at our institution. The objective was to inform the development of a standardised approach to investigation and clinical follow-up. All records of positive biochemical screening for PC/PGL were extracted from the laboratory information system between January 2004 and June 2012. Clinical notes of patients with positive results were reviewed. A total of 2749 biochemical screens were performed during the evaluation period. Of these, 106 (3.9%) performed on 82 patients were positive. Chart review determined that 12/82 patients had histologically confirmed PC/PG. Of the 70 patients remaining, the most common indication for biochemical screening was hypertension and the medical subspecialty most frequently requesting the test was Endocrinology. The primary team carried out repeat testing on 35/70 (50%) patients and in 29 results normalised. Notably, 35/70 (50%) patients did not have any follow-up of positive test results. This study highlights the necessity for a standardised diagnostic protocol for PC/PGL. We suggest that appropriate follow-up of borderline-elevated results should first include repeat biochemical testing. This should be performed under standardised pre-analytical conditions and where possible off all potentially interfering medications, measuring plasma free metadrenalines. © 2015 John Wiley & Sons Ltd.

Differences in the API 20E biochemical patterns of clinical and environmental Vibrio parahaemolyticus isolates.

PubMed

Martinez-Urtaza, Jaime; Lozano-Leon, Antonio; Viña-Feas, Alejandro; de Novoa, Jacobo; Garcia-Martin, Oscar

2006-02-01

Genetic differences in clinical and environmental strains of Vibrio parahaemolyticus have been widely used as criteria in identifying pathogenic isolates. However, few studies have been carried out to assess the differences in biochemical characteristics of V. parahaemolyticus isolates from human and environmental sources. We compared the biochemical profiles obtained by the characterization of V. parahaemolyticus isolates from human infections and the marine environment using the API 20E system. Environmental and clinical isolates showed significant differences in the gelatin and arabinose tests. Additionally, clinical isolates were correctly identified according to the API 20E profile using 0.85% NaCl diluent, but they presented nonspecific profiles with 2% NaCl diluent. In contrast, use of 2% NaCl diluent facilitated correct identification of the environmental isolates. Clinical isolates showed significant differences in up to five biochemical tests with respect to the API 20E database. The API 20E system is widely used in routine identification of bacteria in clinical laboratories, and this discrepancy in an important number of biochemical tests may lead to misidentification of V. parahaemolyticus infection.

A biochemical protocol for the isolation and identification of current species of Vibrio in seafood.

PubMed

Ottaviani, D; Masini, L; Bacchiocchi, S

2003-01-01

We report a biochemical method for the isolation and identification of the current species of vibrios using just one operative protocol. The method involves an enrichment phase with incubation at 30 degrees C for 8-24 h in alkaline peptone water and an isolation phase on thiosulphate-citrate-salt sucrose agar plates incubating at 30 degrees C for 24 h. Four biochemical tests and Alsina's scheme were performed for genus and species identification, respectively. All biochemical tests were optimized as regards conditions of temperature, time of incubation and media composition. The whole standardized protocol was always able to give a correct identification when applied to 25 reference strains of Vibrio and 134 field isolates. The data demonstrated that the assay method allows an efficient recovery, isolation and identification of current species of Vibrio in seafood obtaining results within 2-7 days. This method based on biochemical tests could be applicable even in basic microbiology laboratories, and can be used simultaneously to isolate and discriminate all clinically relevant species of Vibrio.

Hereditary rickets. How genetic alterations explain the biochemical and clinical phenotypes.

PubMed

Papadopoulou, Anna; Gole, Evaggelia; Nicolaidou, Polyxeni

2013-12-01

The reemergence of vitamin D deficiency in the industrialized countries resurrects the "threat" of nutritional rickets, especially among pediatric populations, a fact that may lead to underdiagnosis of hereditary rickets. Today, hereditary rickets may be subdivided into two main groups according to their biochemical profile: the one associated with defects in vitamin D synthesis and action and the second associated with abnormal phosphorus metabolism. The classification of the patients in a particular group of hereditary rickets is determinative of the treatment to follow. This review, through the recent advances on vitamin D and P metabolism, discusses the molecular and biochemical defects associated to each group of inherited rickets, as well as the clinical phenotypes and the recommended therapeutic approaches.

The Glymphatic Hypothesis of Glaucoma: A Unifying Concept Incorporating Vascular, Biomechanical, and Biochemical Aspects of the Disease

PubMed Central

De Groot, Veva; Van Dam, Debby; Audenaert, Kurt; Killer, Hanspeter Esriel; De Deyn, Peter Paul

2017-01-01

The pathophysiology of primary open-angle glaucoma is still largely unknown, although a joint contribution of vascular, biomechanical, and biochemical factors is widely acknowledged. Since glaucoma is a leading cause of irreversible blindness worldwide, exploring its underlying pathophysiological mechanisms is extremely important and challenging. Evidence from recent studies appears supportive of the hypothesis that a “glymphatic system” exists in the eye and optic nerve, analogous to the described “glymphatic system” in the brain. As discussed in the present paper, elucidation of a glymphatic clearance pathway in the eye could provide a new unifying hypothesis of glaucoma that can incorporate many aspects of the vascular, biomechanical, and biochemical theories of the disease. It should be stressed, however, that the few research data currently available cannot be considered as proof of the existence of an “ocular glymphatic system” and that much more studies are needed to validate this possibility. Even though nothing conclusive can yet be said, the recent reports suggesting a paravascular transport system in the eye and optic nerve are encouraging and, if confirmed, may offer new perspectives for the development of novel diagnostic and therapeutic strategies for this devastating disorder. PMID:28948167

The Glymphatic Hypothesis of Glaucoma: A Unifying Concept Incorporating Vascular, Biomechanical, and Biochemical Aspects of the Disease.

PubMed

Wostyn, Peter; De Groot, Veva; Van Dam, Debby; Audenaert, Kurt; Killer, Hanspeter Esriel; De Deyn, Peter Paul

2017-01-01

The pathophysiology of primary open-angle glaucoma is still largely unknown, although a joint contribution of vascular, biomechanical, and biochemical factors is widely acknowledged. Since glaucoma is a leading cause of irreversible blindness worldwide, exploring its underlying pathophysiological mechanisms is extremely important and challenging. Evidence from recent studies appears supportive of the hypothesis that a "glymphatic system" exists in the eye and optic nerve, analogous to the described "glymphatic system" in the brain. As discussed in the present paper, elucidation of a glymphatic clearance pathway in the eye could provide a new unifying hypothesis of glaucoma that can incorporate many aspects of the vascular, biomechanical, and biochemical theories of the disease. It should be stressed, however, that the few research data currently available cannot be considered as proof of the existence of an "ocular glymphatic system" and that much more studies are needed to validate this possibility. Even though nothing conclusive can yet be said, the recent reports suggesting a paravascular transport system in the eye and optic nerve are encouraging and, if confirmed, may offer new perspectives for the development of novel diagnostic and therapeutic strategies for this devastating disorder.

Understanding alterations on blood and biochemical parameters in athletes that use dietary supplements, steroids and illicit drugs.

PubMed

Bordin, Dayanne Mozaner; Bettim, Bárbara Beltrame; Perdona, Gleici Castro; de Campos, Eduardo Geraldo; De Martinis, Bruno Spinosa

2017-02-01

In recent years it was verified there are an alarming growing number of teenagers and young adults using a combination of dietary supplements (DS) anabolic androgenic steroids (AAS) and drugs of abuse. This practice is used to improve physical fitness and appearance, may cause serious side effects. This article shows the alterations in the hematological and renal function parameters associate with these substances in 40 athletes. This research involved three steps: 1-the administration of a self-completion questionnaire ; 2-the assessment of hematological and biochemical parameters of renal function and; 3-toxicological urinalysis. Hematological and biochemical tests were conducted in an accredited laboratory and the toxicological urinalysis was validated in our laboratory using liquid-liquid extraction (LLE) and gas chromatography-mass spectrometry (GC-MS). The testosterone levels in the participants who consumed steroids increased 20-60% and alterations in serum creatinine, urea and uric reached values of up to 1.9; 60.6 and 7.5mg/dL, respectively. The toxicological urinalysis supports self-reports confirming the use of AAS and recreational drugs, putting at risk the health of those athletes increasing the chances of kidney diseases. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems

PubMed Central

Pischel, Dennis; Sundmacher, Kai; Flassig, Robert J.

2017-01-01

Abstract Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples. The method relies on the combination of the sigma point approach to describe extrinsic and external variability and the τ-leaping algorithm to account for the stochasticity due to probabilistic reactions. The comparison of our method to extensive Monte Carlo calculations demonstrates an immense computational advantage while losing an acceptable amount of accuracy. Additionally, the application to parameter optimization problems in stochastic biochemical reaction networks is shown, which is rarely applied due to its huge computational burden. To give further insight, a MATLAB script is provided including the proposed method applied to a simple toy example of gene expression. Availability and implementation: MATLAB code is available at Bioinformatics online. Contact: flassig@mpi-magdeburg.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881987

Tissue Residues, Hematological and Biochemical Effects of Tilmicosin in Broiler Chicken

PubMed Central

Elsayed, Mossad; Elkomy, Ashraf; Morad, Mohamed

2014-01-01

The aim of this study was to determine the blood and tissue concentrations profile and effect of tilmicosin on some hematological and biochemical parameters in broiler chicken. Fifty clinically healthy Hubbard chickens were orally administered 25 mg/kg BW of tilmicosin once daily for 5 consecutive days. Tissue residues of tilmicosin in slaughtered healthy chicken could not be detected by microbiological assay in all tested tissues except in lung (at 96 hours) and liver and kidneys (at 72 hours) after last administration. Tilmicosin caused temporary decrease in the RBCs and WBCs counts and has no effect on hemoglobin (Hb) and packed cell volume concentration (PCV). Also, the effect of tilmicosin on some biochemical parameters was as follows: the concentrations of creatinine, uric acid, electrolytes (sodium, potassium, and calcium), glucose, AST, ALT, ALP, and HDL-cholesterol in the serum of treated chicken did not change in response to the repeated oral administration of tilmicosin. There were only a temporary significant decrease in total protein and albumin concentrations and a significant increase in cholesterol and triglycerides concentrations. Chicken must not be slaughtered before 4 days from the stopping of tilmicosin administration. Tilmicosin makes temporary changes on hematological and biochemical parameters in broiler chicken. PMID:24808972

Tissue residues, hematological and biochemical effects of tilmicosin in broiler chicken.

PubMed

Elsayed, Mossad; Elkomy, Ashraf; Aboubakr, Mohamed; Morad, Mohamed

2014-01-01

The aim of this study was to determine the blood and tissue concentrations profile and effect of tilmicosin on some hematological and biochemical parameters in broiler chicken. Fifty clinically healthy Hubbard chickens were orally administered 25 mg/kg BW of tilmicosin once daily for 5 consecutive days. Tissue residues of tilmicosin in slaughtered healthy chicken could not be detected by microbiological assay in all tested tissues except in lung (at 96 hours) and liver and kidneys (at 72 hours) after last administration. Tilmicosin caused temporary decrease in the RBCs and WBCs counts and has no effect on hemoglobin (Hb) and packed cell volume concentration (PCV). Also, the effect of tilmicosin on some biochemical parameters was as follows: the concentrations of creatinine, uric acid, electrolytes (sodium, potassium, and calcium), glucose, AST, ALT, ALP, and HDL-cholesterol in the serum of treated chicken did not change in response to the repeated oral administration of tilmicosin. There were only a temporary significant decrease in total protein and albumin concentrations and a significant increase in cholesterol and triglycerides concentrations. Chicken must not be slaughtered before 4 days from the stopping of tilmicosin administration. Tilmicosin makes temporary changes on hematological and biochemical parameters in broiler chicken.

Four biochemical tests for identification of probable enteroinvasive Escherichia coli strains.

PubMed

Flores Abuxapqui, J J; Suárez Hoil, G J; Heredia Navarrete, M R; Puc Franco, M A; Vivas Rosel, M L

1999-01-01

Enteroinvasive Escherichia coli (EIEC) share important features with Shigella spp., but EIEC strains are difficult to identify because their biochemical reactions are variable, and Sereny tests or other biological and molecular assays are expensive or hard to perform. The aim of this work was to detect probable enteroinvasive E. coli strains by using four biochemical tests, in children under 5 years of age with and without acute diarrhea. 330 strains of E. coli isolated from children with diarrhea, and 660 strains from children without diarrhea were studied. All strains were tested with the following tests: mucus , lysine and ornithine decarboxylase and motility. The strains which were negative to the four tests were tested by Sereny assay. Twelve strains (3.6%) isolated from children with diarrhea were negative to the tests proposed; eleven were lactose positive and only one was lactose negative. Three strains (0.5%) from children without diarrhea were negative to the tests proposed and were lactose positive. All the 15 strains (100%) were positive in Sereny assay. We recommend the use of these four biochemical tests for initial detection of EIEC strains, because their cost is very low and it is feasible carry out them in small diagnostic laboratories.

Rapid approach to analyze biochemical variation in rat organs by ATR FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Staniszewska, Emilia; Malek, Kamilla; Baranska, Malgorzata

2014-01-01

ATR FTIR spectra were collected from rat tissue homogenates (myocardium, brain, liver, lung, intestine, and kidney) to analyze their biochemical content. Based on the second derivative of an average spectral profile it was possible to assign bands e.g. to triglycerides and cholesterol esters, proteins, phosphate macromolecules (DNA, RNA, phospholipids, phosphorylated proteins) and others (glycogen, lactate). Peaks in the region of 1600-1700 cm-1 related to amide I mode revealed the secondary structure of proteins. The collected spectra do not characterize morphological structure of the investigated tissues but show their different composition. The comparison of spectral information gathered from FTIR spectra of the homogenates and those obtained previously from FTIR imaging of the tissue sections implicates that the presented here approach can be successfully employed in the investigations of biochemical variation in animal tissues. Moreover, it can be used in the pharmacological and pharmacokinetic studies to correlate the overall biochemical status of the tissue with the pathological changes it has undergone.

Biochemical correlates of neurosensory changes in weightlessness

NASA Technical Reports Server (NTRS)

Leach, Carolyn S.; Reschke, Millard F.

1989-01-01

The possible existence of a relationship between space motion sickness and chemical and biochemical variables measured in body fluids is studied. Clinical chemistry and endocrine measurements from blood and urine samples taken before and after Space Shuttle flights were analyzed along with the occurrence of SMS during flight and provocative testing before flight. Significant positive correlations were observed with serum chloride and significant negative correlations with serum phosphate, serum uric acid, and plasma thyroid stimulating hormone.

Percentage of positive prostate biopsies independently predicts biochemical outcome following radiation therapy for prostate cancer.

PubMed

Gabriele, Domenico; Garibaldi, Monica; Girelli, Giuseppe; Taraglio, Stefano; Duregon, Eleonora; Gabriele, Pietro; Guiot, Caterina; Bollito, Enrico

2016-06-01

This work aims to definitely show the ability of percentage of positive biopsy cores (%PC) to independently predict biochemical outcome beyond traditional pretreatment risk-factors in prostate cancer (PCa) patients treated with radiotherapy. A cohort of 2493 men belonging to the EUREKA-2 retrospective multicentric database on (PCa) and treated with external-beam radiation therapy (EBRT) as primary treatment comprised the study population (median follow-up 50 months). A Cox regression time to prostate-specific antigen (PSA) failure analysis was performed to evaluate the predictive power of %PC, both in univariate and multivariate settings, with age, pretreatment PSA, clinical-radiological staging, bioptic Gleason Score (bGS), RT dose and RT +/- ADT as covariates. P statistics for %PC is lower than 0.001 both in univariate and multivariate models. %PC as a continuous variable yields an AUC of 69% in ROC curve analysis for biochemical relapse. Four classes of %PC (1-20%, 21-50%, 51-80% and 81-100%) distinctly split patients for risk of biochemical relapse (overall log-rank test P<0.0001), with biochemical progression free survival (bPFS) at 5-years ranging from 88% to 58% and 10-years bPFS ranging from 80% to 38%. We strongly affirm the usefulness of %PC information beyond main risk factors (PSA, staging and bGS) in predicting biochemical recurrence after EBRT for PCa. The stratification of patients according to %PC may be valuable to further discriminate cases with favourable or adverse prognosis.

Biochemical and Molecular Biological Analyses of space-flown nematodes in Japan, the First International Caenorhabditis elegans Experiment (ICE-First)

PubMed Central

Higashibata, Akira; Higashitani, Atsushi; Adachi, Ryota; Kagawa, Hiroaki; Honda, Shuji; Honda, Yoko; Higashitani, Nahoko; Sasagawa, Yohei; Miyazawa, Yutaka; Szewczyk, Nathaniel J.; Conley, Catharine A.; Fujimoto, Nobuyoshi; Fukui, Keiji; Shimazu, Toru; Kuriyama, Kana; Ishioka, Noriaki

2008-01-01

The first International Caenorhabditis elegans Experiment (ICE-First) was carried out using a Russian Soyuz spacecraft from April 19-30, 2004. This experiment was a part of the program of the DELTA (Dutch Expedition for Life science Technology and Atmospheric research) mission, and the space agencies that participate in the International Space Station (ISS) program formed international research teams. A Japanese research team that conducted by Japan aerospace Exploration Agency (JAXA) investigated the following aspects of the organism: (1) whether meiotic chromosomal dynamics and apoptosis in the germ cells were normal under microgravity conditions, (2) the effect of the space flight on muscle cell development, and (3) the effect of the space flight on protein aggregation. In this article, we summarize the results of these biochemical and molecular biological analyses. PMID:19513185

Effect of Sulforaphane in Men with Biochemical Recurrence after Radical Prostatectomy.

PubMed

Cipolla, Bernard G; Mandron, Eric; Lefort, Jean Marc; Coadou, Yves; Della Negra, Emmanuel; Corbel, Luc; Le Scodan, Ronan; Azzouzi, Abdel Rahmene; Mottet, Nicolas

2015-08-01

Increases in serum levels of prostate-specific antigen (PSA) occur commonly in prostate cancer after radical prostatectomy and are designated "biochemical recurrence." Because the phytochemical sulforaphane has been studied extensively as an anticancer agent, we performed a double-blinded, randomized, placebo-controlled multicenter trial with sulforaphane in 78 patients (mean age, 69 ± 6 years) with increasing PSA levels after radical prostatectomy. Treatment comprised daily oral administration of 60 mg of a stabilized free sulforaphane for 6 months (M0-M6) followed by 2 months without treatment (M6-M8). The study was designed to detect a 0.012 log (ng/mL)/month decrease in the log PSA slope in the sulforaphane group from M0 to M6. The primary endpoint was not reached. For secondary endpoints, median log PSA slopes were consistently lower in sulforaphane-treated men. Mean changes in PSA levels between M6 and M0 were significantly lower in the sulforaphane group (+0.099 ± 0.341 ng/mL) than in placebo (+0.620 ± 1.417 ng/mL; P = 0.0433). PSA doubling time was 86% longer in the sulforaphane than in the placebo group (28.9 and 15.5 months, respectively). PSA increases >20% at M6 were significantly greater in the placebo group (71.8%) than in the sulforaphane group (44.4%); P = 0.0163. Compliance and tolerance were very good. Sulforaphane effects were prominent after 3 months of intervention (M3-M6). After treatment, PSA slopes from M6 to M8 remained the same in the 2 arms. Daily administration of free sulforaphane shows promise in managing biochemical recurrences in prostate cancer after radical prostatectomy. ©2015 American Association for Cancer Research.

Short-term effects of different organic amendments on soil chemical, biochemical and biological indicators

NASA Astrophysics Data System (ADS)

Mondelli, Donato; Aly, Adel; Yirga Dagnachew, Ababu; Piscitelli, Lea; Dumontet, Stefano; Miano, Teodoro

2014-05-01

The limited availability of animal manure and the high cost of good quality compost lead to difficult soil quality management under organic agriculture. Therefore, it is important to find out alternative organic soil amendments and more flexible strategies that are able to sustain crop productivity and maintain and enhance soil quality. A three years study was carried out in the experimental fields of the Mediterranean Agronomic Institute of Bari located in Valenzano, Italy. The main objective of this research is to investigate the effects of different fertility management strategies on soil quality in order to estimate the role of innovative matrices for their use in organic farming. The experiment consists of seven treatments applied to a common crop rotation. The treatments include alternative organic amendments (1- olive mill wastewater OMW, 2- residues of mushroom cultivation MUS, 3- coffee chaff COF), common soil amendments (4- compost COM, 5- faba bean intercropping LEG, 6- cow manure - MAN) and as a reference treatment (7- mineral fertilizer COV). The soil quality was assessed before and after the application of the treatments, through biological (microbial biomass carbon and nitrogen, soil respiration and metabolic quotient), biochemical (soil enzymatic activities: β-glucosidase, alkaline phospatase, urease, fluorescein diacetate (FDA) hydrolysis), and chemical (pH, soil organic carbon, soil organic matter, total nitrogen, available phosphorous, exchangeable potassium, dissolved organic carbon and total dissolved nitrogen) indicators. Based on the results obtained after the second year, all treatments were able to improve various soil chemical parameters as compared to mineral fertilizer. The incorporation of COF and OMW seemed to be more effective in improving soil total N and exchangeable K, while MAN significantly increased available P. All the amendments enhance dissolved organic C, soil respiration, microbial biomass and metabolic quotient as

[Morphological and biochemical adaptations to feeding in some herbivorous gastropods].

PubMed

Aliakrinskaia, O I

2005-01-01

Diet and feeding modes as well as morphological and biochemical adaptations to feeding are analyzed in herbivorous mollusks. The content of hemoglobin in radular tissues and weight properties of the radula are evaluated for different modes of feeding.

Breast cancer diagnosis: Imaging techniques and biochemical markers.

PubMed

Jafari, Seyed Hamed; Saadatpour, Zahra; Salmaninejad, Arash; Momeni, Fatemeh; Mokhtari, Mojgan; Nahand, Javid Sadri; Rahmati, Majid; Mirzaei, Hamed; Kianmehr, Mojtaba

2018-07-01

Breast cancer is a complex disease which is found as the second cause of cancer-associated death among women. Accumulating of evidence indicated that various factors (i.e., gentical and envirmental factors) could be associated with initiation and progression of breast cancer. Diagnosis of breast cancer patients in early stages is one of important aspects of breast cancer treatment. Among of various diagnosis platforms, imaging techniques are main diagnosis approaches which could provide valuable data on patients with breast cancer. It has been showed that various imaging techniques such as mammography, magnetic resonance imaging (MRI), positron-emission tomography (PET), Computed tomography (CT), and single-photon emission computed tomography (SPECT) could be used for diagnosis and monitoring patients with breast cancer in various stages. Beside, imaging techniques, utilization of biochemical biomarkers such as proteins, DNAs, mRNAs, and microRNAs could be employed as new diagnosis and therapeutic tools for patients with breast cancer. Here, we summarized various imaging techniques and biochemical biomarkers could be utilized as diagnosis of patients with breast cancer. Moreover, we highlighted microRNAs and exosomes as new diagnosis and therapeutic biomarkers for monitoring patients with breast cancer. © 2017 Wiley Periodicals, Inc.

Biochemical and genetic analysis of Leigh syndrome patients in Korea.

PubMed

Chae, Jong-Hee; Lee, Jin Sook; Kim, Ki Joong; Hwang, Yong Seung; Hirano, Michio

2008-06-01

Sixteen Korean patients with Leigh syndrome were identified at the Seoul National University Children's Hospital in 2001-2006. Biochemical or molecular defects were identified in 14 patients (87.5%). Thirteen patients had respiratory chain enzyme defects; 9 had complex I deficiency, and 4 had combined defects of complex I+III+IV. Based on the biochemical defects, targeted genetic studies in 4 patients with complex I deficiency revealed two heteroplasmic mitochondrial DNA mutations in ND genes. One patient had the mitochondrial DNA T8993G point mutation. No mitochondrial DNA defects were identified in 11 (68.7%) of our LS patients, who probably have mutations in nuclear DNA. Although a limited study based in a single tertiary medical center, our findings suggest that isolated complex I deficiency may be the most common cause of Leigh syndrome in Korea.

Dynamics of biochemical processes and redox conditions in geochemically linked landscapes of oligotrophic bogs

NASA Astrophysics Data System (ADS)

Inisheva, L. I.; Szajdak, L.; Sergeeva, M. A.

2016-04-01

The biological activity in oligotrophic peatlands at the margins of the Vasyugan Mire has been studied. It is shown found that differently directed biochemical processes manifest themselves in the entire peat profile down to the underlying mineral substrate. Their activity is highly variable. It is argued that the notion about active and inert layers in peat soils is only applicable for the description of their water regime. The degree of the biochemical activity is specified by the physical soil properties. As a result of the biochemical processes, a micromosaic aerobic-anaerobic medium is developed under the surface waterlogged layer of peat deposits. This layer contains the gas phase, including oxygen. It is concluded that the organic and mineral parts of peat bogs represent a single functional system of a genetic peat profile with a clear record of the history of its development.

Biochemical and physiological consequences of the Apollo flight diet.

NASA Technical Reports Server (NTRS)

Hander, E. W.; Leach, C. S.; Fischer, C. L.; Rummel, J.; Rambaut, P.; Johnson, P. C.

1971-01-01

Six male subjects subsisting on a typical Apollo flight diet for five consecutive days were evaluated for changes in biochemical and physiological status. Laboratory examinations failed to demonstrate any significant changes of the kind previously attributed to weightlessness, such as in serum electrolytes, endocrine values, body fluid, or hematologic parameters.

Biochemical and Structural Studies of RNA Modification and Repair

ERIC Educational Resources Information Center

Chan, Chio Mui

2009-01-01

RNA modification, RNA interference, and RNA repair are important events in the cell. This thesis presents three projects related to these three fields. By using both biochemical and structural methods, we characterized enzymatic activities of pseudouridine synthase TruD, solved the structure of "A. aeolicus" GidA, and reconstituted a novel…

Modularization of biochemical networks based on classification of Petri net t-invariants.

PubMed

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-02-08

Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find

Modularization of biochemical networks based on classification of Petri net t-invariants

PubMed Central

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-01-01

Background Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior. With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Methods Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted

Poly(dimethylsiloxane)-Polyurethane Elastomers: Synthesis and Properties of Segmented Copolymers and Related Zwitterionomers.

DTIC Science & Technology

1984-11-01

8217-niethylenediphenylene diisocyanate (MDI) which was chain extended with either 1,4-butanediol (BD) or N -me thyl diethanol ami ne . - g.. ( MDEA ). The MDEA -extended...and then vacuum distilled. Tetrahydrofuran %S 9 4 (Aldrich) was dehydrated over calcium hydride. N -methyldiethanolamne ( MDEA ) (Aldrich) at 97 percent...2CM 2- N -CM2CH OH or MOCH 2CM 2CM2CM2OH MDEA B -EL-MTPS-( -MDI-BD--K-DI-+- TI x or nI X Schem~e 1. Synthetic sche-me for polysiloxa-e-pclyurethane

ECUT: Energy Conversion and Utilization Technologies program. Industry, university and research interest in the US Department of Energy ECUT biocatalysis research activity

NASA Technical Reports Server (NTRS)

Wilcox, R. E.

1983-01-01

The results of a Research Opportunity Notice (RON) disseminated by the Jet Propulsion Laboratory for the U.S. Department of Energy Conversion and Utilization Technologies (ECUT) Program's Biocatalysis Research Activity are presented. The RON was issued in late April of 1983 and solicited expressions of interest from petrochemical and chemical companies, bioengineering firms, biochemical engineering consultants, private research laboratories, and universities for participating in a federal research program to investigate potential applications of biotechnology in producing chemicals. The RON results indicate that broad interest exists within the nation's industry, universities, and research institutes for the Activity and its planned research and development program.

Blood gas and serum biochemical RIs for healthy newborn Murrah buffaloes (Bubalus bubalis).

PubMed

Santana, André M; Silva, Daniela G; Clemente, Virna; Pizauro, Lucas J L; Bernardes, Priscila A; Santana, Clarissa H; Eckersall, Peter D; Fagliari, José J

2018-03-01

There is a lack of published work on RIs for newborn buffaloes. Establishing blood gas and serum biochemical RIs for newborn buffaloes is important for monitoring health. This study establishes blood gas and serum biochemical RIs of newborn buffaloes. Twenty-eight newborn buffaloes, 10-30 days old, were selected. Thirty blood biochemical variables were analyzed. The Anderson-Darling test was used to assess the normality of the distribution. The Dixon test and the Tukey test were used to identify outliers. The RI and 90% CI were determined using standard and robust methods and the Box-Cox transformation. A total of 30 RIs for healthy buffalo calves have been reported in this study. RIs for blood gas variables were reported for pH, partial pressure of oxygen (pO 2 ), partial pressure of carbon dioxide (pCO 2 ), saturation of O 2 (SO 2 ), bicarbonate (cHCO 3 - ), base excess (BE), total carbon dioxide (ctCO 2 ), and anion gap (AG). RIs for serum biochemical variables were reported for glucose (GLU), direct bilirubin (DB), total bilirubin (TB), AST, ALP, GGT, CK, LDH, creatinine (CREA), urea, cholesterol (CHOL), triglycerides (TG), Ca, P, Mg, Na, K, iCa, Cl, iron, total protein (TP), and albumin (ALB). This is the first reported study covering complete serum chemistry and blood gas RIs for healthy 1-month-old Murrah buffaloes. © 2018 American Society for Veterinary Clinical Pathology.

BIOCHEMICAL INDICES OF EXPOSURE TO ENVIRONMENTAL ESTROGENS: A SPECIES COMPARISON

EPA Science Inventory

Existence of endocrine active substances in the aquatic environment has been clearly established in several studies. Exposure of organisms to both natural and synthetic xenoestrogens have been found to alter biochemical homeostatis and, in some cases, result in reproductive and d...

Effect of high wavelengths low intensity light during dark period on physical exercise performance, biochemical and haematological parameters of swimming rats.

PubMed

Beck, W; Gobatto, C

2016-03-01

Nocturnal rodents should be assessed at an appropriate time of day, which leads to a challenge in identifying an adequate environmental light which allows animal visualisation without perturbing physiological homeostasis. Thus, we analysed the influence of high wavelength and low intensity light during dark period on physical exercise and biochemical and haematological parameters of nocturnal rats. We submitted 80 animals to an exhaustive exercise at individualised intensity under two different illuminations during dark period. Red light (> 600 nm; < 15lux) was applied constantly during dark period (EI; for experimental illumination groups) or only for handling and assessments (SI; for standard illumination groups). EI led to worse haematological and biochemical conditions, demonstrating that EI alone can influence physiological parameters and jeopardise result interpretation. SI promotes normal physiological conditions and greater aerobic tolerance than EI, showing the importance of a correct illumination pattern for all researchers that employ nocturnal rats for health/disease or sports performance experiments.

Hematological parameters in relation to age, sex and biochemical values for mute swans (Cygnus olor).

PubMed

Dolka, B; Włodarczyk, R; Zbikowski, A; Dolka, I; Szeleszczuk, P; Kluciński, W

2014-06-01

The knowledge of the correct morphological and biochemical parameters in mute swans is an important indicator of their health status, body condition, adaptation to habitat and useful diagnostic tools in veterinary practice and ecological research. The aim of the study was to obtain hematological parameters in relation to age, sex and serum biochemistry values in wild-living mute swans. We found the significant differences in the erythrocyte count, hematocrit, hemoglobin concentration and erythrocyte sedimentation rate in relation to age of mute swans. There were no differences in hematological values between males and females. The leukogram and H/L ratio did not vary by age and sex in swans. Among of biochemical parameters the slightly increased AST, ALP, CK, K, urea, decreased CHOL and TG values were recorded. As far as we know, this is the first study in which the morphometric parameters of blood cells in mute swans were presented. We found extremely low concentration of lead in blood (at subthreshold level). No blood parasites were found in blood smears. The analysis of body mass and biometric parameters revealed a significant differences dependent on age and sex. No differences in the scaled mass index were found. Our results represent a normal hematologic and blood chemistry values and age-sex related changes, as reference values for the mute swan.

[On necessity to modify biochemical methods for detecting organophosphorus componds in chemical weapons extinction objects (review of literature)].

PubMed

Prokofieva, D S; Shmurak, V I; Sadovnikov, S V; Gontcharov, N V

2015-01-01

The article covers problems of biochemical methods assessing organophosphorus toxic compounds in objects of chemical weapons extinction. The authors present results of works developing new, more specific and selective biochemical methods.

Biochemical Characteristics, Adhesion, and Cytotoxicity of Environmental and Clinical Isolates of Herbaspirillum spp.

PubMed Central

Marques, Ana C. Q.; Paludo, Katia S.; Dallagassa, Cibelle B.; Surek, Monica; Pedrosa, Fábio O.; Souza, Emanuel M.; Cruz, Leonardo M.; LiPuma, John J.; Zanata, Sílvio M.; Rego, Fabiane G. M.

2014-01-01

Herbaspirillum bacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. Here, biochemical tests, matrix-assisted laser deionization–time of flight (MALDI-TOF) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates of Herbaspirillum spp. Discrete biochemical differences were observed between human and environmental strains. All strains adhered to HeLa cells at low densities, and cytotoxic effects were discrete, supporting the view that Herbaspirillum bacteria are opportunists with low virulence potential. PMID:25355763

The predictive value of 2-year posttreatment biopsy after prostate cancer radiotherapy for eventual biochemical outcome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vance, Waseet; Tucker, Susan L.; Crevoisier, Renaud de

2007-03-01

Purpose: To determine the value of a 2-year post-radiotherapy (RT) prostate biopsy for predicting eventual biochemical failure in patients who were treated for localized prostate cancer. Methods and Materials: This study comprised 164 patients who underwent a planned 2-year post-RT prostate biopsy. The independent prognostic value of the biopsy results for forecasting eventual biochemical outcome and overall survival was tested with other factors (the Gleason score, 1992 American Joint Committee on Cancer tumor stage, pretreatment prostate-specific antigen level, risk group, and RT dose) in a multivariate analysis. The current nadir + 2 (CN + 2) definition of biochemical failure wasmore » used. Patients with rising prostate-specific antigen (PSA) or suspicious digital rectal examination before the biopsy were excluded. Results: The biopsy results were normal in 78 patients, scant atypical and malignant cells in 30, carcinoma with treatment effect in 43, and carcinoma without treatment effect in 13. Using the CN + 2 definition, we found a significant association between biopsy results and eventual biochemical failure. We also found that the biopsy status provides predictive information independent of the PSA status at the time of biopsy. Conclusion: A 2-year post-RT prostate biopsy may be useful for forecasting CN + 2 biochemical failure. Posttreatment prostate biopsy may be useful for identifying patients for aggressive salvage therapy.« less

Biochemical signatures mimicking multiple carboxylase deficiency in children with mutations in MT-ATP6.

PubMed

Larson, Austin A; Balasubramaniam, Shanti; Christodoulou, John; Burrage, Lindsay C; Marom, Ronit; Graham, Brett H; Diaz, George A; Glamuzina, Emma; Hauser, Natalie; Heese, Bryce; Horvath, Gabriella; Mattman, Andre; van Karnebeek, Clara; Lane Rutledge, S; Williamson, Amy; Estrella, Lissette; Van Hove, Johan K L; Weisfeld-Adams, James D

2018-01-04

Elevations of specific acylcarnitines in blood reflect carboxylase deficiencies, and have utility in newborn screening for life-threatening organic acidemias and other inherited metabolic diseases. In this report, we describe a newly-identified association of biochemical features of multiple carboxylase deficiency in individuals harboring mitochondrial DNA (mtDNA) mutations in MT-ATP6 and in whom organic acidemias and multiple carboxylase deficiencies were excluded. Using retrospective chart review, we identified eleven individuals with abnormally elevated propionylcarnitine (C3) or hydroxyisovalerylcarnitine (C5OH) with mutations in MT-ATP6, most commonly m.8993T>G in high heteroplasmy or homoplasmy. Most patients were ascertained on newborn screening; most had normal enzymatic or molecular genetic testing to exclude biotinidase and holocarboxylase synthetase deficiencies. MT-ATP6 is associated with some cases of Leigh disease; clinical outcomes in our cohort ranged from death from neurodegenerative disease in early childhood to clinically and developmentally normal after several years of follow-up. These cases expand the biochemical phenotype associated with MT-ATP6 mutations, especially m.8993T>G, to include acylcarnitine abnormalities mimicking carboxylase deficiency states. Clinicians should be aware of this association and its implications for newborn screening, and consider mtDNA sequencing in patients exhibiting similar acylcarnitine abnormalities that are biotin-unresponsive and in whom other enzymatic deficiencies have been excluded. Copyright © 2018 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Comparison of Biochemical Recurrence-Free Survival after Radical Prostatectomy Triggered by Grade Reclassification during Active Surveillance and in Men Newly Diagnosed with Similar Grade Disease.

PubMed

Diniz, Clarissa P; Landis, Patricia; Carter, H Ballentine; Epstein, Jonathan I; Mamawala, Mufaddal

2017-09-01

We compared biochemical recurrence between men on active surveillance who underwent radical prostatectomy triggered by grade reclassification and men diagnosed with similar grade disease treated with immediate radical prostatectomy. We retrospectively analyzed the records of men who underwent surgery from 1995 to 2015 at our institution. We identified 4 groups, including 94 and 56 men on active surveillance who underwent radical prostatectomy following reclassification to Gleason 7 (3 + 4) or greater (grade groups 2 or greater) and Gleason 7 (3 + 4) (grade group 2), and 3,504 and 1,979 in the immediate prostatectomy group diagnosed with grade group 2 or greater and 2, respectively. Biochemical recurrence was assessed by Kaplan-Meir analysis and a multivariable Cox model. Men on active surveillance had a lower incidence of biochemical recurrence than men in the immediate radical prostatectomy groups for biopsy grade groups 2 or greater and 2 (each p <0.05). One, 5 and 10-year biochemical recurrence-free survival for men in the active surveillance group vs the immediate radical prostatectomy group was 97.9% vs 85.5%, 76.6% vs 65.1% and 69.0% vs 54.2% in biopsy grade groups 2 or greater (p = 0.009) and 96.4% vs 91.2%, 89.6% vs 74.0% and 89.6% vs 63.9%, respectively, in biopsy grade group 2 (p = 0.071). For biopsy grade groups 2 or greater there was no significant difference in the risk of biochemical recurrence between the groups after adjusting for age, biopsy extent of cancer and prostate specific antigen density. Patients on active surveillance reclassified to grade groups 2 or greater are at no greater risk for treatment failure than men newly diagnosed with similar grades. Copyright © 2017 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Chromatin: Its history, current research, and the seminal researchers and their philosophy.

PubMed

Deichmann, Ute

2015-01-01

The concept of chromatin as a complex of nucleic acid and proteins in the cell nucleus was developed by cytologists and biochemists in the late 19th century. It was the starting point for biochemical research on DNA and nuclear proteins. Although interest in chromatin declined rapidly at the beginning of the 20th century, a few decades later a new focus on chromatin emerged, which was not only related to its structure, but also to its function in gene regulatory processes in the development of higher organisms. Since the late 20th century, research on chromatin modifications has also been conducted under the label of epigenetics. This article highlights the major phases of chromatin research until the present time and introduces major investigators and their scientific and philosophical outlooks.

The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

2007-03-22

Abstract We derived and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the activemore » site. TM and MA were supported in part by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan. MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.« less

Distinguishing between biochemical and cellular function: Are there peptide signatures for cellular function of proteins?

PubMed

Jain, Shruti; Bhattacharyya, Kausik; Bakshi, Rachit; Narang, Ankita; Brahmachari, Vani

2017-04-01

The genome annotation and identification of gene function depends on conserved biochemical activity. However, in the cell, proteins with the same biochemical function can participate in different cellular pathways and cannot complement one another. Similarly, two proteins of very different biochemical functions are put in the same class of cellular function; for example, the classification of a gene as an oncogene or a tumour suppressor gene is not related to its biochemical function, but is related to its cellular function. We have taken an approach to identify peptide signatures for cellular function in proteins with known biochemical function. ATPases as a test case, we classified ATPases (2360 proteins) and kinases (517 proteins) from the human genome into different cellular function categories such as transcriptional, replicative, and chromatin remodelling proteins. Using publicly available tool, MEME, we identify peptide signatures shared among the members of a given category but not between cellular functional categories; for example, no motif sharing is seen between chromatin remodelling and transporter ATPases, similarly between receptor Serine/Threonine Kinase and Receptor Tyrosine Kinase. There are motifs shared within each category with significant E value and high occurrence. This concept of signature for cellular function was applied to developmental regulators, the polycomb and trithorax proteins which led to the prediction of the role of INO80, a chromatin remodelling protein, in development. This has been experimentally validated earlier for its role in homeotic gene regulation and its interaction with regulatory complexes like the Polycomb and Trithorax complex. Proteins 2017; 85:682-693. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Effects of subchronic extremely low-frequency electromagnetic field exposure on biochemical parameters in rats.

PubMed

Luo, Xue; Ma, Lingjuan; Gao, Peng; Zhang, Yanwen

2017-04-01

The objective of the present study was to systematically determine the effects of 50 Hertz (Hz) magnetic fields (MFs) on biochemical parameters in rats. Sixty-four adult (5 weeks old, 140-165 g) male Sprague-Dawley rats were randomly divided into four groups: sham, 20 µTesla (µT), 100 µT, and 500 µT 50 Hz MF ( n = 16 in each group). The rats in the MF groups were exposed for 2 h daily for up to 4 weeks. Under these experimental conditions, body weight, organ coefficients, biochemical parameters (blood lipids, myocardial enzymes, liver function, and renal function) were measured. We found that 50 Hz MFs had no significant effects on growth or on the majority of blood biochemical parameters, with the exception of creatinine and cholesterol. However, the changes in creatinine and cholesterol were relatively small and unlikely to be clinically relevant.

Brain biochemical correlates of the plasma homocysteine level: a proton magnetic resonance spectroscopy study in the elderly subjects.

PubMed

Chen, Cheng-Sheng; Kuo, Yu-Ting; Tsai, Hui-Yi; Li, Chun-Wei; Lee, Chen-Chang; Yen, Cheng-Fang; Lin, Hsiu-Fen; Ko, Chih-Hung; Juo, Suh-Hang Hank; Yeh, Yi-Chun; Liu, Gin-Chung

2011-07-01

An elevated plasma homocysteine level has been reported to be associated with various neuropsychiatric diseases. However, little is known about the brain biochemical changes associated with the higher plasma homocysteine level. The main goal of this study was to examine the sex difference in brain biochemical concentrations using brain proton magnetic resonance spectroscopy (H MRS), and to elucidate the biochemical changes associated with plasma homocysteine levels by sex in healthy elderly subjects. Seventy elderly subjects without any clinical psychiatric and neurological disease underwent 3-T brain H MRS. MRS spectra were acquired from voxels placed on the left side of the basal ganglia, frontal lobe, and hippocampus. Brain biochemical concentrations were compared between the elderly male and female participants. Correlations between these biochemical concentrations and plasma homocysteine levels by sex were analyzed. Female participants had significantly higher levels of choline in the left frontal lobe and hippocampus, and lower creatine and myo-inositol, in the left basal ganglia than did males. A higher homocysteine level was correlated with a lower N-acetylaspartate (NAA) concentration in the left hippocampus in elderly women (r = -0.44; p = 0.03) but not in elderly men. This study found that there was a sex difference in brain biochemical concentrations in the elderly participants. A higher plasma homocysteine level was associated with a lower NAA in the hippocampus of elderly women. The sex difference in association between brain biochemical concentrations and plasma homocysteine levels needs further investigation. We speculate that after menopause, women lose protection of estrogen from the neurotoxic effects of homocysteine in the hippocampus. Future studies are required to examine this speculation.

Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.

PubMed

Pischel, Dennis; Sundmacher, Kai; Flassig, Robert J

2017-07-15

Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples. The method relies on the combination of the sigma point approach to describe extrinsic and external variability and the τ -leaping algorithm to account for the stochasticity due to probabilistic reactions. The comparison of our method to extensive Monte Carlo calculations demonstrates an immense computational advantage while losing an acceptable amount of accuracy. Additionally, the application to parameter optimization problems in stochastic biochemical reaction networks is shown, which is rarely applied due to its huge computational burden. To give further insight, a MATLAB script is provided including the proposed method applied to a simple toy example of gene expression. MATLAB code is available at Bioinformatics online. flassig@mpi-magdeburg.mpg.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Numerical modeling of gas mixing and bio-chemical transformations during underground hydrogen storage within the project H2STORE

NASA Astrophysics Data System (ADS)

Hagemann, B.; Feldmann, F.; Panfilov, M.; Ganzer, L.

2015-12-01

The change from fossil to renewable energy sources is demanding an increasing amount of storage capacities for electrical energy. A promising technological solution is the storage of hydrogen in the subsurface. Hydrogen can be produced by electrolysis using excessive electrical energy and subsequently converted back into electricity by fuel cells or engine generators. The development of this technology starts with adding small amounts of hydrogen to the high pressure natural gas grid and continues with the creation of pure underground hydrogen storages. The feasibility of hydrogen storage in depleted gas reservoirs is investigated in the lighthouse project H2STORE financed by the German Ministry for Education and Research. The joint research project has project members from the University of Jena, the Clausthal University of Technology, the GFZ Potsdam and the French National Center for Scientic Research in Nancy. The six sub projects are based on laboratory experiments, numerical simulations and analytical work which cover the investigation of mineralogical, geochemical, physio-chemical, sedimentological, microbiological and gas mixing processes in reservoir and cap rocks. The focus in this presentation is on the numerical modeling of underground hydrogen storage. A mathematical model was developed which describes the involved coupled hydrodynamic and microbiological effects. Thereby, the bio-chemical reaction rates depend on the kinetics of microbial growth which is induced by the injection of hydrogen. The model has been numerically implemented on the basis of the open source code DuMuX. A field case study based on a real German gas reservoir was performed to investigate the mixing of hydrogen with residual gases and to discover the consequences of bio-chemical reactions.

Biochemical Reversal of Aging

NASA Astrophysics Data System (ADS)

Ely, John T. A.

2006-03-01

We cite our progress on biochemical reversal of aging. However, it may be circa 2 years before we have necessary substances at low cost. Meanwhile, without them, a number of measures can be adopted providing marked improvement for the problems of aging in modern societies. For example, enzymes are needed to excrete toxins that accelerate aging; Hg is the ultimate toxin that disables all enzymes (including those needed to excrete Hg itself). Low Hg level in the urine, due to loss of excretory ability, causes the diagnosis of Hg toxicity to almost always be missed. Hg sources must be removed from the body! Another example is excess sugar; hyperglycemia decreases intracellular ascorbic acid (AA) by competitively inhibiting the insulin- mediated active transport of AA into cells. Thus, immunity is impaired by low leucocyte AA. AA is needed for new proteins in aging tissues. Humans must supplement AA; their need same as in AA-synthesizing mammals.

Age-dependent biochemical quantities: an approach for calculating reference intervals.

PubMed

Bjerner, J

2007-01-01

A parametric method is often preferred when calculating reference intervals for biochemical quantities, as non-parametric methods are less efficient and require more observations/study subjects. Parametric methods are complicated, however, because of three commonly encountered features. First, biochemical quantities seldom display a Gaussian distribution, and there must either be a transformation procedure to obtain such a distribution or a more complex distribution has to be used. Second, biochemical quantities are often dependent on a continuous covariate, exemplified by rising serum concentrations of MUC1 (episialin, CA15.3) with increasing age. Third, outliers often exert substantial influence on parametric estimations and therefore need to be excluded before calculations are made. The International Federation of Clinical Chemistry (IFCC) currently recommends that confidence intervals be calculated for the reference centiles obtained. However, common statistical packages allowing for the adjustment of a continuous covariate do not make this calculation. In the method described in the current study, Tukey's fence is used to eliminate outliers and two-stage transformations (modulus-exponential-normal) in order to render Gaussian distributions. Fractional polynomials are employed to model functions for mean and standard deviations dependent on a covariate, and the model is selected by maximum likelihood. Confidence intervals are calculated for the fitted centiles by combining parameter estimation and sampling uncertainties. Finally, the elimination of outliers was made dependent on covariates by reiteration. Though a good knowledge of statistical theory is needed when performing the analysis, the current method is rewarding because the results are of practical use in patient care.

Evolution of long-term coloration trends with biochemically unstable ingredients

PubMed Central

Davis, Sarah N.; Andrews, John E.; Badyaev, Alexander V.

2016-01-01

The evolutionarily persistent and widespread use of carotenoid pigments in animal coloration contrasts with their biochemical instability. Consequently, evolution of carotenoid-based displays should include mechanisms to accommodate or limit pigment degradation. In birds, this could involve two strategies: (i) evolution of a moult immediately prior to the mating season, enabling the use of particularly fast-degrading carotenoids and (ii) evolution of the ability to stabilize dietary carotenoids through metabolic modification or association with feather keratins. Here, we examine evolutionary lability and transitions between the two strategies across 126 species of birds. We report that species that express mostly unmodified, fast-degrading, carotenoids have pre-breeding moults, and a particularly short time between carotenoid deposition and the subsequent breeding season. Species that expressed mostly slow-degrading carotenoids in their plumage accomplished this through increased metabolic modification of dietary carotenoids, and the selective expression of these slow-degrading compounds. In these species, the timing of moult was not associated with carotenoid composition of plumage displays. Using repeated samples from individuals of one species, we found that metabolic modification of dietary carotenoids significantly slowed their degradation between moult and breeding season. Thus, the most complex and colourful ornamentation is likely the most biochemically stable in birds, and depends less on ecological factors, such as moult timing and migration tendency. We suggest that coevolution of metabolic modification, selective expression and biochemical stability of plumage carotenoids enables the use of unstable pigments in long-term evolutionary trends in plumage coloration. PMID:27194697

Experimental Theileria lestoquardi infection in sheep: Biochemical and hematological changes.

PubMed

Yaghfoori, Saeed; Mohri, Mehrdad; Razmi, Gholamreza

2017-09-01

Malignant theileriosis (Theileria lestoquardi infection) is a hemoparasitic tick-borne disease that affects both wild and domestic small ruminants. The aim of this study was to evaluate biochemical and hematological characteristics of sheep after being experimentally infected by T. lestoquardi. T. lestoquardi infection was induced in seven Baluchi sheep of six-to-eight months old via experimentally-infected Hyalomma anatolicum adult ticks. Biochemical and hematological parameters were measured twice a week during the three weeks' post infection. Twenty-three biochemical analytes and seven hematological ones were measured. After three to four days infection, body temperature rose above 40 ° C. Maximum and minimum parasitaemia were 3.3% and 0.28%, respectively. Piroplasms and schizont were seen on average from days 7.2 and 4 post infection, respectively. The concentrations and activities of Alb, HDL, ALT, T3, T4, Ca, Fe, Mg, iP, WBC, RBC, PCV, Hb, Plt, neutrophil and lymphocytes significantly decreased (P≤0.05) during experimental infection. However, concentrations and activities of BT, GGT, Glu, BUN, Crea, FIB and Cu significantly increased (P≤0.05). There was no significant change in the serum amounts of Chol, LDL, TG, VLDL and Zn. The observed hypoalbuminemia and increase of FIB concentrations referred to pro-inflammatory cytokines production. Moreover, the raising of GGT activity indicates liver damage, cholestatic disorders or schizont infiltration. The disease stress and corticosteroids are suspected to cause the Glu concentration increase. The present study is aimed at improving the knowledge of malignant theileriosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of class model based on blood biochemical parameters as a diagnostic tool of PSE meat.

PubMed

Qu, Daofeng; Zhou, Xu; Yang, Feng; Tian, Shiyi; Zhang, Xiaojun; Ma, Lin; Han, Jianzhong

2017-06-01

A fast, sensitive and effective method based on the blood biochemical parameters for the detection of PSE meat was developed in this study. A total of 200 pigs were slaughtered in the same slaughterhouse. Meat quality was evaluated by measuring pH, electrical conductivity and color at 45min, 2h and 24h after slaughtering in M. longissimus thoracis et lumborum (LD). Blood biochemical parameters were determined in blood samples collected during carcass bleeding. Principal component analysis (PCA) biplot showed that high levels of exsanguination Creatine Kinase, Lactate Dehydrogenase, Aspertate aminotransferase, blood glucose and lactate were associated with the PSE meat, and the five biochemical parameters were found to be good indicators of PSE meat Discriminant function analysis (DFA) was able to clearly identify PSE meat using the five biochemical parameters as input data, and the class model is an effective diagnostic tool in pigs which can be used to detect the PSE meat and reduce economic loss for the company. Copyright © 2017 Elsevier Ltd. All rights reserved.

Renewable Biochemical Methane Potential through Anaerobic Co-digestion from Selective Feed Stocks

NASA Astrophysics Data System (ADS)

Thara, K.; Navis Karthika, Ignatius; Dheenadayalan, M. S., Dr

2017-08-01

Biochemical Methane Potential (BMP) analysis provides a measure of the anaerobic biodegradability of a given substrate. BMP test is also used to evaluate the potential biogas (methane) production between various Co-digestion substrates. This test is also used to determine the amount of organic carbon in a given material that can be an aerobically converted to methane-Biogas. Studies were carried out for the production of biogas from the leather solid waste. Co-digestion (simultaneous digestion of two or more substrates) studies were carried out in batch reactor using the fleshing (a solid waste generated during the processing of raw hides or skins into finished leather) along with the fruit and vegetable waste at mesophilic condition 35° C). The anaerobic methanogenic seed sludge prepared separately followed by standard BMP test, which was used as the seed inoculums. Recent research on this topic is reviewed in this current paper.

Biochemical and morphological differentiation of acetylcholinesterase-positive efferent fibers in the mouse cochlea.

PubMed

Emmerling, M R; Sobkowicz, H M; Levenick, C V; Scott, G L; Slapnick, S M; Rose, J E

1990-06-01

We have compared the biochemical expression of cholinergic enzymes with the morphological differentiation of efferent nerve fibers and endings in the cochlea of the postnatally developing mouse. Choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) are present in the newborn cochlea at specific activities 63% and 25%, respectively, of their mature levels. The relative increases in ChAT, in AChE, and in its molecular forms over the newborn values start about day 4 and reach maturity by about day 10. The biochemical results correlate well with the massive presence of nerve fibers stained immunocytochemically for ChAT and AChE or enzymatically for AChE in the inner and outer hair cell regions. Ultrastructral studies, however, indicate the presence of only few vesiculated fibers and endings in the inner and outer hair cell regions. The appearance of large, cytologically mature endings occurs only toward the end of the third postnatal week. The discrepancy may be resolved in the electron microscopy using the enzymatic staining for AChE. Labeling is seen on many nonvesiculated fibers and endings in the hair cell regions, suggesting that the majority of the efferent fibers in the perinatal organ may be biochemically differentiated but morphologically immature. The results may imply that the efferents to inner and outer hair cells develop earlier than indicated by previous ultrastructral studies. Moreover, the pattern of development suggests that in the cochlea, as in other tissues, the biochemical differentiation of the efferent innervation may precede the morphological maturation.

Cross-resistance of bisultap resistant strain of Nilaparvata lugens and its biochemical mechanism.

PubMed

Ling, Shanfeng; Zhang, Runjie

2011-02-01

The resistant (R) strain of the planthopper Nilaparvata lugens (Stål) selected for bisultap resistance displayed 7.7-fold resistance to bisultap and also had cross-resistance to nereistoxin (monosultap, thiocyclam, and cartap), chlorpyrifos, dimethoate, and malathion but no cross-resistance to buprofezin, imidacloprid, and fipronil. To find out the biochemical mechanism of resistance to bisultap, biochemical assay was done. The results showed that cytochrome P450 monooxygenases (P450) activity in R strain was 2.71-fold that in susceptible strain (S strain), in which the changed activity for general esterase (EST) was 1.91 and for glutathione S-transferases only 1.32. Piperonyl butoxide (PBO) could significantly inhibit P450 activity (percentage of inhibition [PI]: 37.31%) in the R strain, with ESTs PI = 16.04% by triphenyl phosphate (TPP). The results also demonstrated that diethyl maleate had no synergism with bisultap. However, PBO displayed significant synergism in three different strains, and the synergism increased with resistance (S strain 1.42, Lab strain, 2.24 and R strain, 3.23). TPP also showed synergism for three strains, especially in R strain (synergistic ratio = 2.47). An in vitro biochemical study and in vivo synergistic study indicated that P450 might be play important role in the biochemical mechanism of bisultap resistance and that esterase might be the important factor of bisultap resistance. Acetylcholinesterase (AChE) insensitivity play important role in bisultap resistance. We suggest that buprofezin, imidacloprid, and fipronil could be used in resistance management programs for N. lugens via alternation and rotation with bisultap.

Impact of yoga on biochemical profile of asthmatics: A randomized controlled study

PubMed Central

Agnihotri, Shruti; Kant, Surya; Kumar, Santosh; Mishra, Ranjeet K; Mishra, Satyendra K

2014-01-01

Background: Asthma is a chronic inflammatory disorder of the airways. The chronic inflammation causes an associated increase in airway hyperresponsiveness that leads to recurrent episodes of wheezing, breathlessness, chest tightness, and coughing at night or in the early morning. Most of the studies have reported, as the effects of yoga on bronchial asthma, significant improvements in pulmonary functions, quality of life, and decrease in medication use, but none of the studies has attempted to show the effect of yoga on biochemical changes. Objective: To evaluate the effect of yoga on biochemical profile of asthmatics. Materials and Methods: In the present study, 276 patients of mild to moderate asthma (FEV 1> 60%) aged between 12 to 60 years were recruited from the Department of Pulmonary Medicine, King George's Medical University, U.P., Lucknow, India. They were randomly divided into two groups: Yoga group (with standard medical treatment and yogic intervention) and control group as standard medical treatment (without yogic intervention). At completion of 6 months of the study period, 35 subjects were dropped out, so out of 276 subjects, only 241 subjects completed the whole study (121 subjects from yoga group and 120 subjects from control group). Biochemical assessment was carried out at baseline and after 6 months of the study period. Results: In yoga group, there was significant improvement found in the proportion of hemoglobin and antioxidant superoxide dismutase in comparison to control group and significant decrease was found in total leukocyte count (TLC) and differential leukocytes count in comparison to control group. There was no significant change found in TLC, polymorphs, and monocytes in between group comparison. Conclusions: Yoga group got significantly better improvement in biochemical variables than control group. Result shows that yoga can be practiced as adjuvant therapy with standard inhalation therapy for better outcome of asthma. PMID

Comparative life cycle assessment of lignocellulosic ethanol production: biochemical versus thermochemical conversion.

PubMed

Mu, Dongyan; Seager, Thomas; Rao, P Suresh; Zhao, Fu

2010-10-01

Lignocellulosic biomass can be converted into ethanol through either biochemical or thermochemical conversion processes. Biochemical conversion involves hydrolysis and fermentation while thermochemical conversion involves gasification and catalytic synthesis. Even though these routes produce comparable amounts of ethanol and have similar energy efficiency at the plant level, little is known about their relative environmental performance from a life cycle perspective. Especially, the indirect impacts, i.e. emissions and resource consumption associated with the production of various process inputs, are largely neglected in previous studies. This article compiles material and energy flow data from process simulation models to develop life cycle inventory and compares the fossil fuel consumption, greenhouse gas emissions, and water consumption of both biomass-to-ethanol production processes. The results are presented in terms of contributions from feedstock, direct, indirect, and co-product credits for four representative biomass feedstocks i.e., wood chips, corn stover, waste paper, and wheat straw. To explore the potentials of the two conversion pathways, different technological scenarios are modeled, including current, 2012 and 2020 technology targets, as well as different production/co-production configurations. The modeling results suggest that biochemical conversion has slightly better performance on greenhouse gas emission and fossil fuel consumption, but that thermochemical conversion has significantly less direct, indirect, and life cycle water consumption. Also, if the thermochemical plant operates as a biorefinery with mixed alcohol co-products separated for chemicals, it has the potential to achieve better performance than biochemical pathway across all environmental impact categories considered due to higher co-product credits associated with chemicals being displaced. The results from this work serve as a starting point for developing full life cycle

Comparative Life Cycle Assessment of Lignocellulosic Ethanol Production: Biochemical Versus Thermochemical Conversion

NASA Astrophysics Data System (ADS)

Mu, Dongyan; Seager, Thomas; Rao, P. Suresh; Zhao, Fu

2010-10-01

Lignocellulosic biomass can be converted into ethanol through either biochemical or thermochemical conversion processes. Biochemical conversion involves hydrolysis and fermentation while thermochemical conversion involves gasification and catalytic synthesis. Even though these routes produce comparable amounts of ethanol and have similar energy efficiency at the plant level, little is known about their relative environmental performance from a life cycle perspective. Especially, the indirect impacts, i.e. emissions and resource consumption associated with the production of various process inputs, are largely neglected in previous studies. This article compiles material and energy flow data from process simulation models to develop life cycle inventory and compares the fossil fuel consumption, greenhouse gas emissions, and water consumption of both biomass-to-ethanol production processes. The results are presented in terms of contributions from feedstock, direct, indirect, and co-product credits for four representative biomass feedstocks i.e., wood chips, corn stover, waste paper, and wheat straw. To explore the potentials of the two conversion pathways, different technological scenarios are modeled, including current, 2012 and 2020 technology targets, as well as different production/co-production configurations. The modeling results suggest that biochemical conversion has slightly better performance on greenhouse gas emission and fossil fuel consumption, but that thermochemical conversion has significantly less direct, indirect, and life cycle water consumption. Also, if the thermochemical plant operates as a biorefinery with mixed alcohol co-products separated for chemicals, it has the potential to achieve better performance than biochemical pathway across all environmental impact categories considered due to higher co-product credits associated with chemicals being displaced. The results from this work serve as a starting point for developing full life cycle

Biochemical nature of Russell Bodies.

PubMed

Mossuto, Maria Francesca; Ami, Diletta; Anelli, Tiziana; Fagioli, Claudio; Doglia, Silvia Maria; Sitia, Roberto

2015-07-30

Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.

Fast and Precise Emulation of Stochastic Biochemical Reaction Networks With Amplified Thermal Noise in Silicon Chips.

PubMed

Kim, Jaewook; Woo, Sung Sik; Sarpeshkar, Rahul

2018-04-01

The analysis and simulation of complex interacting biochemical reaction pathways in cells is important in all of systems biology and medicine. Yet, the dynamics of even a modest number of noisy or stochastic coupled biochemical reactions is extremely time consuming to simulate. In large part, this is because of the expensive cost of random number and Poisson process generation and the presence of stiff, coupled, nonlinear differential equations. Here, we demonstrate that we can amplify inherent thermal noise in chips to emulate randomness physically, thus alleviating these costs significantly. Concurrently, molecular flux in thermodynamic biochemical reactions maps to thermodynamic electronic current in a transistor such that stiff nonlinear biochemical differential equations are emulated exactly in compact, digitally programmable, highly parallel analog "cytomorphic" transistor circuits. For even small-scale systems involving just 80 stochastic reactions, our 0.35-μm BiCMOS chips yield a 311× speedup in the simulation time of Gillespie's stochastic algorithm over COPASI, a fast biochemical-reaction software simulator that is widely used in computational biology; they yield a 15 500× speedup over equivalent MATLAB stochastic simulations. The chip emulation results are consistent with these software simulations over a large range of signal-to-noise ratios. Most importantly, our physical emulation of Poisson chemical dynamics does not involve any inherently sequential processes and updates such that, unlike prior exact simulation approaches, they are parallelizable, asynchronous, and enable even more speedup for larger-size networks.

Biochemical characteristics, adhesion, and cytotoxicity of environmental and clinical isolates of Herbaspirillum spp.

PubMed

Marques, Ana C Q; Paludo, Katia S; Dallagassa, Cibelle B; Surek, Monica; Pedrosa, Fábio O; Souza, Emanuel M; Cruz, Leonardo M; LiPuma, John J; Zanata, Sílvio M; Rego, Fabiane G M; Fadel-Picheth, Cyntia M T

2015-01-01

Herbaspirillum bacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. Here, biochemical tests, matrix-assisted laser deionization-time of flight (MALDI-TOF) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates of Herbaspirillum spp. Discrete biochemical differences were observed between human and environmental strains. All strains adhered to HeLa cells at low densities, and cytotoxic effects were discrete, supporting the view that Herbaspirillum bacteria are opportunists with low virulence potential. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Use of biochemical kinetic data to determine strain relatedness among Salmonella enterica subsp. enterica isolates.

PubMed

de la Torre, E; Tello, M; Mateu, E M; Torre, E

2005-11-01

Classical biotyping characterizes strains by creating biotype profiles that consider only positive and negative results for a predefined set of biochemical tests. This method allows Salmonella subspecies to be distinguished but does not allow serotypes and phage types to be distinguished. The objective of this study was to determine the relatedness of isolates belonging to distinct Salmonella enterica subsp. enterica serotypes by using a refined biotyping process that considers the kinetics at which biochemical reactions take place. Using a Vitek GNI+ card for the identification of gram-negative organisms, we determined the biochemical kinetic reactions (28 biochemical tests) of 135 Salmonella enterica subsp. enterica strains of pig origin collected in Spain from 1997 to 2002 (59 Salmonella serotype Typhimurium strains, 25 Salmonella serotype Typhimurium monophasic variant strains, 25 Salmonella serotype Anatum strains, 12 Salmonella serotype Tilburg strains, 7 Salmonella serotype Virchow strains, 6 Salmonella serotype Choleraesuis strains, and 1 Salmonella enterica serotype 4,5,12:-:- strain). The results were expressed as the colorimetric and turbidimetric changes (in percent) and were used to enhance the classical biotype profile by adding kinetic categories. A hierarchical cluster analysis was performed by using the enhanced profiles and resulted in 14 clusters. Six major clusters grouped 94% of all isolates with a similarity of > or =95% within any given cluster, and eight clusters contained a single isolate. The six major clusters grouped not only serotypes of the same type but also phenotypic serotype variations into individual clusters. This suggests that metabolic kinetic reaction data from the biochemical tests commonly used for classic Salmonella enterica subsp. enterica biotyping can possibly be used to determine the relatedness between isolates in an easy and timely manner.

Biochemical, molecular, and clinical diagnoses of patients with cerebral creatine deficiency syndromes.

PubMed

Comeaux, Matthew S; Wang, Jing; Wang, Guoli; Kleppe, Soledad; Zhang, Victor Wei; Schmitt, Eric S; Craigen, William J; Renaud, Deborah; Sun, Qin; Wong, Lee-Jun

2013-07-01

Cerebral creatine deficiency syndromes (CCDS) are a group of inborn errors of creatine metabolism that involve AGAT and GAMT for creatine biosynthesis disorders and SLC6A8 for creatine transporter (CT1) deficiency. Deficiencies in the three enzymes can be distinguished by intermediate metabolite levels, and a definitive diagnosis relies on the presence of deleterious mutations in the causative genes. Mutations and unclassified variants were identified in 41 unrelated patients, and 22 of these mutations were novel. Correlation of sequencing and biochemical data reveals that using plasma guanidinoacetate (GAA) as a biomarker has 100% specificity for both AGAT and GAMT deficiencies, but AGAT deficiency has decreased sensitivity in this assay. Furthermore, the urine creatine:creatinine ratio is an effective screening test with 100% specificity in males suspected of having creatine transporter deficiency. This test has a high false-positive rate due to dietary factors or dilute urine samples and lacks sensitivity in females. We conclude that biochemical screening for plasma GAA and measuring of the urine creatine:creatinine ratio should be performed for suspected CCDS patients prior to sequencing. Also, based on the results of this study, we feel that sequencing should only be considered if a patient has abnormal biochemical results on repeat testing. Copyright © 2013 Elsevier Inc. All rights reserved.

CAP/ACMG proficiency testing for biochemical genetics laboratories: a summary of performance.

PubMed

Oglesbee, Devin; Cowan, Tina M; Pasquali, Marzia; Wood, Timothy C; Weck, Karen E; Long, Thomas; Palomaki, Glenn E

2018-01-01

PurposeTesting for inborn errors of metabolism is performed by clinical laboratories worldwide, each utilizing laboratory-developed procedures. We sought to summarize performance in the College of American Pathologists' (CAP) proficiency testing (PT) program and identify opportunities for improving laboratory quality. When evaluating PT data, we focused on a subset of laboratories that have participated in at least one survey since 2010.MethodsAn analysis of laboratory performance (2004 to 2014) on the Biochemical Genetics PT Surveys, a program administered by CAP and the American College of Medical Genetics and Genomics. Analytical and interpretive performance was evaluated for four tests: amino acids, organic acids, acylcarnitines, and mucopolysaccharides.ResultsSince 2010, 150 laboratories have participated in at least one of four PT surveys. Analytic sensitivities ranged from 88.2 to 93.4%, while clinical sensitivities ranged from 82.4 to 91.0%. Performance was higher for US participants and for more recent challenges. Performance was lower for challenges with subtle findings or complex analytical patterns.ConclusionUS clinical biochemical genetics laboratory proficiency is satisfactory, with a minority of laboratories accounting for the majority of errors. Our findings underscore the complex nature of clinical biochemical genetics testing and highlight the necessity of continuous quality management.

Yield, quality and biochemical properties of various strawberry cultivars under water stress.

PubMed

Adak, Nafiye; Gubbuk, Hamide; Tetik, Nedim

2018-01-01

Although strawberry (Fragaria x ananassa Duch.) species are sensitive to abiotic stress conditions, some cultivars are known to be tolerant to different environmental conditions. We examined the response of different strawberry cultivars to water stress conditions in terms of yield, quality and biochemical features. The trial was conducted under two different irrigation regimes: in grow bags containing cocopeat (control, 30%; water stress, 15% drainage) with four different cultivars (Camarosa, Albion, Amiga and Rubygem). Fruit weight declined by 59.72% and the yield per unit area by 63.62% under water stress conditions as compared to control. Albion and Rubygem were found to be more tolerant and Amiga the most sensitive in terms of yield under stress conditions. Water stress increased all biochemical features in fruits such as total phenol, total anthocyanin, antioxidant activity and sugar contents. Among the cultivars, glucose and fructose was higher in Albion. Considering the rise in global warming, identification of resistant and tolerant cultivars to stress conditions are crucial for future breeding programmes. Our results showed that some of the fruit's physical features were affected negatively by stress conditions whereas many of the biochemical features such as total anthocyanin content, total phenolic content and antioxidant activity were positively modulated. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Physiological and biochemical responses of Ricinus communis seedlings to different temperatures: a metabolomics approach.

PubMed

Ribeiro, Paulo Roberto; Fernandez, Luzimar Gonzaga; de Castro, Renato Delmondez; Ligterink, Wilco; Hilhorst, Henk W M

2014-08-12

response to support growth at higher temperatures. The biochemical changes observed in response to the increasing temperature provide leads into understanding plant adaptation to harsh environmental conditions, which will be very helpful in developing strategies for R. communis crop improvement research.

Biochemical fingerprinting of Vibrio parahaemolyticus by the PhenePlate system: comparison between pandemic and non-pandemic serotypes.

PubMed

Rahman, Mokhlasur; Bhuiyan, N A; Kuhn, I; Ramamurthy, T; Rahman, M; Mollby, R; Nair, G Balakrish

2006-10-01

During recent years a pandemic clone of Vibrio parahaemolyticus has emerged. Isolates of this clone are distributed among several serotypes, but are genotypically related. In the present study, a phenotyping method (biochemical fingerprinting) was used to characterize pandemic and non-pandemic isolates belonging to V. parahaemolyticus. It was found that the pandemic isolates showed a high level of phenotypic homogeneity and a majority of the pandemic isolates belonged to the same biochemical phenotype, whereas non-pandemic V. parahemolyticus isolates were more heterogeneous. In conclusion, biochemical fingerprinting of V. parahaemolyticus can be used as a first screening method to differentiate between pandemic and non-pandemic isolates of V. parahaemolyticus.

[Role of angiotensin II receptor type 2 in predicting biochemical recurrence in the treatment of prostate cancer].

PubMed

Chibichyan, M B; Kogan, M I; Chernogubova, E A; Pavlenko, I A; Matishov, D G

2016-12-01

To identify markers for predicting aggressive forms of prostate cancer. The study retrospectively evaluated expression of angiotensin II type 2 receptors (AT2-R) in prostate needle biopsy tissue from patients with and without biochemical recurrence after combined hormone and radiation therapy. The study findings showed that low expression of AT2-R in prostate tissue was associated with a high risk of biochemical recurrence. The data on the nature of AT2-R expression in prostate tissue of prostate cancer patients may be considered as a tool for predicting biochemical recurrence after combined hormone and radiation therapy. The test has a sensitivity of 87.5% and specificity of 85.71%.

A revision of the Nearctic species of Liancalus Loew (Diptera, Dolichopodidae)

PubMed Central

Runyon, Justin B.; Hurley, Richard L.

2015-01-01

Abstract The genus Liancalus Loew is revised for the Nearctic Region. Seven species are documented from this region including two new species: Liancalus genualis Loew, Liancalus hydrophilus Aldrich, Liancalus limbatus Van Duzee, Liancalus pterodactyl sp. n., Liancalus querulus Osten Sacken, Liancalus similis Aldrich, and Liancalus sonorus sp. n. Lectotypes are designated for the following species: Liancalus genualis, Liancalus hydrophilus, Liancalus querulus, and Liancalus similis. The species are illustrated, a key to males and females is provided, and their distributions mapped. Adults of Liancalus are some of the largest species of Dolichopodidae and commonly occur on waterfalls and vertical seeps. PMID:25755626

Preparation of Chemical Compounds for the U.S. Army Drug Development Program

DTIC Science & Technology

1990-09-14

Aldrich, Lot No. ML0824ML Johns Manville , no Lot No. J.T. Baker, Lot No. A42837 Fisher Scientific Lot No. 885835-60 Ashland, Lot No. 0701768E...Aldrich, Lot No. 03905ET Moore-Tec, No Lot No. Lot Nos. KAPM and KDPA Aaper, Lot Nos. R9529, 89D19-R, 89K06 Kodak, Lot No. 807198C Johns Manville , Lot...89-K06-R and 90-A124-R Fisher, Lot Nos. 881166-60, 895184-36 and 894961-36 Kodak, Lot NO. 807198C Johns Manville Lot Nos. G5P34633 and 3P-291

Low incidence of new biochemical hypogonadism after intensity modulated radiation therapy for prostate cancer.

PubMed

Markovina, Stephanie; Weschenfelder, Débora Cristina; Gay, Hiram; McCandless, Audrey; Carey, Bethany; DeWees, Todd; Knutson, Nels; Michalski, Jeff

2014-01-01

To evaluate serum testosterone and the incidence of biochemical hypogonadism in men treated with intensity modulated radiation therapy (IMRT) for prostate cancer. Serum testosterone was evaluated prospectively in 51 men at pretreatment and at 6-month time points for 2 years posttreatment with IMRT for prostate cancer. Forty-one patients (80%) were treated with definitive intent and 10 patients with postprostatectomy radiation to median total doses of 7380 cGy and 6480 cGy, respectively. No patients received hormone therapy within 12 months of any serum testosterone value. Biochemical hypogonadism was defined as a total serum testosterone level ≤ 300 ng/dL. Incidental testicular dose was calculated using planning software when computed tomography information was available (n = 21) and using a published method of estimation when not available (n = 24), and was available for 45 patients. A statistically significant decrease in testosterone, though small in magnitude, was seen at 6 months after completion of therapy, with no significant difference by 1 year after completion of therapy. There was no increase in biochemical hypogonadism after IMRT. Below-normal pretreatment testosterone was not associated with a transient decrease. Estimated cumulative testicular dose, including dose from daily imaging, was not associated with a change in testosterone, nor was radiation therapy prescription dose or treatment intent (postoperative vs definitive). The mild transient decrease in serum testosterone following IMRT monotherapy for prostate cancer is not associated with new biochemical hypogonadism.

Reassessment of the risk factors for biochemical recurrence in D'Amico intermediate-risk prostate cancer treated using radical prostatectomy.

PubMed

Narita, Shintaro; Mitsuzuka, Koji; Tsuchiya, Norihiko; Koie, Takuya; Kawamura, Sadafumi; Ohyama, Chikara; Tochigi, Tatsuo; Yamaguchi, Takuhiro; Arai, Yoichi; Habuchi, Tomonori

2015-11-01

To assess the risk factors for biochemical recurrence in D'Amico intermediate-risk prostate cancer patients treated using radical prostatectomy. We retrospectively reviewed the medical records of 1268 men with prostate cancer treated using radical prostatectomy without neoadjuvant therapy. The association between various risk factors and biochemical recurrence was then statistically evaluated. The Kaplan-Meier method, log-rank tests and Cox proportional hazards models were used for statistical analysis. In the intermediate-risk group, 96 patients (14.5%) experienced biochemical recurrence during a median follow up of 41 months. In the intermediate-risk group, preoperative prostate-specific antigen level, prostate volume and prostate-specific antigen density were significant preoperative risk factors for biochemical recurrence, whereas other factors including age, primary Gleason 4, clinical stage >T2 and percentage of positive biopsies were not. In multivariate analysis, higher preoperative prostate-specific antigen level and density, and a smaller prostate volume were independent risk factors for biochemical recurrence in the intermediate-risk group. Biochemical recurrence-free survival of patients in the intermediate-risk group with a higher prostate-specific antigen level and density (≥15 ng/mL, ≥0.6 ng/mL/cm(3), respectively), and lower prostate volume (≤10 mL) was comparable with that of high-risk group individuals (P = 0.632, 0.494 and 0.961, respectively). Preoperative prostate-specific antigen, prostate volume and prostate-specific antigen density are significant risk factors for biochemical recurrence in D'Amico intermediate-risk prostate cancer patients treated using radical prostatectomy. Using these variables, a subset of the intermediate-risk patients can be identified as having equivalent outcomes to high-risk patients. © 2015 The Japanese Urological Association.

Osteoarthritis Year in Review 2016: biomarkers (biochemical markers).

PubMed

Mobasheri, A; Bay-Jensen, A-C; van Spil, W E; Larkin, J; Levesque, M C

2017-02-01

The aim of this "Year in Review" article is to summarize and discuss the implications of biochemical marker related articles published between the Osteoarthritis Research Society International (OARSI) 2015 Congress in Seattle and the OARSI 2016 Congress in Amsterdam. The PubMed/MEDLINE bibliographic database was searched using the combined keywords: 'biomarker' and 'osteoarthritis'. The PubMed/MEDLINE literature search was conducted using the Advanced Search Builder function (http://www.ncbi.nlm.nih.gov/pubmed/advanced). Over two hundred new biomarker-related papers were published during the literature search period. Some papers identified new biomarkers whereas others explored the biological properties and clinical utility of existing markers. There were specific references to several adipocytokines including leptin and adiponectin. ADAM Metallopeptidase with Thrombospondin Type 1 motif 4 (ADAMTS-4) and aggrecan ARGS neo-epitope fragment (ARGS) in synovial fluid (SF) and plasma chemokine (CeC motif) ligand 3 (CCL3) were reported as potential new knee biomarkers. New and refined proteomic technologies and novel assays including a fluoro-microbead guiding chip (FMGC) for measuring C-telopeptide of type II collagen (CTX-II) in serum and urine and a novel magnetic nanoparticle-based technology (termed magnetic capture) for collecting and concentrating CTX-II, were described this past year. There has been steady progress in osteoarthritis (OA) biomarker research in 2016. Several novel biomarkers were identified and new technologies have been developed for measuring existing biomarkers. However, there has been no "quantum leap" this past year and identification of novel early OA biomarkers remains challenging. During the past year, OARSI published a set of recommendations for the use of soluble biomarkers in clinical trials, which is a major step forward in the clinical use of OA biomarkers and bodes well for future OA biomarker development. Copyright © 2016 The

Biochemical evaluation of disease activity after pituitary surgery in acromegaly: a critical analysis of patients who spontaneously change disease status.

PubMed

Espinosa-de-Los-Monteros, Ana Laura; Sosa, Ernesto; Cheng, Sonia; Ochoa, Raquel; Sandoval, Carolina; Guinto, Gerardo; Mendoza, Victoria; Hernández, Irma; Molina, Mario; Mercado, Moisés

2006-03-01

The definition of biochemical cure in acromegaly involves both the normalization of IGF-1 and a glucose-suppressed GH level of < 1 ng/ml. These criteria were reached by several consensus meetings, although no evidence-based recommendations as to the optimal time to perform biochemical evaluations were made, nor was the fact that several patients may change biochemically upon long-term follow-up taken into consideration. To identify and characterize biochemical changes in the follow-up of acromegaly. One hundred and twenty-six acromegalic patients seen at a referral centre were followed prospectively (6-108 months) with regard to glucose-suppressed GH levels and IGF-1 concentrations. Eighty-nine patients did not change biochemical status, whereas in 37 (29.3%), one or more changes were identified, mostly during the first year. When glucose-suppressed GH values were discordant with the IGF-1 results, the likelihood of biochemical status modification was significantly greater than when such results were concordant [concordant 19.4%, discordant 57.6%, odds ratio (OR) = 5.6, 95% confidence interval (CI) = 2.3-13.3, P = 0.0001]. Among the changing patients, four out of the nine subjects initially considered as cured remained so at the last follow-up, whereas five became discordant; of the nine initially categorized as active, only three kept such a status at the last evaluation, whereas five became GH discordant and one achieved full biochemical criteria of cure; of 17 initially GH-discordant patients, seven remained so upon the last evaluation, whereas six became concordantly active and four concordantly cured. A significant proportion of acromegalic patients change biochemical status upon long-term follow-up after surgery. Most of these changes occur within the first postoperative year and are more likely to take place if the initial GH postglucose and IGF-1 levels are discordant.

Hematological and Biochemical Parameters in Elite Soccer Players During A Competitive Half Season

PubMed Central

Anđelković, Marija; Baralić, Ivana; Đorđević, Brižita; Stevuljević, Jelena Kotur; Radivojević, Nenad; Dikić, Nenad; Škodrić, Sanja Radojević; Stojković, Mirjana

2015-01-01

Summary Background The purpose of the present study was to report and discuss the hematological and biochemical behavior of elite soccer players, in order to get more insight in the physiological characteristics of these sportsmen and to provide trainers and sports doctors with useful indicators. Methods Nineteen male soccer players volunteered to participate in this study. We followed the young elite soccer players during a competitive half season. Venous blood samples were collected between 9:00 and 10:00 a.m. after an overnight fast (10 h) at baseline, after 45 and 90 days and hematological and biochemical parameters were measured. Results Hemoglobin and hematocrit levels were significantly reduced over the observational period (p<0.05), but erythrocyte count and iron levels remained unchanged. Bilirubin and ferritin levels significantly increased in response to regular soccer training (p<0.05). We observed a significant decrease in muscle enzyme plasma activity during the 90 days study period. ANOVA analysis revealed a significant increase in the leukocyte and neutrophil counts (p<0.05), in parallel with a significant decrease in the lymphocyte count (p<0.05) after the observational period of 90 days. Conclusions Elite soccer players are characterized by significant changes in biochemical and hematological parameters over the half season, which are linked to training workload, as well as adaptation induced by the soccer training. Although the values of the measured parameters fell within the reference range, regular monitoring of the biochemical and hematological parameters is fundamental for the identification of a healthy status and related optimal performances by sport doctors and trainers and selection of a correct workload by trainers. PMID:28356856

European spruce bark beetle (Ips typographus, L.) green attack affects foliar reflectance and biochemical properties

NASA Astrophysics Data System (ADS)

Abdullah, Haidi; Darvishzadeh, Roshanak; Skidmore, Andrew K.; Groen, Thomas A.; Heurich, Marco

2018-02-01

The European spruce bark beetle Ips typographus, L. (hereafter bark beetle), causes major economic loss to the forest industry in Europe, especially in Norway Spruce (Picea abies). To minimise economic loss and preclude a mass outbreak, early detection of bark beetle infestation (so-called ;green attack; stage - a period at which trees are yet to show visual signs of infestation stress) is, therefore, a crucial step in the management of Norway spruce stands. It is expected that a bark beetle infestation at the green attack stage affects a tree's physiological and chemical status. However, the concurrent effect on key foliar biochemical such as foliar nitrogen and chlorophyll as well as spectral responses are not well documented in the literature. Therefore, in this study, the early detection of bark beetle green attacks is investigated by examining foliar biochemical and spectral properties (400-2000 nm). We also assessed whether bark beetle infestation affects the estimation accuracy of foliar biochemicals. An extensive field survey was conducted in the Bavarian Forest National Park (BFNP), Germany, in the early summer of 2015 to collect leaf samples from 120 healthy and green attacked trees. The spectra of the leaf samples were measured using an ASD FieldSpec3 equipped with an integrating sphere. Significant differences (p < 0.05) between healthy and infested needle samples were found in the mean reflectance spectra, with the most pronounced differences being observed in the NIR and SWIR regions between 730 and 1370 nm. Furthermore, significant differences (p < 0.05) were found in the biochemical compositions (chlorophyll and nitrogen concentration) of healthy versus green attacked samples. Our results further demonstrate that the estimation accuracy of foliar chlorophyll and nitrogen concentrations, utilising partial least square regression model, was lower for the infested compared to the healthy trees. We show that early stage of infestation reduces not only

Computer extracted texture features on T2w MRI to predict biochemical recurrence following radiation therapy for prostate cancer

NASA Astrophysics Data System (ADS)

Ginsburg, Shoshana B.; Rusu, Mirabela; Kurhanewicz, John; Madabhushi, Anant

2014-03-01

In this study we explore the ability of a novel machine learning approach, in conjunction with computer-extracted features describing prostate cancer morphology on pre-treatment MRI, to predict whether a patient will develop biochemical recurrence within ten years of radiation therapy. Biochemical recurrence, which is characterized by a rise in serum prostate-specific antigen (PSA) of at least 2 ng/mL above the nadir PSA, is associated with increased risk of metastasis and prostate cancer-related mortality. Currently, risk of biochemical recurrence is predicted by the Kattan nomogram, which incorporates several clinical factors to predict the probability of recurrence-free survival following radiation therapy (but has limited prediction accuracy). Semantic attributes on T2w MRI, such as the presence of extracapsular extension and seminal vesicle invasion and surrogate measure- ments of tumor size, have also been shown to be predictive of biochemical recurrence risk. While the correlation between biochemical recurrence and factors like tumor stage, Gleason grade, and extracapsular spread are well- documented, it is less clear how to predict biochemical recurrence in the absence of extracapsular spread and for small tumors fully contained in the capsule. Computer{extracted texture features, which quantitatively de- scribe tumor micro-architecture and morphology on MRI, have been shown to provide clues about a tumor's aggressiveness. However, while computer{extracted features have been employed for predicting cancer presence and grade, they have not been evaluated in the context of predicting risk of biochemical recurrence. This work seeks to evaluate the role of computer-extracted texture features in predicting risk of biochemical recurrence on a cohort of sixteen patients who underwent pre{treatment 1.5 Tesla (T) T2w MRI. We extract a combination of first-order statistical, gradient, co-occurrence, and Gabor wavelet features from T2w MRI. To identify which of these

The prostate health index PHI predicts oncological outcome and biochemical recurrence after radical prostatectomy - analysis in 437 patients

PubMed Central

Maxeiner, Andreas; Kilic, Ergin; Matalon, Julia; Friedersdorff, Frank; Miller, Kurt; Jung, Klaus; Stephan, Carsten; Busch, Jonas

2017-01-01

The purpose of this study was to investigate the Prostate-Health-Index (PHI) for pathological outcome prediction following radical prostatectomy and also for biochemical recurrence prediction in comparison to established parameters such as Gleason-score, pathological tumor stage, resection status (R0/1) and prostate-specific antigen (PSA). Out of a cohort of 460 cases with preoperative PHI-measurements (World Health Organization calibration: Beckman Coulter Access-2-Immunoassay) between 2001 and 2014, 437 patients with complete follow up data were included. From these 437 patients, 87 (19.9%) developed a biochemical recurrence. Patient characteristics were compared by using chi-square test. Predictors were analyzed by multivariate adjusted logistic and Cox regression. The median follow up for a biochemical recurrence was 65 (range 3-161) months. PHI, PSA, [-2]proPSA, PHI- and PSA-density performed as significant variables (p < 0.05) for cancer aggressiveness: Gleason-score <7 or ≥7 (ISUP grade 1 or ≥2) . Concerning pathological tumor stage discrimination and prediction, variables as PHI, PSA, %fPSA, [-2]proPSA, PHI- and PSA-density significantly discriminated between stages biochemical recurrence prediction PHI, PSA, [-2]proPSA, PHI- and PSA-density were the strongest predictors. In conclusion, due to heterogeneity of time spans to biochemical recurrence, longer follow up periods are crucial. This study with a median follow up of more than 5 years, confirmed a clinical value for PHI as an independent biomarker essential for biochemical recurrence prediction. PMID:29108306

The prostate health index PHI predicts oncological outcome and biochemical recurrence after radical prostatectomy - analysis in 437 patients.

PubMed

Maxeiner, Andreas; Kilic, Ergin; Matalon, Julia; Friedersdorff, Frank; Miller, Kurt; Jung, Klaus; Stephan, Carsten; Busch, Jonas

2017-10-03

The purpose of this study was to investigate the Prostate-Health-Index (PHI) for pathological outcome prediction following radical prostatectomy and also for biochemical recurrence prediction in comparison to established parameters such as Gleason-score, pathological tumor stage, resection status (R0/1) and prostate-specific antigen (PSA). Out of a cohort of 460 cases with preoperative PHI-measurements (World Health Organization calibration: Beckman Coulter Access-2-Immunoassay) between 2001 and 2014, 437 patients with complete follow up data were included. From these 437 patients, 87 (19.9%) developed a biochemical recurrence. Patient characteristics were compared by using chi-square test. Predictors were analyzed by multivariate adjusted logistic and Cox regression. The median follow up for a biochemical recurrence was 65 (range 3-161) months. PHI, PSA, [-2]proPSA, PHI- and PSA-density performed as significant variables (p < 0.05) for cancer aggressiveness: Gleason-score <7 or ≥7 (ISUP grade 1 or ≥2) . Concerning pathological tumor stage discrimination and prediction, variables as PHI, PSA, %fPSA, [-2]proPSA, PHI- and PSA-density significantly discriminated between stages biochemical recurrence prediction PHI, PSA, [-2]proPSA, PHI- and PSA-density were the strongest predictors. In conclusion, due to heterogeneity of time spans to biochemical recurrence, longer follow up periods are crucial. This study with a median follow up of more than 5 years, confirmed a clinical value for PHI as an independent biomarker essential for biochemical recurrence prediction.

Physiological and biochemical responses of the Polychaete Diopatra neapolitana to organic matter enrichment.

PubMed

Carregosa, Vanessa; Velez, Cátia; Pires, Adília; Soares, Amadeu M V M; Figueira, Etelvina; Freitas, Rosa

2014-10-01

Several studies have demonstrated that organic matter enrichment may be associated to aquaculture, leading to impoverished benthic communities and species succession with loss of biodiversity, but very few studies have investigated biochemical and physiological alterations that species affected by aquaculture activities undergo. Thus, in the present study, the effects of the organic enrichment originating from an oyster culture were studied in the Polychaete Diopatra neapolitana, a species already shown to be sensitive to inorganic contamination. For this, physiological responses and biochemical alterations were evaluated. The results obtained revealed that individuals from highly organically enriched areas presented lower capacity to regenerate their body but higher glycogen and protein levels. Furthermore, with increasing organic matter D. neapolitana increased the lipid peroxidation (LPO), the oxidized glutathione content (GSSG) and Glutathione S-transferase activity (GSTs) content, and the activity of the antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD). This study evidenced that organic matter enrichment induced biochemical and physiological alterations in D. neapolitana. Thus, this species was shown to be a good sentinel species to monitor organic contamination. Copyright © 2014 Elsevier B.V. All rights reserved.

Antimicrobial susceptibility and biochemical patterns of Neisseria gonorrhoeae strains in Vejle area, Denmark.

PubMed

Lis-Tønder, J; Cybulski, Z

2009-10-01

Strains of Neisseria gonorrhoeae resistant to penicillin and ciprofloxacin have been isolated worldwide. Increasing number of N. gonorrhoeae that lack the enzyme proline aminopeptidase (proA-negative N. gonorrhoeae) have been detected in many countries all over the world. This study aims to assess the resistance profiles of N. gonorrhoeae isolates sent to the Department of Clinical Microbiology in Vejle, Denmark, between 2003 and 2007, and to analyse their biochemical patterns. Sixty-two strains of N. gonorrhoeae were retrospectively analysed for their susceptibility to penicillin, ciprofloxacin and ceftriaxone. The identification of isolated strains was confirmed using both biochemical and immunological tests. Twenty-one (33.9%) N. gonorrhoeae isolates were resistant to penicillin and 30 (48.4%) were resistant to ciprofloxacin. All strains were susceptible to ceftriaxone. Fifty-six (90.3%) N. gonorrhoeae strains showed API NH biochemical code 10,010 (produced acid from glucose and proline aminopeptidase). Six strains showed code 10,000 that lack the enzyme proline aminopeptidase (proA-negative N. gonorrhoeae). Ceftriaxone should be used as the first-line treatment of gonorrhoea in Vejle community area, Denmark, both for infections with proA-producing and proA-negative N. gonorrhoeae isolates, which circulate in the region.

Biochemical Basis of Sestrin Physiological Activities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Allison; Cho, Chun-Seok; Namkoong, Sim

Excessive accumulation of reactive oxygen species (ROS) and chronic activation of mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) are well-characterized promoters of aging and age-associated degenerative pathologies. Sestrins, a family of highly conserved stress-inducible proteins, are important negative regulators of both ROS and mTORC1 signaling pathways; however, the mechanistic basis of how Sestrins suppress these pathways remains elusive. In the past couple of years, breakthrough discoveries about Sestrin signaling and its molecular nature have markedly increased our biochemical understanding of Sestrin function. These discoveries have also uncovered new potential therapeutic strategies that may eventually enable us to attenuate agingmore » and age-associated diseases.« less