Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

PubMed

Kulasiri, Don

2011-01-01

We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

PubMed Central

Chevalier, Michael W.; El-Samad, Hana

2014-01-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled. PMID:25481130

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

NASA Astrophysics Data System (ADS)

Chevalier, Michael W.; El-Samad, Hana

2014-12-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.

Polyphenol Oxidases in Crops: Biochemical, Physiological and Genetic Aspects

PubMed Central

Taranto, Francesca; Pasqualone, Antonella; Mangini, Giacomo; Tripodi, Pasquale; Miazzi, Monica Marilena; Pavan, Stefano; Montemurro, Cinzia

2017-01-01

Enzymatic browning is a colour reaction occurring in plants, including cereals, fruit and horticultural crops, due to oxidation during postharvest processing and storage. This has a negative impact on the colour, flavour, nutritional properties and shelf life of food products. Browning is usually caused by polyphenol oxidases (PPOs), following cell damage caused by senescence, wounding and the attack of pests and pathogens. Several studies indicated that PPOs play a role in plant immunity, and emerging evidence suggested that PPOs might also be involved in other physiological processes. Genomic investigations ultimately led to the isolation of PPO homologs in several crops, which will be possibly characterized at the functional level in the near future. Here, focusing on the botanic families of Poaceae and Solanaceae, we provide an overview on available scientific literature on PPOs, resulting in useful information on biochemical, physiological and genetic aspects. PMID:28208645

Molecular changes and signaling events occurring in sperm during epididymal maturation

PubMed Central

Gervasi, Maria Gracia; Visconti, Pablo E.

2017-01-01

After leaving the testis, sperm have not yet acquired the ability to move progressively and are unable to fertilize oocytes. To become fertilization-competent they must go through an epididymal maturation process in the male, and capacitation in the female tract. Epididymal maturation can be defined as those changes occurring to sperm in the epididymis that render the sperm the ability to capacitate in the female tract. As part of this process, sperm cells undergo a series of biochemical and physiological changes that require incorporation of new molecules derived from the epididymal epithelium, as well as post-translational modifications of endogenous proteins synthesized during spermiogenesis in the testis. This review will focus on epididymal maturation events, with emphasis in recent advances in the understanding of the molecular basis of this process. PMID:28297559

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

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

Chevalier, Michael W., E-mail: Michael.Chevalier@ucsf.edu; El-Samad, Hana, E-mail: Hana.El-Samad@ucsf.edu

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation timesmore » of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.« less

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.

Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth.

PubMed

Liu, Jinwen; Hai, Guanghui; Wang, Chong; Cao, Shenquan; Xu, Wenjing; Jia, Zhigang; Yang, Chuanping; Wang, Jack P; Dai, Shaojun; Cheng, Yuxiang

2015-08-03

Wood is derived from the secondary growth of tree stems. In this study, we investigated the global changes of protein abundance in Populus early stems using a proteomic approach. Morphological and histochemical analyses revealed three typical stages during Populus early stems, which were the primary growth stage, the transition stage from primary to secondary growth and the secondary growth stage. A total of 231 spots were differentially abundant during various growth stages of Populus early stems. During Populus early stem lignifications, 87 differential spots continuously increased, while 49 spots continuously decreased. These two categories encompass 58.9% of all differential spots, which suggests significant molecular changes from primary to secondary growth. Among 231 spots, 165 unique proteins were identified using LC-ESI-Q-TOF-MS, which were classified into 14 biological function groups. The proteomic characteristics indicated that carbohydrate metabolism, oxido-reduction, protein degradation and secondary cell wall metabolism were the dominantly occurring biochemical processes during Populus early stem development. This study helps in elucidating biochemical processes and identifies potential wood formation-related proteins during tree early stem development. It is a comprehensive proteomic investigation on tree early stem development that, for the first time, reveals the overall molecular networks that occur during Populus early stem lignifications. Copyright © 2015. Published by Elsevier B.V.

Biochemical label-free tissue imaging with subcellular-resolution synchrotron FTIR with focal plane array detector.

PubMed

Kastyak-Ibrahim, M Z; Nasse, M J; Rak, M; Hirschmugl, C; Del Bigio, M R; Albensi, B C; Gough, K M

2012-03-01

The critical questions into the cause of neural degeneration, in Alzheimer disease and other neurodegenerative disorders, are closely related to the question of why certain neurons survive. Answers require detailed understanding of biochemical changes in single cells. Fourier transform infrared microspectroscopy is an excellent tool for biomolecular imaging in situ, but resolution is limited. The mid-infrared beamline IRENI (InfraRed ENvironmental Imaging) at the Synchrotron Radiation Center, University of Wisconsin-Madison, enables label-free subcellular imaging and biochemical analysis of neurons with an increase of two orders of magnitude in pixel spacing over current systems. With IRENI's capabilities, it is now possible to study changes in individual neurons in situ, and to characterize their surroundings, using only the biochemical signatures of naturally-occurring components in unstained, unfixed tissue. We present examples of analyses of brain from two transgenic mouse models of Alzheimer disease (TgCRND8 and 3xTg) that exhibit different features of pathogenesis. Data processing on spectral features for nuclei reveals individual hippocampal neurons, and neurons located in the proximity of amyloid plaque in TgCRND8 mouse. Elevated lipids are detected surrounding and, for the first time, within the dense core of amyloid plaques, offering support for inflammatory and aggregation roles. Analysis of saturated and unsaturated fatty acid ester content in retina allows characterization of neuronal layers. IRENI images also reveal spatially-resolved data with unprecedented clarity and distinct spectral variation, from sub-regions including photoreceptors, neuronal cell bodies and synapses in sections of mouse retina. Biochemical composition of retinal layers can be used to study changes related to disease processes and dietary modification. Copyright © 2011 Elsevier Inc. All rights reserved.

Effect of processing on nutritive values of milk protein.

PubMed

Borad, Sanket G; Kumar, Anuj; Singh, Ashish K

2017-11-22

Milk is an essential source of nutritionally excellent quality protein in human, particularly in vegan diet. Before consumption, milk is invariably processed depending upon final product requirement. This processing may alter the nutritive value of protein in a significant manner. The processing operations like thermal treatment, chemical treatment, biochemical processing, physical treatments, nonconventional treatments, etc. may exert positive or negative influence on nutritional quality of milk proteins. On one side, processing enhances the nutritive and therapeutic values of protein while on other side intermediate or end products generated during protein reactions may cause toxicity and/or antigenicity upon consumption at elevated level. The review discusses the changes occurring in nutritive quality of milk proteins under the influence of various processing operations.

Isotopic inferences of ancient biochemistries - Carbon, sulfur, hydrogen, and nitrogen

NASA Technical Reports Server (NTRS)

Schidlowski, M.; Hayes, J. M.; Kaplan, I. R.

1983-01-01

In processes of biological incorporation and subsequent biochemical processing sizable isotope effects occur as a result of both thermodynamic and kinetic fractionations which take place during metabolic and biosynthetic reactions. In this chapter a review is provided of earlier work and recent studies on isotope fractionations in the biogeochemical cycles of carbon, sulfur, hydrogen, and nitrogen. Attention is given to the biochemistry of carbon isotope fractionation, carbon isotope fractionation in extant plants and microorganisms, isotope fractionation in the terrestrial carbon cycle, the effects of diagenesis and metamorphism on the isotopic composition of sedimentary carbon, the isotopic composition of sedimentary carbon through time, implications of the sedimentary carbon isotope record, the biochemistry of sulfur isotope fractionation, pathways of the biogeochemical cycle of nitrogen, and the D/H ratio in naturally occurring materials.

Recent Advances in Transferable Coarse-Grained Modeling of Proteins

PubMed Central

Kar, Parimal; Feig, Michael

2017-01-01

Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems are employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multi-scale hybrid all-atom/coarse-grained simulations of proteins. PMID:25443957

Use of fibroblast growth factor 2 for expansion of chondrocytes and tissue engineering

NASA Technical Reports Server (NTRS)

Vunjak-Novakovic, Gordana (Inventor); Martin, Ivan (Inventor); Freed, Lisa E. (Inventor); Langer, Robert (Inventor)

2003-01-01

The present invention provides an improved method for expanding cells for use in tissue engineering. In particular the method provides specific biochemical factors to supplement cell culture medium during the expansion process in order to reproduce events occurring during embryonic development with the goal of regenerating tissue equivalents that resemble natural tissues both structurally and functionally. These specific biochemical factors improve proliferation of the cells and are capable of de-differentiation mature cells isolated from tissue so that the differentiation potential of the cells is preserved. The bioactive molecules also maintain the responsiveness of the cells to other bioactive molecules. Specifically, the invention provides methods for expanding chondrocytes in the presence of fibroblast growth factor 2 for use in regeneration of cartilage tissue.

In singulo biochemistry: when less is more.

PubMed

Bustamante, Carlos

2008-01-01

It has been over one-and-a-half decades since methods of single-molecule detection and manipulation were first introduced in biochemical research. Since then, the application of these methods to an expanding variety of problems has grown at a vertiginous pace. While initially many of these experiments led more to confirmatory results than to new discoveries, today single-molecule methods are often the methods of choice to establish new mechanism-based results in biochemical research. Throughout this process, improvements in the sensitivity, versatility, and both spatial and temporal resolution of these techniques has occurred hand in hand with their applications. We discuss here some of the advantages of single-molecule methods over their bulk counterparts and argue that these advantages should help establish them as essential tools in the technical arsenal of the modern biochemist.

When galectins recognize glycans: from biochemistry to physiology and back again.

PubMed

Di Lella, Santiago; Sundblad, Victoria; Cerliani, Juan P; Guardia, Carlos M; Estrin, Dario A; Vasta, Gerardo R; Rabinovich, Gabriel A

2011-09-20

In the past decade, increasing efforts have been devoted to the study of galectins, a family of evolutionarily conserved glycan-binding proteins with multifunctional properties. Galectins function, either intracellularly or extracellularly, as key biological mediators capable of monitoring changes occurring on the cell surface during fundamental biological processes such as cellular communication, inflammation, development, and differentiation. Their highly conserved structures, exquisite carbohydrate specificity, and ability to modulate a broad spectrum of biological processes have captivated a wide range of scientists from a wide spectrum of disciplines, including biochemistry, biophysics, cell biology, and physiology. However, in spite of enormous efforts to dissect the functions and properties of these glycan-binding proteins, limited information about how structural and biochemical aspects of these proteins can influence biological functions is available. In this review, we aim to integrate structural, biochemical, and functional aspects of this bewildering and ancient family of glycan-binding proteins and discuss their implications in physiologic and pathologic settings. © 2011 American Chemical Society

Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance.

PubMed

Ghodke, Harshad; Ho, Han; van Oijen, Antoine M

2018-02-19

Genomic DNA is constantly under threat from intracellular and environmental factors that damage its chemical structure. Uncorrected DNA damage may impede cellular propagation or even result in cell death, making it critical to restore genomic integrity. Decades of research have revealed a wide range of mechanisms through which repair factors recognize damage and co-ordinate repair processes. In recent years, single-molecule live-cell imaging methods have further enriched our understanding of how repair factors operate in the crowded intracellular environment. The ability to follow individual biochemical events, as they occur in live cells, makes single-molecule techniques tremendously powerful to uncover the spatial organization and temporal regulation of repair factors during DNA-repair reactions. In this review, we will cover practical aspects of single-molecule live-cell imaging and highlight recent advances accomplished by the application of these experimental approaches to the study of DNA-repair processes in prokaryotes. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

In vivo biochemistry: quantifying ion and metabolite levels in individual cells or cultures of yeast.

PubMed

Bermejo, Clara; Ewald, Jennifer C; Lanquar, Viviane; Jones, Alexander M; Frommer, Wolf B

2011-08-15

Over the past decade, we have learned that cellular processes, including signalling and metabolism, are highly compartmentalized, and that relevant changes in metabolic state can occur at sub-second timescales. Moreover, we have learned that individual cells in populations, or as part of a tissue, exist in different states. If we want to understand metabolic processes and signalling better, it will be necessary to measure biochemical and biophysical responses of individual cells with high temporal and spatial resolution. Fluorescence imaging has revolutionized all aspects of biology since it has the potential to provide information on the cellular and subcellular distribution of ions and metabolites with sub-second time resolution. In the present review we summarize recent progress in quantifying ions and metabolites in populations of yeast cells as well as in individual yeast cells with the help of quantitative fluorescent indicators, namely FRET metabolite sensors. We discuss the opportunities and potential pitfalls and the controls that help preclude misinterpretation. © The Authors Journal compilation © 2011 Biochemical Society

Insights in the Fruit Flesh Browning Mechanisms in Solanum melongena Genetic Lines with Opposite Postcut Behavior.

PubMed

Docimo, T; Francese, G; De Palma, M; Mennella, D; Toppino, L; Lo Scalzo, R; Mennella, G; Tucci, M

2016-06-08

Color, taste, flavor, nutritional value, and shelf life are important factors determining quality and healthiness of food and vegetables. These factors are strongly affected by browning processes, occurring after fruit or vegetable cutting. Characterization of ten eggplant genotypes for chlorogenic acid (CGA) content, total phenols (TP), polyphenoloxidase (PPO) activity, and browning tendency corroborated a lack of significant correlations between biochemical factors and fruit flesh browning. Further in-depth molecular and biochemical analyses of two divergent eggplant genetic lines, AM199 (high browning) and AM086 (low browning), within 30 min from cutting, highlighted differences in the physiological mechanisms underlying the browning process. qRT-PCR analysis revealed distinct activation mechanisms of CGA biosynthetic and PPO genes in the two genetic lines. Metabolic data on CGA, sugars, and ascorbic acid contents confirmed that their different browning tendency matched with different metabolic responses to cutting. Our findings suggest that the complex mechanism of flesh browning in the two eggplant genetic lines might be mediated by multiple specific factors.

Modeling transformation of soil organic matter through the soil enzyme activity

NASA Astrophysics Data System (ADS)

Tregubova, Polina; Vladimirov, Artem; Vasilyeva, Nadezda

2017-04-01

The sensitivity of soil heterotrophic respiration to changing environmental conditions is widely investigated nowadays but still remain extremely controversial. The mechanisms are still needed to reveal. In this work we model soil C and N biogeochemical cycles based on general principles of soil carbon and nitrogen dynamics with focusing on biochemical processes occurring in the soil based on well known classes of enzymes and organic compounds that they can transform. According to classic theories, exoenzymes and endoenzymes of bacteria and fungi as stable over a long period catalytic components play a significant role in degradation of plant and animal residues, decomposition of biopolymers of different sizes, humification processes and in releasing of labile compounds essential for the microorganism and plant growth and germination. We test the model regimes sensitivity to such environmental factors as temperature and moisture. Modeling the directions and patterns of soil biochemical activity is important for evaluation of soil agricultural productivity as well as its ecological functions.

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases.

PubMed

Tomecki, Rafal; Sikorski, Pawel J; Zakrzewska-Placzek, Monika

2017-07-01

Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans. © 2017 Federation of European Biochemical Societies.

Chemical evolution and the origin of life.

PubMed

Oro, J

1983-01-01

During the last three decades major advances have been made in our understanding of the formation of carbon compounds in the universe and of the occurence of processes of chemical evolution. 1) Carbon and other biogenic elements (C,H,N,O,S and P) are some of the most abundant in the universe. 2) The interstellar medium has been found to contain a diversity of molecules of these elements. 3) Some of these molecules have also been found in comets which are considered the most primordial bodies of the solar system. 4) The atmospheres of the outer planets and their satellites, for example, Titan, are actively involved in the formation of organic compounds which are the precursors of biochemical molecules. 5) Some of these biochemical molecules, such as amino acids, purines and pyrimidines, have been found in carbonaceous chondrites. 6) Laboratory experiments have shown that most of the monomers and oligomers necessary for life can be synthesized under hypothesized but plausible primitive Earth conditions from compounds found in the above cosmic bodies. 7) It appears that the primitive Earth had the necessary and sufficient conditions to allow the chemical synthesis of biomacromolecules and to permit the processes required for the emergence of life on our planet. 8) It is unlikely that the emergence of life occurred in any other body of the solar system, although the examination of the Jovian satellite Europa may provide important clues about the constraints of this evolutionary process. Some of the fundamental principles of chemical evolution are briefly discussed.

[Analysis and research on the degradation and migration of organic pollutants in textile wastewater treatment process by GC-MS].

PubMed

Liu, Wei-jing; Zhang, Long; Wu, Wei; Tu, Yong

2010-04-01

In order to analyze the advantages/disadvantages of the combined treatment process between "physicochemical + biochemical" and "biochemical + physicochemical" in treatment of textile wastewater, gas chromatography-mass spectrometry (GC-MS) was used to determine the degradation process of organic pollutants in this two totally different treatment processes. The same analysis was also conducted to the sludge and discharged water. The results showed that the "physicochemical + biochemical" process displayed a poorer effect than "biochemical + physicochemical" in degrading the organic pollutants. The latter was 6.2% higher than the former in removing the organic pollutants averagely. The difference was mainly manifested in the efficiency of anaerobic hydrolysis in the two coupled processes. Moreover, the implement of "physicochemical + biochemical" process resulted in the migration of plenty of typical organic pollutants to sludge from primary coagulation sedimentation process and to the discharged water, which would cause secondary pollution easily.

The histone shuffle: histone chaperones in an energetic dance

PubMed Central

Das, Chandrima; Tyler, Jessica K.; Churchill, Mair E.A.

2014-01-01

Our genetic information is tightly packaged into a rather ingenious nucleoprotein complex called chromatin in a manner that enables it to be rapidly accessed during genomic processes. Formation of the nucleosome, which is the fundamental unit of chromatin, occurs via a stepwise process that is reversed to enable the disassembly of nucleosomes. Histone chaperone proteins have prominent roles in facilitating these processes as well as in replacing old histones with new canonical histones or histone variants during the process of histone exchange. Recent structural, biophysical and biochemical studies have begun to shed light on the molecular mechanisms whereby histone chaperones promote chromatin assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription. PMID:20444609

Processes influencing seasonal hypoxia in the northern California Current System

PubMed Central

Connolly, T. P.; Hickey, B. M.; Geier, S. L.; Cochlan, W. P.

2010-01-01

This paper delineates the role of physical and biological processes contributing to hypoxia, dissolved oxygen (DO) < 1.4 mL/L, over the continental shelf of Washington State in the northern portion of the California Current System (CCS). In the historical record (1950–1986) during the summer upwelling season, hypoxia is more prevalent and severe off Washington than further south off northern Oregon. Recent data (2003–2005) show that hypoxia over the Washington shelf occurred at levels previously observed in the historical data. 2006 was an exception, with hypoxia covering ~5000 km2 of the Washington continental shelf and DO concentrations below 0.5 mL/L at the inner shelf, lower than any known previous observations at that location. In the four years studied, upwelling of low DO water and changes in source water contribute to interannual variability, but cannot account for seasonal decreases below hypoxic concentrations. Deficits of DO along salinity surfaces, indicating biochemical consumption of DO, vary significantly between surveys, accounting for additional decreases of 0.5–2.5 mL/L by late summer. DO consumption is associated with denitrification, an indicator of biochemical sediment processes. Mass balances of DO and nitrate show that biochemical processes in the water column and sediments each contribute ~50% to the total consumption of DO in near-bottom water. At shorter than seasonal time scales on the inner shelf, along-shelf advection of hypoxic patches and cross-shelf advection of seasonal gradients are both shown to be important, changing DO concentrations by 1.5 mL/L or more over five days. PMID:20463844

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.

Calculation of biochemical net reactions and pathways by using matrix operations.

PubMed Central

Alberty, R A

1996-01-01

Pathways for net biochemical reactions can be calculated by using a computer program that solves systems of linear equations. The coefficients in the linear equations are the stoichiometric numbers in the biochemical equations for the system. The solution of the system of linear equations is a vector of the stoichiometric numbers of the reactions in the pathway for the net reaction; this is referred to as the pathway vector. The pathway vector gives the number of times the various reactions have to occur to produce the desired net reaction. Net reactions may involve unknown numbers of ATP, ADP, and Pi molecules. The numbers of ATP, ADP, and Pi in a desired net reaction can be calculated in a two-step process. In the first step, the pathway is calculated by solving the system of linear equations for an abbreviated stoichiometric number matrix without ATP, ADP, Pi, NADred, and NADox. In the second step, the stoichiometric numbers in the desired net reaction, which includes ATP, ADP, Pi, NADred, and NADox, are obtained by multiplying the full stoichiometric number matrix by the calculated pathway vector. PMID:8804633

Recurrence of Phaeochromocytoma and Abdominal Paraganglioma After Initial Surgical Intervention.

PubMed

Johnston, Philip C; Mullan, Karen R; Atkinson, A Brew; Eatock, Fiona C; Wallace, Helen; Gray, Moyra; Hunter, Steven J

2015-05-01

Clinical and biochemical follow up after surgery for phaeochromocytoma is essential with long term studies demonstrating recurrence frequencies between 6% and 23%. To examine the characteristics and frequency of tumour recurrence in a regional endocrine referral centre, in patients with surgical resection of phaeochromocytoma (P) and abdominal paraganglioma (AP). We identified a cohort of 52 consecutive patients who attended our Regional Endocrinology & Diabetes Centre and retrospectively reviewed their clinical, biochemical and radiological data (between 2002 and 2013). After confirmation of early post-operative remission by negative biochemical testing, tumour recurrence was defined by demonstration of catecholamine excess with confirmatory imaging. Phaeochromocytoma was confirmed histologically in all cases (43:P, 9:AP, mean-age:53 years). Open adrenalectomy was performed in 20 cases and laparoscopically in 32. Hereditary phaeochromocytoma was confirmed by genetic analysis in 12 (23%) patients. Median follow up time from initial surgery was 47 months, (range: 12 - 296 months), 49 patients had no evidence of tumour recurrence at latest follow-up. Three patients (6%) demonstrated tumour development, one in a patient with VHL which occurred in a contralateral adrenal gland, one sporadic case had local recurrence, and an adrenal tumour occurred in a patient with a SDHB gene mutation who had a previous bladder tumour. After initial surgery, the tumours occurred at 8.6, 12.0 and 17.7 years respectively. In this study tumour development occurred in 6% of patients. Although tumour rates were low, careful and sustained clinical and biochemical follow up is advocated, as new tumour development or recurrence may occur long after the initial surgery is performed.

Malodorous volatile organic sulfur compounds: Sources, sinks and significance in inland waters.

PubMed

Watson, Susan B; Jüttner, Friedrich

2017-03-01

Volatile Organic Sulfur Compounds (VOSCs) are instrumental in global S-cycling and greenhouse gas production. VOSCs occur across a diversity of inland waters, and with widespread eutrophication and climate change, are increasingly linked with malodours in organic-rich waterbodies and drinking-water supplies. Compared with marine systems, the role of VOSCs in biogeochemical processes is far less well characterized for inland waters, and often involves different physicochemical and biological processes. This review provides an updated synthesis of VOSCs in inland waters, focusing on compounds known to cause malodours. We examine the major limnological and biochemical processes involved in the formation and degradation of alkylthiols, dialkylsulfides, dialkylpolysulfides, and other organosulfur compounds under different oxygen, salinity and mixing regimes, and key phototropic and heterotrophic microbial producers and degraders (bacteria, cyanobacteria, and algae) in these environs. The data show VOSC levels which vary significantly, sometimes far exceeding human odor thresholds, generated by a diversity of biota, biochemical pathways, enzymes and precursors. We also draw attention to major issues in sampling and analytical artifacts which bias and preclude comparisons among studies, and highlight significant knowledge gaps that need addressing with careful, appropriate methods to provide a more robust understanding of the potential effects of continued global development.

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.

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.

Biochemical composition of deep-sea decapod crustaceans with two different benthic life strategies off the Portuguese south coast

NASA Astrophysics Data System (ADS)

Rosa, R.; Nunes, M. L.

2003-01-01

The objectives of the present study were to characterize the benthic life strategies of Aristeus antennatus (Crustacea: Penaeidea), Parapenaeus longirostris (Crustacea: Penaeidea) and Nephrops norvegicus (Crustacea: Astacidea) on the basis of biochemical composition (proximate chemical composition, total lipids, glycogen and cholesterol contents), and its response to biological and environmental factors (sex, maturation, reproduction, food availability and depth) into account. The specimens were collected at depths between 200 and 600 m off the Portuguese south coast (Algarve). The nektobenthic species ( A. antennatus and P. longirostris) showed higher protein, lipid, cholesterol and glycogen contents, and lower moisture content in the muscle than the benthic-endobenthic species ( N. norvegicus). Consequently, the energy content of the nektobenthic species was also higher. Principal component analyses were used to assess the relationship between the different biochemical contents and to relate them to the biotic and abiotic factors. Depth seems to have the most important role in the observed trends of the biochemical composition. The increase of the ovarian lipid levels occurs as a result of the maturation process. The highest values were obtained in mature N. norvegicus females. The differences can be due to maternal investment (lipid metabolism of the female is geared to the provision of egg lipid), since N. norvegicus produce large lecithotrophic eggs. The biochemical differences observed in the three species did not seem to be due to distinct trophic strategies, but instead were a consequence of depth, which may have a significant interspecific effect on food intake. It was also evident that reproductive cycle has profound effects upon the biochemistry of the three species. Gonadal maturation has large associated energy costs due to the increase in biosynthetic work. Moreover, the biochemical composition would be influenced by or synchronized with seasonal feeding activity or food availability.

Alcohols as alkylating agents in heteroarene C-H functionalization

NASA Astrophysics Data System (ADS)

Jin, Jian; MacMillan, David W. C.

2015-09-01

Redox processes and radical intermediates are found in many biochemical processes, including deoxyribonucleotide synthesis and oxidative DNA damage. One of the core principles underlying DNA biosynthesis is the radical-mediated elimination of H2O to deoxygenate ribonucleotides, an example of `spin-centre shift', during which an alcohol C-O bond is cleaved, resulting in a carbon-centred radical intermediate. Although spin-centre shift is a well-understood biochemical process, it is underused by the synthetic organic chemistry community. We wondered whether it would be possible to take advantage of this naturally occurring process to accomplish mild, non-traditional alkylation reactions using alcohols as radical precursors. Because conventional radical-based alkylation methods require the use of stoichiometric oxidants, increased temperatures or peroxides, a mild protocol using simple and abundant alkylating agents would have considerable use in the synthesis of diversely functionalized pharmacophores. Here we describe the development of a dual catalytic alkylation of heteroarenes, using alcohols as mild alkylating reagents. This method represents the first, to our knowledge, broadly applicable use of unactivated alcohols as latent alkylating reagents, achieved via the successful merger of photoredox and hydrogen atom transfer catalysis. The value of this multi-catalytic protocol has been demonstrated through the late-stage functionalization of the medicinal agents, fasudil and milrinone.

Alcohols as alkylating agents in heteroarene C-H functionalization.

PubMed

Jin, Jian; MacMillan, David W C

2015-09-03

Redox processes and radical intermediates are found in many biochemical processes, including deoxyribonucleotide synthesis and oxidative DNA damage. One of the core principles underlying DNA biosynthesis is the radical-mediated elimination of H2O to deoxygenate ribonucleotides, an example of 'spin-centre shift', during which an alcohol C-O bond is cleaved, resulting in a carbon-centred radical intermediate. Although spin-centre shift is a well-understood biochemical process, it is underused by the synthetic organic chemistry community. We wondered whether it would be possible to take advantage of this naturally occurring process to accomplish mild, non-traditional alkylation reactions using alcohols as radical precursors. Because conventional radical-based alkylation methods require the use of stoichiometric oxidants, increased temperatures or peroxides, a mild protocol using simple and abundant alkylating agents would have considerable use in the synthesis of diversely functionalized pharmacophores. Here we describe the development of a dual catalytic alkylation of heteroarenes, using alcohols as mild alkylating reagents. This method represents the first, to our knowledge, broadly applicable use of unactivated alcohols as latent alkylating reagents, achieved via the successful merger of photoredox and hydrogen atom transfer catalysis. The value of this multi-catalytic protocol has been demonstrated through the late-stage functionalization of the medicinal agents, fasudil and milrinone.

Spatial and Temporal Scales of Surface Water-Groundwater Interactions

NASA Astrophysics Data System (ADS)

Boano, F.

2016-12-01

The interfaces between surface water and groundwater (i.e., river and lake sediments) represent hotspots for nutrient transformation in watersheds. This intense biochemical activity stems from the peculiar physicochemical properties of these interface areas. Here, the exchange of water and nutrients between surface and subsurface environments creates an ecotone region that can support the presence of different microbial species responsible for nutrient transformation. Previous studies have elucidated that water exchange between rivers and aquifers is organized in a complex system of nested flow cells. Each cell entails a range of residence timescales spanning multiple order of magnitudes, providing opportunities for different biochemical reactions to occur. Physically-bases models represent useful tools to deal with the wide range of spatial and temporal scales that characterize surface-subsurface water exchange. This contribution will present insights about how hydrodynamic processes control scale organization for surface water - groundwater interactions. The specific focus will be the influence of exchange processes on microbial activity and nutrient transformation, discussing how groundwater flow at watershed scale controls flow conditions and hence constrain microbial reactions at much smaller scales.

The Mechanobiology of Aging

PubMed Central

Walston, Jeremy; Wirtz, Denis

2016-01-01

Aging is a complex, multifaceted process that induces a myriad of physiological changes over an extended period of time. Aging is accompanied by major biochemical and biomechanical changes at macroscopic and microscopic length scales that affect not only tissues and organs but also cells and subcellular organelles. These changes include transcriptional and epigenetic modifications; changes in energy production within mitochondria; and alterations in the overall mechanics of cells, their nuclei, and their surrounding extracellular matrix. In addition, aging influences the ability of cells to sense changes in extracellular-matrix compliance (mechanosensation) and to transduce these changes into biochemical signals (mechanotransduction). Moreover, following a complex positive-feedback loop, aging is accompanied by changes in the composition and structure of the extracellular matrix, resulting in changes in the mechanics of connective tissues in older individuals. Consequently, these progressive dysfunctions facilitate many human pathologies and deficits that are associated with aging, including cardiovascular, musculoskeletal, and neurodegenerative disorders and diseases. Here, we critically review recent work highlighting some of the primary biophysical changes occurring in cells and tissues that accompany the aging process. PMID:26643020

[Participation of final products of lipid peroxidation in the anticancer mechanism of ionizing radiation and radiomimetic cytostatics].

PubMed

Przybyszewski, W M

2001-01-01

This review reports the evidence for the participation of final products of lipid peroxidation in the anticancer mechanism of ionising radiation and radiomimetic cytostatics. Processes of lipid peroxidation occur endogenously in response to oxidative stress and great diversity of reactive metabolites is formed. However, direct observation of radical reaction in pathophysiology of cells, tissues and organs is limited technically. Most investigations focused on the indirect assessment of their final products, aldehydes. The peroxidative breakdown of polyunsaturated fatty acids is believed to be involved in the regulation of cell division, and antitumor effect through biochemical and genetic processes.

Toward better understanding of postharvest deterioration: biochemical changes in stored cassava (Manihot esculenta Crantz) roots.

PubMed

Uarrota, Virgílio Gavicho; Nunes, Eduardo da Costa; Peruch, Luiz Augusto Martins; Neubert, Enilto de Oliveira; Coelho, Bianca; Moresco, Rodolfo; Domínguez, Moralba Garcia; Sánchez, Teresa; Meléndez, Jorge Luis Luna; Dufour, Dominique; Ceballos, Hernan; Becerra Lopez-Lavalle, Luis Augusto; Hershey, Clair; Rocha, Miguel; Maraschin, Marcelo

2016-05-01

Food losses can occur during production, postharvest, and processing stages in the supply chain. With the onset of worldwide food shortages, interest in reducing postharvest losses in cassava has been increasing. In this research, the main goal was to evaluate biochemical changes and identify the metabolites involved in the deterioration of cassava roots. We found that high levels of ascorbic acid (AsA), polyphenol oxidase (PPO), dry matter, and proteins are correlated with overall lower rates of deterioration. On the other hand, soluble sugars such as glucose and fructose, as well as organic acids, mainly, succinic acid, seem to be upregulated during storage and may play a role in the deterioration of cassava roots. Cultivar Branco (BRA) was most resilient to postharvest physiological deterioration (PPD), while Oriental (ORI) was the most susceptible. Our findings suggest that PPO, AsA, and proteins may play a distinct role in PPD delay.

Recurrence of Phaeochromocytoma and Abdominal Paraganglioma After Initial Surgical Intervention

PubMed Central

Mullan, Karen R; Atkinson, A Brew; Eatock, Fiona C; Wallace, Helen; Gray, Moyra; Hunter, Steven J

2015-01-01

Background Clinical and biochemical follow up after surgery for phaeochromocytoma is essential with long term studies demonstrating recurrence frequencies between 6% and 23%. Aim To examine the characteristics and frequency of tumour recurrence in a regional endocrine referral centre, in patients with surgical resection of phaeochromocytoma (P) and abdominal paraganglioma (AP). Methods We identified a cohort of 52 consecutive patients who attended our Regional Endocrinology & Diabetes Centre and retrospectively reviewed their clinical, biochemical and radiological data (between 2002 and 2013). After confirmation of early post-operative remission by negative biochemical testing, tumour recurrence was defined by demonstration of catecholamine excess with confirmatory imaging. Results Phaeochromocytoma was confirmed histologically in all cases (43:P, 9:AP, mean-age:53years). Open adrenalectomy was performed in 20 cases and laparoscopically in 32. Hereditary phaeochromocytoma was confirmed by genetic analysis in 12 (23%) patients. Median follow up time from initial surgery was 47 months, (range: 12 - 296 months), 49 patients had no evidence of tumour recurrence at latest follow-up. Three patients (6%) demonstrated tumour development, one in a patient with VHL which occurred in a contralateral adrenal gland, one sporadic case had local recurrence, and an adrenal tumour occurred in a patient with a SDHB gene mutation who had a previous bladder tumour. After initial surgery, the tumours occurred at 8.6, 12.0 and 17.7 years respectively. Conclusion In this study tumour development occurred in 6% of patients. Although tumour rates were low, careful and sustained clinical and biochemical follow up is advocated, as new tumour development or recurrence may occur long after the initial surgery is performed. PMID:26170485

In search of mitochondrial mechanisms: interfield excursions between cell biology and biochemistry.

PubMed

Bechtel, William; Abrahamsen, Adele

2007-01-01

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration.

Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes.

PubMed

Huang, Ruiqi; O'Donnell, Andrew J; Barboline, Jessica J; Barkman, Todd J

2016-09-20

Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

PubMed Central

Huang, Ruiqi; O’Donnell, Andrew J.; Barboline, Jessica J.; Barkman, Todd J.

2016-01-01

Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study. PMID:27638206

Analytical considerations and dimensionless analysis for a description of particle interactions in high pressure processes

NASA Astrophysics Data System (ADS)

Rauh, Cornelia; Delgado, Antonio

2010-12-01

High pressures of up to several hundreds of MPa are utilized in a wide range of applications in chemical, bio-, and food engineering, aiming at selective control of (bio-)chemical reactions. Non-uniformity of process conditions may threaten the safety and quality of the resulting products because processing conditions such as pressure, temperature, and treatment history are crucial for the course of (bio-)chemical reactions. Therefore, thermofluid-dynamical phenomena during the high pressure process have to be examined, and numerical tools to predict process uniformity and to optimize the processes have to be developed. Recently applied mathematical models and numerical simulations of laboratory and industrial scale high pressure processes investigating the mentioned crucial phenomena are based on continuum balancing models of thermofluid dynamics. Nevertheless, biological systems are complex fluids containing the relevant (bio-)chemical compounds (enzymes and microorganisms). These compounds are particles that interact with the surrounding medium and between each other. This contribution deals with thermofluid-dynamical interactions of the relevant particulate (bio-)chemical compounds (enzymes and microorganisms) with the surrounding fluid. By consideration of characteristic time and length scales and particle forces, the motion of the (bio-)chemical compounds is characterized.

Alcohols as alkylating agents in heteroarene C–H functionalization

PubMed Central

Jin, Jian; MacMillan, David W. C.

2015-01-01

Redox processes and radical intermediates are found in many biochemical processes, including deoxyribonucleotide synthesis and oxidative DNA damage1. One of the core principles that underlies DNA biosynthesis is the radical-mediated elimnation of H2O to deoxygenate ribonucleotides, an example of ‘spin-center shift’ (SCS)2, during which an alcohol C–O bond is cleaved, resulting in a carbon-centered radical intermediate. While SCS is a well-understood biochemical process, it is underutilized by the synthetic organic chemistry community. We wondered whether it would be possible to take advantage of this naturally occurring process to accomplish mild, non-traditional alkylations using alcohols as radical precursors. Considering traditional radical-based alkylation methods require the use of stoichiometric oxidants, elevated temperatures, or peroxides3–7, the development of a mild protocol using simple and abundant alkylating agents would have significant utility in the synthesis of diversely functionalized pharmacophores. In this manuscript, we describe the successful execution of this idea via the development of a dual catalytic alkylation of heteroarenes using alcohols as mild alkylating reagents. This method represents the first broadly applicable use of unactivated alcohols as latent alkylating reagents, achieved via the successful merger of photoredox and hydrogen atom transfer (HAT) catalysis. The utility of this multi-catalytic protocol has been demonstrated through the late-stage functionalization of the medicinal agents, fasudil and milrinone. PMID:26308895

Förster resonance energy transfer as a tool to study photoreceptor biology

PubMed Central

Hovan, Stephanie C.; Howell, Scott; Park, Paul S.-H.

2010-01-01

Vision is initiated in photoreceptor cells of the retina by a set of biochemical events called phototransduction. These events occur via coordinated dynamic processes that include changes in secondary messenger concentrations, conformational changes and post-translational modifications of signaling proteins, and protein-protein interactions between signaling partners. A complete description of the orchestration of these dynamic processes is still unavailable. Described in this work is the first step in the development of tools combining fluorescent protein technology, Förster resonance energy transfer (FRET), and transgenic animals that have the potential to reveal important molecular insights about the dynamic processes occurring in photoreceptor cells. We characterize the fluorescent proteins SCFP3A and SYFP2 for use as a donor-acceptor pair in FRET assays, which will facilitate the visualization of dynamic processes in living cells. We also demonstrate the targeted expression of these fluorescent proteins to the rod photoreceptor cells of Xenopus laevis, and describe a general method for detecting FRET in these cells. The general approaches described here can address numerous types of questions related to phototransduction and photoreceptor biology by providing a platform to visualize dynamic processes in molecular detail within a native context. PMID:21198205

Reliability of Automated Biochemical Identification of Burkholderia pseudomallei Is Regionally Dependent

PubMed Central

Podin, Yuwana; Kaestli, Mirjam; McMahon, Nicole; Hennessy, Jann; Ngian, Hie Ung; Wong, Jin Shyan; Mohana, Anand; Wong, See Chang; William, Timothy; Mayo, Mark; Baird, Robert W.

2013-01-01

Misidentifications of Burkholderia pseudomallei as Burkholderia cepacia by Vitek 2 have occurred. Multidimensional scaling ordination of biochemical profiles of 217 Malaysian and Australian B. pseudomallei isolates found clustering of misidentified B. pseudomallei isolates from Malaysian Borneo. Specificity of B. pseudomallei identification in Vitek 2 and potentially other automated identification systems is regionally dependent. PMID:23784129

Reliability of automated biochemical identification of Burkholderia pseudomallei is regionally dependent.

PubMed

Podin, Yuwana; Kaestli, Mirjam; McMahon, Nicole; Hennessy, Jann; Ngian, Hie Ung; Wong, Jin Shyan; Mohana, Anand; Wong, See Chang; William, Timothy; Mayo, Mark; Baird, Robert W; Currie, Bart J

2013-09-01

Misidentifications of Burkholderia pseudomallei as Burkholderia cepacia by Vitek 2 have occurred. Multidimensional scaling ordination of biochemical profiles of 217 Malaysian and Australian B. pseudomallei isolates found clustering of misidentified B. pseudomallei isolates from Malaysian Borneo. Specificity of B. pseudomallei identification in Vitek 2 and potentially other automated identification systems is regionally dependent.

Meal-Insulin Cycle: A Visual Summary of the Biochemical Events between Meals

ERIC Educational Resources Information Center

Kalogiannis, Stavros

2017-01-01

In the present article, a scheme that summarizes the biochemical events occurring in the human body after the consumption of a meal is proposed. The scheme illustrates the metabolic sequence as a series of counteracting components occupying opposite positions in a cycle, indicating their opposite actions or physiological states, such as meal…

Herbicide glufosinate inhibits yeast growth and extends longevity during wine fermentation.

PubMed

Vallejo, Beatriz; Picazo, Cecilia; Orozco, Helena; Matallana, Emilia; Aranda, Agustín

2017-09-29

Glufosinate ammonium (GA) is a widely used herbicide that inhibits glutamine synthetase. This inhibition leads to internal amino acid starvation which, in turn, causes the activation of different nutrient sensing pathways. GA also inhibits the enzyme of the yeast Saccharomyces cerevisiae in such a way that, although it is not used as a fungicide, it may alter yeast performance in industrial processes like winemaking. We describe herein how GA indeed inhibits the yeast growth of a wine strain during the fermentation of grape juice. In turn, GA extends longevity in a variety of growth media. The biochemical analysis indicates that GA partially inhibits the nutrient sensing TORC1 pathway, which may explain these phenotypes. The GCN2 kinase mutant is hypersensitive to GA. Hence the control of translation and amino acid biosynthesis is required to also deal with the damaging effects of this pesticide. A global metabolomics analysis under winemaking conditions indicated that an increase in amino acid and in polyamines occurred. In conclusion, GA affects many different biochemical processes during winemaking, which provides us with some insights into both the effect of this herbicide on yeast physiology and into the relevance of the metabolic step for connecting nitrogen and carbon metabolism.

A longitudinal analysis of the effects of age on the blood plasma metabolome in the common marmoset, Callithrix jacchus

PubMed Central

Hoffman, Jessica M.; Tran, ViLinh; Wachtman, Lynn M.; Green, Cara L.; Jones, Dean P.; Promislow, Daniel E.L.

2016-01-01

Primates tend to be long-lived for their size with humans being the longest lived of all primates. There are compelling reasons to understand the underlying age-related processes that shape human lifespan. But the very fact of our long lifespan that makes it so compelling, also makes it especially difficult to study. Thus, in studies of aging, researchers have turned to non-human primate models, including chimpanzees, baboons, and rhesus macaques. More recently, the common marmoset, Callithrix jacchus, has been recognized as a particularly valuable model in studies of aging, given its small size, ease of housing in captivity, and relatively short lifespan. However, little is known about the physiological changes that occur as marmosets age. To begin to fill in this gap, we utilized high sensitivity metabolomics to define the longitudinal biochemical changes associated with age in the common marmoset. We measured 2104 metabolites from blood plasma at three separate time points over a 17-month period, and we completed both a cross-sectional and longitudinal analysis of the metabolome. We discovered hundreds of metabolites associated with age and body weight in both male and female animals. Our longitudinal analysis identified age-associated metabolic pathways that were not found in our cross-sectional analysis. Pathways enriched for age-associated metabolites included tryptophan, nucleotide, and xenobiotic metabolism, suggesting these biochemical pathways might play an important role in the basic mechanisms of aging in primates. Moreover, we found that many metabolic pathways associated with age were sex specific. Our work illustrates the power of longitudinal approaches, even in a short time frame, to discover novel biochemical changes that occur with age. PMID:26805607

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 initiation. Evidence presented herein also suggests there is no detrimental effect on bulb storage life and quality caused by curing at 20 °C, producing a considerable saving in energy and costs. PMID:22234560

Ryan Davis | NREL

Science.gov Websites

design TEA LCA Biochemical conversion process pathways Algal biomass production and conversion pathways Production," Green Chemistry (2015) Process Design and Economics for the Conversion of Lignocellulosic Production," Applied Energy (2011) Process Design and Economics for Biochemical Conversion of

The Interface of Mechanics and Nociception in Joint Pathophysiology: Insights From the Facet and Temporomandibular Joints

PubMed Central

Sperry, Megan M.; Ita, Meagan E.; Kartha, Sonia; Zhang, Sijia; Yu, Ya-Hsin; Winkelstein, Beth

2017-01-01

Chronic joint pain is a widespread problem that frequently occurs with aging and trauma. Pain occurs most often in synovial joints, the body's load bearing joints. The mechanical and molecular mechanisms contributing to synovial joint pain are reviewed using two examples, the cervical spinal facet joints and the temporomandibular joint (TMJ). Although much work has focused on the macroscale mechanics of joints in health and disease, the combined influence of tissue mechanics, molecular processes, and nociception in joint pain has only recently become a focus. Trauma and repeated loading can induce structural and biochemical changes in joints, altering their microenvironment and modifying the biomechanics of their constitutive tissues, which themselves are innervated. Peripheral pain sensors can become activated in response to changes in the joint microenvironment and relay pain signals to the spinal cord and brain where pain is processed and perceived. In some cases, pain circuitry is permanently changed, which may be a potential mechanism for sustained joint pain. However, it is most likely that alterations in both the joint microenvironment and the central nervous system (CNS) contribute to chronic pain. As such, the challenge of treating joint pain and degeneration is temporally and spatially complicated. This review summarizes anatomy, physiology, and pathophysiology of these joints and the sensory pain relays. Pain pathways are postulated to be sensitized by many factors, including degeneration and biochemical priming, with effects on thresholds for mechanical injury and/or dysfunction. Initiators of joint pain are discussed in the context of clinical challenges including the diagnosis and treatment of pain. PMID:28056123

Aging-related anatomical and biochemical changes in lymphatic collectors impair lymph transport, fluid homeostasis, and pathogen clearance

PubMed Central

Zolla, Valerio; Nizamutdinova, Irina Tsoy; Scharf, Brian; Clement, Cristina C; Maejima, Daisuke; Akl, Tony; Nagai, Takashi; Luciani, Paola; Leroux, Jean-Christophe; Halin, Cornelia; Stukes, Sabriya; Tiwari, Sangeeta; Casadevall, Arturo; Jacobs, William R; Entenberg, David; Zawieja, David C; Condeelis, John; Fooksman, David R; Gashev, Anatoliy A; Santambrogio, Laura

2015-01-01

The role of lymphatic vessels is to transport fluid, soluble molecules, and immune cells to the draining lymph nodes. Here, we analyze how the aging process affects the functionality of the lymphatic collectors and the dynamics of lymph flow. Ultrastructural, biochemical, and proteomic analysis indicates a loss of matrix proteins, and smooth muscle cells in aged collectors resulting in a decrease in contraction frequency, systolic lymph flow velocity, and pumping activity, as measured in vivo in lymphatic collectors. Functionally, this impairment also translated into a reduced ability for in vivo bacterial transport as determined by time-lapse microscopy. Ultrastructural and proteomic analysis also indicates a decrease in the thickness of the endothelial cell glycocalyx and loss of gap junction proteins in aged lymph collectors. Redox proteomic analysis mapped an aging-related increase in the glycation and carboxylation of lymphatic’s endothelial cell and matrix proteins. Functionally, these modifications translate into apparent hyperpermeability of the lymphatics with pathogen escaping from the collectors into the surrounding tissue and a decreased ability to control tissue fluid homeostasis. Altogether, our data provide a mechanistic analysis of how the anatomical and biochemical changes, occurring in aged lymphatic vessels, compromise lymph flow, tissue fluid homeostasis, and pathogen transport. PMID:25982749

Physiologic and biochemical aspects of skeletal muscle denervation and reinnervation

NASA Technical Reports Server (NTRS)

Max, S. R.; Mayer, R. F.

1984-01-01

Some of the physiologic and biochemical changes that occur in mammalian skeletal muscle following denervation and reinnervation are considered and some comparisons are made with changes observed following altered motor function. The nature of the trophic influence by which nerves control muscle properties are discussed, including the effects of choline acetyltransferase and acetylcholinesterase and the role of the acetylcholine receptor.

Cellular level models as tools for cytokine design.

PubMed

Radhakrishnan, Mala L; Tidor, Bruce

2010-01-01

Cytokines and growth factors are critical regulators that connect intracellular and extracellular environments through binding to specific cell-surface receptors. They regulate a wide variety of immunological, growth, and inflammatory response processes. The overall signal initiated by a population of cytokine molecules over long time periods is controlled by the subtle interplay of binding, signaling, and trafficking kinetics. Building on the work of others, we abstract a simple kinetic model that captures relevant features from cytokine systems as well as related growth factor systems. We explore a large range of potential biochemical behaviors, through systematic examination of the model's parameter space. Different rates for the same reaction topology lead to a dramatic range of biochemical network properties and outcomes. Evolution might productively explore varied and different portions of parameter space to create beneficial behaviors, and effective human therapeutic intervention might be achieved through altering network kinetic properties. Quantitative analysis of the results reveals the basis for tensions among a number of different network characteristics. For example, strong binding of cytokine to receptor can increase short-term receptor activation and signal initiation but decrease long-term signaling due to internalization and degradation. Further analysis reveals the role of specific biochemical processes in modulating such tensions. For instance, the kinetics of cytokine binding and receptor activation modulate whether ligand-receptor dissociation can generally occur before signal initiation or receptor internalization. Beyond analysis, the same models and model behaviors provide an important basis for the design of more potent cytokine therapeutics by providing insight into how binding kinetics affect ligand potency. (c) 2010 American Institute of Chemical Engineers

Biotechnologies as a Context for Enhancing Junior High-School Students' Ability to Ask Meaningful Questions about Abstract Biological Processes.

ERIC Educational Resources Information Center

Olsher, G.; Dreyfus, A.

1999-01-01

Suggests a new approach to teaching about biochemical cellular processes by stimulating student interest in those biochemical processes that allowed for the outcomes of modern biotechnologies. Discusses the development of students' ability to ask meaningful questions about intra-cellular processes, and the resulting meaningful learning of relevant…

Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

PubMed Central

Li, Fangting

2017-01-01

The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and ‘programmed’, while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic ‘blue-sky’ bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent landscape perspective permits a quantitative discussion of a wide range of biological phenomena as nonlinear, stochastic dynamics. PMID:28490602

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.

Aqua mediated synthesis of bio-active compounds.

PubMed

Panda, Siva S

2013-05-01

Recently the aqueous medium has attracted the interest of organic chemists, and many. Moreover, in the past 20 years, the drug-discovery process has undergone extraordinary changes, and high-throughput biological screening of potential drug candidates has led to an ever-increasing demand for novel drug-like compounds. Noteworthy advantages were observed during the course of study on aqua mediated synthesis of compounds of medicinal importance. The established advantages of water as a solvent for reactions are, water is the most abundant and available resource on the planet and many biochemical processes occur in aqueous medium. This review will focus on describing new developments in the application of water in medicinal chemistry for the synthesis of bio-active compounds possessing various biological properties.

[Signal reception and processing by the retina].

PubMed

Eysel, U

2007-01-01

Phototransduction occurs in the retina, which, as an outsourced part of the brain, fulfills important tasks in neuronal processing for image analysis relevant to perception. Interlinked biochemical cycles with immense amplification factors transform the electromagnetic waves of light into neuronal activity, and photochemical adaptation allows adjustment to light intensities of over more than 10 logarithmic units. Beginning with its dual system of photoreceptors with highly sensible rods and a color sensitive cone system, the retina, with between 50 and 100 main cell types, is characterized by complex neuronal circuits. The resulting center-surround antagonism of the receptive fields serves, amongst other things, to amplify intensity and color contrasts. Specialized ganglion cell types give rise to parallel signaling pathways into the higher visual centers of the brain.

Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

DOEpatents

Holzrichter, J.F.; Siekhaus, W.J.

1997-04-15

A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule. 6 figs.

Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

DOEpatents

Holzrichter, John F.; Siekhaus, Wigbert J.

1997-01-01

A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule.

Conceptual analysis of Physiology of vision in Ayurveda.

PubMed

Balakrishnan, Praveen; Ashwini, M J

2014-07-01

The process by which the world outside is seen is termed as visual process or physiology of vision. There are three phases in this visual process: phase of refraction of light, phase of conversion of light energy into electrical impulse and finally peripheral and central neurophysiology. With the advent of modern instruments step by step biochemical changes occurring at each level of the visual process has been deciphered. Many investigations have emerged to track these changes and helping to diagnose the exact nature of the disease. Ayurveda has described this physiology of vision based on the functions of vata and pitta. Philosophical textbook of ayurveda, Tarka Sangraha, gives certain basics facts of visual process. This article discusses the second and third phase of visual process. Step by step analysis of the visual process through the spectacles of ayurveda amalgamated with the basics of philosophy from Tarka Sangraha has been analyzed critically to generate a concrete idea regarding the physiology and hence thereby interpret the pathology on the grounds of ayurveda based on the investigative reports.

Determination of Biochemical Oxygen Demand of Area Waters: A Bioassay Procedure for Environmental Monitoring

ERIC Educational Resources Information Center

Riehl, Matthew

2012-01-01

A graphical method for determining the 5-day biochemical oxygen demand (BOD5) for a body of water is described. In this bioassay, students collect a sample of water from a designated site, transport it to the laboratory, and evaluate the amount of oxygen consumed by naturally occurring bacteria during a 5-day incubation period. An accuracy check,…

[Experiments using rats on Kosmos biosatellites: morphologic and biochemical studies].

PubMed

Il'in, E A; Kaplanskiĭ, A S; Savina, E A

1989-01-01

Results of morphological and biochemical investigations of rats flown on Cosmos biosatellites are discussed. It is emphasized that most changes occurring during exposure to microgravity are directly or indirectly related to lower musculoskeletal loads which in turn produce deconditioning of different physiological systems and organism as a whole. It is concluded that this deconditioning is associated with both metabolic and structural changes.

"Chemical transformers" from nanoparticle ensembles operated with logic.

PubMed

Motornov, Mikhail; Zhou, Jian; Pita, Marcos; Gopishetty, Venkateshwarlu; Tokarev, Ihor; Katz, Evgeny; Minko, Sergiy

2008-09-01

The pH-responsive nanoparticles were coupled with information-processing enzyme-based systems to yield "smart" signal-responsive hybrid systems with built-in Boolean logic. The enzyme systems performed AND/OR logic operations, transducing biochemical input signals into reversible structural changes (signal-directed self-assembly) of the nanoparticle assemblies, thus resulting in the processing and amplification of the biochemical signals. The hybrid system mimics biological systems in effective processing of complex biochemical information, resulting in reversible changes of the self-assembled structures of the nanoparticles. The bioinspired approach to the nanostructured morphing materials could be used in future self-assembled molecular robotic systems.

Experimental ocean acidification alters the allocation of metabolic energy

PubMed Central

Pan, T.-C. Francis; Applebaum, Scott L.; Manahan, Donal T.

2015-01-01

Energy is required to maintain physiological homeostasis in response to environmental change. Although responses to environmental stressors frequently are assumed to involve high metabolic costs, the biochemical bases of actual energy demands are rarely quantified. We studied the impact of a near-future scenario of ocean acidification [800 µatm partial pressure of CO2 (pCO2)] during the development and growth of an important model organism in developmental and environmental biology, the sea urchin Strongylocentrotus purpuratus. Size, metabolic rate, biochemical content, and gene expression were not different in larvae growing under control and seawater acidification treatments. Measurements limited to those levels of biological analysis did not reveal the biochemical mechanisms of response to ocean acidification that occurred at the cellular level. In vivo rates of protein synthesis and ion transport increased ∼50% under acidification. Importantly, the in vivo physiological increases in ion transport were not predicted from total enzyme activity or gene expression. Under acidification, the increased rates of protein synthesis and ion transport that were sustained in growing larvae collectively accounted for the majority of available ATP (84%). In contrast, embryos and prefeeding and unfed larvae in control treatments allocated on average only 40% of ATP to these same two processes. Understanding the biochemical strategies for accommodating increases in metabolic energy demand and their biological limitations can serve as a quantitative basis for assessing sublethal effects of global change. Variation in the ability to allocate ATP differentially among essential functions may be a key basis of resilience to ocean acidification and other compounding environmental stressors. PMID:25825763

Experimental ocean acidification alters the allocation of metabolic energy.

PubMed

Pan, T-C Francis; Applebaum, Scott L; Manahan, Donal T

2015-04-14

Energy is required to maintain physiological homeostasis in response to environmental change. Although responses to environmental stressors frequently are assumed to involve high metabolic costs, the biochemical bases of actual energy demands are rarely quantified. We studied the impact of a near-future scenario of ocean acidification [800 µatm partial pressure of CO2 (pCO2)] during the development and growth of an important model organism in developmental and environmental biology, the sea urchin Strongylocentrotus purpuratus. Size, metabolic rate, biochemical content, and gene expression were not different in larvae growing under control and seawater acidification treatments. Measurements limited to those levels of biological analysis did not reveal the biochemical mechanisms of response to ocean acidification that occurred at the cellular level. In vivo rates of protein synthesis and ion transport increased ∼50% under acidification. Importantly, the in vivo physiological increases in ion transport were not predicted from total enzyme activity or gene expression. Under acidification, the increased rates of protein synthesis and ion transport that were sustained in growing larvae collectively accounted for the majority of available ATP (84%). In contrast, embryos and prefeeding and unfed larvae in control treatments allocated on average only 40% of ATP to these same two processes. Understanding the biochemical strategies for accommodating increases in metabolic energy demand and their biological limitations can serve as a quantitative basis for assessing sublethal effects of global change. Variation in the ability to allocate ATP differentially among essential functions may be a key basis of resilience to ocean acidification and other compounding environmental stressors.

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.

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

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 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.

Synchrotron X-Ray Visualisation of Ice Formation in Insects during Lethal and Non-Lethal Freezing

PubMed Central

Sinclair, Brent J.; Gibbs, Allen G.; Lee, Wah-Keat; Rajamohan, Arun; Roberts, Stephen P.; Socha, John J.

2009-01-01

Although the biochemical correlates of freeze tolerance in insects are becoming well-known, the process of ice formation in vivo is subject to speculation. We used synchrotron x-rays to directly visualise real-time ice formation at 3.3 Hz in intact insects. We observed freezing in diapausing 3rd instar larvae of Chymomyza amoena (Diptera: Drosophilidae), which survive freezing if it occurs above −14°C, and non-diapausing 3rd instar larvae of C. amoena and Drosophila melanogaster (Diptera: Drosophilidae), neither of which survive freezing. Freezing was readily observed in all larvae, and on one occasion the gut was seen to freeze separately from the haemocoel. There were no apparent qualitative differences in ice formation between freeze tolerant and non-freeze tolerant larvae. The time to complete freezing was positively related to temperature of nucleation (supercooling point, SCP), and SCP declined with decreasing body size, although this relationship was less strong in diapausing C. amoena. Nucleation generally occurred at a contact point with the thermocouple or chamber wall in non-diapausing larvae, but at random in diapausing larvae, suggesting that the latter have some control over ice nucleation. There were no apparent differences between freeze tolerant and non-freeze tolerant larvae in tracheal displacement or distension of the body during freezing, although there was markedly more distension in D. melanogaster than in C. amoena regardless of diapause state. We conclude that although control of ice nucleation appears to be important in freeze tolerant individuals, the physical ice formation process itself does not differ among larvae that can and cannot survive freezing. This suggests that a focus on cellular and biochemical mechanisms is appropriate and may reveal the primary adaptations allowing freeze tolerance in insects. PMID:20011523

21 CFR 315.5 - Evaluation of effectiveness.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 601.34 - Evaluation of effectiveness.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 315.5 - Evaluation of effectiveness.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 315.5 - Evaluation of effectiveness.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 601.34 - Evaluation of effectiveness.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 601.34 - Evaluation of effectiveness.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 315.5 - Evaluation of effectiveness.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 601.34 - Evaluation of effectiveness.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 601.34 - Evaluation of effectiveness.

Code of Federal Regulations, 2013 CFR

2013-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

21 CFR 315.5 - Evaluation of effectiveness.

Code of Federal Regulations, 2013 CFR

2013-04-01

..., physiological, or biochemical assessment is established by demonstrating in a defined clinical setting reliable measurement of function(s) or physiological, biochemical, or molecular process(es). (3) The claim of disease... demonstrating in a defined clinical setting that the test is useful in diagnostic or therapeutic patient...

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.

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.

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

Cooperative structural transitions in amyloid-like aggregation

NASA Astrophysics Data System (ADS)

Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

2017-04-01

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.

The effect of high hydrostatic pressure on the physiological and biochemical properties of pepper (Capsicum annuum L.) seedlings

NASA Astrophysics Data System (ADS)

İşlek, Cemil; Murat Altuner, Ergin; Alpas, Hami

2015-10-01

High hydrostatic pressure is a non-thermal food processing technology, which also has several successful applications in different areas besides food processing. In this study, Capsicum annuum L. (pepper) seeds are subjected to 50, 100, 200 and 300 MPa pressure for 5 min at 25°C and the seedlings of HHP processed seeds are used to compare percentage of seed germination and biochemical properties such as chlorophyll a, b and a/b, proline content, total protein, carotenoid, malondialdehyde, glucose, fructose and phenolic compounds concentrations. As a result of the study, it was observed that there are remarkable changes in terms of biochemical properties especially for seedlings, whose seeds were pressurized at 200 and 300 MPa. More detailed studies are needed to put forward the mechanism behind the changes in biochemical properties.

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.

Microstructure change in wood cell wall fracture from mechanical pretreatment and its influence on enzymatic hydrolysis

Treesearch

Jinxue Jiang; Jinwu Wang; Xiao Zhang; Michael Wolcott

2017-01-01

tMechanical pretreatment is an effective process for chemical or biochemical conversion of woodybiomass. The deconstruction features of the wood cell wall play an important role in its chemical or bio-chemical processing. In this work, we evaluated the wood cell wall fracture in the early stage of mechanicalpretreatment process conducted with various initial moisture...

Fibrous Hydrogels for Cell Encapsulation: A Modular and Supramolecular Approach.

PubMed

Włodarczyk-Biegun, Małgorzata K; Farbod, Kambiz; Werten, Marc W T; Slingerland, Cornelis J; de Wolf, Frits A; van den Beucken, Jeroen J J P; Leeuwenburgh, Sander C G; Cohen Stuart, Martien A; Kamperman, Marleen

2016-01-01

Artificial 3-dimensional (3D) cell culture systems, which mimic the extracellular matrix (ECM), hold great potential as models to study cellular processes under controlled conditions. The natural ECM is a 3D structure composed of a fibrous hydrogel that provides both mechanical and biochemical cues to instruct cell behavior. Here we present an ECM-mimicking genetically engineered protein-based hydrogel as a 3D cell culture system that combines several key features: (1) Mild and straightforward encapsulation meters (1) ease of ut I am not so sure.encapsulation of the cells, without the need of an external crosslinker. (2) Supramolecular assembly resulting in a fibrous architecture that recapitulates some of the unique mechanical characteristics of the ECM, i.e. strain-stiffening and self-healing behavior. (3) A modular approach allowing controlled incorporation of the biochemical cue density (integrin binding RGD domains). We tested the gels by encapsulating MG-63 osteoblastic cells and found that encapsulated cells not only respond to higher RGD density, but also to overall gel concentration. Cells in 1% and 2% (weight fraction) protein gels showed spreading and proliferation, provided a relative RGD density of at least 50%. In contrast, in 4% gels very little spreading and proliferation occurred, even for a relative RGD density of 100%. The independent control over both mechanical and biochemical cues obtained in this modular approach renders our hydrogels suitable to study cellular responses under highly defined conditions.

Japanese quail acute exposure to methamidophos: experimental design, lethal, sub-lethal effects and cholinesterase biochemical and histochemical expression.

PubMed

Foudoulakis, Manousos; Balaskas, Christos; Csato, Attila; Szentes, Csaba; Arapis, Gerassimos

2013-04-15

We exposed the Japanese quail (Coturnix coturnix japonica) to the organophosphate methamidophos using acute oral test. Mortality and sub-lethal effects were recorded in accordance to internationally accepted protocols. In addition cholinesterases were biochemically estimated in tissues of the quail: brain, liver and plasma. Furthermore, brain, liver and duodenum cryostat sections were processed for cholinesterase histochemistry using various substrates and inhibitors. Mortalities occurred mainly in the first 1-2h following application. Sub-lethal effects, such as ataxia, ruffled feathers, tremor, salivation and reduced or no reaction to external stimuli were observed. Biochemical analysis in the brain, liver and plasma indicates a strong cholinesterase dependent inhibition with respect to mortality and sub-lethal effects of the quail. The histochemical staining also indicated a strong cholinesterase inhibition in the organs examined and the analysis of the stained sections allowed for an estimation and interpretation of the intoxication effects of methamidophos, in combination with tissue morphology visible by Haematoxylin and Eosin staining. We conclude that the use of biochemistry and histochemistry for the biomarker cholinesterase, may constitute a significantly novel approach for understanding the results obtained by the acute oral test employed in order to assess the effects of methamidophos and other chemicals known to inhibit this very important nervous system enzyme. Copyright © 2012 Elsevier B.V. All rights reserved.

Assessment of hydrodynamics, biochemical parameters and eddy diffusivity in a semi-enclosed Ionian basin

NASA Astrophysics Data System (ADS)

De Serio, Francesca; Mossa, Michele

2016-11-01

In the framework of the Italian flagship Project RITMARE, during December 2013 a meteo-oceanographic station was installed in the Mar Grande basin, a semi-enclosed bay in Southern Italy, connected to the Ionian Sea. Due to the presence of coastal heavy industry and anthropic pressure, this marine system has experienced environmental degradation over the last decades. Therefore, much monitoring of hydrodynamics and water quality indicators is required. In fact, this monitoring makes it possible to check the real-time biochemical status of the basin and therefore promptly intervene when accidental spills occur, and to create a dataset necessary to calibrate and validate modelling systems providing forecasts. The present paper aims to analyze and discuss the long term and continuous recordings of hydrodynamic and biochemical data collected by this station, available for the period from January 2014 up to December 2014. In detail, hourly measurements of wind, waves, current velocity, water temperature, salinity, chlorophyll and turbidity concentrations were archived in monthly time-series and processed in frequency domain, using the FFT (Fast Fourier Transform), to both delineate the reciprocal effects of drivers and deduce some correlations between parameters (De Serio and Mossa, 2013). Following this, monthly surface current data were processed in order to obtain time-averaged values of the turbulent velocity components, turbulent kinetic energy and turbulent time scales. Based on these calculated turbulent parameters, the horizontal eddy diffusivity was computed with the hypothesis of homogeneous turbulence using two methods, which provided results with the same order of magnitude. These results are of interest for numerical dispersion models. Finally, only referring to the month of December 2014, the time series of the crude oil concentration was available at the station and was examined in depth. The field data enabled us to conclude that the crude oil dispersion process is influenced by the sea turbulence.

Model-Based Design of Biochemical Microreactors

PubMed Central

Elbinger, Tobias; Gahn, Markus; Neuss-Radu, Maria; Hante, Falk M.; Voll, Lars M.; Leugering, Günter; Knabner, Peter

2016-01-01

Mathematical modeling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation, and optimization of metabolic processes in biochemical microreactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first microreactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments of the reactor multienzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions. The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multienzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the microreactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P) was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns, which differ for different experimental arrangements. Furthermore, the total output of G6P increases for scenarios where microcompartimentation of enzymes occurs. These results show that spatially resolved models are needed in the description of the conversion processes. Finally, the enzyme stoichiometry on the nano-beads is determined, which maximizes the production of glucose-6-phosphate. PMID:26913283

Biocatalytic Synthesis of the Rare Sugar Kojibiose: Process Scale-Up and Application Testing.

PubMed

Beerens, Koen; De Winter, Karel; Van de Walle, Davy; Grootaert, Charlotte; Kamiloglu, Senem; Miclotte, Lisa; Van de Wiele, Tom; Van Camp, John; Dewettinck, Koen; Desmet, Tom

2017-07-26

Cost-efficient (bio)chemical production processes are essential to evaluate the commercial and industrial applications of promising carbohydrates and also are essential to ensure economically viable production processes. Here, the synthesis of the naturally occurring disaccharide kojibiose (2-O-α-d-glucopyranosyl-d-glucopyranoside) was evaluated using different Bifidobacterium adolescentis sucrose phosphorylase variants. Variant L341I_Q345S was found to efficiently synthesize kojibiose while remaining fully active after 1 week of incubation at 55 °C. Process optimization allowed kojibiose production at the kilogram scale, and simple but efficient downstream processing, using a yeast treatment and crystallization, resulted in more than 3 kg of highly pure crystalline kojibiose (99.8%). These amounts allowed a deeper characterization of its potential in food applications. It was found to have possible beneficial health effects, including delayed glucose release and potential to trigger SCFA production. Finally, we compared the bulk functionality of highly pure kojibiose to that of sucrose, hereby mapping its potential as a new sweetener in confectionery products.

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 external environment, such as epithelial tissues, may be susceptible to changes in external pH. Such biochemical systems could be adapted to a reduced pH environment by adjustment of weak bonds in an analogous fashion to biochemical adaptation to temperature. Whether such biochemical adaptation to OA exists remains to be discovered. © 2015. Published by The Company of Biologists Ltd.

Implications of electric potentials applied on a denitrifying process.

PubMed

Cadena Ramírez, Arturo; Texier, Anne-Claire; González, Ignacio; Gómez, Jorge

2018-03-20

The effect of three electric potentials (EP) (+104, -187 and -279 mV) applied to the denitrifying process was explored. It was observed that the denitrifying sludge was able to support the oxidation of p-cresol with the application of the EP in the absence of nitrate, but it was unable to drive the denitrification without an organic electron donor. On denitrification, the applied EP uncoupled the oxidative from the reductive process, favoring the p-cresol oxidation over the production of N2. Additionally, biochemical level effects were observed. At +104 and -279 mV potentials, the nitrate and nitrite consumption was affected as well as the p-hydroxybenzoate transformation. However, at -187 mV, effects seemed to occur only on the transport of substrates. This paper presents evidence that denitrification has very characteristic and different physiological behaviors for each EP assayed.

Matt Wecker | NREL

Science.gov Websites

acetaldehyde from bacteria. The idea was to short-sheet the ethanol fermentation pathway to produce ; Biochem. (1995) "Fermentation strategies: Acetaldehyde or ethanol?," Process Biochem. (1987

Biochemistry of HELLP syndrome.

PubMed

Benedetto, Chiara; Marozio, Luca; Tancredi, Annalisa; Picardo, Elisa; Nardolillo, Paola; Tavella, Anna Maria; Salton, Loredana

2011-01-01

The HELLP syndrome is a serious complication of pregnancy characterized by hemolysis (H), elevated liver (EL) enzymes, and low platelet (LP) count that occurs in 0.2-0.6% of all pregnancies and in 10-20% of cases with severe preeclampsia and frequently leads to adverse maternal and perinatal outcome. The exact pathobiology of HELLP syndrome has not been clearly defined. As it is considered a form or a complication of severe preeclampsia, it likely has its origin in aberrant placental development and function resulting in ischemia-producing oxidative stress. However, there is still a debate on whether HELLP must be considered a severe form of preeclampsia or a separate disease entity. It can be described as a placenta-induced disease, as is preeclampsia itself, but with a more acute and predominant inflammatory process typically targeting the liver and with a greater activation of the coagulation system. This occurs during a disordered immunologic process and may be due to a genetic predisposition. In this review, we discuss the main biochemical characteristics of HELLP syndrome, particularly focusing on molecular aspects of placental involvement and maternal systemic responses.

Experimental Monitoring of Cr(VI) Bio-reduction Using Electrochemical Geophysics

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

Birsen Canan; Gary R. Olhoeft; William A. Smith

2007-09-01

Many Department of Energy (DOE) sites are contaminated with highly carcinogenic hexavalent chromium (Cr(VI)). In this research, we explore the feasibility of applying complex resistivity to the detection and monitoring of microbially-induced reduction of hexavalent chromium (Cr(VI)) to a less toxic form (Cr(III)). We hope to measure the change in ionic concentration that occurs during this reduction reaction. This form of reduction promises to be an attractive alternative to more expensive remedial treatment methods. The specific goal of this research is to define the minimum and maximum concentration of the chemical and biological compounds in contaminated samples for which themore » Cr(VI) - Cr(III) reduction processes could be detected via complex resistivity. There are three sets of experiments, each comprised of three sample columns. The first experiment compares three concentrations of Cr(VI) at the same bacterial cell concentration. The second experiment establishes background samples with, and without, Cr(VI) and bacterial cells. The third experiment examines the influence of three different bacterial cell counts on the same concentration of Cr(VI). A polarization relaxation mechanism was observed between 10 and 50 Hz. The polarization mechanism, unfortunately, was not unique to bio-chemically active samples. Spectral analysis of complex resistivity data, however, showed that the frequency where the phase minimum occurred was not constant for bio-chemically active samples throughout the experiment. A significant shifts in phase minima occurred between 10 to 20 Hz from the initiation to completion of Cr(VI) reduction. This phenomena was quantified using the Cole-Cole model and the Marquardt-Levenberg nonlinear least square minimization method. The data suggests that the relaxation time and the time constant of this relaxation are the Cole-Cole parameters most sensitive to changes in biologically-induced reduction of Cr(VI).« less

Monitoring of soluble starch hydrolysis induced by α-amylase from Aspergillus oryzae using ultrasonic spectroscopy

NASA Astrophysics Data System (ADS)

Sierra, Carlos; Resa, Pablo; Buckin, Vitaly; Elvira, Luis

2012-05-01

The online monitoring of enzymatic starch hydrolysis is an important issue for several industrial sectors, mainly in the alimentary industry. Ultrasonic non-invasive methods based on the detection of wave velocity and amplitude changes can be used to study this enzymatic reaction. These wave propagating changes are result of physicalchemical modifications produced in the media by the starch hydrolysis. In this work the starch hydrolysis induced by the enzyme α-amylase from Aspergillus oryzae is studied. This biochemical reaction has been monitored using a high-resolution ultrasonic spectroscopy (HR-US) which is non-invasive and nondestructive. The measured time profiles o of ultrasonic velocity are explained in terms of the starch hydrolysis and the subsequent production of oligosaccharides as a consequence of the enzymatic action. The obtained results have been compared to a conventional off-line technique used in biochemistry, the iodine-starch reaction, a spectrophotometric method to quantify the amount of starch remaining in the medium. The combination of these two types of measurement provides more complete information about the biochemical processes occurred during hydrolysis.

A mathematical model of insulin resistance in Parkinson's disease.

PubMed

Braatz, Elise M; Coleman, Randolph A

2015-06-01

This paper introduces a mathematical model representing the biochemical interactions between insulin signaling and Parkinson's disease. The model can be used to examine the changes that occur over the course of the disease as well as identify which processes would be the most effective targets for treatment. The model is mathematized using biochemical systems theory (BST). It incorporates a treatment strategy that includes several experimental drugs along with current treatments. In the past, BST models of neurodegeneration have used power law analysis and simulation (PLAS) to model the system. This paper recommends the use of MATLAB instead. MATLAB allows for more flexibility in both the model itself and in data analysis. Previous BST analyses of neurodegeneration began treatment at disease onset. As shown in this model, the outcomes of delayed, realistic treatment and full treatment at disease onset are significantly different. The delayed treatment strategy is an important development in BST modeling of neurodegeneration. It emphasizes the importance of early diagnosis, and allows for a more accurate representation of disease and treatment interactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Creating Habitable Zones, at all Scales, from Planets to Mud Micro-Habitats, on Earth and on Mars

NASA Astrophysics Data System (ADS)

Nisbet, Euan; Zahnle, Kevin; Gerasimov, M. V.; Helbert, Jörn; Jaumann, Ralf; Hofmann, Beda A.; Benzerara, Karim; Westall, Frances

The factors that create a habitable planet are considered at all scales, from planetary inventories to micro-habitats in soft sediments and intangibles such as habitat linkage. The possibility of habitability first comes about during accretion, as a product of the processes of impact and volatile inventory history. To create habitability water is essential, not only for life but to aid the continual tectonic reworking and erosion that supply key redox contrasts and biochemical substrates to sustain habitability. Mud or soft sediment may be a biochemical prerequisite, to provide accessible substrate and protection. Once life begins, the habitat is widened by the activity of life, both by its management of the greenhouse and by partitioning reductants (e.g. dead organic matter) and oxidants (including waste products). Potential Martian habitats are discussed: by comparison with Earth there are many potential environmental settings on Mars in which life may once have occurred, or may even continue to exist. The long-term evolution of habitability in the Solar System is considered.

Creating Habitable Zones, at all Scales, from Planets to Mud Micro-Habitats, on Earth and on Mars

NASA Astrophysics Data System (ADS)

Nisbet, Euan; Zahnle, Kevin; Gerasimov, M. V.; Helbert, Jörn; Jaumann, Ralf; Hofmann, Beda A.; Benzerara, Karim; Westall, Frances

2007-03-01

The factors that create a habitable planet are considered at all scales, from planetary inventories to micro-habitats in soft sediments and intangibles such as habitat linkage. The possibility of habitability first comes about during accretion, as a product of the processes of impact and volatile inventory history. To create habitability water is essential, not only for life but to aid the continual tectonic reworking and erosion that supply key redox contrasts and biochemical substrates to sustain habitability. Mud or soft sediment may be a biochemical prerequisite, to provide accessible substrate and protection. Once life begins, the habitat is widened by the activity of life, both by its management of the greenhouse and by partitioning reductants (e.g. dead organic matter) and oxidants (including waste products). Potential Martian habitats are discussed: by comparison with Earth there are many potential environmental settings on Mars in which life may once have occurred, or may even continue to exist. The long-term evolution of habitability in the Solar System is considered.

"Structure and dynamics in complex chemical systems: Gaining new insights through recent advances in time-resolved spectroscopies.” ACS Division of Physical Chemistry Symposium presented at the Fall National ACS Meeting in Boston, MA, August 2015

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

Crawford, Daniel

8-Session Symposium on STRUCTURE AND DYNAMICS IN COMPLEX CHEMICAL SYSTEMS: GAINING NEW INSIGHTS THROUGH RECENT ADVANCES IN TIME-RESOLVED SPECTROSCOPIES. The intricacy of most chemical, biochemical, and material processes and their applications are underscored by the complex nature of the environments in which they occur. Substantial challenges for building a global understanding of a heterogeneous system include (1) identifying unique signatures associated with specific structural motifs within the heterogeneous distribution, and (2) resolving the significance of each of multiple time scales involved in both small- and large-scale nuclear reorganization. This symposium focuses on the progress in our understanding of dynamics inmore » complex systems driven by recent innovations in time-resolved spectroscopies and theoretical developments. Such advancement is critical for driving discovery at the molecular level facilitating new applications. Broad areas of interest include: Structural relaxation and the impact of structure on dynamics in liquids, interfaces, biochemical systems, materials, and other heterogeneous environments.« less

Microgravity research in plant biological systems: Realizing the potential of molecular biology

NASA Technical Reports Server (NTRS)

Lewis, Norman G.; Ryan, Clarence A.

1993-01-01

The sole all-pervasive feature of the environment that has helped shape, through evolution, all life on Earth is gravity. The near weightlessness of the Space Station Freedom space environment allows gravitational effects to be essentially uncoupled, thus providing an unprecedented opportunity to manipulate, systematically dissect, study, and exploit the role of gravity in the growth and development of all life forms. New and exciting opportunities are now available to utilize molecular biological and biochemical approaches to study the effects of microgravity on living organisms. By careful experimentation, we can determine how gravity perception occurs, how the resulting signals are produced and transduced, and how or if tissue-specific differences in gene expression occur. Microgravity research can provide unique new approaches to further our basic understanding of development and metabolic processes of cells and organisms, and to further the application of this new knowledge for the betterment of humankind.

The influence of season on the gonad index and biochemical composition of the sea urchin Paracentrotus lividus from the Golf of Tunis.

PubMed

Arafa, Soumaya; Chouaibi, Moncef; Sadok, Saloua; El Abed, Amor

2012-01-01

Seasonal variation in the gonad weight and biochemical composition of the sea urchin Paracentrotus lividus from the Golf of Tunis (Tunisia) were studied between September 2003 and August 2004. The highest gonad indices occurred in March (16.71%). The spawning period occurred between April and July and resulted in a fall in gonad indices to low level (7.12 ± 0.12%). Protein constituted the main component of the gonad, and lipid and carbohydrate were found at appreciable amounts. Consistent with the gonad cycle, sea urchin biochemical components showed clear seasonal variation with a significant decrease during the spawning period. The polyunsaturated fatty acid (PUFA) group was found at high level (40% of the total fatty acids). Of the PUFA group, eicosapentaenoic (C20:5 n - 3) and eicosatetraenoic (C20:4 n - 3) were the most abundant gonadal lipids. The level of PUFA was significantly affected by temperature variation showing an increase during the cold months and a decrease in the hot months.

The Influence of Season on the Gonad Index and Biochemical Composition of the Sea Urchin Paracentrotus lividus from the Golf of Tunis

PubMed Central

Arafa, Soumaya; Chouaibi, Moncef; Sadok, Saloua; El Abed, Amor

2012-01-01

Seasonal variation in the gonad weight and biochemical composition of the sea urchin Paracentrotus lividus from the Golf of Tunis (Tunisia) were studied between September 2003 and August 2004. The highest gonad indices occurred in March (16.71%). The spawning period occurred between April and July and resulted in a fall in gonad indices to low level (7.12 ± 0.12%). Protein constituted the main component of the gonad, and lipid and carbohydrate were found at appreciable amounts. Consistent with the gonad cycle, sea urchin biochemical components showed clear seasonal variation with a significant decrease during the spawning period. The polyunsaturated fatty acid (PUFA) group was found at high level (40% of the total fatty acids). Of the PUFA group, eicosapentaenoic (C20:5 n − 3) and eicosatetraenoic (C20:4 n − 3) were the most abundant gonadal lipids. The level of PUFA was significantly affected by temperature variation showing an increase during the cold months and a decrease in the hot months. PMID:22629206

Conceptual analysis of Physiology of vision in Ayurveda

PubMed Central

Balakrishnan, Praveen; Ashwini, M. J.

2014-01-01

The process by which the world outside is seen is termed as visual process or physiology of vision. There are three phases in this visual process: phase of refraction of light, phase of conversion of light energy into electrical impulse and finally peripheral and central neurophysiology. With the advent of modern instruments step by step biochemical changes occurring at each level of the visual process has been deciphered. Many investigations have emerged to track these changes and helping to diagnose the exact nature of the disease. Ayurveda has described this physiology of vision based on the functions of vata and pitta. Philosophical textbook of ayurveda, Tarka Sangraha, gives certain basics facts of visual process. This article discusses the second and third phase of visual process. Step by step analysis of the visual process through the spectacles of ayurveda amalgamated with the basics of philosophy from Tarka Sangraha has been analyzed critically to generate a concrete idea regarding the physiology and hence thereby interpret the pathology on the grounds of ayurveda based on the investigative reports. PMID:25336853

Technological and economic aspects of coal biodesulfurisation.

PubMed

Klein, J

1998-01-01

The sulfur found in coal is either part of the molecular coal structure (organically bound sulfur), is contained in minerals such as pyrite (FeS2), or occurs in minor quantities in the form of sulfate and elemental sulfur. When pyrite crystals are finely distributed within the coal matrix, mechanical cleaning can only remove part of the pyrite. It can, however, be removed by microbial action requiring only mild conditions. The process involves simple equipment, almost no chemicals, but relatively long reaction times, and treatment of iron sulfate containing process water. Different process configurations are possible, depending on the coal particle size. Coal with particle sizes of less than 0.5 mm is preferably desulfurised in slurry reactors, while lump coal (> 0.5 mm) should be treated in heaps. Investment and operating costs are estimated for different process configurations on an industrial scale. Concerning the organically bound sulfur in coal there is up to now no promising biochemical pathway for the degradation and/or desulfurisation of such compounds.

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 peroxidase related to the mammalian antimicrobial protein myeloperoxidase in the Euprymna-Vibrio mutualism.

PubMed

Weis, V M; Small, A L; McFall-Ngai, M J

1996-11-26

Many animal-bacteria cooperative associations occur in highly modified host organs that create a unique environment for housing and maintaining the symbionts. It has been assumed that these specialized organs develop through a program of symbiosis-specific or -enhanced gene expression in one or both partners, but a clear example of this process has been lacking. In this study, we provide evidence for the enhanced production of an enzyme in the symbiotic organ of the squid Euprymna scolopes, which harbors a culture of the luminous bacterium Vibrio fischeri. Our data show that this enzyme has a striking biochemical similarity to mammalian myeloperoxidase (MPO; EC 1.11.17), an antimicrobial dianisidine peroxidase that occurs in neutrophils. MPO and the squid peroxidase catalyze the same reaction, have similar apparent subunit molecular masses, and a polyclonal antibody to native human MPO specifically localized a peroxidase-like protein to the bacteria-containing regions of the symbiotic organ. We also provide evidence that a previously described squid cDNA encodes the protein (LO4) that is responsible for the observed dianisidine peroxidase activity. An antibody made against a fragment of LO4 immunoprecipiated dianisidine peroxidase activity from extracts of the symbiotic organ, and reacted against these extracts and human MPO in Western blot analysis. These data suggest that related biochemical mechanisms for the control of bacterial number and growth operate in associations that are as functionally diverse as pathogenesis and mutualism, and as phylogenetically distant as molluscs and mammals.

The rates of protein synthesis and degradation account for the differential response of neurons to spaced and massed training protocols.

PubMed

Naqib, Faisal; Farah, Carole A; Pack, Christopher C; Sossin, Wayne S

2011-12-01

The sensory-motor neuron synapse of Aplysia is an excellent model system for investigating the biochemical changes underlying memory formation. In this system, training that is separated by rest periods (spaced training) leads to persistent changes in synaptic strength that depend on biochemical pathways that are different from those that occur when the training lacks rest periods (massed training). Recently, we have shown that in isolated sensory neurons, applications of serotonin, the neurotransmitter implicated in inducing these synaptic changes during memory formation, lead to desensitization of the PKC Apl II response, in a manner that depends on the method of application (spaced versus massed). Here, we develop a mathematical model of this response in order to gain insight into how neurons sense these different training protocols. The model was developed incrementally, and each component was experimentally validated, leading to two novel findings: First, the increased desensitization due to PKA-mediated heterologous desensitization is coupled to a faster recovery than the homologous desensitization that occurs in the absence of PKA activity. Second, the model suggests that increased spacing leads to greater desensitization due to the short half-life of a hypothetical protein, whose production prevents homologous desensitization. Thus, we predict that the effects of differential spacing are largely driven by the rates of production and degradation of proteins. This prediction suggests a powerful mechanism by which information about time is incorporated into neuronal processing.

Microdissection of black widow spider silk-producing glands.

PubMed

Jeffery, Felicia; La Mattina, Coby; Tuton-Blasingame, Tiffany; Hsia, Yang; Gnesa, Eric; Zhao, Liang; Franz, Andreas; Vierra, Craig

2011-01-11

Modern spiders spin high-performance silk fibers with a broad range of biological functions, including locomotion, prey capture and protection of developing offspring. Spiders accomplish these tasks by spinning several distinct fiber types that have diverse mechanical properties. Such specialization of fiber types has occurred through the evolution of different silk-producing glands, which function as small biofactories. These biofactories manufacture and store large quantities of silk proteins for fiber production. Through a complex series of biochemical events, these silk proteins are converted from a liquid into a solid material upon extrusion. Mechanical studies have demonstrated that spider silks are stronger than high-tensile steel. Analyses to understand the relationship between the structure and function of spider silk threads have revealed that spider silk consists largely of proteins, or fibroins, that have block repeats within their protein sequences. Common molecular signatures that contribute to the incredible tensile strength and extensibility of spider silks are being unraveled through the analyses of translated silk cDNAs. Given the extraordinary material properties of spider silks, research labs across the globe are racing to understand and mimic the spinning process to produce synthetic silk fibers for commercial, military and industrial applications. One of the main challenges to spinning artificial spider silk in the research lab involves a complete understanding of the biochemical processes that occur during extrusion of the fibers from the silk-producing glands. Here we present a method for the isolation of the seven different silk-producing glands from the cobweaving black widow spider, which includes the major and minor ampullate glands [manufactures dragline and scaffolding silk], tubuliform [synthesizes egg case silk], flagelliform [unknown function in cob-weavers], aggregate [makes glue silk], aciniform [synthesizes prey wrapping and egg case threads] and pyriform [produces attachment disc silk]. This approach is based upon anesthetizing the spider with carbon dioxide gas, subsequent separation of the cephalothorax from the abdomen, and microdissection of the abdomen to obtain the silk-producing glands. Following the separation of the different silk-producing glands, these tissues can be used to retrieve different macromolecules for distinct biochemical analyses, including quantitative real-time PCR, northern- and western blotting, mass spectrometry (MS or MS/MS) analyses to identify new silk protein sequences, search for proteins that participate in the silk assembly pathway, or use the intact tissue for cell culture or histological experiments.

Apparatus and method for converting biomass to feedstock for biofuel and biochemical manufacturing processes

DOEpatents

Kania, John; Qiao, Ming; Woods, Elizabeth M.; Cortright, Randy D.; Myren, Paul

2015-12-15

The present invention includes improved systems and methods for producing biomass-derived feedstocks for biofuel and biochemical manufacturing processes. The systems and methods use components that are capable of transferring relatively high concentrations of solid biomass utilizing pressure variations between vessels, and allows for the recovery and recycling of heterogeneous catalyst materials.

Sulfur assimilation and the role of sulfur in plant metabolism: a survey.

PubMed

Droux, Michel

2004-01-01

Sulfur occurs in two major amino-acids, cysteine (Cys) and methionine (Met), essential for the primary and secondary metabolism of the plant. Cys, as the first carbon/nitrogen-reduced sulfur product resulting from the sulfate assimilation pathway, serves as a sulfur donor for Met, glutathione, vitamins, co-factors, and sulfur compounds that play a major role in the growth and development of plant cells. This sulfur imprinting occurs in a myriad of fundamental processes, from photosynthesis to carbon and nitrogen metabolism. Cys and Met occur in proteins, with the former playing a wide range of functions in proteins catalysis. In addition, the sulfur atom in proteins forms part of a redox buffer, as for glutathione, through specific detoxification/protection mechanisms. In this review, a survey of sulfur assimilation from sulfate to Cys, Met and glutathione is presented with highlights on open questions on their respective biosynthetic pathways and regulations that derived from recent findings. These are addressed at the biochemical and molecular levels with respect to the fate of Cys and Met throughout the plant-cell metabolism.

COLDEX-86: Fluid and Electrolyte Changes during Prolonged Cold Water Immersion

DTIC Science & Technology

1990-12-01

4 Urine and blood collections .................. ..................... 5 Sample processing and biochemical analyses...and decaffeinated tea and coffee. Ingestion of fluids was encouraged. After completing the immersion, 16 oz of warm apple or cranberry juice was...day. Sample processing and biochemical analyses. Blood samples (25 ml) were drawn from an antecubital vein with minimum stasis. Each sample was divided

Organogenic nodule formation in hop: a tool to study morphogenesis in plants with biotechnological and medicinal applications.

PubMed

Fortes, Ana M; Santos, Filipa; Pais, Maria S

2010-01-01

The usage of Humulus lupulus for brewing increased the demand for high-quality plant material. Simultaneously, hop has been used in traditional medicine and recently recognized with anticancer and anti-infective properties. Tissue culture techniques have been reported for a wide range of species, and open the prospect for propagation of disease-free, genetically uniform and massive amounts of plants in vitro. Moreover, the development of large-scale culture methods using bioreactors enables the industrial production of secondary metabolites. Reliable and efficient tissue culture protocol for shoot regeneration through organogenic nodule formation was established for hop. The present review describes the histological, and biochemical changes occurring during this morphogenic process, together with an analysis of transcriptional and metabolic profiles. We also discuss the existence of common molecular factors among three different morphogenic processes: organogenic nodules and somatic embryogenesis, which strictly speaking depend exclusively on intrinsic developmental reprogramming, and legume nitrogen-fixing root nodules, which arises in response to symbiosis. The review of the key factors that participate in hop nodule organogenesis and the comparison with other morphogenic processes may have merit as a study presenting recent advances in complex molecular networks occurring during morphogenesis and together, these provide a rich framework for biotechnology applications.

Gene regulation and noise reduction by coupling of stochastic processes

NASA Astrophysics Data System (ADS)

Ramos, Alexandre F.; Hornos, José Eduardo M.; Reinitz, John

2015-02-01

Here we characterize the low-noise regime of a stochastic model for a negative self-regulating binary gene. The model has two stochastic variables, the protein number and the state of the gene. Each state of the gene behaves as a protein source governed by a Poisson process. The coupling between the two gene states depends on protein number. This fact has a very important implication: There exist protein production regimes characterized by sub-Poissonian noise because of negative covariance between the two stochastic variables of the model. Hence the protein numbers obey a probability distribution that has a peak that is sharper than those of the two coupled Poisson processes that are combined to produce it. Biochemically, the noise reduction in protein number occurs when the switching of the genetic state is more rapid than protein synthesis or degradation. We consider the chemical reaction rates necessary for Poisson and sub-Poisson processes in prokaryotes and eucaryotes. Our results suggest that the coupling of multiple stochastic processes in a negative covariance regime might be a widespread mechanism for noise reduction.

Gene regulation and noise reduction by coupling of stochastic processes

PubMed Central

Hornos, José Eduardo M.; Reinitz, John

2015-01-01

Here we characterize the low noise regime of a stochastic model for a negative self-regulating binary gene. The model has two stochastic variables, the protein number and the state of the gene. Each state of the gene behaves as a protein source governed by a Poisson process. The coupling between the the two gene states depends on protein number. This fact has a very important implication: there exist protein production regimes characterized by sub-Poissonian noise because of negative covariance between the two stochastic variables of the model. Hence the protein numbers obey a probability distribution that has a peak that is sharper than those of the two coupled Poisson processes that are combined to produce it. Biochemically, the noise reduction in protein number occurs when the switching of genetic state is more rapid than protein synthesis or degradation. We consider the chemical reaction rates necessary for Poisson and sub-Poisson processes in prokaryotes and eucaryotes. Our results suggest that the coupling of multiple stochastic processes in a negative covariance regime might be a widespread mechanism for noise reduction. PMID:25768447

Gene regulation and noise reduction by coupling of stochastic processes.

PubMed

Ramos, Alexandre F; Hornos, José Eduardo M; Reinitz, John

2015-02-01

Here we characterize the low-noise regime of a stochastic model for a negative self-regulating binary gene. The model has two stochastic variables, the protein number and the state of the gene. Each state of the gene behaves as a protein source governed by a Poisson process. The coupling between the two gene states depends on protein number. This fact has a very important implication: There exist protein production regimes characterized by sub-Poissonian noise because of negative covariance between the two stochastic variables of the model. Hence the protein numbers obey a probability distribution that has a peak that is sharper than those of the two coupled Poisson processes that are combined to produce it. Biochemically, the noise reduction in protein number occurs when the switching of the genetic state is more rapid than protein synthesis or degradation. We consider the chemical reaction rates necessary for Poisson and sub-Poisson processes in prokaryotes and eucaryotes. Our results suggest that the coupling of multiple stochastic processes in a negative covariance regime might be a widespread mechanism for noise reduction.

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

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.

Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

PubMed Central

Smith, Owen K.; Aladjem, Mirit I.

2014-01-01

The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

Cryptic color change in a crab spider (Misumena vatia): identification and quantification of precursors and ommochrome pigments by HPLC.

PubMed

Riou, Mickaël; Christidès, Jean-Philippe

2010-04-01

Mimicry is used widely by arthropods to survive in a hostile environment. Often mimicry is associated with the production of chemical compounds such as pigments. In crab spiders, the change of color is based on a complex physiological process that still is not understood. The aim of this study was to identify and quantify the ommochrome pigments and precursors responsible for the color change in the mimetic crab spider Misumena vatia (Thomisidae). A modified high performance reverse phase ion-pair chromatography technique enabled us to separate and quantify the ommochrome pigments, their precursors, and related metabolites in individual spiders. Compounds such as tryptophan, kynurenine, and kynurenic acid occurred only or mainly in white crab spiders. In contrast, compounds such as 3-hydroxy-kynurenine, xanthommatin, and ommatin D occurred only or mainly in yellow crab spiders. Factor analysis ranked the different color forms in accordance with their metabolites. The biochemical results enabled us to associate the different phases of formation of pigment granules with specific metabolites. Yellow crab spiders contain many unknown ommochrome-like compounds not present in white crab spiders. We also found large quantities of decarboxylated xanthommatin, whose role as precursor of new pathways in ommochrome synthesis needs to be assessed. The catabolism of ommochromes, a process occurring when spiders revert from yellow to white, warrants further study.

The principle of cooperation and life's origin and evolution

NASA Technical Reports Server (NTRS)

Oro, J.; Armangue, G.; Mar, A.

1986-01-01

In simple terms a living entity is a negentropic system that replicates, mutates and evoluves. A number of suggestions have been made, such as directed panspermia, atmospheric photosynthesis, genetic overtaking from inorganic processes, etc., as alternative models to the accepted Oparin-Haldane-Urey model of the origin of life on Earth. This has probably occurred because in spite of tremendous advances in the prebiotic synthesis of biochemical compounds, the fundamental problem of the appearance of the first life--a primordial replicating cell-ancestral to all other forms of extant life, has remained elusive. This is indeed a reflection on the different fundamental nature of the problem involved. Regardless of which were the fundamental processes which occurred on the primitive Earth, it has to end up with the fundamental characteristics of an ancestral protocell. The problem of the emergence of the first ancestral cell was one of synergistic macromolecular cooperation, as it has been discussed by authors recently (COSPAR XXV Plenary Meeting). An analogous situation must have occurred at the time of the appearance of the first eucaryotic organism. Procaryotic life appeared probably during the first 600 million years of Earth history when the Earth was sufficiently cool and continually bombarded (in the late accretion period) by comets and minor bodies of the solar system, when the sea had not yet acquired its present form.

Changes in composition of cuticular biochemicals of the facultatively polygynous ant Petalomyrmex phylax during range expansion in Cameroon with respect to social, spatial and genetic variation.

PubMed

Dalecky, Ambroise; Renucci, Marielle; Tirard, Alain; Debout, Gabriel; Roux, Maurice; Kjellberg, Finn; Provost, Erick

2007-09-01

In social insects, biochemicals found at the surface of the cuticle are involved in the recognition process and in protection against desiccation and pathogens. However, the relative contribution of evolutionary forces in shaping diversity of these biochemicals remains largely unresolved in ants. We determined the composition of epicuticular biochemicals for workers sampled in 12 populations of the ant Petalomyrmex phylax from Cameroon. Genetic variation at 12 microsatellite markers was used to infer population history and to provide null expectations under the neutrality hypothesis. Genetic data suggest a recent southward range expansion of this ant species. Furthermore, there is a decline southward in the numbers of queens present in mature colonies. Here, we contrast the pattern of biochemical variation against genetic, social and spatial parameters. We thus provide the first estimates of the relative contribution of neutral and selective processes on variation of ant cuticular profile. Populations in migration-drift disequilibrium showed reduction of within-population variation for genetic markers as well as for cuticular profiles. In these populations, the cuticular profile became biased towards a limited number of high molecular weight molecules. Within- and among-population biochemical variation was explained by both genetic and social variation and by the spatial distribution of populations. We therefore propose that during range expansion of P. phylax, the composition of epicuticular compounds has been affected by a combination of neutral processes - genetic drift and spatially limited dispersal - and spatially varying selection, social organization and environmental effects.

Current Challenges in Plant Eco-Metabolomics

PubMed Central

Peters, Kristian; Worrich, Anja; Alka, Oliver; Balcke, Gerd; Bruelheide, Helge; Dietz, Sophie; Dührkop, Kai; Heinig, Uwe; Kücklich, Marlen; Müller, Caroline; Poeschl, Yvonne; Pohnert, Georg; Ruttkies, Christoph; Schweiger, Rabea; Shahaf, Nir; Tortosa, Maria; Ueberschaar, Nico; Velasco, Pablo; Weiß, Brigitte M.; van Dam, Nicole M.

2018-01-01

The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant–organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology. PMID:29734799

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.

Feasibility and early outcome of high-dose-rate Ir-192 brachytherapy as monotherapy in two fractions within 1 day for high-/very high-risk prostate cancer.

PubMed

Ashida, Shingo; Yamasaki, Ichiro; Tamura, Kenji; Shimamoto, Tsutomu; Inoue, Keiji; Kariya, Shinji; Kobayashi, Kana; Yamagami, Takuji; Shuin, Taro

2016-05-01

The aim of the present study was to evaluate the feasibility and preliminary outcomes of high-dose-rate (HDR)-brachytherapy as a monotherapy in two fractions within 1 day for localized prostate cancer, including high-/very high-risk cases. Among the 68 patients treated with HDR monotherapy between July 2011 and December 2014, 65 had a minimal follow-up of 12 months without adjuvant androgen deprivation therapy and were enrolled in the present study [42/65 (64.6%) exhibited high-/very high-risk diseases]. HDR monotherapy was performed in two fractions with a minimal interval of 6 h and the prescribed dose was 13.5 Gy (×2). Adverse events (AEs) were assessed using Common Terminology Criteria for Adverse Events (version 4; http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm#ctc_40), and biochemical failure was assessed by the Phoenix definition. The median follow-up time was 30.1 months. The majority of patients had Grade 0-1 acute AEs. Four patients (6.2%) exhibited urinary retention, requiring a Foley catheter. Grade 3 acute AEs occurred at a frequency of 3.1% and hematuria at 1.5%. The majority of patients also exhibited Grade 0-1 chronic AEs. Grade 3 chronic AEs occurred at a frequency of 1.5% and urethral stricture at 1.5%, for which endoscopic treatment was indicated. Acute and chronic gastrointestinal AEs were uncommon, and no Grade 3 or above AEs developed. Biochemical failure occurred in 4 patients who all exhibited high-/very high-risk diseases. Kaplan-Meier estimated that 3 year biochemical failure-free survival was 91.6% overall and 88.0% in high-/very high-risk cases. The present two-fraction 1 day HDR monotherapy is feasible with minimal AEs and achieved acceptable biochemical control of localized prostate cancer, including high-/very high-risk cases, although long-term follow-up is required.

Paternal and maternal factors in preimplantation embryogenesis: interaction with the biochemical environment.

PubMed

Ménézo, Yves J R

2006-05-01

Paternal effect on embryonic development occurs as early as fertilization. Incorrect formation of the spermatozoon due to centrosome defects and abnormal concentrations of any components involved in the activation process lead to failure immediately or in the subsequent cell cycles. Sperm chromosomal abnormalities result in early embryo developmental arrests. Generally poor spermatozoa lead to poor blastocyst formation. Sperm DNA fragmentation may impair even late post-implantation development. The DNA repair capacity of the oocytes is of major importance. Early preimplantation development, i.e. until maternal to zygotic transition, is maternally driven. Maternal mRNAs and proteins are of major importance, as there is an unavoidable turnover of these reserves. Polyadenylation of these mRNAs is precisely controlled, in order to avoid too early or too late transcription and translation of the housekeeping genes. An important set of maternal regulations, such as DNA stability, transcriptional regulation and protection against oxidative stress, are impaired by age. The embryo biochemical endogenous pool is very important and may depend upon the environment, i.e. the culture medium. Paternal, maternal and environmental factors are unavoidable parameters; they become evident when age impairs oocyte quality.

In vitro FTIR microspectroscopy analysis of primary oral squamous carcinoma cells treated with cisplatin and 5-fluorouracil: a new spectroscopic approach for studying the drug-cell interaction.

PubMed

Giorgini, Elisabetta; Sabbatini, Simona; Rocchetti, Romina; Notarstefano, Valentina; Rubini, Corrado; Conti, Carla; Orilisi, Giulia; Mitri, Elisa; Bedolla, Diana E; Vaccari, Lisa

2018-06-22

In the present study, human primary oral squamous carcinoma cells treated with cisplatin and 5-fluorouracil were analyzed, for the first time, by in vitro FTIR Microspectroscopy (FTIRM), to improve the knowledge on the biochemical pathways activated by these two chemotherapy drugs. To date, most of the studies regarding FTIRM cellular analysis have been executed on fixed cells from immortalized cell lines. FTIRM analysis performed on primary tumor cells under controlled hydrated conditions provides more reliable information on the biochemical processes occurring in in vivo tumor cells. This spectroscopic analysis allows to get on the same sample and at the same time an overview of the composition and structure of the most remarkable cellular components. In vitro FTIRM analysis of primary oral squamous carcinoma cells evidenced a time-dependent drug-specific cellular response, also including apoptosis triggering. Furthermore, the univariate and multivariate analyses of IR data evidenced meaningful spectroscopic differences ascribable to alterations affecting cellular proteins, lipids and nucleic acids. These findings suggest for the two drugs different pathways and extents of cellular damage, not provided by conventional cell-based assays (MTT assay and image-based cytometry).

EDAC: Epithelial defence against cancer-cell competition between normal and transformed epithelial cells in mammals.

PubMed

Kajita, Mihoko; Fujita, Yasuyuki

2015-07-01

During embryonic development or under certain pathological conditions, viable but suboptimal cells are often eliminated from the cellular society through a process termed cell competition. Cell competition was originally identified in Drosophila where cells with different properties compete for survival; 'loser' cells are eliminated from tissues and consequently 'winner' cells become dominant. Recent studies have shown that cell competition also occurs in mammals. While apoptotic cell death is the major fate for losers in Drosophila, outcompeted cells show more variable phenotypes in mammals, such as cell death-independent apical extrusion and cellular senescence. Molecular mechanisms underlying these processes have been recently revealed. Especially, in epithelial tissues, normal cells sense and actively eliminate the neighbouring transformed cells via cytoskeletal proteins by the process named epithelial defence against cancer (EDAC). Here, we introduce this newly emerging research field: cell competition in mammals. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

[Origin of the plague microbe Yersinia pestis: structure of the process of speciation].

PubMed

Suntsov, V V

2012-01-01

The origin and evolution of the plague microbe Yersinia pestis are considered in the context of propositions of modern Darwinism. It was shown that the plague pathogen diverged from the pseudotuberculous microbe Yersinia pseudotuberculosis O:1b in the mountain steppe landscapes of Central Asia in the Sartan: 22000-15000 years ago. Speciation occurred in the tarbagan (Marmota sibirica)--flea (Oropsylla silantiewi) parasitic system. The structure of the speciation process included six stages: isolation, genetic drift, enhancement of intrapopulational polymorphism, the beginning of pesticin synthesis (genetic conflict and emergence of hiatus), specialization (stabilization of characteristics), and adaptive irradiation (transformation of the monotypic species Y. pestis tarbagani into a polytypic species). The scenario opens up wide prospects for construction of the molecular phylogeny of the plague microbe Y. pestis and for investigation of the biochemical and molecular-genetic aspects of "Darwinian" evolution of pathogens from many other nature-focal infections.

Mechanism of Cytokinetic Contractile Ring Constriction in Fission Yeast

PubMed Central

Stachowiak, Matthew R.; Laplante, Caroline; Chin, Harvey F.; Guirao, Boris; Karatekin, Erdem; Pollard, Thomas D.; O’Shaughnessy, Ben

2014-01-01

SUMMARY Cytokinesis involves constriction of a contractile actomyosin ring. The mechanisms generating ring tension and setting the constriction rate remain unknown, since the organization of the ring is poorly characterized, its tension was rarely measured, and constriction is coupled to other processes. To isolate ring mechanisms we studied fission yeast protoplasts, where constriction occurs without the cell wall. Exploiting the absence of cell wall and actin cortex, we measured ring tension and imaged ring organization, which was dynamic and disordered. Computer simulations based on the amounts and biochemical properties of the key proteins showed that they spontaneously self-organize into a tension-generating bundle. Together with rapid component turnover, the self-organization mechanism continuously reassembles and remodels the constricting ring. Ring constriction depended on cell shape, revealing that the ring operates close to conditions of isometric tension. Thus, the fission yeast ring sets its own tension, but other processes set the constriction rate. PMID:24914559

Isolation and in vitro binding of mating type plus fertilization tubules from Chlamydomonas.

PubMed

Wilson, Nedra F

2008-01-01

During fertilization in Chlamydomonas, adhesion and fusion of gametes occur at the tip of specialized regions of the plasma membrane, known as mating structures. The mating type minus (mt[-]) structure is a slightly raised dome-shaped region located at the apical end of the cell body. In contrast, the activated mating type plus (mt[+]) structure is an actin-filled, microvillouslike organelle. Interestingly, a similar type of "fusion organelle" is conserved across diverse groups. Chlamydomonas provides an ideal model system for studying the process of gametic cell fusion in that it is amenable to genetic manipulations as well as cell and molecular biological approaches. Moreover, the ease of culturing Chlamydomonas combined with the ability to isolate the mt(+) fertilization tubule and the development of in vitro assays for adhesion makes it an ideal system for biochemical studies focused on dissecting the molecular mechanisms that underlie the complex process of gametic cell fusion.

Does the addition of proteases affect the biogas yield from organic material in anaerobic digestion?

PubMed

Müller, Liane; Kretzschmar, Jörg; Pröter, Jürgen; Liebetrau, Jan; Nelles, Michael; Scholwin, Frank

2016-03-01

The aim of this study was to investigate the biochemical disintegration effect of hydrolytic enzymes in lab scale experiments. Influences of enzyme addition on the biogas yield as well as effects on the process stability were examined. The addition of proteases occurred with low and high dosages in batch and semi-continuous biogas tests. The feed mixture consisted of maize silage, chicken dung and cow manure. Only very high concentrated enzymes caused an increase in biogas production in batch experiments. In semi-continuous biogas tests no positive long-term effects (100 days) were observed. Higher enzyme-dosage led to a reduced biogas-yield (13% and 36% lower than the reference). Phenylacetate and -propionate increased (up to 372 mgl(-1)) before the other volatile fatty acids did. Volatile organic acids rose up to 6.8 gl(-1). The anaerobic digestion process was inhibited. Copyright © 2015 Elsevier Ltd. All rights reserved.

Emerging drugs for the treatment of wound healing.

PubMed

Zielins, Elizabeth R; Brett, Elizabeth A; Luan, Anna; Hu, Michael S; Walmsley, Graham G; Paik, Kevin; Senarath-Yapa, Kshemendra; Atashroo, David A; Wearda, Taylor; Lorenz, H Peter; Wan, Derrick C; Longaker, Michael T

2015-06-01

Wound healing can be characterized as underhealing, as in the setting of chronic wounds, or overhealing, occurring with hypertrophic scar formation after burn injury. Topical therapies targeting specific biochemical and molecular pathways represent a promising avenue for improving and, in some cases normalizing, the healing process. A brief overview of both normal and pathological wound healing has been provided, along with a review of the current clinical guidelines and treatment modalities for chronic wounds, burn wounds and scar formation. Next, the major avenues for wound healing drugs, along with drugs currently in development, are discussed. Finally, potential challenges to further drug development, and future research directions are discussed. The large body of research concerning wound healing pathophysiology has provided multiple targets for topical therapies. Growth factor therapies with the ability to be targeted for localized release in the wound microenvironment are most promising, particularly when they modulate processes in the proliferative phase of wound healing.

Quo vadis plant hormone analysis?

PubMed

Tarkowská, Danuše; Novák, Ondřej; Floková, Kristýna; Tarkowski, Petr; Turečková, Veronika; Grúz, Jiří; Rolčík, Jakub; Strnad, Miroslav

2014-07-01

Plant hormones act as chemical messengers in the regulation of myriads of physiological processes that occur in plants. To date, nine groups of plant hormones have been identified and more will probably be discovered. Furthermore, members of each group may participate in the regulation of physiological responses in planta both alone and in concert with members of either the same group or other groups. The ideal way to study biochemical processes involving these signalling molecules is 'hormone profiling', i.e. quantification of not only the hormones themselves, but also their biosynthetic precursors and metabolites in plant tissues. However, this is highly challenging since trace amounts of all of these substances are present in highly complex plant matrices. Here, we review advances, current trends and future perspectives in the analysis of all currently known plant hormones and the associated problems of extracting them from plant tissues and separating them from the numerous potentially interfering compounds.

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

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States

NASA Astrophysics Data System (ADS)

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M.

2018-03-01

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

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.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

PubMed

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M

2018-03-23

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

Biochemistry of homologous recombination in Escherichia coli.

PubMed Central

Kowalczykowski, S C; Dixon, D A; Eggleston, A K; Lauder, S D; Rehrauer, W M

1994-01-01

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination. Images PMID:7968921

ACTION OF MUTAGENIC AGENTS ON AUXOTROPHIC STRAINS OF STREPTOMYCES

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

Jarai, M.

1962-01-01

The mutagenic effect on Streptomyces auxotrophs of uv and x irradiation and of some chemical agerts was studied. From the observed reverse mutations it was concluded that uv and probably x irradiation have an optimal mutagenic dose. With nine auxotrophic strains it was shown that under the same conditions different gene loci reacted differently to the same mutagenic agent. With uy radiation, mutations occurred most frequently at doses falling within the range of 3500 to 4000 erg/mm/sup 2/. With such doses, the average mutation frequency for singly deficient mutants was 0.8 x 10/sup -6/, for doubly deficient mutants 8.4 xmore » 10/sup -8/. An analysis of the number of mutations as compared to the number of survivors in two biochemical mutants (N-4 and N-11) showed that with N- 4 the highest number of mutations was obtained at doses of 3500 to 4500 erg/mm/ sup 2/, namely, 12 to 15 per 10 surviving conidia, and with strain N-11, the highest frequency was obtained in the same dose range, namely, three to four mutations per 10/sup 6/ surviving conidia. The optimal dose of irradiation corresponds to 90 to 97% lethality. It was shown that, unlike the results with uv irradiation, with x rays no such definite relation existed between optimal dose and frequency of mutations. The highest mutation frequency occurred at doses of 20,000 to 25,000 r, which corresponded to 85 to 91% lethality. Of the chemical substances examined, a definite mutagenic action was exerted by acridine orange, streptomycin, hydroxylamine, phenyl, isocyannte, and 8-quinolinol. The maximum mutagenic frequency for survivors was 41.4 x 10/sup -6/ after uv irradiation (biochemical mutant arg 3-; frequency of sportaneous back mutation, 0.041 x 10/sup -6/). With x irradiation the maximum mutagenic frequency was 3.42 x 10/sup -6/ (biochemical mutant meth 1-; frequency of spontaneous back mutation, 0.28 X 10/sup -6/). With chemical agents the maximum mutation frequencies for the initial conidia number were as follows: acridine orange, 3.65 x 10/sup -6/ (biochemical mutant arg 3-); streptomycin, 2.05 x 10/sup -6/ (biochemical mutant arg 3-); hydroxylamine, 5.81 x 10/sup -6/ (biochemical mutant meth 1/sup -/); phenyl isocyanate, 6.11 x 10/sup -6/ (biochemical mutant meth 1/sup -/); 8- quinolinol, 1.02 x 10/sup -6/ (biochemical mutant meth 1/sup -/). (BBB)« less

Silencing, positive selection and parallel evolution: busy history of primate cytochromes C.

PubMed

Pierron, Denis; Opazo, Juan C; Heiske, Margit; Papper, Zack; Uddin, Monica; Chand, Gopi; Wildman, Derek E; Romero, Roberto; Goodman, Morris; Grossman, Lawrence I

2011-01-01

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.

Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c

PubMed Central

Pierron, Denis; Opazo, Juan C.; Heiske, Margit; Papper, Zack; Uddin, Monica; Chand, Gopi; Wildman, Derek E.; Romero, Roberto; Goodman, Morris; Grossman, Lawrence I.

2011-01-01

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades. PMID:22028846

Organ-coordinated response of early post-germination mahogany seedlings to drought.

PubMed

Horta, Lívia P; Braga, Márcia R; Lemos-Filho, José P; Modolo, Luzia V

2014-04-01

Water deficit tolerance during post-germination stages is critical for seedling recruitment. In this work, we studied the effect of water deficit on morphological and biochemical responses in different organs of newly germinated mahogany (Swietenia macrophylla King) seedlings, a woody species that occurs in the Amazon rainforest. The root : shoot ratio increased under water deficit. The leaf number and water potential were not altered, although reductions in leaf area and stomatal conductance were observed. Osmotic potential became more negative in leaves of seedlings under severe stress. Water deficit increased fructose, glucose, sucrose and myo-inositol levels in leaves. Stems accumulated fructose, glucose and l-proline. Nitric oxide (NO) levels increased in the vascular cylinder of roots under severe stress while superoxide anion levels decreased due to augmented superoxide dismutase activity in this organ. Water deficit induced glutathione reductase activity in both roots and stems. Upon moderate or severe stress, catalase activity decreased in leaves and remained unaffected in the other seedling organs, allowing for an increase of hydrogen peroxide (H2O2) levels in leaves. Overall, the increase of signaling molecules in distinct organs-NO in roots, l-proline in stems and H2O2 and myo-inositol in leaves-contributed to the response of mahogany seedlings to water deficit by triggering biochemical processes that resulted in the attenuation of oxidative stress and the establishment of osmotic adjustment. Therefore, this body of evidence reveals that the development of newly germinated mahogany seedlings may occur in both natural habitats and crop fields even when water availability is greatly limited.

Growth hormone deficiency in children and young adults.

PubMed

Oświęcimska, Joanna; Roczniak, Wojciech; Mikołajczak, Agata; Szymlak, Agnieszka

2016-09-13

Growth hormone (GH) is a naturally occurring polypeptide hormone produced by somatotropic cells in the anterior pituitary. The main function of somatotropin is stimulation of linear growth, but it also affects carbohydrate metabolism, increases bone mass and has potent lipolytic, antinatriuretic and antidiuretic effects. Growth hormone deficiency (GHD) may occur both in children and in adults. At the moment there is no gold standard for the diagnosis of GHD, and the diagnosis should take into account clinical, auxological, biochemical and radiological changes and, if necessary, genetic testing. Recent studies have highlighted that the biochemical diagnosis of GH deficiency is still imperfect. Stimuli used in the tests are non-physiological, and various substances are characterized by a different mechanism of action and potency. A few years ago it was thought that GHD treatment in children must be completed at the end of linear growth. Studies performed in the last two decades have shown that GHD deficiency in adults may result in complex clinical problems, and if untreated shortens the life expectancy and worsens its comfort. Discontinuation of GH therapy after the final height has been reached in fact negatively impacts the physiological processes associated with the transition phase, which is the period of human life between achieving the final height and 25-30 years of age. Given the adverse metabolic effects of GH treatment interruption after linear growth has been completed, the latest recommendations propose reassessment of GH secretion in the period at least one month after cessation of treatment and continuation of the therapy in case of persistent deficit.

Tertiary Hyperparathyroidism

PubMed Central

Davies, D. R.; Dent, C. E.; Watson, Lyal

1968-01-01

In our first 200 cases of primary hyperparathyroidism confirmed by operation 12 were also shown to have a long history either of a malabsorption syndrome or of chronic renal-glomerular failure. We consider that they first went through a phase of secondary hyperparathyroidism, during which one or more of the glands became autonomous adenamata. This then produced the biochemical changes of “primary” hyperparathyroidism, necessitating excision of the adenoma. This condition is best described as “tertiary” hyperparathyroidism. The transition from secondary to tertiary hyperparathyroidism occurred in four of the 12 patients while under our observation. We think the same process can be traced retrospectively in the other eight cases. The concept of tertiary hyperparathyroidism may help to explain the high incidence of other diseases in association with primary hyperparathyroidism. The behaviour of the parathyroid glands provides a valuable model for the investigation of tumour formation in man. All states occurred in our patients with primary hyperparathyroidism, from normal through hyperplasia to adenoma formation and finally to parathyroid carcinoma. PMID:5691200

Relationships between tyrosine, phenylalanine, chlorogenic acid, and ascorbic acid concentrations and blackspot biochemical potential and blackspot susceptibility in stored russet potatoes.

PubMed

Goyer, Aymeric; Pellé, Julien

2018-08-01

Blackspot in potato is an internal tissue discoloration that occurs during handling and transport of potato tubers. Blackspot is cosmetically undesirable and represents a huge economic cost for the potato industry. The aim of this study was to test whether concentrations of certain metabolites in the potato tuber cortex could predict blackspot susceptibility. Seven russet potato varieties were stored for eight months at 8.8 °C. Stored tubers were subjected to mechanical impact and evaluated for blackspot susceptibility. A blackspot susceptibility index was calculated for each variety by determining an index for the percentage of the tuber cortex area that was covered with blackspot, and an index for the intensity of blackspot discoloration. Concentrations of tyrosine, chlorogenic acid, phenylalanine, and ascorbic acid, and blackspot biochemical potential of tubers to synthesize pigments were measured in the tuber cortex. Blackspot indices, metabolites concentrations and blackspot biochemical potential varied significantly between varieties. Tyrosine concentrations strongly, significantly, and positively correlated with blackspot biochemical potential. Phenylalanine concentrations showed good, significant, and positive correlation with blackspot biochemical potential and discoloration index. None of the analyzed metabolites correlated with blackspot susceptibility. Concentrations of tyrosine and phenylalanine explained up to ∼80% of the variation in blackspot biochemical potential between varieties but did not correlate with blackspot susceptibility. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Metal Removal Efficiency And Ecotoxicological Assessment Of Field-Scale Passive Treatment Biochemical Reactors

EPA Science Inventory

Anaerobic biochemical reactors (BCRs) are useful for removing metals from mining-impacted water at remote sites. Removal processes include sorption and precipitation of metal sulfides, carbonates, and hydroxides. A question of interest is whether BCRs remove aquatic toxicity. ...

Sublethal microcystin exposure and biochemical outcomes among hemodialysis patients

EPA Science Inventory

Cyanobacteria are commonly-occurring contaminants of surface waters worldwide. Microcystins, potent hepatotoxins, are among the best characterized cyanotoxins. During November, 2001, a group of 44 hemodialysis patients were exposed to microcystins via contaminated dialysate. Seru...

BIOCHEM-ORCHESTRA: a tool for evaluating chemical speciation and ecotoxicological impacts of heavy metals on river flood plain systems.

PubMed

Vink, J P M; Meeussen, J C L

2007-08-01

The chemical speciation model BIOCHEM was extended with ecotoxicological transfer functions for uptake of metals (As, Cd, Cu, Ni, Pb, and Zn) by plants and soil invertebrates. It was coupled to the object-oriented framework ORCHESTRA to achieve a flexible and dynamic decision support system (DSS) to analyse natural or anthropogenic changes that occur in river systems. The DSS uses the chemical characteristics of soils and sediments as input, and calculates speciation and subsequent uptake by biota at various scenarios. Biotic transfer functions were field-validated, and actual hydrological conditions were derived from long-term monitoring data. The DSS was tested for several scenarios that occur in the Meuse catchment areas, such as flooding and sedimentation of riverine sediments on flood plains. Risks are expressed in terms of changes in chemical mobility, and uptake by flood plain key species (flora and fauna).

A systematic review of the neurobiological aspects of memory in the aging process

PubMed Central

de Oliveira, Eduardo Moreira; Kissaki, Priscilla Tiemi; Ordonez, Tiago Nascimento; Lima-Silva, Thaís Bento

2011-01-01

A systematic review of the neuroanatomical literature was performed to determine the neuropharmacological aspects most relevant to the study of memory processes. Articles were retrieved using the search terms "biology of memory", "memory and aging", "memory impairment", "elderly and memory," and their equivalents in Portuguese. Of the studies surveyed, five studies dealt with epidemiological and demographic issues, 12 were clinical trials i.e. were based on testing and implementation of instruments in human subjects, 33 studies were basic research involving studies of mice, rats and non-human primates, and biochemical and in vitro trials and finally, 52 studies were literature reviews or book chapters which in our view, fell into this category. Conclusions The work sought to highlight which neural networks are most involved in processing information, as well as their location within brain regions and the way in which neurotransmitters interact with each other for the formation of these memories. Moreover, it was shown how memory changes during the normal human aging process, both positively and negatively, by analyzing the morphological alterations that occur in the brain of aging individuals. PMID:29213758

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

Structural and biochemical characterization of N[superscript 5]-carboxyaminoimidazole ribonucleotide synthetase and N[superscript 5]-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus

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

Brugarolas, Pedro; Duguid, Erica M.; Zhang, Wen

With the rapid rise of methicillin-resistant Staphylococcus aureus infections, new strategies against S. aureus are urgently needed. De novo purine biosynthesis is a promising yet unexploited target, insofar as abundant evidence has shown that bacteria with compromised purine biosynthesis are attenuated. Fundamental differences exist within the process by which humans and bacteria convert 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). In bacteria, this transformation occurs through a two-step conversion catalyzed by PurK and PurE; in humans, it is mediated by a one-step conversion catalyzed by class II PurE. Thus, these bacterial enzymes are potential targets for selective antibiotic development. Here,more » the first comprehensive structural and biochemical characterization of PurK and PurE from S. aureus is presented. Structural analysis of S. aureus PurK reveals a nonconserved phenylalanine near the AIR-binding site that occupies the putative position of the imidazole ring of AIR. Mutation of this phenylalanine to isoleucine or tryptophan reduced the enzyme efficiency by around tenfold. The K{sub m} for bicarbonate was determined for the first time for a PurK enzyme and was found to be {approx}18.8 mM. The structure of PurE is described in comparison to that of human class II PurE. It is confirmed biochemically that His38 is essential for function. These studies aim to provide foundations for future structure-based drug-discovery efforts against S. aureus purine biosynthesis.« less

Yeast lipids from cardoon stalks, stranded driftwood and olive tree pruning residues as possible extra sources of oils for producing biofuels and biochemicals.

PubMed

Tasselli, Giorgia; Filippucci, Sara; Borsella, Elisabetta; D'Antonio, Silvia; Gelosia, Mattia; Cavalaglio, Gianluca; Turchetti, Benedetta; Sannino, Ciro; Onofri, Andrea; Mastrolitti, Silvio; De Bari, Isabella; Cotana, Franco; Buzzini, Pietro

2018-01-01

Some lignocellulosic biomass feedstocks occur in Mediterranean Countries. They are still largely unexploited and cause considerable problems due to the lack of cost-effective harvesting, storage and disposal technologies. Recent studies found that some basidiomycetous yeasts are able to accumulate high amount of intracellular lipids for biorefinery processes (i.e., biofuels and biochemicals). Accordingly, the above biomass feedstocks could be used as carbon sources (after their pre-treatment and hydrolysis) for lipid accumulation by oleaginous yeasts. Cardoon stalks, stranded driftwood and olive tree pruning residues were pre-treated with steam-explosion and enzymatic hydrolysis for releasing free mono- and oligosaccharides. Lipid accumulation tests were performed at two temperatures (20 and 25 °C) using Leucosporidium creatinivorum DBVPG 4794, Naganishia adeliensis DBVPG 5195 and Solicoccozyma terricola DBVPG 5870. S. terricola grown on cardoon stalks at 20 °C exhibited the highest lipid production (13.20 g/l), a lipid yield (28.95%) close to the maximum theoretical value and a lipid composition similar to that found in palm oil. On the contrary, N. adeliensis grown on stranded driftwood and olive tree pruning residues exhibited a lipid composition similar to those of olive and almonds oils. A predictive evaluation of the physical properties of the potential biodiesel obtainable by lipids produced by tested yeast strains has been reported and discussed. Lipids produced by some basidiomycetous yeasts grown on Mediterranean lignocellulosic biomass feedstocks could be used as supplementary sources of oils for producing biofuels and biochemicals.

Branched-chain amino acids and brain function.

PubMed

Fernstrom, John D

2005-06-01

Branched-chain amino acids (BCAAs) influence brain function by modifying large, neutral amino acid (LNAA) transport at the blood-brain barrier. Transport is shared by several LNAAs, notably the BCAAs and the aromatic amino acids (ArAAs), and is competitive. Consequently, when plasma BCAA concentrations rise, which can occur in response to food ingestion or BCAA administration, or with the onset of certain metabolic diseases (e.g., uncontrolled diabetes), brain BCAA concentrations rise, and ArAA concentrations decline. Such effects occur acutely and chronically. Such reductions in brain ArAA concentrations have functional consequences: biochemically, they reduce the synthesis and the release of neurotransmitters derived from ArAAs, notably serotonin (from tryptophan) and catecholamines (from tyrosine and phenylalanine). The functional effects of such neurochemical changes include altered hormonal function, blood pressure, and affective state. Although the BCAAs thus have biochemical and functional effects in the brain, few attempts have been made to characterize time-course or dose-response relations for such effects. And, no studies have attempted to identify levels of BCAA intake that might produce adverse effects on the brain. The only "model" of very high BCAA exposure is a very rare genetic disorder, maple syrup urine disease, a feature of which is substantial brain dysfunction but that probably cannot serve as a useful model for excessive BCAA intake by normal individuals. Given the known biochemical and functional effects of the BCAAs, it should be a straightforward exercise to design studies to assess dose-response relations for biochemical and functional effects and, in this context, to explore for adverse effect thresholds.

Hematologic and biochemical characteristics of stranded green sea turtles.

PubMed

March, Duane T; Vinette-Herrin, Kimberly; Peters, Andrew; Ariel, Ellen; Blyde, David; Hayward, Doug; Christidis, Les; Kelaher, Brendan P

2018-05-01

To improve understanding of pathophysiologic processes occurring in green sea turtles ( Chelonia mydas) stranded along the east coast of Australia, we retrospectively examined the hematologic and biochemical blood parameters of 127 green turtles admitted to 2 rehabilitation facilities, Dolphin Marine Magic (DMM) and Taronga Zoo (TZ), between 2002 and 2016. The predominant size class presented was small immature animals (SIM), comprising 88% and 69% of admissions to DMM and TZ, respectively. Significant differences in blood profiles were noted between facility, size, and outcome. Elevated levels of aspartate aminotransferase (AST) and heterophils were poor prognostic indicators in animals from TZ, but not DMM. SIM animals at both institutions had lower protein levels than large older (LO) animals. SIM animals at DMM also had lower hematocrit and monocyte concentration; SIM animals at TZ had lower heterophil counts. Urea was measured for 27 SIM animals from TZ, but the urea-to-uric acid ratio was not prognostically useful. Strong correlations were seen between AST and glutamate dehydrogenase (GDH; r = 0.68) and uric acid and bile acids ( r = 0.72) in the 45 SIM animals from DMM in which additional analytes were measured. χ 2 contingency tests showed that the most recently published reference intervals were not prognostically useful. A paired t-test showed that protein levels rose and heterophil numbers fell in the 15 SIM animals from TZ during the rehabilitation process. Our results indicate that further work is required to identify reliable prognostic biomarkers for green turtles.

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

PubMed Central

Galluzzi, L; Bravo-San Pedro, J M; Vitale, I; Aaronson, S A; Abrams, J M; Adam, D; Alnemri, E S; Altucci, L; Andrews, D; Annicchiarico-Petruzzelli, M; Baehrecke, E H; Bazan, N G; Bertrand, M J; Bianchi, K; Blagosklonny, M V; Blomgren, K; Borner, C; Bredesen, D E; Brenner, C; Campanella, M; Candi, E; Cecconi, F; Chan, F K; Chandel, N S; Cheng, E H; Chipuk, J E; Cidlowski, J A; Ciechanover, A; Dawson, T M; Dawson, V L; De Laurenzi, V; De Maria, R; Debatin, K-M; Di Daniele, N; Dixit, V M; Dynlacht, B D; El-Deiry, W S; Fimia, G M; Flavell, R A; Fulda, S; Garrido, C; Gougeon, M-L; Green, D R; Gronemeyer, H; Hajnoczky, G; Hardwick, J M; Hengartner, M O; Ichijo, H; Joseph, B; Jost, P J; Kaufmann, T; Kepp, O; Klionsky, D J; Knight, R A; Kumar, S; Lemasters, J J; Levine, B; Linkermann, A; Lipton, S A; Lockshin, R A; López-Otín, C; Lugli, E; Madeo, F; Malorni, W; Marine, J-C; Martin, S J; Martinou, J-C; Medema, J P; Meier, P; Melino, S; Mizushima, N; Moll, U; Muñoz-Pinedo, C; Nuñez, G; Oberst, A; Panaretakis, T; Penninger, J M; Peter, M E; Piacentini, M; Pinton, P; Prehn, J H; Puthalakath, H; Rabinovich, G A; Ravichandran, K S; Rizzuto, R; Rodrigues, C M; Rubinsztein, D C; Rudel, T; Shi, Y; Simon, H-U; Stockwell, B R; Szabadkai, G; Tait, S W; Tang, H L; Tavernarakis, N; Tsujimoto, Y; Vanden Berghe, T; Vandenabeele, P; Villunger, A; Wagner, E F; Walczak, H; White, E; Wood, W G; Yuan, J; Zakeri, Z; Zhivotovsky, B; Melino, G; Kroemer, G

2015-01-01

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death. PMID:25236395

Cultivar variability of patatin biochemical characteristics: table versus processing potatoes (Solanum tuberosum L.).

PubMed

Bárta, Jan; Bártová, Veronika; Zdráhal, Zbyněk; Sedo, Ondrej

2012-05-02

Biochemical characteristics of patatin proteins purified by ion-exchange and affinity chromatography from tubers of 20 potato cultivars were studied to evaluate their genotype differences with respect to utility groups, table potato cultivars (TPCs) and processing potato cultivars (PPCs). Both groups of cultivars showed similar values of protein content in dry matter (3.98-7.39%) and of patatin relative abundance (5.40-35.40%). Three mass levels (∼40.6, 41.8, and 42.9 kDa) of purified patatins were found by MALDI-TOF MS within all cultivars. Differences among mass levels corresponding with the mass of sugar antenna (∼1.2 kDa) confirmed the previous concept of different glycosylation extentsin patatin proteins. It was showed that the individual types of patatin varying in their masses occur in the patatin family in a ratio specific for each of the cultivars, with the lowest mass type being the major one. Electrophoretic analyses demonstrated wide cultivar variability in number of patatin forms. Especially 2D-PAGE showed 17-23 detected protein spots independently on the utility group. Specific lipid acyl hydrolase (LAH) activity of purified patatins from the individual tested cultivars varied between 0.92 and 5.46 μmol/(min mg). Patatin samples within most of the TPCs exhibited higher values of specific LAH activity than samples of PPCs. It may be supposed that individual patatin forms do not have similar physiological roles.

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015.

PubMed

Galluzzi, L; Bravo-San Pedro, J M; Vitale, I; Aaronson, S A; Abrams, J M; Adam, D; Alnemri, E S; Altucci, L; Andrews, D; Annicchiarico-Petruzzelli, M; Baehrecke, E H; Bazan, N G; Bertrand, M J; Bianchi, K; Blagosklonny, M V; Blomgren, K; Borner, C; Bredesen, D E; Brenner, C; Campanella, M; Candi, E; Cecconi, F; Chan, F K; Chandel, N S; Cheng, E H; Chipuk, J E; Cidlowski, J A; Ciechanover, A; Dawson, T M; Dawson, V L; De Laurenzi, V; De Maria, R; Debatin, K-M; Di Daniele, N; Dixit, V M; Dynlacht, B D; El-Deiry, W S; Fimia, G M; Flavell, R A; Fulda, S; Garrido, C; Gougeon, M-L; Green, D R; Gronemeyer, H; Hajnoczky, G; Hardwick, J M; Hengartner, M O; Ichijo, H; Joseph, B; Jost, P J; Kaufmann, T; Kepp, O; Klionsky, D J; Knight, R A; Kumar, S; Lemasters, J J; Levine, B; Linkermann, A; Lipton, S A; Lockshin, R A; López-Otín, C; Lugli, E; Madeo, F; Malorni, W; Marine, J-C; Martin, S J; Martinou, J-C; Medema, J P; Meier, P; Melino, S; Mizushima, N; Moll, U; Muñoz-Pinedo, C; Nuñez, G; Oberst, A; Panaretakis, T; Penninger, J M; Peter, M E; Piacentini, M; Pinton, P; Prehn, J H; Puthalakath, H; Rabinovich, G A; Ravichandran, K S; Rizzuto, R; Rodrigues, C M; Rubinsztein, D C; Rudel, T; Shi, Y; Simon, H-U; Stockwell, B R; Szabadkai, G; Tait, S W; Tang, H L; Tavernarakis, N; Tsujimoto, Y; Vanden Berghe, T; Vandenabeele, P; Villunger, A; Wagner, E F; Walczak, H; White, E; Wood, W G; Yuan, J; Zakeri, Z; Zhivotovsky, B; Melino, G; Kroemer, G

2015-01-01

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as 'accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. 'Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.

Molecular modelling and quantum biochemistry computations of a naturally occurring bioremediation enzyme: Alkane hydroxylase from Pseudomonas putida P1.

PubMed

de Sousa, B G; Oliveira, J I N; Albuquerque, E L; Fulco, U L; Amaro, V E; Blaha, C A G

2017-10-01

Many species of bacteria involved in degradation of n-alkanes have an important constitutional metabolic enzyme, the alkane hydroxylase called AlkB, specialized in the conversion of hydrocarbons molecules that can be used as carbon and/or energy source. This enzyme plays an important role in the microbial degradation of oil, chlorinated hydrocarbons, fuel additives, and many other compounds. A number of these enzymes has been biochemically characterized in detail because the potential of alkane hydroxylases to catalyse high added-value reactions is widely recognized. Nevertheless, the industrial and process bioremediation application of them is restricted, owing to their complex biochemistry, challenging process requirements, and the limited number of their three-dimensional structures. Furthermore, AlkB has great potential as biocatalysts for selective transformation of a wide range of chemically inert unreactive alkanes into reactive chemical precursors that can be used as tools for bioremediation and bioprocesses. Aiming to understand the possible ways the AlkB enzyme Pseudomonas putida P1 interacts with octane, octanol and 1-octyne, we consider its suitable biochemical structure taking into account a 3-D homology modelling. Besides, by using a quantum chemistry computational model based on the density functional theory (DFT), we determine possible protein-substrate interaction regions measured by means of its binding energy simulated throughout the Molecular Fractionation with Conjugated Caps (MFCC) approach. Copyright © 2017 Elsevier Inc. All rights reserved.

Endocrine Disruptors Leading to Obesity and Related Diseases.

PubMed

Petrakis, Demetrios; Vassilopoulou, Loukia; Mamoulakis, Charalampos; Psycharakis, Christos; Anifantaki, Aliki; Sifakis, Stavros; Docea, Anca Oana; Tsiaoussis, John; Makrigiannakis, Antonios; Tsatsakis, Aristides M

2017-10-24

The review aims to comprehensively present the impact of exposure to endocrine disruptors (EDs) in relation to the clinical manifestation of obesity and related diseases, including diabetes mellitus, metabolic syndrome, cardiovascular diseases, carcinogenesis and infertility. EDs are strong participants in the obesity epidemic scenery by interfering with cellular morphological and biochemical processes; by inducing inflammatory responses; and by presenting transcriptional and oncogenic activity. Obesity and lipotoxicity enhancement occur through reprogramming and/or remodeling of germline epigenome by exposure to EDs. Specific population groups are vulnerable to ED exposure due to current dietary and environmental conditions. Obesity, morbidity and carcinogenicity induced by ED exposure are an evolving reality. Therefore, a new collective strategic approach is deemed essential, for the reappraisal of current global conditions pertaining to energy management.

Stable-isotope fingerprints of biological agents as forensic tools.

PubMed

Horita, Juske; Vass, Arpad A

2003-01-01

Naturally occurring stable isotopes of light elements in chemical and biological agents may possess unique "stable-isotope fingerprints" depending on their sources and manufacturing processes. To test this hypothesis, two strains of bacteria (Bacillus globigii and Erwinia agglomerans) were grown under controlled laboratory conditions. We observed that cultured bacteria cells faithfully inherited the isotopic composition (hydrogen, carbon, and nitrogen) of media waters and substrates in predictable manners in terms of bacterial metabolism and that even bacterial cells of the same strain, which grew in media water and substrates of different isotopic compositions, have readily distinguishable isotopic signatures. These "stable-isotopic fingerprints" of chemical and biological agents can be used as forensic tools in the event of biochemical terrorist attacks.

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

Metabolomics of AS-1 RBC storage

PubMed Central

Roback, John D.; Josephson, Cassandra D.; Waller, Edmund K.; Newman, James L.; Karatela, Sulaiman; Uppal, Karan; Jones, Dean; Zimring, James C.; Dumont, Larry J.

2014-01-01

Background Population based investigations suggest that red blood cells (RBCs) are therapeutically effective when collected, processed and stored for up to 42 days under validated conditions prior to transfusion. However, some retrospective clinical studies have shown worse patient outcomes when transfused RBCs have been stored for the longest times. Furthermore, studies of RBC persistence in the circulation after transfusion have suggested that considerable donor-to-donor variability exists, and may affect transfusion efficacy. To understand the limitations of current blood storage technologies and to develop approaches to improve RBC storage and transfusion efficacy, we investigated the global metabolic alterations that occur when RBCs are stored in AS-1 (AS1-RBC). Methods Leukoreduced AS1-RBC units prepared from 9 volunteer research donors (12 total donated units) were serially sampled for metabolomics analysis over 42 days of refrigerated storage. Samples were tested by GC/MS and LC/MS/MS, and specific biochemical compounds were identified by comparison to a library of purified standards. Results Over three experiments, 185–264 defined metabolites were quantified in stored RBC samples. Kinetic changes in these biochemicals confirmed known alterations in glycolysis and other pathways previously identified in RBCs stored in SAGM (SAGM-RBC). Furthermore, we identified additional alterations not previously seen in SAGM-RBCs (e.g., stable pentose phosphate pathway flux, progressive decreases in oxidized glutathione), and we delineated changes occurring in other metabolic pathways not previously studied (e.g., S-adenosyl methionine cycle). These data are presented in the context of a detailed comparison with previous studies of SAGM-RBCs from human donors and murine AS1-RBCs. Conclusion Global metabolic profiling of AS1-RBCs revealed a number of biochemical alterations in stored blood that may affect RBC viability during storage as well as therapeutic effectiveness of stored RBCs in transfusion recipients. Significance These results provide future opportunities to more clearly pinpoint the metabolic defects during RBC storage, to identify biomarkers for donor screening and prerelease RBC testing, and to develop improved RBC storage solutions and methodologies. PMID:24636780

Vitamin D-Mediated Hypercalcemia: Mechanisms, Diagnosis, and Treatment

PubMed Central

Tebben, Peter J.; Singh, Ravinder J.

2016-01-01

Hypercalcemia occurs in up to 4% of the population in association with malignancy, primary hyperparathyroidism, ingestion of excessive calcium and/or vitamin D, ectopic production of 1,25-dihydroxyvitamin D [1,25(OH)2D], and impaired degradation of 1,25(OH)2D. The ingestion of excessive amounts of vitamin D3 (or vitamin D2) results in hypercalcemia and hypercalciuria due to the formation of supraphysiological amounts of 25-hydroxyvitamin D [25(OH)D] that bind to the vitamin D receptor, albeit with lower affinity than the active form of the vitamin, 1,25(OH)2D, and the formation of 5,6-trans 25(OH)D, which binds to the vitamin D receptor more tightly than 25(OH)D. In patients with granulomatous disease such as sarcoidosis or tuberculosis and tumors such as lymphomas, hypercalcemia occurs as a result of the activity of ectopic 25(OH)D-1-hydroxylase (CYP27B1) expressed in macrophages or tumor cells and the formation of excessive amounts of 1,25(OH)2D. Recent work has identified a novel cause of non-PTH-mediated hypercalcemia that occurs when the degradation of 1,25(OH)2D is impaired as a result of mutations of the 1,25(OH)2D-24-hydroxylase cytochrome P450 (CYP24A1). Patients with biallelic and, in some instances, monoallelic mutations of the CYP24A1 gene have elevated serum calcium concentrations associated with elevated serum 1,25(OH)2D, suppressed PTH concentrations, hypercalciuria, nephrocalcinosis, nephrolithiasis, and on occasion, reduced bone density. Of interest, first-time calcium renal stone formers have elevated 1,25(OH)2D and evidence of impaired 24-hydroxylase-mediated 1,25(OH)2D degradation. We will describe the biochemical processes associated with the synthesis and degradation of various vitamin D metabolites, the clinical features of the vitamin D-mediated hypercalcemia, their biochemical diagnosis, and treatment. PMID:27588937

A Review: Some biological effects of high LET radiations

NASA Technical Reports Server (NTRS)

Wiley, A., Jr.

1972-01-01

There are qualitative and quantitative differences in the biological damage observed after exposure to high LET radiation as compared to that caused by low LET radiations. This review is concerned with these differences, which are ultimately reflected at the biochemical, cellular and even whole animal levels. In general, high LET radiations seem to produce biochemical damage which is more severe and possibly less repairable. Experimental data for those effects are presented in terms of biochemical RBE's with consideration of both early and late manifestations. An LET independent process by which significant biochemical damage may result from protons, neutrons and negative pion mesons is discussed.

Favorable toxicity and biochemical control using real-time inverse optimization technique for prostate brachytherapy.

PubMed

Raben, Adam; Rusthoven, Kyle E; Sarkar, Abrihup; Glick, Andrew; Benge, Bruce; Jacobs, Dayee; Raben, David

2009-01-01

Favorable dosimetric results have been reported using intraoperative inverse optimization (IO) for permanent prostate brachytherapy. The clinical implications of these improvements in dosimetry are unclear. We review toxicity and early biochemical outcomes for patients implanted using IO technique. Between 2001 and 2007, 165 patients received permanent prostate implants using real-time IO and had >/=3 months of followup. Dose constraints for inverse planning were: the prostate volume receiving 100% of the prescription dose [prostate V(100)] was >95%; the dose received by 90% of the gland [prostate D(90)] was within the 140-180 by dose range; the volume of urethra receiving 150% of the prescription dose [urethra V(150)] was <30%; and the volume of rectal wall receiving 110% of the prescription dose [rectal V(110)] was <1.0 cc. Toxicity was prospectively scored using the Radiation Therapy Oncology Group toxicity scale and the International Prostate Symptom Score questionnaire. Biochemical control was determined using the nadir + 2 ng/mL definition. Mean followup was 30 months (range, 6-63 months). Risk classification was low risk in 89% and intermediate risk in 11%. Iodine-125 sources were used for 161 implants and palladium-103 sources for four implants. The median number of seeds and total activity implanted were 61 and 999 MBq, respectively, for a median prostate volume of 33.6 cc. Late GU and GI morbidity was uncommon. Among patients with at least 24 months followup, 16% had persistent Grade 2-3 urinary morbidity. Grade 2 rectal bleeding occurred in 1 patient (0.6%). Biochemical failure has occurred in only 4 patients at last followup. IO technique for prostate brachytherapy is associated with low rates of late morbidity and excellent early biochemical control. Additionally, the number of seeds and total implanted activity required to achieve a high-quality implant are lower compared with historical controls.

Genetic Counseling and Prenatal Diagnosis of Triploidy During the Second Trimester of Pregnancy

PubMed Central

Kolarski, Milenko; Ahmetovic, Begzudin; Beres, Maja; Topic, Radomir; Nikic, Vedran; Kavecan, Ivana; Sabic, Semin

2017-01-01

Introduction: Triploidy is a lethal chromosomal numeric abnormality, characterized on extra haploid set of chromosomes. It occurs in 2 to 3% of conceptuses and accounts for approximately 20% of chromosomally abnormal first-trimester miscarriages. As such, triploidy is estimated to occur in 1 of 3,500 pregnancies at 12 weeks’, 1 in 30,000 at 16 weeks’, and 1 in 250,000 at 20 weeks’ gestation. Case report: We present a case of second-trimester triploidy diagnosed prenataly at our center. 28-years-old gravida with a first spontaneous pregnancy had early gestational hypertension. Ultrasound examination in 146/7 weeks’ gestation revealed asymmetric intrauterine growth retardation. We recommended biochemical maternal serum screening during second trimester of pregnancy (AFP, HCG, uE3). Result of biochemical screening was indication for cytogenetic analysis from amniotic fluid cells and we recommended early amniocentesis in 156/7 weeks’ gestation. Result showed abnormal karyotype of the fetus (69,XXX triploidy), and DNA analysis confirmed Type-2 Diginy. Parents decided to terminate this pregnancy, and it was done at 22 weeks’ gestation. Conclusion: We emphasize the importance of non-invasive prenatal exminationes-biochemical serum screening during second trimester of pregnancy, and ultrasound examinations in prenatal screening of syndroma Down and other chromosomal abnormalities. PMID:28790549

Microdissection of Black Widow Spider Silk-producing Glands

PubMed Central

Hsia, Yang; Gnesa, Eric; Zhao, Liang; Franz, Andreas; Vierra, Craig

2011-01-01

Modern spiders spin high-performance silk fibers with a broad range of biological functions, including locomotion, prey capture and protection of developing offspring 1,2. Spiders accomplish these tasks by spinning several distinct fiber types that have diverse mechanical properties. Such specialization of fiber types has occurred through the evolution of different silk-producing glands, which function as small biofactories. These biofactories manufacture and store large quantities of silk proteins for fiber production. Through a complex series of biochemical events, these silk proteins are converted from a liquid into a solid material upon extrusion. Mechanical studies have demonstrated that spider silks are stronger than high-tensile steel 3. Analyses to understand the relationship between the structure and function of spider silk threads have revealed that spider silk consists largely of proteins, or fibroins, that have block repeats within their protein sequences 4. Common molecular signatures that contribute to the incredible tensile strength and extensibility of spider silks are being unraveled through the analyses of translated silk cDNAs. Given the extraordinary material properties of spider silks, research labs across the globe are racing to understand and mimic the spinning process to produce synthetic silk fibers for commercial, military and industrial applications. One of the main challenges to spinning artificial spider silk in the research lab involves a complete understanding of the biochemical processes that occur during extrusion of the fibers from the silk-producing glands. Here we present a method for the isolation of the seven different silk-producing glands from the cobweaving black widow spider, which includes the major and minor ampullate glands [manufactures dragline and scaffolding silk] 5,6, tubuliform [synthesizes egg case silk] 7,8, flagelliform [unknown function in cob-weavers], aggregate [makes glue silk], aciniform [synthesizes prey wrapping and egg case threads] 9 and pyriform [produces attachment disc silk] 10. This approach is based upon anesthetizing the spider with carbon dioxide gas, subsequent separation of the cephalothorax from the abdomen, and microdissection of the abdomen to obtain the silk-producing glands. Following the separation of the different silk-producing glands, these tissues can be used to retrieve different macromolecules for distinct biochemical analyses, including quantitative real-time PCR, northern- and western blotting, mass spectrometry (MS or MS/MS) analyses to identify new silk protein sequences, search for proteins that participate in the silk assembly pathway, or use the intact tissue for cell culture or histological experiments. PMID:21248709

Infrared and Raman Microscopy in Cell Biology

PubMed Central

Matthäus, Christian; Bird, Benjamin; Miljković, Miloš; Chernenko, Tatyana; Romeo, Melissa; Diem, Max

2009-01-01

This chapter presents novel microscopic methods to monitor cell biological processes of live or fixed cells without the use of any dye, stains, or other contrast agent. These methods are based on spectral techniques that detect inherent spectroscopic properties of biochemical constituents of cells, or parts thereof. Two different modalities have been developed for this task. One of them is infrared micro-spectroscopy, in which an average snapshot of a cell’s biochemical composition is collected at a spatial resolution of typically 25 mm. This technique, which is extremely sensitive and can collect such a snapshot in fractions of a second, is particularly suited for studying gross biochemical changes. The other technique, Raman microscopy (also known as Raman micro-spectroscopy), is ideally suited to study variations of cellular composition on the scale of subcellular organelles, since its spatial resolution is as good as that of fluorescence microscopy. Both techniques exhibit the fingerprint sensitivity of vibrational spectroscopy toward biochemical composition, and can be used to follow a variety of cellular processes. PMID:19118679

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.

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 assessment model that facilitates effective decision-making regarding lignocellulosic ethanol production.

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 assessment model that facilitates effective decision-making regarding lignocellulosic ethanol production.

Analysis of the coexisting pathways for NO and N2O formation in Chernozem using the (15)N-tracer SimKIM-Advanced model.

PubMed

Stange, Claus Florian; Spott, Oliver; Russow, Rolf

2013-01-01

The nitrogen (N) cycle consists of a variety of microbial processes. These processes often occur simultaneously in soils, but respond differently to local environmental conditions due to process-specific biochemical restrictions (e.g. oxygen levels). Hence, soil nitrogen cycling (e.g. soil N gas production through nitrification and denitrification) is individually affected through these processes, resulting in the complex and highly dynamic behaviour of total soil N turnover. The development and application of methods that facilitate the quantification of individual contributions of coexisting processes is a fundamental prerequisite for (i) understanding the dynamics of soil N turnover and (ii) implementing these processes in ecosystem models. To explain the unexpected results of the triplet tracer experiment (TTE) of Russow et al. (Role of nitrite and nitric oxide in the processes of nitrification and denitrification in soil: results from (15)N tracer experiments. Soil Biol Biochem. 2009;41:785-795) the existing SimKIM model was extended to the SimKIM-Advanced model through the addition of three separate nitrite subpools associated with ammonia oxidation, oxidation of organic nitrogen (Norg), and denitrification, respectively. For the TTE, individual treatments with (15)N ammonium, (15)N nitrate, and (15)N nitrite were conducted under oxic, hypoxic, and anoxic conditions, respectively, to clarify the role of nitric oxide as a denitrification intermediate during N2O formation. Using a split nitrite pool, this analysis model explains the observed differences in the (15)N enrichments in nitric oxide (NO) and nitrous oxide (N2O) which occurred in dependence on different oxygen concentrations. The change from oxic over hypoxic to anoxic conditions only marginally increased the NO and N2O release rates (1.3-fold). The analysis using the model revealed that, under oxic and hypoxic conditions, Norg-based N2O production was the dominant pathway, contributing to 90 and 50 % of the total soil N2O release. Under anoxic conditions, denitrification was the dominant process for soil N2O release. The relative contribution of Norg to the total soil NO release was small. Ammonia oxidation served as the major pathway of soil NO release under oxic and hypoxic conditions, while denitrification was dominant under anoxic conditions. The model parameters for soil with moderate soil organic matter (SOM) content were not scalable to an additional data set for soil with higher SOM content, indicating a strong influence of SOM content on microbial N turnover. Thus, parameter estimation had to be re-calculated for these conditions, highlighting the necessity of individual soil-dependent parameter estimations.

Statistical inference of the generation probability of T-cell receptors from sequence repertoires.

PubMed

Murugan, Anand; Mora, Thierry; Walczak, Aleksandra M; Callan, Curtis G

2012-10-02

Stochastic rearrangement of germline V-, D-, and J-genes to create variable coding sequence for certain cell surface receptors is at the origin of immune system diversity. This process, known as "VDJ recombination", is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Because any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on nonproductive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our probabilistic model predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.

Biochemical, Cellular, Physiological, and Pathological Consequences of Human Loss of N-Glycolylneuraminic Acid.

PubMed

Okerblom, Jonathan; Varki, Ajit

2017-07-04

About 2-3 million years ago, Alu-mediated deletion of a critical exon in the CMAH gene became fixed in the hominin lineage ancestral to humans, possibly through a stepwise process of selection by pathogen targeting of the CMAH product (the sialic acid Neu5Gc), followed by reproductive isolation through female anti-Neu5Gc antibodies. Loss of CMAH has occurred independently in some other lineages, but is functionally intact in Old World primates, including our closest relatives, the chimpanzee. Although the biophysical and biochemical ramifications of losing tens of millions of Neu5Gc hydroxy groups at most cell surfaces remains poorly understood, we do know that there are multiscale effects functionally relevant to both sides of the host-pathogen interface. Hominin CMAH loss might also contribute to understanding human evolution, at the time when our ancestors were starting to use stone tools, increasing their consumption of meat, and possibly hunting. Comparisons with chimpanzees within ethical and practical limitations have revealed some consequences of human CMAH loss, but more has been learned by using a mouse model with a human-like Cmah inactivation. For example, such mice can develop antibodies against Neu5Gc that could affect inflammatory processes like cancer progression in the face of Neu5Gc metabolic incorporation from red meats, display a hyper-reactive immune system, a human-like tendency for delayed wound healing, late-onset hearing loss, insulin resistance, susceptibility to muscular dystrophy pathologies, and increased sensitivity to multiple human-adapted pathogens involving sialic acids. Further studies in such mice could provide a model for other human-specific processes and pathologies involving sialic acid biology that have yet to be explored. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Side effects of the HMG-CoA reductase inhibitors (statins). Lupus erythematosus induced by Atorvastatin therapy].

PubMed

Hydzik, Piotr; Szpak, Dorota

2011-01-01

The paper describes the case of 56 years old woman admitted to the Toxicology Department because of skin lesions, joint and muscle pain and elevated activity of transaminases and creatine phosfokinase as well in biochemical analysis. The symptoms occurred after 6 days of the Atorvastatin therapy. The clinical picture indicated side effects of the hipolipemic therapy, but the presence of the skin lesions suggested drug induced collagenosis (lupus erythrematosus, dermatomyositis). Immunological studies confirmed association with antinuclear antibodies (ANA) and anti-Mi-2 autoantibodies in the serum. Immunosuppressive therapy was ordered with clinical and biochemical improvement.

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

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.

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.

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…

1H NMR-based metabolic profiling for evaluating poppy seed rancidity and brewing.

PubMed

Jawień, Ewa; Ząbek, Adam; Deja, Stanisław; Łukaszewicz, Marcin; Młynarz, Piotr

2015-12-01

Poppy seeds are widely used in household and commercial confectionery. The aim of this study was to demonstrate the application of metabolic profiling for industrial monitoring of the molecular changes which occur during minced poppy seed rancidity and brewing processes performed on raw seeds. Both forms of poppy seeds were obtained from a confectionery company. Proton nuclear magnetic resonance (1H NMR) was applied as the analytical method of choice together with multivariate statistical data analysis. Metabolic fingerprinting was applied as a bioprocess control tool to monitor rancidity with the trajectory of change and brewing progressions. Low molecular weight compounds were found to be statistically significant biomarkers of these bioprocesses. Changes in concentrations of chemical compounds were explained relative to the biochemical processes and external conditions. The obtained results provide valuable and comprehensive information to gain a better understanding of the biology of rancidity and brewing processes, while demonstrating the potential for applying NMR spectroscopy combined with multivariate data analysis tools for quality control in food industries involved in the processing of oilseeds. This precious and versatile information gives a better understanding of the biology of these processes.

Confocal Raman study of aging process in diabetes mellitus human voluntaries

NASA Astrophysics Data System (ADS)

Pereira, Liliane; Téllez Soto, Claudio Alberto; dos Santos, Laurita; Ali, Syed Mohammed; Fávero, Priscila Pereira; Martin, Airton A.

2015-06-01

Accumulation of AGEs [Advanced Glycation End - products] occurs slowly during the human aging process. However, its formation is accelerated in the presence of diabetes mellitus. In this paper, we perform a noninvasive analysis of glycation effect on human skin by in vivo confocal Raman spectroscopy. This technique uses a laser of 785 nm as excitation source and, by the inelastic scattering of light, it is possible to obtain information about the biochemical composition of the skin. Our aim in this work was to characterize the aging process resulting from the glycation process in a group of 10 Health Elderly Women (HEW) and 10 Diabetic Elderly Women (DEW). The Raman data were collected from the dermis at a depth of 70-130 microns. Through the theory of functional density (DFT) the bands positions of hydroxyproline, proline and AGEs (pentosidine and glucosepane) were calculated by using Gaussian 0.9 software. A molecular interpretation of changes in type I collagen was performed by the changes in the vibrational modes of the proline (P) and hydroxyproline (HP). The data analysis shows that the aging effects caused by glycation of proteins degrades type I collagen differently and leads to accelerated aging process.

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.

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B 2 Biosynthesis

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

Barajas, Jesus F.; Zargar, Amin; Pang, Bo

Naturally occurring lactams, such as the polyketide-derived macrolactams, provide a diverse class of natural products that could enhance existing chemically produced lactams. While β-amino acid loading in the fluvirucin B 2 polyketide pathway has been proposed by a previously identified putative biosynthetic gene cluster, biochemical characterization of the complete loading enzymes has not been described. In this paper, we elucidate the complete biosynthetic pathway of the β-amino acid loading pathway in fluvirucin B 2 biosynthesis. We demonstrate the promiscuity of the loading pathway to utilize a range of amino acids and further illustrate the ability to introduce non-native acyl transferasesmore » to selectively transfer β-amino acids onto a PKS loading platform. The results presented here provide a detailed biochemical description of β-amino acid selection and will further aid in future efforts to develop engineered lactam-producing PKS platforms.« less

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.

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B 2 Biosynthesis

DOE PAGES

Barajas, Jesus F.; Zargar, Amin; Pang, Bo; ...

2018-03-30

Naturally occurring lactams, such as the polyketide-derived macrolactams, provide a diverse class of natural products that could enhance existing chemically produced lactams. While β-amino acid loading in the fluvirucin B 2 polyketide pathway has been proposed by a previously identified putative biosynthetic gene cluster, biochemical characterization of the complete loading enzymes has not been described. In this paper, we elucidate the complete biosynthetic pathway of the β-amino acid loading pathway in fluvirucin B 2 biosynthesis. We demonstrate the promiscuity of the loading pathway to utilize a range of amino acids and further illustrate the ability to introduce non-native acyl transferasesmore » to selectively transfer β-amino acids onto a PKS loading platform. The results presented here provide a detailed biochemical description of β-amino acid selection and will further aid in future efforts to develop engineered lactam-producing PKS platforms.« less

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.

Analysis of Lipids and Lipid Rafts in Borrelia.

PubMed

Toledo, Alvaro; Huang, Zhen; Benach, Jorge L; London, Erwin

2018-01-01

Lipid rafts are membrane microdomains that are involved in cellular processes such as protein trafficking and signaling processes, and which play a fundamental role in membrane fluidity and budding. The lipid composition of the membrane and the biochemical characteristics of the lipids found within rafts define the ability of cells to form microdomains and compartmentalize the membrane. In this chapter, we describe the biophysical, biochemical, and molecular approaches used to define and characterize lipid rafts in the Lyme disease agent, Borrelia burgdorferi.

Visualization of Proton and Electron Transfer Processes of a Biochemical Reaction by μSR

NASA Astrophysics Data System (ADS)

Kiyotani, Tamiko; Kobayashi, Masayoshi; Tanaka, Ichiro; Niimura, Nobuo

For the last several years, we have discussed and conducted experiments toward realization of visualization of electron and proton transfer process in an enzyme reaction using muon. As the first step for exploring the useful application of the μSR for the biological system, which is "μSR in Biology". A first μSR experiment on biochemical reaction was conducted using the complex of a digestive enzyme, a kind of serine-protease and the inhibitor at J-PARC and PSI.

Molecular Mechanisms of Neuroplasticity: An Expanding Universe.

PubMed

Gulyaeva, N V

2017-03-01

Biochemical processes in synapses and other neuronal compartments underlie neuroplasticity (functional and structural alterations in the brain enabling adaptation to the environment, learning, memory, as well as rehabilitation after brain injury). This basic molecular level of brain plasticity covers numerous specific proteins (enzymes, receptors, structural proteins, etc.) participating in many coordinated and interacting signal and metabolic processes, their modulation forming a molecular basis for brain plasticity. The articles in this issue are focused on different "hot points" in the research area of biochemical mechanisms supporting neuroplasticity.

Are calcifying matrix vesicles in atherosclerotic lesions of cellular origin?

PubMed

Bobryshev, Yuri V; Killingsworth, Murray C; Huynh, Thuan G; Lord, Reginald S A; Grabs, Anthony J; Valenzuela, Stella M

2007-03-01

Over recent years, the role of matrix vesicles in the initial stages of arterial calcification has been recognized. Matrix calcifying vesicles have been isolated from atherosclerotic arteries and the biochemical composition of calcified vesicles has been studied. No studies have yet been carried out to examine the fine structure of matrix vesicles in order to visualize the features of the consequent stages of their calcification in arteries. In the present work, a high resolution ultrastructural analysis has been employed and the study revealed that matrix vesicles in human atherosclerotic lesions are heterogeneous with two main types which we classified. Type I calcified vesicles were presented by vesicles surrounded by two electron-dense layers and these vesicles were found to be resistant to the calcification process in atherosclerotic lesions in situ. Type II matrix vesicles were presented by vesicles surrounded by several electron-dense layers and these vesicles were found to represent calcifying vesicles in atherosclerotic lesions. To test the hypothesis that calcification of matrix vesicles surrounded by multilayer sheets may occur simply as a physicochemical process, independently from the cell regulation, we produced multilamellar liposomes and induced their calcification in vitro in a manner similar to that occurring in matrix vesicles in atherosclerotic lesions in situ.

Separation of active laccases from Pleurotus sapidus culture supernatant using aqueous two-phase systems in centrifugal partition chromatography.

PubMed

Schwienheer, C; Prinz, A; Zeiner, T; Merz, J

2015-10-01

For the production of bio active compounds, e.g., active enzymes or antibodies, a conserved purification process with a minimum loss of active compounds is necessary. In centrifugal partition chromatography (CPC), the separation effect is based on the different distribution of the components to be separated between two immiscible liquid phases. Thereby, one liquid phase is kept stationary in chambers by a centrifugal field and the mobile phase is pumped through via connecting ducts. Aqueous two phase systems (ATPS) are known to provide benign conditions for biochemical products and seem to be promising when used in CPC for purification tasks. However, it is not known if active biochemical compounds can "survive" the conditions in a CPC where strong shear forces can occur due to the two-phasic flow under centrifugal forces. Therefore, this aspect has been faced within this study by the separation of active laccases from a fermentation broth of Pleurotus sapidus. After selecting a suitable ATPS and operating conditions, the activity yield was calculated and the preservation of the active enzymes could be observed. Therefore, CPC could be shown as potentially suitable for the purification of bio-active compounds. Copyright © 2015 Elsevier B.V. All rights reserved.

Modeling languages for biochemical network simulation: reaction vs equation based approaches.

PubMed

Wiechert, Wolfgang; Noack, Stephan; Elsheikh, Atya

2010-01-01

Biochemical network modeling and simulation is an essential task in any systems biology project. The systems biology markup language (SBML) was established as a standardized model exchange language for mechanistic models. A specific strength of SBML is that numerous tools for formulating, processing, simulation and analysis of models are freely available. Interestingly, in the field of multidisciplinary simulation, the problem of model exchange between different simulation tools occurred much earlier. Several general modeling languages like Modelica have been developed in the 1990s. Modelica enables an equation based modular specification of arbitrary hierarchical differential algebraic equation models. Moreover, libraries for special application domains can be rapidly developed. This contribution compares the reaction based approach of SBML with the equation based approach of Modelica and explains the specific strengths of both tools. Several biological examples illustrating essential SBML and Modelica concepts are given. The chosen criteria for tool comparison are flexibility for constraint specification, different modeling flavors, hierarchical, modular and multidisciplinary modeling. Additionally, support for spatially distributed systems, event handling and network analysis features is discussed. As a major result it is shown that the choice of the modeling tool has a strong impact on the expressivity of the specified models but also strongly depends on the requirements of the application context.

Distribution of phenotypes among Bacillus thuringiensis strains

USDA-ARS?s Scientific Manuscript database

An extensive collection of Bacillus thuringiensis isolates from around the world were phenotypically profiled using standard biochemical tests. Six phenotypic traits occurred in 20-86% of the isolates and were useful in distinguishing isolates: production of urease (U; 20.5% of isolates), hydrolysis...

Influence of cell integrity on textural properties of raw, high pressure, and thermally processed onions.

PubMed

Gonzalez, M E; Jernstedt, J A; Slaughter, D C; Barrett, D M

2010-09-01

The integrity of onion cells and its impact on tissue texture after high pressure and thermal processing was studied. The contribution of cell membranes and the pectic component of cell walls on the texture properties of onion tissue were analyzed. Neutral red (NR) staining of onion parenchyma cell vacuoles was used for the evaluation of cell membrane integrity and microscopic image analysis was used for its quantification. The content of methanol in tissue as a result of pectin methylesterase activity was used to evaluate the pectin component of the middle lamella and cell walls and the hardening effect on the tissue after processing. High pressure treatments consisted of 5-min holding times at 50, 100, 200, 300, or 600 MPa. Thermal treatments consisted of 30-min water bath exposure to 40, 50, 60, 70, or 90 °C. In the high pressure treatments, loss of membrane integrity commenced at 200 MPa and total loss of membrane integrity occurred at 300 MPa and above. In the thermal treatments, membrane integrity was lost between 50 and 60 °C. The texture of onions was influenced by the state of the membranes and texture profiles were abruptly modified once membrane integrity was lost. Hardening of the tissue corresponded with pressure and temperature PME activation and occurred after membrane integrity loss. The texture of vegetables is an important quality attribute that affects consumer preference. Loss of textural integrity also indicates that other biochemical reactions that affect color, flavor, and nutrient content may occur more rapidly. In this study, we analyzed changes in the texture of onions after preservation with heat and high pressure.

Development of constraint-based system-level models of microbial metabolism.

PubMed

Navid, Ali

2012-01-01

Genome-scale models of metabolism are valuable tools for using genomic information to predict microbial phenotypes. System-level mathematical models of metabolic networks have been developed for a number of microbes and have been used to gain new insights into the biochemical conversions that occur within organisms and permit their survival and proliferation. Utilizing these models, computational biologists can (1) examine network structures, (2) predict metabolic capabilities and resolve unexplained experimental observations, (3) generate and test new hypotheses, (4) assess the nutritional requirements of the organism and approximate its environmental niche, (5) identify missing enzymatic functions in the annotated genome, and (6) engineer desired metabolic capabilities in model organisms. This chapter details the protocol for developing genome-scale models of metabolism in microbes as well as tips for accelerating the model building process.

Effects of hypervitaminosis of vitamin B3 on silkworm biology.

PubMed

Etebari, Kayvan; Matindoost, Leila

2004-12-01

A high-dose of vitamin B(3) in silkworm diet interrupts larval feeding and normal growth. High mortality of larvae occurs during molting and they cannot complete this process normally. Also the larvae exhibit nicotinamide hypervitaminosis symptoms such as immobility, dyspepsia, darkening of the skin, inability to excrete normally, exerting brownish fluid from anus and swelling of rectal muscles. Maximum larval weights in 1, 2 and 3 g/l treatments were 2.9, 1.6 and 1.2 g respectively, while maximum larval weight in the control was 5.6 g. Larval stage compared to control had increased 18, 26 and 31 days respectively. The concentration increase of uric acid in haemolymph demonstrates the hyperuricemia, while other measured biochemical compounds show significant decrease; sodium and potassium did not change significantly.

An active second dihydrofolate reductase enzyme is not a feature of rat and mouse, but they do have activity in their mitochondria.

PubMed

Hughes, Linda; Carton, Robert; Minguzzi, Stefano; McEntee, Gráinne; Deinum, Eva E; O'Connell, Mary J; Parle-McDermott, Anne

2015-07-08

The identification of a second functional dihydrofolate reductase enzyme in humans, DHFRL1, led us to consider whether this is also a feature of rodents. We demonstrate that dihydrofolate reductase activity is also a feature of the mitochondria in both rat and mouse but this is not due to a second enzyme. While our phylogenetic analysis revealed that RNA-mediated DHFR duplication events did occur across the mammal tree, the duplicates in brown rat and mouse are likely to be processed pseudogenes. Humans have evolved the need for two separate enzymes while laboratory rats and mice have just one. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Influence of thermal hydrolysis pretreatment on organic transformation characteristics of high solid anaerobic digestion.

PubMed

Han, Yun; Zhuo, Yang; Peng, Dangcong; Yao, Qian; Li, Huijuan; Qu, Qiliang

2017-11-01

The study evaluated the influence of thermal hydrolysis pretreatment (THP) on anaerobic digestion (AD) ability of high solid sludge. The transformation characteristics of organics during the THP+AD process of dewatering sludge from wastewater treatment plant was investigated using a lab-scale THP reactor and four anaerobic digesters. The reduction efficiency of volatile suspended solids using THP+AD exceeded 49%. The acceleration of biogas production during AD was due to the enhancement of protein hydrolysis and acidogenesis by THP. THP had only minimal influence on the improvement of carbohydrate acidogenesis. The hydrolysis of poly phosphates was likely the main reaction of phosphorus transformation. Biochemical generation of sulfide and ammonia nitrogen occurred during the acidogenesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Optimal Cytoplasmic Transport in Viral Infections

PubMed Central

D'Orsogna, Maria R.; Chou, Tom

2009-01-01

For many viruses, the ability to infect eukaryotic cells depends on their transport through the cytoplasm and across the nuclear membrane of the host cell. During this journey, viral contents are biochemically processed into complexes capable of both nuclear penetration and genomic integration. We develop a stochastic model of viral entry that incorporates all relevant aspects of transport, including convection along microtubules, biochemical conversion, degradation, and nuclear entry. Analysis of the nuclear infection probabilities in terms of the transport velocity, degradation, and biochemical conversion rates shows how certain values of key parameters can maximize the nuclear entry probability of the viral material. The existence of such “optimal” infection scenarios depends on the details of the biochemical conversion process and implies potentially counterintuitive effects in viral infection, suggesting new avenues for antiviral treatment. Such optimal parameter values provide a plausible transport-based explanation of the action of restriction factors and of experimentally observed optimal capsid stability. Finally, we propose a new interpretation of how genetic mutations unrelated to the mechanism of drug action may nonetheless confer novel types of overall drug resistance. PMID:20046829

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.

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

Cell adhesion and the immune system: a case study using earthworms.

PubMed

Cooper, E L; Cossarizza, A; Kauschke, E; Franceschi, C

1999-02-15

In the earthworm's immune system, cell adhesion, which occurs by putative receptors on leukocytes, is essential after recognition of self vs. non-self. Confrontation with foreign antigens is a normal event in the environment, replete with microbial pathogens that pose a threat to survival. To better understand what happens when an effector cell first recognizes a foreign target followed by its adhesion to it, isolated leukocytes, in sufficient quantities to be subjected to various analyses, have been extremely beneficial. In vitro approaches when accompanied by biochemical, immunological, and molecular technologies, have opened up new vistas concerning the immune response of earthworms and other invertebrates. The most recent discovery includes the preliminary identification of cell differentiation (CD) markers that play vital roles in recognitive and adhesive events. Certain leukocyte effectors show characteristics of natural killer (NK) cells that may act differently depending upon their source, whether autogeneic, allogeneic, xenogeneic, or expressed under normal or varying environmental conditions including exposure to xenobiotics. At the level of earthworm evolution, there is apparently a dissociation of phagocytosis from the process of killing by NK-like effectors. There are at least three future challenges. First, it is essential to determine the precise nature of the CD markers with respect to their molecular structure. Second, once their molecular and biochemical characteristics have been defined, the role of these markers in cellular and humoral mechanisms must be clarified in order to define effector cell products and resulting immune responses. Third, there is a need to differentiate between the several lytic factors that have been found in earthworms with respect to molecular structure, and biochemical and functional characterization.

Investigating Biochemical and Developmental Dependencies of Lignification with a Click-Compatible Monolignol Analog in Arabidopsis thaliana Stems

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

Pandey, Jyotsna L.; Kiemle, Sarah N.; Richard, Tom L.

Lignin is a key structural component of plant cell walls that provides rigidity, strength, and resistance against microbial attacks. This hydrophobic polymer also serves a crucial role in water transport. Despite its abundance and essential functions, several aspects of lignin biosynthesis and deposition remain cryptic. Lignin precursors are known to be synthesized in the cytoplasm by complex biosynthetic pathways, after which they are transported to the apoplastic space, where they are polymerized via free radical coupling reactions into polymeric lignin. However, the lignin deposition process and the factors controlling it are unclear. In this study, the biochemical and developmental dependenciesmore » of lignification were investigated using a click-compatible monolignol analog, 3-O-propargylcaffeyl alcohol (3-OPC), which can incorporate into both in vitro polymerized lignin and Arabidopsis thaliana tissues. Fluorescence labeling of 3-OPC using click chemistry followed by confocal fluorescence microscopy enabled the detection and imaging of 3-OPC incorporation patterns. These patterns were consistent with endogenous lignification observed in different developmental stages of Arabidopsis stems. However, the concentration of supplied monolignols influenced where lignification occurred at the subcellular level, with low concentrations being deposited in cell corners and middle lamellae and high concentrations also being deposited in secondary walls. Experimental inhibition of multiple lignification factors confirmed that 3-OPC incorporation proceeds via a free radical coupling mechanism involving peroxidases/laccases and reactive oxygen species (ROS). Finally, the presence of peroxide-producing enzymes determined which cell walls lignified: adding exogenous peroxide and peroxidase caused cells that do not naturally lignify in Arabidopsis stems to lignify. In conclusion, 3-OPC accurately mimics natural lignification patterns in different developmental stages of Arabidopsis stems and allows for the dissection of key biochemical and enzymatic factors controlling lignification.« less

Investigating Biochemical and Developmental Dependencies of Lignification with a Click-Compatible Monolignol Analog in Arabidopsis thaliana Stems

PubMed Central

Pandey, Jyotsna L.; Kiemle, Sarah N.; Richard, Tom L.; Zhu, Yimin; Cosgrove, Daniel J.; Anderson, Charles T.

2016-01-01

Lignin is a key structural component of plant cell walls that provides rigidity, strength, and resistance against microbial attacks. This hydrophobic polymer also serves a crucial role in water transport. Despite its abundance and essential functions, several aspects of lignin biosynthesis and deposition remain cryptic. Lignin precursors are known to be synthesized in the cytoplasm by complex biosynthetic pathways, after which they are transported to the apoplastic space, where they are polymerized via free radical coupling reactions into polymeric lignin. However, the lignin deposition process and the factors controlling it are unclear. In this study, the biochemical and developmental dependencies of lignification were investigated using a click-compatible monolignol analog, 3-O-propargylcaffeyl alcohol (3-OPC), which can incorporate into both in vitro polymerized lignin and Arabidopsis thaliana tissues. Fluorescence labeling of 3-OPC using click chemistry followed by confocal fluorescence microscopy enabled the detection and imaging of 3-OPC incorporation patterns. These patterns were consistent with endogenous lignification observed in different developmental stages of Arabidopsis stems. However, the concentration of supplied monolignols influenced where lignification occurred at the subcellular level, with low concentrations being deposited in cell corners and middle lamellae and high concentrations also being deposited in secondary walls. Experimental inhibition of multiple lignification factors confirmed that 3-OPC incorporation proceeds via a free radical coupling mechanism involving peroxidases/laccases and reactive oxygen species (ROS). Finally, the presence of peroxide-producing enzymes determined which cell walls lignified: adding exogenous peroxide and peroxidase caused cells that do not naturally lignify in Arabidopsis stems to lignify. In summary, 3-OPC accurately mimics natural lignification patterns in different developmental stages of Arabidopsis stems and allows for the dissection of key biochemical and enzymatic factors controlling lignification. PMID:27630649

Investigating Biochemical and Developmental Dependencies of Lignification with a Click-Compatible Monolignol Analog in Arabidopsis thaliana Stems

DOE PAGES

Pandey, Jyotsna L.; Kiemle, Sarah N.; Richard, Tom L.; ...

2016-08-31

Lignin is a key structural component of plant cell walls that provides rigidity, strength, and resistance against microbial attacks. This hydrophobic polymer also serves a crucial role in water transport. Despite its abundance and essential functions, several aspects of lignin biosynthesis and deposition remain cryptic. Lignin precursors are known to be synthesized in the cytoplasm by complex biosynthetic pathways, after which they are transported to the apoplastic space, where they are polymerized via free radical coupling reactions into polymeric lignin. However, the lignin deposition process and the factors controlling it are unclear. In this study, the biochemical and developmental dependenciesmore » of lignification were investigated using a click-compatible monolignol analog, 3-O-propargylcaffeyl alcohol (3-OPC), which can incorporate into both in vitro polymerized lignin and Arabidopsis thaliana tissues. Fluorescence labeling of 3-OPC using click chemistry followed by confocal fluorescence microscopy enabled the detection and imaging of 3-OPC incorporation patterns. These patterns were consistent with endogenous lignification observed in different developmental stages of Arabidopsis stems. However, the concentration of supplied monolignols influenced where lignification occurred at the subcellular level, with low concentrations being deposited in cell corners and middle lamellae and high concentrations also being deposited in secondary walls. Experimental inhibition of multiple lignification factors confirmed that 3-OPC incorporation proceeds via a free radical coupling mechanism involving peroxidases/laccases and reactive oxygen species (ROS). Finally, the presence of peroxide-producing enzymes determined which cell walls lignified: adding exogenous peroxide and peroxidase caused cells that do not naturally lignify in Arabidopsis stems to lignify. In conclusion, 3-OPC accurately mimics natural lignification patterns in different developmental stages of Arabidopsis stems and allows for the dissection of key biochemical and enzymatic factors controlling lignification.« less

A Computational Framework for Analyzing Stochasticity in Gene Expression

PubMed Central

Sherman, Marc S.; Cohen, Barak A.

2014-01-01

Stochastic fluctuations in gene expression give rise to distributions of protein levels across cell populations. Despite a mounting number of theoretical models explaining stochasticity in protein expression, we lack a robust, efficient, assumption-free approach for inferring the molecular mechanisms that underlie the shape of protein distributions. Here we propose a method for inferring sets of biochemical rate constants that govern chromatin modification, transcription, translation, and RNA and protein degradation from stochasticity in protein expression. We asked whether the rates of these underlying processes can be estimated accurately from protein expression distributions, in the absence of any limiting assumptions. To do this, we (1) derived analytical solutions for the first four moments of the protein distribution, (2) found that these four moments completely capture the shape of protein distributions, and (3) developed an efficient algorithm for inferring gene expression rate constants from the moments of protein distributions. Using this algorithm we find that most protein distributions are consistent with a large number of different biochemical rate constant sets. Despite this degeneracy, the solution space of rate constants almost always informs on underlying mechanism. For example, we distinguish between regimes where transcriptional bursting occurs from regimes reflecting constitutive transcript production. Our method agrees with the current standard approach, and in the restrictive regime where the standard method operates, also identifies rate constants not previously obtainable. Even without making any assumptions we obtain estimates of individual biochemical rate constants, or meaningful ratios of rate constants, in 91% of tested cases. In some cases our method identified all of the underlying rate constants. The framework developed here will be a powerful tool for deducing the contributions of particular molecular mechanisms to specific patterns of gene expression. PMID:24811315

Regulatory Role of N6 -methyladenosine (m6 A) Methylation in RNA Processing and Human Diseases.

PubMed

Wei, Wenqiang; Ji, Xinying; Guo, Xiangqian; Ji, Shaoping

2017-09-01

N 6 -methyladenosine (m 6 A) modification is an abundant and conservative RNA modification in bacterial and eukaryotic cells. m 6 A modification mainly occurs in the 3' untranslated regions (UTRs) and near the stop codons of mRNA. Diverse strategies have been developed for identifying m 6 A sites in single nucleotide resolution. Dynamic regulation of m 6 A is found in metabolism, embryogenesis, and developmental processes, indicating a possible epigenetic regulation role along RNA processing and exerting biological functions. It has been known that m 6 A editing involves in nuclear RNA export, mRNA degradation, protein translation, and RNA splicing. Deficiency of m 6 A modification will lead to kinds of diseases, such as obesity, cancer, type 2 diabetes mellitus (T2DM), infertility, and developmental arrest. Some specific inhibitors against methyltransferase and demethylase have been developed to selectively regulate m 6 A modification, which may be advantageous for treatment of m 6 A related diseases. J. Cell. Biochem. 118: 2534-2543, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Choice of the laser wavelength for a herpetic keratitis treatment

NASA Astrophysics Data System (ADS)

Razhev, Alexander M.; Bagayev, Sergei N.; Chernikh, Valery V.; Kargapoltsev, Evgeny S.; Trunov, Alexander; Zhupikov, Andrey A.

2002-06-01

For the first time the effect of the UV laser radiation to human eye cornea with herpetic keratitis was experimentally investigated. In experiments the UV radiation of ArF (193 nm), KrCl (223 nm), KrF (248 nm) excimer lasers were used. Optimal laser radiation parameters for the treatment of the herpetic keratitis were determined. The immuno-biochemical investigations were carried out and the results of clinical trials are presented. The maximum ablation rate was obtained for the 248 nm radiation wavelength. The process of healing was successful but in some cases the haze on the surface of the cornea was observed. When used the 193 nm radiation wavelength the corneal surface was clear without any hazes but the epithelization process was slower than for 248 nm wavelength and in some cases the relapse was occurred. The best results for herpetic keratitis treatment have been achieved by utilizing the 223 nm radiation wavelength of the KrCl excimer laser. The use of the 223 nm radiation wavelength allows treating the herpetic keratitis with low traumatic process of ablation and provides high quality of corneal surface.

GROWTH AND DIFFERENTIATION OF MITOCHONDRIA IN THE REGENERATING RAT ADRENAL CORTEX

PubMed Central

Yago, Nagasumi; Seki, Masatoshi; Sekiyama, Shigetaka; Kobayashi, Shigeru; Kurokawa, Hiromi; Iwai, Yuko; Sato, Fumiaki; Shiragai, Akihiro

1972-01-01

Diameters of the circular profiles of spherical mitochondria in parenchymal cells of the zona fasciculata in rat adrenal cortex were measured for intact controls and for the regenerating adrenal cortex on electron micrographs recorded at random. The diameter data were then processed by Bach's method which deals with the sphere size distribution. The structural parameters of the mitochondria were computed with the aid of an electronic computer. The total number of mitochondria in all the parenchymal cells of the zona fasciculata were calculated. The surface area of the inner mitochondrial membrane was then determined stereologically. Biochemical parameters were obtained for the protein, the phospholipid, and the cytochrome P-450 content, per averaged mitochondrion. The number of cytochrome P-450 molecules contained in the inner membrane was determined in terms of the unit surface area and of the unit amount of phospholipid. These correlated biochemical and stereological parameters have led to the following conclusions. (a) The genesis of the mitochondria after the adrenal enucleation is almost completed within 10 days. (b) During the period of mitochondrial proliferation, the mitochondria are small in size and also immature both in the structure and in the function of their inner membrane, (c) These small and immature mitochondria grow through an increase of the phospholipid and protein, and this increase is accompanied by expansion of the area of the membrane surface, (d) An enrichment of the inner membrane with cytochrome P-450 molecules occurs, thus indicating the differentiation of adrenocortical mitochondria. The process of membrane differentiation is not tightly coupled with that of membrane growth. PMID:5009515

Organic Chemicals from Bioprocesses in China

NASA Astrophysics Data System (ADS)

Huang, Jin; Huang, Lei; Lin, Jianping; Xu, Zhinan; Cen, Peilin

Over the last 20 years, China has successfully established a modern biotechnology industry from almost nothing. Presently, China is a major producer of a vast array of products involving bioprocesses, for some China is even the world's top producer. The ever-increasing list of products includes organic acids, amino acids, antibiotics, solvents, chiral chemicals, biopesticides, and biopolymers. Herein, the research and development of bioprocesses in China will be reviewed briefly. We will concentrate on three categories of products: small molecules produced via fermentation, biopolymers produced via fermentation and small chemicals produced by enzyme-catalyzed reactions. In comparison with the traditional chemical process, in which, nonrenewable mineral resources are generally used, products in the first and second categories noted above can use renewable bioresources as raw materials. The bioprocesses are generally energy saving and environmentally benign. For products developed via the third category, although the raw materials still need to be obtained from mineral resources, the biocatalysts are more effective with higher selectivity and productivity, and the bioprocesses occur under ambient temperature and pressure, therefore, these are "green processes." Most of the products such as citric acid, xanthan and acrylamide etc., discussed in this paper have been in large-scale commercial production in China. Also introduced herein are three scientists, Prof. Shen Yinchu, Prof. Ouyang Pingkai and Prof. Chen Guoqiang, and six enterprises, Anhui Fengyuan Biochemical Co. Ltd., Shandong Hiland Biotechnology Co. Ltd., Shandong Fufeng Fermentation Co. Ltd., Shandong Bausch & Lomb-Freda Pharmaceutical Co. Ltd., Zhejiang Hangzhou Xinfu Pharmaceutical Co. Ltd., and Changzhou Changmao Biochemical Engineering Co. Ltd.; they have all contributed a great deal to research and development in the commercialization of bioprocesses.

Biochemical characterization of the THIN-B metallo-beta-lactamase of Janthinobacterium lividum.

PubMed

Docquier, Jean-Denis; Lopizzo, Teresa; Liberatori, Sabrina; Prenna, Manuela; Thaller, Maria Cristina; Frère, Jean-Marie; Rossolini, Gian Maria

2004-12-01

The THIN-B metallo-beta-lactamase, a subclass B3 enzyme produced by the environmental species Janthinobacterium lividum, was overproduced in Escherichia coli by means of a T7-based expression system. The enzyme was purified (>95%) by two ion-exchange chromatography steps and subjected to biochemical analysis. The native THIN-B enzyme is a monomeric protein of 31 kDa. It exhibits the highest catalytic efficiencies with carbapenem substrates and cephalosporins, except for cephaloridine, which acts as a poor inactivator. Individual rate constants for inactivation by chelators were measured, suggesting that inactivation occurred by a mechanism involving formation of a ternary complex.

Biochemical Characterization of the THIN-B Metallo-β-Lactamase of Janthinobacterium lividum

PubMed Central

Docquier, Jean-Denis; Lopizzo, Teresa; Liberatori, Sabrina; Prenna, Manuela; Thaller, Maria Cristina; Frère, Jean-Marie; Rossolini, Gian Maria

2004-01-01

The THIN-B metallo-β-lactamase, a subclass B3 enzyme produced by the environmental species Janthinobacterium lividum, was overproduced in Escherichia coli by means of a T7-based expression system. The enzyme was purified (>95%) by two ion-exchange chromatography steps and subjected to biochemical analysis. The native THIN-B enzyme is a monomeric protein of 31 kDa. It exhibits the highest catalytic efficiencies with carbapenem substrates and cephalosporins, except for cephaloridine, which acts as a poor inactivator. Individual rate constants for inactivation by chelators were measured, suggesting that inactivation occurred by a mechanism involving formation of a ternary complex. PMID:15561856

The epigenetic landscape of mammary gland development and functional differentiation

USDA-ARS?s Scientific Manuscript database

Most of the development and functional differentiation in the mammary gland occur after birth. Epigenetics is defined as the stable alterations in gene expression potential that arise during development and proliferation. Epigenetic changes are mediated at the biochemical level by the chromatin conf...

How Living Things Obtain Energy: A Simpler Explanation.

ERIC Educational Resources Information Center

Igelsrud, Donald E.

1989-01-01

Examines five basic reactions which describe the biochemical pathways for living things obtaining energy. Shows the reactions that occur in respiration after glycolysis, the dehydrogenation reaction, decarboxylation, and two kinds of make-ready reactions which prepare molecules for further dehydrogenation and decarboxylation. Diagrams are…

Ganglioside biochemistry.

PubMed

Kolter, Thomas

2012-01-01

Gangliosides are sialic acid-containing glycosphingolipids. They occur especially on the cellular surfaces of neuronal cells, where they form a complex pattern, but are also found in many other cell types. The paper provides a general overview on their structures, occurrence, and metabolism. Key functional, biochemical, and pathobiochemical aspects are summarized.

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

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.

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.

Focal cryotherapy of localized prostate cancer: a systematic review of the literature.

PubMed

Shah, Taimur Tariq; Ahmed, Hashim; Kanthabalan, Abi; Lau, Benjamin; Ghei, Maneesh; Maraj, Barry; Arya, Manit

2014-11-01

Radical/whole gland treatment for prostate cancer has significant side-effects. Therefore focal treatments such as cryotherapy have been used to treat localized lesions whilst aiming to provide adequate cancer control with minimal side-effects. We performed a systematic review of Pubmed/Medline and Cochrane databases' to yield 9 papers for primary focal prostate cryotherapy and 2 papers for focal salvage treatment (radio-recurrent). The results of 1582 primary patients showed biochemical disease-free survival between 71-93% at 9-70 months follow-up. Incontinence rates were 0-3.6% and ED 0-42%. Recto-urethral fistula occurred in only 2 patients. Salvage focal cryotherapy had biochemical disease-free survival of 50-68% at 3 years. ED occurred in 60-71%. Focal cryotherapy appears to be an effective treatment for primary localized prostate cancer and compares favorably to radical/whole gland treatments in medium-term oncological outcomes and side-effects. Although more studies are needed it is also effective for radio-recurrent cancer with a low complications rates.

Sustained remission of Cushing's disease with mitotane and pituitary irradiation

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

Schteingart, D.E.; Tsao, H.S.; Taylor, C.I.

1980-05-01

Low doses of mitotane were given orally to 36 patients with Cushing's disease, concurrently with or after pituitary cobalt irradiation. Clinical and biochemical remission occurred in 29. The response to treatment occurred early in 17 patients and late in 12. The different pattern of response to mitotane was not related to the dose given or to its serum level. Early biochemical indicators of adrenal suppression with mitotane were a sharp decrease in adrenal response to the infusion of ACTH and in plasma levels of dehydroepiandrosterone sulfate. Although mitotane was given together with pituitary irradiation, initial remission was due mainly tomore » the adrenal effect of mitotane. Plasma ACTH levels were still elevated when cortisol had returned to normal. In seventeen of the 29 patients who responded to treatment drug therapy has been discontinued, and they remain in remission of Cushing's syndrome. Side-effects have been dose dependent, with anorexia, nausea, decreased memory, and gynecomastia in men being the commonest.« less

Porous article with surface functionality and method for preparing same

NASA Technical Reports Server (NTRS)

Koontz, Steven L. (Inventor)

2000-01-01

Porous organic articles having no surface functionality may be treated by remote plasma discharge to thereby introduce functionality to the surface of the article. The functionality is introduced throughout the article's surface, including the exterior surface and the surfaces of the pores. Little or no degradation of the porous organic article occurs as a result of the functionalization. Amino, hydroxyl, carbonyl and carboxyl groups may be introduced to the article. In this way, an essentially inert hydrophobic porous article, made from, for example, polyethylene, can have its surface modified so that the surface becomes hydrophilic. The remote plasma discharge process causes essentially no change in the bulk properties of the organic article. The remote plasma discharge process is preferably conducted so that no photons, and particularly no ultraviolet radiation, is transmitted from the plasma glow to the porous article. The surface-functionalized article may be used, for example, as a solid support in organic synthesis or in the chromatographic purification of organic or biochemicals.

Micro-organisms in latex and natural rubber coagula of Hevea brasiliensis and their impact on rubber composition, structure and properties.

PubMed

Salomez, M; Subileau, M; Intapun, J; Bonfils, F; Sainte-Beuve, J; Vaysse, L; Dubreucq, E

2014-10-01

Natural rubber, produced by coagulation of the latex from the tree Hevea brasiliensis, is an important biopolymer used in many applications for its outstanding properties. Besides polyisoprene, latex is rich in many nonisoprene components such as carbohydrates, proteins and lipids and thereby constitutes a favourable medium for the development of micro-organisms. The fresh rubber coagula obtained by latex coagulation are not immediately processed, allowing the development of various microbial communities. The time period between tree tapping and coagula processing is called maturation, during which an evolution of the properties of the corresponding dry natural rubber occurs. This evolution is partly related to the activity of micro-organisms and to the modification of the biochemical composition. This review synthesizes the current knowledge on microbial populations in latex and natural rubber coagula of H. brasiliensis and the changes they induce on the biochemistry and technical properties of natural rubber during maturation. © 2014 The Society for Applied Microbiology.

REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

PubMed

Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

2011-03-01

RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/. Copyright © 2010 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Morphological, Physiological and Biochemical Impact of Ink Industry Effluent on Germination of Maize (Zea mays), Barley (Hordeum vulgare) and Sorghum (Sorghum bicolor).

PubMed

Zayneb, Chaâbene; Lamia, Khanous; Olfa, Ellouze; Naïma, Jebahi; Grubb, C Douglas; Bassem, Khemakhem; Hafedh, Mejdoub; Amine, Elleuch

2015-11-01

The present study focuses on effects of untreated and treated ink industry wastewater on germination of maize, barley and sorghum. Wastewater had a high chemical oxygen demand (COD) and metal content compared to treated effluent. Germination decreased with increasing COD concentration. Speed of germination also followed the same trend, except for maize seeds exposed to untreated effluent (E), which germinated slightly faster than controls. These alterations of seedling development were mirrored by changes in soluble protein content. E exerted a positive effect on soluble protein content and maximum levels occurred after 10 days with treated effluent using coagulation/flocculation (TEc/f) process and treated effluent using combined process (coagulation/flocculation/biosorption) (TEc/f/b). Likewise, activity of α-amylase was influenced by effluent composition. Its expression depended on the species, exposure time and applied treatment. Nevertheless, current results indicated TEc/f/b had no observable toxic effects on germination and could be a beneficial alternative resource to irrigation water.

Bidirectional synaptic structural plasticity after chronic cocaine administration occurs through Rap1 small GTPase signaling

PubMed Central

Cahill, Michael E.; Bagot, Rosemary C.; Gancarz, Amy M.; Walker, Deena M.; Sun, HaoSheng; Wang, Zi-Jun; Heller, Elizabeth A.; Feng, Jian; Kennedy, Pamela J.; Koo, Ja Wook; Cates, Hannah M.; Neve, Rachael L.; Shen, Li; Dietz, David M.

2016-01-01

Summary Dendritic spines are the sites of most excitatory synapses in the CNS, and opposing alterations in the synaptic structure of medium spiny neurons (MSNs) of the nucleus accumbens, a primary brain reward region, are seen at early vs. late time points after cocaine administration. Here we investigate the time-dependent molecular and biochemical processes that regulate this bidirectional synaptic structural plasticity of NAc MSNs and associated changes in cocaine reward in response to chronic cocaine exposure. Our findings reveal key roles for the bidirectional synaptic expression of the Rap1b small GTPase and an associated local-synaptic protein translation network in this process. The transcriptional mechanisms and pathway-specific inputs to NAc that regulate Rap1b expression are also characterized. Collectively, these findings provide a precise mechanism by which nuclear to synaptic interactions induce “metaplasticity” in NAc MSNs, and we reveal the specific effects of this plasticity on reward behavior in a brain circuit-specific manner. PMID:26844834

Porous article with surface functionality and method for preparing same

NASA Technical Reports Server (NTRS)

Koontz, Steven L. (Inventor)

2004-01-01

Porous organic articles having no surface functionality may be treated by remote plasma discharge to thereby introduce functionality to the surface of the article. The functionality is introduced throughout the article's surface, including the exterior surface and the surfaces of the pores. Little or no degradation of the porous organic article occurs as a result of the functionalization. Amino, hydroxyl, carbonyl and carboxyl groups may be introduced to the article. In this way, an essentially inert hydrophobic porous article, made from, for example, polyethylene, can have its surface modified so that the surface becomes hydrophilic. The remote plasma discharge process causes essentially no change in the bulk properties of the organic article. The remote plasma discharge process is preferably conducted so that no photons, and particularly no ultraviolet radiation, is transmitted from the plasma glow to the porous article. The surface-functionalized article may be used, for example, as a solid support in organic synthesis or in the chromatographic purification of organic or biochemicals.

Nematode sperm maturation triggered by protease involves sperm-secreted serine protease inhibitor (Serpin)

PubMed Central

Zhao, Yanmei; Sun, Wei; Zhang, Pan; Chi, Hao; Zhang, Mei-Jun; Song, Chun-Qing; Ma, Xuan; Shang, Yunlong; Wang, Bin; Hu, Youqiao; Hao, Zhiqi; Hühmer, Andreas F.; Meng, Fanxia; L'Hernault, Steven W.; He, Si-Min; Dong, Meng-Qiu; Miao, Long

2012-01-01

Spermiogenesis is a series of poorly understood morphological, physiological and biochemical processes that occur during the transition of immotile spermatids into motile, fertilization-competent spermatozoa. Here, we identified a Serpin (serine protease inhibitor) family protein (As_SRP-1) that is secreted from spermatids during nematode Ascaris suum spermiogenesis (also called sperm activation) and we showed that As_SRP-1 has two major functions. First, As_SRP-1 functions in cis to support major sperm protein (MSP)-based cytoskeletal assembly in the spermatid that releases it, thereby facilitating sperm motility acquisition. Second, As_SRP-1 released from an activated sperm inhibits, in trans, the activation of surrounding spermatids by inhibiting vas deferens-derived As_TRY-5, a trypsin-like serine protease necessary for sperm activation. Because vesicular exocytosis is necessary to create fertilization-competent sperm in many animal species, components released during this process might be more important modulators of the physiology and behavior of surrounding sperm than was previously appreciated. PMID:22307610

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

Chen, Hang, E-mail: hangchen@mit.edu; Thill, Peter; Cao, Jianshu

In biochemical systems, intrinsic noise may drive the system switch from one stable state to another. We investigate how kinetic switching between stable states in a bistable network is influenced by dynamic disorder, i.e., fluctuations in the rate coefficients. Using the geometric minimum action method, we first investigate the optimal transition paths and the corresponding minimum actions based on a genetic toggle switch model in which reaction coefficients draw from a discrete probability distribution. For the continuous probability distribution of the rate coefficient, we then consider two models of dynamic disorder in which reaction coefficients undergo different stochastic processes withmore » the same stationary distribution. In one, the kinetic parameters follow a discrete Markov process and in the other they follow continuous Langevin dynamics. We find that regulation of the parameters modulating the dynamic disorder, as has been demonstrated to occur through allosteric control in bistable networks in the immune system, can be crucial in shaping the statistics of optimal transition paths, transition probabilities, and the stationary probability distribution of the network.« less

Physical and chemical properties of Nam Prig Noom, a Thai green-chili paste, following ultra-high pressure and thermal processes

NASA Astrophysics Data System (ADS)

Apichartsrangkoon, Arunee; Srisajjalertwaja, Siriwan; Chaikham, Pittaya; Hirun, Sathira

2013-03-01

A study of processing green-chili pastes (Nam Prig Noom) by pressurization (100-600 MPa/30-50°C/20 min), pasteurization (90°C/3-5 min) or sterilization (121°C/4 min), subsequently, their physical, biochemical and microbiological qualities as well as the sensory acceptance were assessed. It was found that pressure at low levels (100-300 MPa) could improve activities of enzyme peroxidase (POD), polyphenoloxidase (PPO) and lypoxygenase (LOX) in the chili paste by more than 100%, while pressures above 500 or 300 MPa combined with heat would significantly inactivate these enzyme activities. Both color parameters and enzyme activities illustrated that though some enzymatic browning occurred with the pressurized products indicated by b* (yellowish) parameter, the magnitude of these browning was still milder than those thermally treated products indicated by-a* (greenness) and L (lightness) parameters, presumably as a consequence of the Maillard reaction. Moreover, the sensory scores were found in accordance with color parameters, firmness and capsaicin contents.

Single-molecule visualization of a formin-capping protein ‘decision complex' at the actin filament barbed end

PubMed Central

Bombardier, Jeffrey P.; Eskin, Julian A.; Jaiswal, Richa; Corrêa, Ivan R.; Xu, Ming-Qun; Goode, Bruce L.; Gelles, Jeff

2015-01-01

Precise control of actin filament length is essential to many cellular processes. Formins processively elongate filaments, whereas capping protein (CP) binds to barbed ends and arrests polymerization. While genetic and biochemical evidence has indicated that these two proteins function antagonistically, the mechanism underlying the antagonism has remained unresolved. Here we use multi-wavelength single-molecule fluorescence microscopy to observe the fully reversible formation of a long-lived ‘decision complex' in which a CP dimer and a dimer of the formin mDia1 simultaneously bind the barbed end. Further, mDia1 displaced from the barbed end by CP can randomly slide along the filament and later return to the barbed end to re-form the complex. Quantitative kinetic analysis reveals that the CP-mDia1 antagonism that we observe in vitro occurs through the decision complex. Our observations suggest new molecular mechanisms for the control of actin filament length and for the capture of filament barbed ends in cells. PMID:26566078

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

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

Trypanosoma vivax Adhesion to Red Blood Cells in Experimentally Infected Sheep

PubMed Central

Boada-Sucre, Alpidio A.; Rossi Spadafora, Marcello Salvatore; Tavares-Marques, Lucinda M.; Finol, Héctor J.; Reyna-Bello, Armando

2016-01-01

Trypanosomosis, a globally occurring parasitic disease, poses as a major obstacle to livestock production in tropical and subtropical regions resulting in tangible economic losses. In Latin America including Venezuela, trypanosomosis of ruminants is mainly caused by Trypanosoma vivax. Biologically active substances produced from trypanosomes, as well as host-trypanosome cellular interactions, contribute to the pathogenesis of anemia in an infection. The aim of this study was to examine with a scanning electron microscope the cellular interactions and alterations in ovine red blood cells (RBC) experimentally infected with T. vivax. Ovine infection resulted in changes of RBC shape as well as the formation of surface holes or vesicles. A frequent observation was the adhesion to the ovine RBC by the trypanosome's free flagellum, cell body, or attached flagellum in a process mediated by the filopodia emission from the trypanosome surface. The observed RBC alterations are caused by mechanical and biochemical damage from host-parasite interactions occurring in the bloodstream. The altered erythrocytes are prone to mononuclear phagocytic removal contributing to the hematocrit decrease during infection. PMID:27293960

Gram-negative sepsis: a dilemma of modern medicine.

PubMed Central

Bone, R C

1993-01-01

Gram-negative sepsis is an increasingly common problem, with up to 300,000 cases occurring each year in the United States alone. Despite the ongoing development of new antibiotics, mortality from gram-negative sepsis remains unacceptably high. To stimulate earlier therapeutic intervention by physicians, a new set of broad definitions has been proposed to define the systemic inflammatory response characteristic of sepsis. In this review, the signs and symptoms of this progressive, injurious process are reviewed and its management is discussed, as are the mechanisms by which bacterial endotoxin triggers the biochemical events that lead to such serious complications as shock, adult respiratory distress syndrome, and disseminated intravascular coagulation. These events often occur even when appropriate antimicrobial therapy has been instituted. An increased understanding of the structure of endotoxin and its role in the development of sepsis, together with advances in hybridoma technology, has led to the development of monoclonal antibodies that bind to endotoxin and significantly attenuate its adverse effects. These agents promise to substantially reduce the morbidity and mortality associated with gram-negative sepsis. PMID:8457980

Effects of coarse-graining on fluctuations in gene expression

NASA Astrophysics Data System (ADS)

Pedraza, Juan; Paulsson, Johan

2008-03-01

Many cellular components are present in such low numbers per cell that random births and deaths of individual molecules can cause significant `noise' in concentrations. But biochemical events do not necessarily occur in steps of individual molecules. Some processes are greatly randomized when synthesis or degradation occurs in large bursts of many molecules in a short time interval. Conversely, each birth or death of a macromolecule could involve several small steps, creating a memory between individual events. Here we present generalized theory for stochastic gene expression, formulating the variance in protein abundance in terms of the randomness of the individual events, and discuss the effective coarse-graining of the molecular hardware. We show that common molecular mechanisms produce gestation and senescence periods that can reduce noise without changing average abundances, lifetimes, or any concentration-dependent control loops. We also show that single-cell experimental methods that are now commonplace in cell biology do not discriminate between qualitatively different stochastic principles, but that this in turn makes them better suited for identifying which components introduce fluctuations.

The nucleolus directly regulates p53 export and degradation.

PubMed

Boyd, Mark T; Vlatkovic, Nikolina; Rubbi, Carlos P

2011-09-05

The correlation between stress-induced nucleolar disruption and abrogation of p53 degradation is evident after a wide variety of cellular stresses. This link may be caused by steps in p53 regulation occurring in nucleoli, as suggested by some biochemical evidence. Alternatively, nucleolar disruption also causes redistribution of nucleolar proteins, potentially altering their interactions with p53 and/or MDM2. This raises the fundamental question of whether the nucleolus controls p53 directly, i.e., as a site where p53 regulatory processes occur, or indirectly, i.e., by determining the cellular localization of p53/MDM2-interacting factors. In this work, transport experiments based on heterokaryons, photobleaching, and micronucleation demonstrate that p53 regulatory events are directly regulated by nucleoli and are dependent on intact nucleolar structure and function. Subcellular fractionation and nucleolar isolation revealed a distribution of ubiquitylated p53 that supports these findings. In addition, our results indicate that p53 is exported by two pathways: one stress sensitive and one stress insensitive, the latter being regulated by activities present in the nucleolus.

Trypanosoma vivax Adhesion to Red Blood Cells in Experimentally Infected Sheep.

PubMed

Boada-Sucre, Alpidio A; Rossi Spadafora, Marcello Salvatore; Tavares-Marques, Lucinda M; Finol, Héctor J; Reyna-Bello, Armando

2016-01-01

Trypanosomosis, a globally occurring parasitic disease, poses as a major obstacle to livestock production in tropical and subtropical regions resulting in tangible economic losses. In Latin America including Venezuela, trypanosomosis of ruminants is mainly caused by Trypanosoma vivax. Biologically active substances produced from trypanosomes, as well as host-trypanosome cellular interactions, contribute to the pathogenesis of anemia in an infection. The aim of this study was to examine with a scanning electron microscope the cellular interactions and alterations in ovine red blood cells (RBC) experimentally infected with T. vivax. Ovine infection resulted in changes of RBC shape as well as the formation of surface holes or vesicles. A frequent observation was the adhesion to the ovine RBC by the trypanosome's free flagellum, cell body, or attached flagellum in a process mediated by the filopodia emission from the trypanosome surface. The observed RBC alterations are caused by mechanical and biochemical damage from host-parasite interactions occurring in the bloodstream. The altered erythrocytes are prone to mononuclear phagocytic removal contributing to the hematocrit decrease during infection.

Mechanical output of myosin II motors is regulated by myosin filament size and actin network mechanics

NASA Astrophysics Data System (ADS)

Stam, Samantha; Alberts, Jonathan; Gardel, Margaret; Munro, Edwin

2013-03-01

The interactions of bipolar myosin II filaments with actin arrays are a predominate means of generating forces in numerous physiological processes including muscle contraction and cell migration. However, how the spatiotemporal regulation of these forces depends on motor mechanochemistry, bipolar filament size, and local actin mechanics is unknown. Here, we simulate myosin II motors with an agent-based model in which the motors have been benchmarked against experimental measurements. Force generation occurs in two distinct regimes characterized either by stable tension maintenance or by stochastic buildup and release; transitions between these regimes occur by changes to duty ratio and myosin filament size. The time required for building force to stall scales inversely with the stiffness of a network and the actin gliding speed of a motor. Finally, myosin motors are predicted to contract a network toward stiffer regions, which is consistent with experimental observations. Our representation of myosin motors can be used to understand how their mechanical and biochemical properties influence their observed behavior in a variety of in vitro and in vivo contexts.

Biochemical markers and protein pattern analysis for canine coagulase-positive staphylococci and their distribution on dog skin.

PubMed

Chanchaithong, Pattrarat; Prapasarakul, Nuvee

2011-08-01

Coagulase-positive staphylococci (CoPS) including S. pseudintermedius, S. schleiferi subsp. coagulans and S. aureus are etiological agents of dermatitis in companion animals and can be zoonotic pathogens. To date no consensual biochemical marker for routine microbiological identification of these species has been identified. The aim of this study was to evaluate biochemical markers and compare the results with the approved molecular method, multiplex-PCR (M-PCR), and confirm their species-specific phenotypic characteristic by using SDS-PAGE. The distribution and frequency of CoPS species were also determined. Three hundred and thirty-seven canine CoPS isolates were obtained from the nasal mucosa, perineum and groins of 66 healthy dogs and were identified by the M-PCR as S. aureus (n=5), S. pseudintermedius (n=263) and S. schleiferi subsp. coagulans (n=69). Selected biochemical tests including the Voges-Proskauer test, mannitol broth fermentation, the assimilation of maltose, galactose, trahalose and lactose using broth medium, were successfully used to distinguish the three species of canine CoPS from other CoPS species. Additionally, species-specific protein patterns were also found to be useful for phenotypic differentiation, with good agreement with the results of M-PCR and the use of biochemical markers. S. aureus occured infrequently on dog skin while co-colonization with S. pseudintermedius and S. schleiferi subsp. coagulans was observed. We propose the use of consensual biochemical markers of canine CoPS with the presence of the unique protein patterns as an alternative tool for conventional laboratory use. Copyright © 2011 Elsevier B.V. All rights reserved.

Water quality and processes affecting dissolved oxygen concentrations in the Blackwater River, Canaan Valley, West Virginia

USGS Publications Warehouse

Waldron, M.C.; Wiley, J.B.

1996-01-01

The water quality and environmental processes affecting dissolved oxygen were determined for the Blackwater River in Canaan Valley, West Virginia. Canaan Valley is oval-shaped (14 miles by 5 miles) and is located in the Allegheny Mountains at an average elevation of 3,200 feet above sea level. Tourism, population, and real estate development have increased in the past two decades. Most streams in Canaan Valley are a dilute calcium magnesium bicarbonate-type water. Streamwater typicaly was soft and low in alkalinity and dissolved solids. Maximum values for specific conductance, hardness, alkalinity, and dissolved solids occurred during low-flow periods when streamflow was at or near baseflow. Dissolved oxygen concentrations are most sensitive to processes affecting the rate of reaeration. The reaeration is affected by solubility (atmospheric pressure, water temperature, humidity, and cloud cover) and processes that determine stream turbulence (stream depth, width, velocity, and roughness). In the headwaters, photosynthetic dissolved oxygen production by benthic algae can result in supersaturated dissolved oxygen concentrations. In beaver pools, dissolved oxygen consumption from sediment oxygen demand and carbonaceous biochemical oxygen demand can result in dissolved oxygen deficits.

Dissecting the hybridization of oligonucleotides to structured complementary sequences.

PubMed

Peracchi, Alessio

2016-06-01

When oligonucleotides hybridize to long target molecules, the process is slowed by the secondary structure in the targets. The phenomenon has been analyzed in several previous studies, but many details remain poorly understood. I used a spectrofluorometric strategy, focusing on the formation/breaking of individual base pairs, to study the kinetics of association between a DNA hairpin and >20 complementary oligonucleotides ('antisenses'). Hybridization rates differed by over three orders of magnitude. Association was toehold-mediated, both for antisenses binding to the target's ends and for those designed to interact with the loop. Binding of these latter, besides being consistently slower, was affected to variable, non-uniform extents by the asymmetric loop structure. Divalent metal ions accelerated hybridization, more pronouncedly when nucleation occurred at the loop. Incorporation of locked nucleic acid (LNA) residues in the antisenses substantially improved the kinetics only when LNAs participated to the earliest hybridization steps. The effects of individual LNAs placed along the antisense indicated that the reaction transition state occurred after invading at least the first base pair of the stem. The experimental approach helps dissect hybridization reactions involving structured nucleic acids. Toehold-dependent, nucleation-invasion models appear fully appropriate for describing such reactions. Estimating the stability of nucleation complexes formed at internal toeholds is the major hurdle for the quantitative prediction of hybridization rates. While analyzing the mechanisms of a fundamental biochemical process (hybridization), this work also provides suggestions for the improvement of technologies that rely on such process. Copyright © 2016 Elsevier B.V. All rights reserved.

Biochemical and physiological processes associated with the differential ozone response in ozone-tolerant and sensitive soybean genotypes

USDA-ARS?s Scientific Manuscript database

Biochemical and physiological traits of two soybean [Glycine max (L.) Merr.] genotypes that differ in sensitivity to ozone (O3) were investigated to determine the possible basis for the differential response. Fiskeby III (O3-tolerant) and Mandarin (Ottawa) (O3-sensitive) were grown in a greenhouse ...

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

Treesearch

Walter C. Shortle; Kevin T. Smith; Rakesh Minocha; Gregory B. Lawrence; Mark B. David

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...

Methods of mesophyll conductance estimation: its impact on key biochemical parameters and photosynthetic limitations in phosphorus-stressed soybean across CO2

USDA-ARS?s Scientific Manuscript database

Photosynthetic potential in C3 plants is largely limited by CO2 diffusion through stomata (Ls) and mesophyll (Lm) and photo-biochemical (Lb) processes. Accurate estimation of mesophyll conductance (gm) using gas exchange (GE) and chlorophyll fluorescence (CF) parameters of the photosynthetic proces...

Services provided in support of the planetary quarantine requirements of the National Aeronautics and Space Administration

NASA Technical Reports Server (NTRS)

Favero, M. S.

1972-01-01

The evaluation is discussed of the terminal sterilization process for unmanned lander spacecraft. Results of biochemical test deviations encountered with the identification schemes are tabulated. Studies to examine the possibility of shifts in biochemical reaction patterns during storage and subculture of the environmental Bacillius isolates are also reported.

Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels.

PubMed

Zeng, Yining; Zhao, Shuai; Yang, Shihui; Ding, Shi-You

2014-06-01

A biochemical platform holds the most promising route toward lignocellulosic biofuels, in which polysaccharides are hydrolyzed by cellulase enzymes into simple sugars and fermented to ethanol by microbes. However, these polysaccharides are cross-linked in the plant cell walls with the hydrophobic network of lignin that physically impedes enzymatic deconstruction. A thermochemical pretreatment process is often required to remove or delocalize lignin, which may also generate inhibitors that hamper enzymatic hydrolysis and fermentation. Here we review recent advances in understanding lignin structure in the plant cell walls and the negative roles of lignin in the processes of converting biomass to biofuels. Perspectives and future directions to improve the biomass conversion process are also discussed. Copyright © 2013. Published by Elsevier Ltd.

Ganglioside Biochemistry

PubMed Central

Kolter, Thomas

2012-01-01

Gangliosides are sialic acid-containing glycosphingolipids. They occur especially on the cellular surfaces of neuronal cells, where they form a complex pattern, but are also found in many other cell types. The paper provides a general overview on their structures, occurrence, and metabolism. Key functional, biochemical, and pathobiochemical aspects are summarized. PMID:25969757

RNA Seq analysis of the role of calcium chloride stress and electron transport in mitochondria for malachite green decolorization by Aspergillus niger.

PubMed

Gomaa, Ola M; Selim, Nabila S; Wee, Josephine; Linz, John E

2017-08-01

Aspergillus niger was previously demonstrated to decolorize the commercial dye malachite green (MG) and this process was enhanced under calcium chloride (CaCl 2 ) treatment. Previous data also suggested that the decolorization process is related to mitochondrial cytochrome c. In the current work, we analyzed in depth the specific relationship between CaCl 2 treatment and MG decolorization. Gene expression analysis (RNA Seq) using Next Generation Sequencing (NGS) revealed up-regulation of 28 genes that are directly or indirectly associated with stress response functions as early as 30min of CaCl 2 treatment; these data further strengthen our previous findings that CaCl 2 treatment induces a stress response in A. niger which enhances the ability to decolorize MG. A significant increase in fluorescence observed by MitoTracker dye suggests that CaCl 2 treatment also increased mitochondrial membrane potential. Isolated mitochondrial membrane protein fractions obtained from A. niger grown under standard growth conditions decolorized MG in the presence of NADH and decolorization was enhanced in samples isolated from CaCl 2 -treated A. niger cultures. Treatment of whole mitochondrial fraction with KCN which inhibits electron transport by cytochrome c oxidase and Triton-X 100 which disrupts mitochondrial membrane integrity suggests that cyanide sensitive cytochrome c oxidase activity is a key biochemical step in MG decolorization. This suggestion was confirmed by the addition of palladium α-lipoic acid complex (PLAC) which resulted in an initial increase in decolorization. Although the role of cytochrome c and cytochrome c oxidase was confirmed at the biochemical level, changes in levels of transcripts encoding these enzymes after CaCl 2 treatment were not found to be statistically significant in RNA Seq analysis. These data suggest that the regulation of cytochrome c enzymes occur predominantly at the post-transcriptional level under CaCl 2 stress. Thus, using global transcriptomics and biochemical approaches, our study provides a molecular association between fungal mitochondrial electron transfer systems and MG decolorization. Copyright © 2017 Elsevier Inc. All rights reserved.

Biochemical and physicochemical analysis of fish protein isolate recovered from red snapper (Lutjanus sp.) by-product using isoelectric solubilization/precipitation method

NASA Astrophysics Data System (ADS)

Pramono, H.; Pujiastuti, D. Y.; Sahidu, A. M.

2018-04-01

The effect of acid- and alkali-process on biochemical and physicochemical characteristics of fish protein isolate from red snapper (Lutjanus sp) by-product was evaluated. Protein recovered by alkali process (16.79%) was higher compared to acid process (13.75%). Reduction of lipid content and total volatile basic nitrogen (TVB-N) exhibited in both treatments indicated both process improved fish protein isolate recovered from red snapper by-product. In addition, the increasing of water holding capacity and oil binding capacity were observed. However, high peroxide value of fish protein isolate was showed in both treatment. This finding indicated that acid and alkali process can be used as a useful method to recover proteins from red snapper by-product. Alkali process gave a protein isolate with better overall quality compared to acid process.

Simulation of anaerobic digestion processes using stochastic algorithm.

PubMed

Palanichamy, Jegathambal; Palani, Sundarambal

2014-01-01

The Anaerobic Digestion (AD) processes involve numerous complex biological and chemical reactions occurring simultaneously. Appropriate and efficient models are to be developed for simulation of anaerobic digestion systems. Although several models have been developed, mostly they suffer from lack of knowledge on constants, complexity and weak generalization. The basis of the deterministic approach for modelling the physico and bio-chemical reactions occurring in the AD system is the law of mass action, which gives the simple relationship between the reaction rates and the species concentrations. The assumptions made in the deterministic models are not hold true for the reactions involving chemical species of low concentration. The stochastic behaviour of the physicochemical processes can be modeled at mesoscopic level by application of the stochastic algorithms. In this paper a stochastic algorithm (Gillespie Tau Leap Method) developed in MATLAB was applied to predict the concentration of glucose, acids and methane formation at different time intervals. By this the performance of the digester system can be controlled. The processes given by ADM1 (Anaerobic Digestion Model 1) were taken for verification of the model. The proposed model was verified by comparing the results of Gillespie's algorithms with the deterministic solution for conversion of glucose into methane through degraders. At higher value of 'τ' (timestep), the computational time required for reaching the steady state is more since the number of chosen reactions is less. When the simulation time step is reduced, the results are similar to ODE solver. It was concluded that the stochastic algorithm is a suitable approach for the simulation of complex anaerobic digestion processes. The accuracy of the results depends on the optimum selection of tau value.

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

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 spores are observed in all deposit layers, mycelium of mushrooms deepens into the peat deposit (to 2 meters) within the limits of aerobic (meter) zone and only in particular months of dry years. The existence of seasonal dynamics of eukaryotic cells, and also capability of yeast and other groups of micromycetes for growth, testifies about vital activity of a number of eukaryotic cells at a depth of 2 meters. Researched peat deposits are biochemically active along the whole profile. But they are different in a microflora number of individual physiological groups either in items of the landscape, or in deposit depth. The largest quantity of aerobic cellulose-fermenting microorganisms is marked during dry years. Anaerobic cellulose-fermenting microorganisms dominate during wet years. The quantity of microbe biomass increases in bottom lifts of peat deposits. This fact testifies about viable condition of microbe complex at depth. The formation process of carbon dioxide in peat deposits of Vasyugan Mire actively occurs during dry years and is defined by hydrothermic conditions of a meter layer of peat deposit. The intensity of CO2 isolation for certain correlates with the temperature in horizon of 0 - 50 sm. and with bog waters level. The study of gas composition for the three years showed that the largest concentration of carbon dioxide in peat soils is marked along the whole profile during a dryer year (0.08 - 2.65 millimole/l), increasing other years' level in about 1.5 0 2 times. Emission of carbon dioxide in peat

A cobalt oxyhydroxide-modified upconversion nanosystem for sensitive fluorescence sensing of ascorbic acid in human plasma

NASA Astrophysics Data System (ADS)

Cen, Yao; Tang, Jun; Kong, Xiang-Juan; Wu, Shuang; Yuan, Jing; Yu, Ru-Qin; Chu, Xia

2015-08-01

Ascorbic acid (AA), a potent antioxidant readily scavenging reactive species, is a crucial micronutrient involved in many biochemical processes. Here, we have developed a cobalt oxyhydroxide (CoOOH)-modified upconversion nanosystem for fluorescence sensing of AA activity in human plasma. The nanosystem consists of upconversion nanoparticles (UCNPs) NaYF4:30% Yb,0.5% Tm@NaYF4, which serve as energy donors, and CoOOH nanoflakes formed on the surface of UCNPs, which act as efficient energy acceptors. The fluorescence resonance energy transfer (FRET) process from the UCNPs to the absorbance of the CoOOH nanoflakes occurs in the nanosystem. The AA-mediated specific redox reaction reduces CoOOH into Co2+, leading to the inhibition of FRET, and resulting in the recovery of upconversion emission spectra. On the basis of these features, the nanosystem can be used for sensing AA activity with sensitivity and selectivity. Moreover, due to the minimizing background interference provided by UCNPs, the nanosystem has been applied to monitoring AA levels in human plasma sample with satisfactory results. The proposed approach may potentially provide an analytical platform for research and clinical diagnosis of AA related diseases.Ascorbic acid (AA), a potent antioxidant readily scavenging reactive species, is a crucial micronutrient involved in many biochemical processes. Here, we have developed a cobalt oxyhydroxide (CoOOH)-modified upconversion nanosystem for fluorescence sensing of AA activity in human plasma. The nanosystem consists of upconversion nanoparticles (UCNPs) NaYF4:30% Yb,0.5% Tm@NaYF4, which serve as energy donors, and CoOOH nanoflakes formed on the surface of UCNPs, which act as efficient energy acceptors. The fluorescence resonance energy transfer (FRET) process from the UCNPs to the absorbance of the CoOOH nanoflakes occurs in the nanosystem. The AA-mediated specific redox reaction reduces CoOOH into Co2+, leading to the inhibition of FRET, and resulting in the recovery of upconversion emission spectra. On the basis of these features, the nanosystem can be used for sensing AA activity with sensitivity and selectivity. Moreover, due to the minimizing background interference provided by UCNPs, the nanosystem has been applied to monitoring AA levels in human plasma sample with satisfactory results. The proposed approach may potentially provide an analytical platform for research and clinical diagnosis of AA related diseases. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03588k

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.

Using a multibiomarker approach and behavioural responses to assess the effects of anthracene in Palaemon serratus.

PubMed

Gravato, Carlos; Almeida, Joana R; Silva, Carlos; Oliveira, Cristiana; Soares, Amadeu M V M

2014-04-01

Polycyclic aromatic hydrocarbons (PAHs) are recognised as one of the main groups of contaminants that assume more importance in the marine environment, enhancing the need of studies concerning their adverse effects and more efficient and ecologically relevant tools for environmental monitoring purposes. This study aims to apply an integrated approach including several multi-level biological responses (accumulation levels, biochemical responses important for different physiological functions and behavioural alterations) to assess the ecological relevance of the effects induced by sub-lethal concentrations of anthracene (ANT) in Palaemon serratus (common prawn). ANT accumulation was assessed by measuring the levels of ANT-type compounds in prawn digestive gland, muscle and eye; biochemical responses were determined using biomarkers involved in biotransformation, oxidative damage, energy production and neurotransmission processes; and behavioural alterations through swimming performance after 96 h exposure bioassay (ANT:16-1,024 μg/L). The rationale behind this approach is to assess the ecologically relevant effects induced by ANT in prawn, given by the association between behavioural alterations with biochemical responses, in search for more efficient tools for environmental risk assessment. Results show a significant decrease of swimming velocity (LOEC=128 μg/L) along with increased levels of ANT-type compounds in digestive gland (LOEC=128 μg/L), muscle (LOEC=256 μg/L) and eye (LOEC=32 μg/L) in prawn exposed to ANT. Increased activities of glutathione peroxidase (GPx) and catalase (CAT), involved in anti-oxidant defence system, were also observed (LOEC=256 μg/L; 1024μg/L, respectively) in the digestive gland of prawn, induction of oxidative damage in lipids (LPO) also occurred (LOEC=32 μg/L). The inhibition of swimming velocity showed a correlation with some biochemical parameters measured, including the levels of ANT-type compounds in tissues and LPO, and thus these may be considered sensitive and ecologically relevant criteria as well as early warning endpoints for assessing polycyclic aromatic compounds exposure effects on marine organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Status of miniature integrated UV resonance fluorescence and Raman sensors for detection and identification of biochemical warfare agents

NASA Astrophysics Data System (ADS)

Hug, William F.; Bhartia, Rohit; Taspin, Alexandre; Lane, Arthur; Conrad, Pamela; Sijapati, Kripa; Reid, Ray D.

2005-11-01

Laser induced native fluorescence (LINF) is the most sensitive method of detection of biological material including microorganisms, virus', and cellular residues. LINF is also a sensitive method of detection for many non-biological materials as well. The specificity with which these materials can be classified depends on the excitation wavelength and the number and location of observation wavelengths. Higher levels of specificity can be obtained using Raman spectroscopy but a much lower levels of sensitivity. Raman spectroscopy has traditionally been employed in the IR to avoid fluorescence. Fluorescence rarely occurs at wavelength below about 270nm. Therefore, when excitation occurs at a wavelength below 250nm, no fluorescence background occurs within the Raman fingerprint region for biological materials. When excitation occurs within electronic resonance bands of the biological target materials, Raman signal enhancement over one million typically occurs. Raman sensitivity within several hundred times fluorescence are possible in the deep UV where most biological materials have strong absorption. Since the Raman and fluorescence emissions occur at different wavelength, both spectra can be observed simultaneously, thereby providing a sensor with unique sensitivity and specificity capability. We will present data on our integrated, deep ultraviolet, LINF/Raman instruments that are being developed for several applications including life detection on Mars as well as biochemical warfare agents on Earth. We will demonstrate the ability to discriminate organic materials based on LINF alone. Together with UV resonance Raman, higher levels of specificity will be demonstrated. In addition, these instruments are being developed as on-line chemical sensors for industrial and municipal waste streams and product quality applications.

Transplantation of Reprogrammed Autologous Stem Cells for Chronic Pain and Drug Abuse

DTIC Science & Technology

2012-10-01

Hyperalgesia and Mechanical Allodynia by Curcumin in a Rat Model of Partial Thickness Thermal Injury Clifford, John Evaluation Of A Non-Invasive System Of...Thermal Injury Garza, Thomas Biochemical Correlates for the Analgesic Action Of Curcumin : A Naturally occurring Anti-inflammatory Agent Greer, Angie

Managing breathlessness: providing comfort at the end of life.

PubMed

Tice, Martha A

2006-04-01

Dyspnea is a common symptom at the end of life. It occurs as the result of a complex mix of physical, biochemical, and perceptual components. When patients and their healthcare providers focus on the "numbers" related to oxygenation, rather than comfort, the individual's quality of life can suffer.

Nutrient-induced modulation of gene expression and cellular functions: modeling epigenetic regulation in bovine cells

USDA-ARS?s Scientific Manuscript database

Volatile fatty acids (VFA), especially butyrate, participate in metabolism both as nutrients and as regulators of histone deacetylation. The major biochemical change that occurs in cells treated with butyrate is the global hyperacetylation of histones. One paradigmatic example of the nutrient-epige...

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

Kleiner, J.B.; Amiel, D.; Harwood, F.L.

A rabbit model for anterior cruciate ligament (ACL) reconstruction using autogenous patellar tendon was utilized to study the early events of autograft cellular dynamics. Biochemical, autoradiographic, histological, and vascular injection techniques demonstrated that the native autograft cell population rapidly necroses. This repopulation occurs without a vascular contribution; cells entering the autograft are reliant upon synovial fluid nutrition.

Effects of glucosinolates and their hydrolysis products on biochemical and performance parameters in broiler chicken diets

USDA-ARS?s Scientific Manuscript database

Glucosinolates are important bioactive molecules and widely found in Brassicaceae species (cress, brussels sprouts, mustard, broccoli, kale, etc.). Depending on the amount of these vegetables consumed, both positive and negative metabolic effects from glucosinolate metabolites may occur. The aim of ...

Effects of glucosinolates and their hydrolysis products on biochemical and performance parameters in broiler chicken diets

USDA-ARS?s Scientific Manuscript database

Glucosinolates are important bioactive molecules and widely found in Brassicaceae species (cress, brussels sprouts, mustard, broccoli, kale etc.). Depending on the amount of these vegetables consumed, both positive and negative metabolic effects from glucosinolate metabolites may occur. The aims of ...

Computer Simulation in Predicting Biochemical Processes and Energy Balance at WWTPs

NASA Astrophysics Data System (ADS)

Drewnowski, Jakub; Zaborowska, Ewa; Hernandez De Vega, Carmen

2018-02-01

Nowadays, the use of mathematical models and computer simulation allow analysis of many different technological solutions as well as testing various scenarios in a short time and at low financial budget in order to simulate the scenario under typical conditions for the real system and help to find the best solution in design or operation process. The aim of the study was to evaluate different concepts of biochemical processes and energy balance modelling using a simulation platform GPS-x and a comprehensive model Mantis2. The paper presents the example of calibration and validation processes in the biological reactor as well as scenarios showing an influence of operational parameters on the WWTP energy balance. The results of batch tests and full-scale campaign obtained in the former work were used to predict biochemical and operational parameters in a newly developed plant model. The model was extended with sludge treatment devices, including anaerobic digester. Primary sludge removal efficiency was found as a significant factor determining biogas production and further renewable energy production in cogeneration. Water and wastewater utilities, which run and control WWTP, are interested in optimizing the process in order to save environment, their budget and decrease the pollutant emissions to water and air. In this context, computer simulation can be the easiest and very useful tool to improve the efficiency without interfering in the actual process performance.

Relationships between pigment composition variation and reflectance for plant species from a coastal savannah in California

NASA Technical Reports Server (NTRS)

Ustin, Susan L.; Sanderson, Eric W.; Grossman, Yaffa; Hart, Quinn J.

1993-01-01

Advances in imaging spectroscopy have indicated that remotely sensed reflectance measurements of the plant canopy may be used to identify and qualify some classes of canopy biochemicals; however, the manner in which differences in biochemical compositions translate into differences is not well understood. Most frequently, multiple linear regression routines have been used to correlate narrow band reflectance values with measured biochemical concentrations. Although some success has been achieved with such methods for given data sets, the bands selected by multiple regression are not consistent between data sets, nor is it always clear what physical or biological basis underlies the correlation. To examine the relationship between biochemical concentration and leaf reflectance signal we chose to focus on the visible spectrum where the primary biochemical absorbances are due to photosynthetic pigments. Pigments provide a range of absorbance features, occur over a range of concentrations in natural samples, and are ecophysiologically important. Concentrations of chlorophyll, for example, have been strongly correlated to foliar nitrogen levels within a species and to photosynthetic capacity across many species. In addition pigments effectively absorb most of the photosynthetically active radiation between 400-700 nm, a spectral region for which silicon detectors have good signal/noise characteristics. Our strategy has been to sample a variety of naturally occurring species to measure leaf reflectance and pigment compositions. We hope to extend our understanding of pigment reflectance effects to interpret small overlapping absorbances of other biochemicals in the infrared region. For this reason, selected samples were also tested to determine total nitrogen, crude protein, cellulose, and lignin levels. Leaf reflectance spectra measured with AVIRIS bandwidths and wavelengths were compared between species and within species and for differences between seasons, for changes in the the shape of the spectra. We attempt to statistically correlate these shape changes with differences in pigment compositions. In parallel with our comparisons of pigment composition and leaf reflectance, we have modified the PROSPECT leaf reflectance model to test the contributions of pigments or pigment group concentrations. PROSPECT considers a leaf as a multi-layer dielectric plane with an uneven surface. Jacquemoud adapted the basic analysis of Allen for surface effects, a leaf thickness factor, and the absorption of water and chlorophyll (actually all pigments) and the plant matrix. Our modifications to PROSPECT in the forward direction include breaking out the pigment concentration parameter into separate components for chlorophyll a and b and a number of xanthophylls and carotenes, and introducing a shift and convolution function to model the spread and shift from their in vitro measurements to their in vivo state. Further, we have considered how the matrix elements (i.e., all biochemicals and structural effects not modeled explicity) vary with species.

Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions

PubMed Central

Lamba, Sanjay; Bera, Soumen; Rashid, Mubasher; Medvinsky, Alexander B.; Acquisti, Claudia; Li, Bai-Lian

2017-01-01

Nitrogen is cycled throughout ecosystems by a suite of biogeochemical processes. The high complexity of the nitrogen cycle resides in an intricate interplay between reversible biochemical pathways alternatively and specifically activated in response to diverse environmental cues. Despite aggressive research, how the fundamental nitrogen biochemical processes are assembled and maintained in fluctuating soil redox conditions remains elusive. Here, we address this question using a kinetic modelling approach coupled with dynamical systems theory and microbial genomics. We show that alternative biochemical pathways play a key role in keeping nitrogen conversion and conservation properties invariant in fluctuating environments. Our results indicate that the biochemical network holds inherent adaptive capacity to stabilize ammonium and nitrate availability, and that the bistability in the formation of ammonium is linked to the transient upregulation of the amo-hao mediated nitrification pathway. The bistability is maintained by a pair of complementary subsystems acting as either source or sink type systems in response to soil redox fluctuations. It is further shown how elevated anthropogenic pressure has the potential to break down the stability of the system, altering substantially ammonium and nitrate availability in the soil, with dramatic effects on biodiversity. PMID:28280580

Aquifer recharge with reclaimed water in the Llobregat Delta. Laboratory batch experiments and field test site.

NASA Astrophysics Data System (ADS)

Tobella, J.

2010-05-01

Summary Spain, as most other Mediterranean countries, faces near future water shortages, generalized pollution and loss of water dependent ecosystems. Aquifer recharge represents a promising option to become a source for indirect potable reuse purposes but presence of pathogens as well as organic and inorganic pollutants should be avoided. To this end, understanding the processes of biogeochemical degradation occurring within the aquifer during infiltration is capital. A set of laboratory batch experiments has been assembled in order to assess the behaviour of selected pesticides, drugs, estrogens, surfactant degradation products, biocides and phthalates under different redox conditions. Data collected during laboratory experiments and monitoring activities at the Sant Vicenç dels Horts test site will be used to build and calibrate a numerical model (i) of the physical-chemical-biochemical processes occurring in the batches and (ii) of multicomponent reactive transport in the unsaturated/saturated zone at the test site. Keywords Aquifer recharge, batch experiments, emerging micropollutants, infiltration, numerical model, reclaimed water, redox conditions, Soil Aquifer Treatment (SAT). 1. Introduction In Spain, the Llobregat River and aquifers, which supply water to Barcelona, have been overexploited for years and therefore, suffer from serious damages: the river dries up on summer, riparian vegetation has disappeared and seawater has intruded the aquifer. In a global context, solutions to water stress problems are urgently needed yet must be sustainable, economical and safe. Recent developments of analytical techniques detect the presence of the so-called "emerging" organic micropollutants in water and soils. Such compounds may affect living organisms when occurring in the environment at very low concentrations (microg/l or ng/l). In wastewater and drinking water treatment plants, a remarkable removal of these chemicals from water can be obtained only using advanced and costly treatments. Nevertheless, a number of studies are demonstrating that physical, chemical and biochemical processes associated with water movement within the subsoil represent a natural alternative way to reduce the presence of these contaminants. This processes are called Soil Aquifer Treatment (SAT). Aquifer recharge will become a source for indirect potable reuse purposes as long as the presence of pathogens and organic and inorganic pollutants is avoided. To this end, understanding the biogeochemical degradation processes occurring within the aquifer during infiltration is capital. 2. Laboratory batch experiments A set of laboratory batch experiments has been assembled to assess the behaviour of selected pesticides, drugs, estrogens, surfactant degradation products, biocides and phthalates under different redox conditions. The setup of the experiments consists of glass bottles containing 120 g of soil and 240 ml of synthetic water spiked with the mix of micropollutants. A source of easily degradable organic carbon and, depending on the type of test, electron acceptors are added in order to yield aerobic respiration and nitrate/iron/manganese/sulphate reduction conditions. The evolution of the processes is monitored by sacrificing duplicate bottles according to a defined schedule and analysing water for major and minor components as well as for micropollutants. Results from biotic tests are compared with abiotic ones in order to discern biodegradation from other chemical processes. The soil, the synthetic water and the micropollutants selected for the experiments are representative of a test site in the nearby of Barcelona (Spain) where artificial recharge of groundwater through ponds is going to be performed using river water or tertiary effluent from a waste water treatment plant. The results of the experiments improve the knowledge on the behaviour of the selected micropollutants under different redox conditions and provide with useful information on the conditions to develop at the test site during artificial recharge. The data collected during the laboratory experiments and in the test site will be used to build and calibrate a numerical model of the physical-chemical-biochemical processes developing in the batches and of multicomponent reactive transport in the unsaturated/saturated zone in the test site area. 3. Field test site The infiltration site of Sant Vicenç dels Horts has been selected to assessing the biogeochemical processes occurring during SAT. The system consists of two ponds that have been built as compensatory measure for the reduction in natural recharge caused by the construction of the High Speed Train Line. The first pond acts as a decantation pond while the second one acts as an infiltration basin (Figure 1). Recharge water comes from the tertiary treatment plant of the El Prat de Llobregat WWTP and the river (?). The CUADLL (Lower Llobregat Aquifer End-Users Community) is now managing the system operation. Tasks that are currently being carried out at this Test Site aims at (i) improving the local experience on MAR through infiltration ponds operational aspects and (ii) monitoring the changes in water quality during the recharge processes (unsaturated and saturated zone). Special attention is being paid to the fate of emerging organic pollutants (pharmaceuticals, surfactants, pesticides, etc.). The yielding of the monitoring will be compared with the results from the laboratory batch experiments on the behaviour of selected emerging organic pollutants. To this end, observation wells have been constructed, pressure / temperature / electrical conductivity transducers have been installed and the vadose zone under the infiltration pond has been instrumented (tensiometers, water content probes and suction cups). In addition double ring and infiltration tests have been performed in order to forecast the infiltration capacity of the basin.

Functional analysis of H. sapiens DNA polymerase γ spacer mutation W748S with and without common variant E1143G

PubMed Central

Palin, Eino JH; Lesonen, Annamari; Farr, Carol L; Euro, Liliya; Suomalainen, Anu; Kaguni, Laurie S

2010-01-01

Mitochondrial DNA polymerase, POLG, is the sole DNA polymerase found in animal mitochondria. In humans, POLGα W748S in cis with an E1143G mutation has been linked to a new type of recessive ataxia, MIRAS, which is the most common inherited ataxia in Finland. We investigated the biochemical phenotypes of the W748S amino acid change, using recombinant human POLG. We measured processive and non-processive DNA polymerase activity, DNA binding affinity, enzyme processivity, and subunit interaction with recombinant POLGβ. In addition, we studied the effects of the W748S and E1143G mutations in primary human cell cultures using retroviral transduction. Here, we examined cell viability, mitochondrial DNA copy number, and products of mitochondrial translation. Our results indicate that the W748S mutant POLGα does not exhibit a clear biochemical phenotype, making it indistinguishable from wild type POLGα and as such, fail to replicate previously published results. Furthermore, results from the cell models were concurrent with the findings from patients, and support our biochemical findings. PMID:20153822

Search for biochemical fossils on earth and non-biological organic molecules on Jupiter, Saturn and Titan

NASA Astrophysics Data System (ADS)

Nagy, Bartholomew

1982-07-01

Recognizable remnants of ancient biochemicals may survive under mild/moderate geological environments. Acyclic isoprenoid hydrocarbons, cyclic hydrocarbons with terpenoid carbon skeletons (e.g. hopanes) and vanadyl and nickel porphyrins have been isolated from organic matter, including petroleum, in Phanerozoic sedimentary rocks. Remnants of lignin have also been found. Usually, carbohydrates do not survive long; they degrade and/or react with other organic substances to form macromolecular matter. Proteins, e.g. apparently those in dinosaur bone collagen, break down relatively rapidly. Life arose during the Precambrian and potential biochemical fossils, e.g. n-alkanes, 2,5-dimethylfuran have been isolated from Precambrian kerogens. Traces of hydrocarbons, NH3, PH3 occur on Jupiter and Saturn. Hydrocarbons, N2 and HCN, the latter a key intermediary in the laboratory abiological syntheses of amino acids and nucleic acid bases, are present on Titan where life could not have evolved. Precursor abiological organic molecules of some complexity may have been synthesized on Titan and the Jovian planets.

Methods for Discovery of Novel Cellulosomal Cellulases Using Genomics and Biochemical Tools.

PubMed

Ben-David, Yonit; Dassa, Bareket; Bensoussan, Lizi; Bayer, Edward A; Moraïs, Sarah

2018-01-01

Cell wall degradation by cellulases is extensively explored owing to its potential contribution to biofuel production. The cellulosome is an extracellular multienzyme complex that can degrade the plant cell wall very efficiently, and cellulosomal enzymes are therefore of great interest. The cellulosomal cellulases are defined as enzymes that contain a dockerin module, which can interact with a cohesin module contained in multiple copies in a noncatalytic protein, termed scaffoldin. The assembly of the cellulosomal cellulases into the cellulosomal complex occurs via specific protein-protein interactions. Cellulosome systems have been described initially only in several anaerobic cellulolytic bacteria. However, owing to ongoing genome sequencing and metagenomic projects, the discovery of novel cellulosome-producing bacteria and the description of their cellulosomal genes have dramatically increased in the recent years. In this chapter, methods for discovery of novel cellulosomal cellulases from a DNA sequence by bioinformatics and biochemical tools are described. Their biochemical characterization is also described, including both the enzymatic activity of the putative cellulases and their assembly into mature designer cellulosomes.

Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination.

PubMed

Buisson, Rémi; Dion-Côté, Anne-Marie; Coulombe, Yan; Launay, Hélène; Cai, Hong; Stasiak, Alicja Z; Stasiak, Andrzej; Xia, Bing; Masson, Jean-Yves

2010-10-01

Inherited mutations in human PALB2 are associated with a predisposition to breast and pancreatic cancers. PALB2's tumor-suppressing effect is thought to be based on its ability to facilitate BRCA2's function in homologous recombination. However, the biochemical properties of PALB2 are unknown. Here we show that human PALB2 binds DNA, preferentially D-loop structures, and directly interacts with the RAD51 recombinase to stimulate strand invasion, a vital step of homologous recombination. This stimulation occurs through reinforcing biochemical mechanisms, as PALB2 alleviates inhibition by RPA and stabilizes the RAD51 filament. Moreover, PALB2 can function synergistically with a BRCA2 chimera (termed piccolo, or piBRCA2) to further promote strand invasion. Finally, we show that PALB2-deficient cells are sensitive to PARP inhibitors. Our studies provide the first biochemical insights into PALB2's function with piBRCA2 as a mediator of homologous recombination in DNA double-strand break repair.

Efficient ethanol production from dried oil palm trunk treated by hydrothermolysis and subsequent enzymatic hydrolysis.

PubMed

Eom, In-Yong; Yu, Ju-Hyun; Jung, Chan-Duck; Hong, Kyung-Sik

2015-01-01

Oil palm trunk (OPT) is a valuable bioresource for the biorefinery industry producing biofuels and biochemicals. It has the distinct feature of containing a large amount of starch, which, unlike cellulose, can be easily solubilized by water when heated and hydrolyzed to glucose by amylolytic enzymes without pretreatment for breaking down the biomass recalcitrance. Therefore, it is suggested as beneficial to extract most of the starch from OPT through autoclaving and subsequent amylolytic hydrolysis prior to pretreatment. However, this treatment requires high capital and operational costs, and there could be a high probability of microbial contamination during starch processing. In terms of biochemical conversion of OPT, this study aimed to develop a simple and efficient ethanol conversion process without any chemical use such as acids and bases or detoxification. For comparison with the proposed efficient ethanol conversion process, OPT was subjected to hydrothermal treatment at 180 °C for 30 min. After enzymatic hydrolysis of PWS, 43.5 g of glucose per 100 g dry biomass was obtained, which corresponds to 81.3 % of the theoretical glucose yield. Through subsequent alcohol fermentation, 81.4 % ethanol yield of the theoretical ethanol yield was achieved. To conduct the proposed new process, starch in OPT was converted to ethanol through enzymatic hydrolysis and subsequent fermentation prior to hydrothermal treatment, and the resulting slurry was subjected to identical processes that were applied to control. Consequently, a high-glucose yield of 96.3 % was achieved, and the resulting ethanol yield was 93.5 %. The proposed new process was a simple method for minimizing the loss of starch during biochemical conversion and maximizing ethanol production as well as fermentable sugars from OPT. In addition, this methodology offers the advantage of reducing operational and capital costs due to minimizing the process for ethanol production by excluding expensive processes related to detoxification prior to enzymatic hydrolysis and fermentation such as washing/conditioning and solid-liquid separation of pretreated slurry. The potential future use of xylose-digestible microorganisms could further increase the ethanol yield from the proposed process, thereby increasing its effectiveness for the conversion of OPT into biofuels and biochemicals.

Biochemical Storage Lesions Occurring in Nonirradiated and Irradiated Red Blood Cells: A Brief Review

PubMed Central

Adams, F.; Bellairs, G.; Bird, A. R.; Oguntibeju, O. O.

2015-01-01

Red blood cells undergo a series of biochemical fluctuations during 35–42-day storage period at 1°C to 6°C. The sodium/potassium pump is immobilised causing a decrease in intracellular potassium with an increase in cytoplasmic sodium levels, glucose levels decline, and acidosis occurs as a result of low pH levels. The frailty of stored erythrocytes triggers the formation of haemoglobin-containing microparticles and the release of cell-free haemoglobin which may add to transfusion difficulties. Lipid peroxidation, oxidative stress to band 3 structures, and other morphological and structural molecular changes also occur leading to spheroechinocytes and osmotic fragility. These changes that transpire in the red cells during the storage period are referred to as “storage lesions.” It is well documented that gamma irradiation exacerbates storage lesions and the reports of increased potassium levels leading to adverse reactions observed in neonates and infants have been of particular concern. There are, however, remarkably few systematic studies comparing the in vitro storage lesions of irradiated and nonirradiated red cell concentrates and it has been suggested that the impact of storage lesions on leucocyte reduced red blood cell concentrate (RBCC) is incomplete. The review examines storage lesions in red blood cells and their adverse effects in reference to blood transfusion. PMID:25710038

Responds of Bone Cells to Microgravity: Ground-Based Research

NASA Astrophysics Data System (ADS)

Zhang, Jian; Li, Jingbao; Xu, Huiyun; Yang, Pengfei; Xie, Li; Qian, Airong; Zhao, Yong; Shang, Peng

2015-11-01

Severe loss of bone occurs due to long-duration spaceflight. Mechanical loading stimulates bone formation, while bone degradation happens under mechanical unloading. Bone remodeling is a dynamic process in which bone formation and bone resorption are tightly coupled. Increased bone resorption and decreased bone formation caused by reduced mechanical loading, generally result in disrupted bone remodeling. Bone remodeling is orchestrated by multiple bone cells including osteoblast, osteocyte, osteoclast and mesenchymal stem cell. It is yet not clear that how these bone cells sense altered gravity, translate physical stimulus into biochemical signals, and then regulate themselves structurally and functionally. In this paper, studies elucidating the bioeffects of microgravity on bone cells (osteoblast, osteocyte, osteoclast, mesenchymal stem cell) using various platforms including spaceflight and ground-based simulated microgravity were summarized. Promising gravity-sensitive signaling pathways and protein molecules were proposed.

Roth spots in pyridoxine dependent epilepsy

PubMed Central

Bok, Levinus A; Halbertsma, Feico; Kerkhoff, Frank; Jakobs, Cornelis; Duijsters, Carola; Willemsen, Michèl

2011-01-01

Pyridoxine dependent epilepsy (PDE) is a rare metabolic defect in the degradation of lysine. The authors report a patient with metabolic and DNA confirmed PDE, on the fifth day of life ophthalmoscopy showed bilateral multiple white centred retinal haemorrhages, so called Roth spots. Roth spots are non-specific haemorrhagic signs that occur in a variety of conditions of acute systemic insults in homeostasis – most often infections- which relate to retinal capillary damage and the ensuing reparative process. No biochemical or microbiological signs of infection were present in blood and liquor. MRI of the brain showed an abnormal diffusion signal with increased apparent diffusion coefficient and little blood around the tentorium. The knowledge of the pathogenesis of PDE is still limited. The presence of Roth spots is suggestive for a pathogenic mechanism of vasogenic damage in PDE. PMID:22688935

Comparative biology of the neuronal ceroid-lipofuscinoses (NCL): an overview.

PubMed

Jolly, R D

1995-06-05

Multiple forms of ceroid-lipofuscinosis occur in human beings and animals. They are characterized by brain and retinal atrophy associated with selective necrosis of neurons. This neurodegenerative disease appears associated with the disease process rather than storage of fluorescent lipopigment per se, and there is now growing evidence that pathogenesis may involve mitochondria rather than a primary defect of lysosomal catabolism. Of the forms of ceroid-lipofuscinosis studied, most but not all reflect accumulation of subunit c of mitochondrial ATP synthase. If there is a common denominator between all forms other than the presence of fluorescent lipopigment, then it may be the accumulation of hydrophobic protein. Analogous diseases in animals can be expected to reflect the same spectrum of biochemical changes, and they warrant in-depth study to help understand the pathogenesis and heterogeneity of the group.

Indolethylamine-N-methyltransferase Polymorphisms: Genetic and Biochemical Approaches for Study of Endogenous N,N,-dimethyltryptamine.

PubMed

Dean, Jon G

2018-01-01

N,N -dimethyltryptamine (DMT) is a powerful serotonergic psychedelic whose exogenous administration elicits striking psychedelic effects in humans. Studies have identified DMT and analogous compounds (e.g., 5-hydroxy-DMT, 5-methoxy-DMT) alongside of an enzyme capable of synthesizing DMT endogenously from tryptamine, indolethylamine- N -methyltransferase (INMT), in human and several other mammalian tissues. Subsequently, multiple hypotheses for the physiological role of endogenous DMT have emerged, from proposed immunomodulatory functions to an emphasis on the overlap between the mental states generated by exogenous DMT and naturally occurring altered states of consciousness; e.g., schizophrenia. However, no clear relationship between endogenous DMT and naturally occurring altered states of consciousness has yet been established from in vivo assays of DMT in bodily fluids. The advent of genetic screening has afforded the capability to link alterations in the sequence of specific genes to behavioral and molecular phenotypes via expression of identified single nucleotide polymorphisms (SNPs) in cell and animal models. As SNPs in INMT may impact endogenous DMT synthesis and levels via changes in INMT expression and/or INMT structure and function, these combined genetic and biochemical approaches circumvent the limitations of assaying DMT in bodily fluids and may augment data from prior in vitro and in vivo work. Therefore, all reported SNPs in INMT were amassed from genetic and biochemical literature and genomic databases to consolidate a blueprint for future studies aimed at elucidating whether DMT plays a physiological role.

Indolethylamine-N-methyltransferase Polymorphisms: Genetic and Biochemical Approaches for Study of Endogenous N,N,-dimethyltryptamine

PubMed Central

Dean, Jon G.

2018-01-01

N,N-dimethyltryptamine (DMT) is a powerful serotonergic psychedelic whose exogenous administration elicits striking psychedelic effects in humans. Studies have identified DMT and analogous compounds (e.g., 5-hydroxy-DMT, 5-methoxy-DMT) alongside of an enzyme capable of synthesizing DMT endogenously from tryptamine, indolethylamine-N-methyltransferase (INMT), in human and several other mammalian tissues. Subsequently, multiple hypotheses for the physiological role of endogenous DMT have emerged, from proposed immunomodulatory functions to an emphasis on the overlap between the mental states generated by exogenous DMT and naturally occurring altered states of consciousness; e.g., schizophrenia. However, no clear relationship between endogenous DMT and naturally occurring altered states of consciousness has yet been established from in vivo assays of DMT in bodily fluids. The advent of genetic screening has afforded the capability to link alterations in the sequence of specific genes to behavioral and molecular phenotypes via expression of identified single nucleotide polymorphisms (SNPs) in cell and animal models. As SNPs in INMT may impact endogenous DMT synthesis and levels via changes in INMT expression and/or INMT structure and function, these combined genetic and biochemical approaches circumvent the limitations of assaying DMT in bodily fluids and may augment data from prior in vitro and in vivo work. Therefore, all reported SNPs in INMT were amassed from genetic and biochemical literature and genomic databases to consolidate a blueprint for future studies aimed at elucidating whether DMT plays a physiological role. PMID:29740267

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

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.

Refeeding Syndrome: A Literature Review

PubMed Central

Khan, L. U. R.; Ahmed, J.; Khan, S.; MacFie, J.

2011-01-01

Refeeding syndrome (RFS) describes the biochemical changes, clinical manifestations, and complications that can occur as a consequence of feeding a malnourished catabolic individual. RFS has been recognised in the literature for over fifty years and can result in serious harm and death. Crude estimates of incidence, morbidity, and mortality are available for specific populations. RFS can occur in any individual but more commonly occurs in at-risk populations. Increased awareness amongst healthcare professionals is likely to reduce morbidity and mortality. This review examines the physiology of RFS and describes the clinical manifestations. A management strategy is described. The importance of a multidisciplinary approach is emphasized. PMID:20886063

Stability of Intercellular Exchange of Biochemical Substances Affected by Variability of Environmental Parameters

NASA Astrophysics Data System (ADS)

Mihailović, Dragutin T.; Budinčević, Mirko; Balaž, Igor; Mihailović, Anja

Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters at almost all stages of the process. Since communication is one of essential processes for functioning of living systems it is of interest to investigate conditions for its stability. Using previously developed simplified model of bacterial communication in a form of coupled difference logistic equations we investigate stability of exchange of signaling molecules under variability of internal and external parameters.

Method and apparatus for energy efficient self-aeration in chemical, biochemical, and wastewater treatment processes

DOEpatents

Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR

2002-05-28

The present invention is a pulse spilling self-aerator (PSSA) that has the potential to greatly lower the installation, operation, and maintenance cost associated with aerating and mixing aqueous solutions. Currently, large quantities of low-pressure air are required in aeration systems to support many biochemical production processes and wastewater treatment plants. Oxygen is traditionally supplied and mixed by a compressor or blower and a mechanical agitator. These systems have high-energy requirements and high installation and maintenance costs. The PSSA provides a mixing and aeration capability that can increase operational efficiency and reduce overall cost.

[Healing process of claw lesions in dairy cows in alpine mountain pastures].

PubMed

Lischer, C J; Wehrle, M; Geyer, H; Lutz, B; Ossent, P

2000-07-01

The field study investigated severity, localisation and incidence of claw lesions of dairy cows and their healing process during a period of three months on selected mountain pastures in the central part of Switzerland. In 60 cows, which were at least 120 days in their lactation, the healing process was compared with the biochemical profiles. In 141 cows 197 claw lesions were recorded. Diagnosed were only sole ulcers (38%) and white line lesions (62%). In the first and second half of the summer term, the number of claw lesions was equal, although more severe lesions occurred mainly during the second half (89%). The lesions were treated surgically and the affected claw was elevated on a wood block or a plastic shoe. Average time for formation of a close layer of horn was 14 days. A delayed healing process was observed in dairy cows with an milk yield over 5500 kg per lactation, as well as in the second half of the summer term. Cows with a delayed healing process had significantly higher concentrations of free fatty acids and beta-hydroxybutyrate, and higher plasma enzyme activities for AST than cows with adequate healing process. This indicates that cows with a relatively high milk production touch upon the limits of their physical capacity under harder conditions on alpine pastures, which may affect also the healing process of claw lesions.

40 CFR 405.41 - Specialized definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... STANDARDS DAIRY PRODUCTS PROCESSING POINT SOURCE CATEGORY Butter Subcategory § 405.41 Specialized... term “BOD5 input” shall mean the biochemical oxygen demand of the materials entered into process. It...

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system.

PubMed

Lopes, Ana R; Bello, Diana; Prieto-Fernández, Ángeles; Trasar-Cepeda, Carmen; Manaia, Célia M; Nunes, Olga C

2015-08-01

The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.

Alzheimer disease and cognitive impairment associated with diabetes mellitus type 2: associations and a hypothesis.

PubMed

Domínguez, R O; Pagano, M A; Marschoff, E R; González, S E; Repetto, M G; Serra, J A

2014-01-01

Epidemiological studies have demonstrated that patients with diabetes mellitus have an increased risk of developing Alzheimer disease, but the relationship between the 2 entities is not clear. Both diseases exhibit similar metabolic abnormalities: disordered glucose metabolism, abnormal insulin receptor signalling and insulin resistance, oxidative stress, and structural abnormalities in proteins and β-amyloid deposits. Different hypotheses have emerged from experimental work in the last two decades. One of the most comprehensive relates the microvascular damage in diabetic polyneuritis with the central nervous system changes occurring in Alzheimer disease. Another hypothesis considers that cognitive impairment in both diabetes and Alzheimer disease is linked to a state of systemic oxidative stress. Recently, attenuation of cognitive impairment and normalisation of values in biochemical markers for oxidative stress were found in patients with Alzheimer disease and concomitant diabetes. Antidiabetic drugs may have a beneficial effect on glycolysis and its end products, and on other metabolic alterations. Diabetic patients are at increased risk for developing Alzheimer disease, but paradoxically, their biochemical alterations and cognitive impairment are less pronounced than in groups of dementia patients without diabetes. A deeper understanding of interactions between the pathogenic processes of both entities may lead to new therapeutic strategies that would slow or halt the progression of impairment. Copyright © 2013 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

Exogenously applied zinc and copper mitigate salinity effect in maize (Zea mays L.) by improving key physiological and biochemical attributes.

PubMed

Iqbal, Muhammad Naveed; Rasheed, Rizwan; Ashraf, Muhammad Yasin; Ashraf, Muhammad Arslan; Hussain, Iqbal

2018-06-07

Zinc or copper deficiency and salinity are known soil problems and often occur simultaneously in agriculture soils. Plants undergo various changes in physiological and biochemical processes to respond to high salt in the growing medium. There is lack of information on the relation of exogenous application of Zn and Cu with important salinity tolerance mechanisms in plants. Therefore, the present study was conducted to determine the effect of foliar Zn and Cu on two maize cultivars (salt-tolerant cv. Yousafwala Hybrid and salt-sensitive cv. Hybrid 1898). Salinity caused a significant reduction in water and turgor potentials, stomatal conductance, and transpiration and photosynthetic rate, while increase in glycine betaine, proline, total soluble sugars, and total free amino acids was evident in plants under saline regimes. Furthermore, there was significant decline in P, N, Ca, K, Mn, Fe, Zn, and Cu and increase in Na and Cl contents in plants fed with NaCl salinity. Nitrate reductase activity was lower in salt-stressed plants. However, foliar application of Zn and Cu circumvented salinity effect on water relations, photosynthesis, and nutrition and this was attributed to the better antioxidant system and enhanced accumulation of glycine betaine, proline, total free amino acids, and sugars. The results of the present study suggested that Zn application was superior to Cu for mediating plant defense responses under salinity.

Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice.

PubMed

Lakatos, Anita; Goldberg, Natalie R S; Blurton-Jones, Mathew

2017-03-10

We previously demonstrated that transplantation of murine neural stem cells (NSCs) can improve motor and cognitive function in a transgenic model of Dementia with Lewy Bodies (DLB). These benefits occurred without changes in human α-synuclein pathology and were mediated in part by stem cell-induced elevation of brain-derived neurotrophic factor (BDNF). However, instrastriatal NSC transplantation likely alters the brain microenvironment via multiple mechanisms that may synergize to promote cognitive and motor recovery. The underlying neurobiology that mediates such restoration no doubt involves numerous genes acting in concert to modulate signaling within and between host brain cells and transplanted NSCs. In order to identify functionally connected gene networks and additional mechanisms that may contribute to stem cell-induced benefits, we performed weighted gene co-expression network analysis (WGCNA) on striatal tissue isolated from NSC- and vehicle-injected wild-type and DLB mice. Combining continuous behavioral and biochemical data with genome wide expression via network analysis proved to be a powerful approach; revealing significant alterations in immune response, neurotransmission, and mitochondria function. Taken together, these data shed further light on the gene network and biological processes that underlie the therapeutic effects of NSC transplantation on α-synuclein induced cognitive and motor impairments, thereby highlighting additional therapeutic targets for synucleinopathies.

Raman Spectroscopic Analysis of Biochemical Changes in Individual Triglyceride-Rich Lipoproteins in the Pre- and Postprandial State

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

Chan, J; Motton, D; Rutledge, J

2004-09-13

Individual triglyceride-rich lipoprotein (TGRL) particles derived from human volunteers are non-destructively analyzed by laser tweezers Raman microspectroscopy and information on their composition and distribution is obtained. The Raman signature of single optically trapped very low-density lipoproteins (VLDL), a subclass of TGRL, which play an important role in cardiovascular disease, exhibits distinct peaks associated with molecular vibrations of fatty acids, proteins, lipids, and structural rearrangements of lipids. Our analysis of pre- and postprandial VLDL exhibits the signature of biochemical changes in individual lipoprotein particles following the consumption of meals. Interaction of VLDL with endothelium leads to the breakdown of complex triacylglycerolsmore » and the formation of a highly ordered core of free saturated fatty acids in the particle. A particle distribution analysis reveals trends in the degree to which this process has occurred in particles at different times during the postprandial period. Differences in particle distributions based on the different ratios of polyunsaturated to saturated fats in the consumed meals are also easily discerned. Individual lipoprotein particles hydrolyzed in-vitro through addition of lipoprotein lipase (LpL) exhibit strikingly similar changes in their Raman spectra. These results demonstrate the feasibility of monitoring the dynamics of lipid metabolism of individual TGRL particles as they interact with LpL in the endothelial cell wall using Raman spectroscopy.« less

40 CFR 405.31 - Specialized definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... STANDARDS DAIRY PRODUCTS PROCESSING POINT SOURCE CATEGORY Cultured Products Subcategory § 405.31 Specialized... term “BOD5 input” shall mean the biochemical oxygen demand of the materials entered into process. It...

40 CFR 405.91 - Specialized definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... STANDARDS DAIRY PRODUCTS PROCESSING POINT SOURCE CATEGORY Condensed Milk Subcategory § 405.91 Specialized... term “BOD5 input” shall mean the biochemical oxygen demand of the materials entered into process. It...

40 CFR 405.21 - Specialized definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... STANDARDS DAIRY PRODUCTS PROCESSING POINT SOURCE CATEGORY Fluid Products Subcategory § 405.21 Specialized... term “BOD5 input” shall mean the biochemical oxygen demand of the materials entered into process. It...

Run-length encoding graphic rules, biochemically editable designs and steganographical numeric data embedment for DNA-based cryptographical coding system.

PubMed

Kawano, Tomonori

2013-03-01

There have been a wide variety of approaches for handling the pieces of DNA as the "unplugged" tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based digital barcodes, water marks and cryptography. In the present article, novel designs of artificial genes as the media for storing the digitally compressed data for images are proposed for bio-computing purpose while natural genes principally encode for proteins. Furthermore, the proposed system allows cryptographical application of DNA through biochemically editable designs with capacity for steganographical numeric data embedment. As a model case of image-coding DNA technique application, numerically and biochemically combined protocols are employed for ciphering the given "passwords" and/or secret numbers using DNA sequences. The "passwords" of interest were decomposed into single letters and translated into the font image coded on the separate DNA chains with both the coding regions in which the images are encoded based on the novel run-length encoding rule, and the non-coding regions designed for biochemical editing and the remodeling processes revealing the hidden orientation of letters composing the original "passwords." The latter processes require the molecular biological tools for digestion and ligation of the fragmented DNA molecules targeting at the polymerase chain reaction-engineered termini of the chains. Lastly, additional protocols for steganographical overwriting of the numeric data of interests over the image-coding DNA are also discussed.

Computational study of noise in a large signal transduction network.

PubMed

Intosalmi, Jukka; Manninen, Tiina; Ruohonen, Keijo; Linne, Marja-Leena

2011-06-21

Biochemical systems are inherently noisy due to the discrete reaction events that occur in a random manner. Although noise is often perceived as a disturbing factor, the system might actually benefit from it. In order to understand the role of noise better, its quality must be studied in a quantitative manner. Computational analysis and modeling play an essential role in this demanding endeavor. We implemented a large nonlinear signal transduction network combining protein kinase C, mitogen-activated protein kinase, phospholipase A2, and β isoform of phospholipase C networks. We simulated the network in 300 different cellular volumes using the exact Gillespie stochastic simulation algorithm and analyzed the results in both the time and frequency domain. In order to perform simulations in a reasonable time, we used modern parallel computing techniques. The analysis revealed that time and frequency domain characteristics depend on the system volume. The simulation results also indicated that there are several kinds of noise processes in the network, all of them representing different kinds of low-frequency fluctuations. In the simulations, the power of noise decreased on all frequencies when the system volume was increased. We concluded that basic frequency domain techniques can be applied to the analysis of simulation results produced by the Gillespie stochastic simulation algorithm. This approach is suited not only to the study of fluctuations but also to the study of pure noise processes. Noise seems to have an important role in biochemical systems and its properties can be numerically studied by simulating the reacting system in different cellular volumes. Parallel computing techniques make it possible to run massive simulations in hundreds of volumes and, as a result, accurate statistics can be obtained from computational studies. © 2011 Intosalmi et al; licensee BioMed Central Ltd.

Biochemical characterization of embryogenic calli of Vanilla planifolia in response to two years of thidiazuron treatment.

PubMed

Kodja, Hippolyte; Noirot, Michel; Khoyratty, Shahnoo S; Limbada, Hafsah; Verpoorte, Robert; Palama, Tony Lionel

2015-11-01

Vanilla planifolia embryogenic calli were cultured for two years on a medium containing thidiazuron (TDZ). Due to the presence of TDZ, these calli were under permanent chemical treatment and the differentiation of adventitious shoots from protocorm-like-bodies (PLBs) was blocked. When embryogenic calli were transferred onto a medium without TDZ, shoot organogenesis and plantlet regeneration occurred. To gain better knowledge about the biochemical and molecular processes involved in the morphoregulatory role of TDZ, hormonal and metabolomic analyses were performed. Our results indicate that in the presence of TDZ, embryogenic calli contained a high amount of abscisic acid (ABA) essentially metabolized into abscisic acid glucosyl ester (ABAGE) and phaseic acid (PA), which was the most abundant. When transferred onto a medium without TDZ, shoot regeneration and development take place in four stages that include: embryogenic calli growth, differentiation of PLBs from meristmatic cells zones (MCZ), shoot organogenesis from PLBs and the elongation of well-formed shoots. From a hormonal perspective, the significant reduction in ABA metabolism and its readjustment in the ABAGE pathway triggered PLBs formation. However, this first morphogenesis was stimulated by a strong reduction in IAA metabolism. The organogenesis of PLBs into shoots is associated with an increase in ABA catabolism and a gradual shift in cellular metabolism towards shoot differentiation. Thus, the initiation of the elongation process in shoots is correlated with an alteration in metabolite composition, including an increase in energy reserves (sucrose/starch) and a rapid decrease in alanine content. Our data highlighted the relationship between endogenous hormone signalling, carbohydrate metabolism and shoot organogenesis in Orchid plants. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Low temperature and UV curable sol-gel coatings for long lasting optical fiber biosensors

NASA Astrophysics Data System (ADS)

Otaduy, D.; Villar, A.; Gomez-Herrero, E.; Goitandia, A. M.; Gorritxategi, E.; Quintana, I.

2010-04-01

The use of optical fibers as sensing element is increasing in clinical, pharmaceutical and industrial applications. Excellent light delivery, long interaction length, low cost and ability not only to excite the target molecules but also to capture the emitted light from the targets are the hallmarks of optical fiber as biosensors. In biosensors based on fiber optics the interaction with the analyte can occur within an element of the optical fiber. One of the techniques for this kind of biosensors is to remove the fiber optic cladding and substitute it for biological coatings that will interact with the parameter to sensorize. The deposition of these layers can be made by sol-gel technology. The sol-gel technology is being increasingly used mainly due to the high versatility to tailor their optical features. Incorporation of suitable chemical and biochemical sensing agents have allowed determining pH, gases, and biochemical species, among others. Nonetheless, the relatively high processing temperatures and short lifetime values mean severe drawbacks for a successful exploitation of sol-gel based coated optical fibres. With regard to the latter, herein we present the design, preparation and characterization of novel sol-gel coated optical fibres. Low temperature and UV curable coating formulations were optimized to achieve a good adhesion and optical performance. The UV photopolymerizable formulation was comprised by glycidoxypropyltrimethoxysilane (GLYMO), Tetraethylorthosilicate (TEOS) and an initiator. While the thermoset coating was prepared by using 3-aminopropyltrimethoxysilane, GLYMO, and TEOS as main reagents. Both curable sol-gel coated fibres were analysed by FTIR, SEM and optical characterization. Furthermore, in the present work a new technique for silica cladding removal has been developed by ultra-short pulses laser processing, getting good dimensional accuracy and surface integrity.

How Do Fruits Ripen?

ERIC Educational Resources Information Center

Sargent, Steven A.

2005-01-01

A fruit is alive, and for it to ripen normally, many biochemical reactions must occur in a proper order. After pollination, proper nutrition, growing conditions, and certain plant hormones cause the fruit to develop and grow to proper size. During this time, fruits store energy in the form of starch and sugars, called photosynthates because they…

EVALUATION OF ALTERED SENSITIVITY OF OLDER ADULTS TO ENVIRONMENTAL AGENTS USING PHYSIOLOGICALLY BASED PHARMACOKINETIC (PBPK) MODELING

EPA Science Inventory

The population of older Americans is increasing due to the aging of the Baby Boomers as well as an increase in the average life span. A number of physiological and biochemical changes occur during aging that could influence the relationship between exposure, dose, and response to...

G6PD deficiency from lyonization after hematopoietic stem cell transplantation from female heterozygous donors.

PubMed

Au, W-Y; Pang, A; Lam, K K Y; Song, Y-Q; Lee, W-M; So, J C C; Kwong, Y-L

2007-10-01

To determine whether during hematopoietic stem cell transplantation (HSCT), X-chromosome inactivation (lyonization) of donor HSC might change after engraftment in recipients, the glucose-6-phosphate dehydrogenase (G6PD) gene of 180 female donors was genotyped by PCR/allele-specific primer extension, and MALDI-TOF mass spectrometry/Sequenom MassARRAY analysis. X-inactivation was determined by semiquantitative PCR for the HUMARA gene before/after HpaII digestion. X-inactivation was preserved in most cases post-HSCT, although altered skewing of lyonization might occur to either of the X-chromosomes. Among pre-HSCT clinicopathologic parameters analyzed, only recipient gender significantly affected skewing. Seven donors with normal G6PD biochemically but heterozygous for G6PD mutants were identified. Owing to lyonization changes, some donor-recipient pairs showed significantly different G6PD levels. In one donor-recipient pair, extreme lyonization affecting the wild-type G6PD allele occurred, causing biochemical G6PD deficiency in the recipient. In HSCT from asymptomatic female donors heterozygous for X-linked recessive disorders, altered lyonization might cause clinical diseases in the recipients.

Algebraic properties of automata associated to Petri nets and applications to computation in biological systems.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Biochemical and genetic regulatory networks are often modeled by Petri nets. We study the algebraic structure of the computations carried out by Petri nets from the viewpoint of algebraic automata theory. Petri nets comprise a formalized graphical modeling language, often used to describe computation occurring within biochemical and genetic regulatory networks, but the semantics may be interpreted in different ways in the realm of automata. Therefore, there are several different ways to turn a Petri net into a state-transition automaton. Here, we systematically investigate different conversion methods and describe cases where they may yield radically different algebraic structures. We focus on the existence of group components of the corresponding transformation semigroups, as these reflect symmetries of the computation occurring within the biological system under study. Results are illustrated by applications to the Petri net modelling of intermediary metabolism. Petri nets with inhibition are shown to be computationally rich, regardless of the particular interpretation method. Along these lines we provide a mathematical argument suggesting a reason for the apparent all-pervasiveness of inhibitory connections in living systems.

Biochemical quality of the pharmaceutically licensed plasma OctaplasLG after implementation of a novel prion protein (PrPSc) removal technology and reduction of the solvent/detergent (S/D) process time.

PubMed

Heger, A; Svae, T-E; Neisser-Svae, A; Jordan, S; Behizad, M; Römisch, J

2009-10-01

A new chromatographic step for the selective binding of pathological prion proteins (PrP(Sc)) to an affinity ligand, developed and optimized for PrP(Sc) capture and attached to synthetic resin particles (PRDT, USA; ProMetic BioSciences Ltd, Isle of Man, UK) was implemented into the manufacturing process of the solvent/detergent (S/D) treated biopharmaceutical quality plasma Octaplas. Pilot batches of Octaplas with the implemented chromatographic step [labelled as OctaplasLG (ligand gel)] were manufactured by Octapharma PPGmbH, Vienna, Austria. The biochemical quality was compared directly after manufacturing as well as after 18 months storage. All samples were tested on global coagulation parameters, fibrinogen levels, activities of coagulation factors and protease inhibitors, ADAMTS13 levels, as well as markers of activated coagulation and fibrinolysis. In addition, von Willebrand factor multimeric analysis was performed. The incorporation of this novel chromatography into the large-scale routine manufacturing process was shown to be technically feasible and the performance of the column was assessed to be excellent. The biochemical studies showed that Octaplas and OctaplasLG produced without and with the new column, respectively, demonstrate an identical biochemical quality. OctaplasLG remained stable over a period of 18 months stored frozen. A parallel reduction of the S/D virus inactivation step from 4-4.5 to 1-1.5 h led to significantly higher activities of plasmin inhibitor. The studies confirmed that the affinity ligand chromatography under the developed conditions can be introduced into the Octaplas manufacturing process, as a mean to reduce potentially present PrP(Sc), without hampering the proven quality of this product.

Enzyme activities by indicator of quality in organic soil

NASA Astrophysics Data System (ADS)

Raigon Jiménez, Mo; Fita, Ana Delores; Rodriguez Burruezo, Adrián

2016-04-01

The analytical determination of biochemical parameters, as soil enzyme activities and those related to the microbial biomass is growing importance by biological indicator in soil science studies. The metabolic activity in soil is responsible of important processes such as mineralization and humification of organic matter. These biological reactions will affect other key processes involved with elements like carbon, nitrogen and phosphorus , and all transformations related in soil microbial biomass. The determination of biochemical parameters is useful in studies carried out on organic soil where microbial processes that are key to their conservation can be analyzed through parameters of the metabolic activity of these soils. The main objective of this work is to apply analytical methodologies of enzyme activities in soil collections of different physicochemical characteristics. There have been selective sampling of natural soils, organic farming soils, conventional farming soils and urban soils. The soils have been properly identified conserved at 4 ° C until analysis. The enzyme activities determinations have been: catalase, urease, cellulase, dehydrogenase and alkaline phosphatase, which bring together a representative group of biological transformations that occur in the soil environment. The results indicate that for natural and agronomic soil collections, the values of the enzymatic activities are within the ranges established for forestry and agricultural soils. Organic soils are generally higher level of enzymatic, regardless activity of the enzyme involved. Soil near an urban area, levels of activities have been significantly reduced. The vegetation cover applied to organic soils, results in greater enzymatic activity. So the quality of these soils, defined as the ability to maintain their biological productivity is increased with the use of cover crops, whether or spontaneous species. The practice of cover based on legumes could be used as an ideal choice for the recovery of degraded soils, because these soils have the highest levels of enzymatic activities.

The rapid yellowing of spruce at a mountain site in the Central Black Forest (Germany). Combined effects of Mg deficiency and ozone on biochemical, physiological and structural properties of the chloroplasts.

PubMed

Siefermann-Harms, Dorothea; Boxler-Baldoma, Carmen; von Wilpert, Klaus; Heumann, Hans-Günther

2004-04-01

Biochemical, physiological and ultrastructural changes of the chloroplasts were examined in the course of the rapid yellowing process of spruce (Picea abies (L.) Karst.) at a Mg-deficient and ozone polluted mountain site (Schöllkopf mountain, Central Black Forest, Germany, 840 m a.s.l.). While at an early stage of yellowing the chlorophyll (Chl) content of the needles decreased slowly, significant changes occurred in the chloroplasts: The lability of the light-harvesting Chl a/b protein complex LHC II increased; the thylakoid cross-sectional area of chloroplasts in the outer mesophyll of the needles decreased, and their Chl fluorescence showed typical changes like the decrease of Fv/Fm and the increase of the photoinhibitory Fv quenching. Later on, the Chl content decreased rapidly, the changes in the chloroplasts continued and the needles turned yellow. Lutein and the pigments of the xanthophyll cycle were enhanced in relation to Chl a. Light and dark reactions of the xanthophyll cycle were highly active indicating efficient proton pumping and NADPH formation. The ratio of nonappressed to appressed thylakoid membranes increased with decreasing Fv/Fm suggesting that structural and fluorescence properties of the chloroplasts were related. The response of the needles to defined shading and improved Mg supply was also examined. The combined effects of strong sun light, low levels of non-Chl-bound Mg (Mg(free)) and ozone concentrations exceeding 80 microg m(-3) are shown to be necessary to induce the rapid yellowing process. For needles with Mg(free) < 0.12 mg g(-1) needle dry matter, the lability of the LHC II was correlated with the ozone concentration suggesting that the destabilization of the LHC II plays a central role in the rapid yellowing process.

Efficacy of Acorus calamus on collagen maturation on full thickness cutaneous wounds in rats

PubMed Central

Ponrasu, Thangavel; Madhukumar, Karuppanan Natarajan; Ganeshkumar, Moorthy; Iyappan, Kuttalam; Sangeethapriya, Vilvanathan; Gayathri, Vinaya Subramani; Suguna, Lonchin

2014-01-01

Background: The rhizomes of Acorus calamus and their essential oil are widely used in the flavoring industry and production of alcoholic beverages in Europe. Recent reports have confirmed the presence of several pharmacological components in the rhizomes of A. calamus. Objective: The objective of this study was to find out the efficacy of topical administration of ethanolic extract of A. calamus on dermal wound healing in rats. Wound healing is a natural process occurring in living organisms, which results in a complete or partial remodeling of injured tissue and ultimately progresses to the formation of a fibrous scar. Several natural products have been reported to augment the wound healing process. Materials and Methods: An ethanolic extract of A. calamus was prepared and its wound-healing efficacy was studied. An excision wound was made on the back of the rat and 200 μL (40 mg/kg body weight) of the A. calamus extract was applied topically once daily for the treated wounds. The control wounds were treated with 200 μL of phosphate buffered saline. Results: The granulation tissues formed were removed at 4, 8 and 12 days and biochemical parameters such as deoxyribonucleic acid, total protein, total collagen, hexosamine and uronic acids were measured. The amount of type I/III collagen formed in control and treated wound tissues was evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The epithelialization time, tensile strength and histological examination of the wounds were also studied. Biochemical analyses of the granulation tissues revealed a significant increase in collagen, hexosamine and uronic acid when compared with the control. The tensile strength of extract treated wounds was found to increase by 112%. A significant reduction in lipid peroxide levels suggested that A. calamus possesses antioxidant components. Conclusions: The results strongly confirm the beneficial effects of A. calamus in augmenting the wound healing process. PMID:24991107

Biochemical study of leaf browning in minimally processed leaves of lettuce (Lactuca sativa L. var. acephala).

PubMed

Degl'Innocenti, E; Guidi, L; Pardossi, A; Tognoni, F

2005-12-28

A series of biochemical parameters, including the concentration of total ascorbic acid (ASA(tot)) and the activities of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), and peroxidases (PODs), was investigated during cold storage (72 h at 4 degrees C in the dark) in fresh-cut (minimally processed) leaves of two lettuce (Lactuca sativa L. var. acephala) cultivars differing in the susceptibility to tissue browning: Green Salade Bowl (GSB), susceptible, and Red Salade Bowl (RSB), resistant. The two cultivars showed differences also at the biochemical level. The content in ASA(tot) increased in RSB, as a consequence of increased DHA concentration; conversely, ASA(tot) diminished in GSB, in which ASA was not detectable after 72 h of storage, thus suggesting a disappearance of ascorbate (both ASA and DHA) into nonactive forms. The antioxidant capacity (as determined by using FRAP analysis) decreased significantly during storage in RSB, while a strong increase was observed in GSB. PAL activity increased soon after processing reaching a maximum by 3 h, then it declined to a relatively constant value in RSB, while in GSB it showed a tendency to decrease in the first few hours from harvest and processing. POD activity, at least for chlorogenic acid, increased significantly during storage only in GSB.

A model for traumatic brain injury using laser induced shockwaves

NASA Astrophysics Data System (ADS)

Selfridge, A.; Preece, D.; Gomez, V.; Shi, L. Z.; Berns, M. W.

2015-08-01

Traumatic brain injury (TBI) represents a major treatment challenge in both civilian and military medicine; on the cellular level, its mechanisms are poorly understood. As a method to study the dysfunctional repair mechanisms following injury, laser induced shock waves (LIS) are a useful way to create highly precise, well characterized mechanical forces. We present a simple model for TBI using laser induced shock waves as a model for damage. Our objective is to develop an understanding of the processes responsible for neuronal death, the ways in which we can manipulate these processes to improve cell survival and repair, and the importance of these processes at different levels of biological organization. The physics of shock wave creation has been modeled and can be used to calculate forces acting on individual neurons. By ensuring that the impulse is in the same regime as that occurring in practical TBI, the LIS model can ensure that in vitro conditions and damage are similar to those experienced in TBI. This model will allow for the study of the biochemical response of neurons to mechanical stresses, and can be combined with microfluidic systems for cell growth in order to better isolate areas of damage.

Multi-Faceted Functions of Secretory IgA at Mucosal Surfaces

PubMed Central

Corthésy, Blaise

2013-01-01

Secretory IgA (SIgA) plays an important role in the protection and homeostatic regulation of intestinal, respiratory, and urogenital mucosal epithelia separating the outside environment from the inside of the body. This primary function of SIgA is referred to as immune exclusion, a process that limits the access of numerous microorganisms and mucosal antigens to these thin and vulnerable mucosal barriers. SIgA has been shown to be involved in avoiding opportunistic pathogens to enter and disseminate in the systemic compartment, as well as tightly controlling the necessary symbiotic relationship existing between commensals and the host. Clearance by peristalsis appears thus as one of the numerous mechanisms whereby SIgA fulfills its function at mucosal surfaces. Sampling of antigen-SIgA complexes by microfold (M) cells, intimate contact occurring with Peyer’s patch dendritic cells (DC), down-regulation of inflammatory processes, modulation of epithelial, and DC responsiveness are some of the recently identified processes to which the contribution of SIgA has been underscored. This review aims at presenting, with emphasis at the biochemical level, how the molecular complexity of SIgA can serve these multiple and non-redundant modes of action. PMID:23874333

Cyanogenesis in Cassava1

PubMed Central

White, Wanda L.B.; Arias-Garzon, Diana I.; McMahon, Jennifer M.; Sayre, Richard T.

1998-01-01

In the cyanogenic crop cassava (Manihot esculenta, Crantz), the final step in cyanide production is the conversion of acetone cyanohydrin, the deglycosylation product of linamarin, to cyanide plus acetone. This process occurs spontaneously at pH greater than 5.0 or enzymatically and is catalyzed by hydroxynitrile lyase (HNL). Recently, it has been demonstrated that acetone cyanohydrin is present in poorly processed cassava root food products. Since it has generally been assumed that HNL is present in all cassava tissues, we reinvestigated the enzymatic properties and tissue-specific distribution of HNL in cassava. We report the development of a rapid two-step purification protocol for cassava HNL, which yields an enzyme that is catalytically more efficient than previously reported (Hughes, J., Carvalho, F., and Hughes, M. [1994] Arch Biochem Biophys 311: 496–502). Analyses of the distribution of HNL activity and protein indicate that the accumulation of acetone cyanohydrin in roots is due to the absence of HNL, not to inhibition of the enzyme. Furthermore, the absence of HNL in roots and stems is associated with very low steady-state HNL transcript levels. It is proposed that the lack of HNL in cassava roots accounts for the high acetone cyanohydrin levels in poorly processed cassava food products. PMID:9536038

Removal of organic impurities in waste glycerol from biodiesel production process through the acidification and coagulation processes.

PubMed

Xie, Qiao-Guang; Taweepreda, Wirach; Musikavong, Charongpun; Suksaroj, Chaisri

2012-01-01

Treatment of waste glycerol, a by-product of the biodiesel production process, can reduce water pollution and bring significant economic benefits for biodiesel facilities. In the present study, hydrochloric acid (HCl) was used as acidification to convert soaps into salts and free fatty acids which were recovered after treatment. The pH value, dosages of polyaluminum chloride (PACl) and dosage of polyacrylamide (PAM) were considered to be the factors that can influence coagulation efficiency. The pH value of waste glycerol was adjusted to a pH range of 3-9. The PACl and PAM added were in the range of 1-6 g/L and 0.005-0.07 g/L. The results showed best coagulation efficiency occurs at pH 4 when dosage of PACl and PAM were 2 and 0.01 g/L. The removal of chemical oxygen demand (COD), biochemical oxygen demand (BOD(5)), total suspended solids (TSS) and soaps were 80, 68, 97 and 100%, respectively. The compositions of organic matters in the treated waste glycerol were glycerol (288 g/L), methanol (3.8 g/L), and other impurities (0.3 g/L).

Differences in irradiation susceptibility and turnover between mucosal and connective tissue-type mast cells of mice

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

Fukuzumi, T.; Waki, N.; Kanakura, Y.

Although precursors of mast cells are derived from the bone marrow, phenotypes of mast cells are influenced by the tissues in which final differentiation occurs. Connective tissue-type mast cells (CTMC) and mucosal mast cells (MMC) are different in morphological, biochemical, immunological, and functional criteria. The purpose of the present study was to obtain information about the differentiation process of MMC. First, we compared changes in irradiation susceptibility in mice during the differentiation process of CTMC and MMC. The decrease in irradiation susceptibility was remarkable in the CTMC differentiation process, but it was moderate in that of MMC. Some morphologically identifiablemore » CTMC in the peritoneal cavity had proliferative potential and were highly radioresistant, whereas such a radioresistant population of MMC was not detectable in the gastric mucosa. Second, we estimated the turnover of CTMC and MMC by determining the proportion of mast cells that were labeled with continuously administered bromodeoxyuridine. The turnover of MMC was significantly faster than that of CTMC. The absence of the radioresistant mast cell population in the gastric mucosa appeared to be related to the short life span of MMC.« less

Polyphenols in foods are more complex than often thought.

PubMed

Cheynier, Véronique

2005-01-01

Dietary polyphenols show a great diversity of structures, ranging from rather simple molecules (monomers and oligomers) to polymers. Higher-molecular-weight structures (with molecular weights of > 500) are usually designated as tannins, which refers to their ability to interact with proteins. Among them, condensed tannins (proanthocyanidins) are particularly important because of their wide distribution in plants and their contributions to major food qualities. All phenolic compounds are highly unstable and rapidly transformed into various reaction products when the plant cells are damaged (for instance, during food processing), thus adding to the complexity of dietary polyphenol composition. The polyphenol composition of plant-derived foods and beverages depends on that of the raw material used but also on the extraction process and subsequent biochemical and chemical reactions of plant polyphenols. The occurrence of specific tannin-like compounds (ie, thearubigins and theaflavins) arising from enzymatic oxidation is well documented in black tea. Various chemical reactions involving anthocyanins and/or flavanols have been demonstrated to occur during red wine aging. Current knowledge regarding the reaction mechanisms involved in some of these processes and the structures of the resulting products is reviewed. Their effects on organoleptic and nutritional quality are also discussed.

40 CFR 405.61 - Specialized definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... STANDARDS DAIRY PRODUCTS PROCESSING POINT SOURCE CATEGORY Natural and Processed Cheese Subcategory § 405.61... subpart. (b) The term “BOD5 input” shall mean the biochemical oxygen demand of the materials entered into...

Effect of altitude on biochemical composition and quality of green arabica coffee beans can be affected by shade and postharvest processing method.

PubMed

Worku, Mohammed; de Meulenaer, Bruno; Duchateau, Luc; Boeckx, Pascal

2018-03-01

Although various studies have assessed altitude, shade and postharvest processing effects on biochemical content and quality of coffee beans, data on their interactions are scarce. The individual and interactive effects of these factors on the caffeine, chlorogenic acids (CGA) and sucrose contents as well as physical and sensory qualities of green coffee beans from large plantations in southwestern Ethiopia were evaluated. Caffeine and CGA contents decreased with increasing altitude; they respectively declined 0.12 and 1.23gkg -1 100m -1 . Sucrose content increased with altitude; however, the altitude effect was significant for wet-processed beans (3.02gkg -1 100m -1 ), but not for dry-processed beans (0.36g kg -1 100m -1 ). Similarly, sucrose content increased with altitude with much stronger effect for coffee grown without shade (2.11gkg -1 100m -1 ) compared to coffee grown under shade (0.93gkg -1 100m -1 ). Acidity increased with altitude when coffee was grown under shade (0.22 points 100m -1 ), but no significant altitude effect was observed on coffee grown without shade. Beans grown without shade showed a higher physical quality score for dry (37.2) than for wet processing (29.1). These results generally underline the complex interaction effects between altitude and shade or postharvest processing on biochemical composition and quality of green arabica coffee beans. Copyright © 2017. Published by Elsevier Ltd.

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.

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.

Vitreous humour - routine or alternative material for analysis in forensic medicine.

PubMed

Markowska, Joanna; Szopa, Monika; Zawadzki, Marcin; Piekoszewski, Wojciech

2017-01-01

Biological materials used in toxicological analyses in forensic medicine traditionally include blood, urine and vitreous humour. Forensic use of the vitreous body is mostly due to the need to assess the endogenous concentration of ethyl alcohol in the process of human body decomposition. The vitreous body is an underestimated biological material, even though its biochemical properties and anatomical location make it suitable for specific forensic toxicology tests as a reliable material for the preparation of forensic expert opinions. Based on the available literature the paper gathers information on the biochemical structure of the vitreous body, ways to secure the material after collection and its use in postmortem diagnostics. Specific applications of the vitreous humour for biochemical and toxicological tests are discussed, with a focus on its advantages and limitations in forensic medical assessment which are attributable to its biochemical properties, anatomical location and limited scientific studies on the distribution of xenobiotics in the vitreous body.

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.

TERMINAL ELECTRON ACCEPTING PROCESSES IN THE ALLUVIAL SEDIMENTS OF A HEADWATER STREAM

EPA Science Inventory

Chemical fluxes between catchments and streams are influenced by biochemical processes in the groundwater-stream water (GW-SW) ecotone, the interface between stream surface water and groundwater. Terminal electron accepting processes (TEAPs) that are utilized in respiration of ...

Development of efficient, integrated cellulosic biorefineries : LDRD final report.

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

Teh, Kwee-Yan; Hecht, Ethan S.; Shaddix, Christopher R.

2010-09-01

Cellulosic ethanol, generated from lignocellulosic biomass sources such as grasses and trees, is a promising alternative to conventional starch- and sugar-based ethanol production in terms of potential production quantities, CO{sub 2} impact, and economic competitiveness. In addition, cellulosic ethanol can be generated (at least in principle) without competing with food production. However, approximately 1/3 of the lignocellulosic biomass material (including all of the lignin) cannot be converted to ethanol through biochemical means and must be extracted at some point in the biochemical process. In this project we gathered basic information on the prospects for utilizing this lignin residue material inmore » thermochemical conversion processes to improve the overall energy efficiency or liquid fuel production capacity of cellulosic biorefineries. Two existing pretreatment approaches, soaking in aqueous ammonia (SAA) and the Arkenol (strong sulfuric acid) process, were implemented at Sandia and used to generated suitable quantities of residue material from corn stover and eucalyptus feedstocks for subsequent thermochemical research. A third, novel technique, using ionic liquids (IL) was investigated by Sandia researchers at the Joint Bioenergy Institute (JBEI), but was not successful in isolating sufficient lignin residue. Additional residue material for thermochemical research was supplied from the dilute-acid simultaneous saccharification/fermentation (SSF) pilot-scale process at the National Renewable Energy Laboratory (NREL). The high-temperature volatiles yields of the different residues were measured, as were the char combustion reactivities. The residue chars showed slightly lower reactivity than raw biomass char, except for the SSF residue, which had substantially lower reactivity. Exergy analysis was applied to the NREL standard process design model for thermochemical ethanol production and from a prototypical dedicated biochemical process, with process data supplied by a recent report from the National Research Council (NRC). The thermochemical system analysis revealed that most of the system inefficiency is associated with the gasification process and subsequent tar reforming step. For the biochemical process, the steam generation from residue combustion, providing the requisite heating for the conventional pretreatment and alcohol distillation processes, was shown to dominate the exergy loss. An overall energy balance with different potential distillation energy requirements shows that as much as 30% of the biomass energy content may be available in the future as a feedstock for thermochemical production of liquid fuels.« less

Valsartan-induced acute pancreatitis.

PubMed

Can, Burak; Sali, Mursel; Batman, Adnan; Yilmaz, Hasan; Korkmaz, Ugur; Celebi, Altay; Senturk, Omer; Hulagu, Sadettin

2014-01-01

Gastrointestinal toxicity is uncommon among patients treated with angiotensin II receptor antagonists. A 58-year-old man presented with nausea, vomiting and constant pain in the epigastrium that radiated to the flanks. He received treatment with valsartan (160 mg daily) for hypertension. The clinical, biochemical and radiological findings were compatible with a diagnosis of acute pancreatitis. After the patient achieved a clinical and biochemical recovery, the valsartan therapy was started again. Six weeks later, he returned to the hospital with an attack of pancreatitis. Subsequently, he returned with repeated attacks of pancreatitis twice, and the valsartan was discontinued. Ten months after the treatment, the patient had no complaints. When severe abdominal symptoms occur for no apparent reason during treatment with valsartan, a diagnosis of pancreatitis should be considered.

Hemoglobin Variants: Biochemical Properties and Clinical Correlates

PubMed Central

Thom, Christopher S.; Dickson, Claire F.; Gell, David A.; Weiss, Mitchell J.

2013-01-01

Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples. PMID:23388674

Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster.

PubMed

Okada, Hirokazu; Ebhardt, H Alexander; Vonesch, Sibylle Chantal; Aebersold, Ruedi; Hafen, Ernst

2016-09-01

The manner by which genetic diversity within a population generates individual phenotypes is a fundamental question of biology. To advance the understanding of the genotype-phenotype relationships towards the level of biochemical processes, we perform a proteome-wide association study (PWAS) of a complex quantitative phenotype. We quantify the variation of wing imaginal disc proteomes in Drosophila genetic reference panel (DGRP) lines using SWATH mass spectrometry. In spite of the very large genetic variation (1/36 bp) between the lines, proteome variability is surprisingly small, indicating strong molecular resilience of protein expression patterns. Proteins associated with adult wing size form tight co-variation clusters that are enriched in fundamental biochemical processes. Wing size correlates with some basic metabolic functions, positively with glucose metabolism but negatively with mitochondrial respiration and not with ribosome biogenesis. Our study highlights the power of PWAS to filter functional variants from the large genetic variability in natural populations.

Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode.

PubMed

Rebello, Karina M; Barros, Juliana S L; Mota, Ester M; Carvalho, Paulo C; Perales, Jonas; Lenzi, Henrique L; Neves-Ferreira, Ana G C

2011-08-24

Angiostrongylus costaricensis is a nematode helminth that causes an intestinal acute inflammatory process known as abdominal angiostrongyliasis, which is a poorly understood human disease occurring in Latin America. Our aim was to study the proteomic profiles of adult parasites focusing on immunogenic proteins. Total cellular extracts from both genders showed similar 2-DE profiles, with 60% of all protein spots focused between pH 5-7 and presenting molecular masses from 20.1 to 66 kDa. A total of 53 different dominant proteins were identified in our dataset and were mainly associated with the following over-represented Gene Ontology Biological Process terms: "macromolecule metabolic process", "developmental process", "response to stress", and "biological regulation". Female and male immunoblots showed similar patterns of reactive proteins. Immunoreactive spots identified by MALDI-PSD were found to represent heat shock proteins, a putative abnormal DAuer Formation family member, and galectins. To date, very few biochemical analyses have focused on the nematode Angiostrongylus costaricensis. As such, our results contribute to a better understanding of its biology and the mechanisms underlying the host-parasite relationship associated with this species. Moreover, our findings represent a first step in the search for candidate proteins for diagnostic assays and the treatment of this parasitic infection. Copyright © 2011 Elsevier B.V. All rights reserved.

Modelling and analysis of the sugar cataract development process using stochastic hybrid systems.

PubMed

Riley, D; Koutsoukos, X; Riley, K

2009-05-01

Modelling and analysis of biochemical systems such as sugar cataract development (SCD) are critical because they can provide new insights into systems, which cannot be easily tested with experiments; however, they are challenging problems due to the highly coupled chemical reactions that are involved. The authors present a stochastic hybrid system (SHS) framework for modelling biochemical systems and demonstrate the approach for the SCD process. A novel feature of the framework is that it allows modelling the effect of drug treatment on the system dynamics. The authors validate the three sugar cataract models by comparing trajectories computed by two simulation algorithms. Further, the authors present a probabilistic verification method for computing the probability of sugar cataract formation for different chemical concentrations using safety and reachability analysis methods for SHSs. The verification method employs dynamic programming based on a discretisation of the state space and therefore suffers from the curse of dimensionality. To analyse the SCD process, a parallel dynamic programming implementation that can handle large, realistic systems was developed. Although scalability is a limiting factor, this work demonstrates that the proposed method is feasible for realistic biochemical systems.

Phototropism: growing towards an understanding of plant movement.

PubMed

Liscum, Emmanuel; Askinosie, Scott K; Leuchtman, Daniel L; Morrow, Johanna; Willenburg, Kyle T; Coats, Diana Roberts

2014-01-01

Phototropism, or the differential cell elongation exhibited by a plant organ in response to directional blue light, provides the plant with a means to optimize photosynthetic light capture in the aerial portion and water and nutrient acquisition in the roots. Tremendous advances have been made in our understanding of the molecular, biochemical, and cellular bases of phototropism in recent years. Six photoreceptors and their associated signaling pathways have been linked to phototropic responses under various conditions. Primary detection of directional light occurs at the plasma membrane, whereas secondary modulatory photoreception occurs in the cytoplasm and nucleus. Intracellular responses to light cues are processed to regulate cell-to-cell movement of auxin to allow establishment of a trans-organ gradient of the hormone. Photosignaling also impinges on the transcriptional regulation response established as a result of changes in local auxin concentrations. Three additional phytohormone signaling pathways have also been shown to influence phototropic responsiveness, and these pathways are influenced by the photoreceptor signaling as well. Here, we will discuss this complex dance of intra- and intercellular responses that are regulated by these many systems to give rise to a rapid and robust adaptation response observed as organ bending.

Phototropism: Growing towards an Understanding of Plant Movement[OPEN

PubMed Central

Liscum, Emmanuel; Askinosie, Scott K.; Leuchtman, Daniel L.; Morrow, Johanna; Willenburg, Kyle T.; Coats, Diana Roberts

2014-01-01

Phototropism, or the differential cell elongation exhibited by a plant organ in response to directional blue light, provides the plant with a means to optimize photosynthetic light capture in the aerial portion and water and nutrient acquisition in the roots. Tremendous advances have been made in our understanding of the molecular, biochemical, and cellular bases of phototropism in recent years. Six photoreceptors and their associated signaling pathways have been linked to phototropic responses under various conditions. Primary detection of directional light occurs at the plasma membrane, whereas secondary modulatory photoreception occurs in the cytoplasm and nucleus. Intracellular responses to light cues are processed to regulate cell-to-cell movement of auxin to allow establishment of a trans-organ gradient of the hormone. Photosignaling also impinges on the transcriptional regulation response established as a result of changes in local auxin concentrations. Three additional phytohormone signaling pathways have also been shown to influence phototropic responsiveness, and these pathways are influenced by the photoreceptor signaling as well. Here, we will discuss this complex dance of intra- and intercellular responses that are regulated by these many systems to give rise to a rapid and robust adaptation response observed as organ bending. PMID:24481074

Classification of the degenerative grade of lesions of supraspinatus rotator cuff tendons by FT-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Palma Fogazza, Bianca; da Silva Carvalho, Carolina; Godoy Penteado, Sergio; Meneses, Cláudio S.; Abrahão Martin, Airton; da Silva Martinho, Herculano

2007-02-01

FT-Raman spectroscopy was employed to access the biochemical alterations occurring on the degenerative process of the rotator cuff supraspinatus tendons. The spectral characteristic variations in the 351 spectra of samples of 39 patients were identified with the help of Principal Components Analysis. The main variations occurred in the 840-911; 1022- 1218; 1257; 1270; 1300; 1452; 1663; and 1751 cm -1 regions corresponding to the vibrational bands of proline, hydroxiproline, lipids, nucleic acids, carbohydrates, collagen, and elastin. These alterations are compatible with the pathology alterations reported on the literature. Scattering plots of PC 4 vs PC 2 and PC 3 vs PC 2 contrasted with histopathological analysis has enabled the spectral classification of the data into normal and degenerated groups of tendons. By depicting empiric lines the estimated sensibility and specificity were 39,6 % and 97,8 %, respectively for PC 4 vs PC 2 and 36,0 % and 100 %, respectively for PC 3 vs PC 2. These results indicate that Raman spectroscopy can be used to probe the general tendon quality and could be applied as co adjuvant element in the usual arthroscopy surgery apparatus to guide the procedure and possibly infer about the probability of rerupture.

Role of chemical and mechanical stimuli in mediating bone fracture healing.

PubMed

Zhang, Lihai; Richardson, Martin; Mendis, Priyan

2012-08-01

Bone is a remarkable living tissue that provides a framework for animal body support and motion. However, under excessive loads and deformations, bone is prone is to damage through fracture. Furthermore, once the bone is weakened by osteoporosis, bone fracture can occur even after only minimal trauma. Various techniques have been developed to treat bone fractures. Successful treatment outcomes depend on a fundamental understanding of the biochemical and biomechanical environments of the fracture site. Various cell types (e.g. mesenchymal stem cells, chondrocytes, osteoblasts and osteoclasts) within the fracture site tightly control the healing process by responding to the chemical and mechanical microenvironment. However, these mechanochemical regulatory mechanisms remain poorly understood at the system level owing to the large range of variables, such as age, sex and disease-associated material properties of the tissue. Computational modelling can play an important role in unravelling this complexity by combining mechanochemical interactions, revealing the dominant controlling processes and optimizing system behaviour, thereby enabling the development and evaluation of treatment strategies for individual patients. © 2011 The Authors. Clinical and Experimental Pharmacology and Physiology © 2011 Blackwell Publishing Asia Pty Ltd.

In vivo Raman spectroscopy for biochemical monitoring of the human cervix throughout pregnancy.

PubMed

O'Brien, Christine M; Vargis, Elizabeth; Rudin, Amy; Slaughter, James C; Thomas, Giju; Newton, J Michael; Reese, Jeff; Bennett, Kelly A; Mahadevan-Jansen, Anita

2018-05-01

The cervix must undergo significant biochemical remodeling to allow for successful parturition. This process is not fully understood, especially in instances of spontaneous preterm birth. In vivo Raman spectroscopy is an optical technique that can be used to investigate the biochemical composition of tissue longitudinally and noninvasively in human beings, and has been utilized to measure physiology and disease states in a variety of medical applications. The purpose of this study is to measure in vivo Raman spectra of the cervix throughout pregnancy in women, and to identify biochemical markers that change with the preparation for delivery and postpartum repair. In all, 68 healthy pregnant women were recruited. Raman spectra were measured from the cervix of each patient monthly in the first and second trimesters, weekly in the third trimester, and at the 6-week postpartum visit. Raman spectra were measured using an in vivo Raman system with an optical fiber probe to excite the tissue with 785 nm light. A spectral model was developed to highlight spectral regions that undergo the most changes throughout pregnancy, which were subsequently used for identifying Raman peaks for further analysis. These peaks were analyzed longitudinally to determine if they underwent significant changes over the course of pregnancy (P < .05). Finally, 6 individual components that comprise key biochemical constituents of the human cervix were measured to extract their contributions in spectral changes throughout pregnancy using a linear combination method. Patient factors including body mass index and parity were included as variables in these analyses. Raman peaks indicative of extracellular matrix proteins (1248 and 1254 cm -1 ) significantly decreased (P < .05), while peaks corresponding to blood (1233 and 1563 cm -1 ) significantly increased (P < .0005) in a linear manner throughout pregnancy. In the postpartum cervix, significant increases in peaks corresponding to actin (1003, 1339, and 1657 cm -1 ) and cholesterol (1447 cm -1 ) were observed when compared to late gestation, while signatures from blood significantly decreased. Postpartum actin signals were significantly higher than early pregnancy, whereas extracellular matrix proteins and water signals were significantly lower than early weeks of gestation. Parity had a significant effect on blood and extracellular matrix protein signals, with nulliparous patients having significant increases in blood signals throughout pregnancy, and higher extracellular matrix protein signals in early pregnancy compared to patients with prior pregnancies. Body mass index significantly affected actin signal contribution, with low body mass index patients showing decreasing actin contribution throughout pregnancy and high body mass index patients demonstrating increasing actin signals. Raman spectroscopy was successfully used to biochemically monitor cervical remodeling in pregnant women during prenatal visits. This foundational study has demonstrated sensitivity to known biochemical dynamics that occur during cervical remodeling, and identified patient variables that have significant effects on Raman spectra throughout pregnancy. Raman spectroscopy has the potential to improve our understanding of cervical maturation, and be used as a noninvasive preterm birth risk assessment tool to reduce the incidence, morbidity, and mortality caused by preterm birth. Copyright © 2018. Published by Elsevier Inc.

Bioremediation of cyanotoxins.

PubMed

Edwards, Christine; Lawton, Linda A

2009-01-01

Cyanobacteria are a diverse group of mainly aquatic microorganisms which occur globally. Eutrophication (nutrient enrichment) of water bodies, often as a result of human activities, results in prolific grow of cyanobacteria that develop into a thick scum or bloom. Many of these blooms are toxic due to the production of hepatotoxins (microcystins and cylindrospermopsin) and/or neurotoxins (saxitoxins and anatoxins) posing a serious health hazard to humans and animals. The presence of these cyanotoxins is of particular concern in drinking water supplies where conventional water treatment often fails to eliminate them. Hence, there is significant interest in water treatment strategies that ensure the removal of cyanotoxins, with the exploitation of microbes being on such possible approach. As naturally occurring compounds it is assumed that these toxins are readily biodegraded. Furthermore, there is no significant evidence of their accumulation in the environment and their relative stable under a wide range of physico-chemical conditions, suggests biodegradation is the main route for their natural removal from the environment. Microcystins, as the most commonly occurring toxins, have been the most widely studied and hence form the main focus here. The review provides an overview of research into the biodegradation of cyanotoxin, including evidence for natural bioremediation, screening and isolation of toxin biodegrading bacteria, genetic and biochemical elucidation of a degradation pathway along with attempts to harness them for bioremediation through bioactive water treatment processes.

Apoptotic natural cell death in developing primate dopamine midbrain neurons occurs during a restricted period in the second trimester of gestation

PubMed Central

Morrow, Bret A.; Roth, Robert H.; Redmond, D. Eugene; Sladek, John R.; Elsworth, John D.

2012-01-01

Natural cell death (NCD) by apoptosis is a normal developmental event in most neuronal populations, and is a determinant of the eventual size of a population. We decided to examine the timing and extent of NCD of the midbrain dopamine system in a primate species, as dopamine deficiency or excess has been implicated in several disorders. Genetic or environmental differences may alter the extent of NCD and predispose individuals to neurological or psychiatric diseases. In developing rats, NCD in the midbrain dopamine system has been observed to start at the end of gestation and peak in the postnatal period. In fetal monkey brains, apoptosis in midbrain DA neurons was identified histologically by chromatin clumping in tyrosine hydroxylase-positive cells, and confirmed by TUNEL and active caspase-3 staining. A distinct peak of NCD occurred at about E80, midway through gestation in this species. We estimate that at least 50% of the population may be lost in this process. In other brains we determined biochemically that the onset of apoptosis coincides with the time of greatest rate of increase of striatal DA concentration. Thus, marked apoptotic NCD occurs in the primate midbrain dopamine system half-way through gestation, and appears to be associated with the rapid developmental increase in striatal dopamine innervation. PMID:17313945

Nitrogen fixation on early Mars and other terrestrial planets: experimental demonstration of abiotic fixation reactions to nitrite and nitrate.

PubMed

Summers, David P; Khare, Bishun

2007-04-01

Understanding the abiotic fixation of nitrogen is critical to understanding planetary evolution and the potential origin of life on terrestrial planets. Nitrogen, an essential biochemical element, is certainly necessary for life as we know it to arise. The loss of atmospheric nitrogen can result in an incapacity to sustain liquid water and impact planetary habitability and hydrological processes that shape the surface. However, our current understanding of how such fixation may occur is almost entirely theoretical. This work experimentally examines the chemistry, in both gas and aqueous phases, that would occur from the formation of NO and CO by the shock heating of a model carbon dioxide/nitrogen atmosphere such as is currently thought to exist on early terrestrial planets. The results show that two pathways exist for the abiotic fixation of nitrogen from the atmosphere into the crust: one via HNO and another via NO(2). Fixation via HNO, which requires liquid water, could represent fixation on a planet with liquid water (and hence would also be a source of nitrogen for the origin of life). The pathway via NO(2) does not require liquid water and shows that fixation could occur even when liquid water has been lost from a planet's surface (for example, continuing to remove nitrogen through NO(2) reaction with ice, adsorbed water, etc.).

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

Factors predicting biochemical recurrence after radical prostatectomy among patients with clinical T3 prostate cancer.

PubMed

Otsuka, Masafumi; Kamasako, Tomohiko; Uemura, Toshihiro; Takeshita, Nobushige; Shinozaki, Tetsuo; Kobayashi, Masayuki; Komaru, Atsushi; Fukasawa, Satoshi

2018-06-19

The effectiveness of cancer control is unclear after radical prostatectomy for patients with clinical T3 prostate cancer. We retrospectively reviewed 1409 patients who underwent radical prostatectomy between April 2007 and December 2014, including 210 patients with cT3 prostate cancer. Nine patients who received neoadjuvant hormonal therapy and three patients who were lost to follow-up were excluded from the analysis. Clinical staging was performed by an experienced radiologist using preoperative magnetic resonance imaging findings. We analyzed the predictors of biochemical recurrence using Cox proportional hazard analyses. A total of 113 patients (57%) underwent radical retropubic prostatectomy and 85 patients (43%) underwent robot-assisted radical prostatectomy. The median follow-up period was 36 months. Downstaging occurred for 60 patients (30%), positive surgical margins were identified in 117 patients (59%), and biochemical recurrence was observed for 89 patients (45%). In the multivariate analyses, the independent preoperative predictors of biochemical recurrence were ≥50% proportion of positive biopsy cores [hazard ratio (HR): 2.858, P < 0.0001] and a biopsy Gleason score of ≥8 (HR: 1.800, P = 0.0093). The independent post-operative predictors of biochemical recurrence were positive surgical margins (HR: 2.490, P = 0.0018) and seminal vesicle invasion (HR: 2.750, P < 0.0001). Among patients with cT3 prostate cancer, the percentage of positive biopsy cores and the biopsy Gleason score should be considered to select treatment. Compared with radical retropubic prostatectomy, robot-assisted radical prostatectomy may be a feasible treatment option in this setting.

A thermochemical-biochemical hybrid processing of lignocellulosic biomass for producing fuels and chemicals.

PubMed

Shen, Yanwen; Jarboe, Laura; Brown, Robert; Wen, Zhiyou

2015-12-01

Thermochemical-biological hybrid processing uses thermochemical decomposition of lignocellulosic biomass to produce a variety of intermediate compounds that can be converted into fuels and chemicals through microbial fermentation. It represents a unique opportunity for biomass conversion as it mitigates some of the deficiencies of conventional biochemical (pretreatment-hydrolysis-fermentation) and thermochemical (pyrolysis or gasification) processing. Thermochemical-biological hybrid processing includes two pathways: (i) pyrolysis/pyrolytic substrate fermentation, and (ii) gasification/syngas fermentation. This paper provides a comprehensive review of these two hybrid processing pathways, including the characteristics of fermentative substrates produced in the thermochemical stage and microbial utilization of these compounds in the fermentation stage. The current challenges of these two biomass conversion pathways include toxicity of the crude pyrolytic substrates, the inhibition of raw syngas contaminants, and the mass-transfer limitations in syngas fermentation. Possible approaches for mitigating substrate toxicities are discussed. The review also provides a summary of the current efforts to commercialize hybrid processing. Copyright © 2015 Elsevier Inc. All rights reserved.

LASER BIOLOGY AND MEDICINE: Combined application of optical methods to increase the information content of optical coherent tomography in diagnostics of neoplastic processes

NASA Astrophysics Data System (ADS)

Kuranov, R. V.; Sapozhnikova, V. V.; Shakhova, N. M.; Gelikonov, V. M.; Zagainova, E. V.; Petrova, S. A.

2002-11-01

A combined application of optical methods [optical coherent tomography (OCT), cross-polarisation optical coherent tomography, and fluorescence spectroscopy] is proposed for obtaining information on morphological and biochemical changes occurring in tissues in norm and pathology. It is shown that neoplastic and scar changes in esophagus can be distinguished using a combination of polarisation and standard OCT due to the difference between the depolarising properties of the tissues caused by the structural properties of collagenic fibres in stroma. It is shown that OCT combined with fluorescence spectroscopy with the use of 5-aminolevulinic acid is promising for determining the boundaries of carcinoma of the uterine cervix and vulva. It is found that the tumour boundary detected by optical methods coincides with the morphological boundary and extends beyond colposcopically determined boundary by about 2 mm.

Detection of biotin in individual sea urchin oocytes using a bioluminescence binding assay.

PubMed

Feltus, A; Grosvenor, A L; Conover, R C; Anderson, K W; Daunert, S

2001-04-01

The ability to detect biomolecules in single cells is important in order to fully understand the processes by which many biochemical events occur. To that end, we have developed a bioluminescence binding assay capable of measuring the intracellular biotin content of individual cells. The assay depends on competition between an aequorin-biotin conjugate (AEQ-biotin) and free biotin within the oocytes for binding sites on the protein avidin. The assay is performed by microinjecting each component into the oocytes and following the resulting bioluminescence within the oocyte upon triggering of aequorin. Results obtained using sea urchin oocytes show that the assay performed within the cells behaves in a manner consistent with assay theory. Using the assay, the individual biotin content of the oocytes is an average of approximately 20 amol. To our knowledge, this is the first reported multicomponent binding assay to be performed inside an intact single cell.

Physiological links of circadian clock and biological clock of aging.

PubMed

Liu, Fang; Chang, Hung-Chun

2017-07-01

Circadian rhythms orchestrate biochemical and physiological processes in living organisms to respond the day/night cycle. In mammals, nearly all cells hold self-sustained circadian clocks meanwhile couple the intrinsic rhythms to systemic changes in a hierarchical manner. The suprachiasmatic nucleus (SCN) of the hypothalamus functions as the master pacemaker to initiate daily synchronization according to the photoperiod, in turn determines the phase of peripheral cellular clocks through a variety of signaling relays, including endocrine rhythms and metabolic cycles. With aging, circadian desynchrony occurs at the expense of peripheral metabolic pathologies and central neurodegenerative disorders with sleep symptoms, and genetic ablation of circadian genes in model organisms resembled the aging-related features. Notably, a number of studies have linked longevity nutrient sensing pathways in modulating circadian clocks. Therapeutic strategies that bridge the nutrient sensing pathways and circadian clock might be rational designs to defy aging.

A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution.

PubMed

Jha, Ramesh K; Bingen, Jeremy M; Johnson, Christopher W; Kern, Theresa L; Khanna, Payal; Trettel, Daniel S; Strauss, Charlie E M; Beckham, Gregg T; Dale, Taraka

2018-06-01

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. Here we demonstrate the optimization of an Escherichia coli- based biosensor in a robust microbial strain for the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators.

Characterization of decellularized scaffold derived from porcine meniscus for tissue engineering applications

NASA Astrophysics Data System (ADS)

Gao, Shuang; Yuan, Zhiguo; Xi, Tingfei; Wei, Xiaojuan; Guo, Quanyi

2016-06-01

Menisci are fundamental fibrocartilaginous organs in knee joints. The injury in meniscus can impair normal knee function and predisposes patients to osteoarthritis. This study prepared decellularized meniscus scaffolds using a 1% (w/w) sodium dodecyl sulfate solution and sufficient rinsing steps. Complete cell removal was verified by hematoxylin and eosin staining and DNA content assay. Decellularized menisci had accordant tension properties to intact ones, but with declined compression properties. This occurred because the collagen fiber was not damaged but glycosaminoglycans was significantly lost during the decellularization process, which was confirmed by biochemical assay and histology staining. In vitro cytotoxicity assay demonstrated that decellularized meniscus scaffolds have no toxicity on L929 murine fibroblasts and porcine chondrocytes. Further experiment showed that porcine chondrocytes could adhere and proliferate on the scaffold surface, and some cells even could infiltrate into the scaffold. All results showed the potential of this decellularized meniscus to be the scaffolds in tissue engineering.

Spectroscopy on the wing: naturally inspired SERS substrates for biochemical analysis.

PubMed

Garrett, Natalie L; Vukusic, Peter; Ogrin, Feodor; Sirotkin, Evgeny; Winlove, C Peter; Moger, Julian

2009-03-01

We show that naturally occurring chitinous nanostructures found on the wings of the Graphium butterfly can be used as substrates for surface-enhanced Raman scattering when coated with a thin film of gold or silver. The substrates were found to exhibit excellent biocompatibility and sensitivity, making them ideal for protein assaying. An assay using avidin/biotin binding showed that the substrates could be used to quantify protein binding directly from changes in the surface-enhanced Raman scattering (SERS) spectra and were sensitive over a concentration range comparable with a typical enzyme-linked immunosorbent assays (ELISA) assay. A biomimetic version of the wing nanostructures produced using a highly reproducible, large-scale fabrication process, yielded comparable enhancement factors and biocompatibility. The excellent biocompatibility of the wings and biomimetic substrates is unparalleled by other lithographically produced substrates, and this could pave the way for widespread application of ultrasensitive SERS-based bioassays.

Characterization of choline trimethylamine-lyase expands the chemistry of glycyl radical enzymes.

PubMed

Craciun, Smaranda; Marks, Jonathan A; Balskus, Emily P

2014-07-18

The recently identified glycyl radical enzyme (GRE) homologue choline trimethylamine-lyase (CutC) participates in the anaerobic conversion of choline to trimethylamine (TMA), a widely distributed microbial metabolic transformation that occurs in the human gut and is linked to disease. The proposed biochemical function of CutC, C-N bond cleavage, represents new reactivity for the GRE family. Here we describe the in vitro characterization of CutC and its activating protein CutD. We have observed CutD-mediated formation of a glycyl radical on CutC using EPR spectroscopy and have demonstrated that activated CutC processes choline to trimethylamine and acetaldehyde. Surveys of potential alternate CutC substrates uncovered a strict specificity for choline. Homology modeling and mutagenesis experiments revealed essential CutC active site residues. Overall, this work establishes that CutC is a GRE of unique function and a molecular marker for anaerobic choline metabolism.

Factors and pathways involved in capacitation: how are they regulated?

PubMed Central

Jin, Shi-Kai; Yang, Wan-Xi

2017-01-01

In mammals, fertilization occurs via a comprehensive progression of events. Freshly ejaculated sperm have yet to acquire progressive motility or fertilization ability. They must first undergo a series of biochemical and physiological changes, collectively known as capacitation. Capacitation is a significant prerequisite to fertilization. During the process of capacitation, changes in membrane properties, intracellular ion concentration and the activities of enzymes, together with other protein modifications, induce multiple signaling events and pathways in defined media in vitro or in the female reproductive tract in vivo. These, in turn, stimulate the acrosome reaction and prepare spermatozoa for penetration of the egg zona pellucida prior to fertilization. In the present review, we conclude all mainstream factors and pathways regulate capacitation and highlight their crosstalk. We also summarize the relationship between capacitation and assisted reproductive technology or human disease. In the end, we sum up the open questions and future avenues in this field. PMID:27690295

Anionic lipids and the maintenance of membrane electrostatics in eukaryotes.

PubMed

Platre, Matthieu Pierre; Jaillais, Yvon

2017-02-01

A wide range of signaling processes occurs at the cell surface through the reversible association of proteins from the cytosol to the plasma membrane. Some low abundant lipids are enriched at the membrane of specific compartments and thereby contribute to the identity of cell organelles by acting as biochemical landmarks. Lipids also influence membrane biophysical properties, which emerge as an important feature in specifying cellular territories. Such parameters are crucial for signal transduction and include lipid packing, membrane curvature and electrostatics. In particular, membrane electrostatics specifies the identity of the plasma membrane inner leaflet. Membrane surface charges are carried by anionic phospholipids, however the exact nature of the lipid(s) that powers the plasma membrane electrostatic field varies among eukaryotes and has been hotly debated during the last decade. Herein, we discuss the role of anionic lipids in setting up plasma membrane electrostatics and we compare similarities and differences that were found in different eukaryotic cells.

A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution

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

Jha, Ramesh K.; Bingen, Jeremy M.; Johnson, Christopher W.

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. In this study, we demonstrate the optimization of an Escherichia coli-based biosensor in a robust microbial strain formore » the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators.« less

Growth of Bacterial Colonies

NASA Astrophysics Data System (ADS)

Warren, Mya; Hwa, Terence

2013-03-01

On hard agar gel, there is insufficient surface hydration for bacteria to swim or swarm. Instead, growth occurs in colonies of close-packed cells, which expand purely due to repulsive interactions: individual bacteria push each other out of the way through the force of their growth. In this way, bacterial colonies represent a new type of ``active'' granular matter. In this study, we investigate the physical, biochemical, and genetic elements that determine the static and dynamic aspects of this mode of bacterial growth for E. coli. We characterize the process of colony expansion empirically, and use discrete and continuum models to examine the extent to which our observations can be explained by the growth characteristics of non-communicating cells, coupled together by physical forces, nutrients, and waste products. Our results challenge the commonly accepted modes of bacterial colony growth and provide insight into sources of growth limitation in crowded bacterial communities.

Bioenergetics of Mammalian Sperm Capacitation

PubMed Central

Ferramosca, Alessandra; Zara, Vincenzo

2014-01-01

After ejaculation, the mammalian male gamete must undergo the capacitation process, which is a prerequisite for egg fertilization. The bioenergetics of sperm capacitation is poorly understood despite its fundamental role in sustaining the biochemical and molecular events occurring during gamete activation. Glycolysis and mitochondrial oxidative phosphorylation (OXPHOS) are the two major metabolic pathways producing ATP which is the primary source of energy for spermatozoa. Since recent data suggest that spermatozoa have the ability to use different metabolic substrates, the main aim of this work is to present a broad overview of the current knowledge on the energy-producing metabolic pathways operating inside sperm mitochondria during capacitation in different mammalian species. Metabolism of glucose and of other energetic substrates, such as pyruvate, lactate, and citrate, is critically analyzed. Such knowledge, besides its obvious importance for basic science, could eventually translate into the development of novel strategies for treatment of male infertility, artificial reproduction, and sperm selection methods. PMID:24791005

Bioenergetics of mammalian sperm capacitation.

PubMed

Ferramosca, Alessandra; Zara, Vincenzo

2014-01-01

After ejaculation, the mammalian male gamete must undergo the capacitation process, which is a prerequisite for egg fertilization. The bioenergetics of sperm capacitation is poorly understood despite its fundamental role in sustaining the biochemical and molecular events occurring during gamete activation. Glycolysis and mitochondrial oxidative phosphorylation (OXPHOS) are the two major metabolic pathways producing ATP which is the primary source of energy for spermatozoa. Since recent data suggest that spermatozoa have the ability to use different metabolic substrates, the main aim of this work is to present a broad overview of the current knowledge on the energy-producing metabolic pathways operating inside sperm mitochondria during capacitation in different mammalian species. Metabolism of glucose and of other energetic substrates, such as pyruvate, lactate, and citrate, is critically analyzed. Such knowledge, besides its obvious importance for basic science, could eventually translate into the development of novel strategies for treatment of male infertility, artificial reproduction, and sperm selection methods.

Utilization of plasmas for graphene synthesis

NASA Astrophysics Data System (ADS)

Shashurin, Alexey; Keidar, Michael

2013-10-01

Graphene is a one-atom-thick planar sheet of carbon atoms that are densely packed in a honeycomb crystal lattice. Grapheen has tremendous range of potential applications ranging from high-speed transistors to electrochemical energy storage devices and biochemical sensors. Methods of graphene synthesis include mechanical exfoliation, epitaxial growth on SiC, CVD and colloidal suspensions. In this work the utilization of plasmas in synthesis process is considered. Types of carbonaceous structures produced by the anodic arc and regions of their synthesis were studied. Ultimate role of substrate temperature and transformations occurring with various carbonaceous structures generated in plasma discharge were considered. Formation of graphene film on copper substrate was detected at temperatures around the copper melting point. The film was consisted of several layers graphene flakes having typical sizes of about 200 nm. Time required for crystallization of graphene on externally heated substrates was determined. This work was supported by National Science Foundation (NSF Grant No. CBET-1249213).

Relevance of Chemical Kinetics for Medicine: The Case of Nitric Oxide

NASA Astrophysics Data System (ADS)

Balaban, Alexandru T.; Seitz, William

2003-06-01

Nitric oxide, NO, is central to many physiological processes including regulation of blood pressure and nerve signal transmission. Enzymes in endothelial cells and in the brain of mammals continuously synthesize it—generally in low and carefully regulated concentrations. The well known reaction of NO with oxygen to produce toxic nitrogen dioxide, NO2, has a rate which is bimolecular in NO. High concentrations of NO, as are found often in industrial plants or cigarettes, react rapidly with oxygen to produce toxic NO2. However, the half-life of NO at low NO concentrations as found in solutions and gases occurring in blood vessels, brains, and lungs is sufficiently long for biochemical purposes. Kinetics, then, determines the harmful versus helpful aspects of nitric oxide. At concentrations below 80 ppm NO is used in hospitals for lung vasodilation of preterm newborns and patients with pulmonary distress.

Alternative Medicine in Diabetes - Role of Angiogenesis, Oxidative Stress, and Chronic Inflammation

PubMed Central

El-Refaei, Mohamed F.; Abduljawad, Suha H.; Alghamdi, Ahmed H.

2014-01-01

Diabetes is a chronic metabolic disorder that is characterized by hyperglycemia due to lack of or resistance to insulin. Patients with diabetes are frequently afflicted with ischemic vascular disease and impaired wound healing. Type 2 diabetes is known to accelerate atherosclerotic processes, endothelial cell dysfunction, glycosylation of extracellular matrix proteins, and vascular denervation. Herbal medicines and naturally occurring substances may positively affect diabetes management, and could thus be utilized as cost-effective means of supporting treatment in developing countries. Natural treatments have been used in these countries for a long time to treat diabetes. The present review analyses the features of aberrant angiogenesis, abnormalities in growth factors, oxidative stress, and metabolic derangements relevant to diabetes, and how herbal substances and their active chemical constituents may counteract these events. Evidence for possible biochemical effectiveness and limitations of herbal medicines are given, as well as details regarding the role of cytokines and nitric oxide. PMID:26177484

Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.

PubMed

Clifton, Ben E; Kaczmarski, Joe A; Carr, Paul D; Gerth, Monica L; Tokuriki, Nobuhiko; Jackson, Colin J

2018-04-23

The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.

A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution

DOE PAGES

Jha, Ramesh K.; Bingen, Jeremy M.; Johnson, Christopher W.; ...

2018-06-01

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. In this study, we demonstrate the optimization of an Escherichia coli-based biosensor in a robust microbial strain formore » the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators.« less

Combined application of optical methods to increase the information content of optical coherent tomography in diagnostics of neoplastic processes

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

Kuranov, R V; Sapozhnikova, V V; Shakhova, N M

2002-11-30

A combined application of optical methods [optical coherent tomography (OCT), cross-polarisation optical coherent tomography, and fluorescence spectroscopy] is proposed for obtaining information on morphological and biochemical changes occurring in tissues in norm and pathology. It is shown that neoplastic and scar changes in esophagus can be distinguished using a combination of polarisation and standard OCT due to the difference between the depolarising properties of the tissues caused by the structural properties of collagenic fibres in stroma. It is shown that OCT combined with fluorescence spectroscopy with the use of 5-aminolevulinic acid is promising for determining the boundaries of carcinoma ofmore » the uterine cervix and vulva. It is found that the tumour boundary detected by optical methods coincides with the morphological boundary and extends beyond colposcopically determined boundary by about 2 mm. (laser biology and medicine)« less

Photosynthesis.

PubMed

Johnson, Matthew P

2016-10-31

Photosynthesis sustains virtually all life on planet Earth providing the oxygen we breathe and the food we eat; it forms the basis of global food chains and meets the majority of humankind's current energy needs through fossilized photosynthetic fuels. The process of photosynthesis in plants is based on two reactions that are carried out by separate parts of the chloroplast. The light reactions occur in the chloroplast thylakoid membrane and involve the splitting of water into oxygen, protons and electrons. The protons and electrons are then transferred through the thylakoid membrane to create the energy storage molecules adenosine triphosphate (ATP) and nicotinomide-adenine dinucleotide phosphate (NADPH). The ATP and NADPH are then utilized by the enzymes of the Calvin-Benson cycle (the dark reactions), which converts CO 2 into carbohydrate in the chloroplast stroma. The basic principles of solar energy capture, energy, electron and proton transfer and the biochemical basis of carbon fixation are explained and their significance is discussed. © 2016 The Author(s).

Cadmium and mercury nephrotoxicity

NASA Astrophysics Data System (ADS)

Nicholson, J. K.

1983-08-01

Despite increasing attempts to control environmental pollution, changes in the distribution and bioavailability of toxic metals like mercury and cadmium are still occurring. Apart from natural processes, other contributory factors include the gradual spread of industrialization, the use of sewage sludge as a fertilizer and the acidification of Northern Hemisphere ground-water. Animals (including man and domestic varieties) can accumulate harmful concentrations of toxic metals1-5. We therefore looked for damage to the kidneys in seabirds contaminated with mercury and cadmium and made comparisons with kidneys from three other groups of animals: seabirds from an uncontaminated colony, metal-dosed birds and metal-dosed mice. We report here that, comparing all these groups of animals, invididuals with comparatively high levels of metals had nephrotoxic lesions of a similar type and severity. Moreover, the metal concentrations at which damage began and at which biochemical changes could be detected were below those presently considered as relatively safe for humans by the World Health Organization.

The Macrophage in the Development of Experimental Crescentic Glomerulonephritis

PubMed Central

Thomson, Napier M.; Holdsworth, Stephen R.; Glasgow, Eric F.; Atkins, Robert C.

1979-01-01

The role played by the macrophage in the development of injury in rabbit nephrotoxic nephritis (NTN) has been assessed by electron microscopy and glomerular culture of renal tissue obtained by several biopsies during the course of the disease. These observations have been correlated with the other immune, cellular, and biochemical events occurring in the glomerulus, ie, deposition of immunoglobulin and complement, proteinuria, polymorphonuclear leukocyte (PMN) exudation, fibrin deposition, crescent formation, and renal failure. A biphasic macrophage accumulation was detected, corresponding to the heterologous and autologous phases of the disease. In the autologous or crescentic phase, macrophages accumulated within the glomerular tuft from Day 5; their appearance coincided with the accumulation of PMN and development of proteinuria. Fibrin deposition in Bowman's space, which commenced on Days 6 and 7, was rapidly followed by the migration of macrophages from the glomeruli into Bowman's space. Within Bowman's space, macrophages were observed to phagocytose fibrin, transform into epithelioid and giant cells, and accumulate to form a substantial proportion of the cells forming the crescent. The inflammatory process of PMN exudation, macrophage accumulation, fibrin deposition, and crescent formation and the degree of renal failure reached a maximum by Days 12 to 14. Thereafter, resolution of the inflammatory process occurred so that by Day 40 macrophages had disappeared from the glomeruli. However, varying degrees of glomerular damage and renal failure persisted, occurring largely as a result of glomerulosclerosis and sclerosis of crescents. The tissue culture studies also demonstrated mesangial cell proliferation during the inflammatory process but did not show any abnormality of epithelial cell activity. This study demonstrates that the macrophages participate in NTN by accumulating in damaged glomeruli then migrating into Bowman's space (probably in response to fibrin deposition) where they undergo granulomatous transformation and accumulate, contributing to crescent formation. ImagesFigure 2Figure 3Figure 4Figure 1 PMID:371409

The application of Fourier transform infrared microspectroscopy for the study of diseased central nervous system tissue.

PubMed

Caine, Sally; Heraud, Philip; Tobin, Mark J; McNaughton, Donald; Bernard, Claude C A

2012-02-15

In the last two decades the field of infrared spectroscopy has seen enormous advances in both instrumentation and the development of bioinformatic methods for spectral analysis, allowing the examination of a large variety of healthy and diseased samples, including biological fluids, isolated cells, whole tissues, and tissue sections. The non-destructive nature of the technique, together with the ability to directly probe biochemical changes without the addition of stains or contrast agents, enables a range of complementary analyses. This review focuses on the application of Fourier transform infrared (FTIR) microspectroscopy to analyse central nervous system tissues, with the aim of understanding the biochemical and structural changes associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, transmissible spongiform encephalopathies, multiple sclerosis, as well as brain tumours. Modern biospectroscopic methods that combine FTIR microspectroscopy with bioinformatic analysis constitute a powerful new methodology that can discriminate pathology from normal healthy tissue in a rapid, unbiased fashion, with high sensitivity and specificity. Notably, the ability to detect protein secondary structural changes associated with Alzheimer's plaques, neurons in Parkinson's disease, and in some spectra from meningioma, as well as in the animal models of Alzheimer's disease, transmissible spongiform encephalopathies, and multiple sclerosis, illustrates the power of this technology. The capacity to offer insight into the biochemical and structural changes underpinning aetio-pathogenesis of diseases in tissues provides both a platform to investigate early pathologies occurring in a variety of experimentally induced and naturally occurring central nervous system diseases, and the potential to evaluate new therapeutic approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

Common biochemical defects linkage between post-traumatic stress disorders, mild traumatic brain injury (TBI) and penetrating TBI.

PubMed

Prasad, Kedar N; Bondy, Stephen C

2015-03-02

Post-traumatic stress disorder (PTSD) is a complex mental disorder with psychological and emotional components, caused by exposure to single or repeated extreme traumatic events found in war, terrorist attacks, natural or man-caused disasters, and by violent personal assaults and accidents. Mild traumatic brain injury (TBI) occurs when the brain is violently rocked back and forth within the skull following a blow to the head or neck as in contact sports, or when in close proximity to a blast pressure wave following detonation of explosives in the battlefield. Penetrating TBI occurs when an object penetrates the skull and damages the brain, and is caused by vehicle crashes, gunshot wound to the head, and exposure to solid fragments in the proximity of explosions, and other combat-related head injuries. Despite clinical studies and improved understanding of the mechanisms of cellular damage, prevention and treatment strategies for patients with PTSD and TBI remain unsatisfactory. To develop an improved plan for treating and impeding progression of PTSD and TBI, it is important to identify underlying biochemical changes that may play key role in the initiation and progression of these disorders. This review identifies three common biochemical events, namely oxidative stress, chronic inflammation and excitotoxicity that participate in the initiation and progression of these conditions. While these features are separately discussed, in many instances, they overlap. This review also addresses the goal of developing novel treatments and drug regimens, aimed at combating this triad of events common to, and underlying, injury to the brain. Copyright © 2014 Elsevier B.V. All rights reserved.

Extended-Spectrum β-lactamase (ESBL) producing Enterobacter aerogenes phenotypically misidentified as Klebsiella pneumoniae or K. terrigena

PubMed Central

Claeys, Geert; De Baere, Thierry; Wauters, Georges; Vandecandelaere, Patricia; Verschraegen, Gerda; Muylaert, An; Vaneechoutte, Mario

2004-01-01

Background Enterobacter aerogenes and Klebsiella pneumoniae are common isolates in clinical microbiology and important as producers of extended spectrum β-lactamases (ESBL). The discrimination between both species, which is routinely based on biochemical characteristics, is generally accepted to be straightforward. Here we report that genotypically unrelated strains of E. aerogenes can be misidentified as K. pneumoniae by routine laboratories using standard biochemical identification and using identification automates. Results Ten clinical isolates, identified as K. pneumoniae or K. terrigena with the routinely used biochemical tests and with API-20E, were identified as E. aerogenes by tDNA-PCR – an identification that was confirmed by 16S rRNA gene sequencing for five of these isolates. Misidentification also occurred when using the automated identification systems Vitek 2 and Phoenix, and was due to delayed positivity for ornithine decarboxylase and motility. Subculture and prolonged incubation resulted in positive results for ornithine decarboxylase and for motility. It could be shown by RAPD-analysis that the E. aerogenes strains belonged to different genotypes. Conclusions Clinical E. aerogenes isolates can be easily misidentified as Klebsiella due to delayed positivity for ornithine decarboxylase and motility. The phenomenon may be widespread, since it was shown to occur among genotypically unrelated strains from different hospitals and different isolation dates. A useful clue for correct identification is the presence of an inducible β-lactamase, which is highly unusual for K. pneumoniae. In several instances, the use of genotypic techniques like tDNA-PCR may circumvent problems of phenotypic identification. PMID:15619329

Natural outbreak of Streptococcus agalactiae (GBS) infection in wild giant Queensland grouper, Epinephelus lanceolatus (Bloch), and other wild fish in northern Queensland, Australia.

PubMed

Bowater, R O; Forbes-Faulkner, J; Anderson, I G; Condon, K; Robinson, B; Kong, F; Gilbert, G L; Reynolds, A; Hyland, S; McPherson, G; Brien, J O'; Blyde, D

2012-03-01

Ninety-three giant Queensland grouper, Epinephelus lanceolatus (Bloch), were found dead in Queensland, Australia, from 2007 to 2011. Most dead fish occurred in northern Queensland, with a peak of mortalities in Cairns in June 2008. In 2009, sick wild fish including giant sea catfish, Arius thalassinus (Rüppell), and javelin grunter, Pomadasys kaakan (Cuvier), also occurred in Cairns. In 2009 and 2010, two disease epizootics involving wild stingrays occurred at Sea World marine aquarium. Necropsy, histopathology, bacteriology and PCR determined that the cause of deaths of 12 giant Queensland grouper, three wild fish, six estuary rays, Dasyatis fluviorum (Ogilby), one mangrove whipray, Himantura granulata (Macleay), and one eastern shovelnose ray, Aptychotrema rostrata (Shaw), was Streptococcus agalactiae septicaemia. Biochemical testing of 34 S. agalactiae isolates from giant Queensland grouper, wild fish and stingrays showed all had identical biochemical profiles. The 16S rRNA gene sequences of isolates confirmed all isolates were S. agalactiae; genotyping of selected S. agalactiae isolates showed the isolates from giant Queensland grouper were serotype Ib, whereas isolates from wild fish and stingrays closely resembled serotype II. This is the first report of S. agalactiae from wild giant Queensland grouper and other wild tropical fish and stingray species in Queensland, Australia. © 2012 Blackwell Publishing Ltd and State of Queensland.

Nutrition and Musculoskeletal Function: Skylab Experiment Series Number M070

NASA Technical Reports Server (NTRS)

Raumbaut, P. C.

1972-01-01

The M070 experiments are expected to give medical investigators precise information on a variety of biochemical changes occurring during exposure to space flight. Sufficient control data are being generated by baseline studies to differentiate those effects that are caused by weightless flight and those that are caused by other abnormal conditions that normally accompany spaceflight.

Amino Acid Complementarity: A Biochemical Exemplar of Stoichiometry for General and Health Sciences Chemistry

ERIC Educational Resources Information Center

Vitz, Ed

2005-01-01

The standard introduction to stoichiometry and simple exemplars can motivate students to learn the stoichiometric studies and the condensation reaction that occurs between amino acids to form the peptide bond. This topic can be integrated into general chemistry courses as an alternative to inclusion of a separate biochemistry course that could be…

Run-length encoding graphic rules, biochemically editable designs and steganographical numeric data embedment for DNA-based cryptographical coding system

PubMed Central

Kawano, Tomonori

2013-01-01

There have been a wide variety of approaches for handling the pieces of DNA as the “unplugged” tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based digital barcodes, water marks and cryptography. In the present article, novel designs of artificial genes as the media for storing the digitally compressed data for images are proposed for bio-computing purpose while natural genes principally encode for proteins. Furthermore, the proposed system allows cryptographical application of DNA through biochemically editable designs with capacity for steganographical numeric data embedment. As a model case of image-coding DNA technique application, numerically and biochemically combined protocols are employed for ciphering the given “passwords” and/or secret numbers using DNA sequences. The “passwords” of interest were decomposed into single letters and translated into the font image coded on the separate DNA chains with both the coding regions in which the images are encoded based on the novel run-length encoding rule, and the non-coding regions designed for biochemical editing and the remodeling processes revealing the hidden orientation of letters composing the original “passwords.” The latter processes require the molecular biological tools for digestion and ligation of the fragmented DNA molecules targeting at the polymerase chain reaction-engineered termini of the chains. Lastly, additional protocols for steganographical overwriting of the numeric data of interests over the image-coding DNA are also discussed. PMID:23750303

Continuous monitoring of dissolved gases with membrane inlet mass spectrometry to fingerprint river biochemical activity

NASA Astrophysics Data System (ADS)

Vautier, Camille; Chatton, Eliot; Abbott, Benjamin; Harjung, Astrid; Labasque, Thierry; Guillou, Aurélie; Pannard, Alexandrine; Piscart, Christophe; Laverman, Anniet; Kolbe, Tamara; Massé, Stéphanie; de Dreuzy, Jean-Raynald; Thomas, Zahra; Aquilina, Luc; Pinay, Gilles

2017-04-01

Water quality in rivers results from biogeochemical processes in contributing hydrological compartments (soils, aquifers, hyporheic and riparian zones) and biochemical activity in the river network itself. Consequently, chemical fluxes fluctuate on multiple spatial and temporal scales, leading eventually to complex concentration signals in rivers. We characterized these fluctuations with innovative continuous monitoring of dissolved gases, to quantify transport and reaction processes occurring in different hydrological compartments. We performed stream-scale experiments in two headwater streams in Brittany, France. Factorial injections of inorganic nitrogen (NH4NO3), inorganic phosphate (P2O5) and multiple sources of labile carbon (acetate, tryptophan) were implemented in the two streams. We used a new field application of membrane inlet mass spectrometry to continuously monitor dissolved gases for multiple day-night periods (Chatton et al., 2016). Quantified gases included He, O2, N2, CO2, CH4, N2O, and 15N of dissolved N2 and N2O. We calibrated and assessed the methodology with well-established complementary techniques including gas chromatography and high-frequency water quality sensors. Wet chemistry and radon analysis complemented the study. The analyses provided several methodological and ecological insights and demonstrated that high frequency variations linked to background noise can be efficiently determined and filtered to derive effective fluxes. From a more fundamental point of view, the tested stream segments were fully characterized with extensive sampling of riverbeds and laboratory experiments, allowing scaling of point-level microbial and invertebrate diversity and activity on in-stream processing. This innovative technology allows fully-controlled in-situ experiments providing rich information with a high signal to noise ratio. We present the integrated nutrient demand and uptake and discuss limiting processes and elements at the reach and catchment scales. Eliot Chatton, Thierry Labasque, Jérôme de La Bernardie, Nicolas Guihéneuf, Olivier Bour, Luc Aquilina. 2016. Field Continuous Measurement of Dissolved Gases with a CF-MIMS: Applications to the Physics and Biogeochemistry of Groundwater Flow. Environ. Sci. Technol.

[Mercury (and...) through the centuries].

PubMed

Kłys, Małgorzata

2010-01-01

Mercury has a long history, fascinating in its many aspects. Through the centuries--from ancient times to the present day--the metal in its various forms, also known under the name "quicksilver", accompanied the man and was used for diversified purposes. Today, mercury is employed in manufacturing thermometers, barometers, vacuum pumps and explosives. It is also used in silver and gold mining processes. Mercury compounds play a significant role in dentistry, pharmaceutical industry and crop protection. The contemporary use of mercury markedly decreases, but historically speaking, the archives abound in materials that document facts and events occurring over generations and the immense intellectual effort aiming at discovering the true properties and mechanisms of mercury activity. Mercury toxicity, manifested in destruction of biological membranes and binding of the element with proteins, what disturbs biochemical processes occurring in the body, was discovered only after many centuries of the metal exerting its effect on the lives of individuals and communities. For centuries, mercury was present in the work of alchemists, who searched for the universal essence or quintessence and the so-called philosopher's stone. In the early modern era, between the 16th and 19th centuries, mercury was used to manufacture mirrors. Mercury compounds were employed as a medication against syphilis, which plagued mankind for more than four hundred years--from the Middle Ages till mid 20th century, when the discovery of penicillin became the turning point. This extremely toxic therapy resulted in much suffering, individual tragedies, chronic poisonings leading to fatalities and dramatic sudden deaths. In the last fifty years, there even occurred attempts of mentally imbalanced individuals at injecting themselves with metallic mercury, also as a performance-enhancing drug. Instances of mass mercury poisoning occurred many times in the past in consequence of eating food products poisoned with organic mercury compounds originating from the natural environment.

Effect of Temperature on Biochemical Composition, Growth and Reproduction of the Ornamental Red Cherry Shrimp Neocaridina heteropoda heteropoda (Decapoda, Caridea)

PubMed Central

Tropea, Carolina; Stumpf, Liane; López Greco, Laura Susana

2015-01-01

The effect of water temperature on biochemical composition, growth and reproduction of the ornamental shrimp, Neocaridina heteropoda heteropoda, was investigated to determine the optimum temperature for its culture. The effect of embryo incubation temperature on the subsequent performance of juveniles was also evaluated. Ovigerous females and recently hatched juveniles (JI) were maintained during egg incubation and for a 90-day period, respectively, at three temperatures (24, 28 and 32°C). Incubation period increased with decreasing water temperature, but the number and size of JI were similar among treatments. At day 30 of the 90-day period, body weight and growth increment (GI) at 24°C were lower than those at 28 and 32°C. On subsequent days, GI at 24°C exceeded that at 28 and 32°C, leading to a similar body weight among treatments. These results suggest growth was delayed at 24°C, but only for 30 days after hatching. The lipid concentration tended to be lowest, intermediate and highest at 28, 32 and 24°C, respectively, possibly as a consequence of the metabolic processes involved in growth and ovarian maturation. Protein and glycogen concentrations were similar among treatments. Both the growth trajectory and biochemical composition of shrimps were affected by the temperature experienced during the 90-day growth period independently of the embryo incubation temperature. During the growth period, shrimps reached sexual maturity and mated, with the highest proportion of ovigerous females occurring at 28°C. All the females that matured and mated at 32°C lost their eggs, indicating a potentially stressful effect of high temperature on ovarian maturation. Based on high survival and good growth performance of shrimps at the three temperatures tested over the 90-day period it is concluded that N. heteropoda heteropoda is tolerant to a wide range of water temperatures, with 28°C being the optimum temperature for its culture. PMID:25768918

Biochemical Process Development and Integration | Bioenergy | NREL

Science.gov Websites

Process Development We develop and scale fermentation processes that produce fuels and chemicals from guide experimental designs. Our newly updated fermentation laboratory houses 38 bench-scale fermentors current projects cover the fermentation spectrum including anaerobic, micro-aerobic, aerobic, and gas-to

FATE AND EFFECTS OF PHOSPHORUS ADDITIONS IN SOILS UNDER N2-FIXING RED ALDER

EPA Science Inventory

Soil phosphorus (P) dynamics are controlled by the interaction of geochemical, biochemical and biological processes, and changing species composition or management may alter the relative importance of these processes. We examined the role of these processes in two plantations of...

Identifying Opportunities for Vertical Integration of Biochemistry and Clinical Medicine.

PubMed

Wendelberger, Karen J.; Burke, Rebecca; Haas, Arthur L.; Harenwattananon, Marisa; Simpson, Deborah

1998-01-01

Objectives: Retention of basic science knowledge, as judged by National Board of Medical Examiners' (NBME) data, suffers due to lack of apparent relevance and isolation of instruction from clinical application, especially in biochemistry. However, the literature reveals no systematic process for identifying key biochemical concepts and associated clinical conditions. This study systematically identified difficult biochemical concepts and their common clinical conditions as a critical step towards enhancing relevance and retention of biochemistry.Methods: A multi-step/ multiple stakeholder process was used to: (1) identify important biochemistry concepts; (2) determine students' perceptions of concept difficulty; (3) assess biochemistry faculty, student, and clinical teaching scholars' perceived relevance of identified concepts; and (4) identify associated common clinical conditions for relevant and difficult concepts. Surveys and a modified Delphi process were used to gather data, subsequently analyzed using SPSS for Windows.Results: Sixteen key biochemical concepts were identified. Second year medical students rated 14/16 concepts as extremely difficult while fourth year students rated nine concepts as moderately to extremely difficult. On average, each teaching scholar generated common clinical conditions for 6.2 of the 16 concepts, yielding a set of seven critical concepts and associated clinical conditions.Conclusions: Key stakeholders in the instructional process struggle to identify biochemistry concepts that are critical, difficult to learn and associated with common clinical conditions. However, through a systematic process beginning with identification of concepts and associated clinical conditions, relevance of basic science instruction can be enhanced.

The National Niemann-Pick Type C1 Disease Database: correlation of lipid profiles, mutations, and biochemical phenotypes

PubMed Central

Garver, William S.; Jelinek, David; Meaney, F. John; Flynn, James; Pettit, Kathleen M.; Shepherd, Glen; Heidenreich, Randall A.; Vockley, Cate M. Walsh; Castro, Graciela; Francis, Gordon A.

2010-01-01

Niemann-Pick type C1 disease (NPC1) is an autosomal recessive lysosomal storage disorder characterized by neonatal jaundice, hepatosplenomegaly, and progressive neurodegeneration. The present study provides the lipid profiles, mutations, and corresponding associations with the biochemical phenotype obtained from NPC1 patients who participated in the National NPC1 Disease Database. Lipid profiles were obtained from 34 patients (39%) in the survey and demonstrated significantly reduced plasma LDL cholesterol (LDL-C) and increased plasma triglycerides in the majority of patients. Reduced plasma HDL cholesterol (HDL-C) was the most consistent lipoprotein abnormality found in male and female NPC1 patients across age groups and occurred independent of changes in plasma triglycerides. A subset of 19 patients for whom the biochemical severity of known NPC1 mutations could be correlated with their lipid profile showed a strong inverse correlation between plasma HDL-C and severity of the biochemical phenotype. Gene mutations were available for 52 patients (59%) in the survey, including 52 different mutations and five novel mutations (Y628C, P887L, I923V, A1151T, and 3741_3744delACTC). Together, these findings provide novel information regarding the plasma lipoprotein changes and mutations in NPC1 disease, and suggest plasma HDL-C represents a potential biomarker of NPC1 disease severity. PMID:19744920

Hematologic and plasma biochemical changes associated with fenbendazole administration in Hermann's tortoises (testudo hermanni).

PubMed

Neiffer, Donald L; Lydick, Dianna; Burks, Kyle; Doherty, Donna

2005-12-01

Toxicosis associated with benzimidazole anthelmintics has been reported with increasing frequency in zoologic collections. Clinical signs, clinicopathologic abnormalities, and gross and histologic lesions are primarily the result of damage to the gastrointestinal and hematopoietic systems. Profound leukopenia, especially granulocytopenia, is the most common and severe clinicopathologic change associated with benzimidazole administration. Death usually occurs from overwhelming systemic bacterial and/or fungal infections secondary to severe immunosuppression. In this 125-day study, six male Hermann's tortoises (Testudo hermanni) were treated orally with two 5-day courses of fenbendazole 2 wk apart at a dosage of 50 mg/kg. Serial blood samples were used to assess hematologic and plasma biochemical changes before, during, and following the treatment period. Although the tortoises remained healthy, blood sampling indicated an extended heteropenia with transient hypoglycemia, hyperuricemia, hyperphosphatemia, and equivocal hyperproteinemia/hyperglobulinemia, which were considered to be in response to fenbendazole administration. Changes in several other clinicopathologic parameters appeared to correlate with fenbendazole administration. The hematologic and biochemical changes seen in the healthy animals in this study should be considered when treating compromised tortoises with fenbendazole. Hematologic and plasma biochemical status of tortoises/reptiles should be determined before treatment and monitored during the treatment period. The risk of mortality of an individual from nematode infection should be assessed relative to the potential for metabolic alteration and secondary septicemia following damage to hematopoietic and gastrointestinal systems by fenbendazole.

Economic feasibility of biochemical processes for the upgrading of crudes and the removal of sulfur, nitrogen, and trace metals from crude oil -- Benchmark cost establishment of biochemical processes on the basis of conventional downstream technologies. Final report FY95

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

Premuzic, E.T.

1996-08-01

During the past several years, a considerable amount of work has been carried out showing that microbially enhanced oil recovery (MEOR) is promising and the resulting biotechnology may be deliverable. At Brookhaven National Laboratory (BNL), systematic studies have been conducted which dealt with the effects of thermophilic and thermoadapted bacteria on the chemical and physical properties of selected types of crude oils at elevated temperatures and pressures. Current studies indicate that during the biotreatment several chemical and physical properties of crude oils are affected. The oils are (1) emulsified; (2) acidified; (3) there is a qualitative and quantitative change inmore » light and heavy fractions of the crudes; (4) there are chemical changes in fractions containing sulfur compounds; (5) there is an apparent reduction in the concentration of trace metals; and (6) the qualitative and quantitative changes appear to be microbial species dependent; and (7) there is a distinction between biodegraded and biotreated oils. The downstream biotechnological crude oil processing research performed thus far is of laboratory scale and has focused on demonstrating the technical feasibility of downstream processing with different types of biocatalysts under a variety of processing conditions. Quantitative economic analysis is the topic of the present project which investigates the economic feasibility of the various biochemical downstream processes which hold promise in upgrading of heavy crudes, such as those found in California, e.g., Monterey-type, Midway Sunset, Honda crudes, and others.« less

Discerning the biochemical stability of pyrogenic C in soils

NASA Astrophysics Data System (ADS)

De la Rosa, José M.; Paneque, Marina; Contreras-Bernal, Lidia; Miller, Ana Z.; Knicker, Heike

2016-04-01

The soil organic matter (SOM) constitutes approximately 2/3 of the global terrestrial C pool, which corresponds to estimated 4000 Pg to a depth of 3 m [1] and therefore, the dynamics of organic carbon (OC) in soils control a large part of the terrestrial C cycle. The term Pyrogenic Carbon (PyC) comprises the whole range of pyrogenic organic materials, from partly charred material through charcoal to soot produced during fire, as well as technical chars (biochars) produced by pyrolysis of biomass. The previously common assumption of PyC being inert has long been proven wrong [2]. In theory, the pyrogenic process confers these materials a longer mean residence time in the soils than their precursors, thus the application of PyC in general and particularly biochar to soil is proposed as a valid approach to establish a significant, long-term sink for atmospheric carbon dioxide in terrestrial ecosystems [3]. Nevertheless, the knowledge concerning the biochemical recalcitrance of PyOM in soils is still limited. This study combines the analysis by 13C solid state Nuclear Magnetic Resonance Spectroscopy (13C NMR), Field Emission Scanning Electron Microscopy (FESEM), analytical pyrolysis (Py-GC/MS) and CO2 emissions in incubated pots of burned and unburned soils as well as in biochar amended and un-amended soils. By using this integrated approach we achieved a more complete understanding of the stability of different forms of PyC in the soil and the chemical changes occurring during aging. Significant differences are found between the stability of PyC. They depend on the nature of the source material, surficial properties of PyC, the pyrolysis process and the soil conditions during aging. Acknowledgements: The Marie Skłodowska-Curie actions (PCIG12-GA-2012-333784-Biocharisma project and PIEF-GA-2012-328689-DECAVE project), and the Spanish Ministry of Economy and Competitiveness (MINECO) (project PCGL2012-37041) are thanked for the financial support of the present study. References: [1] Hernández-Soriano M.C., Peña A., Mingorance MD., 2013. Env. Toxicol. Chem. 32(5), 1027-1032. [2] De la Rosa J.M., Knicker H., 2011. Soil Biol. Biochem. 43, 2368-2373. [3] Sohi S., Lopez-Capel E., Krull E., Bol R., 2009. Rep. No. 05/09. CSIRO. 1834-6618.

Biochemical marker reference values across pediatric, adult, and geriatric ages: establishment of robust pediatric and adult reference intervals on the basis of the Canadian Health Measures Survey.

PubMed

Adeli, Khosrow; Higgins, Victoria; Nieuwesteeg, Michelle; Raizman, Joshua E; Chen, Yunqi; Wong, Suzy L; Blais, David

2015-08-01

Biological covariates such as age and sex can markedly influence biochemical marker reference values, but no comprehensive study has examined such changes across pediatric, adult, and geriatric ages. The Canadian Health Measures Survey (CHMS) collected comprehensive nationwide health information and blood samples from children and adults in the household population and, in collaboration with the Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER), examined biological changes in biochemical markers from pediatric to geriatric age, establishing a comprehensive reference interval database for routine disease biomarkers. The CHMS collected health information, physical measurements, and biosamples (blood and urine) from approximately 12 000 Canadians aged 3-79 years and measured 24 biochemical markers with the Ortho Vitros 5600 FS analyzer or a manual microplate. By use of CLSI C28-A3 guidelines, we determined age- and sex-specific reference intervals, including corresponding 90% CIs, on the basis of specific exclusion criteria. Biochemical marker reference values exhibited dynamic changes from pediatric to geriatric age. Most biochemical markers required some combination of age and/or sex partitioning. Two or more age partitions were required for all analytes except bicarbonate, which remained constant throughout life. Additional sex partitioning was required for most biomarkers, except bicarbonate, total cholesterol, total protein, urine iodine, and potassium. Understanding the fluctuations in biochemical markers over a wide age range provides important insight into biological processes and facilitates clinical application of biochemical markers to monitor manifestation of various disease states. The CHMS-CALIPER collaboration addresses this important evidence gap and allows the establishment of robust pediatric and adult reference intervals. © 2015 American Association for Clinical Chemistry.

Biochemical Platform Processing Integration

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

None

The objective of this project is to facilitate deployment of enzyme-based biomass conversion technology. The immediate goal is to explore integration issues that impact process performance and to demonstrate improved performance of the lower-cost enzymes being developed by Genencor and Novozymes.

In-vitro synthesis of drug metabolites and their screening/characterization using liquid chromatography-mass spectrometry (LC-MS)

USDA-ARS?s Scientific Manuscript database

Drug metabolism is a biochemical process by which drugs and xenobiotics are chemically modified to metabolites, primarily by liver enzymes. Metabolites may sometimes affect cellular therapeutic or toxicological processes, therefore knowledge of metabolic processes is essential for understanding drug...

Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability

PubMed Central

Deerinck, Thomas J.; Chen, Yibang; He, John C.; Ellisman, Mark H.; Iyengar, Ravi

2017-01-01

Kidney podocytes’ function depends on fingerlike projections (foot processes) that interdigitate with those from neighboring cells to form the glomerular filtration barrier. The integrity of the barrier depends on spatial control of dynamics of actin cytoskeleton in the foot processes. We determined how imbalances in regulation of actin cytoskeletal dynamics could result in pathological morphology. We obtained 3-D electron microscopy images of podocytes and used quantitative features to build dynamical models to investigate how regulation of actin dynamics within foot processes controls local morphology. We find that imbalances in regulation of actin bundling lead to chaotic spatial patterns that could impair the foot process morphology. Simulation results are consistent with experimental observations for cytoskeletal reconfiguration through dysregulated RhoA or Rac1, and they predict compensatory mechanisms for biochemical stability. We conclude that podocyte morphology, optimized for filtration, is intrinsically fragile, whereby local transient biochemical imbalances may lead to permanent morphological changes associated with pathophysiology. PMID:28301477

Differentiation of Staphylococcus aureus from freshly slaughtered poultry and strains 'endemic' to processing plants by biochemical and physiological tests.

PubMed

Mead, G C; Norris, A P; Bratchell, N

1989-02-01

A comparison was made of 27 'endemic' strains of Staphylococcus aureus and 35 strains from freshly slaughtered birds, isolated at five commercial slaughterhouses processing chickens or turkeys. Of 112 biochemical and physiological tests used, 74 gave results which differed among the strains. Cluster analysis revealed several distinct groupings which were influenced by strain type, processing plant and bird origin; these included a single group at the 72% level of similarity containing most of the 'endemic' strains. In comparison with strains from freshly slaughtered birds, a higher proportion of 'endemic' strains produced fibrinolysin, alpha-glucosidase and urease and were beta-haemolytic on sheep-blood agar. The 'endemic' type also showed a greater tendency to coagulate human but not bovine plasma, and to produce mucoid growth and clumping. The last two properties, relevant to colonization of processing equipment, were less evident in heart infusion broth than in richer media or process water collected during defeathering of the birds.

Characteristics of 263K Scrapie Agent in Multiple Hamster Species

PubMed Central

Barbian, Kent D.; Race, Brent; Favara, Cynthia; Gardner, Don; Taubner, Lara; Porcella, Stephen; Race, Richard

2009-01-01

Transmissible spongiform encephalopathy (TSE) diseases are known to cross species barriers, but the pathologic and biochemical changes that occur during transmission are not well understood. To better understand these changes, we infected 6 hamster species with 263K hamster scrapie strain and, after each of 3 successive passages in the new species, analyzed abnormal proteinase K (PK)–resistant prion protein (PrPres) glycoform ratios, PrPres PK sensitivity, incubation periods, and lesion profiles. Unique 263K molecular and biochemical profiles evolved in each of the infected hamster species. Characteristics of 263K in the new hamster species seemed to correlate best with host factors rather than agent strain. Furthermore, 2 polymorphic regions of the prion protein amino acid sequence correlated with profile differences in these TSE-infected hamster species. PMID:19193264

Study of a number of biochemical indices of the blood and tissue of dogs after prolonged gamma-radiation

NASA Technical Reports Server (NTRS)

Alers, I.; Alersova, E.; Praslichka, T.; Mishurova, E.; Sedlakova, A.; Malatova, Z.; Akhunov, A. A.; Markelov, B. A.

1974-01-01

The glucose content in blood and the lipid content in serum and tissues of dogs exposed to chronic radiation for 3 and 5 years were studied. In tissues of these animals, the concentration of soluble DNA and DNA contained in DNP was studied in the spleen, lymph node (deep cervical node) and bone marrow of thigh bones. Results indicate that chronic gamma irradiation significantly changes concentrations of glucose in the blood, and that of several lipids in serum and tissues. A reduction in the concentration of DNP in tested organs reflects changes in the relative number of cells with various nuclear cytoplasmic ratios; most pronounced changes in biochemical indices occur in dogs exposed to chronic gamma radiation in doses of 125 rad per year.

Ultrasensitive biochemical sensing device and method of sensing analytes

DOEpatents

Pinchuk, Anatoliy

2017-06-06

Systems and methods biochemically sense a concentration of a ligand using a sensor having a substrate having a metallic nanoparticle array formed onto a surface of the substrate. A light source is incident on the surface. A matrix is deposited over the nanoparticle array and contains a protein adapted to binding the ligand. A detector detects s-polarized and p-polarized light from the reflective surface. Spacing of nanoparticles in the array and wavelength of light are selected such that plasmon resonance occurs with an isotropic point such that -s and -p polarizations of the incident light result in substantially identical surface Plasmon resonance, wherein binding of the ligand to the protein shifts the resonance such that differences between the -S and -P polarizations give in a signal indicative of presence of the ligand.

Techno-economic comparison of biojet fuel production from lignocellulose, vegetable oil and sugar cane juice.

PubMed

Diederichs, Gabriel Wilhelm; Ali Mandegari, Mohsen; Farzad, Somayeh; Görgens, Johann F

2016-09-01

In this study, a techno-economic comparison was performed considering three processes (thermochemical, biochemical and hybrid) for production of jet fuel from lignocellulosic biomass (2G) versus two processes from first generation (1G) feedstocks, including vegetable oil and sugar cane juice. Mass and energy balances were constructed for energy self-sufficient versions of these processes, not utilising any fossil energy sources, using ASPEN Plus® simulations. All of the investigated processes obtained base minimum jet selling prices (MJSP) that is substantially higher than the market jet fuel price (2-4 fold). The 1G process which converts vegetable oil, obtained the lowest MJSPs of $2.22/kg jet fuel while the two most promising 2G processes- the thermochemical (gasification and Fischer-Tropsch synthesis) and hybrid (gasification and biochemical upgrading) processes- reached MJSPs of $2.44/kg and $2.50/kg jet fuel, respectively. According to the economic sensitivity analysis, the feedstock cost and fixed capital investment have the most influence on the MJSP. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biological, biochemical and histological features of Bradybaena similaris (Gastropoda: Pulmonata) infected by Heterorabditis indica (Rhabditida: Heterorhabditidae) strain LPP1.

PubMed

Tunholi, Victor Menezes; Tunholi-Alves, Vinícius Menezes; Monteiro, Caio Oliveira; Silva, Lidiane Cristina da; Dolinski, Cláudia de Melo; Castro, Rosane Nora; Bittencourt, Vânia Rita Elias Pinheiro; Silva, Jairo Pinheiro da; Freire Martins, Isabella Vilhena

2017-08-01

This study investigated the possible biological, biochemical and histological changes in Bradybaena similaris(Gastropoda: Pulmonata) infected by Heterorhabditis indica (Rhabditida: Heterorhabditidae), strain LPP1. Two groups of 16 snails were formed: the control group (unexposed) and the treated group, which was exposed for three weeks to infective juveniles (J 3 ) of H. indica LPP1. The experiment was conducted in duplicate, using a total of 64 snails. After the exposure period, the snails were dissected to collect the hemolymph and tissues, for evaluation of the physiological changes caused by the infection. The number of eggs laid/snail and the viability of these eggs were also assessed as indicators of the reproductive activity of B. similaris. Intense glycogenolysis was accompanied by a significant reduction (p < 0.05) in the glucose content of the hemolymph of the exposed snails, indicating that infection by H. indica induces breakdown of the host's glycemic homeostasis. Significant variations (p < 0.05) in the lactate dehydrogenase activity occurred together with changes in the concentration of pyruvic and lactic acid in the hemolymph of the infected B. similaris snails, corroborating the transition from aerobic to anaerobic metabolism in the hosts. These metabolic alterations reflect the parasitic castration process in this interface. The results suggest that the use of H. indica LPP1 is a potential alternative for biological control of B. similaris. Copyright © 2017 Elsevier Inc. All rights reserved.

Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism

PubMed Central

Faraldo-Gómez, José D.

2017-01-01

The membrane transporter anion exchanger 1 (AE1), or band 3, is a key component in the processes of carbon-dioxide transport in the blood and urinary acidification in the renal collecting duct. In both erythrocytes and the basolateral membrane of the collecting-duct α-intercalated cells, the role of AE1 is to catalyze a one-for-one exchange of chloride for bicarbonate. After decades of biochemical and functional studies, the structure of the transmembrane region of AE1, which catalyzes the anion-exchange reaction, has finally been determined. Each protomer of the AE1 dimer comprises two repeats with inverted transmembrane topologies, but the structures of these repeats differ. This asymmetry causes the putative substrate-binding site to be exposed only to the extracellular space, consistent with the expectation that anion exchange occurs via an alternating-access mechanism. Here, we hypothesize that the unknown, inward-facing conformation results from inversion of this asymmetry, and we propose a model of this state constructed using repeat-swap homology modeling. By comparing this inward-facing model with the outward-facing experimental structure, we predict that the mechanism of AE1 involves an elevator-like motion of the substrate-binding domain relative to the nearly stationary dimerization domain and to the membrane plane. This hypothesis is in qualitative agreement with a wide range of biochemical and functional data, which we review in detail, and suggests new avenues of experimentation. PMID:29167180

Biochemical factors modulating female genital sexual arousal physiology.

PubMed

Traish, Abdulmaged M; Botchevar, Ella; Kim, Noel N

2010-09-01

Female genital sexual arousal responses are complex neurophysiological processes consisting of central and peripheral components that occur following sexual stimulation. The peripheral responses in sexual arousal include genital vasocongestion, engorgement and lubrication resulting from a surge of vaginal and clitoral blood flow. These hemodynamic events are mediated by a host of neurotransmitters and vasoactive agents. To discuss the role of various biochemical factors modulating female genital sexual arousal responses. A comprehensive literature review was conducted using the PubMed database and citations were selected, based on topical relevance, and examined for study methodology and major findings. Data from peer-reviewed publications. Adrenergic as well as non-adrenergic non-cholinergic neurotransmitters play an important role in regulating genital physiological responses by mediating vascular and non-vascular smooth muscle contractility. Vasoactive peptides and neuropeptides also modulate genital sexual responses by regulating vascular and non-vascular smooth muscle cells and epithelial function. The endocrine milieu, particularly sex steroid hormones, is critical in the maintenance of tissue structure and function. Reduced levels of estrogens and androgen are associated with dramatic alterations in genital tissue structure, including the nerve network, as well as the response to physiological modulators. Furthermore, estrogen and androgen deficiency is associated with reduced expression of sex steroid receptors and most importantly with attenuated genital blood flow and lubrication in response to pelvic nerve stimulation. This article provides an integrated framework describing the physiological and molecular basis of various pathophysiological conditions associated with female genital sexual arousal dysfunction. © 2010 International Society for Sexual Medicine.

[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.

Crystallization and preliminary crystallographic analysis of Abp, a GH27 β-L-arabinopyranosidase from Geobacillus stearothermophilus.

PubMed

Lansky, Shifra; Salama, Rachel; Solomon, Vered H; Belrhali, Hassan; Shoham, Yuval; Shoham, Gil

2013-06-01

Geobacillus stearothermophilus T-6 is a thermophilic soil bacterium that possesses an extensive system for the utilization of hemicellulose. The bacterium produces a small number of endo-acting extracellular enzymes that cleave high-molecular-weight hemicellulolytic polymers into short decorated oligosaccharides, which are further hydrolysed into the respective sugar monomers by a battery of intracellular glycoside hydrolases. One of these intracellular processing enzymes is β-L-arabinopyranosidase (Abp), which is capable of removing β-L-arabinopyranose residues from naturally occurring arabino-polysaccharides. As arabino-polymers constitute a significant part of the hemicellulolytic content of plant biomass, their efficient enzymatic degradation presents an important challenge for many potential biotechnological applications. This aspect has led to an increasing interest in the biochemical characterization and structural analysis of this and related hemicellulases. Abp from G. stearothermophilus T-6 has recently been cloned, overexpressed, purified, biochemically characterized and crystallized in our laboratory, as part of its complete structure-function study. The best crystals obtained for this enzyme belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with average unit-cell parameters a = 107.7, b = 202.2, c = 287.3 Å. Full diffraction data sets to 2.3 Å resolution have been collected for both the wild-type enzyme and its D197A catalytic mutant from flash-cooled crystals at 100 K, using synchrotron radiation. These data are currently being used for a high-resolution three-dimensional structure determination of Abp.

Examining the architecture of cellular computing through a comparative study with a computer

PubMed Central

Wang, Degeng; Gribskov, Michael

2005-01-01

The computer and the cell both use information embedded in simple coding, the binary software code and the quadruple genomic code, respectively, to support system operations. A comparative examination of their system architecture as well as their information storage and utilization schemes is performed. On top of the code, both systems display a modular, multi-layered architecture, which, in the case of a computer, arises from human engineering efforts through a combination of hardware implementation and software abstraction. Using the computer as a reference system, a simplistic mapping of the architectural components between the two is easily detected. This comparison also reveals that a cell abolishes the software–hardware barrier through genomic encoding for the constituents of the biochemical network, a cell's ‘hardware’ equivalent to the computer central processing unit (CPU). The information loading (gene expression) process acts as a major determinant of the encoded constituent's abundance, which, in turn, often determines the ‘bandwidth’ of a biochemical pathway. Cellular processes are implemented in biochemical pathways in parallel manners. In a computer, on the other hand, the software provides only instructions and data for the CPU. A process represents just sequentially ordered actions by the CPU and only virtual parallelism can be implemented through CPU time-sharing. Whereas process management in a computer may simply mean job scheduling, coordinating pathway bandwidth through the gene expression machinery represents a major process management scheme in a cell. In summary, a cell can be viewed as a super-parallel computer, which computes through controlled hardware composition. While we have, at best, a very fragmented understanding of cellular operation, we have a thorough understanding of the computer throughout the engineering process. The potential utilization of this knowledge to the benefit of systems biology is discussed. PMID:16849179

Examining the architecture of cellular computing through a comparative study with a computer.

PubMed

Wang, Degeng; Gribskov, Michael

2005-06-22

The computer and the cell both use information embedded in simple coding, the binary software code and the quadruple genomic code, respectively, to support system operations. A comparative examination of their system architecture as well as their information storage and utilization schemes is performed. On top of the code, both systems display a modular, multi-layered architecture, which, in the case of a computer, arises from human engineering efforts through a combination of hardware implementation and software abstraction. Using the computer as a reference system, a simplistic mapping of the architectural components between the two is easily detected. This comparison also reveals that a cell abolishes the software-hardware barrier through genomic encoding for the constituents of the biochemical network, a cell's "hardware" equivalent to the computer central processing unit (CPU). The information loading (gene expression) process acts as a major determinant of the encoded constituent's abundance, which, in turn, often determines the "bandwidth" of a biochemical pathway. Cellular processes are implemented in biochemical pathways in parallel manners. In a computer, on the other hand, the software provides only instructions and data for the CPU. A process represents just sequentially ordered actions by the CPU and only virtual parallelism can be implemented through CPU time-sharing. Whereas process management in a computer may simply mean job scheduling, coordinating pathway bandwidth through the gene expression machinery represents a major process management scheme in a cell. In summary, a cell can be viewed as a super-parallel computer, which computes through controlled hardware composition. While we have, at best, a very fragmented understanding of cellular operation, we have a thorough understanding of the computer throughout the engineering process. The potential utilization of this knowledge to the benefit of systems biology is discussed.

Biochemical characteristics of a free cyanide and total nitrogen assimilating Fusarium oxysporum EKT01/02 isolate from cyanide contaminated soil.

PubMed

Akinpelu, Enoch A; Adetunji, Adewole T; Ntwampe, Seteno K O; Nchu, Felix; Mekuto, Lukhanyo

2017-10-01

Sustainability of nutrient requirements for microbial proliferation on a large scale is a challenge in bioremediation processes. This article presents data on biochemical properties of a free cyanide resistant and total nitrogen assimilating fungal isolate from the rhizosphere of Zea mays (maize) growing in soil contaminated with a cyanide-based pesticide. DNA extracted from this isolate were PCR amplified using universal primers; TEF1-α and ITS. The raw sequence files are available on the NCBI database. Characterisation using biochemical data was obtained using colorimetric reagents analysed with VITEK ® 2 software version 7.01. The data will be informative in selection of biocatalyst for environmental engineering application.

Barnacle cement: a polymerization model based on evolutionary concepts

PubMed Central

Dickinson, Gary H.; Vega, Irving E.; Wahl, Kathryn J.; Orihuela, Beatriz; Beyley, Veronica; Rodriguez, Eva N.; Everett, Richard K.; Bonaventura, Joseph; Rittschof, Daniel

2009-01-01

Summary Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate and invertebrate blood clotting, barnacle cement polymerization was shown to involve proteolytic activation of enzymes and structural precursors, transglutaminase cross-linking and assembly of fibrous proteins. Proteolytic activation of structural proteins maximizes the potential for bonding interactions with other proteins and with the surface. Transglutaminase cross-linking reinforces cement integrity. Remarkably, epitopes and sequences homologous to bovine trypsin and human transglutaminase were identified in barnacle cement with tandem mass spectrometry and/or western blotting. Akin to blood clotting, the peptides generated during proteolytic activation functioned as signal molecules, linking a molecular level event (protein aggregation) to a behavioral response (barnacle larval settlement). Our results draw attention to a highly conserved protein polymerization mechanism and shed light on a long-standing biochemical puzzle. We suggest that barnacle cement polymerization is a specialized form of wound healing. The polymerization mechanism common between barnacle cement and blood may be a theme for many marine animal glues. PMID:19837892

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.

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 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

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.

[Dynamics of biomacromolecules in coherent electromagnetic radiation field].

PubMed

Leshcheniuk, N S; Apanasevich, E E; Tereshenkov, V I

2014-01-01

It is shown that induced oscillations and periodic displacements of the equilibrium positions occur in biomacromolecules in the absence of electromagnetic radiation absorption, due to modulation of interaction potential between atoms and groups of atoms forming the non-valence bonds in macromolecules by the external electromagnetic field. Such "hyperoscillation" state causes inevitably the changes in biochemical properties of macromolecules and conformational transformation times.

Extreme low temperature tolerance in woody plants

Treesearch

G. Richard Strimbeck; Paul G. Schaberg; Carl G. Fossdal; Wolfgang P. Schroder; Trygve D. Kjellsen

2015-01-01

Woody plants in boreal to arctic environments and high mountains survive prolonged exposure to temperatures below -40°C and minimum temperatures below -60°C, and laboratory tests show that many of these species can also survive immersion in liquid nitrogen at -196°C. Studies of biochemical changes that occur during acclimation, including recent proteomic and...

Alternative carbohydrate reserves used in the daily cycle of crassulacean acid metabolism

Treesearch

C.C. Black; J.-Q. Chen; R.L. Doong; M.N. Angelov; Shi-Jean S. Sung

1996-01-01

Each day a massive interlocked biochemical cycle occurs in the green tissues of crassulacean acid metabolism plants.The function of this interlocked cycle, in its simplest context, is to furnish most of the CO2 for CAM plant photosynthesis.In this unified presentation our aims are (1) to divide CAM plants into two metabolic groups, (2) to...

Prediction of the First Variceal Haemorrhage

PubMed Central

1997-01-01

We followed 87 cirrhotic patients with esophageal varices and without previous hemorrhage for a mean period of 24 mo to prospectively evaluate the occurance of variceal bleeding within (early) or after (late) 6 mo from entry and the contribution of portal Doppler ultrasound parameters to the prediction of early and late hemorrhage. Clinical, biochemical, endoscopic and portal Doppler ultrasound parameters were recorded at entry. Variceal bleeding occurred in 22 patients (25.3%). Nine (40.9%) bled within the first 6 mo. Cox regression analysis identified variceal size, cherry-red spots, serum bilirubin and congestion index of the portal vein (the ratio of portal vein [cross-sectional area] and portal blood flow velocity) as the only independent predictors of first variceal hemorrhage. Discriminant analysis was used to find the prognostic index cut off points to identify patients who bled within 6 mo (prognostic group 1) or after 6 mo (prognostic group 2) or remained free of bleeding (prognostic group 3). The cumulative proportion of patients correctly classified was 73% in prognostic group 1, 47% in prognostic group 2 and more than 80% in prognostic group 3. The addition of Doppler ultrasound flowmetry to clinical, biochemical and endoscopic parameter only improved the classification of patients with early bleeding. PMID:9184882

Structuring evolution: biochemical networks and metabolic diversification in birds.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2016-08-25

Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

Neuropathologic Studies of the Baltimore Longitudinal Study of Aging (BLSA)

PubMed Central

O’Brien, Richard J.; Resnick, Susan M.; Zonderman, Alan B.; Ferrucci, Luigi; Crain, Barbara J.; Pletnikova, Olga; Rudow, Gay; Iacono, Diego; Riudavets, Miguel A.; Driscoll, Ira; Price, Donald L.; Martin, Lee J.; Troncoso, Juan C.

2010-01-01

The Baltimore Longitudinal Study of Aging (BLSA) was established in 1958 and is one the oldest prospective studies of aging in the USA and the world. The BLSA is supported by the National Institute of Aging (NIA) and its mission is to learn what happens to people as they get old and how to sort out changes due to aging and from those due to disease or other causes. In 1986, an autopsy program combined with comprehensive neurologic and cognitive evaluations was established in collaboration with the Johns Hopkins University Alzheimer’s Disease Research Center (ADRC). Since then, 211 subjects have undergone autopsy. Here we review the key clinical neuropathological correlations from this autopsy series. The focus is on the morphological and biochemical changes that occur in normal aging, and the early neuropathological changes of neurodegenerative diseases, especially Alzheimer’s disease (AD). We highlight the combined clinical, pathologic, morphometric, and biochemical evidence of asymptomatic AD, a state characterized by normal clinical evaluations in subjects with abundant AD pathology. We conclude that in some individuals, successful cognitive aging results from compensatory mechanisms that occur at the neuronal level (i.e., neuronal hypertrophy and synaptic plasticity) whereas a failure of compensation may culminate in disease. PMID:19661626

GREET Pretreatment Module

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

Adom, Felix K.; Dunn, Jennifer B.; Han, Jeongwoo

2014-09-01

A wide range of biofuels and biochemicals can be produced from cellulosic biomass via different pretreatment technologies that yield sugars. Process simulations of dilute acid and ammonia fiber expansion pretreatment processes and subsequent hydrolysis were developed in Aspen Plus for four lignocellulosic feedstocks (corn stover, miscanthus, switchgrass, and poplar). This processing yields sugars that can be subsequently converted to biofuels or biochemical. Material and energy consumption data from Aspen Plus were then compiled in a new Greenhouses Gases, Regulated Emissions, and Energy Use in Transportation (GREET TM) pretreatment module. The module estimates the cradle-to-gate fossil energy consumption (FEC) and greenhousemore » gas (GHG) emissions associated with producing fermentable sugars. This report documents the data and methodology used to develop this module and the cradle-to-gate FEC and GHG emissions that result from producing fermentable sugars.« less

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

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.

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.

Methamphetamine fails to alter the noradrenergic integrity of the heart.

PubMed

Ruffoli, Riccardo; Soldani, Paola; Pasquali, Livia; Ruggieri, Stefano; Paparelli, Antonio; Fornai, Francesco

2008-10-01

The chronic use of methamphetamine leads to cardiomyopathy and a nigrostriatal dopamine deficiency that partly mimics what occurs in Parkinson's disease. This study examines the cardiac effects occurring after chronic administration of methamphetamine and parkinsonism-inducing neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. Despite the similarities concerning the nigrostriatal dopamine denervation, methamphetamine failed to produce chronic norepinephrine depletion in the heart, thus contrasting with what occurs in Parkinson's disease or after administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. These data suggest that the chronic cardiovascular effects induced by methamphetamine rely on biochemical changes which differ from those activated by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine or during the course of Parkinson's disease.

Prostate specific antigen bounce is related to overall survival in prostate brachytherapy.

PubMed

Hinnen, Karel A; Monninkhof, Evelyn M; Battermann, Jan J; van Roermund, Joep G H; Frank, Steven J; van Vulpen, Marco

2012-02-01

To investigate the association between prostate specific antigen (PSA) bounce and disease outcome after prostate brachytherapy. We analyzed 975 patients treated with (125)I implantation monotherapy between 1992 and 2006. All patients had tumor Stage ≤ 2c, Gleason score ≤ 7 prostate cancer, a minimum follow-up of 2 years with at least four PSA measurements, and no biochemical failure in the first 2 years. Median follow-up was 6 years. Bounce was defined as a PSA elevation of +0.2 ng/mL with subsequent decrease to previous nadir. We used the Phoenix +2 ng/mL definition for biochemical failure. Additional endpoints were disease-specific and overall survival. Multivariate Cox regression analysis was performed to adjust for potential confounding factors. Bounce occurred in 32% of patients, with a median time to bounce of 1.6 years. More than 90% of bounces took place in the first 3 years after treatment and had disappeared within 2 years of onset. Ten-year freedom from biochemical failure, disease-specific survival, and overall survival rates were, respectively, 90%, 99%, and 88% for the bounce group and 70%, 93%, and 82% for the no-bounce group. Only 1 patient (0.3%) died of prostate cancer in the bounce group, compared with 40 patients (6.1%) in the no-bounce group. Adjusted for confounding, a 70% biochemical failure risk reduction was observed for patients experiencing a bounce (hazard ratio 0.31; 95% confidence interval 0.20-0.48). A PSA bounce after prostate brachytherapy is strongly related to better outcome in terms of biochemical failure, disease-specific survival, and overall survival. Copyright © 2012 Elsevier Inc. All rights reserved.

Walking the C4 pathway: past, present, and future.

PubMed

Furbank, Robert T

2017-01-01

The year 2016 marks 50 years since the publication of the seminal paper by Hatch and Slack describing the biochemical pathway we now know as C 4 photosynthesis. This review provides insight into the initial discovery of this pathway, the clues which led Hatch and Slack and others to these definitive experiments, some of the intrigue which surrounds the international activities which led up to the discovery, and personal insights into the future of this research field. While the biochemical understanding of the basic pathways came quickly, the role of the bundle sheath intermediate CO 2 pool was not understood for a number of years, and the nature of C 4 as a biochemical CO 2 pump then linked the unique Kranz anatomy of C 4 plants to their biochemical specialization. Decades of "grind and find biochemistry" and leaf physiology fleshed out the regulation of the pathway and the differences in physiological response to the environment between C 3 and C 4 plants. The more recent advent of plant transformation then high-throughput RNA and DNA sequencing and synthetic biology has allowed us both to carry out biochemical experiments and test hypotheses in planta and to better understand the evolution-driven molecular and genetic changes which occurred in the genomes of plants in the transition from C 3 to C 4 Now we are using this knowledge in attempts to engineer C 4 rice and improve the C 4 engine itself for enhanced food security and to provide novel biofuel feedstocks. The next 50 years of photosynthesis will no doubt be challenging, stimulating, and a drawcard for the best young minds in plant biology. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Walking the C4 pathway: past, present, and future.

PubMed

Furbank, Robert T

2016-07-01

The year 2016 marks 50 years since the publication of the seminal paper by Hatch and Slack describing the biochemical pathway we now know as C4 photosynthesis. This review provides insight into the initial discovery of this pathway, the clues which led Hatch and Slack and others to these definitive experiments, some of the intrigue which surrounds the international activities which led up to the discovery, and personal insights into the future of this research field. While the biochemical understanding of the basic pathways came quickly, the role of the bundle sheath intermediate CO2 pool was not understood for a number of years, and the nature of C4 as a biochemical CO2 pump then linked the unique Kranz anatomy of C4 plants to their biochemical specialization. Decades of "grind and find biochemistry" and leaf physiology fleshed out the regulation of the pathway and the differences in physiological response to the environment between C3 and C4 plants. The more recent advent of plant transformation then high-throughput RNA and DNA sequencing and synthetic biology has allowed us both to carry out biochemical experiments and test hypotheses in planta and to better understand the evolution-driven molecular and genetic changes which occurred in the genomes of plants in the transition from C3 to C4 Now we are using this knowledge in attempts to engineer C4 rice and improve the C4 engine itself for enhanced food security and to provide novel biofuel feedstocks. The next 50 years of photosynthesis will no doubt be challenging, stimulating, and a drawcard for the best young minds in plant biology. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Characterizing canopy biochemistry from imaging spectroscopy and its application to ecosystem studies

USGS Publications Warehouse

Kokaly, R.F.; Asner, Gregory P.; Ollinger, S.V.; Martin, M.E.; Wessman, C.A.

2009-01-01

For two decades, remotely sensed data from imaging spectrometers have been used to estimate non-pigment biochemical constituents of vegetation, including water, nitrogen, cellulose, and lignin. This interest has been motivated by the important role that these substances play in physiological processes such as photosynthesis, their relationships with ecosystem processes such as litter decomposition and nutrient cycling, and their use in identifying key plant species and functional groups. This paper reviews three areas of research to improve the application of imaging spectrometers to quantify non-pigment biochemical constituents of plants. First, we examine recent empirical and modeling studies that have advanced our understanding of leaf and canopy reflectance spectra in relation to plant biochemistry. Next, we present recent examples of how spectroscopic remote sensing methods are applied to characterize vegetation canopies, communities and ecosystems. Third, we highlight the latest developments in using imaging spectrometer data to quantify net primary production (NPP) over large geographic areas. Finally, we discuss the major challenges in quantifying non-pigment biochemical constituents of plant canopies from remotely sensed spectra.

Synergistic Effects of Nitrogen and Potassium on Quantitative Limitations to Photosynthesis in Rice ( Oryza sativa L.).

PubMed

Hou, Wenfeng; Yan, Jinyao; Jákli, Bálint; Lu, Jianwei; Ren, Tao; Cong, Rihuan; Li, Xiaokun

2018-05-23

The inhibition of the net CO 2 assimilation ( A) during photosynthesis is one of the major physiological effects of both nitrogen (N) and potassium (K) deficiencies on rice growth. Whether the reduction in A arises from a limitation in either the diffusion and biochemical fixation of CO 2 or photochemical energy conversion is still debated in relation to N and K deficiencies. In this study, the gas exchange parameters of rice under different N and K levels were evaluated and limitations within the photosynthetic carbon capture process were quantified. A was increased by 17.3 and 12.1% for the supply of N and K, respectively. The suitable N/K ratio should be maintained from 1.42 to 1.50. The limitation results indicated that A is primarily limited by the biochemical process. The stomatal conductance ( L S ), mesophyll conductance ( L M ), and biochemical ( L B ) limitations were regulated by 26.6-79.9, 24.4-54.1, and 44.1-75.2%, respectively, with the N and K supply.

Microbial Production of Short Chain Fatty Acids from Lignocellulosic Biomass: Current Processes and Market.

PubMed

Baumann, Ivan; Westermann, Peter

2016-01-01

Biological production of organic acids from conversion of biomass derivatives has received increased attention among scientists and engineers and in business because of the attractive properties such as renewability, sustainability, degradability, and versatility. The aim of the present review is to summarize recent research and development of short chain fatty acids production by anaerobic fermentation of nonfood biomass and to evaluate the status and outlook for a sustainable industrial production of such biochemicals. Volatile fatty acids (VFAs) such as acetic acid, propionic acid, and butyric acid have many industrial applications and are currently of global economic interest. The focus is mainly on the utilization of pretreated lignocellulosic plant biomass as substrate (the carbohydrate route) and development of the bacteria and processes that lead to a high and economically feasible production of VFA. The current and developing market for VFA is analyzed focusing on production, prices, and forecasts along with a presentation of the biotechnology companies operating in the market for sustainable biochemicals. Finally, perspectives on taking sustainable product of biochemicals from promise to market introduction are reviewed.

Microbial Production of Short Chain Fatty Acids from Lignocellulosic Biomass: Current Processes and Market

PubMed Central

Baumann, Ivan

2016-01-01

Biological production of organic acids from conversion of biomass derivatives has received increased attention among scientists and engineers and in business because of the attractive properties such as renewability, sustainability, degradability, and versatility. The aim of the present review is to summarize recent research and development of short chain fatty acids production by anaerobic fermentation of nonfood biomass and to evaluate the status and outlook for a sustainable industrial production of such biochemicals. Volatile fatty acids (VFAs) such as acetic acid, propionic acid, and butyric acid have many industrial applications and are currently of global economic interest. The focus is mainly on the utilization of pretreated lignocellulosic plant biomass as substrate (the carbohydrate route) and development of the bacteria and processes that lead to a high and economically feasible production of VFA. The current and developing market for VFA is analyzed focusing on production, prices, and forecasts along with a presentation of the biotechnology companies operating in the market for sustainable biochemicals. Finally, perspectives on taking sustainable product of biochemicals from promise to market introduction are reviewed. PMID:27556042

Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

PubMed

Bowsher, Clive G

2011-02-15

Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

Microbiological and biochemical survey on the transition of fermentative processes in Fukuyama pot vinegar brewing.

PubMed

Okazaki, Sachiko; Furukawa, Soichi; Ogihara, Hirokazu; Kawarai, Taketo; Kitada, Chika; Komenou, Akiko; Yamasaki, Makari

2010-06-01

Traditional brewing of Fukuyama pot vinegar is a process that has been continued in Fukuyama, Kagoshima, Japan, for almost 200 years. The entire process proceeds from raw materials, including steamed rice, rice koji (steamed rice grown with a fungus, Aspergillus oryzae) and water, to produce vinegar in roughly capped large pots laid in the open air. No special fermentative manipulation is required, except for scattering dried rice koji (called furi-koji) on the surface of the mash to form a cap-like mat on the surface at the start of brewing. As the biochemical mechanism of the natural transition of the fermentative processes during brewing has not been fully explained, we conducted a microbiological and biochemical study on the transition. First, a distinct biochemical change was observed in the brewing of spring preparation; that is, a sharp decline in pH from 6.5 to 3.5 within the first 5 days of brewing was observed due to lactic acid fermentation. Alcoholic fermentation also proceeded with a sharp increase to 4.5% ethanol within the first 5 days under the acidic conditions, suggesting that saccharification and both fermentations proceed in parallel. Acidic conditions and ethanol accumulation restricted the growth of most microorganisms in the mash, and in turn provided a favorable growth condition for acetic acid bacteria which are acid resistant and "ethanol-philic." Acetic acid was detected from day 16 and gradually increased in concentration, reaching a maximum of 7% at day 70 that was maintained thereafter. Empirically furi-koji naturally sinks into the mash after around day 40 by an unknown mechanism, allowing acetic acid bacteria to easily form pellicles on the mash surface and promoting efficient acetic acid fermentation. Dominant microbial species involved in the three fermentations were identified by denaturing gradient gel electrophoresis analysis using PCR-amplified defined-regions of small rDNA from microorganisms in the brewing mash or colony direct PCR applied to isolated microorganisms from the mash.

German Multicenter Study Investigating 177Lu-PSMA-617 Radioligand Therapy in Advanced Prostate Cancer Patients.

PubMed

Rahbar, Kambiz; Ahmadzadehfar, Hojjat; Kratochwil, Clemens; Haberkorn, Uwe; Schäfers, Michael; Essler, Markus; Baum, Richard P; Kulkarni, Harshad R; Schmidt, Matthias; Drzezga, Alexander; Bartenstein, Peter; Pfestroff, Andreas; Luster, Markus; Lützen, Ulf; Marx, Marlies; Prasad, Vikas; Brenner, Winfried; Heinzel, Alexander; Mottaghy, Felix M; Ruf, Juri; Meyer, Philipp Tobias; Heuschkel, Martin; Eveslage, Maria; Bögemann, Martin; Fendler, Wolfgang Peter; Krause, Bernd Joachim

2017-01-01

177 Lu-labeled PSMA-617 is a promising new therapeutic agent for radioligand therapy (RLT) of patients with metastatic castration-resistant prostate cancer (mCRPC). Initiated by the German Society of Nuclear Medicine, a retrospective multicenter data analysis was started in 2015 to evaluate efficacy and safety of 177 Lu-PSMA-617 in a large cohort of patients. One hundred forty-five patients (median age, 73 y; range, 43-88 y) with mCRPC were treated with 177 Lu-PSMA-617 in 12 therapy centers between February 2014 and July 2015 with 1-4 therapy cycles and an activity range of 2-8 GBq per cycle. Toxicity was categorized by the common toxicity criteria for adverse events (version 4.0) on the basis of serial blood tests and the attending physician's report. The primary endpoint for efficacy was biochemical response as defined by a prostate-specific antigen decline ≥ 50% from baseline to at least 2 wk after the start of RLT. A total of 248 therapy cycles were performed in 145 patients. Data for biochemical response in 99 patients as well as data for physician-reported and laboratory-based toxicity in 145 and 121 patients, respectively, were available. The median follow-up was 16 wk (range, 2-30 wk). Nineteen patients died during the observation period. Grade 3-4 hematotoxicity occurred in 18 patients: 10%, 4%, and 3% of the patients experienced anemia, thrombocytopenia, and leukopenia, respectively. Xerostomia occurred in 8%. The overall biochemical response rate was 45% after all therapy cycles, whereas 40% of patients already responded after a single cycle. Elevated alkaline phosphatase and the presence of visceral metastases were negative predictors and the total number of therapy cycles positive predictors of biochemical response. The present retrospective multicenter study of 177 Lu-PSMA-617 RLT demonstrates favorable safety and high efficacy exceeding those of other third-line systemic therapies in mCRPC patients. Future phase II/III studies are warranted to elucidate the survival benefit of this new therapy in patients with mCRPC. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

The Global Spike: Conserved Dendritic Properties Enable Unique Ca2+ Spike Generation in Low-Threshold Spiking Neurons.

PubMed

Connelly, William M; Crunelli, Vincenzo; Errington, Adam C

2015-11-25

Low-threshold Ca(2+) spikes (LTS) are an indispensible signaling mechanism for neurons in areas including the cortex, cerebellum, basal ganglia, and thalamus. They have critical physiological roles and have been strongly associated with disorders including epilepsy, Parkinson's disease, and schizophrenia. However, although dendritic T-type Ca(2+) channels have been implicated in LTS generation, because the properties of low-threshold spiking neuron dendrites are unknown, the precise mechanism has remained elusive. Here, combining data from fluorescence-targeted dendritic recordings and Ca(2+) imaging from low-threshold spiking cells in rat brain slices with computational modeling, the cellular mechanism responsible for LTS generation is established. Our data demonstrate that key somatodendritic electrical conduction properties are highly conserved between glutamatergic thalamocortical neurons and GABAergic thalamic reticular nucleus neurons and that these properties are critical for LTS generation. In particular, the efficiency of soma to dendrite voltage transfer is highly asymmetric in low-threshold spiking cells, and in the somatofugal direction, these neurons are particularly electrotonically compact. Our data demonstrate that LTS have remarkably similar amplitudes and occur synchronously throughout the dendritic tree. In fact, these Ca(2+) spikes cannot occur locally in any part of the cell, and hence we reveal that LTS are generated by a unique whole-cell mechanism that means they always occur as spatially global spikes. This all-or-none, global electrical and biochemical signaling mechanism clearly distinguishes LTS from other signals, including backpropagating action potentials and dendritic Ca(2+)/NMDA spikes, and has important consequences for dendritic function in low-threshold spiking neurons. Low-threshold Ca(2+) spikes (LTS) are critical for important physiological processes, including generation of sleep-related oscillations, and are implicated in disorders including epilepsy, Parkinson's disease, and schizophrenia. However, the mechanism underlying LTS generation in neurons, which is thought to involve dendritic T-type Ca(2+) channels, has remained elusive due to a lack of knowledge of the dendritic properties of low-threshold spiking cells. Combining dendritic recordings, two-photon Ca(2+) imaging, and computational modeling, this study reveals that dendritic properties are highly conserved between two prominent low-threshold spiking neurons and that these properties underpin a whole-cell somatodendritic spike generation mechanism that makes the LTS a unique global electrical and biochemical signal in neurons. Copyright © 2015 Connelly et al.

Using Simple Manipulatives to Improve Student Comprehension of a Complex Biological Process: Protein Synthesis

ERIC Educational Resources Information Center

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

The effect of ascorbic acid ingestion on the biochemical and physicochemical risk factors associated with calcium oxalate kidney stone formation.

PubMed

Auer, B L; Auer, D; Rodgers, A L

1998-03-01

The present study was undertaken to determine the effect of ingestion of large doses of vitamin C on urinary oxalate excretion and on a number of other biochemical and physicochemical risk factors associated with calcium oxalate urolithiasis. A further objective was to determine urinary ascorbate excretion and to relate it qualitatively to ingested levels of the vitamin and oxalate excretion. Ten healthy males participated in a protocol in which 4 g ascorbic acid was ingested for 5 days. Urines (24 h) were collected prior to, during and after the protocol. The urine collection procedure was designed to allow for the analysis of oxalate in the presence and absence of an EDTA preservative and for the analysis of ascorbic acid by manual titration using 2,6 dichlorophenolindophenol. Physicochemical risk factors such as the calcium oxalate relative supersaturation and Tiselius risk index were calculated from urine composition. The results showed that erroneously high analytical oxalate levels occur in the asence of preservative. In the preserved samples there was no significant increase in oxalate excretion at any stage of the protocol. Ascorbate excretion increased when vitamin C ingestion commenced but levelled out after 24 hours suggesting that saturation of the metabolic pool is reached within 24 hours after which ingested ascorbic acid is excreted unmetabolized in the urine. While transient statistically significant changes occurred in some of the biochemical risk factors, they were not regarded as being clinically significant. There were no changes in either the calcium oxalate relative supersaturation or Tiselius risk index. It is concluded that ingestion of large doses of ascorbic acid does not affect the principal risk factors associated with calcium oxalate kidney stone formation.

Canine Degenerative Myelopathy: Biochemical characterization of superoxide dismutase 1 in the first naturally occurring non-human amyotrophic lateral sclerosis model1

PubMed Central

Crisp, Matthew J.; Beckett, Jeffrey; Coates, Joan R.; Miller, Timothy M.

2013-01-01

Mutations in canine superoxide dismutase 1 (SOD1) have recently been shown to cause canine degenerative myelopathy, a disabling neurodegenerative disorder affecting specific breeds of dogs characterized by progressive motor neuron loss and paralysis until death, or more common, euthanasia. This discovery makes canine degenerative myelopathy the first and only naturally occurring non-human model of amyotrophic lateral sclerosis (ALS), closely paralleling the clinical, pathological, and genetic presentation of its human counterpart, SOD1-mediated familial ALS. To further understand the biochemical role that canine SOD1 plays in this disease and how it may be similar to human SOD1, we characterized the only two SOD1 mutations described in affected dogs to date, E40K and T18S. We show that a detergent-insoluble species of mutant SOD1 is present in spinal cords of affected dogs that increases with disease progression. Our in vitro results indicate that both canine SOD1 mutants form enzymatically active dimers, arguing against a loss of function in affected homozygous animals. Further studies show that these mutants, like most human SOD1 mutants, have an increased propensity to form aggregates in cell culture, with 10-20% of cells possessing visible aggregates. Creation of the E40K mutation in human SOD1 recapitulates the normal enzymatic activity but not the aggregation propensity seen with the canine mutant. Our findings lend strong biochemical support to the toxic role of SOD1 in canine degenerative myelopathy and establish close parallels for the role mutant SOD1 plays in both canine and human disorders. PMID:23707216

Canine degenerative myelopathy: biochemical characterization of superoxide dismutase 1 in the first naturally occurring non-human amyotrophic lateral sclerosis model.

PubMed

Crisp, Matthew J; Beckett, Jeffrey; Coates, Joan R; Miller, Timothy M

2013-10-01

Mutations in canine superoxide dismutase 1 (SOD1) have recently been shown to cause canine degenerative myelopathy, a disabling neurodegenerative disorder affecting specific breeds of dogs characterized by progressive motor neuron loss and paralysis until death, or more common, euthanasia. This discovery makes canine degenerative myelopathy the first and only naturally occurring non-human model of amyotrophic lateral sclerosis (ALS), closely paralleling the clinical, pathological, and genetic presentation of its human counterpart, SOD1-mediated familial ALS. To further understand the biochemical role that canine SOD1 plays in this disease and how it may be similar to human SOD1, we characterized the only two SOD1 mutations described in affected dogs to date, E40K and T18S. We show that a detergent-insoluble species of mutant SOD1 is present in spinal cords of affected dogs that increases with disease progression. Our in vitro results indicate that both canine SOD1 mutants form enzymatically active dimers, arguing against a loss of function in affected homozygous animals. Further studies show that these mutants, like most human SOD1 mutants, have an increased propensity to form aggregates in cell culture, with 10-20% of cells possessing visible aggregates. Creation of the E40K mutation in human SOD1 recapitulates the normal enzymatic activity but not the aggregation propensity seen with the canine mutant. Our findings lend strong biochemical support to the toxic role of SOD1 in canine degenerative myelopathy and establish close parallels for the role mutant SOD1 plays in both canine and human disorders. Copyright © 2013 Elsevier Inc. All rights reserved.

Intranuclear Aggregates Precede Clinical Onset in Oculopharyngeal Muscular Dystrophy.

PubMed

van der Sluijs, B M; Raz, V; Lammens, M; van den Heuvel, L P; Voermans, N C; van Engelen, B G M

2016-03-03

Oculopharyngeal muscular dystrophy (OPMD) has long been characterized by a combination of bilateral ptosis and dysphagia and subsequent limb girdle weakness. The role of the typical intranuclear inclusion in the pathophysiology is unresolved. The aim of this study was to describe the clinical and histopathological features of oculopharyngeal muscular dystrophy (OPMD). We examined this in a Dutch cohort including presymptomatic Ala-expanded-PABPN1 carriers and late symptomatic patients. We performed a prospective, observational study in OPMD patients and adult children of genetically confirmed OPMD patients. The study includes a structured history, a detailed neurological examination, muscle histology and biochemical analysis. Forty patients and 18 adult children participated in this study, among whom were six presymptomatic mutation carriers. One patient died during the study and had given permission to autopsy. In addition to the characteristic OPMD symptoms including ptosis and dysphagia, other symptoms such as limb girdle and axial weakness, and external ophthalmoplegia were frequently observed. Intranuclear aggregates were observed in the biopsies of presymptomatic carriers. Biochemical analysis of the biopsies of the presymptomatic carriers showed no mitochondrial dysfunction. The autopsy showed that muscle weakness correlated with histopathological findings in five different muscles in an individual patient. The main findings of this nationwide study are the presence of intranuclear aggregates before clinical onset and the absence of mitochondrial changes in Ala-expanded-PABPN1 carriers. This indicates that the expression of Ala-expanded-PABPN1 causes the formation of nuclear aggregates before the onset of muscle weakness. Normal results of biochemical analysis in presymptomatic carriers suggest that possible mitochondrial dysfunction occurs later. Furthermore we confirmed that limb girdle weakness occurs frequently in Dutch OPMD patients. This study thus expands the OPMD research towards characterization of presymptomatic carriers.

Different phospholipase-C-coupled receptors differentially regulate capacitative and non-capacitative Ca2+ entry in A7r5 cells

PubMed Central

Moneer, Zahid; Pino, Irene; Taylor, Emily J. A.; Broad, Lisa M.; Liu, Yingjie; Tovey, Stephen C.; Staali, Leila; Taylor, Colin W.

2005-01-01

Several receptors, including those for AVP (Arg8-vasopressin) and 5-HT (5-hydroxytryptamine), share an ability to stimulate PLC (phospholipase C) and so production of IP3 (inositol 1,4,5-trisphosphate) and DAG (diacylglycerol) in A7r5 vascular smooth muscle cells. Our previous analysis of the effects of AVP on Ca2+ entry [Moneer, Dyer and Taylor (2003) Biochem. J. 370, 439–448] showed that arachidonic acid released from DAG stimulated NO synthase. NO then stimulated an NCCE (non-capacitative Ca2+ entry) pathway, and, via cGMP and protein kinase G, it inhibited CCE (capacitative Ca2+ entry). This reciprocal regulation ensured that, in the presence of AVP, all Ca2+ entry occurred via NCCE to be followed by a transient activation of CCE only when AVP was removed [Moneer and Taylor (2002) Biochem. J. 362, 13–21]. We confirm that, in the presence of AVP, all Ca2+ entry occurs via NCCE, but 5-HT, despite activating PLC and evoking release of Ca2+ from intracellular stores, stimulates Ca2+ entry only via CCE. We conclude that two PLC-coupled receptors differentially regulate CCE and NCCE. We also address evidence that, in some A7r5 cells lines, AVP fails either to stimulate NCCE or inhibit CCE [Brueggemann, Markun, Barakat, Chen and Byron (2005) Biochem. J. 388, 237–244]. Quantitative PCR analysis suggests that these cells predominantly express TRPC1 (transient receptor potential canonical 1), whereas cells in which AVP reciprocally regulates CCE and NCCE express a greater variety of TRPC subtypes (TRPC1=6>2>3). PMID:15918794

Dynamic control and information processing in chemical reaction systems by tuning self-organization behavior

NASA Astrophysics Data System (ADS)

Lebiedz, Dirk; Brandt-Pollmann, Ulrich

2004-09-01

Specific external control of chemical reaction systems and both dynamic control and signal processing as central functions in biochemical reaction systems are important issues of modern nonlinear science. For example nonlinear input-output behavior and its regulation are crucial for the maintainance of the life process that requires extensive communication between cells and their environment. An important question is how the dynamical behavior of biochemical systems is controlled and how they process information transmitted by incoming signals. But also from a general point of view external forcing of complex chemical reaction processes is important in many application areas ranging from chemical engineering to biomedicine. In order to study such control issues numerically, here, we choose a well characterized chemical system, the CO oxidation on Pt(110), which is interesting per se as an externally forced chemical oscillator model. We show numerically that tuning of temporal self-organization by input signals in this simple nonlinear chemical reaction exhibiting oscillatory behavior can in principle be exploited for both specific external control of dynamical system behavior and processing of complex information.

Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations

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

Gupta, Chinmaya; López, José Manuel; Azencott, Robert

Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemicalmore » Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay.« less

BASIC BIOCHEMICAL AND CLINICAL ASPECTS OF NONINVASIVE TESTS HELIC.

PubMed

Dmitrienko, M A; Dmitrienko, V S; Kornienko, E A; Parolova, N I; Colomina, E O; Aronov, E B

Biochemical process that lay in the core of non-invasive detection of Helico ho cter pylod with the help of HELIC Ammonia breath test, manufactured by AMA Co Ltd., St.Petersburg, is shown. Patents from various countries, describing ammonia as H.pyiori diagnostic marker, are reviewed. Approaches for evaluation of efficacy of the test-system are analyzed, validation and verification data is provided. High diagnostic characteristics are confirmed by the results of comparative studies on patients of different age groups, reaching 97% sensitivity and 96% specificity.

Time-lapse Raman imaging of osteoblast differentiation

PubMed Central

Hashimoto, Aya; Yamaguchi, Yoshinori; Chiu, Liang-da; Morimoto, Chiaki; Fujita, Katsumasa; Takedachi, Masahide; Kawata, Satoshi; Murakami, Shinya; Tamiya, Eiichi

2015-01-01

Osteoblastic mineralization occurs during the early stages of bone formation. During this mineralization, hydroxyapatite (HA), a major component of bone, is synthesized, generating hard tissue. Many of the mechanisms driving biomineralization remain unclear because the traditional biochemical assays used to investigate them are destructive techniques incompatible with viable cells. To determine the temporal changes in mineralization-related biomolecules at mineralization spots, we performed time-lapse Raman imaging of mouse osteoblasts at a subcellular resolution throughout the mineralization process. Raman imaging enabled us to analyze the dynamics of the related biomolecules at mineralization spots throughout the entire process of mineralization. Here, we stimulated KUSA-A1 cells to differentiate into osteoblasts and conducted time-lapse Raman imaging on them every 4 hours for 24 hours, beginning 5 days after the stimulation. The HA and cytochrome c Raman bands were used as markers for osteoblastic mineralization and apoptosis. From the Raman images successfully acquired throughout the mineralization process, we found that β-carotene acts as a biomarker that indicates the initiation of osteoblastic mineralization. A fluctuation of cytochrome c concentration, which indicates cell apoptosis, was also observed during mineralization. We expect time-lapse Raman imaging to help us to further elucidate osteoblastic mineralization mechanisms that have previously been unobservable. PMID:26211729

Bioinspired catalytic generation of high-valent cobalt-oxo species by the axially coordinated CoPc on pyridine-functionalized MWCNTs for the elimination of organic contaminants

NASA Astrophysics Data System (ADS)

Li, Nan; Wang, Ying; Wu, Chenren; Lu, Wangyang; Pei, Kemei; Chen, Wenxing

2018-03-01

Enzymes have always been a source of inspiration for the design and improvement of catalysts. Many examples are occurring in heme/non-heme metalloenzymes with the generation of active high-valent metal-oxo intermediates that are controlled by the surrounding amino acids/protein and axial residue ligands, facilitating the efficient oxidation of substrates in biochemical processes. Here, the high-valent cobalt-oxo species have been formed during the heterolysis of H2O2 activated by the bioinspired catalyst, axially coordinated cobalt phthalocyanine (CoPc) on pyridine-functionalized multi-walled carbon nanotubes (MWCNTs-Py), characterized by ultraviolet-visible and X-ray photoelectron spectroscopy. Formation process of the active cobalt-oxo species has been further confirmed by electrospray ionization mass spectrometry analysis and the results from the density functional theory (B3LYP/6-311G) calculations. Such high-valent cobalt-oxo species exhibit high reactivity and enough persistence for the oxidation of the target substrate, C.I. Acid Red 1. The oxidation products are nearly biodegradable small molecules identified by ultra-performance liquid chromatography/high-definition mass spectrometry. This strategy provides a foundation on developing efficient and persistent catalytic system, in particular oxidation processes based on the complex catalysts with N4 macrocycle structures.

Oxidative stability of fermented meat products.

PubMed

Wójciak, Karolina M; Dolatowski, Zbigniew J

2012-04-02

Meat and meat products, which form a major part of our diet, are very susceptible to quality changes resulting from oxidative processes. Quality of fermented food products depends on the course of various physicochemical and biochemical processes. Oxidation of meat components in raw ripening products may be the result of enzymatic changes occurring as a result of activity of enzymes originating in tissues and microorganisms, as well as lipid peroxidation by free radicals. Primary and secondary products of lipid oxidation are extremely reactive and react with other components of meat, changing their physical and chemical properties. Oxidised proteins take on a yellowish, red through brown hue. Products of lipid and protein degradation create a specific flavour and aroma ; furthermore, toxic substances (such as biogenic amines or new substances) are formed as a result of interactions between meat components, e.g. protein-lipid or protein-protein combinations, as well as transverse bonds in protein structures. Oxidation of meat components in raw ripening products is a particularly difficult process. On the one hand it is essential, since the enzymatic and non-enzymatic lipid oxidation creates flavour and aroma compounds characteristic for ripening products; on the other hand excessive amounts or transformations of those compounds may cause the fermented meat product to become a risk to health.

Time-lapse Raman imaging of osteoblast differentiation

NASA Astrophysics Data System (ADS)

Hashimoto, Aya; Yamaguchi, Yoshinori; Chiu, Liang-Da; Morimoto, Chiaki; Fujita, Katsumasa; Takedachi, Masahide; Kawata, Satoshi; Murakami, Shinya; Tamiya, Eiichi

2015-07-01

Osteoblastic mineralization occurs during the early stages of bone formation. During this mineralization, hydroxyapatite (HA), a major component of bone, is synthesized, generating hard tissue. Many of the mechanisms driving biomineralization remain unclear because the traditional biochemical assays used to investigate them are destructive techniques incompatible with viable cells. To determine the temporal changes in mineralization-related biomolecules at mineralization spots, we performed time-lapse Raman imaging of mouse osteoblasts at a subcellular resolution throughout the mineralization process. Raman imaging enabled us to analyze the dynamics of the related biomolecules at mineralization spots throughout the entire process of mineralization. Here, we stimulated KUSA-A1 cells to differentiate into osteoblasts and conducted time-lapse Raman imaging on them every 4 hours for 24 hours, beginning 5 days after the stimulation. The HA and cytochrome c Raman bands were used as markers for osteoblastic mineralization and apoptosis. From the Raman images successfully acquired throughout the mineralization process, we found that β-carotene acts as a biomarker that indicates the initiation of osteoblastic mineralization. A fluctuation of cytochrome c concentration, which indicates cell apoptosis, was also observed during mineralization. We expect time-lapse Raman imaging to help us to further elucidate osteoblastic mineralization mechanisms that have previously been unobservable.

Yeast community associated with the solid state fermentation of traditional Chinese Maotai-flavor liquor.

PubMed

Wu, Qun; Chen, Liangqiang; Xu, Yan

2013-09-02

Yeasts are the most important group of microorganisms contributing to liquor quality in the solid-state fermentation process of Chinese Maotai-flavor liquor. There occurred a complex yeast community structure during this process, including stages of Daqu (the starter) making, stacking fermentation on the ground and liquor fermentation in the pits. In the Daqu making stage, few yeast strains accumulated. However, the stacking fermentation stage accumulated nine yeast species with different physio-biochemical characteristics. But only four species kept dominant until liquor fermentation, which were Zygosaccharomyces bailii, Saccharomyces cerevisiae, Pichia membranifaciens, and Schizosaccharomyces pombe, implying their important functions in liquor making. The four species tended to inhabit in different locations of the stack and pits during stacking and liquor fermentation, due to the condition heterogeneity of the solid-state fermentation, including the different fermentation temperature profiles and oxygen density in different locations. Moreover, yeast population was much larger in the upper layer than that in the middle and bottom layers in liquor fermentation, which was in accordance with the profile of reducing sugar consumption and ethanol production. This was a systematical investigation of yeast community structure dynamics in the Maotai-flavor liquor fermentation process. It would be of help to understand the fermentative mechanism in solid-state fermentation for Maotai-flavor liquor. © 2013.

Metabolomics-Based Elucidation of Active Metabolic Pathways in Erythrocytes and HSC-Derived Reticulocytes.

PubMed

Srivastava, Anubhav; Evans, Krystal J; Sexton, Anna E; Schofield, Louis; Creek, Darren J

2017-04-07

A detailed analysis of the metabolic state of human-stem-cell-derived erythrocytes allowed us to characterize the existence of active metabolic pathways in younger reticulocytes and compare them to mature erythrocytes. Using high-resolution LC-MS-based untargeted metabolomics, we found that reticulocytes had a comparatively much richer repertoire of metabolites, which spanned a range of metabolite classes. An untargeted metabolomics analysis using stable-isotope-labeled glucose showed that only glycolysis and the pentose phosphate pathway actively contributed to the biosynthesis of metabolites in erythrocytes, and these pathways were upregulated in reticulocytes. Most metabolite species found to be enriched in reticulocytes were residual pools of metabolites produced by earlier erythropoietic processes, and their systematic depletion in mature erythrocytes aligns with the simplification process, which is also seen at the cellular and the structural level. Our work shows that high-resolution LC-MS-based untargeted metabolomics provides a global coverage of the biochemical species that are present in erythrocytes. However, the incorporation of stable isotope labeling provides a more accurate description of the active metabolic processes that occur in each developmental stage. To our knowledge, this is the first detailed characterization of the active metabolic pathways of the erythroid lineage, and it provides a rich database for understanding the physiology of the maturation of reticulocytes into mature erythrocytes.

Ophthalmic acid is a marker of oxidative stress in plants as in animals.

PubMed

Servillo, Luigi; Castaldo, Domenico; Giovane, Alfonso; Casale, Rosario; D'Onofrio, Nunzia; Cautela, Domenico; Balestrieri, Maria Luisa

2018-04-01

Ophthalmic acid (OPH), γ-glutamyl-L-2-aminobutyryl-glycine, a tripeptide analogue of glutathione (GSH), has recently captured considerable attention as a biomarker of oxidative stress in animals. The OPH and GSH biosynthesis, as well as some biochemical behaviors, are very similar. Here, we sought to investigate the presence of OPH in plants and its possible relationship with GSH, known to possess multiple functions in the plant development, growth and response to environmental changes. HPLC-ESI-MS/MS analysis was used to examine the occurrence of OPH in leaves from various plant species, and flours from several plant seeds. Different types of oxidative stress, i.e., water, dark, paraquat, and cadmium stress, were induced in rye, barley, oat, and winter wheat leaves to evaluate the effects on the levels of OPH and its metabolic precursors. OPH and its dipeptide precursor, γ-glutamyl-2-aminobutyric acid, were found to occur in phylogenetically distant plants. Interestingly, the levels of OPH were tightly associated with the oxidative stress tested. Levels of OPH precursors, γ-glutamyl-2-aminobutyric acid and 2-aminobutyric acid, the latter efficiently formed in plants via biosynthetic pathways absent in the animal kingdom, were also found to increase during oxidative stress. OPH occurs in plants and its levels are tightly associated with oxidative stress. OPH behaves as an oxidative stress marker and its biogenesis might occur through a biochemical pathway common to many living organisms. Copyright © 2018 Elsevier B.V. All rights reserved.

Modeling nitrous oxide production during biological nitrogen removal via nitrification and denitrification: extensions to the general ASM models.

PubMed

Ni, Bing-Jie; Ruscalleda, Maël; Pellicer-Nàcher, Carles; Smets, Barth F

2011-09-15

Nitrous oxide (N(2)O) can be formed during biological nitrogen (N) removal processes. In this work, a mathematical model is developed that describes N(2)O production and consumption during activated sludge nitrification and denitrification. The well-known ASM process models are extended to capture N(2)O dynamics during both nitrification and denitrification in biological N removal. Six additional processes and three additional reactants, all involved in known biochemical reactions, have been added. The validity and applicability of the model is demonstrated by comparing simulations with experimental data on N(2)O production from four different mixed culture nitrification and denitrification reactor study reports. Modeling results confirm that hydroxylamine oxidation by ammonium oxidizers (AOB) occurs 10 times slower when NO(2)(-) participates as final electron acceptor compared to the oxic pathway. Among the four denitrification steps, the last one (N(2)O reduction to N(2)) seems to be inhibited first when O(2) is present. Overall, N(2)O production can account for 0.1-25% of the consumed N in different nitrification and denitrification systems, which can be well simulated by the proposed model. In conclusion, we provide a modeling structure, which adequately captures N(2)O dynamics in autotrophic nitrification and heterotrophic denitrification driven biological N removal processes and which can form the basis for ongoing refinements.

Steam gasification of a thermally pretreated high lignin corn stover simultaneous saccharification and fermentation digester residue

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

Howe, Daniel T.; Taasevigen, Danny; Garcia-Perez, Manuel

Efficient conversion of all components in lignocellulosic biomass is essential to realizing economic feasibility of biorefineries. However, when utilizing biochemical pathways, lignin cannot be fermented. Furthermore, the high lignin and high ash residue resulting from simultaneous saccharification and fermentation (SSF) reactors is difficult to thermochemically process due to feed line plugging and bed agglomeration. In this study a corn stover SSF digester residue was thermally pretreated at 300°C for 22.5 minutes (min) and then gasified in a bubbling fluidized bed gasifier to study the effect of thermal pretreatment on its processing behavior. Untreated, pelletized SSF residue was gasified at themore » same conditions to establish the baseline processing behavior. Results indicate that the thermal pretreatment process removes a substantial portion of the polar and non-polar extractives, with a resultant increase in the concentration of lignin, cellulose, and ash. Feed line plugging was not observed, although bed agglomeration was occurring at similar rates for both feedstocks, suggesting that overall ash content is the most important factor affecting bed agglomeration. Benzene, phenol, and polyaromatic hydrocarbons in the tar were present at higher concentrations in the treated material, with higher tar loading in the product gas. Total product gas generation is lower for the treated material, although the overall gas composition does not change.« less

Development of reactor configurations for an electrofuels platform utilizing genetically modified iron oxidizing bacteria for the reduction of CO2 to biochemicals.

PubMed

Guan, Jingyang; Berlinger, Sarah A; Li, Xiaozheng; Chao, Zhongmou; Sousa E Silva, Victor; Banta, Scott; West, Alan C

2017-03-10

Electrofuels processes are potentially promising platforms for biochemical production from CO 2 using renewable energy. When coupled to solar panels, this approach could avoid the inefficiencies of photosynthesis and there is no competition with food agriculture. In addition, these systems could potentially be used to store intermittent or stranded electricity generated from other renewable sources. Here we develop reactor configurations for continuous electrofuels processes to convert electricity and CO 2 to isobutyric acid (IBA) using genetically modified (GM) chemolithoautotrophic Acidithiobacillus ferrooxidans. These cells oxidize ferrous iron which can be electrochemically reduced. During two weeks of cultivation on ferrous iron, stable cell growth and continuous IBA production from CO 2 were achieved in a process where media was circulated between electrochemical and biochemical rectors. An alternative process with an additional electrochemical cell for accelerated ferrous production was developed, and this system achieved an almost three-fold increase in steady state cell densities, and an almost 4-fold increase in the ferrous iron oxidation rate. Combined, this led to an almost 8-fold increase in the steady state volumetric productivity of IBA up to 0.063±0.012mg/L/h, without a decline in energy efficiency from previous work. Continued development of reactor configurations which can increase the delivery of energy to the genetically modified cells will be required to increase product titers and volumetric productivities. Copyright © 2017 Elsevier B.V. All rights reserved.

Proton mediated control of biochemical reactions with bioelectronic pH modulation

NASA Astrophysics Data System (ADS)

Deng, Yingxin; Miyake, Takeo; Keene, Scott; Josberger, Erik E.; Rolandi, Marco

2016-04-01

In Nature, protons (H+) can mediate metabolic process through enzymatic reactions. Examples include glucose oxidation with glucose dehydrogenase to regulate blood glucose level, alcohol dissolution into carboxylic acid through alcohol dehydrogenase, and voltage-regulated H+ channels activating bioluminescence in firefly and jellyfish. Artificial devices that control H+ currents and H+ concentration (pH) are able to actively influence biochemical processes. Here, we demonstrate a biotransducer that monitors and actively regulates pH-responsive enzymatic reactions by monitoring and controlling the flow of H+ between PdHx contacts and solution. The present transducer records bistable pH modulation from an “enzymatic flip-flop” circuit that comprises glucose dehydrogenase and alcohol dehydrogenase. The transducer also controls bioluminescence from firefly luciferase by affecting solution pH.

Nanodiscs in Membrane Biochemistry and Biophysics.

PubMed

Denisov, Ilia G; Sligar, Stephen G

2017-03-22

Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.

Loss of trabeculae by mechano-biological means may explain rapid bone loss in osteoporosis.

PubMed

Mulvihill, Brianne M; McNamara, Laoise M; Prendergast, Patrick J

2008-10-06

Osteoporosis is characterized by rapid and irreversible loss of trabecular bone tissue leading to increased bone fragility. In this study, we hypothesize two causes for rapid loss of bone trabeculae; firstly, the perforation of trabeculae is caused by osteoclasts resorbing a cavity so deep that it cannot be refilled and, secondly, the increases in bone tissue elastic modulus lead to increased propensity for trabecular perforation. These hypotheses were tested using an algorithm that was based on two premises: (i) bone remodelling is a turnover process that repairs damaged bone tissue by resorbing and returning it to a homeostatic strain level and (ii) osteoblast attachment is under biochemical control. It was found that a mechano-biological algorithm based on these premises can simulate the remodelling cycle in a trabecular strut where damaged bone is resorbed to form a pit that is subsequently refilled with new bone. Furthermore, the simulation predicts that there is a depth of resorption cavity deeper than which refilling of the resorption pits is impossible and perforation inevitably occurs. However, perforation does not occur by a single fracture event but by continual removal of microdamage after it forms beneath the resorption pit. The simulation also predicts that perforations would occur more easily in trabeculae that are more highly mineralized (stiffer). Since both increased osteoclast activation rates and increased mineralization have been measured in osteoporotic bone, either or both may contribute to the rapid loss of trabecular bone mass observed in osteoporotic patients.

Biological activity of antitumoural MGBG: the structural variable.

PubMed

Marques, M P M; Gil, F P S C; Calheiros, R; Battaglia, V; Brunati, A M; Agostinelli, E; Toninello, A

2008-05-01

The present study aims at determining the structure-activity relationships (SAR's) ruling the biological function of MGBG (methylglyoxal bis(guanylhydrazone)), a competitive inhibitor of S-adenosyl-L-methionine decarboxylase displaying anticancer activity, involved in the biosynthesis of the naturally occurring polyamines spermidine and spermine. In order to properly understand its biochemical activity, MGBG's structural preferences at physiological conditions were ascertained, by quantum mechanical (DFT) calculations.

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 effects of chlorpyrifos on two developmental stages of Xenopus laevis.

PubMed

Richards, Sean M; Kendall, Ron J

2002-09-01

Abstract-The effects of a 96-h static exposure to chlorpyrifos were examined in two developmental stages of larval Xenopus laevis (premetamorph and metamorph). Measures of effect included mortality, deformity, cholinesterase (ChE) activity, and DNA and protein concentration. All parameters indicated that metamorphs were more sensitive than were premetamorphs. For larvae exposed as premetamorphs, the median lethal concentration and median effective concentration were 14.6 mg/L and 1.71 mg/L; for those exposed as metamorphs, values were 0.56 mg/L and 0.24 mg/L, respectively. Cholinesterase activity was the most sensitive biochemical parameter. Exposure to chlorpyrifos at 0.01 mg/L caused significant decreases in the ChE activity of metamorphs; 0.1 mg/L significantly decreased premetamorph ChE activity. Metamorph DNA was significantly decreased at 0.1 mg/L; premetamorph DNA was not reduced until exposure to 1.0 mg/L. Whole-body protein was the least sensitive biochemical measure of effect. Premetamorphs did not experience a reduction in protein concentrations. Metamorph protein concentration was significantly decreased at 1.0 mg/L. Based on current surface water data, the most sensitive effect would not have a high probability (< or = 4.2%) of occurring in the environment.

Mechanisms for Variation of Cellular P Stoichiometry: Diverse Cellular Phosphorus Allocation Strategies Across Microbial Groups from the Sargasso Sea

NASA Astrophysics Data System (ADS)

Popendorf, K.; Duhamel, S.

2016-02-01

Phosphorus is the least abundant of the three major macronutrients that define the canonical Redfield ratio, but its place in the backbone of nucleic acids and as an energy trafficking molecule lays a lower bound of cellular phosphorus content that is essential for all life. In addition to forming DNA, RNA, and adenosine triphosphate (ATP), significant amounts of cellular phosphorus may also be allocated to the production of phospholipids and polyphosphate. These latter two biochemicals in particular may occur in significant but highly variable amounts across different microbial groups, and the variation in cellular allocation to these biochemicals may be a contributing factor in defining the elemental stoichiometry of microbes. We investigated this variation in cellular phosphorus allocation across the most abundant microbial groups in the P-depleted Sargasso Sea: Prochlorococcus, Synechococcus, and heterotrophic bacteria. By coupling radioisotope tracing of phosphate and ATP with cell sorting flow cytometry and subsequent biochemical extractions, we made novel measurements of the P allocation to DNA, phospholipids, and polyphosphate in individual microbial groups from environmental populations. These results provide new insights into the cellular mechanisms of variation in stoichiometry and different microbial strategies for adaptation to low-P environments.

Improved ADM1 model for anaerobic digestion process considering physico-chemical reactions.

PubMed

Zhang, Yang; Piccard, Sarah; Zhou, Wen

2015-11-01

The "Anaerobic Digestion Model No. 1" (ADM1) was modified in the study by improving the bio-chemical framework and integrating a more detailed physico-chemical framework. Inorganic carbon and nitrogen balance terms were introduced to resolve the discrepancies in the original bio-chemical framework between the carbon and nitrogen contents in the degraders and substrates. More inorganic components and solids precipitation processes were included in the physico-chemical framework of ADM1. The modified ADM1 was validated with the experimental data and used to investigate the effects of calcium ions, magnesium ions, inorganic phosphorus and inorganic nitrogen on anaerobic digestion in batch reactor. It was found that the entire anaerobic digestion process might exist an optimal initial concentration of inorganic nitrogen for methane gas production in the presence of calcium ions, magnesium ions and inorganic phosphorus. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational modelling of oxygenation processes in enzymes and biomimetic model complexes.

PubMed

de Visser, Sam P; Quesne, Matthew G; Martin, Bodo; Comba, Peter; Ryde, Ulf

2014-01-11

With computational resources becoming more efficient and more powerful and at the same time cheaper, computational methods have become more and more popular for studies on biochemical and biomimetic systems. Although large efforts from the scientific community have gone into exploring the possibilities of computational methods for studies on large biochemical systems, such studies are not without pitfalls and often cannot be routinely done but require expert execution. In this review we summarize and highlight advances in computational methodology and its application to enzymatic and biomimetic model complexes. In particular, we emphasize on topical and state-of-the-art methodologies that are able to either reproduce experimental findings, e.g., spectroscopic parameters and rate constants, accurately or make predictions of short-lived intermediates and fast reaction processes in nature. Moreover, we give examples of processes where certain computational methods dramatically fail.

Understanding force-generating microtubule systems through in vitro reconstitution

PubMed Central

Kok, Maurits; Dogterom, Marileen

2016-01-01

ABSTRACT Microtubules switch between growing and shrinking states, a feature known as dynamic instability. The biochemical parameters underlying dynamic instability are modulated by a wide variety of microtubule-associated proteins that enable the strict control of microtubule dynamics in cells. The forces generated by controlled growth and shrinkage of microtubules drive a large range of processes, including organelle positioning, mitotic spindle assembly, and chromosome segregation. In the past decade, our understanding of microtubule dynamics and microtubule force generation has progressed significantly. Here, we review the microtubule-intrinsic process of dynamic instability, the effect of external factors on this process, and how the resulting forces act on various biological systems. Recently, reconstitution-based approaches have strongly benefited from extensive biochemical and biophysical characterization of individual components that are involved in regulating or transmitting microtubule-driven forces. We will focus on the current state of reconstituting increasingly complex biological systems and provide new directions for future developments. PMID:27715396

Assessment of Rho GTPase signaling during neurite outgrowth.

PubMed

Feltrin, Daniel; Pertz, Olivier

2012-01-01

Rho GTPases are key regulators of the cytoskeleton during the process of neurite outgrowth. Based on overexpression of dominant-positive and negative Rho GTPase constructs, the classic view is that Rac1 and Cdc42 are important for neurite elongation whereas RhoA regulates neurite retraction in response to collapsing agents. However, recent work has suggested a much finer control of spatiotemporal Rho GTPase signaling in this process. Understanding this complexity level necessitates a panel of more sensitive tools than previously used. Here, we discuss a novel assay that enables the biochemical fractionation of the neurite from the soma of differentiating N1E-115 neuronal-like cells. This allows for spatiotemporal characterization of a large number of protein components, interactions, and post-translational modifications using classic biochemical and also proteomics approaches. We also provide protocols for siRNA-mediated knockdown of genes and sensitive assays that allow quantitative analysis of the neurite outgrowth process.

Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses

PubMed Central

Teissandier, Aurélie; Onésime, Djamila; Loux, Valentin; Monnet, Christophe; Irlinger, Françoise; Landaud, Sophie; Leclercq-Perlat, Marie-Noëlle; Bento, Pascal; Fraud, Sébastien; Gibrat, Jean-François; Aubert, Julie; Fer, Frédéric; Guédon, Eric; Pons, Nicolas; Kennedy, Sean; Beckerich, Jean-Marie; Swennen, Dominique; Bonnarme, Pascal

2015-01-01

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process. PMID:25867897

Amyloid Precursor Protein Processing and Alzheimer’s Disease

PubMed Central

O’Brien, Richard J.; Wong, Philip C.

2011-01-01

Alzheimer’s disease (AD), the leading cause of dementia worldwide, is characterized by the accumulation of the β-amyloid peptide (Aβ) within the brain along with hyperphosphorylated and cleaved forms of the microtubule-associated protein tau. Genetic, biochemical, and behavioral research suggest that physiologic generation of the neurotoxic Aβ peptide from sequential amyloid precursor protein (APP) proteolysis is the crucial step in the development of AD. APP is a single-pass transmembrane protein expressed at high levels in the brain and metabolized in a rapid and highly complex fashion by a series of sequential proteases, including the intramembranous γ-secretase complex, which also process other key regulatory molecules. Why Aβ accumulates in the brains of elderly individuals is unclear but could relate to changes in APP metabolism or Aβ elimination. Lessons learned from biochemical and genetic studies of APP processing will be crucial to the development of therapeutic targets to treat AD. PMID:21456963

In Vitro Measurements of Metabolism for Application in Pharmacokinetic Modeling

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

Lipscomb, John C.; Poet, Torka S.

2008-04-01

Abstract Human risk and exposure assessments require dosimetry information. Species-specific tissue dose response will be driven by physiological and biochemical processes. While metabolism and pharmacokinetic data are often not available in humans, they are much more available in laboratory animals; metabolic rate constants can be readily derived in vitro. The physiological differences between laboratory animals and humans are known. Biochemical processes, especially metabolism, can be measured in vitro and extrapolated to account for in vivo metabolism through clearance models or when linked to a physiologically based biological (PBPK) model to describe the physiological processes, such as drug delivery to themore » metabolic organ. This review focuses on the different organ, cellular, and subcellular systems that can be used to measure in vitro metabolic rate constants and how that data is extrapolated to be used in biokinetic modeling.« less

Humic Substances: Determining Potential Molecular Regulatory Processes in Plants

PubMed Central

Shah, Zahid Hussain; Rehman, Hafiz M.; Akhtar, Tasneem; Alsamadany, Hameed; Hamooh, Bahget T.; Mujtaba, Tahir; Daur, Ihsanullah; Al Zahrani, Yahya; Alzahrani, Hind A. S.; Ali, Shawkat; Yang, Seung H.; Chung, Gyuhwa

2018-01-01

Humic substances (HSs) have considerable effects on soil fertility and crop productivity owing to their unique physiochemical and biochemical properties, and play a vital role in establishing biotic and abiotic interactions within the plant rhizosphere. A comprehensive understanding of the mode of action and tissue distribution of HS is, however, required, as this knowledge could be useful for devising advanced rhizospheric management practices. These substances trigger various molecular processes in plant cells, and can strengthen the plant’s tolerance to various kinds of abiotic stresses. HS manifest their effects in cells through genetic, post-transcriptional, and post-translational modifications of signaling entities that trigger different molecular, biochemical, and physiological processes. Understanding of such fundamental mechanisms will provide a better perspective for defining the cues and signaling crosstalk of HS that mediate various metabolic and hormonal networks operating in plant systems. Various regulatory activities and distribution strategies of HS have been discussed in this review. PMID:29593751

[The biochemical carcinogenesis of selected heavy metals in bladder cancer].

PubMed

Rorbach-Dolata, Anna; Marchewka, Zofia; Piwowar, Agnieszka

2015-01-01

Bladder cancer takes the second place in the classification of morbidity of urinary system cancers. Many chemical factors take part in cancerogenesis. It is suggested that exposure to heavy metals such as arsenic, chromium, nickel and cadmium as well as its metabolites may trigger the bladder cancer through inducing excessive reactive oxygen species production and oxidative stress formation which are responsible for DNA damage. In patients with bladder cancer is observed the disorder of processes regulated by p-53, including apoptosis. There are many patients with bladder cancer with confirmed absence of retinoblastoma protein, which is responsible of holding on the process of coming up the cells with mutation into synthesis, where the replication process undergoes. It is mentioned that excessive expression of proto-oncogenes may also cause the bladder cancer. The article concerns biochemical effects of exposure to chosen heavy metals and their potential role in bladder cancer progression.

Anomalous diffusion and scaling in coupled stochastic processes

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

Bel, Golan; Nemenman, Ilya

2009-01-01

Inspired by problems in biochemical kinetics, we study statistical properties of an overdamped Langevin processes with the friction coefficient depending on the state of a similar, unobserved, process. Integrating out the latter, we derive the Pocker-Planck the friction coefficient of the first depends on the state of the second. Integrating out the latter, we derive the Focker-Planck equation for the probability distribution of the former. This has the fonn of diffusion equation with time-dependent diffusion coefficient, resulting in an anomalous diffusion. The diffusion exponent can not be predicted using a simple scaling argument, and anomalous scaling appears as well. Themore » diffusion exponent of the Weiss-Havlin comb model is derived as a special case, and the same exponent holds even for weakly coupled processes. We compare our theoretical predictions with numerical simulations and find an excellent agreement. The findings caution against treating biochemical systems with unobserved dynamical degrees of freedom by means of standandard, diffusive Langevin descritpion.« less

Aflatoxin-induced biochemical changes in liver of mice and its mitigation by black tea extract.

PubMed

Jha, Anamika; Shah, Komal; Verma, Ramtej J

2012-01-01

Aflatoxin belongs to the class of naturally occurring mycotoxins, food contaminants having potent carcinogenicity. We have evaluated the ameliorative role of black tea extract on aflatoxin-induced biochemical changes in the liver of albino male mice. Adult male mice were orally administered with 750 and 1500 pg of aflatoxin in 0.2 mL olive oil/kg b.w./day for 30 days. Oral administration of aflatoxin caused, as compared with controls, significant, dose-dependent reduction in DNA, RNA, protein and glycogen contents; however, cholesterol content and phsphorylase activity were significantly increased. Black tea is one of the most potent antioxidants containing numerous bioactive phytonurtients having therapeutic applications. Aflatoxin-induced changes in the liver of mice were significantly ameliorated on co-treatment of black tea extract (2% infusion in water).

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

The digestive system of the "stick bug" Cladomorphus phyllinus (Phasmida, Phasmatidae): a morphological, physiological and biochemical analysis.

PubMed

Monteiro, Emiliano C; Tamaki, Fábio K; Terra, Walter R; Ribeiro, Alberto F

2014-03-01

This work presents a detailed morphofunctional study of the digestive system of a phasmid representative, Cladomorphus phyllinus. Cells from anterior midgut exhibit a merocrine secretion, whereas posterior midgut cells show a microapocrine secretion. A complex system of midgut tubules is observed in the posterior midgut which is probably related to the luminal alkalization of this region. Amaranth dye injection into the haemolymph and orally feeding insects with dye indicated that the anterior midgut is water-absorbing, whereas the Malpighian tubules are the main site of water secretion. Thus, a putative counter-current flux of fluid from posterior to anterior midgut may propel enzyme digestive recycling, confirmed by the low rate of enzyme excretion. The foregut and anterior midgut present an acidic pH (5.3 and 5.6, respectively), whereas the posterior midgut is highly alkaline (9.1) which may be related to the digestion of hemicelluloses. Most amylase, trypsin and chymotrypsin activities occur in the foregut and anterior midgut. Maltase is found along the midgut associated with the microvillar glycocalix, while aminopeptidase occurs in the middle and posterior midgut in membrane bound forms. Both amylase and trypsin are secreted mainly by the anterior midgut through an exocytic process as revealed by immunocytochemical data. Copyright © 2013 Elsevier Ltd. All rights reserved.

Morphodynamics of a growing microbial colony driven by cell death

NASA Astrophysics Data System (ADS)

Ghosh, Pushpita; Levine, Herbert

2017-11-01

Bacterial cells can often self-organize into multicellular structures with complex spatiotemporal morphology. In this work, we study the spatiotemporal dynamics of a growing microbial colony in the presence of cell death. We present an individual-based model of nonmotile bacterial cells which grow and proliferate by consuming diffusing nutrients on a semisolid two-dimensional surface. The colony spreads by growth forces and sliding motility of cells and undergoes cell death followed by subsequent disintegration of the dead cells in the medium. We model cell death by considering two possible situations: In one of the cases, cell death occurs in response to the limitation of local nutrients, while the other case corresponds to an active death process, known as apoptotic or programmed cell death. We demonstrate how the colony morphology is influenced by the presence of cell death. Our results show that cell death facilitates transitions from roughly circular to highly branched structures at the periphery of an expanding colony. Interestingly, our results also reveal that for the colonies which are growing in higher initial nutrient concentrations, cell death occurs much earlier compared to the colonies which are growing in lower initial nutrient concentrations. This work provides new insights into the branched patterning of growing bacterial colonies as a consequence of complex interplay among the biochemical and mechanical effects.

Single-molecule Analysis of Inhibitory Pausing States of V1-ATPase*

PubMed Central

Uner, Naciye Esma; Nishikawa, Yoshihiro; Okuno, Daichi; Nakano, Masahiro; Yokoyama, Ken; Noji, Hiroyuki

2012-01-01

V1-ATPase, the hydrophilic V-ATPase domain, is a rotary motor fueled by ATP hydrolysis. Here, we found that Thermus thermophilus V1-ATPase shows two types of inhibitory pauses interrupting continuous rotation: a short pause (SP, 4.2 s) that occurred frequently during rotation, and a long inhibitory pause (LP, >30 min) that terminated all active rotations. Both pauses occurred at the same angle for ATP binding and hydrolysis. Kinetic analysis revealed that the time constants of inactivation into and activation from the SP were too short to represent biochemically predicted ADP inhibition, suggesting that SP is a newly identified inhibitory state of V1-ATPase. The time constant of inactivation into LP was 17 min, consistent with one of the two time constants governing the inactivation process observed in bulk ATPase assay. When forcibly rotated in the forward direction, V1 in LP resumed active rotation. Solution ADP suppressed the probability of mechanical activation, suggesting that mechanical rotation enhanced inhibitory ADP release. These features were highly consistent with mechanical activation of ADP-inhibited F1, suggesting that LP represents the ADP-inhibited state of V1-ATPase. Mechanical activation largely depended on the direction and angular displacement of forced rotation, implying that V1-ATPase rotation modulates the off rate of ADP. PMID:22736762

Average oxidation state of carbon in proteins

PubMed Central

Dick, Jeffrey M.

2014-01-01

The formal oxidation state of carbon atoms in organic molecules depends on the covalent structure. In proteins, the average oxidation state of carbon (ZC) can be calculated as an elemental ratio from the chemical formula. To investigate oxidation–reduction (redox) patterns, groups of proteins from different subcellular locations and phylogenetic groups were selected for comparison. Extracellular proteins of yeast have a relatively high oxidation state of carbon, corresponding with oxidizing conditions outside of the cell. However, an inverse relationship between ZC and redox potential occurs between the endoplasmic reticulum and cytoplasm. This trend provides support for the hypothesis that protein transport and turnover are ultimately coupled to the maintenance of different glutathione redox potentials in subcellular compartments. There are broad changes in ZC in whole-genome protein compositions in microbes from different environments, and in Rubisco homologues, lower ZC tends to occur in organisms with higher optimal growth temperature. Energetic costs calculated from thermodynamic models are consistent with the notion that thermophilic organisms exhibit molecular adaptation to not only high temperature but also the reducing nature of many hydrothermal fluids. Further characterization of the material requirements of protein metabolism in terms of the chemical conditions of cells and environments may help to reveal other linkages among biochemical processes with implications for changes on evolutionary time scales. PMID:25165594

Bioengineering thermodynamics of biological cells.

PubMed

Lucia, Umberto

2015-12-01

Cells are open complex thermodynamic systems. They can be also regarded as complex engines that execute a series of chemical reactions. Energy transformations, thermo-electro-chemical processes and transports phenomena can occur across the cells membranes. Moreover, cells can also actively modify their behaviours in relation to changes in their environment. Different thermo-electro-biochemical behaviours occur between health and disease states. But, all the living systems waste heat, which is no more than the result of their internal irreversibility. This heat is dissipated into the environment. But, this wasted heat represent also a sort of information, which outflows from the cell toward its environment, completely accessible to any observer. The analysis of irreversibility related to this wasted heat can represent a new approach to study the behaviour of the cells themselves and to control their behaviours. So, this approach allows us to consider the living systems as black boxes and analyze only the inflows and outflows and their changes in relation to the modification of the environment. Therefore, information on the systems can be obtained by analyzing the changes in the cell heat wasted in relation to external perturbations. The bioengineering thermodynamics bases are summarized and used to analyse possible controls of the calls behaviours based on the control of the ions fluxes across the cells membranes.

Co-regulation of photosynthetic processes under potassium deficiency across CO2 levels in soybean: mechanisms of limitations and adaptations

USDA-ARS?s Scientific Manuscript database

Plants photosynthesis-related traits are often co-regulated to capture light and CO2 to optimize the rate of CO2 fixation (A) via photo-biochemical processes. However, potassium (K) limitations and adaptations strategies of photosynthetic processes across CO2 levels are not well understood. To evalu...

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 0.01 hour{sup −1}.« less

Metabolism. Part III: Lipids.

ERIC Educational Resources Information Center

Bodner, George M.

1986-01-01

Describes the metabolic processes of complex lipids, including saponification, activation and transport, and the beta-oxidation spiral. Discusses fatty acid degradation in regard to biochemical energy and ketone bodies. (TW)

The Pathway of Oligomeric DNA Melting Investigated by Molecular Dynamics Simulations

PubMed Central

Wong, Ka-Yiu; Pettitt, B. Montgomery

2008-01-01

Details of the reaction coordinate for DNA melting are fundamental to much of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved. To clarify the reaction mechanism of the melting transition of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair DNA duplex, d(A12)·d(T12), with explicit salt water at 400 K. Analysis of the trajectory reveals the various biochemically important processes that occur on different timescales. Peeling (including fraying from the ends), searching for Watson-Crick complements, and dissociation are recognizable processes. However, we find that basepair searching for Watson-Crick complements along a strand is not mechanistically tied to or directly accessible from the dissociation steps of strand melting. A three-step melting mechanism is proposed where the untwisting of the duplex is determined to be the major component of the reaction coordinate at the barrier. Though the observations are limited to the characteristics of the system being studied, they provide important insight into the mechanism of melting of other more biologically relevant forms of DNA, which will certainly differ in details from those here. PMID:18952784

Cycling of beryllium and carbon through hillslope soils in Iowa

USGS Publications Warehouse

Harden, J.W.; Fries, T.L.; Pavich, M.J.

2002-01-01

Isotopes of Be and C were used to reconstruct loess accumulation, hillslope evolution, and agricultural modification in soils of western Iowa. While both elements are derived from additions by the atmosphere (via plants in the case of carbon), the differences in element cycling allow erosional and depositional processes to be separated from biochemical processing. Based on 10Be, loess accumulation likely occurred simultaneously with hillslope degradation. Rates of loess accumulation declined five-fold between early stages (late Pleistocene and early Holocene) and later stages (late Holocene) of accumulation, but the absolute timing of accumulation requires independent dating methods. Based on 14C measurements, plant inputs and decomposition are significant near the surface, but below 1-1.5 m carbon inputs are minimal and decomposition is nearly arrested. The amount of carbon below 1.5 m is constant (0.1%) and is composed of soil organic matter that was buried by loess. Agricultural modification results in a dramatic redistribution of 10Be through soil erosion and deposition. By contrast, the redistribution of soil organic matter is masked by the rapid cycling of C through the topsoil as it continually decomposes and is replaced by plant inputs.

The microbial arsenic cycle in Mono Lake, California

USGS Publications Warehouse

Oremland, Ronald S.; Stolz, John F.; Hollibaugh, James T.

2004-01-01

Significant concentrations of dissolved inorganic arsenic can be found in the waters of a number of lakes located in the western USA and in other water bodies around the world. These lakes are often situated in arid, volcanic terrain. The highest concentrations of arsenic occur in hypersaline, closed basin soda lakes and their remnant brines. Although arsenic is a well-known toxicant to eukaryotes and prokaryotes alike, some prokaryotes have evolved biochemical mechanisms to exploit arsenic oxyanions (i.e., arsenate and arsenite); they can use them either as an electron acceptor for anaerobic respiration (arsenate), or as an electron donor (arsenite) to support chemoautotrophic fixation of CO2 into cell carbon. Unlike in freshwater or marine ecosystems, these processes may assume quantitative significance with respect to the carbon cycle in arsenic-rich soda lakes. For the past several years our research has focused on the occurrence and biogeochemical manifestations of these processes in Mono Lake, a particularly arsenic-rich environment. Herein we review some of our findings concerning the biogeochemical arsenic cycle in this lake, with the hope that it may broaden the understanding of the influence of microorganisms upon the speciation of arsenic in more common, less “extreme” environments, such as drinking water aquifers.

Emerging facets of prokaryotic glycosylation

PubMed Central

Schäffer, Christina; Messner, Paul

2017-01-01

Glycosylation of proteins is one of the most prevalent post-translational modifications occurring in nature, with a wide repertoire of biological implications. Pathways for the main types of this modification, the N- and O-glycosylation, can be found in all three domains of life—the Eukarya, Bacteria and Archaea—thereby following common principles, which are valid also for lipopolysaccharides, lipooligosaccharides and glycopolymers. Thus, studies on any glycoconjugate can unravel novel facets of the still incompletely understood fundamentals of protein N- and O-glycosylation. While it is estimated that more than two-thirds of all eukaryotic proteins would be glycosylated, no such estimate is available for prokaryotic glycoproteins, whose understanding is lagging behind, mainly due to the enormous variability of their glycan structures and variations in the underlying glycosylation processes. Combining glycan structural information with bioinformatic, genetic, biochemical and enzymatic data has opened up an avenue for in-depth analyses of glycosylation processes as a basis for glycoengineering endeavours. Here, the common themes of glycosylation are conceptualised for the major classes of prokaryotic (i.e. bacterial and archaeal) glycoconjugates, with a special focus on glycosylated cell-surface proteins. We describe the current knowledge of biosynthesis and importance of these glycoconjugates in selected pathogenic and beneficial microbes. PMID:27566466