Biochemical Processes (biochemical + process)

Distribution by Scientific Domains


Selected Abstracts


cDNA cloning and characterization of a novel calmodulin-like protein from pearl oyster Pinctada fucata

FEBS JOURNAL, Issue 19 2005
Shuo Li
Calcium metabolism in oysters is a very complicated and highly controlled physiological and biochemical process. However, the regulation of calcium metabolism in oyster is poorly understood. Our previous study showed that calmodulin (CaM) seemed to play a regulatory role in the process of oyster calcium metabolism. In this study, a full-length cDNA encoding a novel calmodulin-like protein (CaLP) with a long C-terminal sequence was identified from pearl oyster Pinctada fucata, expressed in Escherichia coli and characterized in vitro. The oyster CaLP mRNA was expressed in all tissues tested, with the highest levels in the mantle that is a key organ involved in calcium secretion. In situ hybridization analysis reveals that CaLP mRNA is expressed strongly in the outer and inner epithelial cells of the inner fold, the outer epithelial cells of the middle fold, and the dorsal region of the mantle. The oyster CaLP protein, with four putative Ca2+ -binding domains, is highly heat-stable and has a potentially high affinity for calcium. CaLP also displays typical Ca2+ -dependent electrophoretic shift, Ca2+ -binding activity and significant Ca2+ -induced conformational changes. Ca2+ -dependent affinity chromatography analysis demonstrated that oyster CaLP was able to interact with some different target proteins from those of oyster CaM in the mantle and the gill. In summary, our results have demonstrated that the oyster CaLP is a novel member of the CaM superfamily, and suggest that the oyster CaLP protein might play a different role from CaM in the regulation of oyster calcium metabolism. [source]


Quantitative sodium imaging with a flexible twisted projection pulse sequence

MAGNETIC RESONANCE IN MEDICINE, Issue 6 2010
Aiming Lu
Abstract The quantification of sodium MR images from an arbitrary intensity scale into a bioscale fosters image interpretation in terms of the spatially resolved biochemical process of sodium ion homeostasis. A methodology for quantifying tissue sodium concentration using a flexible twisted projection imaging sequence is proposed that allows for optimization of tradeoffs between readout time, signal-to-noise ratio efficiency, and sensitivity to static field susceptibility artifacts. The gradient amplitude supported by the slew rate at each k -space radius regularizes the readout gradient waveform design to avoid slew rate violation. Static field inhomogeneity artifacts are corrected using a frequency-segmented conjugate phase reconstruction approach, with field maps obtained quickly from coregistered proton imaging. High-quality quantitative sodium images have been achieved in phantom and volunteer studies with real isotropic spatial resolution of 7.5 × 7.5 × 7.5 mm3 for the slow T2 component in ,8 min on a clinical 3-T scanner. After correcting for coil sensitivity inhomogeneity and water fraction, the tissue sodium concentration in gray matter and white matter was measured to be 36.6 ± 0.6 ,mol/g wet weight and 27.6 ± 1.2 ,mol/g wet weight, respectively. Magn Reson Med 63:1583,1593, 2010. © 2010 Wiley-Liss, Inc. [source]


Fundamentals of neuronal apoptosis relevant to pediatric anesthesia

PEDIATRIC ANESTHESIA, Issue 5 2010
MORGAN BLAYLOCK PhD
Summary The programmed cell death or apoptosis is a complex biochemical process that has risen to prominence in pediatric anesthesia. Preclinical studies report a dose-dependant neuronal apoptosis during synaptogenesis following exposure to intravenous and volatile anesthetic agents. Although emerging clinical data do not universally indicate an increased neurodegenerative risk of general anesthesia in early human life, a great deal of uncertainty was created within the pediatric anesthesia community. This was at least partially caused by the demand of understanding of basic science concepts and knowledge of apoptosis frequently out of reach to the clinician. It is, however, important for the pediatric anesthesiologist to be familiar with the basic science concepts of neuronal apoptosis to be able to critically evaluate current and future preclinical data in this area and future clinical studies. This current review describes the extrinsic and intrinsic pathways involved in the cell death process and discusses techniques commonly employed to determine apoptosis. In addition, potential mechanisms of anesthesia-induced neuronal apoptosis are illustrated in this review. [source]


Environmental performance of lignocellulosic bioethanol production from Alfalfa stems

BIOFUELS, BIOPRODUCTS AND BIOREFINING, Issue 2 2010
Sara González-García
Abstract A ,well-to-wheel' analysis was conducted for bioethanol obtained from alfalfa stems by means of the Life Cycle Assessment (LCA) methodology. This analysis was compared with two blends of conventional gasoline with bioethanol (E10 and E85), all used in a mid-size car. A biochemical process including enzymatic hydrolysis and simultaneous saccharification and fermentation was considered. The life cycles of the fuels include gasoline production, alfalfa agriculture, lignocellulosic bioethanol production, blend production, and finally the use of fuels. The production of the alfalfa plant has two products: high-protein leaves for animal feed (the main driving force) and high-fiber stems. In this study, we assumed two allocation procedures based on mass and protein content, the latter reflecting the greater value of the leaves. According to the results, the use of bioethanol-based fuels leads to reduced global warming potential. A reduction in fossil fuel extraction of up to 72% could be achieved when pure bioethanol is used as transport fuel. On the contrary, bioethanol fuels are not the most suitable option when assessing acidification, eutrophication, and photochemical oxidant formation impact categories, mainly due to the higher impact from the upstream processes (specifically agricultural activities). LCA methodology helped to identify the key areas in the bioethanol production where researchers and technicians need to work to improve the environmental performance, paying special attention to enzyme production, onsite energy generation and distillation processes as well as agricultural activities. Copyright © 2010 Society of Chemical Industry and John Wiley & Sons, Ltd [source]


Optimal Synthesis of Protein Purification Processes

BIOTECHNOLOGY PROGRESS, Issue 4 2001
Elsa Vásquez-Alvarez
There has been an increasing interest in the development of systematic methods for the synthesis of purification steps for biotechnological products, which are often the most difficult and costly stages in a biochemical process. Chromatographic processes are extensively used in the purification of multicomponent biotechnological systems. One of the main challenges in the synthesis of purification processes is the appropriate selection and sequencing of chromatographic steps that are capable of producing the desired product at an acceptable cost and quality. This paper describes mathematical models and solution strategies based on mixed integer linear programming (MILP) for the synthesis of multistep purification processes. First, an optimization model is proposed that uses physicochemical data on a protein mixture, which contains the desired product, to select a sequence of operations with the minimum number of steps from a set of candidate chromatographic techniques that must achieve a specified purity level. Since several sequences that have the minimum number of steps may satisfy the purity level, it is possible to obtain the one that maximizes final purity. Then, a second model that may use the total number of steps obtained in the first model generates a solution with the maximum purity of the product. Whenever the sequence does not affect the final purity or more generally does not impact the objective function, alternative models that are of smaller size are developed for the optimal selection of steps. The models are tested in several examples, containing up to 13 contaminants and a set of 22 candidate high-resolution steps, generating sequences of six operations, and are compared to the current synthesis approaches. [source]


The structure at 2.5,Å resolution of human basophilic leukemia-expressed protein BLES03

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2005
Eduard Bitto
The crystal structure of the human basophilic leukemia-expressed protein (BLES03, p5326, Hs.433573) was determined by single-wavelength anomalous diffraction and refined to an R factor of 18.8% (Rfree = 24.5%) at 2.5,Å resolution. BLES03 shows no detectable sequence similarity to any functionally characterized proteins using state-of-the-art sequence-comparison tools. The structure of BLES03 adopts a fold similar to that of eukaryotic transcription initiation factor 4E (eIF4E), a protein involved in the recognition of the cap structure of eukaryotic mRNA. In addition to fold similarity, the electrostatic surface potentials of BLES03 and eIF4E show a clear conservation of basic and acidic patches. In the crystal lattice, the acidic amino-terminal helices of BLES03 monomers are bound within the basic cavity of symmetry-related monomers in a manner analogous to the binding of mRNA by eIF4E. Interestingly, the gene locus encoding BLES03 is located between genes encoding the proteins DRAP1 and FOSL1, both of which are involved in transcription initiation. It is hypothesized that BLES03 itself may be involved in a biochemical process that requires recognition of nucleic acids. [source]


Microbial biodegradation of polyaromatic hydrocarbons

FEMS MICROBIOLOGY REVIEWS, Issue 6 2008
Ri-He Peng
Abstract Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites. [source]


Rates Of Postglacial rock weathering on glacially scoured outcrops (Abisko,Riksgränsen area, 68°N)

GEOGRAFISKA ANNALER SERIES A: PHYSICAL GEOGRAPHY, Issue 3-4 2002
Françoise André, Marie
Ice,polished quartz veins, feldspar phenocrysts and quartzite layers were used as reference surfaces to assess the impact of Postglacial rock weathering in Lapland (68°N). Over 3200 measurements were carried out on roches moutonées and glaciofluvially scoured outcrops distributed within three study areas covering 8 km2. Inferred weathering rates demonstrate that 10,000 years of Holocene weathering did not significantly modify the geometry of Weichselian rock surfaces. However, rates of general surface lowering range from 1 to 25, depending on the rock type, with average values at 0.2 mm ka,1 for homogeneous crystalline rocks (irrespective of their acidity and grain size), 1 mm ka,1 for biotite,rich crystalline rocks, and 5 mm ka,1 for carbonate sedimentary rocks. Accelerated rates were recorded in weathering pits and along joints with values up to ten times higher than on the rest of the rock surface. Comparisons with cold and temperate areas suggest that solution rates of carbonate rocks are highly dependent on climate conditions, whilst granular disintegration of crystalline rocks operates at the same rate whatever the environment. It probably means that microgelivation is not efficient on ice,polished crystalline outcrops even under harsh climate conditions, and that granular disintegration proceeds under various climates from the same ubiquitous combination of biochemical processes. Last, the weathering state of Late,Weichselian roches moutonées can be usefully compared to that of Preglacial tors of the nearby Kiruna area. [source]


Captopril and its synthesis from chiral intermediates

JOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 2 2001
R Chirumamilla
Abstract Captopril is an antihypertensive agent that inhibits the angiotensin-converting enzyme of the renin,angiotensin system. Chiral intermediates are used in the synthesis of the drug. These intermediates are obtained by resolution of racemic compounds or by chemical, biocatalytic methods and or by asymmetric synthesis by biocatalytic process. This article reviews the various chemical and biochemical processes involved in the synthesis of the chiral drug, including the pharmacological action of captopril. © 2001 Society of Chemical Industry [source]


Insights from comparative analyses of aging in birds and mammals

AGING CELL, Issue 2 2010
Robert E. Ricklefs
Summary Many laboratory models used in aging research are inappropriate for understanding senescence in mammals, including humans, because of fundamental differences in life history, maintenance in artificial environments, and selection for early aging and high reproductive rate. Comparative studies of senescence in birds and mammals reveal a broad range in rates of aging among a variety of taxa with similar physiology and patterns of development. These comparisons suggest that senescence is a shared property of all vertebrates with determinate growth, that the rate of senescence has been modified by evolution in response to the potential life span allowed by extrinsic mortality factors, and that most variation among species in the rate of senescence is independent of commonly ascribed causes of aging, such as oxidative damage. Individuals of potentially long-lived species, particularly birds, appear to maintain high condition to near the end of life. Because most individuals in natural populations of such species die of aging-related causes, these populations likely harbor little genetic variation for mechanisms that could extend life further, or these mechanisms are very costly. This, and the apparent evolutionary conservatism in the rate of increase in mortality with age, suggests that variation in the rate of senescence reflects fundamental changes in organism structure, likely associated with the rate of development, rather than physiological or biochemical processes influenced by a few genes. Understanding these evolved differences between long-lived and short-lived organisms would seem to be an essential foundation for designing therapeutic interventions with respect to human aging and longevity. [source]


How to account for the lipid effect on carbon stable-isotope ratio (,13C): sample treatment effects and model bias

JOURNAL OF FISH BIOLOGY, Issue 4 2008
K. Mintenbeck
This study investigated the impact of lipid extraction, CaCO3 removal and of both treatments combined on fish tissue ,13C, ,15N and C:N ratio. Furthermore, the suitability of empirical ,13C lipid normalization and correction models was examined. ,15N was affected by lipid extraction (increase of up to 1·65,) and by the combination of both treatments, while acidification alone showed no effect. The observed shift in ,15N represents a significant bias in trophic level estimates, i.e. lipid-extracted samples are not suitable for ,15N analysis. C:N and ,13C were significantly affected by lipid extraction, proportional to initial tissue lipid content. For both variables, rates of change with lipid content (,C:N and ,,13C) were species specific. All tested lipid normalization and correction models produced biased estimates of fish tissue ,13C, probably due to a non-representative database and incorrect assumptions and generalizations the models were based on. Improved models need a priori more extensive and detailed studies of the relationships between lipid content, C:N and ,13C, as well as of the underlying biochemical processes. [source]


WATER MOTION, MARINE MACROALGAL PHYSIOLOGY, AND PRODUCTION

JOURNAL OF PHYCOLOGY, Issue 3 2000
Catriona L. Hurd
Water motion is a key determinant of marine macroalgal production, influencing directly or indirectly physiological rates and community structure. Our understanding of how marine macroalgae interact with their hydrodynamic environment has increased substantially over the past 20 years, due to the application of tools such as flow visualization to aquatic vegetation, and in situ measurements of seawater velocity and turbulence. This review considers how the hydrodynamic environment in which macroalgae grow influences their ability to acquire essential resources and how macroalgae might respond physiologically to fluctuations in their hydrodynamic regime with a focus on: (1) the biochemical processes occurring within the diffusion boundary layer (DBL) that might reduce rates of macroalgal production; (2) time scales over which measurements of velocity and DBL processes should be made, discussing the likelihood of in situ mass transfer limitation; (3) if and how macroalgal morphology influences resource acquisition in slow flows; and (4) ecobiomechanics and how hydrodynamic drag might influence resource acquisition and allocation. Finally, the concept that macroalgal production is enhanced in wave-exposed versus sheltered habitats is discussed. [source]


Bayesian analysis of single-molecule experimental data

JOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 3 2005
S. C. Kou
Summary., Recent advances in experimental technologies allow scientists to follow biochemical processes on a single-molecule basis, which provides much richer information about chemical dynamics than traditional ensemble-averaged experiments but also raises many new statistical challenges. The paper provides the first likelihood-based statistical analysis of the single-molecule fluorescence lifetime experiment designed to probe the conformational dynamics of a single deoxyribonucleic acid (DNA) hairpin molecule. The conformational change is initially treated as a continuous time two-state Markov chain, which is not observable and must be inferred from changes in photon emissions. This model is further complicated by unobserved molecular Brownian diffusions. Beyond the simple two-state model, a competing model that models the energy barrier between the two states of the DNA hairpin as an Ornstein,Uhlenbeck process has been suggested in the literature. We first derive the likelihood function of the simple two-state model and then generalize the method to handle complications such as unobserved molecular diffusions and the fluctuating energy barrier. The data augmentation technique and Markov chain Monte Carlo methods are developed to sample from the posterior distribution desired. The Bayes factor calculation and posterior estimates of relevant parameters indicate that the fluctuating barrier model fits the data better than the simple two-state model. [source]


Fluorometric Analysis of DNA Unwinding (FADU) as a Method for Detecting Repair-induced DNA Strand Breaks in UV-irradiated Mammalian Cells,

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2000
Christa Baumstark-Khan
ABSTRACT Fluorometric analysis of DNA unwinding (FADU assay) was originally designed to detect X-ray,induced DNA damage in repair-proficient and repair-deficient mammalian cell lines. The method was modified and applied to detect DNA strand breaks in Chinese hamster ovary (CHO) cells exposed to ionizing radiation as well as to UV light. Exposed cells were allowed to repair damaged DNA by incubation for up to 1 h after exposure under standard growth conditions in the presence and in the absence of the DNA synthesis inhibitor aphidicolin. Thereafter, cell lysates were mixed with 0.15 M sodium hydroxide, and DNA unwinding took place at pH 12.1 for 30 min at 20°C. The amount of DNA remaining double-stranded after alkaline reaction was detected by binding to the Hoechst 33258 dye (bisbenzimide) and measuring the fluorescence. After exposure to X-rays DNA strand breaks were observed in all cell lines immediately after exposure with subsequent restitution of high molecular weight DNA during postexposure incubation. In contrast, after UV exposure delayed production of DNA strand break was observed only in cell lines proficient for nucleotide excision repair of DNA photoproducts. Here strand break production was enhanced when the polymerization step was inhibited by adding the repair inhibitor aphidicolin during repair incubation. These results demonstrate that the FADU approach is suitable to distinguish between different DNA lesions (strand breaks versus base alterations) preferentially induced by different environmental radiations (X-rays versus UV) and to distinguish between the different biochemical processes during damage repair (incision versus polymerization and ligation). [source]


Gene expression associated with N-induced shifts in resource allocation in poplar

PLANT CELL & ENVIRONMENT, Issue 5 2003
J. E. K. COOKE
ABSTRACT Surprisingly little is known about molecular mechanisms by which nitrogen (N) availability acts to modulate the growth of forest trees. To address this issue, differential display was used in conjunction with filter-based arrays to identify 52 partial cDNA clones that were significantly regulated within days in response to limiting or luxuriant levels of NH4NO3 fertilization in Populus trichocarpa Torr. & Gray × deltoides Bartr. ex Marsh. A subset of these cDNAs also demonstrated shifts in expression patterns in stem-girdled trees, a manipulative physiology technique that disrupts phloem transport. Stem girdling also induced changes in glutamine and asparagine pools which were correlated with the observed changes in expression profiles for these genes. The identity of these genes provides insight into biochemical processes that are altered by N availability in poplar. Carbon,nitrogen interactions appear to figure prominently in the N-response. The gene expression data suggest that N availability modulates the partitioning of C and N resources into metabolic fates that have the potential to alter both wood quality and quantity, including synthesis of vegetative storage proteins, cell wall components, and terpenoids. [source]


Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2006
Inger V. H. Kjærsgård Dr.
Abstract Multivariate data analysis has been combined with proteomics to enhance the recovery of information from 2-DE of cod muscle proteins during different storage conditions. Proteins were extracted according to 11 different storage conditions and samples were resolved by 2-DE. Data generated by 2-DE was subjected to principal component analysis (PCA) and discriminant partial least squares regression (DPLSR). Applying PCA to 2-DE data revealed the samples to form groups according to frozen storage time, whereas differences due to different storage temperatures or chilled storage in modified atmosphere packing did not lead to distinct changes in protein pattern. Applying DPLSR to the 2-DE data enabled the selection of protein spots critical for differentiation between 3 and 6,months frozen storage with 12,months frozen storage. Some of these protein spots have been identified by MS/MS, revealing myosin light chain 1, 2 and 3, triose-phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, aldolase A and two ,-actin fragments, and a nuclease diphosphate kinase B fragment to change in concentration, during frozen storage. Application of proteomics, multivariate data analysis and MS/MS to analyse protein changes in cod muscle proteins during storage has revealed new knowledge on the issue and enables a better understanding of biochemical processes occurring. [source]


A study of Streptococcus thermophilus proteome by integrated analytical procedures and differential expression investigations

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 1 2006
Simona Arena
Abstract Streptococcus thermophilus is a Gram-positive bacterium belonging to the group of lactic acid bacteria, among which several genera play an essential role in manufacture of food products. Recently, a genomic consortium sequenced and annotated its entire genome, which has been demonstrated to contain 1900 coding sequences. In this study, we have revealed the expression products of almost 200 different genes using a proteomic strategy combining 2-DE plus MALDI-TOF PMF and differential 1-DE plus ,LC-ESI-IT-MS/MS. Thus, a number of cellular pathways related to important physiological processes were described at the proteomic level. Almost 50 genes were related to multiple electrophoretic species, whose heterogeneity was mainly due to variability in pI values. A 2-DE reference map obtained for lactose-grown cells was compared with those obtained after heat, cold, acid, oxidative and starvation stresses. Protein up/down-regulation measurements demonstrated that adaptation to different environmental challenges may involve the contribution of unique as well as combined physiological mechanisms. Common regulatory sites in the promoter region of genes whose expression was induced after stress were identified. These results provide a better comprehension of biochemical processes related to stress resistance in S. thermophilus, allowing defining the molecular bases of adaptative responses or markers for the identification of strains with potential industrial applications. [source]


Crystallization of gankyrin, an oncoprotein that interacts with CDK4 and the S6b (rpt3) ATPase of the 19S regulator of the 26S proteasome

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2003
Szymon Krzywda
Gankyrin is an oncoprotein overexpressed in hepatocarcinoma cells that binds to the cell-cycle regulator CDK4 and the S6b ATPase subunit of the regulatory component of the proteasome. It belongs to the family of ankyrin-repeat proteins that appear to mediate protein,protein interactions in diverse biochemical processes. Gankyrin has been crystallized from polyethylene glycol solutions and diffraction data have been obtained from these crystals that extend to 2.1,Å spacing. [source]


The early history of 32P as a radioactive tracer in biochemical research: A personal memoir

BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 3 2005
Howard Gest
The concept of using radioactive isotopes as "tracers" of chemical conversions was conceived and developed by inorganic chemist Georg de Hevesy (Nobel Laureate in Chemistry 1943). In 1935, he began to apply the technique to various biological processes using 32P, and his experiments revealed the dynamic character of physiology and metabolism. Following de Hevesy's lead, Samuel Ruben (University of California, Berkeley) exploited 32P in 1937,38 for investigation of phospholipid metabolism. Between 1937 and 1940, Ruben and colleague Martin Kamen spearheaded tracer studies in various biological systems using 32P, short-lived 11C, and other radioactive isotopes. During this period, Kamen was responsible for cyclotron-produced radioactive tracers and was able to sustain de Hevesy's research by supplying him with 32P. In 1940, Ruben and Kamen discovered long-lived 14C, which later proved to be a very powerful tool for analysis of complex biochemical processes, such as the path of carbon in photosynthesis. Between 1946 and 1950, 32P was used in studies of bacteriophage replication and photosynthetic metabolism. This memoir surveys the history of these early investigations. [source]


Structure of the adenylation domain of NAD+ -dependent DNA ligase from Staphylococcus aureus

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009
Seungil Han
DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5,-phosphate and 3,-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD+ -dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD+ -dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD+ -binding pocket and the `C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors. [source]


Antimetabolite incorporation into DNA: Structural and thermodynamic basis for anticancer activity

BIOPOLYMERS, Issue 3 2002
William H. Gmeiner
Abstract Antimetabolites are a class of effective anticancer drugs that structurally resemble naturally occurring biochemicals and interfere in essential biochemical processes. In this review, the recent literature describing investigations of the structural and thermodynamic basis for the anticancer activity of three antipyrimidines [1-,- D -arabinofuranosyl cytidine (AraC). 2,,2,-difluoro deoxycytidine (dFdC), and 5-fluoro-2,-deoxyuridine (FdUrd)] is summarized. Our laboratory, and others, have shown that misincorporation of any of these three antipyrimidines into DNA perturbs the structure and decreases the stability of duplex DNA. These data are useful for rationalizing the effects of antipyrimidine misincorporation on the activities of proteins required for DNA replication and repair such as DNA topoisomerase 1 and DNA polymerases. The studies completed to date and summarized in this review demonstrate the utility of investigations into the structure,function relationships between antipyrimidine-substituted DNA complexed with DNA-modifying proteins for the purpose of understanding the basis for effective antipyrimidine cancer chemotherapy and the future design of novel anticancer drugs. © 2002 Wiley Periodicals, Inc. Biopolymers (Nucleic Acid Sci) 65: 180,189, 2002 [source]


Modeling biochemical processes based on systems biology concepts

BIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009
Article first published online: 21 NOV 200
No abstract is available for this article. [source]


Development of a large-scale biocalorimeter to monitor and control bioprocesses

BIOTECHNOLOGY & BIOENGINEERING, Issue 2 2002
D. Voisard
Abstract Calorimetry has shown real potential at bench-scale for chemical and biochemical processes. The aim of this work was therefore to scale-up the system by adaptation of a standard commercially available 300-L pilot-scale bioreactor. To achieve this, all heat flows entering or leaving the bioreactor were identified and the necessary instrumentation implemented to enable on-line monitoring and dynamic heat balance estimation. Providing that the signals are sufficiently precise, such a heat balance would enable calculation of the heat released or taken up during an operational (bio)process. Two electrical Wattmeters were developed, the first for determination of the power consumption by the stirrer motor and the second for determination of the power released by an internal calibration heater. Experiments were designed to optimize the temperature controller of the bioreactor such that it was sufficiently rapid so as to enable the heat accumulation terms to be neglected. Further calibration experiments were designed to correlate the measured stirring power to frictional heat losses of the stirrer into the reaction mass. This allows the quantitative measurement of all background heat flows and the on-line quantitative calculation of the (bio)process power. Three test fermentations were then performed with B. sphaericus 1593M, a spore-forming bacterium pathogenic to mosquitoes. A first batch culture was performed on a complex medium, to enable optimization of the calorimeter system. A second batch culture, on defined medium containing three carbon sources, was used to show the fast, accurate response of the heat signal and the ability to perfectly monitor the different growth phases associated with growth on mixed substrates, in particular when carbon sources became depleted. A maximum heat output of 1100 W was measured at the end of the log-phase. A fed-batch culture on the same defined medium was then carried out with the feed rate controlled as a function of the calorimeter signal. A maximum heat output of 2250 W was measured at the end of the first log-phase. This work demonstrates that real-time quantitative calorimetry is not only possible at pilot-scale, but could be readily applied at even larger scales. The technique requires simple, readily available devices for determination of the few necessary heat flows, making it a robust, cost-effective technique for process development and routine monitoring and control of production processes. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 125,138, 2002 [source]


Kinetic Modeling of the Autotrophic Growth of Pavlova lutheri: Study of the Combined Influence of Light and Temperature

BIOTECHNOLOGY PROGRESS, Issue 4 2003
Ana P. Carvalho
The optimization and control of biochemical processes require the previous establishment of mathematical models that can describe the effect of process variables on their actual kinetics. Environmental temperature is a modulating factor to which the algal cells respond continuously by adjusting their rates of cellular reactions, their nutritional requirements, and, consequently, their biomass composition. Light intensity is an exhaustible resource, indispensable to autotrophic organisms. The effects of light intensity and temperature on growth of the microalga Pavlova lutheri, which have hardly been considered to date in a simultaneous fashion, were experimentally assessed using a factorial experimental design; in this way, the effects of each variable independently and their interactions could be quantified, using maximum biomass (Xmax) or maximum specific growth rate (,max) as objective functions. The preliminary results produced indicated that light intensity plays a more important role on ,max than temperature; in the case of Xmax, both temperature and, to a lesser extent, light intensity do apparently play a role. The highest values of Xmax were associated with low temperatures and high light intensities; a similar behavior could be observed for ,max concerning light intensity, although the dependency on temperature did not seem to be as important. A more complex mechanistic model was then postulated, incorporating light and temperature as input variables, which was successfully fitted to the experimental data generated during batch cultivation of P. lutheri. [source]


Flavor of Cheddar Cheese: A Chemical and Sensory Perspective

COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY, Issue 4 2003
T.K. Singh
ABSTRACT Considerable knowledge has been accumulated on the biochemical processes occurring during ripening of Cheddar cheese, which in turn has major consequences on flavor and texture development. The present review outlines major metabolic pathways and agents involved in the modification of milk constituents in Cheddar cheese ripening. Mechanisms of volatile flavor and off-flavor production and recent developments in the analysis, both sensory and instrumental, of Cheddar flavor and flavor compounds are also detailed here. [source]